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Sample records for substrate based inhibitor

  1. Biosensors based on enzyme field-effect transistors for determination of some substrates and inhibitors.

    Science.gov (United States)

    Dzyadevych, Sergei V; Soldatkin, Alexey P; Korpan, Yaroslav I; Arkhypova, Valentyna N; El'skaya, Anna V; Chovelon, Jean-Marc; Martelet, Claude; Jaffrezic-Renault, Nicole

    2003-10-01

    This paper is a review of the authors' publications concerning the development of biosensors based on enzyme field-effect transistors (ENFETs) for direct substrates or inhibitors analysis. Such biosensors were designed by using immobilised enzymes and ion-selective field-effect transistors (ISFETs). Highly specific, sensitive, simple, fast and cheap determination of different substances renders them as promising tools in medicine, biotechnology, environmental control, agriculture and the food industry. The biosensors based on ENFETs and direct enzyme analysis for determination of concentrations of different substrates (glucose, urea, penicillin, formaldehyde, creatinine, etc.) have been developed and their laboratory prototypes were fabricated. Improvement of the analytical characteristics of such biosensors may be achieved by using a differential mode of measurement, working solutions with different buffer concentrations and specific agents, negatively or positively charged additional membranes, or genetically modified enzymes. These approaches allow one to decrease the effect of the buffer capacity influence on the sensor response in an aim to increase the sensitivity of the biosensors and to extend their dynamic ranges. Biosensors for the determination of concentrations of different toxic substances (organophosphorous pesticides, heavy metal ions, hypochlorite, glycoalkaloids, etc.) were designed on the basis of reversible and/or irreversible enzyme inhibition effect(s). The conception of an enzymatic multibiosensor for the determination of different toxic substances based on the enzyme inhibition effect is also described. We will discuss the respective advantages and disadvantages of biosensors based on the ENFETs developed and also demonstrate their practical application.

  2. Chemical probing of the human sirtuin 5 active site reveals its substrate acyl specificity and peptide-based inhibitors.

    Science.gov (United States)

    Roessler, Claudia; Nowak, Theresa; Pannek, Martin; Gertz, Melanie; Nguyen, Giang T T; Scharfe, Michael; Born, Ilona; Sippl, Wolfgang; Steegborn, Clemens; Schutkowski, Mike

    2014-09-26

    Sirtuins are NAD(+)-dependent deacetylases acting as sensors in metabolic pathways and stress response. In mammals there are seven isoforms. The mitochondrial sirtuin 5 is a weak deacetylase but a very efficient demalonylase and desuccinylase; however, its substrate acyl specificity has not been systematically analyzed. Herein, we investigated a carbamoyl phosphate synthetase 1 derived peptide substrate and modified the lysine side chain systematically to determine the acyl specificity of Sirt5. From that point we designed six potent peptide-based inhibitors that interact with the NAD(+) binding pocket. To characterize the interaction details causing the different substrate and inhibition properties we report several X-ray crystal structures of Sirt5 complexed with these peptides. Our results reveal the Sirt5 acyl selectivity and its molecular basis and enable the design of inhibitors for Sirt5. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. S1 pocket fingerprints of human and bacterial methionine aminopeptidases determined using fluorogenic libraries of substrates and phosphorus based inhibitors

    Czech Academy of Sciences Publication Activity Database

    Poreba, M.; Gajda, A.; Pícha, Jan; Jiráček, Jiří; Marschner, A.; Klein, Ch. D.; Salvesen, G. S.; Drag, M.

    2012-01-01

    Roč. 94, č. 3 (2012), s. 704-710 ISSN 0300-9084 R&D Projects: GA MŠk(CZ) LC06077 Institutional research plan: CEZ:AV0Z40550506 Keywords : methionine aminopeptidase * substrate library * protease * enzyme * inhibitor * substrate specificity Subject RIV: CC - Organic Chemistry Impact factor: 3.142, year: 2012

  4. pKa modulation of the acid/base catalyst within GH32 and GH68: a role in substrate/inhibitor specificity?

    Directory of Open Access Journals (Sweden)

    Shuguang Yuan

    Full Text Available Glycoside hydrolases of families 32 (GH32 and 68 (GH68 belong to clan GH-J, containing hydrolytic enzymes (sucrose/fructans as donor substrates and fructosyltransferases (sucrose/fructans as donor and acceptor substrates. In GH32 members, some of the sugar substrates can also function as inhibitors, this regulatory aspect further adding to the complexity in enzyme functionalities within this family. Although 3D structural information becomes increasingly available within this clan and huge progress has been made on structure-function relationships, it is not clear why some sugars bind as inhibitors without being catalyzed. Conserved aspartate and glutamate residues are well known to act as nucleophile and acid/bases within this clan. Based on the available 3D structures of enzymes and enzyme-ligand complexes as well as docking simulations, we calculated the pKa of the acid-base before and after substrate binding. The obtained results strongly suggest that most GH-J members show an acid-base catalyst that is not sufficiently protonated before ligand entrance, while the acid-base can be fully protonated when a substrate, but not an inhibitor, enters the catalytic pocket. This provides a new mechanistic insight aiming at understanding the complex substrate and inhibitor specificities observed within the GH-J clan. Moreover, besides the effect of substrate entrance on its own, we strongly suggest that a highly conserved arginine residue (in the RDP motif rather than the previously proposed Tyr motif (not conserved provides the proton to increase the pKa of the acid-base catalyst.

  5. Mechanism-based population pharmacokinetic modelling in diabetes: vildagliptin as a tight binding inhibitor and substrate of dipeptidyl peptidase IV

    Science.gov (United States)

    Landersdorfer, Cornelia B; He, Yan-Ling; Jusko, William J

    2012-01-01

    AIMS To assess the pharmacokinetics of vildagliptin at different doses and build a mechanism-based population model that simultaneously describes vildagliptin pharmacokinetics and its effects on DPP-4 activity based on underlying physiology and biology. METHODS Vildagliptin concentrations and DPP-4 activity vs. time from 13 type 2 diabetic patients after oral vildagliptin 10, 25 or 100 mg and placebo twice daily for 28 days were co-modelled. NONMEM VI and S-ADAPT were utilized for population modelling. RESULTS A target-mediated drug disposition (TMDD) model accounting for capacity-limited high affinity binding of vildagliptin to DPP-4 in plasma and tissues had good predictive performance. Modelling the full time course of the vildagliptin-DPP-4 interaction suggested parallel vildagliptin dissociation from DPP-4 by a slow first-order process and hydrolysis by DPP-4 to an inactive metabolite as a disposition mechanism. Due to limited amounts of DPP-4, vildagliptin concentrations increased slightly more than dose proportionally. This newly proposed model and the parameter estimates are supported by published in vitro studies. Mean parameter estimates (inter-individual coefficient of variation) were: non-saturable clearance 36 l h−1 (25%), central volume of distribution 22 l (37%), half-life of dissociation from DPP-4 1.1 h (94%) and half-life of hydrolysis 6.3 h (81%). CONCLUSIONS Vildagliptin is both an inhibitor and substrate for DPP-4. By utilizing the TMDD approach, slow dissociation of vildagliptin from DPP-4 was found in patients and the half-life of hydrolysis by DPP-4 estimated. This model can be used to predict DPP-4 inhibition effects of other dosage regimens and be modified for other DPP-4 inhibitors to differentiate their properties. PMID:22442826

  6. Predicting the effect of cytochrome P450 inhibitors on substrate drugs: analysis of physiologically based pharmacokinetic modeling submissions to the US Food and Drug Administration.

    Science.gov (United States)

    Wagner, Christian; Pan, Yuzhuo; Hsu, Vicky; Grillo, Joseph A; Zhang, Lei; Reynolds, Kellie S; Sinha, Vikram; Zhao, Ping

    2015-01-01

    The US Food and Drug Administration (FDA) has seen a recent increase in the application of physiologically based pharmacokinetic (PBPK) modeling towards assessing the potential of drug-drug interactions (DDI) in clinically relevant scenarios. To continue our assessment of such approaches, we evaluated the predictive performance of PBPK modeling in predicting cytochrome P450 (CYP)-mediated DDI. This evaluation was based on 15 substrate PBPK models submitted by nine sponsors between 2009 and 2013. For these 15 models, a total of 26 DDI studies (cases) with various CYP inhibitors were available. Sponsors developed the PBPK models, reportedly without considering clinical DDI data. Inhibitor models were either developed by sponsors or provided by PBPK software developers and applied with minimal or no modification. The metric for assessing predictive performance of the sponsors' PBPK approach was the R predicted/observed value (R predicted/observed = [predicted mean exposure ratio]/[observed mean exposure ratio], with the exposure ratio defined as [C max (maximum plasma concentration) or AUC (area under the plasma concentration-time curve) in the presence of CYP inhibition]/[C max or AUC in the absence of CYP inhibition]). In 81 % (21/26) and 77 % (20/26) of cases, respectively, the R predicted/observed values for AUC and C max ratios were within a pre-defined threshold of 1.25-fold of the observed data. For all cases, the R predicted/observed values for AUC and C max were within a 2-fold range. These results suggest that, based on the submissions to the FDA to date, there is a high degree of concordance between PBPK-predicted and observed effects of CYP inhibition, especially CYP3A-based, on the exposure of drug substrates.

  7. Design, chemical synthesis and kinetic studies of trypsin chromogenic substrates based on the proteinase binding loop of Cucurbita maxima trypsin inhibitor (CMTI-III).

    Science.gov (United States)

    Lesner, A; Brzozowski, K; Kupryszewski, G; Rolka, K

    2000-03-05

    A series of trypsin chromogenic substrates with formula: Y-Ala-X-Abu-Pro-Lys-pNA, where X = Gly, Ala, Abu, Val, Leu, Phe, Ser, Glu and Y = Ac, H; pNA = p-nitroanilide was synthesized. The Cucurbita maxima trypsin inhibitor CMTI-III molecule was used as a vehicle to design the trypsin substrates. To evaluate the influence of position P(4) on the substrate-enzyme interaction, kinetic parameters of newly synthesized substrates with bovine beta-trypsin were determined. The increasing hydrophobicity of the amino acid residue (Gly, Ala, Abu, Val) introduced in position P(4) significantly enhanced the substrate specificity (k(cat)/K(m)) which was over 8 times higher for the last residue than that for the first one. The introduction of residues with more hydrophilic side chain (Glu, Ser) in this position reduced the value of this parameter. These results correspond well with those obtained using molecular dynamics of bovine beta-trypsin with monosubstituted CMTI-I analogues, indicating that in both trypsin substrate and inhibitor position 4 plays an important role in the interaction with the enzyme. Copyright 2000 Academic Press.

  8. Human leukocyte and porcine pancreatic elastase: X-ray crystal structures, mechanism, substrate specificity, and mechanism-based inhibitors

    International Nuclear Information System (INIS)

    Bode, W.; Meyer, E. Jr.; Powers, J.C.

    1989-01-01

    The serine protease family of enzymes is one of the most widely studied group of enzymes, as evidenced by the fact that more crystal structures are available for individuals of this superfamily than for any other homologous group of enzymes. These enzymes contain a conserved triad of catalytic residues including Ser-195, His-57, and Asp-102. The active-site serine is very nucleophilic, and serine proteases are inhibited by specific serine protease reagents such as diisopropyl phosphorofluoridate (DFP), phenylmethanesulfonyl fluoride, and 3,4-dichloroisocoumarin. Elastases are a group of proteases that possess the ability to cleave the important connective tissue protein elastin. Elastin has the unique property of elastic recoil, is widely distributed in vertebrate tissue, and is particularly abundant in the lungs, arteries, skin, and ligaments. Human neutrophil elastase and pancreatic elastase are two major serine proteases that cleave elastin. Neutrophil elastase is found in the dense granules of polymorphonuclear leukycytes and is essential for phagocytosis and defense against infection by invading microorganisms. Pancreatic elastase is stored as an inactive zymogen in the pancreas and is secreted into the intestines where it becomes activated by trypsin and then participates in digestion. Both elastases cleave substrates at peptide bonds where the P 1 residue is an amino acid residue with a small alkyl side chain

  9. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.

    Science.gov (United States)

    Rawlings, Neil D; Waller, Matthew; Barrett, Alan J; Bateman, Alex

    2014-01-01

    Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfill the need for an integrated source of information about these. The database has hierarchical classifications in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. Recent developments include the following. A community annotation project has been instigated in which acknowledged experts are invited to contribute summaries for peptidases. Software has been written to provide an Internet-based data entry form. Contributors are acknowledged on the relevant web page. A new display showing the intron/exon structures of eukaryote peptidase genes and the phasing of the junctions has been implemented. It is now possible to filter the list of peptidases from a completely sequenced bacterial genome for a particular strain of the organism. The MEROPS filing pipeline has been altered to circumvent the restrictions imposed on non-interactive blastp searches, and a HMMER search using specially generated alignments to maximize the distribution of organisms returned in the search results has been added.

  10. Substrate and inhibitor specificity of kynurenine monooxygenase from Cytophaga hutchinsonii.

    Science.gov (United States)

    Phillips, Robert S; Anderson, Andrew D; Gentry, Harvey G; Güner, Osman F; Bowen, J Phillip

    2017-04-15

    Kynurenine monooxygenase (KMO) is a potential drug target for treatment of neurodegenerative disorders such as Huntington's and Alzheimer's diseases. We have evaluated substituted kynurenines as substrates or inhibitors of KMO from Cytophaga hutchinsonii. Kynurenines substituted with a halogen at the 5-position are excellent substrates, with values of k cat and k cat /K m comparable to or higher than kynurenine. However, kynurenines substituted in the 3-position are competitive inhibitors, with K I values lower than the K m for kynurenine. Bromination also enhances inhibition, and 3,5-dibromokynurenine is a potent competitive inhibitor with a K I value of 1.5μM. A pharmacophore model of KMO was developed, and predicted that 3,4-dichlorohippuric acid would be an inhibitor. The K I for this compound was found to be 34μM, thus validating the pharmacophore model. We are using these results and our model to design more potent inhibitors of KMO. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Structural and functional analysis of cyclin D1 reveals p27 and substrate inhibitor binding requirements.

    Science.gov (United States)

    Liu, Shu; Bolger, Joshua K; Kirkland, Lindsay O; Premnath, Padmavathy N; McInnes, Campbell

    2010-12-17

    An alternative strategy for inhibition of the cyclin dependent kinases (CDKs) in antitumor drug discovery is afforded through the substrate recruitment site on the cyclin positive regulatory subunit. Critical CDK substrates such as the Rb and E2F families must undergo cyclin groove binding before phosphorylation, and hence inhibitors of this interaction also block substrate specific kinase activity. This approach offers the potential to generate highly selective and cell cycle specific CDK inhibitors and to reduce the inhibition of transcription mediated through CDK7 and 9, commonly observed with ATP competitive compounds. While highly potent peptide and small molecule inhibitors of CDK2/cyclin A, E substrate recruitment have been reported, little information has been generated on the determinants of inhibitor binding to the cyclin groove of the CDK4/cyclin D1 complex. CDK4/cyclin D is a validated anticancer drug target and continues to be widely pursued in the development of new therapeutics based on cell cycle blockade. We have therefore investigated the structural basis for peptide binding to its cyclin groove and have examined the features contributing to potency and selectivity of inhibitors. Peptidic inhibitors of CDK4/cyclin D of pRb phosphorylation have been synthesized, and their complexes with CDK4/cyclin D1 crystal structures have been generated. Based on available structural information, comparisons of the cyclin grooves of cyclin A2 and D1 are presented and provide insights into the determinants for peptide binding and the basis for differential binding and inhibition. In addition, a complex structure has been generated in order to model the interactions of the CDKI, p27(KIP)¹, with cyclin D1. This information has been used to shed light onto the endogenous inhibition of CDK4 and also to identify unique aspects of cyclin D1 that can be exploited in the design of cyclin groove based CDK inhibitors. Peptidic and nonpeptidic compounds have been

  12. Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1

    Energy Technology Data Exchange (ETDEWEB)

    Lewis-Ballester, Ariel; Pham, Khoa N.; Batabyal, Dipanwita; Karkashon, Shay; Bonanno, Jeffrey B.; Poulos, Thomas L.; Yeh, Syun-Ru (Einstein); (UCI)

    2017-11-22

    Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an attractive cancer immunotherapeutic target owing to its role in promoting tumoral immune escape. However, drug development has been hindered by limited structural information. Here, we report the crystal structures of hIDO1 in complex with its substrate, Trp, an inhibitor, epacadostat, and/or an effector, indole ethanol (IDE). The data reveal structural features of the active site (Sa) critical for substrate activation; in addition, they disclose a new inhibitor-binding mode and a distinct small molecule binding site (Si). Structure-guided mutation of a critical residue, F270, to glycine perturbs the Si site, allowing structural determination of an inhibitory complex, where both the Sa and Si sites are occupied by Trp. The Si site offers a novel target site for allosteric inhibitors and a molecular explanation for the previously baffling substrate-inhibition behavior of the enzyme. Taken together, the data open exciting new avenues for structure-based drug design.

  13. Potent Inhibitors of the Hepatitis C Virus NS3 Protease: Design and Synthesis of Macrocyclic Substrate-Based [beta]-Strand Mimics

    Energy Technology Data Exchange (ETDEWEB)

    Goudreau, Nathalie; Brochu, Christian; Cameron, Dale R.; Duceppe, Jean-Simon; Faucher, Anne-Marie; Ferland, Jean-Marie; Grand-Maître, Chantal; Poirier, Martin; Simoneau, Bruno; Tsantrizos, Youla S. (Boehringer)

    2008-06-30

    The virally encoded NS3 protease is essential to the life cycle of the hepatitis C virus (HCV), an important human pathogen causing chronic hepatitis, cirrhosis of the liver, and hepatocellular carcinoma. The design and synthesis of 15-membered ring {beta}-strand mimics which are capable of inhibiting the interactions between the HCV NS3 protease enzyme and its polyprotein substrate will be described. The binding interactions between a macrocyclic ligand and the enzyme were explored by NMR and molecular dynamics, and a model of the ligand/enzyme complex was developed.

  14. Corrosion Finishing/Coating Systems for DoD Metallic Substrates Based on Non-Chromate Inhibitors and UV Curable, Zero VOC Materials

    Science.gov (United States)

    2010-08-01

    decrease the effective deposition rate of CeCCs by slowing the nucleation process, improving coating quality and corrosion resistance. Investigations on...Release, October 1, 2004. 3. “ Electrodeposition of Cerium Based Coatings for Corrosion Protection of Aluminum Alloys”, J. O. Stoffer, T.J. O’Keefe, S...Chloride Environments”, Materials Letters, 61 (17), 3378 (2007). B. Technical Reports 1. Philip Jones, May 2007, MS Thesis , Impact of Processing

  15. Engineering the substrate and inhibitor specificities of human coagulation Factor VIIa

    DEFF Research Database (Denmark)

    Larsen, Katrine S; Østergaard, Henrik; Bjelke, Jais R

    2007-01-01

    The remarkably high specificity of the coagulation proteases towards macromolecular substrates is provided by numerous interactions involving the catalytic groove and remote exosites. For FVIIa [activated FVII (Factor VII)], the principal initiator of coagulation via the extrinsic pathway, several...... for FVIIa by marked changes in primary substrate specificity and decreased rates of antithrombin III inhibition. Interestingly, these changes do not necessarily coincide with an altered ability to activate Factor X, demonstrating that inhibitor and macromolecular substrate selectivity may be engineered...

  16. Discovery and Characterization of Novel Nonsubstrate and Substrate NAMPT Inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Wilsbacher, Julie L.; Cheng, Min; Cheng, Dong; Trammell, Samuel A.J.; Shi, Yan; Guo, Jun; Koeniger, Stormy L.; Kovar, Peter J.; He, Yupeng; Selvaraju, Sujatha; Heyman, H. Robin; Sorensen, Bryan K.; Clark, Richard F.; Hansen, T. Matthew; Longenecker, Kenton L.; Raich, Diana; Korepanova, Alla V.; Cepa, Steven; Towne, Danli L.; Abraham, Vivek C.; Tang, Hua; Richardson, Paul L.; McLoughlin, Shaun M.; Badagnani, Ilaria; Curtin, Michael L.; Michaelides, Michael R.; Maag, David; Buchanan, F. Gregory; Chiang, Gary G.; Gao, Wenqing; Rosenberg, Saul H.; Brenner, Charles; Tse, Chris (AbbVie)

    2017-05-03

    Cancer cells are highly reliant on NAD+-dependent processes, including glucose metabolism, calcium signaling, DNA repair, and regulation of gene expression. Nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme for NAD+ salvage from nicotinamide, has been investigated as a target for anticancer therapy. Known NAMPT inhibitors with potent cell activity are composed of a nitrogen-containing aromatic group, which is phosphoribosylated by the enzyme. Here, we identified two novel types of NAM-competitive NAMPT inhibitors, only one of which contains a modifiable, aromatic nitrogen that could be a phosphoribosyl acceptor. Both types of compound effectively deplete cellular NAD+, and subsequently ATP, and produce cell death when NAMPT is inhibited in cultured cells for more than 48 hours. Careful characterization of the kinetics of NAMPT inhibition in vivo allowed us to optimize dosing to produce sufficient NAD+ depletion over time that resulted in efficacy in an HCT116 xenograft model. Our data demonstrate that direct phosphoribosylation of competitive inhibitors by the NAMPT enzyme is not required for potent in vitro cellular activity or in vivo antitumor efficacy. Mol Cancer Ther; 16(7); 1236–45.

  17. Turning a Substrate Peptide into a Potent Inhibitor for the Histone Methyltransferase SETD8

    Energy Technology Data Exchange (ETDEWEB)

    Judge, Russell A.; Zhu, Haizhong; Upadhyay, Anup K.; Bodelle, Pierre M.; Hutchins, Charles W.; Torrent, Maricel; Marin, Violeta L.; Yu, Wenyu; Vedadi, Masoud; Li, Fengling; Brown, Peter J.; Pappano, William N.; Sun, Chaohong; Petros, Andrew M.

    2016-12-08

    SETD8 is a histone H4–K20 methyltransferase that plays an essential role in the maintenance of genomic integrity during mitosis and in DNA damage repair, making it an intriguing target for cancer research. While some small molecule inhibitors for SETD8 have been reported, the structural binding modes for these inhibitors have not been revealed. Using the complex structure of the substrate peptide bound to SETD8 as a starting point, different natural and unnatural amino acid substitutions were tested, and a potent (Ki 50 nM, IC50 0.33 μM) and selective norleucine containing peptide inhibitor has been obtained.

  18. SAR and characterization of non-substrate isoindoline urea inhibitors of nicotinamide phosphoribosyltransferase (NAMPT)

    Energy Technology Data Exchange (ETDEWEB)

    Curtin, Michael L.; Heyman, H. Robin; Clark, Richard F.; Sorensen, Bryan K.; Doherty, George A.; Hansen, T. Matthew; Frey, Robin R.; Sarris, Kathy A.; Aguirre, Ana L.; Shrestha, Anurupa; Tu, Noah; Woller, Kevin; Pliushchev, Marina A.; Sweis, Ramzi F.; Cheng, Min; Wilsbacher, Julie L.; Kovar, Peter J.; Guo, Jun; Cheng, Dong; Longenecker, Kenton L.; Raich, Diana; Korepanova, Alla V.; Soni, Nirupama B.; Algire, Mikkel A.; Richardson, Paul L.; Marin, Violeta L.; Badagnani, Ilaria; Vasudevan, Anil; Buchanan, F.Greg; Maag, David; Chiang, Gary G.; Tse, Chris; Michaelides, Michael R. (AbbVie)

    2017-08-01

    Herein we disclose SAR studies that led to a series of isoindoline ureas which we recently reported were first-in-class, non-substrate nicotinamide phosphoribosyltransferase (NAMPT) inhibitors. Modification of the isoindoline and/or the terminal functionality of screening hit 5 provided inhibitors such as 52 and 58 with nanomolar antiproliferative activity and preclinical pharmacokinetics properties which enabled potent antitumor activity when dosed orally in mouse xenograft models. X-ray crystal structures of two inhibitors bound in the NAMPT active-site are discussed.

  19. Identification of cytochrome P450 2D6 and 2C9 substrates and inhibitors by QSAR analysis

    DEFF Research Database (Denmark)

    Jónsdóttir, Svava Ósk; Ringsted, Tine; Nikolov, Nikolai G.

    2012-01-01

    This paper presents four new QSAR models for CYP2C9 and CYP2D6 substrate recognition and inhibitor identification based on human clinical data. The models were used to screen a large data set of environmental chemicals for CYP activity, and to analyze the frequency of CYP activity among these com......This paper presents four new QSAR models for CYP2C9 and CYP2D6 substrate recognition and inhibitor identification based on human clinical data. The models were used to screen a large data set of environmental chemicals for CYP activity, and to analyze the frequency of CYP activity among...... these compounds. A large fraction of these chemicals were found to be CYP active, and thus potentially capable of affecting human physiology. 20% of the compounds within applicability domain of the models were predicted to be CYP2C9 substrates, and 17% to be inhibitors. The corresponding numbers for CYP2D6 were 9...... of specific CYP activity. An overrepresentation was seen for poly-aromatic hydrocarbons (group of procarcinogens) among CYP2C9 active and mutagenic compounds compared to CYP2C9 inactive and mutagenic compounds. The mutagenicity was predicted with a QSAR model based on Ames in vitro test data....

  20. HIV-1 integrase inhibitors are substrates for the multidrug transporter MDR1-P-glycoprotein

    Directory of Open Access Journals (Sweden)

    Cara Andrea

    2007-03-01

    Full Text Available Abstract Background The discovery of diketoacid-containing derivatives as inhibitors of HIV-1 Integrase (IN (IN inhibitors, IINs has played a major role in validating this enzyme as an important target for antiretroviral therapy. Since the in vivo efficacy depends on access of these drugs to intracellular sites where HIV-1 replicates, we determined whether the IINs are recognized by the multidrug transporter MDR1-P-glycoprotein (P-gp thereby reducing their intracellular accumulation. To address the effect of IINs on drug transport, nine quinolonyl diketo acid (DKA derivatives active on the HIV-1 IN strand transfer (ST step and with EC50 ranging from 1.83 to >50 μm in cell-based assays were tested for their in vitro interaction with P-gp in the CEM-MDR cell system. IINs were investigated for the inhibition and induction of the P-gp function and expression as well as for multidrug resistance (MDR reversing ability. Results The HIV-1 IINs act as genuine P-gp substrates by inhibiting doxorubicin efflux and inducing P-gp functional conformation changes as evaluated by the modulation of UIC2 mAb epitope. Further, IINs chemosensitize MDR cells to vinblastine and induce P-gp expression in drug sensitive revertants of CEM-MDR cells. Conclusion To our knowledge, this is the first demonstration that HIV-1 IINs are P-gp substrates. This biological property may influence the absorption, distribution and elimination of these novels anti HIV-1 compounds.

  1. Identification of putative substrates for cynomolgus monkey cytochrome P450 2C8 by substrate depletion assays with 22 human P450 substrates and inhibitors.

    Science.gov (United States)

    Hosaka, Shinya; Murayama, Norie; Satsukawa, Masahiro; Uehara, Shotaro; Shimizu, Makiko; Iwasaki, Kazuhide; Iwano, Shunsuke; Uno, Yasuhiro; Yamazaki, Hiroshi

    2016-07-01

    Cynomolgus monkeys are widely used in drug developmental stages as non-human primate models. Previous studies used 89 compounds to investigate species differences associated with cytochrome P450 (P450 or CYP) function that reported monkey specific CYP2C76 cleared 19 chemicals, and homologous CYP2C9 and CYP2C19 metabolized 17 and 30 human CYP2C9 and/or CYP2C19 substrates/inhibitors, respectively. In the present study, 22 compounds selected from viewpoints of global drug interaction guidances and guidelines were further evaluated to seek potential substrates for monkey CYP2C8, which is highly homologous to human CYP2C8 (92%). Amodiaquine, montelukast, quercetin and rosiglitazone, known as substrates or competitive inhibitors of human CYP2C8, were metabolically depleted by recombinant monkey CYP2C8 at relatively high rates. Taken together with our reported findings of the slow eliminations of amodiaquine and montelukast by monkey CYP2C9, CYP2C19 and CYP2C76, the present results suggest that these at least four chemicals may be good marker substrates for monkey CYP2C8. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  2. Human inter-α-inhibitor is a substrate for factor XIIIa and tissue transglutaminase

    DEFF Research Database (Denmark)

    Sonne-Schmidt, Carsten Scavenius; Sanggaard, Kristian W; Nikolajsen, Camilla L

    2011-01-01

    that inter-α-inhibitor is cross-linked to the fibrin clot in a 1:20 ratio relative to the known factor XIIIa substrate α2-antiplasmin. This interaction may protect fibrin or other Lys-donating proteins from adventitious proteolysis by increasing the local concentration of bikunin. In addition, the reaction...... may influence the TSG-6/heavy Chain 2-mediated transfer of heavy chains observed during inflammation....

  3. Plasmin substrate binding site cooperativity guides the design of potent peptide aldehyde inhibitors.

    Science.gov (United States)

    Swedberg, Joakim E; Harris, Jonathan M

    2011-10-04

    Perioperative bleeding is a cause of major blood loss and is associated with increased rates of postoperative morbidity and mortality. To combat this, antifibrinolytic inhibitors of the serine protease plasmin are commonly used to reduce bleeding during surgery. The most effective and previously widely used of these is the broad range serine protease inhibitor aprotinin. However, adverse clinical outcomes have led to use of alternative serine lysine analogues to inhibit plasmin. These compounds suffer from low selectivity and binding affinity. Consequently, a concerted effort to discover potent and selective plasmin inhibitors has developed. This study used a noncombinatorial peptide library to define plasmin's extended substrate specificity and guide the design of potent transition state analogue inhibitors. The various substrate binding sites of plasmin were found to exhibit a higher degree of cooperativity than had previously been appreciated. Peptide sequences capitalizing on these features produced high-affinity inhibitors of plasmin. The most potent of these, Lys-Met(sulfone)-Tyr-Arg-H [KM(O(2))YR-H], inhibited plasmin with a K(i) of 3.1 nM while maintaining 25-fold selectivity over plasma kallikrein. Furthermore, 125 nM (0.16 μg/mL) KM(O(2))YR-H attenuated fibrinolysis in vitro with an efficacy similar to that of 15 nM (0.20 μg/mL) aprotinin. To date, this is the most potent peptide inhibitor of plasmin that exhibits selectivity against plasma kallikrein, making this compound an attractive candidate for further therapeutic development.

  4. Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Manchi C.M.; Kuppan, Gokulan; Shetty, Nishant D.; Owen, Joshua L.; Ioerger, Thomas R.; Sacchettini, James C. (TAM)

    2009-12-01

    S-adenosylhomocysteine hydrolase (SAHH) is a ubiquitous enzyme that plays a central role in methylation-based processes by maintaining the intracellular balance between S-adenosylhomocysteine (SAH) and S-adenosylmethionine. We report the first prokaryotic crystal structure of SAHH, from Mycobacterium tuberculosis (Mtb), in complex with adenosine (ADO) and nicotinamide adenine dinucleotide. Structures of complexes with three inhibitors are also reported: 3{prime}-keto aristeromycin (ARI), 2-fluoroadenosine, and 3-deazaadenosine. The ARI complex is the first reported structure of SAHH complexed with this inhibitor, and confirms the oxidation of the 3{prime} hydroxyl to a planar keto group, consistent with its prediction as a mechanism-based inhibitor. We demonstrate the in vivo enzyme inhibition activity of the three inhibitors and also show that 2-fluoradenosine has bactericidal activity. While most of the residues lining the ADO-binding pocket are identical between Mtb and human SAHH, less is known about the binding mode of the homocysteine (HCY) appendage of the full substrate. We report the 2.0 {angstrom} resolution structure of the complex of SAHH cocrystallized with SAH. The most striking change in the structure is that binding of HCY forces a rotation of His363 around the backbone to flip out of contact with the 5{prime} hydroxyl of the ADO and opens access to a nearby channel that leads to the surface. This complex suggests that His363 acts as a switch that opens up to permit binding of substrate, then closes down after release of the cleaved HCY. Differences in the entrance to this access channel between human and Mtb SAHH are identified.

  5. Pyrimidine nucleoside analogues, potential chemotherapeutic agents, and substrates/inhibitors in various enzyme systems

    International Nuclear Information System (INIS)

    Kulikowski, T.; Bretner, M.; Felczak, K.; Drabikowska, A.; Shugar, D.

    1998-01-01

    Full text. Pyrimidine nucleoside analogues are an important class of compounds with antimetabolic (antitumor, antiparasitic and antiviral) properties. The synthesis of thiated nucleoside and nucleotide analogues, determination of structures, conformation and dissociation constans, their potential chemotherapeutic activities, and their substrate/inhibitor properties in various enzyme systems, with emphasis on enzymes related to chemotherapeutic activities, were investigated. In the series of thionated inhibitors of thymidylate synthase (TS), potential antitumor agents, regioselective syntheses were elaborated for 2- and 4-thio, and 2,4-dithio derivatives of 2'-deoxyuridine (dUrd), 5-fluoro-2'-deoxyuridine (FdUrd), and several other 5-fluoro-, 5-bromo- and 5-trifluoromethyl congeners, and the 2-thio derivatives of FdUrd and its α-anomer, which proved to be selective agents with high cytotoxicities correlated with the inhibitory activities vs TS of their corresponding 5'-monophosphates. Regioslective syntheses were also elaborated for 2'-deoxycytidin e and 5-fluoro-2'-deoxycitidine derivatives. Solution conformation of these nucleosides were deduced from high-resolution (500 MHz) 1 H NMR spectra. Substrate/inhibitor properties of 2-thio-2'-deoxycitidine (S 2 dCyd) and 5-fluoro-2-thio-2'-deoxycitidine ( S 2 FdCyd) with respect to human leukemic spleen deoxycytidine kinase have been examined. Both are substrates, and also good inhibitors, of phosphorylation of 2'-deoxycitidine and 2'-deoxyadenosine. Particular attention was directed to the specificity of t he NTP phosphate donor for several nucleoside kinases, and procedures have been developed for distinguishing between ATP and other NTP donors, a problem of importance in chemotherapy with nucleoside analogues. Biological properties of the newly synthetize d thiated pyrimidine 2',3'-dideoxy-3'-fluoronucleosides, S 2 ,3'-FddUrd and S 2 ,3'-FddThd, were also investigated. Thiated 3'-fluoronucleosides were moderate

  6. Crosstalk between Substrates and Rho-Associated Kinase Inhibitors in Cryopreservation of Tissue-Engineered Constructs

    Directory of Open Access Journals (Sweden)

    Arindam Bit

    2017-01-01

    Full Text Available It is documented that human mesenchymal stem cells (hMSCs can be differentiated into various types of cells to present a tool for tissue engineering and regenerative medicine. Thus, the preservation of stem cells is a crucial factor for their effective long-term storage that further facilitates their continuous supply and transportation for application in regenerative medicine. Cryopreservation is the most important, practicable, and the only established mechanism for long-term preservation of cells, tissues, and organs, and engineered tissues; thus, it is the key step for the improvement of tissue engineering. A significant portion of MSCs loses cellular viability while freeze-thawing, which represents an important technical limitation to achieving sufficient viable cell numbers for maximum efficacy. Several natural and synthetic materials are extensively used as substrates for tissue engineering constructs and cryopreservation because they promote cell attachment and proliferation. Rho-associated kinase (ROCK inhibitors can improve the physiological function and postthaw viability of cryopreserved MSCs. This review proposes a crosstalk between substrate topology and interaction of cells with ROCK inhibitors. It is shown that incorporation of ionic nanoparticles in the presence of an external electrical field improves the generation of ROCK inhibitors to safeguard cellular viability for the enhanced cryopreservation of engineered tissues.

  7. Novel diamide-based inhibitors of IMPDH.

    Science.gov (United States)

    Gu, Henry H; Iwanowicz, Edwin J; Guo, Junqing; Watterson, Scott H; Shen, Zhongqi; Pitts, William J; Dhar, T G Murali; Fleener, Catherine A; Rouleau, Katherine; Sherbina, N Z; Witmer, Mark; Tredup, Jeffrey; Hollenbaugh, Diane

    2002-05-06

    A series of novel amide-based small molecule inhibitors of inosine monophosphate dehydrogenase is described. The synthesis and the structure-activity relationships (SARs) derived from in vitro studies are presented.

  8. A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior.

    Science.gov (United States)

    Kromann-Hansen, Tobias; Oldenburg, Emil; Yung, Kristen Wing Yu; Ghassabeh, Gholamreza H; Muyldermans, Serge; Declerck, Paul J; Huang, Mingdong; Andreasen, Peter A; Ngo, Jacky Chi Ki

    2016-07-15

    A peptide segment that binds the active site of a serine protease in a substrate-like manner may behave like an inhibitor or a substrate. However, there is sparse information on which factors determine the behavior a particular peptide segment will exhibit. Here, we describe the first x-ray crystal structure of a nanobody in complex with a serine protease. The nanobody displays a new type of interaction between an antibody and a serine protease as it inserts its complementary determining region-H3 loop into the active site of the protease in a substrate-like manner. The unique binding mechanism causes the nanobody to behave as a strong inhibitor as well as a poor substrate. Intriguingly, its substrate behavior is incomplete, as 30-40% of the nanobody remained intact and inhibitory after prolonged incubation with the protease. Biochemical analysis reveals that an intra-loop interaction network within the complementary determining region-H3 of the nanobody balances its inhibitor versus substrate behavior. Collectively, our results unveil molecular factors, which may be a general mechanism to determine the substrate versus inhibitor behavior of other protease inhibitors. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior*

    Science.gov (United States)

    Kromann-Hansen, Tobias; Oldenburg, Emil; Yung, Kristen Wing Yu; Ghassabeh, Gholamreza H.; Muyldermans, Serge; Declerck, Paul J.; Huang, Mingdong; Andreasen, Peter A.; Ngo, Jacky Chi Ki

    2016-01-01

    A peptide segment that binds the active site of a serine protease in a substrate-like manner may behave like an inhibitor or a substrate. However, there is sparse information on which factors determine the behavior a particular peptide segment will exhibit. Here, we describe the first x-ray crystal structure of a nanobody in complex with a serine protease. The nanobody displays a new type of interaction between an antibody and a serine protease as it inserts its complementary determining region-H3 loop into the active site of the protease in a substrate-like manner. The unique binding mechanism causes the nanobody to behave as a strong inhibitor as well as a poor substrate. Intriguingly, its substrate behavior is incomplete, as 30–40% of the nanobody remained intact and inhibitory after prolonged incubation with the protease. Biochemical analysis reveals that an intra-loop interaction network within the complementary determining region-H3 of the nanobody balances its inhibitor versus substrate behavior. Collectively, our results unveil molecular factors, which may be a general mechanism to determine the substrate versus inhibitor behavior of other protease inhibitors. PMID:27226628

  10. Structure of S. aureus HPPK and the discovery of a new substrate site inhibitor.

    Directory of Open Access Journals (Sweden)

    Sandeep Chhabra

    Full Text Available The first structural and biophysical data on the folate biosynthesis pathway enzyme and drug target, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (SaHPPK, from the pathogen Staphylococcus aureus is presented. HPPK is the second essential enzyme in the pathway catalysing the pyrophosphoryl transfer from cofactor (ATP to the substrate (6-hydroxymethyl-7,8-dihydropterin, HMDP. In-silico screening identified 8-mercaptoguanine which was shown to bind with an equilibrium dissociation constant, K(d, of ∼13 µM as measured by isothermal titration calorimetry (ITC and surface plasmon resonance (SPR. An IC(50 of ∼41 µM was determined by means of a luminescent kinase assay. In contrast to the biological substrate, the inhibitor has no requirement for magnesium or the ATP cofactor for competitive binding to the substrate site. The 1.65 Å resolution crystal structure of the inhibited complex showed that it binds in the pterin site and shares many of the key intermolecular interactions of the substrate. Chemical shift and (15N heteronuclear NMR measurements reveal that the fast motion of the pterin-binding loop (L2 is partially dampened in the SaHPPK/HMDP/α,β-methylene adenosine 5'-triphosphate (AMPCPP ternary complex, but the ATP loop (L3 remains mobile on the µs-ms timescale. In contrast, for the SaHPPK/8-mercaptoguanine/AMPCPP ternary complex, the loop L2 becomes rigid on the fast timescale and the L3 loop also becomes more ordered--an observation that correlates with the large entropic penalty associated with inhibitor binding as revealed by ITC. NMR data, including (15N-(1H residual dipolar coupling measurements, indicate that the sulfur atom in the inhibitor is important for stabilizing and restricting important motions of the L2 and L3 catalytic loops in the inhibited ternary complex. This work describes a comprehensive analysis of a new HPPK inhibitor, and may provide a foundation for the development of novel antimicrobials targeting

  11. Identification of the hot spot residues for pyridine derivative inhibitor CCT251455 and ATP substrate binding on monopolar spindle 1 (MPS1) kinase by molecular dynamic simulation.

    Science.gov (United States)

    Chen, Kai; Duan, Wenxiu; Han, Qianqian; Sun, Xuan; Li, Wenqian; Hu, Shuangyun; Wan, Jiajia; Wu, Jiang; Ge, Yushu; Liu, Dan

    2018-03-08

    Protein kinase monopolar spindle 1 plays an important role in spindle assembly checkpoint at the onset of mitosis. Over expression of MPS1 correlated with a wide range of human tumors makes it an attractive target for finding an effective and specific inhibitor. In this work, we performed molecular dynamics simulations of protein MPS1 itself as well as protein bound systems with the inhibitor and natural substrate based on crystal structures. The reported orally bioavailable 1 h-pyrrolo [3,2-c] pyridine inhibitors of MPS1 maintained stable binding in the catalytic site, while natural substrate ATP could not stay. Comparative study of stability and flexibility of three systems reveals position shifting of β-sheet region within the catalytic site, which indicates inhibition mechanism was through stabilizing the β-sheet region. Binding free energies calculated with MM-GB/PBSA method shows different binding affinity for inhibitor and ATP. Finally, interactions between protein and inhibitor during molecular dynamic simulations were measured and counted. Residue Gly605 and Leu654 were suggested as important hot spots for stable binding of inhibitor by molecular dynamic simulation. Our results reveal an important position shifting within catalytic site for non-inhibited proteins. Together with hot spots found by molecular dynamic simulation, the results provide important information of inhibition mechanism and will be referenced for designing novel inhibitors.

  12. A specific and potent inhibitor of glucosylceramide synthase for substrate inhibition therapy of Gaucher disease.

    Science.gov (United States)

    McEachern, Kerry Anne; Fung, John; Komarnitsky, Svetlana; Siegel, Craig S; Chuang, Wei-Lien; Hutto, Elizabeth; Shayman, James A; Grabowski, Gregory A; Aerts, Johannes M F G; Cheng, Seng H; Copeland, Diane P; Marshall, John

    2007-07-01

    An approach to treating Gaucher disease is substrate inhibition therapy which seeks to abate the aberrant lysosomal accumulation of glucosylceramide. We have identified a novel inhibitor of glucosylceramide synthase (Genz-112638) and assessed its activity in a murine model of Gaucher disease (D409V/null). Biochemical characterization of Genz-112638 showed good potency (IC(50) approximately 24nM) and specificity against the target enzyme. Mice that received drug prior to significant accumulation of substrate (10 weeks of age) showed reduced levels of glucosylceramide and number of Gaucher cells in the spleen, lung and liver when compared to age-matched control animals. Treatment of older mice that already displayed significant amounts of tissue glucosylceramide (7 months old) resulted in arrest of further accumulation of the substrate and appearance of additional Gaucher cells in affected organs. These data indicate that substrate inhibition therapy with Genz-112638 represents a viable alternate approach to enzyme therapy to treat the visceral pathology in Gaucher disease.

  13. Substrate-derived triazolo- and azapeptides as inhibitors of cathepsins K and S.

    Science.gov (United States)

    Galibert, Matthieu; Wartenberg, Mylène; Lecaille, Fabien; Saidi, Ahlame; Mavel, Sylvie; Joulin-Giet, Alix; Korkmaz, Brice; Brömme, Dieter; Aucagne, Vincent; Delmas, Agnès F; Lalmanach, Gilles

    2018-01-20

    Cathepsin (Cat) K is a critical bone-resorbing protease and is a relevant target for the treatment of osteoporosis and bone metastasis, while CatS is an attractive target for drugs in autoimmune diseases (e.g. rheumatoid arthritis), emphysema or neuropathic pain. Despite major achievements, current pharmacological inhibitors are still lacking in safety and may have damaging side effects. A promising strategy for developing safer reversible and competitive inhibitors as new lead compounds could be to insert non-cleavable bonds at the scissile P1-P1' position of selective substrates of CatS and CatK. Accordingly, we introduced a 1,4-disubstituted 1,2,3-triazole heterocycle that mimics most of the features of a trans-amide bond, or we incorporated a semicarbazide bond (azaGly residue) by replacing the α-carbon of the glycyl residue at P1 by a nitrogen atom. AzaGly-containing peptidomimetics inhibited powerfully their respective target proteases in the nM range, while triazolopeptides were weaker inhibitors (Ki in the μM range). The selectivity of the azaGly CatS inhibitor (1b) was confirmed by using spleen lysates from wild-type vs CatS-deficient mice. Alternatively, the azaGly bradykinin-derived CatK inhibitor (2b) potently inhibited CatK (Ki = 9 nM) and impaired its kininase activity in vitro. Molecular modeling studies support that the semicarbazide bond of 2b is more favorable than the 1,2,3-triazole linkage of the bradykinin-derived pseudopeptide 2a to preserve an effective affinity towards CatK, its protease target. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  14. A metal-based inhibitor of NEDD8-activating enzyme.

    Directory of Open Access Journals (Sweden)

    Hai-Jing Zhong

    Full Text Available A cyclometallated rhodium(III complex [Rh(ppy(2(dppz](+ (1 (where ppy=2-phenylpyridine and dppz=dipyrido[3,2-a:2',3'-c]phenazine dipyridophenazine has been prepared and identified as an inhibitor of NEDD8-activating enzyme (NAE. The complex inhibited NAE activity in cell-free and cell-based assays, and suppressed the CRL-regulated substrate degradation and NF-κB activation in human cancer cells with potency comparable to known NAE inhibitor MLN4924. Molecular modeling analysis suggested that the overall binding mode of 1 within the binding pocket of the APPBP1/UBA3 heterodimer resembled that for MLN4924. Complex 1 is the first metal complex reported to suppress the NEDDylation pathway via inhibition of the NEDD8-activating enzyme.

  15. Novel peptide-based protease inhibitors

    DEFF Research Database (Denmark)

    Roodbeen, Renée

    of novel peptide-based protease inhibitors, efforts were made towards improved methods for peptide synthesis. The coupling of Fmoc-amino acids onto N-methylated peptidyl resins was investigated. These couplings can be low yielding and the effect of the use of microwave heating combined with the coupling...

  16. Quantification of gamma-secretase modulation differentiates inhibitor compound selectivity between two substrates Notch and amyloid precursor protein

    Directory of Open Access Journals (Sweden)

    Yang Ting

    2008-11-01

    Full Text Available Abstract Background Deposition of amyloid-β protein (Aβ is a major pathological hallmark of Alzheimer's disease (AD. Aβ is generated from γ-secretase cleavage of amyloid precursor protein (APP. In addition to APP, γ-secretase also cleaves other type I integral membrane proteins, including the Notch receptor, a key molecule involved in embryonic development. Results To explore selective γ-secretase inhibitors, a combination of five methods was used to systematically determine these inhibitors' profiles on the γ-secretase cleavage of APP and Notch. When two potent γ-secretase inhibitors, compound E (cpd E and DAPT, were used in a conventional in vitro γ-secretase activity assay, cpd E completely blocked Aβ generation from the cleavage of substrate APP C100, but only had a minor effect on Notch cleavage and NICD generation. Next, cpd E and DAPT were applied to HEK293 cells expressing a truncated Notch substrate NotchΔE. Both cpd E and DAPT were more potent in blocking Aβ generation than NICD generation. Third, a reporter construct was created that carried the NICD targeting promoter with three Su(H binding sequences followed by the luciferase gene. We found that the inhibition of NICD generation by cpd E and DAPT was consistent with the reduced expression of luciferase gene driven by this Notch targeting promoter. Fourth, levels of "Notch-Aβ-like" (Nβ* peptide derived from two previously reported chimeric APP with its transmembrane domain or the juxtamembrane portion replaced by the Notch sequence were quantified. Measurement of Nβ* peptides by ELISA confirmed that EC50's of cpd E were much higher for Nβ* than Aβ. Finally, the expression levels of Notch target gene her6 in cpd E or DAPT-treated zebrafish were correlated with the degree of tail curvature due to defective somitogenesis, a well characterized Notch phenotype in zebrafish. Conclusion Our ELISA-based quantification of Aβ and Nβ* in combination with the test in

  17. [Enzyme kinetic glucose determination by the glucose dehydrogenase method. Enzyme kinetic substrate determination using competitive inhibitors, II (author's transl)].

    Science.gov (United States)

    Müller-Matthesius, R

    1975-05-01

    The sensitivity of enzyme kinetic substrate determinations can be improved with the aid of competitive inhibitors. As an example, the determination of glucose dehydrogenase in the presence of potassium thiocyanate is described. The method has the advantage of rapid operation with satisfactory precision.

  18. Mo-Si-B-Based Coatings for Ceramic Base Substrates

    Science.gov (United States)

    Perepezko, John Harry (Inventor); Sakidja, Ridwan (Inventor); Ritt, Patrick (Inventor)

    2015-01-01

    Alumina-containing coatings based on molybdenum (Mo), silicon (Si), and boron (B) ("MoSiB coatings") that form protective, oxidation-resistant scales on ceramic substrate at high temperatures are provided. The protective scales comprise an aluminoborosilicate glass, and may additionally contain molybdenum. Two-stage deposition methods for forming the coatings are also provided.

  19. Substrate structures for InP-based devices

    International Nuclear Information System (INIS)

    Wanlass, M.W.; Sheldon, P.

    1990-01-01

    A substrate structure for an InP-based semiconductor device having an InP based film is described. The substrate structure includes a substrate region having a lightweight bulk substrate and an upper GaAs layer. An interconnecting region is disposed between the substrate region and the InP-based device. The interconnecting region includes a compositionally graded intermediate layer substantially lattice-matched at the opposite end to the InP=based film. The interconnecting region further includes a dislocation mechanism disposed between the GaAs layer and the InP-based film in cooperation with the graded intermediate layer, the buffer mechanism blocking and inhibiting propagation of threading dislocations between the substrate region, and the InP-based device

  20. Structure-Based Search for New Inhibitors of Cholinesterases

    Directory of Open Access Journals (Sweden)

    Barbara Malawska

    2013-03-01

    Full Text Available Cholinesterases are important biological targets responsible for regulation of cholinergic transmission, and their inhibitors are used for the treatment of Alzheimer’s disease. To design new cholinesterase inhibitors, of different structure-based design strategies was followed, including the modification of compounds from a previously developed library and a fragment-based design approach. This led to the selection of heterodimeric structures as potential inhibitors. Synthesis and biological evaluation of selected candidates confirmed that the designed compounds were acetylcholinesterase inhibitors with IC50 values in the mid-nanomolar to low micromolar range, and some of them were also butyrylcholinesterase inhibitors.

  1. Graphene based strain sensor with LCP substrate

    Science.gov (United States)

    Nie, M.; Yang, H. S.; Xia, Y. H.

    2018-02-01

    A flexible strain sensor constructed by an efficient, low-cost fabrication strategy is presented in this paper. It is assembled by adhering grid-like graphene on LCP substrate. Kinds of measurement setup have been designed to verify that the proposed flexible sensor device is suitable to be used in health monitoring system. From the experiment results, it can be proved that the sensor exhibits the following features: ultra-light, relatively good sensitivity, high reversibility, superior physical robustness, easy fabrication. With the great performance of this flexible strain sensor, it is considered to play an important role in body monitoring, structural health monitoring system, fatigue detection and healthcare systems in the near future.

  2. Importance of the Extracellular Loop 4 in the Human Serotonin Transporter for Inhibitor Binding and Substrate Translocation.

    Science.gov (United States)

    Rannversson, Hafsteinn; Wilson, Pamela; Kristensen, Kristina Birch; Sinning, Steffen; Kristensen, Anders Skov; Strømgaard, Kristian; Andersen, Jacob

    2015-06-05

    The serotonin transporter (SERT) terminates serotonergic neurotransmission by performing reuptake of released serotonin, and SERT is the primary target for antidepressants. SERT mediates the reuptake of serotonin through an alternating access mechanism, implying that a central substrate site is connected to both sides of the membrane by permeation pathways, of which only one is accessible at a time. The coordinated conformational changes in SERT associated with substrate translocation are not fully understood. Here, we have identified a Leu to Glu mutation at position 406 (L406E) in the extracellular loop 4 (EL4) of human SERT, which induced a remarkable gain-of-potency (up to >40-fold) for a range of SERT inhibitors. The effects were highly specific for L406E relative to six other mutations in the same position, including the closely related L406D mutation, showing that the effects induced by L406E are not simply charge-related effects. Leu(406) is located >10 Å from the central inhibitor binding site indicating that the mutation affects inhibitor binding in an indirect manner. We found that L406E decreased accessibility to a residue in the cytoplasmic pathway. The shift in equilibrium to favor a more outward-facing conformation of SERT can explain the reduced turnover rate and increased association rate of inhibitor binding we found for L406E. Together, our findings show that EL4 allosterically can modulate inhibitor binding within the central binding site, and substantiates that EL4 has an important role in controlling the conformational equilibrium of human SERT. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Importance of the Extracellular Loop 4 in the Human Serotonin Transporter for Inhibitor Binding and Substrate Translocation*

    Science.gov (United States)

    Rannversson, Hafsteinn; Wilson, Pamela; Kristensen, Kristina Birch; Sinning, Steffen; Kristensen, Anders Skov; Strømgaard, Kristian; Andersen, Jacob

    2015-01-01

    The serotonin transporter (SERT) terminates serotonergic neurotransmission by performing reuptake of released serotonin, and SERT is the primary target for antidepressants. SERT mediates the reuptake of serotonin through an alternating access mechanism, implying that a central substrate site is connected to both sides of the membrane by permeation pathways, of which only one is accessible at a time. The coordinated conformational changes in SERT associated with substrate translocation are not fully understood. Here, we have identified a Leu to Glu mutation at position 406 (L406E) in the extracellular loop 4 (EL4) of human SERT, which induced a remarkable gain-of-potency (up to >40-fold) for a range of SERT inhibitors. The effects were highly specific for L406E relative to six other mutations in the same position, including the closely related L406D mutation, showing that the effects induced by L406E are not simply charge-related effects. Leu406 is located >10 Å from the central inhibitor binding site indicating that the mutation affects inhibitor binding in an indirect manner. We found that L406E decreased accessibility to a residue in the cytoplasmic pathway. The shift in equilibrium to favor a more outward-facing conformation of SERT can explain the reduced turnover rate and increased association rate of inhibitor binding we found for L406E. Together, our findings show that EL4 allosterically can modulate inhibitor binding within the central binding site, and substantiates that EL4 has an important role in controlling the conformational equilibrium of human SERT. PMID:25903124

  4. Systemic inflammation is linked to low arginine and high ADMA plasma levels resulting in an unfavourable NOS substrate-to-inhibitor ratio: the Hoorn Study

    NARCIS (Netherlands)

    van der Zwan, L.P.; Scheffer, P.G.; Dekker, J.M.; Stehouwer, C.D.A.; Heine, R.J.; Teerlink, T.

    2011-01-01

    Inflammation is associated with a reduced availability of NO in the vasculature. We investigated the possible involvement of altered levels of the substrate (arginine) and the inhibitor [ADMA (asymmetric ω-N

  5. Abundance, genetic diversity and sensitivity to demethylation inhibitor fungicides of Aspergillus fumigatus isolates from organic substrates with special emphasis on compost.

    Science.gov (United States)

    Santoro, Karin; Matić, Slavica; Gisi, Ulrich; Spadaro, Davide; Pugliese, Massimo; Gullino, Maria L

    2017-12-01

    Aspergillus fumigatus is a widespread fungus that colonizes dead organic substrates but it can also cause fatal human diseases. Aspergilloses are treated with demethylation inhibitor (DMI) fungicides; however, resistant isolates appeared recently in the medical and also environmental area. The present study aims at molecular characterizing and quantifying A. fumigatus in major environmental habitats and determining its sensitivity to medical and agricultural DMI fungicides. A. fumigatus was isolated only rarely from soil and meadow/forest organic matter but high concentrations (10 3 to 10 7  cfu/g) were detected in substrates subjected to elevated temperatures, such as compost and silage. High genetic diversity of A. fumigatus from compost was found based on SSR markers, distinguishing among fungal isolates even when coming from the same substrate sample, while subclustering was observed based on mutations in cyp51A gene. Several cyp51A amino acid substitutions were found in 15 isolates, although all isolates were fully sensitive to the tested DMI fungicides, with exception of one isolate in combination with one fungicide. This study suggests that the tested A. fumigatus isolates collected in Italy, Spain and Hungary from the fungus' major living habitats (compost) and commercial growing substrates are not potential carriers for DMI resistance in the environment. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  6. Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring.

    Science.gov (United States)

    Imamura, Haruna; Wagih, Omar; Niinae, Tomoya; Sugiyama, Naoyuki; Beltrao, Pedro; Ishihama, Yasushi

    2017-04-07

    Protein kinase A (PKA or cAMP-dependent protein kinase) is a serine/threonine kinase that plays essential roles in the regulation of proliferation, differentiation, and apoptosis. To better understand the functions of PKA, it is necessary to elucidate the direct interplay between PKA and their substrates in living human cells. To identify kinase target substrates in a high-throughput manner, we first quantified the change of phosphoproteome in the cells of which PKA activity was perturbed by drug stimulations. LC-MS/MS analyses identified 2755 and 3191 phosphopeptides from experiments with activator or inhibitor of PKA. To exclude potential indirect targets of PKA, we built a computational model to characterize the kinase sequence specificity toward the substrate target site based on known kinase-substrate relationships. Finally, by combining the sequence recognition model with the quantitative changes in phosphorylation measured in the two drug perturbation experiments, we identified 29 reliable candidates of PKA targeting residues in living cells including 8 previously known substrates. Moreover, 18 of these sites were confirmed to be site-specifically phosphorylated in vitro. Altogether this study proposed a confident list of PKA substrate candidates, expanding our knowledge of PKA signaling network.

  7. Differential gene expression for suicide-substrate serine proteinase inhibitors (serpins) in vegetative and grain tissues of barley

    DEFF Research Database (Denmark)

    Roberts, T.H.; Marttila, S.; Rasmussen, S.K.

    2003-01-01

    centres in vitro, were ubiquitous at low levels, but the protein could not be detected. EST analysis showed that expression of genes for serpins with BSZx-type reactive centres in vegetative tissues is widespread in the plant kingdom, suggesting a common regulatory function. For BSZ4 and BSZ7, expression...... their irreversible inhibitory mechanism in the inhibition of exogenous proteinases capable of breaking down seed storage proteins, and in the defence of specific cell types in vegetative tissues.......Proteins of the serpin superfamily (similar to43 kDa) from mature cereal grains are in vitro suicide-substrate inhibitors of specific mammalian serine proteinases of the chymotrypsin family. However, unlike the 'standard-mechanism' serine proteinase inhibitors (

  8. Inhibitors

    Science.gov (United States)

    ... JM, and the Hemophilia Inhibitor Research Study Investigators. Validation of Nijmegen-Bethesda assay modifications to allow inhibitor ... webinars on blood disorders Language: English (US) Español (Spanish) File Formats Help: How do I view different ...

  9. Structural Insights into TMB-1 and the Role of Residues 119 and 228 in Substrate and Inhibitor Binding.

    Science.gov (United States)

    Skagseth, Susann; Christopeit, Tony; Akhter, Sundus; Bayer, Annette; Samuelsen, Ørjan; Leiros, Hanna-Kirsti S

    2017-08-01

    Metallo-β-lactamases (MBLs) threaten the effectiveness of β-lactam antibiotics, including carbapenems, and are a concern for global public health. β-Lactam/β-lactamase inhibitor combinations active against class A and class D carbapenemases are used, but no clinically useful MBL inhibitor is currently available. Tripoli metallo-β-lactamase-1 (TMB-1) and TMB-2 are members of MBL subclass B1a, where TMB-2 is an S228P variant of TMB-1. The role of S228P was studied by comparisons of TMB-1 and TMB-2, and E119 was investigated through the construction of site-directed mutants of TMB-1, E119Q, E119S, and E119A (E119Q/S/A). All TMB variants were characterized through enzyme kinetic studies. Thermostability and crystallization analyses of TMB-1 were performed. Thiol-based inhibitors were investigated by determining the 50% inhibitory concentrations (IC 50 ) and binding using surface plasmon resonance (SPR) for analysis of TMB-1. Thermostability measurements found TMB-1 to be stabilized by high NaCl concentrations. Steady-state enzyme kinetics analyses found substitutions of E119, in particular, substitutions associated with the penicillins, to affect hydrolysis to some extent. TMB-2 with S228P showed slightly reduced catalytic efficiency compared to TMB-1. The IC 50 levels of the new thiol-based inhibitors were 0.66 μM (inhibitor 2a) and 0.62 μM (inhibitor 2b), and the equilibrium dissociation constant ( K D ) of inhibitor 2a was 1.6 μM; thus, both were more potent inhibitors than l-captopril (IC 50 = 47 μM; K D = 25 μM). The crystal structure of TMB-1 was resolved to 1.75 Å. Modeling of inhibitor 2b in the TMB-1 active site suggested that the presence of the W64 residue results in T-shaped π-π stacking and R224 cation-π interactions with the phenyl ring of the inhibitor. In sum, the results suggest that residues 119 and 228 affect the catalytic efficiency of TMB-1 and that inhibitors 2a and 2b are more potent inhibitors for TMB-1 than l-captopril. Copyright

  10. Secretory leukocyte protease inhibitor (SLPI is, like its homologue trappin-2 (pre-elafin, a transglutaminase substrate.

    Directory of Open Access Journals (Sweden)

    Kévin Baranger

    Full Text Available Human lungs contain secretory leukocyte protease inhibitor (SLPI, elafin and its biologically active precursor trappin-2 (pre-elafin. These important low-molecular weight inhibitors are involved in controlling the potentially deleterious proteolytic activities of neutrophil serine proteases including elastase, proteinase 3 and cathepsin G. We have shown previously that trappin-2, and to a lesser extent, elafin can be linked covalently to various extracellular matrix proteins by tissue transglutaminases and remain potent protease inhibitors. SLPI is composed of two distinct domains, each of which is about 40% identical to elafin, but it lacks consensus transglutaminase sequence(s, unlike trappin-2 and elafin. We investigated the actions of type 2 tissue transglutaminase and plasma transglutaminase activated factor XIII on SLPI. It was readily covalently bound to fibronectin or elastin by both transglutaminases but did not compete with trappin-2 cross-linking. Cross-linked SLPI still inhibited its target proteases, elastase and cathepsin G. We have also identified the transglutamination sites within SLPI, elafin and trappin-2 by mass spectrometry analysis of tryptic digests of inhibitors cross-linked to mono-dansyl cadaverin or to a fibronectin-derived glutamine-rich peptide. Most of the reactive lysine and glutamine residues in SLPI are located in its first N-terminal elafin-like domain, while in trappin-2, they are located in both the N-terminal cementoin domain and the elafin moiety. We have also demonstrated that the transglutamination substrate status of the cementoin domain of trappin-2 can be transferred from one protein to another, suggesting that it may provide transglutaminase-dependent attachment properties for engineered proteins. We have thus added to the corpus of knowledge on the biology of these potential therapeutic inhibitors of airway proteases.

  11. Green inhibitors. Rare Earth based systems

    International Nuclear Information System (INIS)

    Aballe, A.; Bethencourt, M.; Botana, F.J.; Perez, J.; Rodriguez, M.A.; Marcos, M.

    1997-01-01

    Lanthanum, Cerium and Samarium chlorides have been investigated as uniform and pitting corrosion inhibitors of AISI 434 and AISI 304 stainless steels and AA 5083 Al-Mg alloy in 3.5% Na Cl aerated aqueous solutions. Their inhibitor power was evaluated by using electrochemical techniques such as Linear and Cyclic Polarisation. In each case, the highest protection degree was found in the solution dropped with 500 ppm of CeCl 3 . Similar results were obtained for additions of 500 ppm of LaCl 3 . Scanning Electron Microscopy and Energy Dispersive Spectroscopy allowed us to confirm the cathodic nature of the inhibition process. (Author) 27 refs

  12. Novel guanidine-based inhibitors of inosine monophosphate dehydrogenase.

    Science.gov (United States)

    Iwanowicz, Edwin J; Watterson, Scott H; Liu, Chunjian; Gu, Henry H; Mitt, Toomas; Leftheris, Katerina; Barrish, Joel C; Fleener, Catherine A; Rouleau, Katherine; Sherbina, N Z; Hollenbaugh, Diane L

    2002-10-21

    A series of novel guanidine-based small molecule inhibitors of inosine monophosphate dehydrogenase (IMPDH) was explored. IMPDH catalyzes the rate determining step in guanine nucleotide biosynthesis and is a target for anticancer, immunosuppressive and antiviral therapy. The synthesis and the structure-activity relationships (SARs), derived from in vitro studies, for this new series of inhibitors is given.

  13. Interactions of barley alpha-amylase isozymes with Ca2+, substrates and proteinaceous inhibitors

    DEFF Research Database (Denmark)

    Abou Hachem, Maher; Bozonnet, Sophie; Willemoes, Martin

    2006-01-01

    discovered 'sugar tongs' site in domain C of AMY1 is thus critical for binding to starch granules. Furthermore, mutations of binding sites mostly reduced the degree of multiple attack in amylose hydrolysis. AMY1 has higher substrate affinity than AMY2, but isozyme chimeras with AMY2 domain C and other...

  14. Substrate-Competitive Activity-Based Profiling of Ester Prodrug Activating Enzymes.

    Science.gov (United States)

    Xu, Hao; Majmudar, Jaimeen D; Davda, Dahvid; Ghanakota, Phani; Kim, Ki H; Carlson, Heather A; Showalter, Hollis D; Martin, Brent R; Amidon, Gordon L

    2015-09-08

    Understanding the mechanistic basis of prodrug delivery and activation is critical for establishing species-specific prodrug sensitivities necessary for evaluating preclinical animal models and potential drug-drug interactions. Despite significant adoption of prodrug methodologies for enhanced pharmacokinetics, functional annotation of prodrug activating enzymes is laborious and often unaddressed. Activity-based protein profiling (ABPP) describes an emerging chemoproteomic approach to assay active site occupancy within a mechanistically similar enzyme class in native proteomes. The serine hydrolase enzyme family is broadly reactive with reporter-linked fluorophosphonates, which have shown to provide a mechanism-based covalent labeling strategy to assay the activation state and active site occupancy of cellular serine amidases, esterases, and thioesterases. Here we describe a modified ABPP approach using direct substrate competition to identify activating enzymes for an ethyl ester prodrug, the influenza neuraminidase inhibitor oseltamivir. Substrate-competitive ABPP analysis identified carboxylesterase 1 (CES1) as an oseltamivir-activating enzyme in intestinal cell homogenates. Saturating concentrations of oseltamivir lead to a four-fold reduction in the observed rate constant for CES1 inactivation by fluorophosphonates. WWL50, a reported carbamate inhibitor of mouse CES1, blocked oseltamivir hydrolysis activity in human cell homogenates, confirming CES1 is the primary prodrug activating enzyme for oseltamivir in human liver and intestinal cell lines. The related carbamate inhibitor WWL79 inhibited mouse but not human CES1, providing a series of probes for analyzing prodrug activation mechanisms in different preclinical models. Overall, we present a substrate-competitive activity-based profiling approach for broadly surveying candidate prodrug hydrolyzing enzymes and outline the kinetic parameters for activating enzyme discovery, ester prodrug design, and

  15. Structure-Based Design of Potent and Selective 3-Phosphoinositide-Dependent Kinase-1 (PDK1) Inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Medina, Jesus R.; Becker, Christopher J.; Blackledge, Charles W.; Duquenne, Celine; Feng, Yanhong; Grant, Seth W.; Heerding, Dirk; Li, William H.; Miller, William H.; Romeril, Stuart P.; Scherzer, Daryl; Shu, Arthur; Bobko, Mark A.; Chadderton, Antony R.; Dumble, Melissa; Gardiner, Christine M.; Gilbert, Seth; Liu, Qi; Rabindran, Sridhar K.; Sudakin, Valery; Xiang, Hong; Brady, Pat G.; Campobasso, Nino; Ward, Paris; Axten, Jeffrey M. (GSKPA)

    2014-10-02

    Phosphoinositide-dependent protein kinase-1(PDK1) is a master regulator of the AGC family of kinases and an integral component of the PI3K/AKT/mTOR pathway. As this pathway is among the most commonly deregulated across all cancers, a selective inhibitor of PDK1 might have utility as an anticancer agent. Herein we describe our lead optimization of compound 1 toward highly potent and selective PDK1 inhibitors via a structure-based design strategy. The most potent and selective inhibitors demonstrated submicromolar activity as measured by inhibition of phosphorylation of PDK1 substrates as well as antiproliferative activity against a subset of AML cell lines. In addition, reduction of phosphorylation of PDK1 substrates was demonstrated in vivo in mice bearing OCl-AML2 xenografts. These observations demonstrate the utility of these molecules as tools to further delineate the biology of PDK1 and the potential pharmacological uses of a PDK1 inhibitor.

  16. Experimental and Simulation Identification of Xanthohumol as an Inhibitor and Substrate of ABCB1

    Directory of Open Access Journals (Sweden)

    Fangming Liu

    2018-04-01

    Full Text Available Xanthohumol (XN is a well-known prenylated flavonoid found in Humulus lupulus L. It is involved in several pharmacological activities, including the sensitization of doxorubicin-resistant breast cancer (MCF-7/ADR cells to doxorubicin (DOX through a reduction in cell viability and stemness. In the present study, we revealed another mechanism to further explain the reverse of the drug resistance of XN. In the MCF-7/ADR cell line, we found that XN inhibited the efflux functions of ATP-binding cassette subfamily B member 1 (ABCB1. We also observed that XN was a substrate of ABCB1 and stimulated its ATPase activity. Moreover, our results revealed that XN showed a synergic effect with the ABCB1 substrate colchicine (COL in the MCF-7/ADR cell line. Further, we showed that XN bound to the central transmembrane domain (TMD site, overlapping with the DOX binding site. This mechanism was supported by molecular modeling and simulation data, which revealed that XN bound to the ABCB1 transmembrane domain, where doxorubicin also binds, and its binding affinity was stronger than that of doxorubicin, resulting in less protein and ligand position fluctuation. These results support the XN-induced reversal of drug resistance via the inhibition of ABCB1-mediated transport of doxorubicin, stimulating ABCB1 ATPase activity and acting as a substrate of ABCB1.

  17. Substrate Specificity and Inhibitor Sensitivity of Plant UDP-Sugar Producing Pyrophosphorylases

    Directory of Open Access Journals (Sweden)

    Daniel Decker

    2017-09-01

    Full Text Available UDP-sugars are essential precursors for glycosylation reactions producing cell wall polysaccharides, sucrose, glycoproteins, glycolipids, etc. Primary mechanisms of UDP sugar formation involve the action of at least three distinct pyrophosphorylases using UTP and sugar-1-P as substrates. Here, substrate specificities of barley and Arabidopsis (two isozymes UDP-glucose pyrophosphorylases (UGPase, Arabidopsis UDP-sugar pyrophosphorylase (USPase and Arabidopsis UDP-N-acetyl glucosamine pyrophosphorylase2 (UAGPase2 were investigated using a range of sugar-1-phosphates and nucleoside-triphosphates as substrates. Whereas all the enzymes preferentially used UTP as nucleotide donor, they differed in their specificity for sugar-1-P. UGPases had high activity with D-Glc-1-P, but could also react with Fru-1-P and Fru-2-P (Km values over 10 mM. Contrary to an earlier report, their activity with Gal-1-P was extremely low. USPase reacted with a range of sugar-1-phosphates, including D-Glc-1-P, D-Gal-1-P, D-GalA-1-P (Km of 1.3 mM, β-L-Ara-1-P and α-D-Fuc-1-P (Km of 3.4 mM, but not β-L-Fuc-1-P. In contrast, UAGPase2 reacted only with D-GlcNAc-1-P, D-GalNAc-1-P (Km of 1 mM and, to some extent, D-Glc-1-P (Km of 3.2 mM. Generally, different conformations/substituents at C2, C4, and C5 of the pyranose ring of a sugar were crucial determinants of substrate specificity of a given pyrophosphorylase. Homology models of UDP-sugar binding to UGPase, USPase and UAGPase2 revealed more common amino acids for UDP binding than for sugar binding, reflecting differences in substrate specificity of these proteins. UAGPase2 was inhibited by a salicylate derivative that was earlier shown to affect UGPase and USPase activities, consistent with a common structural architecture of the three pyrophosphorylases. The results are discussed with respect to the role of the pyrophosphorylases in sugar activation for glycosylated end-products.

  18. Novel amide-based inhibitors of inosine 5'-monophosphate dehydrogenase.

    Science.gov (United States)

    Watterson, Scott H; Liu, Chunjian; Dhar, T G Murali; Gu, Henry H; Pitts, William J; Barrish, Joel C; Fleener, Catherine A; Rouleau, Katherine; Sherbina, N Z; Hollenbaugh, Diane L; Iwanowicz, Edwin J

    2002-10-21

    A series of novel amide-based small molecule inhibitors of inosine monophosphate dehydrogenase (IMPDH) was explored. The synthesis and the structure-activity relationships (SARs) derived from in vitro studies are described.

  19. Multiple Linear Regression Analysis Indicates Association of P-Glycoprotein Substrate or Inhibitor Character with Bitterness Intensity, Measured with a Sensor.

    Science.gov (United States)

    Yano, Kentaro; Mita, Suzune; Morimoto, Kaori; Haraguchi, Tamami; Arakawa, Hiroshi; Yoshida, Miyako; Yamashita, Fumiyoshi; Uchida, Takahiro; Ogihara, Takuo

    2015-09-01

    P-glycoprotein (P-gp) regulates absorption of many drugs in the gastrointestinal tract and their accumulation in tumor tissues, but the basis of substrate recognition by P-gp remains unclear. Bitter-tasting phenylthiocarbamide, which stimulates taste receptor 2 member 38 (T2R38), increases P-gp activity and is a substrate of P-gp. This led us to hypothesize that bitterness intensity might be a predictor of P-gp-inhibitor/substrate status. Here, we measured the bitterness intensity of a panel of P-gp substrates and nonsubstrates with various taste sensors, and used multiple linear regression analysis to examine the relationship between P-gp-inhibitor/substrate status and various physical properties, including intensity of bitter taste measured with the taste sensor. We calculated the first principal component analysis score (PC1) as the representative value of bitterness, as all taste sensor's outputs shared significant correlation. The P-gp substrates showed remarkably greater mean bitterness intensity than non-P-gp substrates. We found that Km value of P-gp substrates were correlated with molecular weight, log P, and PC1 value, and the coefficient of determination (R(2) ) of the linear regression equation was 0.63. This relationship might be useful as an aid to predict P-gp substrate status at an early stage of drug discovery. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

  20. The use of LeuT as a model in elucidating binding sites for substrates and inhibitors in neurotransmitter transporters

    DEFF Research Database (Denmark)

    Løland, Claus Juul

    2015-01-01

    Background: The mammalian neurotransmitter transporters are complex proteins playing a central role in synaptic transmission between neurons by rapid reuptake of neurotransmitters. The proteins which transport dopamine, noradrenaline and serotonin belong to the Neurotransmitter:Sodium Symporters...... (NSS). Due to their important role, dysfunctions are associated with several psychiatric and neurological diseases and they also serve as targets for a wide range of therapeutic and illicit drugs. Despite the central physiological and pharmacological importance, direct evidence on structure......–function relationships on mammalian NSS proteins has so far been unsuccessful. The crystal structure of the bacterial NSS protein, LeuT, has been a turning point in structural investigations. Scope of review: To provide an update on what is known about the binding sites for substrates and inhibitors in the Leu...

  1. Inhibiting properties and adsorption of an amine based fatty acid corrosion inhibitor on carbon steel in aqueous carbon dioxide solutions

    Energy Technology Data Exchange (ETDEWEB)

    Buchweishaija, Joseph

    1997-12-31

    Carbon dioxide corrosion is a major corrosion problem in oil and gas production systems and many organic inhibitors have been tested and used to protect the substrate from corrosion. This thesis studies the mechanism of interaction of the inhibitor molecule with the metallic substrate and how this affects the dissolution rate of the metal. The performance of a commercial amine based fatty acid corrosion inhibitor has been investigated using rotating cylinder electrodes and carbon steel electrodes in CO{sub 2} saturated formation water in the temperature range between 35 to 80{sup o}C. The corrosion process was monitored by electrochemical impedance measurements, and at the end of each experiment full polarization curves were recorded. When the inhibitor was applied on noncorroded electrodes, high inhibitor performance, over 99.7%, was observed independent of temperature. On precorroded electrodes inhibitor performance was found to depend on temperature and time of precorrosion. Above 60{sup o}C, the inhibitor performance decreased with increasing time of precorrosion, presumably because of the formation of a corrosion film of either iron carbonate or a combination of iron carbonate and iron carbide which prevent the inhibitor from reaching the surface. The inhibitor protection efficiency was assumed to be associated with the degree of inhibitor coverage at the material surface, and adsorption isotherms have been calculated in the concentration range between 0.1 ppm and 100 ppm. A Langmuir isotherm was found to give the best fit. The inhibitor performance on a 2 days precorroded rotating electrode was investigated at different solution pH ranging between 4.5 and 6.5 at 35{sup o}C. 130 refs., 80 figs., 22 tabs.

  2. Structure and function based design of Plasmodium-selective proteasome inhibitors

    Science.gov (United States)

    Li, Hao; O'Donoghue, Anthony J.; van der Linden, Wouter A.; Xie, Stanley C.; Yoo, Euna; Foe, Ian T.; Tilley, Leann; Craik, Charles S.; da Fonseca, Paula C. A.; Bogyo, Matthew

    2016-01-01

    The proteasome is a multi-component protease complex responsible for regulating key processes such as the cell cycle and antigen presentation1. Compounds that target the proteasome are potentially valuable tools for the treatment of pathogens that depend on proteasome function for survival and replication. In particular, proteasome inhibitors have been shown to be toxic for the malaria parasite Plasmodium falciparum at all stages of its life cycle2-5. Most compounds that have been tested against the parasite also inhibit the mammalian proteasome resulting in toxicity that precludes their use as therapeutic agents2,6. Therefore, better definition of the substrate specificity and structural properties of the Plasmodium proteasome could enable the development of compounds with sufficient selectivity to allow their use as anti-malarial agents. To accomplish this goal, we used a substrate profiling method to uncover differences in the specificities of the human and P. falciparum proteasome. We designed inhibitors based on amino acid preferences specific to the parasite proteasome, and found that they preferentially inhibit the β 2 subunit. We determined the structure of the P. falciparum 20S proteasome bound to the inhibitor using cryo-electron microscopy (cryo-EM) and single particle analysis, to a resolution of 3.6 Å. These data reveal the unusually open P. falciparum β2 active site and provide valuable information regarding active site architecture that can be used to further refine inhibitor design. Furthermore, consistent with the recent finding that the proteasome is important for stress pathways associated with resistance of artemisinin (ART) family anti-malarials7,8, we observed growth inhibition synergism with low doses of this β 2 selective inhibitor in ART sensitive and resistant parasites. Finally, we demonstrated that a parasite selective inhibitor could be used to attenuate parasite growth in vivo without significant toxicity to the host. Thus, the

  3. Structure- and function-based design of Plasmodium-selective proteasome inhibitors.

    Science.gov (United States)

    Li, Hao; O'Donoghue, Anthony J; van der Linden, Wouter A; Xie, Stanley C; Yoo, Euna; Foe, Ian T; Tilley, Leann; Craik, Charles S; da Fonseca, Paula C A; Bogyo, Matthew

    2016-02-11

    The proteasome is a multi-component protease complex responsible for regulating key processes such as the cell cycle and antigen presentation. Compounds that target the proteasome are potentially valuable tools for the treatment of pathogens that depend on proteasome function for survival and replication. In particular, proteasome inhibitors have been shown to be toxic for the malaria parasite Plasmodium falciparum at all stages of its life cycle. Most compounds that have been tested against the parasite also inhibit the mammalian proteasome, resulting in toxicity that precludes their use as therapeutic agents. Therefore, better definition of the substrate specificity and structural properties of the Plasmodium proteasome could enable the development of compounds with sufficient selectivity to allow their use as anti-malarial agents. To accomplish this goal, here we use a substrate profiling method to uncover differences in the specificities of the human and P. falciparum proteasome. We design inhibitors based on amino-acid preferences specific to the parasite proteasome, and find that they preferentially inhibit the β2-subunit. We determine the structure of the P. falciparum 20S proteasome bound to the inhibitor using cryo-electron microscopy and single-particle analysis, to a resolution of 3.6 Å. These data reveal the unusually open P. falciparum β2 active site and provide valuable information about active-site architecture that can be used to further refine inhibitor design. Furthermore, consistent with the recent finding that the proteasome is important for stress pathways associated with resistance of artemisinin family anti-malarials, we observe growth inhibition synergism with low doses of this β2-selective inhibitor in artemisinin-sensitive and -resistant parasites. Finally, we demonstrate that a parasite-selective inhibitor could be used to attenuate parasite growth in vivo without appreciable toxicity to the host. Thus, the Plasmodium proteasome is a

  4. Structure based design of 11β-HSD1 inhibitors.

    Science.gov (United States)

    Singh, Suresh; Tice, Colin

    2010-11-01

    Controlling elevated tissue-specific levels of cortisol may provide a novel therapeutic approach for treating metabolic syndrome. This concept has spurred large scale medicinal chemistry efforts in the pharmaceutical industry for the design of 11β-HSD1 inhibitors. High resolution X-ray crystal structures of inhibitors in complex with the enzyme have facilitated the structure-based design of diverse classes of molecules. A summary of binding modes, trends in structure-activity relationships, and the pharmacodynamic data of inhibitors from each class is presented.

  5. Cigarette smoke toxicants as substrates and inhibitors for human cytosolic SULTs

    International Nuclear Information System (INIS)

    Yasuda, Shin; Idell, Steven; Fu Jian; Carter, Glendora; Snow, Rhodora; Liu, M.-C.

    2007-01-01

    The current study was designed to examine the role of sulfation in the metabolism of cigarette smoke toxicants and clarify whether these toxicants, by serving as substrates for the cytosolic sulfotransferases (SULTs), may interfere with the sulfation of key endogenous compounds. By metabolic labeling, [ 35 S]sulfated species were found to be generated and released into the media of HepG2 human hepatoma cells and primary human lung endothelial cells labeled with [ 35 S]sulfate in the presence of cigarette smoke extract (CSE). Concomitantly, several [ 35 S]sulfated metabolites observed in the medium in the absence of CSE either decreased or disappeared. Eleven previously prepared human cytosolic SULTs were tested for sulfating activity with CSE and known cigarette smoke toxicants as substrates. Activity data revealed SULT1A1, SULT1A2, SULT1A3, and SULT1C2 as major enzymes responsible for their sulfation. To examine their inhibitory effects on the sulfation of 17β-estradiol by SULT1A1, enzymatic assays were performed in the presence of three representative toxicant compounds, namely N-hydroxy-4-aminobiphenyl (N-OH-4-ABP), 4-aminobiphenyl (4-ABP) and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). IC 50 values determined for the sulfation of 17β-estradiol by SULT1A1 were 11.8 μM, 28.2 μM, and 500 μM, respectively, for N-OH-4-ABP, 4-ABP and PhIP. Kinetic analyses indicated that the mechanism underlying the inhibition of 17β-estradiol sulfation by these cigarette smoke toxicants is of a mixed competitive-noncompetitive type. Metabolic labeling experiments clearly showed inhibition of the production of [ 35 S]sulfated 17β-estradiol by N-OH-4-ABP in a concentration-dependent manner in HepG2 cells. Taken together, these results suggest that sulfation plays a significant role in the metabolism of cigarette smoke compounds. By serving as substrates for SULTs, cigarette smoke toxicants may interfere with the metabolism of 17β-estradiol and other endogenous

  6. Kinetic analysis of enzyme systems with suicide substrate in the presence of a reversible competitive inhibitor, tested by simulated progress curves.

    Science.gov (United States)

    Moruno-Dávila, M A; Garrido-del Solo, C; García-Moreno, M; Havsteen, B H; Garcia-Sevilla, F; Garcia-Cánovas, F; Varón, R

    2001-02-01

    The use of suicide substrates remains a very important and useful method in enzymology for studying enzyme mechanisms and designing potential drugs. Suicide substrates act as modified substrates for the target enzymes and bind to the active site. Therefore the presence of a competitive reversible inhibitor decreases the rate of substrate-induced inactivation and protects the enzyme from this inactivation. This lowering on the inactivation rate has evident physiological advantages, since it allows the easy acquisition of experimental data and facilitates kinetic data analysis by providing another variable (inhibitor concentration). However despite the importance of the simultaneous action of a suicide substrate and a competitive reversible inhibition, to date no corresponding kinetic analysis has been carried out. Therefore we present a general kinetic analysis of a Michaelis-Menten reaction mechanism with double inhibition caused by both, a suicide substrate and a competitive reversible inhibitor. We assume rapid equilibrium of the reversible reaction steps involved, while the time course equations for the reaction product have been derived with the assumption of a limiting enzyme. The goodness of the analytical solutions has been tested by comparison with the simulated curves obtained by numerical integration. A kinetic data analysis to determine the corresponding kinetic parameters from the time progress curve of the product is suggested. In conclusion, we present a complete kinetic analysis of an enzyme reaction mechanism as described above in an attempt to fill a gap in the theoretical treatment of this type of system.

  7. Microarray-based screening of heat shock protein inhibitors.

    Science.gov (United States)

    Schax, Emilia; Walter, Johanna-Gabriela; Märzhäuser, Helene; Stahl, Frank; Scheper, Thomas; Agard, David A; Eichner, Simone; Kirschning, Andreas; Zeilinger, Carsten

    2014-06-20

    Based on the importance of heat shock proteins (HSPs) in diseases such as cancer, Alzheimer's disease or malaria, inhibitors of these chaperons are needed. Today's state-of-the-art techniques to identify HSP inhibitors are performed in microplate format, requiring large amounts of proteins and potential inhibitors. In contrast, we have developed a miniaturized protein microarray-based assay to identify novel inhibitors, allowing analysis with 300 pmol of protein. The assay is based on competitive binding of fluorescence-labeled ATP and potential inhibitors to the ATP-binding site of HSP. Therefore, the developed microarray enables the parallel analysis of different ATP-binding proteins on a single microarray. We have demonstrated the possibility of multiplexing by immobilizing full-length human HSP90α and HtpG of Helicobacter pylori on microarrays. Fluorescence-labeled ATP was competed by novel geldanamycin/reblastatin derivatives with IC50 values in the range of 0.5 nM to 4 μM and Z(*)-factors between 0.60 and 0.96. Our results demonstrate the potential of a target-oriented multiplexed protein microarray to identify novel inhibitors for different members of the HSP90 family. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. The Role of Factor XIa (FXIa) Catalytic Domain Exosite Residues in Substrate Catalysis and Inhibition by the Kunitz Protease Inhibitor Domain of Protease Nexin 2*

    Science.gov (United States)

    Su, Ya-Chi; Miller, Tara N.; Navaneetham, Duraiswamy; Schoonmaker, Robert T.; Sinha, Dipali; Walsh, Peter N.

    2011-01-01

    To select residues in coagulation factor XIa (FXIa) potentially important for substrate and inhibitor interactions, we examined the crystal structure of the complex between the catalytic domain of FXIa and the Kunitz protease inhibitor (KPI) domain of a physiologically relevant FXIa inhibitor, protease nexin 2 (PN2). Six FXIa catalytic domain residues (Glu98, Tyr143, Ile151, Arg3704, Lys192, and Tyr5901) were subjected to mutational analysis to investigate the molecular interactions between FXIa and the small synthetic substrate (S-2366), the macromolecular substrate (factor IX (FIX)) and inhibitor PN2KPI. Analysis of all six Ala mutants demonstrated normal Km values for S-2366 hydrolysis, indicating normal substrate binding compared with plasma FXIa; however, all except E98A and K192A had impaired values of kcat for S-2366 hydrolysis. All six Ala mutants displayed deficient kcat values for FIX hydrolysis, and all were inhibited by PN2KPI with normal values of Ki except for K192A, and Y5901A, which displayed increased values of Ki. The integrity of the S1 binding site residue, Asp189, utilizing p-aminobenzamidine, was intact for all FXIa mutants. Thus, whereas all six residues are essential for catalysis of the macromolecular substrate (FIX), only four (Tyr143, Ile151, Arg3704, and Tyr5901) are important for S-2366 hydrolysis; Glu98 and Lys192 are essential for FIX but not S-2366 hydrolysis; and Lys192 and Tyr5901 are required for both inhibitor and macromolecular substrate interactions. PMID:21778227

  9. Plasmonic crystal based solid substrate for biomedical application of SERS

    Science.gov (United States)

    Morasso, Carlo F.; Mehn, Dora; Picciolini, Silvia; Vanna, Renzo; Bedoni, Marzia; Gramatica, Furio; Pellacani, Paola; Frangolho, Ana; Marchesini, Gerardo; Valsesia, Andrea

    2014-02-01

    Surface Enhanced Raman Spectroscopy is a powerful analytical technique that combines the excellent chemical specificity of Raman spectroscopy with the good sensitivity provided by the enhancement of the signal observed when a molecule is located on (or very close to) the surface of suitable nanostructured metallic materials. The availability of cheap, reliable and easy to use SERS substrates would pave the road to the development of bioanalytical tests that can be used in clinical practice. SERS, in fact, is expected to provide not only higher sensitivity and specificity, but also the simultaneous and markedly improved detection of several targets at the same time with higher speed compared to the conventional analytical methods. Here, we present the SERS activity of 2-D plasmonic crystals made by polymeric pillars embedded in a gold matrix obtained through the combination of soft-lithography and plasma deposition techniques on a transparent substrates. The use of a transparent support material allowed us to perform SERS detection from support side opening the possibility to use these substrates in combination with microfluidic devices. In order to demonstrate the potentialities for bioanalytical applications, we used our SERS active gold surface to detect the oxidation product of apomorphine, a well-known drug molecule used in Parkinson's disease which has been demonstrated being difficult to study by traditional HPLC based approaches.

  10. New cholesterol esterase inhibitors based on rhodanine and thiazolidinedione scaffolds

    DEFF Research Database (Denmark)

    Heng, Sabrina; Tieu, William; Hautmann, Stephanie

    2011-01-01

    We present a new class of inhibitors of pancreatic cholesterol esterase (CEase) based on 'priviledged' 5-benzylidenerhodanine and 5-benzylidene-2,4-thiazolidinedione structural scaffolds. The lead structures (5-benzylidenerhodanine 4a and 5-benzylidene-2,4-thiazolidinedione 4b) were identified in...

  11. Nanoscale contacts to organic molecules based on layered semiconductor substrates

    Energy Technology Data Exchange (ETDEWEB)

    Strobel, Sebastian

    2009-06-15

    This work reports on the integration of organic molecules as nanoelectronic device units on semiconductor substrates. Two novel preparation methods for sub-10-nm separated metal electrodes are presented using current microelectronics process technology. The first method utilises AlGaAs/GaAs heterostructures grown by molecular beam epitaxy (MBE) as mold to create planar metal electrodes employing a newly developed, high resolution nanotransfer printing (nTP) process. The second method uses commercially available Silicon-on-Insulator (SOI) substrates as base material for the fabrication of nanogap electrode devices. This sandwich-like material stack consists of a silicon substrate, a thin silicon oxide layer, and a capping silicon layer on top. Electronic transport measurements verified their excellent electrical properties at liquid helium temperatures. Specifically tailored nanogap devices featured an electrode insulation in the GW range even up to room temperature as well as within aqueous electrolyte solution. Finally, the well defined layer architecture facilitated the fabrication of electrodes with gap separations below-10-nm to be directly bridged by molecules. Approximately 12-nm-long conjugated molecules with extended -electron system were assembled onto the devices from solution. A large conductance gap was observed with a steep increase in current at a bias voltage of V{sub T}{approx}{+-}1.5 V. Theoretical calculations based on density functional theory and non-equilibrium Green's function formalism confirmed the measured non-linear IV-characteristics qualitatively and lead to the conclusion that the conductance gap mainly originates from the oxygen containing linker. Temperature dependent investigations of the conductance indicated a hopping charge transport mechanism through the central part of the molecule for bias voltages near but below V{sub T}. (orig.)

  12. Interrogating the Molecular Basis for Substrate Recognition in Serotonin and Dopamine Transporters with High-Affinity Substrate-Based Bivalent Ligands

    DEFF Research Database (Denmark)

    Andersen, Jacob; Ladefoged, Lucy Kate; Kristensen, Trine N. Bjerre

    2016-01-01

    insight into substrate recognition in SERT and DAT. An optimized bivalent ligand comprising two serotonin moieties binds SERT with 3,800-fold increased affinity compared to that of serotonin, suggesting that the human transporters have two distinct substrate binding sites. We show that the bivalent...... ligands are inhibitors of SERT and an experimentally validated docking model suggests that the bivalent compounds bind with one substrate moiety in the central binding site (the S1 site), whereas the other substrate moiety binds in a distinct binding site (the S2 site). A systematic study of nonconserved...

  13. Design of Selective Substrates and Activity-Based Probes for Hydrolase Important for Pathogenesis 1 (HIP1) from Mycobacterium tuberculosis.

    Science.gov (United States)

    Lentz, Christian S; Ordonez, Alvaro A; Kasperkiewicz, Paulina; La Greca, Florencia; O'Donoghue, Anthony J; Schulze, Christopher J; Powers, James C; Craik, Charles S; Drag, Marcin; Jain, Sanjay K; Bogyo, Matthew

    2016-11-11

    Although serine proteases are important mediators of Mycobacterium tuberculosis (Mtb) virulence, there are currently no tools to selectively block or visualize members of this family of enzymes. Selective reporter substrates or activity-based probes (ABPs) could provide a means to monitor infection and response to therapy using imaging methods. Here, we use a combination of substrate selectivity profiling and focused screening to identify optimized reporter substrates and ABPs for the Mtb "Hydrolase important for pathogenesis 1" (Hip1) serine protease. Hip1 is a cell-envelope-associated enzyme with minimal homology to host proteases, making it an ideal target for probe development. We identified substituted 7-amino-4-chloro-3-(2-bromoethoxy)isocoumarins as irreversible inhibitor scaffolds. Furthermore, we used specificity data to generate selective reporter substrates and to further optimize a selective chloroisocoumarin inhibitor. These new reagents are potentially useful in delineating the roles of Hip1 during pathogenesis or as diagnostic imaging tools for specifically monitoring Mtb infections.

  14. Proline-Based Carbamates as Cholinesterase Inhibitors

    Directory of Open Access Journals (Sweden)

    Hana Pizova

    2017-11-01

    Full Text Available Series of twenty-five benzyl (2S-2-(arylcarbamoylpyrrolidine-1-carboxylates was prepared and completely characterized. All the compounds were tested for their in vitro ability to inhibit acetylcholinesterase (AChE and butyrylcholinesterase (BChE, and the selectivity of compounds to individual cholinesterases was determined. Screening of the cytotoxicity of all the compounds was performed using a human monocytic leukaemia THP-1 cell line, and the compounds demonstrated insignificant toxicity. All the compounds showed rather moderate inhibitory effect against AChE; benzyl (2S-2-[(2-chlorophenylcarbamoyl]pyrrolidine-1-carboxylate (IC50 = 46.35 μM was the most potent agent. On the other hand, benzyl (2S-2-[(4-bromophenyl-] and benzyl (2S-2-[(2-bromophenylcarbamoyl]pyrrolidine-1-carboxylates expressed anti-BChE activity (IC50 = 28.21 and 27.38 μM, respectively comparable with that of rivastigmine. The ortho-brominated compound as well as benzyl (2S-2-[(2-hydroxyphenylcarbamoyl]pyrrolidine-1-carboxylate demonstrated greater selectivity to BChE. The in silico characterization of the structure–inhibitory potency for the set of proline-based carbamates considering electronic, steric and lipophilic properties was provided using comparative molecular surface analysis (CoMSA and principal component analysis (PCA. Moreover, the systematic space inspection with splitting data into the training/test subset was performed to monitor the statistical estimators performance in the effort to map the probability-guided pharmacophore pattern. The comprehensive screening of the AChE/BChE profile revealed potentially relevant structural and physicochemical features that might be essential for mapping of the carbamates inhibition efficiency indicating qualitative variations exerted on the reaction site by the substituent in the 3′-/4′-position of the phenyl ring. In addition, the investigation was completed by a molecular docking study of recombinant human AChE.

  15. Real-time zymography and reverse zymography: a method for detecting activities of matrix metalloproteinases and their inhibitors using FITC-labeled collagen and casein as substrates.

    Science.gov (United States)

    Hattori, Shunji; Fujisaki, Hitomi; Kiriyama, Tomomi; Yokoyama, Tsukao; Irie, Shinkichi

    2002-02-01

    Zymography and reverse zymography are widely used techniques for identifying the proteolytic activity of enzymes and the presence of protease inhibitors in polyacrylamide gels. In the current studies, we utilized a fluorescein-isothiocyanate-labeled substrate to develop novel zymographic and reverse zymographic methods for detecting matrix metalloproteinases and tissue inhibitors of the metalloproteinases, respectively. Using a transilluminator, the results can be observed visually without stopping the enzymatic reaction. For this reason, we have named these methods real-time zymography and real-time reverse zymography. These methods have the following advantages compared with conventional protocols: (1) because the reaction can be repeatedly monitored on the polyacrylamide gels, optimization of the incubation time can be achieved without preliminary analyses; (2) higher sensitivity is achieved with a lower amount of substrate than with conventional methods; (3) a semi-quantitative analysis of matrix metalloproteinases is possible. An additional advantage of the real-time reverse zymography is that, because the fluorescence detection is specific for substrate digestion, the inhibitor bands can be easily distinguished from contaminating proteins.

  16. Oxindole based oxadiazole hybrid analogs: Novel α-glucosidase inhibitors.

    Science.gov (United States)

    Taha, Muhammad; Imran, Syahrul; Rahim, Fazal; Wadood, Abdul; Khan, Khalid Mohammed

    2018-02-01

    Inhibition of α-glucosidase is an effective strategy for controlling post-prandial hyperglycemia in diabetic patients. Beside these α-glucosidase inhibitors has been also used as anti-obesity and anti-viral drugs. Keeping in view the greater importance of α-glucosidase inhibitors here in this study we are presenting oxindole based oxadiazoles hybrid analogs (1-20) synthesis, characterized by different spectroscopic techniques including 1 H NMR and EI-MS and their α-glucosidase inhibitory activity. All compounds were found potent inhibitors for the enzyme with IC 50 values ranging between 1.25 ± 0.05 and 268.36 ± 4.22 µM when compared with the standard drug acarbose having IC 50 value 895.09 ± 2.04 µM. Our study identifies novel series of potent α-glucosidase inhibitors and further investigation on this may led to the lead compounds. A structure activity relationship has been established for all compounds. The interactions of the active compounds and enzyme active site were established with the help of molecular docking studies. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Base-modified GDP-mannose derivatives and their substrate activity towards a yeast mannosyltransferase.

    Science.gov (United States)

    Collier, Alice; Wagner, Gerd K

    2017-11-27

    We have previously developed a new class of inhibitors and chemical probes for glycosyltransferases through base-modification of the sugar-nucleotide donor. The key feature of these donor analogues is the presence of an additional substituent at the nucleobase. To date, the application of this general concept has been limited to UDP-sugars and UDP-sugar-dependent glycosyltransferases. Herein, we report for the first time the application of our approach to a GDP-mannose-dependent mannosyltransferase. We have prepared four GDP-mannose derivatives with an additional substituent at either position 6 or 8 of the nucleobase. These donor analogues were recognised as donor substrates by the mannosyltransferase Kre2p from yeast, albeit with significantly lower turnover rates than the natural donor GDP-mannose. The presence of the additional substituent also redirected enzyme activity from glycosyl transfer to donor hydrolysis. Taken together, our results suggest that modification of the donor nucleobase is, in principle, a viable strategy for probe and inhibitor development against GDP-mannose-dependent GTs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Design, synthesis and evaluation of a potent substrate analog inhibitor identified by scanning Ala/Phe mutagenesis, mimicking substrate co-evolution, against multidrug-resistant HIV-1 protease

    International Nuclear Information System (INIS)

    Yedidi, Ravikiran S.; Muhuhi, Joseck M.; Liu, Zhigang; Bencze, Krisztina Z.; Koupparis, Kyriacos; O’Connor, Carrie E.; Kovari, Iulia A.; Spaller, Mark R.; Kovari, Ladislau C.

    2013-01-01

    Highlights: •Inhibitors against MDR HIV-1 protease were designed, synthesized and evaluated. •Lead peptide (6a) showed potent inhibition (IC 50 : 4.4 nM) of MDR HIV-1 protease. •(6a) Showed favorable binding isotherms against NL4-3 and MDR proteases. •(6a) Induced perturbations in the 15 N-HSQC spectrum of MDR HIV-1 protease. •Molecular modeling suggested that (6a) may induce total flap closure inMDR protease. -- Abstract: Multidrug-resistant (MDR) clinical isolate-769, human immunodeficiency virus type-1 (HIV-1) protease (PDB ID: (1TW7)), was shown to exhibit wide-open flaps and an expanded active site cavity, causing loss of contacts with protease inhibitors. In the current study, the expanded active site cavity of MDR769 HIV-1 protease was screened with a series of peptide-inhibitors that were designed to mimic the natural substrate cleavage site, capsid/p2. Scanning Ala/Phe chemical mutagenesis approach was incorporated into the design of the peptide series to mimic the substrate co-evolution. Among the peptides synthesized and evaluated, a lead peptide (6a) with potent activity (IC 50 : 4.4 nM) was identified against the MDR769 HIV-1 protease. Isothermal titration calorimetry data showed favorable binding profile for 6aagainst both wild type and MDR769 HIV-1 protease variants. Nuclear magnetic resonance spectrum of 15 N-labeled MDR769 HIV-1 protease in complex with 6a showed some major perturbations in chemical shift, supporting the peptide induced conformational changes in protease. Modeling analysis revealed multiple contacts between 6a and MDR769 HIV-1 protease. The lead peptide-inhibitor, 6a, with high potency and good binding profile can be used as the basis for developing potent small molecule inhibitors against MDR variants of HIV

  19. Design, synthesis and evaluation of a potent substrate analog inhibitor identified by scanning Ala/Phe mutagenesis, mimicking substrate co-evolution, against multidrug-resistant HIV-1 protease

    Energy Technology Data Exchange (ETDEWEB)

    Yedidi, Ravikiran S. [Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201 (United States); Muhuhi, Joseck M. [Department of Chemistry, Wayne State University, Detroit, MI 48202 (United States); Liu, Zhigang [Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201 (United States); Bencze, Krisztina Z. [Department of Chemistry, Fort Hays State University, Hays, KS 67601 (United States); Koupparis, Kyriacos [Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201 (United States); Department of Chemistry, Wayne State University, Detroit, MI 48202 (United States); O’Connor, Carrie E.; Kovari, Iulia A. [Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201 (United States); Spaller, Mark R. [Department of Chemistry, Wayne State University, Detroit, MI 48202 (United States); Kovari, Ladislau C., E-mail: kovari@med.wayne.edu [Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201 (United States)

    2013-09-06

    Highlights: •Inhibitors against MDR HIV-1 protease were designed, synthesized and evaluated. •Lead peptide (6a) showed potent inhibition (IC{sub 50}: 4.4 nM) of MDR HIV-1 protease. •(6a) Showed favorable binding isotherms against NL4-3 and MDR proteases. •(6a) Induced perturbations in the {sup 15}N-HSQC spectrum of MDR HIV-1 protease. •Molecular modeling suggested that (6a) may induce total flap closure inMDR protease. -- Abstract: Multidrug-resistant (MDR) clinical isolate-769, human immunodeficiency virus type-1 (HIV-1) protease (PDB ID: (1TW7)), was shown to exhibit wide-open flaps and an expanded active site cavity, causing loss of contacts with protease inhibitors. In the current study, the expanded active site cavity of MDR769 HIV-1 protease was screened with a series of peptide-inhibitors that were designed to mimic the natural substrate cleavage site, capsid/p2. Scanning Ala/Phe chemical mutagenesis approach was incorporated into the design of the peptide series to mimic the substrate co-evolution. Among the peptides synthesized and evaluated, a lead peptide (6a) with potent activity (IC{sub 50}: 4.4 nM) was identified against the MDR769 HIV-1 protease. Isothermal titration calorimetry data showed favorable binding profile for 6aagainst both wild type and MDR769 HIV-1 protease variants. Nuclear magnetic resonance spectrum of {sup 15}N-labeled MDR769 HIV-1 protease in complex with 6a showed some major perturbations in chemical shift, supporting the peptide induced conformational changes in protease. Modeling analysis revealed multiple contacts between 6a and MDR769 HIV-1 protease. The lead peptide-inhibitor, 6a, with high potency and good binding profile can be used as the basis for developing potent small molecule inhibitors against MDR variants of HIV.

  20. The role of a second-shell residue in modifying substrate and inhibitor interactions in the SHV beta-lactamase: a study of ambler position Asn276.

    Science.gov (United States)

    Drawz, Sarah M; Bethel, Christopher R; Hujer, Kristine M; Hurless, Kelly N; Distler, Anne M; Caselli, Emilia; Prati, Fabio; Bonomo, Robert A

    2009-06-02

    Inhibitor-resistant class A beta-lactamases of the TEM and SHV families that arise by single amino acid substitutions are a significant threat to the efficacy of beta-lactam/beta-lactamase inhibitor combinations. To better understand the basis of the inhibitor-resistant phenotype in SHV, we performed mutagenesis to examine the role of a second-shell residue, Asn276. Of the 19 variants expressed in Escherichia coli, only the Asn276Asp enzyme demonstrated reduced susceptibility to ampicillin/clavulanate (MIC increased from 50/2 --> 50/8 microg/mL) while maintaining high-level resistance to ampicillin (MIC = 8192 microg/mL). Steady-state kinetic analyses of Asn276Asp revealed slightly diminished k(cat)/K(m) for all substrates tested. In contrast, we observed a 5-fold increase in K(i) for clavulanate (7.4 +/- 0.9 microM for Asn276Asp vs 1.4 +/- 0.2 microM for SHV-1) and a 40% reduction in k(inact)/K(I) (0.013 +/- 0.002 microM(-1 )s(-1) for Asn276Asp vs 0.021 +/- 0.004 microM(-1) s(-1) for SHV-1). Timed electrospray ionization mass spectrometry of clavulanate-inhibited SHV-1 and SHV Asn276Asp showed nearly identical mass adducts, arguing for a similar pathway of inactivation. Molecular modeling shows that novel electrostatic interactions are formed between Arg244Neta2 and both 276AspOdelta1 and Odelta2; these new forces restrict the spatial position of Arg244, a residue important in the recognition of the C(3)/C(4) carboxylate of beta-lactam substrates and inhibitors. Testing the functional consequences of this interaction, we noted considerable free energy costs (+DeltaDeltaG) for substrates and inhibitors. A rigid carbapenem (meropenem) was most affected by the Asn276Asp substitution (46-fold increase in K(i) vs SHV-1). We conclude that residue 276 is an important second-shell residue in class A beta-lactamase-mediated resistance to substrates and inhibitors, and only Asn is able to precisely modulate the conformational flexibility of Arg244 required for successful

  1. Systemic delivery of a glucosylceramide synthase inhibitor reduces CNS substrates and increases lifespan in a mouse model of type 2 Gaucher disease.

    Directory of Open Access Journals (Sweden)

    Mario A Cabrera-Salazar

    Full Text Available Neuropathic Gaucher disease (nGD, also known as type 2 or type 3 Gaucher disease, is caused by a deficiency of the enzyme glucocerebrosidase (GC. This deficiency impairs the degradation of glucosylceramide (GluCer and glucosylsphingosine (GluSph, leading to their accumulation in the brains of patients and mouse models of the disease. These accumulated substrates have been thought to cause the severe neuropathology and early death observed in patients with nGD and mouse models. Substrate accumulation is evident at birth in both nGD mouse models and humans affected with the most severe type of the disease. Current treatment of non-nGD relies on the intravenous delivery of recombinant human glucocerebrosidase to replace the missing enzyme or the administration of glucosylceramide synthase inhibitors to attenuate GluCer production. However, the currently approved drugs that use these mechanisms do not cross the blood brain barrier, and thus are not expected to provide a benefit for the neurological complications in nGD patients. Here we report the successful reduction of substrate accumulation and CNS pathology together with a significant increase in lifespan after systemic administration of a novel glucosylceramide synthase inhibitor to a mouse model of nGD. To our knowledge this is the first compound shown to cross the blood brain barrier and reduce substrates in this animal model while significantly enhancing its lifespan. These results reinforce the concept that systemically administered glucosylceramide synthase inhibitors could hold enhanced therapeutic promise for patients afflicted with neuropathic lysosomal storage diseases.

  2. Systemic delivery of a glucosylceramide synthase inhibitor reduces CNS substrates and increases lifespan in a mouse model of type 2 Gaucher disease.

    Science.gov (United States)

    Cabrera-Salazar, Mario A; Deriso, Matthew; Bercury, Scott D; Li, Lingyun; Lydon, John T; Weber, William; Pande, Nilesh; Cromwell, Mandy A; Copeland, Diane; Leonard, John; Cheng, Seng H; Scheule, Ronald K

    2012-01-01

    Neuropathic Gaucher disease (nGD), also known as type 2 or type 3 Gaucher disease, is caused by a deficiency of the enzyme glucocerebrosidase (GC). This deficiency impairs the degradation of glucosylceramide (GluCer) and glucosylsphingosine (GluSph), leading to their accumulation in the brains of patients and mouse models of the disease. These accumulated substrates have been thought to cause the severe neuropathology and early death observed in patients with nGD and mouse models. Substrate accumulation is evident at birth in both nGD mouse models and humans affected with the most severe type of the disease. Current treatment of non-nGD relies on the intravenous delivery of recombinant human glucocerebrosidase to replace the missing enzyme or the administration of glucosylceramide synthase inhibitors to attenuate GluCer production. However, the currently approved drugs that use these mechanisms do not cross the blood brain barrier, and thus are not expected to provide a benefit for the neurological complications in nGD patients. Here we report the successful reduction of substrate accumulation and CNS pathology together with a significant increase in lifespan after systemic administration of a novel glucosylceramide synthase inhibitor to a mouse model of nGD. To our knowledge this is the first compound shown to cross the blood brain barrier and reduce substrates in this animal model while significantly enhancing its lifespan. These results reinforce the concept that systemically administered glucosylceramide synthase inhibitors could hold enhanced therapeutic promise for patients afflicted with neuropathic lysosomal storage diseases.

  3. Repositioning the substrate activity screening (SAS) approach as a fragment-based method for identification of weak binders.

    Science.gov (United States)

    Gladysz, Rafaela; Cleenewerck, Matthias; Joossens, Jurgen; Lambeir, Anne-Marie; Augustyns, Koen; Van der Veken, Pieter

    2014-10-13

    Fragment-based drug discovery (FBDD) has evolved into an established approach for "hit" identification. Typically, most applications of FBDD depend on specialised cost- and time-intensive biophysical techniques. The substrate activity screening (SAS) approach has been proposed as a relatively cheap and straightforward alternative for identification of fragments for enzyme inhibitors. We have investigated SAS for the discovery of inhibitors of oncology target urokinase (uPA). Although our results support the key hypotheses of SAS, we also encountered a number of unreported limitations. In response, we propose an efficient modified methodology: "MSAS" (modified substrate activity screening). MSAS circumvents the limitations of SAS and broadens its scope by providing additional fragments and more coherent SAR data. As well as presenting and validating MSAS, this study expands existing SAR knowledge for the S1 pocket of uPA and reports new reversible and irreversible uPA inhibitor scaffolds. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Silica-Based Sol-Gel Coating on Magnesium Alloy with Green Inhibitors

    Directory of Open Access Journals (Sweden)

    Vinod Upadhyay

    2017-06-01

    Full Text Available In this work, the performances of several natural organic inhibitors were investigated in a sol-gel system (applied on the magnesium alloy Mg AZ31B substrate. The inhibitors were quinaldic acid (QDA, betaine (BET, dopamine hydrochloride (DOP, and diazolidinyl urea (DZU. Thin, uniform, and defect-free sol-gel coatings were prepared with and without organic inhibitors, and applied on the Mg AZ31B substrate. SEM and EDX were performed to analyze the coating surface properties, the adhesion to the substrate, and the thickness. Electrochemical measurements, including electrochemical impedance spectroscopy (EIS and anodic potentiodynamic polarization scan (PDS, were performed on the coated samples to characterize the coatings’ protective properties. Also, hydrogen evolution measurement—an easy method to measure magnesium corrosion—was performed in order to characterize the efficiency of coating protection on the magnesium substrate. Moreover, scanning vibrating electrode technique (SVET measurements were performed to examine the efficiency of the coatings loaded with inhibitors in preventing and containing corrosion events in defect areas. From the testing results it was observed that the formulated sol-gel coatings provided a good barrier to the substrate, affording some protection even without the presence of inhibitors. Finally, when the inhibitors’ performances were compared, the QDA-doped sol-gel was able to contain the corrosion event at the defect.

  5. Two-way pharmacokinetic interaction studies between saxagliptin and cytochrome P450 substrates or inhibitors: simvastatin, diltiazem extended-release, and ketoconazole

    Directory of Open Access Journals (Sweden)

    Patel C

    2011-06-01

    Full Text Available Chirag G Patel, Li Li, Suzette Girgis, David M Kornhauser, Ernest U Frevert, David W BoultonBristol-Myers Squibb, Princeton, NJ, USABackground: Many medicines, including several cholesterol-lowering agents (eg, lovastatin, simvastatin, antihypertensives (eg, diltiazem, nifedipine, verapamil, and antifungals (eg, ketoconazole are metabolized by and/or inhibit the cytochrome P450 (CYP 3A4 metabolic pathway. These types of medicines are commonly coprescribed to treat comorbidities in patients with type 2 diabetes mellitus (T2DM and the potential for drug-drug interactions of these medicines with new medicines for T2DM must be carefully evaluated.Objective: To investigate the effects of CYP3A4 substrates or inhibitors, simvastatin (substrate, diltiazem (moderate inhibitor, and ketoconazole (strong inhibitor on the pharmacokinetics and safety of saxagliptin, a CYP3A4/5 substrate; and the effects of saxagliptin on these agents in three separate studies.Methods: Healthy subjects were administered saxagliptin 10 mg or 100 mg. Simvastatin, diltiazem extended-release, and ketoconazole doses of 40 mg once daily, 360 mg once daily, and 200 mg twice daily, respectively, were used to determine two-way pharmacokinetic interactions.Results: Coadministration of simvastatin, diltiazem extended-release, or ketoconazole increased mean area under the concentration-time curve values (AUC of saxagliptin by 12%, 109%, and 145%, respectively, versus saxagliptin alone. Mean exposure (AUC of the CYP3A4-generated active metabolite of saxagliptin, 5-hydroxy saxagliptin, decreased with coadministration of simvastatin, diltiazem, and ketoconazole by 2%, 34%, and 88%, respectively. All adverse events were considered mild or moderate in all three studies; there were no serious adverse events or deaths.Conclusion: Saxagliptin, when coadministered with simvastatin, diltiazem extended-release, or ketoconazole, was safe and generally well tolerated in healthy subjects. Clinically

  6. Importance of the Extracellular Loop 4 in the Human Serotonin Transporter for Inhibitor Binding and Substrate Translocation

    DEFF Research Database (Denmark)

    Rannversson, Hafsteinn; Wilson, Pamela; Kristensen, Kristina Birch

    2015-01-01

    ) in the extracellular loop 4 (EL4) of human SERT, which induced a remarkable gain-of-potency (up to >40-fold) for a range of SERT inhibitors. The effects were highly specific for L406E relative to six other mutations in the same position, including the closely related L406D mutation, showing that the effects induced...... to favor a more outward-facing conformation of SERT can explain the reduced turnover rate and increased association rate of inhibitor binding we found for L406E. Together, our findings show that EL4 allosterically can modulate inhibitor binding within the central binding site, and substantiates that EL4...

  7. Metabolic Effects of a Succinic Acid<Based Substrate Antihypoxant

    Directory of Open Access Journals (Sweden)

    B. N. Shakh

    2014-01-01

    Full Text Available The paper discusses promises for clinical use of substrate antihypoxants.Objective: to investigate the efficacy of succinate containing  substrate  antihypoxants  on  systemic  oxygen  consumption,  blood  buffer  capacity,  and  changes  in  the  mixed venous blood level of lactate when they are used in gravely sick patients and victims with marked metabolic posthypoxic disorders.Subjects and methods. The trial enrolled 30 patients and victims who had sustained an episode of severe hypoxia of mixed genesis, the severity of which was evaluated by the APACHE II scale and amounted to 23 to 30 scores with a 46 to 70.3% risk of death. The standard infusion program in this group involved the succinate-containing drug 1.5% reamberin solution  in  a  total  dose  of  800  ml.  A  comparison  group  included  15  patients  who  had  undergone  emergency  extensive surgery for abdominal diseases. 400 ml of 10% glucose solution was used as an infusion medium. Oxygen consumption (VO2ml/min and carbon dioxide production (VCO2ml/min were measured before infusion and monitored for 2 hours. Arterial blood gases and acid-base balance (ABB parameters and mixed venous blood lactate levels were examined. Measurements were made before and 30 minutes after the infusion of reamberin or glucose solution.Results. Infusion of 1.5% reamberin solution was followed by a significant increase in minute oxygen consumption from 281.5±21.2 to 310.4±24.4 ml/min. CO2 production declined (on average, from 223.3±6.5 to 206.5±7.59 ml/min. During infusion of 10% glucose solution, all the patients of the comparison group showed a rise in oxygen consumption from 303.6±33.86 to 443.13±32.1 ml/min, i.e. about 1.5-fold. VCO2 changed similarly. The intravenous infusion of 800 ml of 1.5% reamberin solution raised arterial blood buffer capacity, which was reflected by changes in pH, BE, and HCO3. There was a clear trend for lactate values to drop in the

  8. A New Assay for Measurement of Acetylcholinesterase and Butyrylcholinesterase in Canine Whole Blood Combining Specific Substrates and Ethopropazine Hydrochloride as a Selective Butyrylcholinesterase Inhibitor

    Directory of Open Access Journals (Sweden)

    F Tecles, A Tvarijonaviciute and JJ Cerón*

    2013-11-01

    Full Text Available In the present report, a new assay combining specific substrates and a selective BChE inhibitor (ethopropazine hydrochloride was used to measure both AChE and BChE in canine whole blood samples. Acetylthiocholine iodide (ATCI and butyrylthiocholine iodide (BTCI were used as substrates, whereas 2,2’-dithiodipiridine was used as chromophore. Ethopropazine concentration inhibiting over 95% BChE with minimum AChE inhibition was fixed at 0.3mM. The results confirmed that whole blood cholinesterase activity measured with BTCI in absence of ethopropazine corresponded with serum BChE, whereas whole blood cholinesterase analysed with ATCI in presence of ethopropazine reflected mainly erythrocytes and plasma AChE activity. This procedure showed good repeatability, it was easy and fast, and can be routinely used in veterinary laboratories.

  9. Fragment-based discovery of a potent NAMPT inhibitor.

    Science.gov (United States)

    Korepanova, Alla; Longenecker, Kenton L; Pratt, Steve D; Panchal, Sanjay C; Clark, Richard F; Lake, Marc; Gopalakrishnan, Sujatha M; Raich, Diana; Sun, Chaohong; Petros, Andrew M

    2017-12-12

    NAMPT expression is elevated in many cancers, making this protein a potential target for anticancer therapy. We have carried out both NMR based and TR-FRET based fragment screens against human NAMPT and identified six novel binders with a range of potencies. Co-crystal structures were obtained for two of the fragments bound to NAMPT while for the other four fragments force-field driven docking was employed to generate a bound pose. Based on structural insights arising from comparison of the bound fragment poses to that of bound FK866 we were able to synthetically elaborate one of the fragments into a potent NAMPT inhibitor. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Peptide-based proteasome inhibitors in anticancer drug design.

    Science.gov (United States)

    Micale, Nicola; Scarbaci, Kety; Troiano, Valeria; Ettari, Roberta; Grasso, Silvana; Zappalà, Maria

    2014-09-01

    The identification of the key role of the eukaryotic 26S proteasome in regulated intracellular proteolysis and its importance as a target in many pathological conditions wherein the proteasomal activity is defective (e.g., malignancies, autoimmune diseases, neurodegenerative diseases, etc.) prompted several research groups to the development of specific inhibitors of this multicatalytic complex with the aim of obtaining valid drug candidates. In regard to the anticancer therapy, the peptide boronate bortezomib (Velcade®) represents the first molecule approved by FDA for the treatment of multiple myeloma in 2003 and mantle cell lymphoma in 2006. Since then, a plethora of molecules targeting the proteasome have been identified as potential anticancer agents and a few of them reached clinical trials or are already in the market (i.e., carfilzomib; Kyprolis®). In most cases, the design of new proteasome inhibitors (PIs) takes into account a proven peptide or pseudopeptide motif as a base structure and places other chemical entities throughout the peptide skeleton in such a way to create an efficacious network of interactions within the catalytic sites. The purpose of this review is to provide an in-depth look at the current state of the research in the field of peptide-based PIs, specifically those ones that might find an application as anticancer agents. © 2014 Wiley Periodicals, Inc.

  11. Superhydrophobic SERS substrates based on silicon hierarchical nanostructures

    Science.gov (United States)

    Chen, Xuexian; Wen, Jinxiu; Zhou, Jianhua; Zheng, Zebo; An, Di; Wang, Hao; Xie, Weiguang; Zhan, Runze; Xu, Ningsheng; Chen, Jun; She, Juncong; Chen, Huanjun; Deng, Shaozhi

    2018-02-01

    Silicon nanostructures have been cultivated as promising surface enhanced Raman scattering (SERS) substrates in terms of their low-loss optical resonance modes, facile functionalization, and compatibility with today’s state-of-the-art CMOS techniques. However, unlike their plasmonic counterparts, the electromagnetic field enhancements induced by silicon nanostructures are relatively small, which restrict their SERS sensing limit to around 10-7 M. To tackle this problem, we propose here a strategy for improving the SERS performance of silicon nanostructures by constructing silicon hierarchical nanostructures with a superhydrophobic surface. The hierarchical nanostructures are binary structures consisted of silicon nanowires (NWs) grown on micropyramids (MPs). After being modified with perfluorooctyltriethoxysilane (PFOT), the nanostructure surface shows a stable superhydrophobicity with a high contact angle of ˜160°. The substrate can allow for concentrating diluted analyte solutions into a specific area during the evaporation of the liquid droplet, whereby the analytes are aggregated into a small volume and can be easily detected by the silicon nanostructure SERS substrate. The analyte molecules (methylene blue: MB) enriched from an aqueous solution lower than 10-8 M can be readily detected. Such a detection limit is ˜100-fold lower than the conventional SERS substrates made of silicon nanostructures. Additionally, the detection limit can be further improved by functionalizing gold nanoparticles onto silicon hierarchical nanostructures, whereby the superhydrophobic characteristics and plasmonic field enhancements can be combined synergistically to give a detection limit down to ˜10-11 M. A gold nanoparticle-functionalized superhydrophobic substrate was employed to detect the spiked melamine in liquid milk. The results showed that the detection limit can be as low as 10-5 M, highlighting the potential of the proposed superhydrophobic SERS substrate in

  12. Nanowires-based light emitters on thermally and electrically conductive substrates and of making same

    KAUST Repository

    Ooi, Boon S.; Zhao, Chao; Ng, Tien Khee

    2017-01-01

    Elemental or compound semiconductors on metal substrates and methods of growing them are provided. The methods can include the steps of: (i) providing a metal substrate; (ii) adding an interlayer on a surface of the metal substrate, and (iii) growing semiconductor nanowires on the interlayer using a semiconductor epitaxy growth system to form the elemental or compound semiconductor. The method can include direct growth of high quality group III-V and group III-N based materials in the form of nanowires and nanowires-based devices on metal substrates. The nanowires on all- metal scheme greatly simplifies the fabrication process of nanowires based high power light emitters.

  13. Nanowires-based light emitters on thermally and electrically conductive substrates and of making same

    KAUST Repository

    Ooi, Boon S.

    2017-04-27

    Elemental or compound semiconductors on metal substrates and methods of growing them are provided. The methods can include the steps of: (i) providing a metal substrate; (ii) adding an interlayer on a surface of the metal substrate, and (iii) growing semiconductor nanowires on the interlayer using a semiconductor epitaxy growth system to form the elemental or compound semiconductor. The method can include direct growth of high quality group III-V and group III-N based materials in the form of nanowires and nanowires-based devices on metal substrates. The nanowires on all- metal scheme greatly simplifies the fabrication process of nanowires based high power light emitters.

  14. Thermodynamic and Structure Guided Design of Statin Based Inhibitors of 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase

    Energy Technology Data Exchange (ETDEWEB)

    Sarver, Ronald W.; Bills, Elizabeth; Bolton, Gary; Bratton, Larry D.; Caspers, Nicole L.; Dunbar, James B.; Harris, Melissa S.; Hutchings, Richard H.; Kennedy, Robert M.; Larsen, Scott D.; Pavlovsky, Alexander; Pfefferkorn, Jeffrey A.; Bainbridge, Graeme (Pfizer)

    2008-10-02

    Clinical studies have demonstrated that statins, 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) inhibitors, are effective at lowering mortality levels associated with cardiovascular disease; however, 2--7% of patients may experience statin-induced myalgia that limits compliance with a treatment regimen. High resolution crystal structures, thermodynamic binding parameters, and biochemical data were used to design statin inhibitors with improved HMGR affinity and therapeutic index relative to statin-induced myalgia. These studies facilitated the identification of imidazole 1 as a potent (IC{sub 50} = 7.9 nM) inhibitor with excellent hepatoselectivity (>1000-fold) and good in vivo efficacy. The binding of 1 to HMGR was found to be enthalpically driven with a {Delta}H of -17.7 kcal/M. Additionally, a second novel series of bicyclic pyrrole-based inhibitors was identified that induced order in a protein flap of HMGR. Similar ordering was detected in a substrate complex, but has not been reported in previous statin inhibitor complexes with HMGR.

  15. Substrate and Inhibitor-Specific Conformational Changes in the Human Serotonin Transporter Revealed by Voltage-Clamp Fluorometry

    DEFF Research Database (Denmark)

    Söderhielm, Pella C; Andersen, Jacob; Munro, Lachlan

    2015-01-01

    of TM6, Ala419 in the interface between TM8 and extracellular loop (EL) 4, and Leu481 in EL5. The reporter positions were used for time-resolved measurement of conformational changes during 5-HT transport and binding of cocaine and the selective serotonin reuptake inhibitors fluoxetine and escitalopram...... changes overall, which included movements within or around TM1b, EL4, and EL5. Taken together, our data lead us to suggest that competitive inhibitors stabilize hSERT in a state that is different from the apo outward-open conformation as well as inward-facing conformations....

  16. Experimental Study on Inkjet-Printed Passive UHF RFID Tags on Versatile Paper-Based Substrates

    Directory of Open Access Journals (Sweden)

    Han He

    2016-01-01

    Full Text Available We present the possibilities and challenges of passive UHF RFID tag antennas manufactured by inkjet printing silver nanoparticle ink on versatile paper-based substrates. The most efficient manufacturing parameters, such as the pattern resolution, were determined and the optimal number of printed layers was evaluated for each substrate material. Next, inkjet-printed passive UHF RFID tags were fabricated on each substrate with the optimized parameters and number of layers. According to our measurements, the tags on different paper substrates showed peak read ranges of 4–6.5 meters and the tags on different cardboard substrates exhibited peak read ranges of 2–6 meters. Based on their wireless performance, these inkjet-printed paper-based passive UHF RFID tags are sufficient for many future wireless applications and comparable to tags fabricated on more traditional substrates, such as polyimide.

  17. Aqueous Molecular Dynamics Simulations of the M. tuberculosis Enoyl-ACP Reductase-NADH System and Its Complex with a Substrate Mimic or Diphenyl Ethers Inhibitors

    Directory of Open Access Journals (Sweden)

    Camilo Henrique da Silva Lima

    2015-10-01

    Full Text Available Molecular dynamics (MD simulations of 12 aqueous systems of the NADH-dependent enoyl-ACP reductase from Mycobacterium tuberculosis (InhA were carried out for up to 20–40 ns using the GROMACS 4.5 package. Simulations of the holoenzyme, holoenzyme-substrate, and 10 holoenzyme-inhibitor complexes were conducted in order to gain more insight about the secondary structure motifs of the InhA substrate-binding pocket. We monitored the lifetime of the main intermolecular interactions: hydrogen bonds and hydrophobic contacts. Our MD simulations demonstrate the importance of evaluating the conformational changes that occur close to the active site of the enzyme-cofactor complex before and after binding of the ligand and the influence of the water molecules. Moreover, the protein-inhibitor total steric (ELJ and electrostatic (EC interaction energies, related to Gly96 and Tyr158, are able to explain 80% of the biological response variance according to the best linear equation, pKi = 7.772 − 0.1885 × Gly96 + 0.0517 × Tyr158 (R2 = 0.80; n = 10, where interactions with Gly96, mainly electrostatic, increase the biological response, while those with Tyr158 decrease. These results will help to understand the structure-activity relationships and to design new and more potent anti-TB drugs.

  18. Coplanar transitions based on aluminum nitride interposer substrate for terabit transceivers

    DEFF Research Database (Denmark)

    Dong, Yunfeng; Johansen, Tom Keinicke; Zhurbenko, Vitaliy

    2017-01-01

    This paper presents two types of coplanar transitions based on aluminum nitride (AlN) substrate for interposer designs of terabit transceivers. The designs of coupled coplanar waveguide (CCPW), coupled line, coplanar waveguide (CPW), and coplanar stripline (CPS) based on AlN substrate are explained...

  19. A ph sensor based on a flexible substrate

    Science.gov (United States)

    Huang, Wen-Ding

    implanted inside the esophagus. Our pH electrode can monitor the pH changes of gastric juice in real time when the reflux happening in the esophagus. Our micro flexible pH sensor performed clear responses in each distinct pH reflux episode quickly and accurately comparing with the other commercial pH monitoring system. For the food freshness monitoring applications, we used the flexible pH sensor as a freshness indicator to monitor the pH changing profile during the food spoilage procedure. The sensor was then embedded with radio frequency identification (RFID) based passive telemetry enabling remote monitoring of food freshness. In the result, our pH-wireless RFID system presented 633Hz/pH of the sensitivity in the frequency calibration. The calibration of stability and dynamical response of the RFID system were also demonstrated before the test on food freshness monitoring. Finally, a white fish meat for long term spoilage procedure monitoring was applied and tested by using our wireless IrOx pH sensing system. Our RFID pH sensing module is able to monitor, collect and transmit the pH information continuously for 18 hours during the food spoilage procedure. In this dissertation, a micro size of IrOx/AgCl pH sensor was fabricated on a flexible substrate. The physical properties of the IrO x thin film was verified in the work. The different sensing capability such as the sensitivity, stability, reversibility, response time, repeatability, selectivity, and temperature dependence was then demonstrated in this work. After the different in-vitro tests, the pH sensor were embedded with our passive RFID circuitry for the in-vivo GERD diagnosis and food freshness monitoring application. Our wireless pH sensing system was able to deliver the accurate and quick pH sensing data wirelessly. In conclusion, our deformable IrOx pH electrodes have been demonstrated with the advantages of accommodating and conforming sensors in small spaces or curved surfaces. This miniature IrOx pH sensor

  20. A novel yeast cell-based screen identifies flavone as a tankyrase inhibitor

    International Nuclear Information System (INIS)

    Yashiroda, Yoko; Okamoto, Reika; Hatsugai, Kaori; Takemoto, Yasushi; Goshima, Naoki; Saito, Tamio; Hamamoto, Makiko; Sugimoto, Yoshikazu; Osada, Hiroyuki; Seimiya, Hiroyuki; Yoshida, Minoru

    2010-01-01

    The telomere-associated protein tankyrase 1 is a poly(ADP-ribose) polymerase and is considered to be a promising target for cancer therapy, especially for BRCA-associated cancers. However, an efficient assay system for inhibitor screening has not been established, mainly due to the difficulty of efficient preparation of the enzyme and its substrate. Here, we report a cell-based assay system for detecting inhibitory activity against tankyrase 1. We found that overexpression of the human tankyrase 1 gene causes a growth defect in the fission yeast Schizosaccharomyces pombe. Chemicals that restore the growth defect phenotype can be identified as potential tankyrase 1 inhibitors. We performed a high-throughput screen using this system, and identified flavone as a compound that restores the growth of yeast cells overexpressing tankyrase 1. Indeed, flavone inhibited poly(ADP-ribosyl)ation of proteins caused by overexpression of tankyrase 1 in yeast cells. This system allows rapid identification of inhibitory activity against tankyrase 1 and is amenable to high-throughput screening using robotics.

  1. Detection of Benzoic Acid by an Amperometric Inhibitor Biosensor Based on Mushroom Tissue Homogenate

    Directory of Open Access Journals (Sweden)

    Mustafa Kemal Sezgintürk

    2005-01-01

    Full Text Available An amperometric benzoic acid-sensing inhibitor biosensor was prepared by immobilizing mushroom (Agaricus bisporus tissue homogenate on a Clark-type oxygen electrode. The effects of the quantity of mushroom tissue homogenate, the quantity of gelatin and the effect of the crosslinking agent glutaraldehyde percent on the biosensor were studied. The optimum concentration of phenol used as substrate was 200 μM. The bioanalytical properties of the proposed biosensor, such as dependence of the biosensor response on the pH value and the temperature, were investigated. The biosensor responded linearly to benzoic acid in a concentration range of 25–100 μM. Standard deviation (s.d. was ±0.49 μM for 7 successive determinations at a concentration of 75 μM. The inhibitor biosensor based on mushroom tissue homogenate was applied for the determination of benzoic acid in fizzy lemonade, some fruits and groundwater samples. Results were compared to those obtained using AOAC method, showing a good agreement.

  2. A human fatty acid synthase inhibitor binds β-ketoacyl reductase in the keto-substrate site.

    Science.gov (United States)

    Hardwicke, Mary Ann; Rendina, Alan R; Williams, Shawn P; Moore, Michael L; Wang, Liping; Krueger, Julie A; Plant, Ramona N; Totoritis, Rachel D; Zhang, Guofeng; Briand, Jacques; Burkhart, William A; Brown, Kristin K; Parrish, Cynthia A

    2014-09-01

    Human fatty acid synthase (hFAS) is a complex, multifunctional enzyme that is solely responsible for the de novo synthesis of long chain fatty acids. hFAS is highly expressed in a number of cancers, with low expression observed in most normal tissues. Although normal tissues tend to obtain fatty acids from the diet, tumor tissues rely on de novo fatty acid synthesis, making hFAS an attractive metabolic target for the treatment of cancer. We describe here the identification of GSK2194069, a potent and specific inhibitor of the β-ketoacyl reductase (KR) activity of hFAS; the characterization of its enzymatic and cellular mechanism of action; and its inhibition of human tumor cell growth. We also present the design of a new protein construct suitable for crystallography, which resulted in what is to our knowledge the first co-crystal structure of the human KR domain and includes a bound inhibitor.

  3. High quality silicon-based substrates for microwave and millimeter wave passive circuits

    Science.gov (United States)

    Belaroussi, Y.; Rack, M.; Saadi, A. A.; Scheen, G.; Belaroussi, M. T.; Trabelsi, M.; Raskin, J.-P.

    2017-09-01

    Porous silicon substrate is very promising for next generation wireless communication requiring the avoidance of high-frequency losses originating from the bulk silicon. In this work, new variants of porous silicon (PSi) substrates have been introduced. Through an experimental RF performance, the proposed PSi substrates have been compared with different silicon-based substrates, namely, standard silicon (Std), trap-rich (TR) and high resistivity (HR). All of the mentioned substrates have been fabricated where identical samples of CPW lines have been integrated on. The new PSi substrates have shown successful reduction in the substrate's effective relative permittivity to values as low as 3.7 and great increase in the substrate's effective resistivity to values higher than 7 kΩ cm. As a concept proof, a mm-wave bandpass filter (MBPF) centred at 27 GHz has been integrated on the investigated substrates. Compared with the conventional MBPF implemented on standard silicon-based substrates, the measured S-parameters of the PSi-based MBPF have shown high filtering performance, such as a reduction in insertion loss and an enhancement of the filter selectivity, with the joy of having the same filter performance by varying the temperature. Therefore, the efficiency of the proposed PSi substrates has been well highlighted. From 1994 to 1995, she was assistant of physics at (USTHB), Algiers . From 1998 to 2011, she was a Researcher at characterization laboratory in ionized media and laser division at the Advanced Technologies Development Center. She has integrated the Analog Radio Frequency Integrated Circuits team as Researcher since 2011 until now in Microelectronic and Nanotechnology Division at Advanced Technologies Development Center (CDTA), Algiers. She has been working towards her Ph.D. degree jointly at CDTA and Ecole Nationale Polytechnique, Algiers, since 2012. Her research interest includes fabrication and characterization of microwave passive devices on porous

  4. Fragment-based approaches to the discovery of kinase inhibitors.

    Science.gov (United States)

    Mortenson, Paul N; Berdini, Valerio; O'Reilly, Marc

    2014-01-01

    Protein kinases are one of the most important families of drug targets, and aberrant kinase activity has been linked to a large number of disease areas. Although eminently targetable using small molecules, kinases present a number of challenges as drug targets, not least obtaining selectivity across such a large and relatively closely related target family. Fragment-based drug discovery involves screening simple, low-molecular weight compounds to generate initial hits against a target. These hits are then optimized to more potent compounds via medicinal chemistry, usually facilitated by structural biology. Here, we will present a number of recent examples of fragment-based approaches to the discovery of kinase inhibitors, detailing the construction of fragment-screening libraries, the identification and validation of fragment hits, and their optimization into potent and selective lead compounds. The advantages of fragment-based methodologies will be discussed, along with some of the challenges associated with using this route. Finally, we will present a number of key lessons derived both from our own experience running fragment screens against kinases and from a large number of published studies.

  5. Steric Hindrance as a Basis for Structure-Based Design of Selective Inhibitors of Protein-Tyrosine Phosphatases

    DEFF Research Database (Denmark)

    Iversen, L. F.; Andersen, H. S.; Møller, K. B.

    2001-01-01

    Utilizing structure-based design, we have previously demonstrated that it is possible to obtain selective inhibitors of protein-tyrosine phosphatase 1B (PTP1B). A basic nitrogen was introduced into a general PTP inhibitor to form a salt bridge to Asp48 in PTP1B and simultaneously cause repulsion...... in PTPs containing an asparagine in the equivalent position [Iversen, L. F., et al. (2000) J. Biol. Chem. 275, 10300−10307]. Further, we have recently demonstrated that Gly259 in PTP1B forms the bottom of a gateway that allows easy access to the active site for a broad range of substrates, while bulky...... in accessibility to the active site among various PTPs. We show that a general, low-molecular weight PTP inhibitor can be developed into a highly selective inhibitor for PTP1B and TC-PTP by introducing a substituent, which is designed to address the region around residues 258 and 259. Detailed enzyme kinetic...

  6. Crystal structure of an FIV/HIV chimeric protease complexed with the broad-based inhibitor, TL-3

    Directory of Open Access Journals (Sweden)

    Elder John H

    2007-01-01

    Full Text Available Abstract We have obtained the 1.7 Å crystal structure of FIV protease (PR in which 12 critical residues around the active site have been substituted with the structurally equivalent residues of HIV PR (12X FIV PR. The chimeric PR was crystallized in complex with the broad-based inhibitor TL-3, which inhibits wild type FIV and HIV PRs, as well as 12X FIV PR and several drug-resistant HIV mutants 1234. Biochemical analyses have demonstrated that TL-3 inhibits these PRs in the order HIV PR > 12X FIV PR > FIV PR, with Ki values of 1.5 nM, 10 nM, and 41 nM, respectively 234. Comparison of the crystal structures of the TL-3 complexes of 12X FIV and wild-typeFIV PR revealed theformation of additinal van der Waals interactions between the enzyme inhibitor in the mutant PR. The 12X FIV PR retained the hydrogen bonding interactions between residues in the flap regions and active site involving the enzyme and the TL-3 inhibitor in comparison to both FIV PR and HIV PR. However, the flap regions of the 12X FIV PR more closely resemble those of HIV PR, having gained several stabilizing intra-flap interactions not present in wild type FIV PR. These findings offer a structural explanation for the observed inhibitor/substrate binding properties of the chimeric PR.

  7. Crius: A Novel Fragment-Based Algorithm of De Novo Substrate Prediction for Enzymes.

    Science.gov (United States)

    Yao, Zhiqiang; Jiang, Shuiqin; Zhang, Lujia; Gao, Bei; He, Xiao; Zhang, John Z H; Wei, Dongzhi

    2018-05-03

    The study of enzyme substrate specificity is vital for developing potential applications of enzymes. However, the routine experimental procedures require lot of resources in the discovery of novel substrates. This article reports an in silico structure-based algorithm called Crius, which predicts substrates for enzyme. The results of this fragment-based algorithm show good agreements between the simulated and experimental substrate specificities, using a lipase from Candida antarctica (CALB), a nitrilase from Cyanobacterium syechocystis sp. PCC6803 (Nit6803), and an aldo-keto reductase from Gluconobacter oxydans (Gox0644). This opens new prospects of developing computer algorithms that can effectively predict substrates for an enzyme. This article is protected by copyright. All rights reserved. © 2018 The Protein Society.

  8. GaN-based light-emitting diodes on various substrates: a critical review.

    Science.gov (United States)

    Li, Guoqiang; Wang, Wenliang; Yang, Weijia; Lin, Yunhao; Wang, Haiyan; Lin, Zhiting; Zhou, Shizhong

    2016-05-01

    GaN and related III-nitrides have attracted considerable attention as promising materials for application in optoelectronic devices, in particular, light-emitting diodes (LEDs). At present, sapphire is still the most popular commercial substrate for epitaxial growth of GaN-based LEDs. However, due to its relatively large lattice mismatch with GaN and low thermal conductivity, sapphire is not the most ideal substrate for GaN-based LEDs. Therefore, in order to obtain high-performance and high-power LEDs with relatively low cost, unconventional substrates, which are of low lattice mismatch with GaN, high thermal conductivity and low cost, have been tried as substitutes for sapphire. As a matter of fact, it is not easy to obtain high-quality III-nitride films on those substrates for various reasons. However, by developing a variety of techniques, distincts progress has been made during the past decade, with high-performance LEDs being successfully achieved on these unconventional substrates. This review focuses on state-of-the-art high-performance GaN-based LED materials and devices on unconventional substrates. The issues involved in the growth of GaN-based LED structures on each type of unconventional substrate are outlined, and the fundamental physics behind these issues is detailed. The corresponding solutions for III-nitride growth, defect control, and chip processing for each type of unconventional substrate are discussed in depth, together with a brief introduction to some newly developed techniques in order to realize LED structures on unconventional substrates. This is very useful for understanding the progress in this field of physics. In this review, we also speculate on the prospects for LEDs on unconventional substrates.

  9. Bacillus subtilis RapA phosphatase domain interaction with its substrate, phosphorylated Spo0F, and its inhibitor, the PhrA peptide.

    Science.gov (United States)

    Diaz, Alejandra R; Core, Leighton J; Jiang, Min; Morelli, Michela; Chiang, Christina H; Szurmant, Hendrik; Perego, Marta

    2012-03-01

    Rap proteins in Bacillus subtilis regulate the phosphorylation level or the DNA-binding activity of response regulators such as Spo0F, involved in sporulation initiation, or ComA, regulating competence development. Rap proteins can be inhibited by specific peptides generated by the export-import processing pathway of the Phr proteins. Rap proteins have a modular organization comprising an amino-terminal alpha-helical domain connected to a domain formed by six tetratricopeptide repeats (TPR). In this study, the molecular basis for the specificity of the RapA phosphatase for its substrate, phosphorylated Spo0F (Spo0F∼P), and its inhibitor pentapeptide, PhrA, was analyzed in part by generating chimeric proteins with RapC, which targets the DNA-binding domain of ComA, rather than Spo0F∼P, and is inhibited by the PhrC pentapeptide. In vivo analysis of sporulation efficiency or competence-induced gene expression, as well as in vitro biochemical assays, allowed the identification of the amino-terminal 60 amino acids as sufficient to determine Rap specificity for its substrate and the central TPR3 to TPR5 (TPR3-5) repeats as providing binding specificity toward the Phr peptide inhibitor. The results allowed the prediction and testing of key residues in RapA that are essential for PhrA binding and specificity, thus demonstrating how the widespread structural fold of the TPR is highly versatile, using a common interaction mechanism for a variety of functions in eukaryotic and prokaryotic organisms.

  10. Metformin Is a Substrate and Inhibitor of the Human Thiamine Transporter, THTR-2 (SLC19A3).

    Science.gov (United States)

    Liang, Xiaomin; Chien, Huan-Chieh; Yee, Sook Wah; Giacomini, Marilyn M; Chen, Eugene C; Piao, Meiling; Hao, Jia; Twelves, Jolyn; Lepist, Eve-Irene; Ray, Adrian S; Giacomini, Kathleen M

    2015-12-07

    The biguanide metformin is widely used as first-line therapy for the treatment of type 2 diabetes. Predominately a cation at physiological pH's, metformin is transported by membrane transporters, which play major roles in its absorption and disposition. Recently, our laboratory demonstrated that organic cation transporter 1, OCT1, the major hepatic uptake transporter for metformin, was also the primary hepatic uptake transporter for thiamine, vitamin B1. In this study, we tested the reverse, i.e., that metformin is a substrate of thiamine transporters (THTR-1, SLC19A2, and THTR-2, SLC19A3). Our study demonstrated that human THTR-2 (hTHTR-2), SLC19A3, which is highly expressed in the small intestine, but not hTHTR-1, transports metformin (Km = 1.15 ± 0.2 mM) and other cationic compounds (MPP(+) and famotidine). The uptake mechanism for hTHTR-2 was pH and electrochemical gradient sensitive. Furthermore, metformin as well as other drugs including phenformin, chloroquine, verapamil, famotidine, and amprolium inhibited hTHTR-2 mediated uptake of both thiamine and metformin. Species differences in the substrate specificity of THTR-2 between human and mouse orthologues were observed. Taken together, our data suggest that hTHTR-2 may play a role in the intestinal absorption and tissue distribution of metformin and other organic cations and that the transporter may be a target for drug-drug and drug-nutrient interactions.

  11. Ligand and structure-based classification models for Prediction of P-glycoprotein inhibitors

    DEFF Research Database (Denmark)

    Klepsch, Freya; Poongavanam, Vasanthanathan; Ecker, Gerhard Franz

    2014-01-01

    an algorithm based on Euclidean distance. Results show that random forest and SVM performed best for classification of P-gp inhibitors and non-inhibitors, correctly predicting 73/75 % of the external test set compounds. Classification based on the docking experiments using the scoring function Chem...

  12. Surface-enhanced Raman spectroscopy based on conical holed enhancing substrates

    International Nuclear Information System (INIS)

    Chen, Yao; Chen, Zeng-Ping; Zuo, Qi; Shi, Cai-Xia; Yu, Ru-Qin

    2015-01-01

    In this contribution, surface-enhanced Raman spectroscopy (SERS) based on conical holed glass substrates deposited with silver colloids was reported for the first time. It combines the advantages of both dry SERS assays based on plane films deposited with silver colloids and wet SERS assays utilizing cuvettes or capillary tubes. Compared with plane glass substrates deposited with silver colloids, the conical holed glass substrates deposited with silver colloids exhibited five-to ten-folds of increase in the rate of signal enhancement, due to the internal multiple reflections of both the excitation laser beam and the Raman scattering photons within conical holes. The application of conical holed glass substrates could also yield significantly stronger and more reproducible SERS signals than SERS assays utilizing capillary tubes to sample the mixture of silver colloids and the solution of the analyte of interest. The conical holed glass substrates in combination with the multiplicative effects model for surface-enhanced Raman spectroscopy (MEM SERS ) achieved quite sensitive and precise quantification of 6-mercaptopurine in complex plasma samples with an average relative prediction error of about 4% and a limit of detection of about 0.02 μM using a portable i-Raman 785H spectrometer. It is reasonable to expect that SERS technique based on conical holed enhancing substrates in combination with MEM SERS model can be developed and extended to other application areas such as drug detection, environmental monitoring, and clinic analysis, etc. - Highlights: • A novel conical holed SERS enhancing substrate was designed and manufactured. • The optimal conical holed glass substrates can produce stronger SERS signal. • The novel substrates can overcome the shortcomings of both dry and wet methods. • The novel substrates coupled with MEM SERS can realize quantitative SERS assays

  13. Discovery of new Gyrase β inhibitors via structure based modeling.

    Science.gov (United States)

    Al-Nadaf, Afaf H; Salah, Sajeda A; Taha, Mutasem O

    2018-03-19

    Gyrase B is an essential enzyme in the prokaryotes which became an attractive target for antibacterial agents. In our study, we implemented a wide range of docking configurations to dock 120 inhibitors into the in the ATP- binding pocket of Gyrase B enzyme (PDB code: 4GEE). LigandFit docking engines and six scoring functions were utilized in the study. Furthermore, the ligands were docked in their ionized and unionized forms into the hydrous and anhydrous binding pocket. We used docking-based Comparative Intermolecular Contacts Analysis (db-CICA) which is a novel methodology to validate and identify the optimal docking configurations. Three docking configurations were found to achieve self-consistent db-CICA models. The resulting db-CICA models were used to construct corresponding pharmacophoric models that were used to screen the National Cancer Institute (NCI) list of compounds. In-vitro study represents antibacterial activities for twelve hit molecules with the most active having IC 50 of 20.9 μM. Copyright © 2018. Published by Elsevier Ltd.

  14. Prospective iterative trial of proteasome inhibitor-based desensitization.

    Science.gov (United States)

    Woodle, E S; Shields, A R; Ejaz, N S; Sadaka, B; Girnita, A; Walsh, R C; Alloway, R R; Brailey, P; Cardi, M A; Abu Jawdeh, B G; Roy-Chaudhury, P; Govil, A; Mogilishetty, G

    2015-01-01

    A prospective iterative trial of proteasome inhibitor (PI)-based therapy for reducing HLA antibody (Ab) levels was conducted in five phases differing in bortezomib dosing density and plasmapheresis timing. Phases included 1 or 2 bortezomib cycles (1.3 mg/m(2) × 6-8 doses), one rituximab dose and plasmapheresis. HLA Abs were measured by solid phase and flow cytometry (FCM) assays. Immunodominant Ab (iAb) was defined as highest HLA Ab level. Forty-four patients received 52 desensitization courses (7 patients enrolled in multiple phases): Phase 1 (n = 20), Phase 2 (n = 12), Phase 3 (n = 10), Phase 4 (n = 5), Phase 5 (n = 5). iAb reductions were observed in 38 of 44 (86%) patients and persisted up to 10 months. In Phase 1, a 51.5% iAb reduction was observed at 28 days with bortezomib alone. iAb reductions increased with higher bortezomib dosing densities and included class I, II, and public antigens (HLA DRβ3, HLA DRβ4 and HLA DRβ5). FCM median channel shifts decreased in 11/11 (100%) patients by a mean of 103 ± 54 mean channel shifts (log scale). Nineteen out of 44 patients (43.2%) were transplanted with low acute rejection rates (18.8%) and de novo DSA formation (12.5%). In conclusion, PI-based desensitization consistently and durably reduces HLA Ab levels providing an alternative to intravenous immune globulin-based desensitization. © Copyright 2014 The American Society of Transplantation and the American Society of Transplant Surgeons.

  15. Crystal Structure of the Homo sapiens Kynureninase-3-Hydroxyhippuric Acid Inhibitor Complex: Insights into the Molecular Basis Of Kynureninase Substrate Specificity

    Energy Technology Data Exchange (ETDEWEB)

    Lima,Santiago; Kumar,Sunil; Gawandi,Vijay; Momany,Cory; Phillips,Robert S.; (Georgia)

    2009-02-23

    Homo sapiens kynureninase is a pyridoxal-5'-phosphate dependent enzyme that catalyzes the hydrolytic cleavage of 3-hydroxykynurenine to yield 3-hydroxyanthranilate and L-alanine as part of the tryptophan catabolic pathway leading to the de novo biosynthesis of NAD{sup +}. This pathway results in quinolinate, an excitotoxin that is an NMDA receptor agonist. High levels of quinolinate have been correlated with the etiology of neurodegenerative disorders such as AIDS-related dementia and Alzheimer's disease. We have synthesized a novel kynureninase inhibitor, 3-hydroxyhippurate, cocrystallized it with human kynureninase, and solved the atomic structure. On the basis of an analysis of the complex, we designed a series of His-102, Ser-332, and Asn-333 mutants. The H102W/N333T and H102W/S332G/N333T mutants showed complete reversal of substrate specificity between 3-hydroxykynurenine and L-kynurenine, thus defining the primary residues contributing to substrate specificity in kynureninases.

  16. Zr-based conversion coatings for multi-metal substrates

    NARCIS (Netherlands)

    Cerezo Palacios, J.M.

    2015-01-01

    In this PhD work, a new surface treatment based on the application of Zr-based conversion coatings by immersion in a Cu containing Zr-based conversion solution was investigated as a replacement of the traditional phosphating process for the automotive industry. Nowadays most of the cars are made of

  17. Effects of substrate on piezoelectricity of electrospun poly(vinylidene fluoride)-nanofiber-based energy generators.

    Science.gov (United States)

    Lee, Byoung-Sun; Park, Boongik; Yang, Ho-Sung; Han, Jin Woo; Choong, Chweelin; Bae, Jihyun; Lee, Kihwan; Yu, Woong-Ryeol; Jeong, Unyong; Chung, U-In; Park, Jong-Jin; Kim, Ohyun

    2014-03-12

    We report the effects of various substrates and substrate thicknesses on electrospun poly(vinylidene fluoride) (PVDF)-nanofiber-based energy harvesters. The electrospun PVDF nanofibers showed an average diameter of 84.6 ± 23.5 nm. A high relative β-phase fraction (85.2%) was achieved by applying high voltage during electrospinning. The prepared PVDF nanofibers thus generated considerable piezoelectric potential in accordance with the sound-driven mechanical vibrations of the substrates. Slide glass, poly(ethylene terephthalate), poly(ethylene naphthalate), and paper substrates were used to investigate the effects of the intrinsic and extrinsic substrate properties on the piezoelectricity of the energy harvesters. The thinnest paper substrate (66 μm) with a moderate Young's modulus showed the highest voltage output (0.4885 V). We used high-performance 76, 66, and 33 μm thick papers to determine the effect of paper thickness on the output voltage. The thinnest paper substrate resulted in the highest voltage output (0.7781 V), and the numerical analyses of the sound-driven mechanical deformation strongly support the hypothesis that substrate thickness has a considerable effect on piezoelectric performance.

  18. Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design.

    Directory of Open Access Journals (Sweden)

    Yuan-Ping Pang

    2009-11-01

    Full Text Available Botulinum neurotoxin serotype A (BoNTA causes a life-threatening neuroparalytic disease known as botulism. Current treatment for post exposure of BoNTA uses antibodies that are effective in neutralizing the extracellular toxin to prevent further intoxication but generally cannot rescue already intoxicated neurons. Effective small-molecule inhibitors of BoNTA endopeptidase (BoNTAe are desirable because such inhibitors potentially can neutralize the intracellular BoNTA and offer complementary treatment for botulism. Previously we reported a serotype-selective, small-molecule BoNTAe inhibitor with a K(i (app value of 3.8+/-0.8 microM. This inhibitor was developed by lead identification using virtual screening followed by computer-aided optimization of a lead with an IC(50 value of 100 microM. However, it was difficult to further improve the lead from micromolar to even high nanomolar potency due to the unusually large enzyme-substrate interface of BoNTAe. The enzyme-substrate interface area of 4,840 A(2 for BoNTAe is about four times larger than the typical protein-protein interface area of 750-1,500 A(2. Inhibitors must carry several functional groups to block the unusually large interface of BoNTAe, and syntheses of such inhibitors are therefore time-consuming and expensive. Herein we report the development of a serotype-selective, small-molecule, and competitive inhibitor of BoNTAe with a K(i value of 760+/-170 nM using synthesis-based computer-aided molecular design (SBCAMD. This new approach accounts the practicality and efficiency of inhibitor synthesis in addition to binding affinity and selectivity. We also report a three-dimensional model of BoNTAe in complex with the new inhibitor and the dynamics of the complex predicted by multiple molecular dynamics simulations, and discuss further structural optimization to achieve better in vivo efficacy in neutralizing BoNTA than those of our early micromolar leads. This work provides new insight

  19. Vacuum-based surface modification of organic and metallic substrates

    Science.gov (United States)

    Torres, Jessica

    Surface physico-chemical properties play an important role in the development and performance of materials in different applications. Consequently, understanding the chemical and physical processes involved during surface modification strategies is of great scientific and technological importance. This dissertation presents results from the surface modification of polymers, organic films and metallic substrates with reactive species, with the intent of simulating important modification processes and elucidating surface property changes of materials under different environments. The reactions of thermally evaporated copper and titanium with halogenated polytetrafluoroethylene (PTFE) and polyvinyl chloride (PVC) are used to contrast the interaction of metals with polymers. Results indicate that reactive metallization is thermodynamically favored when the metal-halogen bond strength is greater than the carbon-halogen bond strength. X-ray post-metallization treatment results in an increase in metal-halide bond formation due to the production of volatile halogen species in the polymer that react with the metallic overlayer. The reactions of atomic oxygen (AO) and atomic chlorine with polyethylene (PE) and self-assembled monolayers (SAMs) films were followed to ascertain the role of radical species during plasma-induced polymer surface modification. The reactions of AO with X-ray modified SAMs are initially the dominated by the incorporation of new oxygen containing functionality at the vacuum/film interface, leading to the production of volatile carbon containing species such as CO2 that erodes the hydrocarbon film. The reaction of atomic chlorine species with hydrocarbon SAMs, reveals that chlorination introduces C-Cl and C-Cl2 functionalities without erosion. A comparison of the reactions of AO and atomic chlorine with PE reveal a maximum incorporation of the corresponding C-O and C-Cl functionalities at the polymer surface. A novel method to prepare phosphorous

  20. PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites.

    Directory of Open Access Journals (Sweden)

    Jiangning Song

    Full Text Available The ability to catalytically cleave protein substrates after synthesis is fundamental for all forms of life. Accordingly, site-specific proteolysis is one of the most important post-translational modifications. The key to understanding the physiological role of a protease is to identify its natural substrate(s. Knowledge of the substrate specificity of a protease can dramatically improve our ability to predict its target protein substrates, but this information must be utilized in an effective manner in order to efficiently identify protein substrates by in silico approaches. To address this problem, we present PROSPER, an integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four different proteases. PROSPER utilizes established specificity information for these proteases (derived from the MEROPS database with a machine learning approach to predict protease cleavage sites by using different, but complementary sequence and structure characteristics. Features used by PROSPER include local amino acid sequence profile, predicted secondary structure, solvent accessibility and predicted native disorder. Thus, for proteases with known amino acid specificity, PROSPER provides a convenient, pre-prepared tool for use in identifying protein substrates for the enzymes. Systematic prediction analysis for the twenty-four proteases thus far included in the database revealed that the features we have included in the tool strongly improve performance in terms of cleavage site prediction, as evidenced by their contribution to performance improvement in terms of identifying known cleavage sites in substrates for these enzymes. In comparison with two state-of-the-art prediction tools, PoPS and SitePrediction, PROSPER achieves greater accuracy and coverage. To our knowledge, PROSPER is the first comprehensive server capable of predicting cleavage sites of multiple proteases within a single substrate

  1. Structure-based discovery of inhibitors of the YycG histidine kinase

    DEFF Research Database (Denmark)

    Qin, X.; Zhang, J.; Xu, B.

    2006-01-01

    inhibitors of YycG histidine kinase thus are of potential value as leads for developing new antibiotics against infecting staphylococci. The structure-based virtual screening (SBVS) technology can be widely used in screening potential inhibitors of other bacterial TCSs, since it is more rapid and efficacious...... than traditional screening technology....

  2. Identification of novel and potent isoquinoline aminooxazole-based IMPDH inhibitors.

    Science.gov (United States)

    Chen, Ping; Norris, Derek; Haslow, Kristin D; Murali Dhar, T G; Pitts, William J; Watterson, Scott H; Cheney, Daniel L; Bassolino, Donna A; Fleener, Catherine A; Rouleau, Katherine A; Hollenbaugh, Diane L; Townsend, Robert M; Barrish, Joel C; Iwanowicz, Edwin J

    2003-04-07

    Screening of our in-house compound collection led to the discovery of 5-bromo-6-amino-2-isoquinoline 1 as a weak inhibitor of IMPDH. Subsequent optimization of 1 afforded a series of novel 2-isoquinolinoaminooxazole-based inhibitors, represented by 17, with single-digit nanomolar potency against the enzyme.

  3. 3-cyanoindole-based inhibitors of inosine monophosphate dehydrogenase: synthesis and initial structure-activity relationships.

    Science.gov (United States)

    Dhar, T G Murali; Shen, Zhongqi; Gu, Henry H; Chen, Ping; Norris, Derek; Watterson, Scott H; Ballentine, Shelley K; Fleener, Catherine A; Rouleau, Katherine A; Barrish, Joel C; Townsend, Robert; Hollenbaugh, Diane L; Iwanowicz, Edwin J

    2003-10-20

    A series of novel small molecule inhibitors of inosine monophosphate dehydrogenase (IMPDH), based upon a 3-cyanoindole core, were explored. IMPDH catalyzes the rate determining step in guanine nucleotide biosynthesis and is a target for anticancer, immunosuppressive and antiviral therapy. The synthesis and the structure-activity relationships (SAR), derived from in vitro studies, for this new series of inhibitors is given.

  4. Identification of novel malarial cysteine protease inhibitors using structure-based virtual screening of a focused cysteine protease inhibitor library.

    Science.gov (United States)

    Shah, Falgun; Mukherjee, Prasenjit; Gut, Jiri; Legac, Jennifer; Rosenthal, Philip J; Tekwani, Babu L; Avery, Mitchell A

    2011-04-25

    Malaria, in particular that caused by Plasmodium falciparum , is prevalent across the tropics, and its medicinal control is limited by widespread drug resistance. Cysteine proteases of P. falciparum , falcipain-2 (FP-2) and falcipain-3 (FP-3), are major hemoglobinases, validated as potential antimalarial drug targets. Structure-based virtual screening of a focused cysteine protease inhibitor library built with soft rather than hard electrophiles was performed against an X-ray crystal structure of FP-2 using the Glide docking program. An enrichment study was performed to select a suitable scoring function and to retrieve potential candidates against FP-2 from a large chemical database. Biological evaluation of 50 selected compounds identified 21 diverse nonpeptidic inhibitors of FP-2 with a hit rate of 42%. Atomic Fukui indices were used to predict the most electrophilic center and its electrophilicity in the identified hits. Comparison of predicted electrophilicity of electrophiles in identified hits with those in known irreversible inhibitors suggested the soft-nature of electrophiles in the selected target compounds. The present study highlights the importance of focused libraries and enrichment studies in structure-based virtual screening. In addition, few compounds were screened against homologous human cysteine proteases for selectivity analysis. Further evaluation of structure-activity relationships around these nonpeptidic scaffolds could help in the development of selective leads for antimalarial chemotherapy.

  5. Paper based Flexible and Conformal SERS Substrate for Rapid Trace Detection on Real-world Surfaces

    Science.gov (United States)

    Singamaneni, Srikanth; Lee, Chang; Tian, Limei

    2011-03-01

    One of the important but often overlooked considerations in the design of surface enhanced Raman scattering (SERS) substrates for trace detection is the efficiency of sample collection. Conventional designs based on rigid substrates such as silicon, alumina, and glass resist conformal contact with the surface under investigation, making the sample collection inefficient. We demonstrate a novel SERS substrate based on common filter paper adsorbed with gold nanorods, which allows conformal contact with real-world surfaces, thus dramatically enhancing the sample collection efficiency compared to conventional rigid substrates. We demonstrate the detection of trace amounts of analyte (140 pg spread over 4 cm2) by simply swabbing the surface under investigation with the novel SERS substrate. The hierarchical fibrous structure of paper serves as a 3D vasculature for easy uptake and transport of the analytes to the electromagnetic hot spots in the paper. Simple yet highly efficient and cost effective SERS substrate demonstrated here brings SERS based trace detection closer to real-world applications. We acknowledge the financial support from Center for Materials Innovation at Washington University.

  6. Assessment of cerebral P-glycoprotein expression and function with PET by combined [11C]inhibitor and [11C]substrate scans in rats

    International Nuclear Information System (INIS)

    Müllauer, Julia; Karch, Rudolf; Bankstahl, Jens P.; Bankstahl, Marion; Stanek, Johann; Wanek, Thomas; Mairinger, Severin; Müller, Markus; Löscher, Wolfgang; Langer, Oliver; Kuntner, Claudia

    2013-01-01

    Introduction: The adenosine triphosphate-binding cassette (ABC) transporter P-glycoprotein (Pgp) protects the brain from accumulation of lipophilic compounds by active efflux transport across the blood–brain barrier. Changes in Pgp function/expression may occur in neurological disorders, such as epilepsy, Alzheimer’s or Parkinson’s disease. In this work we investigated the suitability of the radiolabeled Pgp inhibitors [ 11 C]elacridar and [ 11 C]tariquidar to visualize Pgp density in rat brain with PET. Methods: Rats underwent a first PET scan with [ 11 C]elacridar (n = 5) or [ 11 C]tariquidar (n = 6) followed by a second scan with the Pgp substrate (R)-[ 11 C]verapamil after administration of unlabeled tariquidar at a dose which half-maximally inhibits cerebral Pgp (3 mg/kg). Compartmental modeling using an arterial input function and Logan graphical analysis were used to estimate rate constants and volumes of distribution (V T ) of radiotracers in different brain regions. Results: Brain PET signals of [ 11 C]elacridar and [ 11 C]tariquidar were very low (∼ 0.5 standardized uptake value, SUV). There was a significant negative correlation between V T and K 1 (i.e. influx rate constant from plasma into brain) values of [ 11 C]elacridar or [ 11 C]tariquidar and V T and K 1 values of (R)-[ 11 C]verapamil in different brain regions which was consistent with binding of [ 11 C]inhibitors to Pgp and efflux of (R)-[ 11 C]verapamil by Pgp. Conclusion: The small Pgp binding signals obtained with [ 11 C]elacridar and [ 11 C]tariquidar limit the applicability of these tracers to measure cerebral Pgp density. PET tracers with higher (i.e. subnanomolar) binding affinities will be needed to visualize the low density of Pgp in brain

  7. Secretion of apolipoproteins A-I and B by HepG2 cells: regulation by substrates and metabolic inhibitors.

    Science.gov (United States)

    Kempen, H J; Imbach, A P; Giller, T; Neumann, W J; Hennes, U; Nakada, N

    1995-08-01

    It was the aim of this study to i) compare the effects of glucose and other hexoses with that of oleate on secretion of apolipoproteins (apos) A-I and B by HepG2 cells, and ii) document the effect of various metabolic inhibitors on the secretion of these apos in the absence or presence of extra glucose/oleate. i) The addition of 10 mM glucose increased secretion of apoA-I and apoB, as measured by enzyme immunoassay, by about 60% when cells were incubated for 48 h in DMEM + 10% fetal calf serum. The addition of extra glucose also increased the mRNA levels for these apos. Increased radioactivity was also found in these apolipoproteins by immunoprecipitation after metabolic labeling with [35S]methionine for 48 h. However, in a pulse-chase experiment (15 min labeling, 2 h chase), glucose was found to increase apoA-I synthesis but not apoB synthesis. More labeled apoB appeared in the medium during the chase because glucose inhibited its intracellular degradation. The effect of glucose on secretion of these apos could be mimicked by fructose and mannose but not by 6-deoxyglucose, showing that the hexoses must enter the cells and be phosphorylated. In contrast, the addition of 0.5 mM oleate had a weak inhibitory effect on secretion of apoA-I whereas it increased the secretion of apoB by more than twofold. The combination of 10 mM glucose and 0.5 mM oleate had no greater effect than glucose alone on apoA-I secretion but increased apoB secretion by fourfold. ii) Inhibiting glycolysis (by glucosamine) lowered secretion of both apoA-I and apoB, while inhibiting lipogenesis (using 8-Br-cyclic AMP or 5-(tetradecyloxy)-2-furancarboxylic acid (TOFA)) did not affect apoA-I secretion but clearly decreased that of apoB. However, the inhibitory effect of TOFA on apoB secretion was much smaller in the presence of 0.5 mM oleate instead of extra glucose. Actinomycin-D and cycloheximide strongly suppressed the stimulatory effect of glucose on secretion of both apolipoproteins

  8. Investigation of graphene based miniaturized terahertz antenna for novel substrate materials

    Directory of Open Access Journals (Sweden)

    Rajni Bala

    2016-03-01

    Full Text Available The selection of appropriate substrate material acts as a performance regulator for miniaturized graphene patch antenna. The substrate material not only controls the transport properties of graphene but also influences the resonant properties of the graphene patch antenna. The edge fed microstrip line graphene based rectangular patch antenna is designed here for operating in the frequency range 2.67–2.92 THz for wireless applications. The performance is investigated for silicon nitride, aluminum oxide, boron nitride, silica and quartz substrate materials on the basis of return loss, voltage standing wave ratio (VSWR, absorption cross section, bandwidth and radiation efficiency. The comparison of results shows that silicon nitride exhibits overall excellent performance by the virtue of having higher bandwidth and radiation efficiency as compared to other chosen substrate materials.

  9. Identifying suitable substrates for high-quality graphene-based heterostructures

    Science.gov (United States)

    Banszerus, L.; Janssen, H.; Otto, M.; Epping, A.; Taniguchi, T.; Watanabe, K.; Beschoten, B.; Neumaier, D.; Stampfer, C.

    2017-06-01

    We report on a scanning confocal Raman spectroscopy study investigating the strain-uniformity and the overall strain and doping of high-quality chemical vapour deposited (CVD) graphene-based heterostuctures on a large number of different substrate materials, including hexagonal boron nitride (hBN), transition metal dichalcogenides, silicon, different oxides and nitrides, as well as polymers. By applying a hBN-assisted, contamination free, dry transfer process for CVD graphene, high-quality heterostructures with low doping densities and low strain variations are assembled. The Raman spectra of these pristine heterostructures are sensitive to substrate-induced doping and strain variations and are thus used to probe the suitability of the substrate material for potential high-quality graphene devices. We find that the flatness of the substrate material is a key figure for gaining, or preserving high-quality graphene.

  10. Structure-Based Design and Synthesis of Potent and Selective Matrix Metalloproteinase 13 Inhibitors.

    Science.gov (United States)

    Choi, Jun Yong; Fuerst, Rita; Knapinska, Anna M; Taylor, Alexander B; Smith, Lyndsay; Cao, Xiaohang; Hart, P John; Fields, Gregg B; Roush, William R

    2017-07-13

    We describe the use of comparative structural analysis and structure-guided molecular design to develop potent and selective inhibitors (10d and (S)-17b) of matrix metalloproteinase 13 (MMP-13). We applied a three-step process, starting with a comparative analysis of the X-ray crystallographic structure of compound 5 in complex with MMP-13 with published structures of known MMP-13·inhibitor complexes followed by molecular design and synthesis of potent but nonselective zinc-chelating MMP inhibitors (e.g., 10a and 10b). After demonstrating that the pharmacophores of the chelating inhibitors (S)-10a, (R)-10a, and 10b were binding within the MMP-13 active site, the Zn 2+ chelating unit was replaced with nonchelating polar residues that bridged over the Zn 2+ binding site and reached into a solvent accessible area. After two rounds of structural optimization, these design approaches led to small molecule MMP-13 inhibitors 10d and (S)-17b, which bind within the substrate-binding site of MMP-13 and surround the catalytically active Zn 2+ ion without chelating to the metal. These compounds exhibit at least 500-fold selectivity versus other MMPs.

  11. Amino acid derivatives are substrates or non-transported inhibitors of the amino acid transporter PAT2 (slc36a2).

    Science.gov (United States)

    Edwards, Noel; Anderson, Catriona M H; Gatfield, Kelly M; Jevons, Mark P; Ganapathy, Vadivel; Thwaites, David T

    2011-01-01

    The H(+)-coupled amino acid transporter PAT2 (SLC36A2) transports the amino acids proline, glycine, alanine and hydroxyproline. A physiological role played by PAT2 in amino acid reabsorption in the renal proximal tubule is demonstrated by mutations in SLC36A2 that lead to an iminoglycinuric phenotype (imino acid and glycine uria) in humans. A number of proline, GABA and tryptophan derivatives were examined to determine if they function either as transported substrates or non-transported inhibitors of PAT2. The compounds were investigated following heterologous expression of rat PAT2 in Xenopus laevis oocytes. PAT2 function was characterised by: radiotracer uptake and competition (cis-inhibition) studies; radiotracer efflux and trans-stimulation; and measurement of substrate-induced positive inward current by two-electrode voltage-clamp. In general, the proline derivatives appeared to be transported substrates and the relative ability to induce current flow was closely related to the inhibitory effects on PAT2-mediated l-[(3)H]proline uptake. In contrast, certain heterocyclic GABA derivatives (e.g. l-pipecolic acid) were translocated only slowly. Finally, the tryptophan derivatives inhibited PAT2 function but did not undergo transport. l-Proline uptake was inhibited by 5-hydroxy-l-tryptophan (IC(50) 1.6±0.4mM), α-methyl-d,l-tryptophan (3.5±1.5mM), l-tryptophan, 1-methyl-l-tryptophan and indole-3-propionic acid. Although neither 5-hydroxy-l-tryptophan nor α-methyl-d,l-tryptophan were able to elicit inward current in PAT2-expressing oocytes both reduced the current evoked by l-proline. 5-Hydroxy-l-tryptophan and α-methyl-d,l-tryptophan were unable to trans-stimulate l-proline efflux from PAT2-expressing oocytes, confirming that the two compounds act as non-transported blockers of PAT2. These two tryptophan derivatives should prove valuable experimental tools in future investigations of the physiological roles of PAT2. Copyright © 2010 Elsevier B.V. All rights

  12. [Advances on enzymes and enzyme inhibitors research based on microfluidic devices].

    Science.gov (United States)

    Hou, Feng-Hua; Ye, Jian-Qing; Chen, Zuan-Guang; Cheng, Zhi-Yi

    2010-06-01

    With the continuous development in microfluidic fabrication technology, microfluidic analysis has evolved from a concept to one of research frontiers in last twenty years. The research of enzymes and enzyme inhibitors based on microfluidic devices has also made great progress. Microfluidic technology improved greatly the analytical performance of the research of enzymes and enzyme inhibitors by reducing the consumption of reagents, decreasing the analysis time, and developing automation. This review focuses on the development and classification of enzymes and enzyme inhibitors research based on microfluidic devices.

  13. A Potent Peptidomimetic Inhibitor of Botulinum Neurotoxin Serotype A has a Very Different Conformation than SNAP-25 Substrate

    Science.gov (United States)

    2008-10-07

    Fort Detrick, Frederick, MD 21702, USA 3Target Structure-Based Drug Discovery Group, SAIC-Frederick, Inc. 4Developmental Therapeutics Program National...additional binding surfaces identified in the vicinity of the I1-binding sites, will be useful for the development of effica- cious antibotulinum drugs ...in a competent orientation for attack by the catalytic water in the protease, resulting in the cleavage of the peptide bond. A cocrystal structure of

  14. Novel inhibitors of IMPDH: a highly potent and selective quinolone-based series.

    Science.gov (United States)

    Watterson, Scott H; Carlsen, Marianne; Dhar, T G Murali; Shen, Zhongqi; Pitts, William J; Guo, Junqing; Gu, Henry H; Norris, Derek; Chorba, John; Chen, Ping; Cheney, Daniel; Witmer, Mark; Fleener, Catherine A; Rouleau, Katherine; Townsend, Robert; Hollenbaugh, Diane L; Iwanowicz, Edwin J

    2003-02-10

    A series of novel quinolone-based small molecule inhibitors of inosine monophosphate dehydrogenase (IMPDH) was explored. The synthesis and the structure-activity relationships (SARs) derived from in vitro studies are described.

  15. Identification by shape-based virtual screening and evaluation of new tyrosinase inhibitors

    Directory of Open Access Journals (Sweden)

    Qi Li

    2018-01-01

    Full Text Available Targeting tyrosinase is considered to be an effective way to control the production of melanin. Tyrosinase inhibitor is anticipated to provide new therapy to prevent skin pigmentation, melanoma and neurodegenerative diseases. Herein, we report our results in identifying new tyrosinase inhibitors. The shape-based virtual screening was performed to discover new tyrosinase inhibitors. Thirteen potential hits derived from virtual screening were tested by biological determinations. Compound 5186-0429 exhibited the most potent inhibitory activity. It dose-dependently inhibited the activity of tyrosinase, with the IC50 values 6.2 ± 2.0 µM and 10.3 ± 5.4 µM on tyrosine and L-Dopa formation, respectively. The kinetic study of 5186-0429 demonstrated that this compound acted as a competitive inhibitor. We believe the discoveries here could serve as a good starting point for further design of potent tyrosinase inhibitor.

  16. Investigation of specificity determinants in bacterial tRNA-guanine transglycosylase reveals queuine, the substrate of its eucaryotic counterpart, as inhibitor.

    Directory of Open Access Journals (Sweden)

    Inna Biela

    Full Text Available Bacterial tRNA-guanine transglycosylase (Tgt catalyses the exchange of the genetically encoded guanine at the wobble position of tRNAs(His,Tyr,Asp,Asn by the premodified base preQ1, which is further converted to queuine at the tRNA level. As eucaryotes are not able to synthesise queuine de novo but acquire it through their diet, eucaryotic Tgt directly inserts the hypermodified base into the wobble position of the tRNAs mentioned above. Bacterial Tgt is required for the efficient pathogenicity of Shigella sp, the causative agent of bacillary dysentery and, hence, it constitutes a putative target for the rational design of anti-Shigellosis compounds. Since mammalian Tgt is known to be indirectly essential to the conversion of phenylalanine to tyrosine, it is necessary to create substances which only inhibit bacterial but not eucaryotic Tgt. Therefore, it seems of utmost importance to study selectivity-determining features within both types of proteins. Homology models of Caenorhabditis elegans Tgt and human Tgt suggest that the replacement of Cys158 and Val233 in bacterial Tgt (Zymomonas mobilis Tgt numbering by valine and accordingly glycine in eucaryotic Tgt largely accounts for the different substrate specificities. In the present study we have created mutated variants of Z. mobilis Tgt in order to investigate the impact of a Cys158Val and a Val233Gly exchange on catalytic activity and substrate specificity. Using enzyme kinetics and X-ray crystallography, we gained evidence that the Cys158Val mutation reduces the affinity to preQ1 while leaving the affinity to guanine unaffected. The Val233Gly exchange leads to an enlarged substrate binding pocket, that is necessary to accommodate queuine in a conformation compatible with the intermediately covalently bound tRNA molecule. Contrary to our expectations, we found that a priori queuine is recognised by the binding pocket of bacterial Tgt without, however, being used as a substrate.

  17. Developing upconversion nanoparticle-based smart substrates for remote temperature sensing

    Science.gov (United States)

    Coker, Zachary; Marble, Kassie; Alkahtani, Masfer; Hemmer, Philip; Yakovlev, Vladislav V.

    2018-02-01

    Recent developments in understanding of nanomaterial behaviors and synthesis have led to their application across a wide range of commercial and scientific applications. Recent investigations span from applications in nanomedicine and the development of novel drug delivery systems to nanoelectronics and biosensors. In this study, we propose the application of a newly engineered temperature sensitive water-based bio-compatible core/shell up-conversion nanoparticle (UCNP) in the development of a smart substrate for remote temperature sensing. We developed this smart substrate by dispersing functionalized nanoparticles into a polymer solution and then spin-coating the solution onto one side of a microscope slide to form a thin film substrate layer of evenly dispersed nanoparticles. By using spin-coating to deposit the particle solution we both create a uniform surface for the substrate while simultaneously avoid undesired particle agglomeration. Through this investigation, we have determined the sensitivity and capabilities of this smart substrate and conclude that further development can lead to a greater range of applications for this type smart substrate and use in remote temperature sensing in conjunction with other microscopy and spectroscopy investigations.

  18. Synthesis and characterisation of substrate-based peptides as inhibitors of histone demethylase KDM4C

    DEFF Research Database (Denmark)

    Nielsen, Simon D; Leurs, Ulrike; Bergner, Magnus

    2016-01-01

    different series of peptides were designed and synthesized. One series contained N-acylated H3K9 and two series introduced triazoles in this position via click chemistry to enable facile variation of headgroups. As the click reaction is compatible with free amino acids this was performed on an azido...

  19. A recombinant fusion protein-based, fluorescent protease assay for high throughput-compatible substrate screening.

    Science.gov (United States)

    Bozóki, Beáta; Gazda, Lívia; Tóth, Ferenc; Miczi, Márió; Mótyán, János András; Tőzsér, József

    2018-01-01

    In connection with the intensive investigation of proteases, several methods have been developed for analysis of the substrate specificity. Due to the great number of proteases and the expected target molecules to be analyzed, time- and cost-efficient high-throughput screening (HTS) methods are preferred. Here we describe the development and application of a separation-based HTS-compatible fluorescent protease assay, which is based on the use of recombinant fusion proteins as substrates of proteases. The protein substrates used in this assay consists of N-terminal (hexahistidine and maltose binding protein) fusion tags, cleavage sequences of the tobacco etch virus (TEV) and HIV-1 proteases, and a C-terminal fluorescent protein (mApple or mTurquoise2). The assay is based on the fluorimetric detection of the fluorescent proteins, which are released from the magnetic bead-attached substrates by the proteolytic cleavage. The protease assay has been applied for activity measurements of TEV and HIV-1 proteases to test the suitability of the system for enzyme kinetic measurements, inhibition studies, and determination of pH optimum. We also found that denatured fluorescent proteins can be renatured after SDS-PAGE of denaturing conditions, but showed differences in their renaturation abilities. After in-gel renaturation both substrates and cleavage products can be identified by in-gel UV detection. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Inoculation of sphagnum-based soil substrate with entomopathogenic fungus Isaria fumosorosea (Hypocreales: Cordycipitaceae)

    Science.gov (United States)

    Zemek, Rostislav; Konopická, Jana; Bohatá, Andrea

    2018-04-01

    Convenient ecological alternative to broad-spectrum chemical pesticides is the utilization of natural enemies, like predators, parasitoids and microorganisms. A substantial number of microbial biopesticides based on entomopathogenic fungi have been developed worldwide since 1960s. Beauveria bassiana (Balsamo-Crivelli) Vuillemin, Metarhizium anisopliae (Metchnikoff) Sorokin, Isaria fumosorosea (Wize), and B. brongniartii (Saccardo) Petch are the most common species used in commercially produced mycopesticides. Besides direct biological pest control, these fungi could be also used in preventive application programs, particularly in ornamental or nursery plants to provide better control against pests. The aim of the present study was to investigate potential of pre-colonization of sphagnum-based soil substrate with I. fumosorosea strain CCM 8367 which was found earlier to be highly virulent against several pest species. We developed simple laboratory apparatus for application of fungal spore suspension into the substrate. Suspension was prepared from blastospores obtained by submerged cultivation on potato dextrose broth (PDB) medium using an orbital shaker. Inoculated substrate was placed into plastic bags and stored at constant temperature for six months. Every month, samples were analyzed for concentration of colony forming units (CFU) by elution and selective medium technique. The results showed that at 20°C the fungus successfully colonized the soil substrate and persisted there although the mean concentration slightly decreased from 5.89×104 to 2.76×104 CFU per milliliter of substrate during the experiment. Temperature 30°C had negative effect on survival of the fungus and is not recommended for long-term storage of pre-inoculated substrate. We can conclude that I. fumosorosea-colonized substrate can be convenient for preventive and permanent protection of various plants against soil-dwelling pests.

  1. Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors.

    Science.gov (United States)

    Andersen, Jannik N; Sathyanarayanan, Sriram; Di Bacco, Alessandra; Chi, An; Zhang, Theresa; Chen, Albert H; Dolinski, Brian; Kraus, Manfred; Roberts, Brian; Arthur, William; Klinghoffer, Rich A; Gargano, Diana; Li, Lixia; Feldman, Igor; Lynch, Bethany; Rush, John; Hendrickson, Ronald C; Blume-Jensen, Peter; Paweletz, Cloud P

    2010-08-04

    Although we have made great progress in understanding the complex genetic alterations that underlie human cancer, it has proven difficult to identify which molecularly targeted therapeutics will benefit which patients. Drug-specific modulation of oncogenic signaling pathways in specific patient subpopulations can predict responsiveness to targeted therapy. Here, we report a pathway-based phosphoprofiling approach to identify and quantify clinically relevant, drug-specific biomarkers for phosphatidylinositol 3-kinase (PI3K) pathway inhibitors that target AKT, phosphoinositide-dependent kinase 1 (PDK1), and PI3K-mammalian target of rapamycin (mTOR). We quantified 375 nonredundant PI3K pathway-relevant phosphopeptides, all containing AKT, PDK1, or mitogen-activated protein kinase substrate recognition motifs. Of these phosphopeptides, 71 were drug-regulated, 11 of them by all three inhibitors. Drug-modulated phosphoproteins were enriched for involvement in cytoskeletal reorganization (filamin, stathmin, dynamin, PAK4, and PTPN14), vesicle transport (LARP1, VPS13D, and SLC20A1), and protein translation (S6RP and PRAS40). We then generated phosphospecific antibodies against selected, drug-regulated phosphorylation sites that would be suitable as biomarker tools for PI3K pathway inhibitors. As proof of concept, we show clinical translation feasibility for an antibody against phospho-PRAS40(Thr246). Evaluation of binding of this antibody in human cancer cell lines, a PTEN (phosphatase and tensin homolog deleted from chromosome 10)-deficient mouse prostate tumor model, and triple-negative breast tumor tissues showed that phospho-PRAS40(Thr246) positively correlates with PI3K pathway activation and predicts AKT inhibitor sensitivity. In contrast to phosphorylation of AKT(Thr308), the phospho-PRAS40(Thr246) epitope is highly stable in tissue samples and thus is ideal for immunohistochemistry. In summary, our study illustrates a rational approach for discovery of drug

  2. Semiconductor-based, large-area, flexible, electronic devices on {110} oriented substrates

    Science.gov (United States)

    Goyal, Amit

    2014-08-05

    Novel articles and methods to fabricate the same resulting in flexible, oriented, semiconductor-based, electronic devices on {110} textured substrates are disclosed. Potential applications of resulting articles are in areas of photovoltaic devices, flat-panel displays, thermophotovoltaic devices, ferroelectric devices, light emitting diode devices, computer hard disc drive devices, magnetoresistance based devices, photoluminescence based devices, non-volatile memory devices, dielectric devices, thermoelectric devices and quantum dot laser devices.

  3. Effects of Incretin-Based Therapies and SGLT2 Inhibitors on Skeletal Health.

    Science.gov (United States)

    Egger, Andrea; Kraenzlin, Marius E; Meier, Christian

    2016-12-01

    Anti-diabetic drugs are widely used and are essential for adequate glycemic control in patients with type 2 diabetes. Recently, marketed anti-diabetic drugs include incretin-based therapies (GLP-1 receptor agonists and DPP-4 inhibitors) and sodium-glucose co-transporter 2 (SGLT2) inhibitors. In contrast to well-known detrimental effects of thiazolidinediones on bone metabolism and fracture risk, clinical data on the safety of incretin-based therapies is limited. Based on meta-analyses of trials investigating the glycemic-lowering effect of GLP-1 receptor agonists and DPP4 inhibitors, it seems that incretin-based therapies are not associated with an increase in fracture risk. Sodium-glucose co-transporter 2 inhibitors may alter calcium and phosphate homeostasis as a result of secondary hyperparathyroidism induced by increased phosphate reabsorption. Although these changes may suggest detrimental effects of SGLT-2 inhibitors on skeletal integrity, treatment-related direct effects on bone metabolism seem unlikely. Observed changes in BMD, however, seem to result from increased bone turnover in the early phase of drug-induced weight loss. Fracture risk, which is observed in older patients with impaired renal function and elevated cardiovascular disease risk treated with SGLT2 inhibitors, seems to be independent of direct effects on bone but more likely to be associated with falls and changes in hydration status secondary to osmotic diuresis.

  4. Tubulin Inhibitor-Based Antibody-Drug Conjugates for Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Hao Chen

    2017-08-01

    Full Text Available Antibody-drug conjugates (ADCs are a class of highly potent biopharmaceutical drugs generated by conjugating cytotoxic drugs with specific monoclonal antibodies through appropriate linkers. Specific antibodies used to guide potent warheads to tumor tissues can effectively reduce undesired side effects of the cytotoxic drugs. An in-depth understanding of antibodies, linkers, conjugation strategies, cytotoxic drugs, and their molecular targets has led to the successful development of several approved ADCs. These ADCs are powerful therapeutics for cancer treatment, enabling wider therapeutic windows, improved pharmacokinetic/pharmacodynamic properties, and enhanced efficacy. Since tubulin inhibitors are one of the most successful cytotoxic drugs in the ADC armamentarium, this review focuses on the progress in tubulin inhibitor-based ADCs, as well as lessons learned from the unsuccessful ADCs containing tubulin inhibitors. This review should be helpful to facilitate future development of new generations of tubulin inhibitor-based ADCs for cancer therapy.

  5. Hot spot-based design of small-molecule inhibitors for protein-protein interactions.

    Science.gov (United States)

    Guo, Wenxing; Wisniewski, John A; Ji, Haitao

    2014-06-01

    Protein-protein interactions (PPIs) are important targets for the development of chemical probes and therapeutic agents. From the initial discovery of the existence of hot spots at PPI interfaces, it has been proposed that hot spots might provide the key for developing small-molecule PPI inhibitors. However, there has been no review on the ways in which the knowledge of hot spots can be used to achieve inhibitor design, nor critical examination of successful examples. This Digest discusses the characteristics of hot spots and the identification of druggable hot spot pockets. An analysis of four examples of hot spot-based design reveals the importance of this strategy in discovering potent and selective PPI inhibitors. A general procedure for hot spot-based design of PPI inhibitors is outlined. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. SOLVENT-BASED TO WATERBASED ADHESIVE-COATED SUBSTRATE RETROFIT - VOLUME II: PROCESS OVERVIEW

    Science.gov (United States)

    This volume presents initial results of a study to identify the issues and barriers associated with retrofitting existing solvent-based equipment to accept waterbased adhesives as part of an EPA effort to improve equipment cleaning in the coated and laminated substrate manufactur...

  7. Global patterns and substrate-based mechanisms of the terrestrial nitrogen cycle

    DEFF Research Database (Denmark)

    Niu, Shuli; Classen, Aimee Taylor; Dukes, Jeffrey S.

    2016-01-01

    availability but increase exponentially and become the dominant fate of N at high loading rates. The original N saturation hypothesis emphasises sequential N saturation from plant uptake to soil retention before N losses occur. However, biogeochemical models that simulate simultaneous competition for soil N...... substrates by multiple processes match the observed patterns of N losses better than models based on sequential competition. To enable better prediction of terrestrial N cycle responses to N loading, we recommend that future research identifies the response functions of different N processes to substrate...

  8. Malonate-based inhibitors of mammalian serine racemase: Kinetic characterization and structure-based computational study

    Czech Academy of Sciences Publication Activity Database

    Vorlová, Barbora; Nachtigallová, Dana; Jirásková-Vaníčková, Jana; Ajani, Haresh; Jansa, Petr; Řezáč, Jan; Fanfrlík, Jindřich; Otyepka, M.; Hobza, Pavel; Konvalinka, Jan; Lepšík, Martin

    2015-01-01

    Roč. 89, Jan 7 (2015), s. 189-197 ISSN 0223-5234 R&D Projects: GA ČR GBP208/12/G016 Grant - others:GA MŠk(CZ) ED2.1.00/03.0058 Program:ED Institutional support: RVO:61388963 Keywords : NMDA receptor * pyridoxal-5 '-phosphate-dependent enzyme * human/mouse serine racemase * malonate-based inhibitors * semiempirical quantum mechanical calculations Subject RIV: CE - Biochemistry Impact factor: 3.902, year: 2015

  9. The discovery of novel tartrate-based TNF-[alpha] converting enzyme (TACE) inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Rosner, Kristin E.; Guo, Zhuyan; Orth, Peter; Shipps, Jr., Gerald W.; Belanger, David B.; Chan, Tin Yau; Curran, Patrick J.; Dai, Chaoyang; Deng, Yongqi; Girijavallabhan, Vinay M.; Hong, Liwu; Lavey, Brian J.; Lee, Joe F.; Li, Dansu; Liu, Zhidan; Popovici-Muller, Janeta; Ting, Pauline C.; Vaccaro, Henry; Wang, Li; Wang, Tong; Yu, W.; Zhou, G.; Niu, X.; Sun, J.; Kozlowski, J.A.; Lundell, D.J.; Madison, V.; McKittrick, B.; Piwinski, J.J.; Shih, N.Y.; Siddiqui, M. Arshad; Strickland, Corey O. (SPRI)

    2010-09-17

    A novel series of TNF-{alpha} convertase (TACE) inhibitors which are non-hydroxamate have been discovered. These compounds are bis-amides of L-tartaric acid (tartrate) and coordinate to the active site zinc in a tridentate manner. They are selective for TACE over other MMP's. We report the first X-ray crystal structure for a tartrate-based TACE inhibitor.

  10. The discovery of glycine and related amino acid-based factor Xa inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Kohrt, Jeffrey T.; Filipski, Kevin J.; Cody, Wayne L.; Bigge, Christopher F.; La, Frances; Welch, Kathleen; Dahring, Tawny; Bryant, John W.; Leonard, Daniele; Bolton, Gary; Narasimhan, Lakshmi; Zhang, Erli; Peterson, J. Thomas; Haarer, Staci; Sahasrabudhe, Vaishali; Janiczek, Nancy; Desiraju, Shrilakshmi; Hena, Mostofa; Fiakpui, Charles; Saraswat, Neerja; Sharma, Raman; Sun, Shaoyi; Maiti, Samarendra N.; Leadley, Robert; Edmunds, Jeremy J. (Naeja); (Pfizer)

    2010-12-03

    Herein, we report on the identification of three potent glycine and related amino acid-based series of FXa inhibitors containing a neutral P1 chlorophenyl pharmacophore. A X-ray crystal structure has shown that constrained glycine derivatives with optimized N-substitution can greatly increase hydrophobic interactions in the FXa active site. Also, the substitution of a pyridone ring for a phenylsulfone ring in the P4 sidechain resulted in an inhibitor with enhanced oral bioavailability.

  11. Optical Characterization of SERS Substrates Based on Porous Au Films Prepared by Pulsed Laser Deposition

    Directory of Open Access Journals (Sweden)

    V. V. Strelchuk

    2015-01-01

    Full Text Available The SERS (surface enhanced Raman spectroscopy substrates based on nanocomposite porous films with gold nanoparticles (Au NPs arrays were formed using the method of the pulsed laser deposition from the back low-energy flux of erosion torch particles on the glass substrate fixed at the target plain. The dependencies of porosity, and morphology of the surface of the film regions located near and far from the torch axis on the laser ablation regime, laser pulses energy density, their number, and argon pressure in the vacuum chamber, were ascertained. The Au NPs arrays with the controllable extinction spectra caused by the local surface plasmon resonance were prepared. The possibility of the formation of SERS substrates for the detection of the Rhodamine 6G molecules with the concentration 10−10 Mol/L with the enhancement factor 4·107 was shown.

  12. Growth of carbon nanotubes by Fe-catalyzed chemical vapor processes on silicon-based substrates

    Science.gov (United States)

    Angelucci, Renato; Rizzoli, Rita; Vinciguerra, Vincenzo; Fortuna Bevilacqua, Maria; Guerri, Sergio; Corticelli, Franco; Passini, Mara

    2007-03-01

    In this paper, a site-selective catalytic chemical vapor deposition synthesis of carbon nanotubes on silicon-based substrates has been developed in order to get horizontally oriented nanotubes for field effect transistors and other electronic devices. Properly micro-fabricated silicon oxide and polysilicon structures have been used as substrates. Iron nanoparticles have been obtained both from a thin Fe film evaporated by e-gun and from iron nitrate solutions accurately dispersed on the substrates. Single-walled nanotubes with diameters as small as 1 nm, bridging polysilicon and silicon dioxide “pillars”, have been grown. The morphology and structure of CNTs have been characterized by SEM, AFM and Raman spectroscopy.

  13. Structure-Based Design of Novel HIV-1 Protease Inhibitors to Combat Drug Resistance

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh,A.; Sridhar, P.; Leshchenko, S.; Hussain, A.; Li, J.; Kovalevsky, A.; Walters, D.; Wedelind, J.; Grum-Tokars, V.; et al.

    2006-01-01

    Structure-based design and synthesis of novel HIV protease inhibitors are described. The inhibitors are designed specifically to interact with the backbone of HIV protease active site to combat drug resistance. Inhibitor 3 has exhibited exceedingly potent enzyme inhibitory and antiviral potency. Furthermore, this inhibitor maintains impressive potency against a wide spectrum of HIV including a variety of multi-PI-resistant clinical strains. The inhibitors incorporated a stereochemically defined 5-hexahydrocyclopenta[b]furanyl urethane as the P2-ligand into the (R)-(hydroxyethylamino)sulfonamide isostere. Optically active (3aS,5R,6aR)-5-hydroxy-hexahydrocyclopenta[b]furan was prepared by an enzymatic asymmetrization of meso-diacetate with acetyl cholinesterase, radical cyclization, and Lewis acid-catalyzed anomeric reduction as the key steps. A protein-ligand X-ray crystal structure of inhibitor 3-bound HIV-1 protease (1.35 Angstroms resolution) revealed extensive interactions in the HIV protease active site including strong hydrogen bonding interactions with the backbone. This design strategy may lead to novel inhibitors that can combat drug resistance.

  14. Evaluation of the thiazole Schiff bases as β-glucuronidase inhibitors and their in silico studies.

    Science.gov (United States)

    Khan, Khalid Mohammed; Karim, Aneela; Saied, Sumayya; Ambreen, Nida; Rustamova, Xayale; Naureen, Shagufta; Mansoor, Sajid; Ali, Muhammad; Perveen, Shahnaz; Choudhary, M Iqbal; Morales, Guillermo Antonio

    2014-05-01

    Twenty eight (28) derivatives 2-29 were synthesized and four analogs were found to exhibit single-digit IC(50) values as β-glucuronidase inhibitors. Molecular modeling indicates that three factors: substituent R, lone pair on the nitrogen of azomethine part, and the interactions made by the main skeleton of the molecule, determined the enzyme inhibitory potential of these compounds. The planar conformation of the molecules allows them to fit deep inside the pocket while blocking the entry of other physiological substrates seems to play an important role in their activity.

  15. Circumvention of breast cancer resistance protein (BCRP)-mediated resistance to camptothecins in vitro using non-substrate drugs or the BCRP inhibitor GF120918.

    Science.gov (United States)

    Maliepaard, M; van Gastelen, M A; Tohgo, A; Hausheer, F H; van Waardenburg, R C; de Jong, L A; Pluim, D; Beijnen, J H; Schellens, J H

    2001-04-01

    This study was aimed at characterizing the role of BCRP/MXR/ABCP (BCRP) in resistance of the human ovarian tumor cell lines T8 and MX3 to camptothecins more extensively and investigating whether resistance can be reversed by inhibiting BCRP by GF120918. Camptothecins studied were topotecan, CPT-11, and its active metabolite SN-38, 9-aminocamptothecin, and the novel experimental camptothecins NX211, DX8951f, and BNP1350. Notably, DX8951f and BNP1350 appeared to be very poor substrates for BCRP, with much lower resistance factors observed both in T8 and MX3 cells than observed for the other camptothecins tested. In the presence of a nontoxic dose level of GF120918, the intracellular accumulation of topotecan in the T8 and MX3 cells was completely restored to the intracellular levels observed in the sensitive IGROV1 parental cell line. This resulted in almost complete reversal of drug resistance to topotecan and to most of the other topoisomerase I drugs tested in the T8 cell line and to complete reversal in the MX3 cells. However, coincubation of DX8951f or BNP1350 with GF120918 did not affect the cytotoxicity of either of these drugs significantly. From the combined data, we conclude that the affinities of topoisomerase I drugs for BCRP are, in decreasing order: SN-38 > topotecan > 9-aminocamptothecin approximately CPT-11 > NX211 > DX8951f > BNP1350. Furthermore, GF120918 appears to be a potent reversal agent of BCRP-mediated resistance to camptothecins, with almost complete reversal noted at 100 nM. Potential BCRP-mediated resistance to topoisomerase I inhibitors can also be avoided by using the BCRP-insensitive drugs DX8951f or BNP1350. This observation may have important clinical implications for future development of novel camptothecins.

  16. Design, synthesis and crystallographic analysis of nitrile-based broad-spectrum peptidomimetic inhibitors for coronavirus 3C-like proteases.

    Science.gov (United States)

    Chuck, Chi-Pang; Chen, Chao; Ke, Zhihai; Wan, David Chi-Cheong; Chow, Hak-Fun; Wong, Kam-Bo

    2013-01-01

    Coronaviral infection is associated with up to 5% of respiratory tract diseases. The 3C-like protease (3CL(pro)) of coronaviruses is required for proteolytic processing of polyproteins and viral replication, and is a promising target for the development of drugs against coronaviral infection. We designed and synthesized four nitrile-based peptidomimetic inhibitors with different N-terminal protective groups and different peptide length, and examined their inhibitory effect on the in-vitro enzymatic activity of 3CL(pro) of severe-acute-respiratory-syndrome-coronavirus. The IC(50) values of the inhibitors were in the range of 4.6-49 μM, demonstrating that the nitrile warhead can effectively inactivate the 3CL(pro) autocleavage process. The best inhibitor, Cbz-AVLQ-CN with an N-terminal carbobenzyloxy group, was ~10x more potent than the other inhibitors tested. Crystal structures of the enzyme-inhibitor complexes showed that the nitrile warhead inhibits 3CL(pro) by forming a covalent bond with the catalytic Cys145 residue, while the AVLQ peptide forms a number of favourable interactions with the S1-S4 substrate-binding pockets. We have further showed that the peptidomimetic inhibitor, Cbz-AVLQ-CN, has broad-spectrum inhibition against 3CL(pro) from human coronavirus strains 229E, NL63, OC43, HKU1, and infectious bronchitis virus, with IC(50) values ranging from 1.3 to 3.7 μM, but no detectable inhibition against caspase-3. In summary, we have shown that the nitrile-based peptidomimetic inhibitors are effective against 3CL(pro), and they inhibit 3CL(pro) from a broad range of coronaviruses. Our results provide further insights into the future design of drugs that could serve as a first line defence against coronaviral infection. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  17. MOVPE and characterization of GaN-based structures on alternative substrates

    Energy Technology Data Exchange (ETDEWEB)

    Dikme, Y.

    2006-06-20

    This study involves growth experiments of GaN-based layer structures on silicon (Si), lithium aluminate (LiAlO{sub 2}) and the composite substrate SiCOI. Substrate specific preparation and growth procedures were developed. Because of the different lattice constants and thermal expansion coefficients between GaN and the substrate materials and because of the high depositions temperatures (>1000 C) complex interlayers are required to create a crossover from the substrate to the GaN layer and to prevent substrate/layer bowing and cracks developing in the epitaxial layers. Crystallographic, thermal and electronic properties of these materials were investigated and the developed layers were used as buffer layers for electronic and opto electronic devices. On Si AlN/GaN distributed Bragg reflectors (DBR), InGaN/GaN multiple quantum well (MQW) and AlGaN/GaN HEMT (high electron mobility transistor) were demonstrated. The transistor structures showed high power densities, which were comparable to industrially fabricated devices. As well as the reflection of a certain wavelength region, the DBR layers additionally showed positive influence on succeeding GaN top layer optical properties. For the first time laser emission of an optically pumped InGaN/GaN MQW on Si was demonstrated with low excitation density and a high operating temperature. GaN-based structures were deposited on LiAlO2 in the m-plane crystal orientation; that do not exhibit polarization mechanisms in growth direction. For the deposition of coalesced GaN films a seal-coating of the LiAlO{sub 2} surface was developed and finally LED structures were grown on these substrates. For the first time electroluminescence of LED structures on LiAlO{sub 2} was achieved. The growth on the composite substrate SiCOI was initiated with an HT AlN layer and it was demonstrated that SiCOI is comparable to a bulk SiC substrate for the GaN-based epitaxy. The developed and investigated layer structure served as buffer for the

  18. Kynurenine 3-monooxygenase from Pseudomonas fluorescens: substrate-like inhibitors both stimulate flavin reduction and stabilize the flavin-peroxo intermediate yet result in the production of hydrogen peroxide.

    Science.gov (United States)

    Crozier-Reabe, Karen R; Phillips, Robert S; Moran, Graham R

    2008-11-25

    Kynurenine 3-monooxygenase (KMO) is a flavin-dependent hydroxylase that catalyzes the conversion of l-kynurenine (l-Kyn) to 3-hydroxykynurenine (3OHKyn) in the pathway for tryptophan catabolism. KMO inhibition has been widely suggested as an early treatment for stroke and other neurological disorders that involve ischemia. We have investigated the reductive and the oxidative half-reactions of a stable form of KMO from Pseudomonas fluorescens (KMO). The binding of l-Kyn by the enzyme is relatively slow and involves at least two reversible steps. The rate constant for reduction of the flavin cofactor by NADPH increases by a factor of approximately 2.5 x 10(3) when l-Kyn is bound. The rate of reduction of the KMO.l-Kyn complex is 160 s(-1), and the K(d) for the NADPH complex is 200 microM with charge-transfer absorption bands for the KMO(RED).l-Kyn.NADP(+) complex accumulating after reduction. The reduction potential of KMO is -188 mV and is unresponsive to the addition of l-Kyn or other inhibitory ligands. KMO inhibitors whose structures are reminiscent of l-Kyn such as m-nitrobenzoylalanine and benzoylalanine also stimulate reduction of flavin by NADPH and, in the presence of dioxygen, result in the stoichiometric liberation of hydrogen peroxide, diminishing the perceived therapeutic potential of inhibitors of this type. In the presence of the native substrate, the oxidative half-reaction exhibits triphasic absorbance data. A spectrum consistent with that of a peroxyflavin species accumulates and then decays to yield the oxidized enzyme. This species then undergoes minor spectral changes that, based on flavin difference spectra defined in the presence of 3OHKyn, can be correlated with product release. The oxidative half-reaction observed in the presence of saturating benzoylalanine or m-nitrobenzoylalanine also shows the accumulation of a peroxyflavin species that then decays to yield hydrogen peroxide without hydroxylation.

  19. Enhanced Neural Cell Adhesion and Neurite Outgrowth on Graphene-Based Biomimetic Substrates

    Directory of Open Access Journals (Sweden)

    Suck Won Hong

    2014-01-01

    Full Text Available Neural cell adhesion and neurite outgrowth were examined on graphene-based biomimetic substrates. The biocompatibility of carbon nanomaterials such as graphene and carbon nanotubes (CNTs, that is, single-walled and multiwalled CNTs, against pheochromocytoma-derived PC-12 neural cells was also evaluated by quantifying metabolic activity (with WST-8 assay, intracellular oxidative stress (with ROS assay, and membrane integrity (with LDH assay. Graphene films were grown by using chemical vapor deposition and were then coated onto glass coverslips by using the scooping method. Graphene sheets were patterned on SiO2/Si substrates by using photolithography and were then covered with serum for a neural cell culture. Both types of CNTs induced significant dose-dependent decreases in the viability of PC-12 cells, whereas graphene exerted adverse effects on the neural cells just at over 62.5 ppm. This result implies that graphene and CNTs, even though they were the same carbon-based nanomaterials, show differential influences on neural cells. Furthermore, graphene-coated or graphene-patterned substrates were shown to substantially enhance the adhesion and neurite outgrowth of PC-12 cells. These results suggest that graphene-based substrates as biomimetic cues have good biocompatibility as well as a unique surface property that can enhance the neural cells, which would open up enormous opportunities in neural regeneration and nanomedicine.

  20. PDMS as a sacrificial substrate for SU-8-based biomedical and microfluidic applications

    International Nuclear Information System (INIS)

    Patel, Jasbir N; Kaminska, Bozena; Gray, Bonnie L; Gates, Byron D

    2008-01-01

    We describe a new fabrication process utilizing polydimethylesiloxane (PDMS) as a sacrificial substrate layer for fabricating free-standing SU-8-based biomedical and microfluidic devices. The PDMS-on-glass substrate permits SU-8 photo patterning and layer-to-layer bonding. We have developed a novel PDMS-based process which allows the SU-8 structures to be easily peeled off from the substrate after complete fabrication. As an example, a fully enclosed microfluidic chip has been successfully fabricated utilizing the presented new process. The enclosed microfluidic chip uses adhesive bonding technology and the SU-8 layers from 10 µm to 450 µm thick for fully enclosed microchannels. SU-8 layers as large as the glass substrate are successfully fabricated and peeled off from the PDMS layer as single continuous sheets. The fabrication results are supported by optical microscopy and profilometry. The peel-off force for the 120 µm thick SU-8-based chips is measured using a voice coil actuator (VCA). As an additional benefit the release step leaves the input and the output of the microchannels accessible to the outside world facilitating interconnecting to the external devices

  1. Peptide-Based Selective Inhibitors of Matrix Metalloproteinase-Mediated Activities

    Directory of Open Access Journals (Sweden)

    Margaret W. Ndinguri

    2012-11-01

    Full Text Available The matrix metalloproteinases (MMPs exhibit a broad array of activities, some catalytic and some non-catalytic in nature. An overall lack of selectivity has rendered small molecule, active site targeted MMP inhibitors problematic in execution. Inhibitors that favor few or individual members of the MMP family often take advantage of interactions outside the enzyme active site. We presently focus on peptide-based MMP inhibitors and probes that do not incorporate conventional Zn2+ binding groups. In some cases, these inhibitors and probes function by binding only secondary binding sites (exosites, while others bind both exosites and the active site. A myriad of MMP mediated-activities beyond selective catalysis can be inhibited by peptides, particularly cell adhesion, proliferation, motility, and invasion. Selective MMP binding peptides comprise highly customizable, unique imaging agents. Areas of needed improvement for MMP targeting peptides include binding affinity and stability.

  2. Virtual Lead Identification of Farnesyltransferase Inhibitors Based on Ligand and Structure-Based Pharmacophore Techniques

    Directory of Open Access Journals (Sweden)

    Nizar M. Mhaidat

    2013-05-01

    Full Text Available Farnesyltransferase enzyme (FTase is considered an essential enzyme in the Ras signaling pathway associated with cancer. Thus, designing inhibitors for this enzyme might lead to the discovery of compounds with effective anticancer activity. In an attempt to obtain effective FTase inhibitors, pharmacophore hypotheses were generated using structure-based and ligand-based approaches built in Discovery Studio v3.1. Knowing the presence of the zinc feature is essential for inhibitor’s binding to the active site of FTase enzyme; further customization was applied to include this feature in the generated pharmacophore hypotheses. These pharmacophore hypotheses were thoroughly validated using various procedures such as ROC analysis and ligand pharmacophore mapping. The validated pharmacophore hypotheses were used to screen 3D databases to identify possible hits. Those which were both high ranked and showed sufficient ability to bind the zinc feature in active site, were further refined by applying drug-like criteria such as Lipiniski’s “rule of five” and ADMET filters. Finally, the two candidate compounds (ZINC39323901 and ZINC01034774 were allowed to dock using CDOCKER and GOLD in the active site of FTase enzyme to optimize hit selection.

  3. Covalent docking of selected boron-based serine beta-lactamase inhibitors

    Science.gov (United States)

    Sgrignani, Jacopo; Novati, Beatrice; Colombo, Giorgio; Grazioso, Giovanni

    2015-05-01

    AmpC β-lactamase is a hydrolytic enzyme conferring resistance to β-lactam antibiotics in multiple Gram-negative bacteria. Therefore, identification of non-β-lactam compounds able to inhibit the enzyme is crucial for the development of novel antibacterial therapies. In general, AmpC inhibitors have to engage the highly solvent-exposed catalytic site of the enzyme. Therefore, understanding the implications of ligand-protein induced-fit and water-mediated interactions behind the inhibitor-enzyme recognition process is fundamental for undertaking structure-based drug design process. Here, we focus on boronic acids, a promising class of beta-lactamase covalent inhibitors. First, we optimized a docking protocol able to reproduce the experimentally determined binding mode of AmpC inhibitors bearing a boronic group. This goal was pursued (1) performing rigid and flexible docking calculations aiming to establish the role of the side chain conformations; and (2) investigating the role of specific water molecules in shaping the enzyme active site and mediating ligand protein interactions. Our calculations showed that some water molecules, conserved in the majority of the considered X-ray structures, are needed to correctly predict the binding pose of known covalent AmpC inhibitors. On this basis, we formalized our findings in a docking and scoring protocol that could be useful for the structure-based design of new boronic acid AmpC inhibitors.

  4. Electrical characteristics of SiGe-base bipolar transistors on thin-film SOI substrates

    International Nuclear Information System (INIS)

    Liao, Shu-Hui; Chang, Shu-Tong

    2010-01-01

    This paper, based on two-dimensional simulations, provides a comprehensive analysis of the electrical characteristics of the Silicon germanium (SiGe)-base bipolar transistors on thin-film siliconon-insulator (SOI) substrates. The impact of the buried oxide thickness (T OX ), the emitter width (W E ), and the lateral distance between the edge of the intrinsic base and the reach-through region (L col ) on both the AC and DC device characteristics was analyzed in detail. Regarding the DC characteristics, the simulation results suggest that a thicker T OX gives a larger base-collector breakdown voltage (BV CEO ), whereas reducing the T OX leads to an enhanced maximum electric field at the B-C junction. As for the AC characteristics, cut-off frequency (f T ) increases slightly with increasing buried oxide thickness and finally saturates to a constant value when the buried oxide thickness is about 0.15 μm. The collector-substrate capacitance (C CS ) decreases with increasing buried oxide thickness while the maximum oscillation frequency (f max ) increases with increasing buried oxide thickness. Furthermore, the impact of self-heating effects in the device was analyzed in various areas. The thermal resistance as a function of the buried oxide thickness indicates that the thermal resistance of the SiGe-base bipolar transistor on a SOI substrate is slightly higher than that of a bulk SiGe-base bipolar transistor. The thermal resistance is reduced by ∼37.89% when the emitter width is increased by a factor of 5 for a fixed buried oxide thickness of 0.1 μm. All the results can be used to design and optimize SiGe-base bipolar transistors on SOI substrates with minimum thermal resistance to enhance device performance.

  5. Dihydrooxonate is a substrate of Dihydroorrotate Dehydrogenase (DHOD) providing evidence for involvement of crsteine and serine residues in base catalysis

    DEFF Research Database (Denmark)

    Björnberg, Olof; Jordan, Douglas B.; Palfey, Bruce Allan

    2001-01-01

    pKa of the 5-position in the substrate. Oxonate, the oxidation product of dihydrooxonate, was a competitive inhibitor versus dihydroorotate, and DHODA was the most sensitive of the three enzymes. DHODA was reinvestigated with respect to product inhibition by orotate. The results suggest a classical...... one-site ping-pong mechanism with fumarate as electron acceptor, while the kinetics with ferricyanide is highly dependent on the detailed reaction conditions....

  6. Design of an SolidWorks-based household substrate cultivation device

    Science.gov (United States)

    Yi, Guo; Yueying, Wang

    2018-03-01

    Rapid urbanization has caused increasingly severe environmental problems and smaller tillable land area. Even worse, negative reports on vegetable production are repeatedly found. In this case, home gardening has become an inexorable trend. To meet demand for vegetable cultivation in the home environment, an SolidWorks-based household substrate cultivation device has been designed. This device is composed of the cultivation tank, upright post, base, irrigation system, supplemental lighting system and control system. The household substrate cultivation device manufactured based on the design results has shown in practice that this device features an esthetic appearance, low cost, automatic irrigation and lighting supplementation, good vegetable growing conditions, full of ornamental value and practicability and thus is suitable for vegetable growing in the home environment. Hence it has a higher promotion value in the home gardening field.

  7. Modeling of the rough spherical nanoparticles manipulation on a substrate based on the AFM nanorobot

    Science.gov (United States)

    Zakeri, M.; Faraji, J.

    2014-12-01

    In this paper, dynamic behavior of the rough spherical micro/nanoparticles during pulling/pushing on the flat substrate has been investigated and analyzed. For this purpose, at first, two hexagonal roughness models (George and Cooper) were studied and then evaluations for adhesion force were determined for rough particle manipulation on flat substrate. These two models were then changed by using of the Rabinovich theory. Evaluations were determined for contact adhesion force between rough particle and flat substrate; depth of penetration evaluations were determined by the Johnson-Kendall-Roberts contact mechanic theory and the Schwartz method and according to Cooper and George roughness models. Then, the novel contact theory was used to determine a dynamic model for rough micro/nanoparticle manipulation on flat substrate. Finally, simulation of particle dynamic behavior was implemented during pushing of rough spherical gold particles with radii of 50, 150, 400, 600, and 1,000 nm. Results derived from simulations of particles with several rates of roughness on flat substrate indicated that compared to results for flat particles, inherent roughness on particles might reduce the rate of critical force needed for sliding and rolling given particles. Given a fixed radius for roughness value and increased roughness height, evaluations for sliding and rolling critical forces showed greater reduction. Alternately, the rate of critical force was shown to reduce relative to an increased roughness radius. With respect to both models, based on the George roughness model, the predicted rate of adhesion force was greater than that determined in the Cooper roughness model, and as a result, the predicted rate of critical force based on the George roughness model was closer to the critical force value of flat particle.

  8. Solution Structure of a Novel C2-Symmetrical Bifunctional Bicyclic Inhibitor Based on SFTI-1

    International Nuclear Information System (INIS)

    Jaulent, Agnes M.; Brauer, Arnd B. E.; Matthews, Stephen J.; Leatherbarrow, Robin J.

    2005-01-01

    A novel bifunctional bicyclic inhibitor has been created that combines features both from the Bowman-Birk inhibitor (BBI) proteins, which have two distinct inhibitory sites, and from sunflower trypsin inhibitor-1 (SFTI-1), which has a compact bicyclic structure. The inhibitor was designed by fusing together a pair of reactive loops based on a sequence derived from SFTI-1 to create a backbone-cyclized disulfide-bridged 16-mer peptide. This peptide has two symmetrically spaced trypsin binding sites. Its synthesis and biological activity have been reported in a previous communication [Jaulent and Leatherbarrow, 2004, PEDS 17, 681]. In the present study we have examined the three-dimensional structure of the molecule. We find that the new inhibitor, which has a symmetrical 8-mer half-cystine CTKSIPP'I' motif repeated through a C 2 symmetry axis also shows a complete symmetry in its three-dimensional structure. Each of the two loops adopts the expected canonical conformation common to all BBIs as well as SFTI-1. We also find that the inhibitor displays a strong and unique structural identity, with a notable lack of minor conformational isomers that characterise most reactive site loop mimics examined to date as well as SFTI-1. This suggests that the presence of the additional cyclic loop acts to restrict conformational mobility and that the deliberate introduction of cyclic symmetry may offer a general route to locking the conformation of β-hairpin structures

  9. Model-based confirmation of alternative substrates of mitochondrial electron transport chain.

    Science.gov (United States)

    Kleessen, Sabrina; Araújo, Wagner L; Fernie, Alisdair R; Nikoloski, Zoran

    2012-03-30

    Discrimination of metabolic models based on high throughput metabolomics data, reflecting various internal and external perturbations, is essential for identifying the components that contribute to the emerging behavior of metabolic processes. Here, we investigate 12 different models of the mitochondrial electron transport chain (ETC) in Arabidopsis thaliana during dark-induced senescence in order to elucidate the alternative substrates to this metabolic pathway. Our findings demonstrate that the coupling of the proposed computational approach, based on dynamic flux balance analysis, with time-resolved metabolomics data results in model-based confirmations of the hypotheses that, during dark-induced senescence in Arabidopsis, (i) under conditions where the main substrate for the ETC are not fully available, isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase are able to donate electrons to the ETC, (ii) phytanoyl-CoA does not act even as an indirect substrate of the electron transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase complex, and (iii) the mitochondrial γ-aminobutyric acid transporter has functional significance in maintaining mitochondrial metabolism. Our study provides a basic framework for future in silico studies of alternative pathways in mitochondrial metabolism under extended darkness whereby the role of its components can be computationally discriminated based on available molecular profile data.

  10. Nonnucleoside Reverse-transcriptase Inhibitor- vs Ritonavir-boosted Protease Inhibitor-based Regimens for Initial Treatment of HIV Infection

    DEFF Research Database (Denmark)

    Borges, Álvaro H; Lundh, Andreas; Tendal, Britta

    2016-01-01

    BACKGROUND: Previous studies suggest that nonnucleoside reverse-transcriptase inhibitors (NNRTIs) cause faster virologic suppression, while ritonavir-boosted protease inhibitors (PI/r) recover more CD4 cells. However, individual trials have not been powered to compare clinical outcomes. METHODS: ...

  11. Design and synthesis of 3,3'-biscoumarin-based c-Met inhibitors.

    Science.gov (United States)

    Xu, Jimin; Ai, Jing; Liu, Sheng; Peng, Xia; Yu, Linqian; Geng, Meiyu; Nan, Fajun

    2014-06-14

    A library of biscoumarin-based c-Met inhibitors was synthesized, based on optimization of 3,3'-biscoumarin hit 3, which was identified as a non-ATP competitive inhibitor of c-Met from a diverse library of coumarin derivatives. Among these compounds, 38 and 40 not only showed potent enzyme activities with IC50 values of 107 nM and 30 nM, respectively, but also inhibited c-Met phosphorylation in BaF3/TPR-Met and EBC-1 cells.

  12. Origin of magnetic switching field distribution in bit patterned media based on pre-patterned substrates

    OpenAIRE

    Pfau , B; Günther , C.M.; Guehrs , E; Hauet , Thomas; Yang , H; Vinh , L.; Xu , X; Yaney , D; Rick , R; Eisebitt , S; Hellwig , O

    2011-01-01

    International audience; Using a combination of synchrotron radiation based magnetic imaging and high-resolution transmission electron microscopy we reveal systematic correlations between the magnetic switching field and the internal nanoscale structure of individual islands in bit patterned media fabricated by Co/Pd-multilayer deposition onto pre-patterned substrates. We find that misaligned grains at the island periphery are a common feature independent of the island switching field, while i...

  13. Silicon nanowire-based tunneling field-effect transistors on flexible plastic substrates.

    Science.gov (United States)

    Lee, Myeongwon; Koo, Jamin; Chung, Eun-Ae; Jeong, Dong-Young; Koo, Yong-Seo; Kim, Sangsig

    2009-11-11

    A technique to implement silicon nanowire (SiNW)-based tunneling field-effect transistors (TFETs) on flexible plastic substrates is developed for the first time. The p-i-n configured Si NWs are obtained from an Si wafer using a conventional top-down CMOS-compatible technology, and they are then transferred onto the plastic substrate. Based on gate-controlled band-to-band tunneling (BTBT) as their working principle, the SiNW-based TFETs show normal p-channel switching behavior with a threshold voltage of -1.86 V and a subthreshold swing of 827 mV/dec. In addition, ambipolar conduction is observed due to the presence of the BTBT between the heavily doped p+ drain and n+ channel regions, indicating that our TFETs can operate in the n-channel mode as well. Furthermore, the BTBT generation rates for both the p-channel and n-channel operating modes are nearly independent of the bending state (strain = 0.8%) of the plastic substrate.

  14. Silicon nanowire-based tunneling field-effect transistors on flexible plastic substrates

    International Nuclear Information System (INIS)

    Lee, Myeongwon; Koo, Jamin; Chung, Eun-Ae; Jeong, Dong-Young; Kim, Sangsig; Koo, Yong-Seo

    2009-01-01

    A technique to implement silicon nanowire (SiNW)-based tunneling field-effect transistors (TFETs) on flexible plastic substrates is developed for the first time. The p-i-n configured Si NWs are obtained from an Si wafer using a conventional top-down CMOS-compatible technology, and they are then transferred onto the plastic substrate. Based on gate-controlled band-to-band tunneling (BTBT) as their working principle, the SiNW-based TFETs show normal p-channel switching behavior with a threshold voltage of -1.86 V and a subthreshold swing of 827 mV/dec. In addition, ambipolar conduction is observed due to the presence of the BTBT between the heavily doped p + drain and n + channel regions, indicating that our TFETs can operate in the n-channel mode as well. Furthermore, the BTBT generation rates for both the p-channel and n-channel operating modes are nearly independent of the bending state (strain = 0.8%) of the plastic substrate.

  15. Silicon nanowire-based tunneling field-effect transistors on flexible plastic substrates

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Myeongwon; Koo, Jamin; Chung, Eun-Ae; Jeong, Dong-Young; Kim, Sangsig [Department of Electrical Engineering and Institute for Nano Science, Korea University, 5-1, Anam-Dong, Seongbuk-Gu, Seoul 136-701 (Korea, Republic of); Koo, Yong-Seo, E-mail: sangsig@korea.ac.k [Department of Electrical Engineering, Seokyeong University, 16-1, Jungneung-dong, Seongbuk-gu, Seoul 136-704 (Korea, Republic of)

    2009-11-11

    A technique to implement silicon nanowire (SiNW)-based tunneling field-effect transistors (TFETs) on flexible plastic substrates is developed for the first time. The p-i-n configured Si NWs are obtained from an Si wafer using a conventional top-down CMOS-compatible technology, and they are then transferred onto the plastic substrate. Based on gate-controlled band-to-band tunneling (BTBT) as their working principle, the SiNW-based TFETs show normal p-channel switching behavior with a threshold voltage of -1.86 V and a subthreshold swing of 827 mV/dec. In addition, ambipolar conduction is observed due to the presence of the BTBT between the heavily doped p{sup +} drain and n{sup +} channel regions, indicating that our TFETs can operate in the n-channel mode as well. Furthermore, the BTBT generation rates for both the p-channel and n-channel operating modes are nearly independent of the bending state (strain = 0.8%) of the plastic substrate.

  16. Synthesis and Evaluation of Bicyclo[3.1.0]hexane-Based UDP-Galf Analogues as Inhibitors of the Mycobacterial Galactofuranosyltransferase GlfT2

    Directory of Open Access Journals (Sweden)

    Todd L. Lowary

    2016-08-01

    Full Text Available UDP-galactofuranose (UDP-Galf is the donor substrate for both bifunctional galactofuranosyltransferases, GlfT1 and GlfT2, which are involved in the biosynthesis of mycobacterial galactan. In this paper, a group of UDP-Galf mimics were synthesized via reductive amination of a bicyclo[3.1.0]hexane-based amine by reacting with aromatic, linear, or uridine-containing aldehydes. These compounds were evaluated against GlfT2 using a coupled spectrophotometric assay, and were shown to be weak inhibitors of the enzyme.

  17. Dye-sensitized solar cells based on different nano-oxides on plastic PET substrate

    Science.gov (United States)

    Mikula, Milan; Gemeiner, Pavol; Beková, Zuzana; Dvonka, Vladimír; Búc, Dalibor

    2015-01-01

    Polyethylene-terephthalate (PET) foils and glass slides coated with thin conductive layers were used as substrates for TiO2 or ZnO based photoactive electrodes of dye-sensitized solar cells (DSSC) with organo-metallic Ru-dye, standard iodine electrolyte and Pt coated FTO/glass counterelectrode (CE). Different compositions of nanoparticle oxides in forms of alcohol pastes as well as the CE paste were applied onto the substrates by screen printing or by doctor blade techniques. Photocurrents and I-V loading characteristics were measured depending on the solar cell structure and preparation, including the oxide composition, electrode conductivity and the dye type. The influence of thin TiO2 blocking layer prepared by sol-gel technique is also discussed.

  18. Multistep Cylindrical Structure Analysis at Normal Incidence Based on Water-Substrate Broadband Metamaterial Absorbers

    Science.gov (United States)

    Fang, Chonghua

    2018-01-01

    A new multistep cylindrical structure based on water-substrate broadband metamaterial absorbers is designed to reduce the traditional radar cross-section (RCS) of a rod-shaped object. The proposed configuration consists of two distinct parts. One of these components is formed by a four-step cylindrical metal structure, whereas the other one is formed by a new water-substrate broadband metamaterial absorber. The designed structure can significantly reduce the radar cross section more than 10 dB from 4.58 to 18.42 GHz which is the 86.5 % bandwidth of from C-band to 20 GHz. The results of measurement show reasonably good accordance with the simulated ones, which verifies the ability and effect of the proposed design.

  19. Phase characterization of Re-based diffusion barrier layer on Nb substrate

    International Nuclear Information System (INIS)

    Sugiarti, Eni; Wang, Youngmin; Hashimoto, Naoyuki; Ohnuki, Somei; Narita, Toshio

    2011-01-01

    An electron microscopy phase characterization was carried out for a Re-based diffusion barrier layer, which was deposited on the Nb substrate used as an ultra high temperature material. The coating process produced three layers; an outer Cr(Re) layer, an intermediate Cr-Nb-Re layer, and an inner Nb(Re) layer. The Cr-Nb-Re layer is considered to act as a diffusion barrier layer between the substrate and the outer Cr(Re) reservoir layer. The Cr(Re) and Nb(Re) layers are in single phase with a similar bcc structures, but they are different in structure from the intermediate layer, which is composed of a dual phase of Re 63 Cr 20 Nb 17 with a cubic structure and Nb 42 Re 33 Cr 25 with a hexagonal structure determined by transmission electron microscopy (TEM) in this study. (author)

  20. Glycosylase-mediated repair of radiation-induced DNA bases: substrate specificities and mechanisms

    International Nuclear Information System (INIS)

    D'ham, Cedric

    1998-01-01

    Cellular DNA is subject to permanent damage and repair processes. One way to restore the integrity of DNA involves the base excision repair pathway. Glycosylases are the key-enzymes of this process. The present work deals with the determination of the substrate specificity and the mechanism of action of three glycosylases: endonuclease III and Fpg of Escherichia coli and Ogg1 of Saccharomyces cerevisiae. The present manuscript is divided into four parts: Endonuclease III-mediated excision of 5,6-dihydro-thymine and 5-hydroxy-5,6-dihydro-thymine from γ-irradiated DNA was analyzed by a gas chromatography-mass spectrometry assay, including a liquid chromatography pre-purification step. This was found to be necessary in order to separate the cis and trans isomers of 6-hydroxy-5,6-dihydro-thymine from the 5-hydroxy-5,6-dihydro-thymine. Modified oligonucleotides that contained a unique lesion, including thymine glycol, 5,6-dihydro-thymine and 5-hydroxy-cytosine were synthesized to assess the substrate specificity of endonuclease III and Fpg. The order of preference of the enzymes for the substrates was determined by the measurement of the Michaelis constants of the kinetics. Furthermore, the mechanism of action of endonuclease III has been reconsidered, after analysis using the MALDI mass spectrometry technique. These studies reveal that hydrolysis is the main pathway by which endonuclease III cleaves the DNA backbone. Using a modified oligonucleotide, 8-oxo-7,8-dihydro-adenine was shown to be a product of excision of the Ogg1 enzyme. The role of the complementary base towards the lesion was found to be preponderant in the damage excision. A last chapter concerns the synthesis and the characterization of the four isomers of 5(6)-hydroxy-6(5)-hydroperoxides of thymine. These products may be substrates for endonuclease III or Fpg. (author) [fr

  1. DFT-based inhibitor and promoter selection criteria for pentagonal ...

    Indian Academy of Sciences (India)

    Methane hydrate formation inhibition by methanol and ethylene glycol as well as methane hydrate stabilization by cyclopentane and tetrahydrofuran are critically analysed based on the interaction energy, free energy change, dipole moment and infrared frequency calculation. Calculation of free energy change for formation ...

  2. Improved Potency of Indole-Based NorA Efflux Pump Inhibitors: From Serendipity toward Rational Design and Development.

    Science.gov (United States)

    Buonerba, Federica; Lepri, Susan; Goracci, Laura; Schindler, Bryan D; Seo, Susan M; Kaatz, Glenn W; Cruciani, Gabriele

    2017-01-12

    The NorA efflux pump is a potential drug target for reversal of resistance to selected antibacterial agents, and recently we described indole-based inhibitor candidates. Herein we report a second class of inhibitors derived from them but with significant differences in shape and size. In particular, compounds 13 and 14 are very potent inhibitors in that they demonstrated the lowest IC 50 values (2 μM) ever observed among all indole-based compounds we have evaluated.

  3. A cell-based fluorescent glucose transporter assay for SGLT2 inhibitor discovery

    Directory of Open Access Journals (Sweden)

    Yi Huan

    2013-04-01

    Full Text Available The sodium/glucose cotransporter 2 (SGLT2 is responsible for the majority of glucose reabsorption in the kidney, and currently, SGLT2 inhibitors are considered as promising hypoglycemic agents for the treatment of type 2 diabetes mellitus. By constructing CHO cell lines that stably express the human SGLT2 transmembrane protein, along with a fluorescent glucose transporter assay that uses 2-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-ylamino]2-deoxyglucose (2-NBDG as a glucose analog, we have developed a nonradioactive, cell-based assay for the discovery and characterization of SGLT2 inhibitors.

  4. Some observations on phosphate based corrosion inhibitors in preventing carbon steel corrosion

    International Nuclear Information System (INIS)

    Anupkumar, B.; Satpathy, K.K.

    2000-01-01

    Among the various types of phosphonic acid based inhibitors assayed, namely HEDP, ATMP and a commercial corrosion inhibitor (code named Betz), it was found that Betz has the maximum amount of organic phosphate followed by HEDP and ATMP. The corrosion rate studies show that Betz gives the highest inhibition efficiency followed by HEDP and ATMP. This shows that organic phosphate plays a significant role in corrosion protection. However, it was observed that due to synergestic effect, HEDP in the presence of Zn 2+ gave a better corrosion protection than Betz. The results are discussed in the light of available literature. (author)

  5. Identification of p38α MAP kinase inhibitors by pharmacophore based virtual screening

    DEFF Research Database (Denmark)

    Gangwal, Rahul P; Das, Nihar R; Thanki, Kaushik

    2014-01-01

    The p38α mitogen-activated protein (MAP) kinase plays a vital role in treating many inflammatory diseases. In the present study, a combined ligand and structure based pharmacophore model was developed to identify potential DFG-in selective p38 MAP kinase inhibitors. Conformations of co...

  6. SVMDLF: A novel R-based Web application for prediction of dipeptidyl peptidase 4 inhibitors.

    Science.gov (United States)

    Chandra, Sharat; Pandey, Jyotsana; Tamrakar, Akhilesh K; Siddiqi, Mohammad Imran

    2017-12-01

    Dipeptidyl peptidase 4 (DPP4) is a well-known target for the antidiabetic drugs. However, currently available DPP4 inhibitor screening assays are costly and labor-intensive. It is important to create a robust in silico method to predict the activity of DPP4 inhibitor for the new lead finding. Here, we introduce an R-based Web application SVMDLF (SVM-based DPP4 Lead Finder) to predict the inhibitor of DPP4, based on support vector machine (SVM) model, predictions of which are confirmed by in vitro biological evaluation. The best model generated by MACCS structure fingerprint gave the Matthews correlation coefficient of 0.87 for the test set and 0.883 for the external test set. We screened Maybridge database consisting approximately 53,000 compounds. For further bioactivity assay, six compounds were shortlisted, and of six hits, three compounds showed significant DPP4 inhibitory activities with IC 50 values ranging from 8.01 to 10.73 μm. This application is an OpenCPU server app which is a novel single-page R-based Web application for the DPP4 inhibitor prediction. The SVMDLF is freely available and open to all users at http://svmdlf.net/ocpu/library/dlfsvm/www/ and http://www.cdri.res.in/svmdlf/. © 2017 John Wiley & Sons A/S.

  7. Structure of matrix metalloproteinase-3 with a platinum-based inhibitor.

    Science.gov (United States)

    Belviso, Benny Danilo; Caliandro, Rocco; Siliqi, Dritan; Calderone, Vito; Arnesano, Fabio; Natile, Giovanni

    2013-06-18

    An X-ray investigation has been performed with the aim of characterizing the binding sites of a platinum-based inhibitor (K[PtCl3(DMSO)]) of matrix metalloproteinase-3 (stromelysin-1). The platinum complex targets His224 in the S1' specificity loop, representing the first step in the selective inhibition process (PDB ID code 4JA1).

  8. Novel indole-based inhibitors of IMPDH: introduction of hydrogen bond acceptors at indole C-3.

    Science.gov (United States)

    Watterson, Scott H; Dhar, T G Murali; Ballentine, Shelley K; Shen, Zhongqi; Barrish, Joel C; Cheney, Daniel; Fleener, Catherine A; Rouleau, Katherine A; Townsend, Robert; Hollenbaugh, Diane L; Iwanowicz, Edwin J

    2003-04-07

    The development of a series of novel indole-based inhibitors of 5'-inosine monophosphate dehydrogenase (IMPDH) is described. Various hydrogen bond acceptors at C-3 of the indole were explored. The synthesis and the structure-activity relationships (SARs) derived from in vitro studies are outlined.

  9. Synthesis, pharmacological evaluation and molecular docking studies of pyrimidinedione based DPP-4 inhibitors as antidiabetic agents

    Science.gov (United States)

    Jha, Vibhu; Bhadoriya, Kamlendra Singh

    2018-04-01

    Dipeptidyl peptidase-4 (DPP-4) inhibitors are a class of newly developed antidiabetic drugs that bock DPP-4. DPP-4 is responsible for degradation of incretins harmones such as GLP-1 (Glucagon like Peptide) and GIP (Gastric inhibitory polypeptide) that maintain blood-glucose level. Pyrimidinedione based compounds were designed and synthesized for DPP-4 inhibitory activity. These heterocycles were designed by taking Alogliptin as a reference DPP-4 inhibitors and synthesized as N-methylated and N-benzylated pyrimidinediones. These compounds were subjected to DPP-4 assay, five out of nine synthesized compounds have shown in vitro DPP-4 inhibitory activity in significant range. Further, molecular docking studies of these compounds were performed on DPP-4 subunit and compared with natural DPP-4 inhibitors like Flavone, Resveratrol, Quercetin, Diprotin A. Docking studies have led to the conclusion that there are some identical amino acid interactions as Tyr 666 and Tyr 662, seen in both synthesized compounds and natural DPP-4 inhibitors. This study completely gives a good scope for further derivatisation and optimization of synthesized compounds to get clinical candidate as DPP-4 inhibitor for antidiabetic activity.

  10. Fragment-Based Discovery of a Potent, Orally Bioavailable Inhibitor That Modulates the Phosphorylation and Catalytic Activity of ERK1/2.

    Science.gov (United States)

    Heightman, Tom D; Berdini, Valerio; Braithwaite, Hannah; Buck, Ildiko M; Cassidy, Megan; Castro, Juan; Courtin, Aurélie; Day, James E H; East, Charlotte; Fazal, Lynsey; Graham, Brent; Griffiths-Jones, Charlotte M; Lyons, John F; Martins, Vanessa; Muench, Sandra; Munck, Joanne M; Norton, David; O'Reilly, Marc; Palmer, Nick; Pathuri, Puja; Reader, Michael; Rees, David C; Rich, Sharna J; Richardson, Caroline; Saini, Harpreet; Thompson, Neil T; Wallis, Nicola G; Walton, Hugh; Wilsher, Nicola E; Woolford, Alison J-A; Cooke, Michael; Cousin, David; Onions, Stuart; Shannon, Jonathan; Watts, John; Murray, Christopher W

    2018-05-31

    Aberrant activation of the MAPK pathway drives cell proliferation in multiple cancers. Inhibitors of BRAF and MEK kinases are approved for the treatment of BRAF mutant melanoma, but resistance frequently emerges, often mediated by increased signaling through ERK1/2. Here, we describe the fragment-based generation of ERK1/2 inhibitors that block catalytic phosphorylation of downstream substrates such as RSK but also modulate phosphorylation of ERK1/2 by MEK without directly inhibiting MEK. X-ray crystallographic and biophysical fragment screening followed by structure-guided optimization and growth from the hinge into a pocket proximal to the C-α helix afforded highly potent ERK1/2 inhibitors with excellent kinome selectivity. In BRAF mutant cells, the lead compound suppresses pRSK and pERK levels and inhibits proliferation at low nanomolar concentrations. The lead exhibits tumor regression upon oral dosing in BRAF mutant xenograft models, providing a promising basis for further optimization toward clinical pERK1/2 modulating ERK1/2 inhibitors.

  11. A Yellow Emitting InGaN/GaN Nanowires-based Light Emitting Diode Grown on Scalable Quartz Substrate

    KAUST Repository

    Prabaswara, Aditya

    2017-05-08

    The first InGaN/GaN nanowires-based yellow (λ = 590 nm) light-emitting diodes on scalable quartz substrates are demonstrated, by utilizing a thin Ti/TiN interlayer to achieve simultaneous substrate conductivity and transparency.

  12. A Yellow Emitting InGaN/GaN Nanowires-based Light Emitting Diode Grown on Scalable Quartz Substrate

    KAUST Repository

    Prabaswara, Aditya; Ng, Tien Khee; Zhao, Chao; Janjua, Bilal; Alyamani, Ahmed; El-desouki, Munir; Ooi, Boon S.

    2017-01-01

    The first InGaN/GaN nanowires-based yellow (λ = 590 nm) light-emitting diodes on scalable quartz substrates are demonstrated, by utilizing a thin Ti/TiN interlayer to achieve simultaneous substrate conductivity and transparency.

  13. Theoretical study on the interaction of pyrrolopyrimidine derivatives as LIMK2 inhibitors: insight into structure-based inhibitor design.

    Science.gov (United States)

    Shen, Mingyun; Zhou, Shunye; Li, Youyong; Li, Dan; Hou, Tingjun

    2013-10-01

    LIM kinases (LIMKs), downstream of Rho-associated protein kinases (ROCKs) and p21-activated protein kinases (PAKs), are shown to be promising targets for the treatment of cancers. In this study, the inhibition mechanism of 41 pyrrolopyrimidine derivatives as LIMK2 inhibitors was explored through a series of theoretical approaches. First, a model of LIMK2 was generated through molecular homology modeling, and the studied inhibitors were docked into the binding active site of LIMK2 by the docking protocol, taking into consideration the flexibility of the protein. The binding poses predicted by molecular docking for 17 selected inhibitors with different bioactivities complexed with LIMK2 underwent molecular dynamics (MD) simulations, and the binding free energies for the complexes were predicted by using the molecular mechanics/generalized born surface area (MM/GBSA) method. The predicted binding free energies correlated well with the experimental bioactivities (r(2) = 0.63 or 0.62). Next, the free energy decomposition analysis was utilized to highlight the following key structural features related to biological activity: (1) the important H-bond between Ile408 and pyrrolopyrimidine, (2) the H-bonds between the inhibitors and Asp469 and Gly471 which maintain the stability of the DFG-out conformation, and (3) the hydrophobic interactions between the inhibitors and several key residues (Leu337, Phe342, Ala345, Val358, Lys360, Leu389, Ile408, Leu458 and Leu472). Finally, a variety of LIMK2 inhibitors with a pyrrolopyrimidine scaffold were designed, some of which showed improved potency according to the predictions. Our studies suggest that the use of molecular docking with MD simulations and free energy calculations could be a powerful tool for understanding the binding mechanism of LIMK2 inhibitors and for the design of more potent LIMK2 inhibitors.

  14. Discovery of novel EGFR tyrosine kinase inhibitors by structure-based virtual screening.

    Science.gov (United States)

    Li, Siyuan; Sun, Xianqiang; Zhao, Hongli; Tang, Yun; Lan, Minbo

    2012-06-15

    By using of structure-based virtual screening, 13 novel epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors were discovered from 197,116 compounds in the SPECS database here. Among them, 8 compounds significantly inhibited EGFR kinase activity with IC(50) values lower than 10 μM. 3-{[1-(3-Chloro-4-fluorophenyl)-3,5-dioxo-4-pyrazolidinylidene]methyl}phenyl 2-thiophenecarboxylate (13), particularly, was the most potent inhibitor possessing the IC(50) value of 3.5 μM. The docking studies also provide some useful information that the docking models of the 13 compounds are beneficial to find a new path for designing novel EGFR inhibitors. Copyright © 2012 Elsevier Ltd. All rights reserved.

  15. Fabrication of digital microfluidic devices on flexible paper-based and rigid substrates via screen printing

    Science.gov (United States)

    Yafia, Mohamed; Shukla, Saurabh; Najjaran, Homayoun

    2015-05-01

    In this work, a new fabrication method is presented for digital microfluidic (DMF) devices in which the electrodes are generated using the screen printing technique. This method is applicable to both rigid and flexible substrates. The proposed screen printing approach, as a batch printing technique, is advantageous to the widely reported DMF fabrication methods in terms of fabrication time, cost and capability of mass production. Screen printing provides an effective means for printing different types of conductive materials on a variety of substrates. Specifically, screen printing of conductive silver and carbon based inks is performed on paper, glass and wax paper. As a result, the fabricated DMF devices are characterized by being flexible, disposable and incinerable. Hence, the main advantage of screen printing carbon based inks on paper substrates is more pronounced for point-of-care applications that require a large number of low cost DMF chips, and laboratory setups that lack sophisticated microfabrication facilities. The resolution of the printed DMF electrodes generated by this technique is examined for proof of concept using manual screen printing, but higher resolution screens and automated machines are available off-the-shelf, if needed. Another contribution of this research is the improved actuation techniques that facilitate droplet transport in electrode configurations with relatively large electrode spacing to alleviate the disadvantage of lower resolution screens. Thus, we were able to reduce the cost of fabrication significantly without compromising the DMF performance. The paper-based devices have already shown to be effective in continuous microfluidics domain, so the investigation of their applicability in DMF systems is worthwhile. With this in mind, successful integration of a paper-based microchannel with paper-based digital microfluidic chip is demonstrated in this work.

  16. Fabrication of digital microfluidic devices on flexible paper-based and rigid substrates via screen printing

    International Nuclear Information System (INIS)

    Yafia, Mohamed; Shukla, Saurabh; Najjaran, Homayoun

    2015-01-01

    In this work, a new fabrication method is presented for digital microfluidic (DMF) devices in which the electrodes are generated using the screen printing technique. This method is applicable to both rigid and flexible substrates. The proposed screen printing approach, as a batch printing technique, is advantageous to the widely reported DMF fabrication methods in terms of fabrication time, cost and capability of mass production. Screen printing provides an effective means for printing different types of conductive materials on a variety of substrates. Specifically, screen printing of conductive silver and carbon based inks is performed on paper, glass and wax paper. As a result, the fabricated DMF devices are characterized by being flexible, disposable and incinerable. Hence, the main advantage of screen printing carbon based inks on paper substrates is more pronounced for point-of-care applications that require a large number of low cost DMF chips, and laboratory setups that lack sophisticated microfabrication facilities. The resolution of the printed DMF electrodes generated by this technique is examined for proof of concept using manual screen printing, but higher resolution screens and automated machines are available off-the-shelf, if needed. Another contribution of this research is the improved actuation techniques that facilitate droplet transport in electrode configurations with relatively large electrode spacing to alleviate the disadvantage of lower resolution screens. Thus, we were able to reduce the cost of fabrication significantly without compromising the DMF performance. The paper-based devices have already shown to be effective in continuous microfluidics domain, so the investigation of their applicability in DMF systems is worthwhile. With this in mind, successful integration of a paper-based microchannel with paper-based digital microfluidic chip is demonstrated in this work. (note)

  17. A high-throughput colorimetric screening assay for terpene synthase activity based on substrate consumption.

    Directory of Open Access Journals (Sweden)

    Maiko Furubayashi

    Full Text Available Terpene synthases catalyze the formation of a variety of terpene chemical structures. Systematic mutagenesis studies have been effective in providing insights into the characteristic and complex mechanisms of C-C bond formations and in exploring the enzymatic potential for inventing new chemical structures. In addition, there is growing demand to increase terpene synthase activity in heterologous hosts, given the maturation of metabolic engineering and host breeding for terpenoid synthesis. We have developed a simple screening method for the cellular activities of terpene synthases by scoring their substrate consumption based on the color loss of the cell harboring carotenoid pathways. We demonstrate that this method can be used to detect activities of various terpene synthase or prenyltransferase genes in a high-throughput manner, irrespective of the product type, enabling the mutation analysis and directed evolution of terpene synthases. We also report the possibility for substrate-specific screening system of terpene synthases by taking advantage of the substrate-size specificity of C30 and C40 carotenoid pathways.

  18. Printed hydrogen sulfide gas sensor on paper substrate based on polyaniline composite

    International Nuclear Information System (INIS)

    Sarfraz, J.; Ihalainen, P.; Määttänen, A.; Peltonen, J.; Lindén, M.

    2013-01-01

    The fabrication of a hydrogen sulfide (H 2 S) sensor based on polyaniline (PANI)-metal salt (CuCl 2 ) composite is demonstrated. The sensing film was produced by screen printing and spray coating of the sensing material on interdigitated silver electrodes inkjet-printed on a paper substrate. The H 2 S sensing functionality with respect to pH and metal salt concentration was optimized. In addition, the long term stability and humidity effects on the sensor performance were investigated. The printed chemiresistors showed more than five orders of magnitude change in resistance within 20 min of exposure of 15 ppm H 2 S at room temperature. The relatively fast kinetics and large response of the sensor can be explained by the formation of Cu 2 S and subsequent protonation of PANI. In addition, the relatively large roughness and porosity of the paper substrate offers an increased surface sensing area. - Highlights: • pH, salt concentration, film thickness, cross sensitivity • Printed sensor on paper substrate • Commercial polyaniline against special morphologies

  19. Screen-Printed Flexible Bandstop Filter on Polyethylene Terephthalate Substrate Based on Ag Nanoparticles

    Directory of Open Access Journals (Sweden)

    Rajendra Dhakal

    2015-01-01

    Full Text Available We present a low-power, cost-effective, highly reproducible, and disposable bandstop filter by employing high-throughput screen-printing technology. We apply large-scale printing strategies using silver-nanoparticle-based ink for the metallization of conductive wires to fabricate a bandstop filter on a polyethylene terephthalate (PET substrate. The filter exhibits an attenuation pole at 4.35 GHz with excellent in-and-out band characteristics. These characteristics reflect a rejection depth that is better than −25 dB with a return loss of −0.75 dB at the normal orientation of the PET substrate. In addition, the filter characteristics are observed at various bending angles (0°, 10°, and 20° of the PET substrate with an excellent relative standard deviation of less than 0.5%. These results confirm the accuracy, reproducibility, and independence of the resonance frequency. This screen-printing technology for well-defined nanostructures is more favorable than other complex photolithographic processes because it overcomes signal losses due to uneven surface distributions and thereby reveals a homogeneous distribution. Moreover, the proposed methodology enables incremental steps in the process of producing highly flexible and cost-effective printed-electronic radio devices.

  20. Improved Peak Capacity for Capillary Electrophoretic Separations of Enzyme Inhibitors with Activity-Based Detection Using Magnetic Bead Microreactors

    Science.gov (United States)

    Yan, Xiaoyan; Gilman, S. Douglass

    2010-01-01

    A technique for separating and detecting enzyme inhibitors was developed using capillary electrophoresis with an enzyme microreactor. The on-column enzyme microreactor was constructed using NdFeB magnet(s) to immobilize alkaline phosphatase-coated superparamagnetic beads (2.8 μm diameter) inside a capillary before the detection window. Enzyme inhibition assays were performed by injecting a plug of inhibitor into a capillary filled with the substrate, AttoPhos. Product generated in the enzyme microreactor was detected by laser-induced fluorescence. Inhibitor zones electrophoresed through the capillary, passed through the enzyme microreactor, and were observed as negative peaks due to decreased product formation. The goal of this study was to improve peak capacities for inhibitor separations relative to previous work, which combined continuous engagement electrophoretically mediated microanalysis (EMMA) and transient engagement EMMA to study enzyme inhibition. The effects of electric field strength, bead injection time and inhibitor concentrations on peak capacity and peak width were investigated. Peak capacities were increased to ≥20 under optimal conditions of electric field strength and bead injection time for inhibition assays with arsenate and theophylline. Five reversible inhibitors of alkaline phosphatase (theophylline, vanadate, arsenate, L-tryptophan and tungstate) were separated and detected to demonstrate the ability of this technique to analyze complex inhibitor mixtures. PMID:20024913

  1. An Al₂O₃ Gating Substrate for the Greater Performance of Field Effect Transistors Based on Two-Dimensional Materials.

    Science.gov (United States)

    Yang, Hang; Qin, Shiqiao; Zheng, Xiaoming; Wang, Guang; Tan, Yuan; Peng, Gang; Zhang, Xueao

    2017-09-22

    We fabricated 70 nm Al₂O₃ gated field effect transistors based on two-dimensional (2D) materials and characterized their optical and electrical properties. Studies show that the optical contrast of monolayer graphene on an Al₂O₃/Si substrate is superior to that on a traditional 300 nm SiO₂/Si substrate (2.4 times). Significantly, the transconductance of monolayer graphene transistors on the Al₂O₃/Si substrate shows an approximately 10-fold increase, due to a smaller dielectric thickness and a higher dielectric constant. Furthermore, this substrate is also suitable for other 2D materials, such as WS₂, and can enhance the transconductance remarkably by 61.3 times. These results demonstrate a new and ideal substrate for the fabrication of 2D materials-based electronic logic devices.

  2. Structural and photoluminescence properties of Si-based nanosheet bundles rooted on Si substrates

    Science.gov (United States)

    Yuan, Peiling; Tamaki, Ryo; Kusazaki, Shinya; Atsumi, Nanae; Saito, Yuya; Kumazawa, Yuki; Ahsan, Nazmul; Okada, Yoshitaka; Ishida, Akihiro; Tatsuoka, Hirokazu

    2018-04-01

    Si-based nanosheet bundles were synthesized by the extraction of Ca atoms from CaSi2 microwalls grown on Si substrates by inositol hexakisphosphate solution or thermal treatment in FeCl2 vapor. The structural and photoluminescence properties of the Si-based nanosheet bundles were examined. The photoluminescence emissions in the visible region were clearly observed, and the temperature and excitation intensity dependences of the emissions were characterized. The observed Si-based nanosheets consist of thin Si layers, and a superlattice-like layered structural model is proposed to describe the Si-based nanosheet bundle structures and their photoluminescence property. The photoluminescence property of the nanosheets significantly depends on their treatment process. The luminescence mechanism of the nanosheets was discussed.

  3. The Discovery of Aurora Kinase Inhibitor by Multi-Docking-Based Virtual Screening

    Directory of Open Access Journals (Sweden)

    Jun-Tae Kim

    2014-11-01

    Full Text Available We report the discovery of aurora kinase inhibitor using the fragment-based virtual screening by multi-docking strategy. Among a number of fragments collected from eMololecules, we found four fragment molecules showing potent activity (>50% at 100 μM against aurora kinase. Based on the explored fragment scaffold, we selected two compounds in our synthesized library and validated the biological activity against Aurora kinase.

  4. Combinatorial Pharmacophore-Based 3D-QSAR Analysis and Virtual Screening of FGFR1 Inhibitors

    Directory of Open Access Journals (Sweden)

    Nannan Zhou

    2015-06-01

    Full Text Available The fibroblast growth factor/fibroblast growth factor receptor (FGF/FGFR signaling pathway plays crucial roles in cell proliferation, angiogenesis, migration, and survival. Aberration in FGFRs correlates with several malignancies and disorders. FGFRs have proved to be attractive targets for therapeutic intervention in cancer, and it is of high interest to find FGFR inhibitors with novel scaffolds. In this study, a combinatorial three-dimensional quantitative structure-activity relationship (3D-QSAR model was developed based on previously reported FGFR1 inhibitors with diverse structural skeletons. This model was evaluated for its prediction performance on a diverse test set containing 232 FGFR inhibitors, and it yielded a SD value of 0.75 pIC50 units from measured inhibition affinities and a Pearson’s correlation coefficient R2 of 0.53. This result suggests that the combinatorial 3D-QSAR model could be used to search for new FGFR1 hit structures and predict their potential activity. To further evaluate the performance of the model, a decoy set validation was used to measure the efficiency of the model by calculating EF (enrichment factor. Based on the combinatorial pharmacophore model, a virtual screening against SPECS database was performed. Nineteen novel active compounds were successfully identified, which provide new chemical starting points for further structural optimization of FGFR1 inhibitors.

  5. A New Kind of Circular Polarization Leaky-Wave Antenna Based on Substrate Integrated Waveguide

    Directory of Open Access Journals (Sweden)

    Chong Zhang

    2015-01-01

    Full Text Available A new kind of circular polarization leaky-wave antenna with N-shaped slots cut in the upper side of substrate integrated waveguide (SIW is investigated and presented. The radiation pattern and polarization axial ratio of the leaky-wave antenna are studied. The results show that the width of N-shaped slots has significant effect on the circular polarization property of the antenna. By properly choosing structural parameters, the SIW based leaky-wave antenna can realize circular polarization with excellent axial ratio in 8 GHz satellite band.

  6. Low-Cost Lattice Matching Si Based Composite Substrates for HgCdTe

    Science.gov (United States)

    2013-09-01

    211). ..............................................5 Figure 3. Relationship between calculated alloy compositions based on Se/CdTe BEP ratio and...Se:CdTe beam equivalent pressure ( BEP ) ratios. During CdSeTe growth, Se and Te are in competition for the same nucleation sites. If we assume that all...therefore, x(cal) = ΦSe/ΦCd = 2ΦSe/ΦCdTe, where Φ is the BEP of the material, measured by the nude ion gauge at the substrate position. Figure 3 shows the

  7. Activity-based assay for human mono-ADP-ribosyltransferases ARTD7/PARP15 and ARTD10/PARP10 aimed at screening and profiling inhibitors.

    Science.gov (United States)

    Venkannagari, Harikanth; Fallarero, Adyary; Feijs, Karla L H; Lüscher, Bernhard; Lehtiö, Lari

    2013-05-13

    Poly(ADP-ribose) polymerases (PARPs) or diphtheria toxin like ADP-ribosyl transferases (ARTDs) are enzymes that catalyze the covalent modification of proteins by attachment of ADP-ribose units to the target amino acid residues or to the growing chain of ADP-ribose. A subclass of the ARTD superfamily consists of mono-ADP-ribosyl transferases that are thought to modify themselves and other substrate proteins by covalently adding only a single ADP-ribose moiety to the target. Many of the ARTD enzymes are either established or potential drug targets and a functional activity assay for them will be a valuable tool to identify selective inhibitors for each enzyme. Existing assays are not directly applicable for screening of inhibitors due to the different nature of the reaction and different target molecules. We modified and applied a fluorescence-based assay previously described for PARP1/ARTD1 and tankyrase/ARTD5 for screening of PARP10/ARTD10 and PARP15/ARTD7 inhibitors. The assay measures the amount of NAD(+) present after chemically converting it to a fluorescent analog. We demonstrate that by using an excess of a recombinant acceptor protein the performance of the activity-based assay is excellent for screening of compound libraries. The assay is homogenous and cost effective, making it possible to test relatively large compound libraries. This method can be used to screen inhibitors of mono-ARTDs and profile inhibitors of the enzyme class. The assay was optimized for ARTD10 and ARTD7, but it can be directly applied to other mono-ARTDs of the ARTD superfamily. Profiling of known ARTD inhibitors against ARTD10 and ARTD7 in a validatory screening identified the best inhibitors with submicromolar potencies. Only few of the tested ARTD inhibitors were potent, implicating that there is a need to screen new compound scaffolds. This is needed to create small molecules that could serve as biological probes and potential starting points for drug discovery projects against

  8. Systemic Delivery of a Glucosylceramide Synthase Inhibitor Reduces CNS Substrates and Increases Lifespan in a Mouse Model of Type 2 Gaucher Disease

    OpenAIRE

    Cabrera-Salazar, Mario A.; DeRiso, Matthew; Bercury, Scott D.; Li, Lingyun; Lydon, John T.; Weber, William; Pande, Nilesh; Cromwell, Mandy A.; Copeland, Diane; Leonard, John; Cheng, Seng H.; Scheule, Ronald K.

    2012-01-01

    Neuropathic Gaucher disease (nGD), also known as type 2 or type 3 Gaucher disease, is caused by a deficiency of the enzyme glucocerebrosidase (GC). This deficiency impairs the degradation of glucosylceramide (GluCer) and glucosylsphingosine (GluSph), leading to their accumulation in the brains of patients and mouse models of the disease. These accumulated substrates have been thought to cause the severe neuropathology and early death observed in patients with nGD and mouse models. Substrate a...

  9. Association between selective serotonin reuptake inhibitors and upper gastrointestinal bleeding: population based case-control study

    Science.gov (United States)

    de Abajo, Francisco José; Rodríguez, Luis Alberto García; Montero, Dolores

    1999-01-01

    Objective To examine the association between selective serotonin reuptake inhibitors and risk of upper gastrointestinal bleeding. Design Population based case-control study. Setting General practices included in the UK general practice research database. Subjects 1651 incident cases of upper gastrointestinal bleeding and 248 cases of ulcer perforation among patients aged 40 to 79 years between April 1993 and September 1997, and 10 000 controls matched for age, sex, and year that the case was identified. Interventions Review of computer profiles for all potential cases, and an internal validation study to confirm the accuracy of the diagnosis on the basis of the computerised information. Main outcome measures Current use of selective serotonin reuptake inhibitors or other antidepressants within 30 days before the index date. Results Current exposure to selective serotonin reuptake inhibitors was identified in 3.1% (52 of 1651) of patients with upper gastrointestinal bleeding but only 1.0% (95 of 10 000) of controls, giving an adjusted rate ratio of 3.0 (95% confidence interval 2.1 to 4.4). This effect measure was not modified by sex, age, dose, or treatment duration. A crude incidence of 1 case per 8000 prescriptions was estimated. A small association was found with non-selective serotonin reuptake inhibitors (relative risk 1.4, 1.1 to 1.9) but not with antidepressants lacking this inhibitory effect. None of the groups of antidepressants was associated with ulcer perforation. The concurrent use of selective serotonin reuptake inhibitors with non-steroidal anti-inflammatory drugs increased the risk of upper gastrointestinal bleeding beyond the sum of their independent effects (15.6, 6.6 to 36.6). A smaller interaction was also found between selective serotonin reuptake inhibitors and low dose aspirin (7.2, 3.1 to 17.1). Conclusions Selective serotonin reuptake inhibitors increase the risk of upper gastrointestinal bleeding. The absolute effect is, however

  10. Neural Substrates of Similarity and Rule-based Strategies in Judgment

    Directory of Open Access Journals (Sweden)

    Bettina eVon Helversen

    2014-10-01

    Full Text Available Making accurate judgments is a core human competence and a prerequisite for success in many areas of life. Plenty of evidence exists that people can employ different judgment strategies to solve identical judgment problems. In categorization, it has been demonstrated that similarity-based and rule-based strategies are associated with activity in different brain regions. Building on this research, the present work tests whether solving two identical judgment problems recruits different neural substrates depending on people's judgment strategies. Combining cognitive modeling of judgment strategies at the behavioral level with functional magnetic resonance imaging (fMRI, we compare brain activity when using two archetypal judgment strategies: a similarity-based exemplar strategy and a rule-based heuristic strategy. Using an exemplar-based strategy should recruit areas involved in long-term memory processes to a larger extent than a heuristic strategy. In contrast, using a heuristic strategy should recruit areas involved in the application of rules to a larger extent than an exemplar-based strategy. Largely consistent with our hypotheses, we found that using an exemplar-based strategy led to relatively higher BOLD activity in the anterior prefrontal and inferior parietal cortex, presumably related to retrieval and selective attention processes. In contrast, using a heuristic strategy led to relatively higher activity in areas in the dorsolateral prefrontal and the temporal-parietal cortex associated with cognitive control and information integration. Thus, even when people solve identical judgment problems, different neural substrates can be recruited depending on the judgment strategy involved.

  11. Substrate-Based Noble-Metal Nanomaterials: Shape Engineering and Applications

    Science.gov (United States)

    Hajfathalian, Maryam

    Nanostructures have potential for use in state-of-the-art applications such as sensing, imaging, therapeutics, drug delivery, and electronics. The ability to fabricate and engineer these nanoscale materials is essential for the continued development of such devices. Because the morphological features of nanomaterials play a key role in determining chemical and physical properties, there is great interest in developing and improving methods capable of controlling their size, shape, and composition. While noble nanoparticles have opened the door to promising applications in fields such as imaging, cancer targeting, photothermal treatment, drug delivery, catalysis and sensing, the synthetic processes required to form these nanoparticles on surfaces are not well-developed. Herein is a detailed account on efforts for adapting established solution-based seed-mediated synthetic protocols to structure in a substrate-based platform. These syntheses start by (i) defining heteroepitaxially oriented nanostructured seeds at site-specific locations using lithographic or directed-assembly techniques, and then (ii) transforming the seeds using either a solution or vapor phase processing route to activate kinetically- or thermodynamically-driven growth modes, to arrive at nanocrystals with complex and useful geometries. The first series of investigations highlight synthesis-routes based on heterogeneous nucleation, where templates serve as nucleation sites for metal atoms arriving in the vapor phase. In the first research direction, the vapor-phase heterogeneous nucleation of Ag on Au was carried out at high temperatures, where the Ag vapor was sourced from a sublimating foil onto adjacent Au templates. This process transformed both the composition and morphology of the initial Au Wulff-shaped nanocrystals to a homogeneous AuAg nanoprism. In the second case, the vapor-phase heterogeneous nucleation of Cu atoms on Au nanocrystal templates was investigated by placing a Cu foil next

  12. Thermal bubble inkjet printing of water-based graphene oxide and graphene inks on heated substrate

    Science.gov (United States)

    Huang, Simin; Shen, Ruoxi; Qian, Bo; Li, Lingying; Wang, Wenhao; Lin, Guanghui; Zhang, Xiaofei; Li, Peng; Xie, Yonglin

    2018-04-01

    Stable-jetting water-based graphene oxide (GO) and graphene (GR) inks without any surfactant or stabilizer are prepared from an unstable-jetting water-based starting solvent, with many thermal bubble inkjet satellite drops, by simply increasing the material concentration. The concentration-dependent thermal bubble inkjet droplet generation process is studied in detail. To overcome the low concentration properties of water-based thermal bubble inkjet inks, the substrate temperature is tuned below 60 °C to achieve high-quality print lines. Due to the difference in hydrophilicity and hydrophobicity of the 2D materials, the printed GO lines show a different forming mechanism from that of the GR lines. The printed GO lines are reduced by thermal annealing and by ascorbic acid, respectively. The reduced GO lines exhibit electrical conductivity of the same order of magnitude as that of the GR lines.

  13. De novo fragment-based design of inhibitors of DXS guided by spin-diffusion-based NMR spectroscopy

    NARCIS (Netherlands)

    Masini, T.; Pilger, J.; Kroezen, B. S.; Illarionov, B.; Lottmann, P.; Fischer, M.; Griesinger, C.; Hirsch, A. K. H.

    We applied for the first time an innovative ligand-based NMR methodology (STI) to a medicinal-chemistry project aimed at the development of inhibitors for the enzyme 1-deoxy-D-xylulose-5-phosphate synthase (DXS). DXS is the first enzyme of the 2C-methyl-D-erythritol-4-phosphate (MEP) pathway,

  14. Sensing element for detection of polar organic vapours on the base of polyaniline-composite - Effect of substrate surface area

    International Nuclear Information System (INIS)

    Olejnik, Robert; Babar, Dipak Gorakh; Slobodian, Petr; Matyas, Jiri

    2016-01-01

    Conductive polymer polyaniline (PANI) was synthesized by oxidative polymerization of aniline hydrochloride as a source of aniline and ammonium persulfate as an oxidation agent. The polymerization process is relatively easy and cheap. The reaction was carried out in presence of polymer substrate, in our case polyethylene terephthalate (PET) as a representative of smooth surface substrate and polyvinylidenfluoride (PVDF) nanofibers membrane as a representative of porous substrate. Both these substrates were covered by polyaniline (PANI) and used as a sensing element for organic vapors detection. The detection was made by measuring and the record of the change of resistivity during adsorption and desorption of saturated vapors. The result shows that sensitivity decreases with increasing polarity of chosen solvent in order N,N- Dimethylformamide (DMF), N,N-Dimethylacetamide (DMAc) and Dimethyl sulfoxide (DMSO). The PANI base sensing element on PVDF substrate improves sensitivity, selectivity and it also has good reversibility and repeatability. (paper)

  15. Silica-based microstructures on nonplanar substrates by femtosecond laser-induced nonlinear lithography

    International Nuclear Information System (INIS)

    Mizoshiri, M; Nishiyama, H; Hirata, Y; Nishii, J

    2009-01-01

    We developed a technique for the formation of nonplanar surfaces of inorganic optical materials by a combined process of nonlinear lithography and plasma etching. This technique can be used to fabricate structures even on non-flat substrates, which is difficult using current semiconductor technology. Three-dimensional patterns were written directly inside a positive-tone photoresist using femtosecond laser-induced nonlinear optical absorption. The patterns were then transferred to underlying nonplanar substrates by the ion beam etching technique. For the lithographic process, we obtained a minimum feature size of 900 nm, which is below the diffraction limit. We demonstrated the fabrication of silica-based hybrid diffractive-refractive lenses. Fresnel zone plates with smooth surfaces were obtained on convex microlenses. When a 633-nm-wavelength He-Ne laser was coupled normally to the hybrid lens, the primary focal length was measured as 630 μm. This hybridization shifted the focal length by 200 μm, which agreed with the theoretical value. Our process is useful for the precise fabrication of nonplanar structures based on inorganic materials.

  16. Progress in the Development of SERS-Active Substrates Based on Metal-Coated Porous Silicon.

    Science.gov (United States)

    Bandarenka, Hanna V; Girel, Kseniya V; Zavatski, Sergey A; Panarin, Andrei; Terekhov, Sergei N

    2018-05-21

    The present work gives an overview of the developments in surface-enhanced Raman scattering (SERS) with metal-coated porous silicon used as an active substrate. We focused this review on the research referenced to SERS-active materials based on porous silicon, beginning from the patent application in 2002 and enclosing the studies of this year. Porous silicon and metal deposition technologies are discussed. Since the earliest studies, a number of fundamentally different plasmonic nanostructures including metallic dendrites, quasi-ordered arrays of metallic nanoparticles (NPs), and metallic nanovoids have been grown on porous silicon, defined by the morphology of this host material. SERS-active substrates based on porous silicon have been found to combine a high and well-reproducible signal level, storage stability, cost-effective technology and handy use. They make it possible to identify and study many compounds including biomolecules with a detection limit varying from milli- to femtomolar concentrations. The progress reviewed here demonstrates the great prospects for the extensive use of the metal-coated porous silicon for bioanalysis by SERS-spectroscopy.

  17. Progress in the Development of SERS-Active Substrates Based on Metal-Coated Porous Silicon

    Directory of Open Access Journals (Sweden)

    Hanna V. Bandarenka

    2018-05-01

    Full Text Available The present work gives an overview of the developments in surface-enhanced Raman scattering (SERS with metal-coated porous silicon used as an active substrate. We focused this review on the research referenced to SERS-active materials based on porous silicon, beginning from the patent application in 2002 and enclosing the studies of this year. Porous silicon and metal deposition technologies are discussed. Since the earliest studies, a number of fundamentally different plasmonic nanostructures including metallic dendrites, quasi-ordered arrays of metallic nanoparticles (NPs, and metallic nanovoids have been grown on porous silicon, defined by the morphology of this host material. SERS-active substrates based on porous silicon have been found to combine a high and well-reproducible signal level, storage stability, cost-effective technology and handy use. They make it possible to identify and study many compounds including biomolecules with a detection limit varying from milli- to femtomolar concentrations. The progress reviewed here demonstrates the great prospects for the extensive use of the metal-coated porous silicon for bioanalysis by SERS-spectroscopy.

  18. Computational study of some benzamidine-based inhibitors of thrombin-like snake venom proteinases

    Science.gov (United States)

    Henriques, Elsa S.; Nascimento, Marco A. C.; Ramos, Maria João

    Pit viper venoms contain a number of serine proteinases that, despite their observed coagulant thrombin-like action in vitro, exhibit a paradoxical benign defibrinogenating (anticoagulant) action in vivo, with clinical applications in preventing thrombi and improved blood circulation. Considering that several benzamidine-based inhibitors, some highly selective to thrombin, also inhibit the enzymatic activity of such venombins, the modeling of their enzyme-inhibitor interactions could provide valuable information on the topological factors that determine the divergences in activity. The first step, and the object of the present study, was to derive the necessary set of parameters, consistent with the CHARMM force field, and to perform molecular dynamics (MD) simulations on a few selected representatives of the inhibitors in question under physiological conditions. Bonding and van der Waals parameters were derived by analogy to similar ones in the existing force field. Net atomic charges were obtained with a restrained fitting to the molecular electrostatic potential generated at B3LYP/6-31G(d) level. The parameters were refined to reproduce the available experimental geometries and crystal data, and the MD simulations of the free inhibitors in aqueous solution at 298 K provided an insightful description of their available conformational space.

  19. A dual-color fluorescence-based platform to identify selective inhibitors of Akt signaling.

    Directory of Open Access Journals (Sweden)

    Aranzazú Rosado

    Full Text Available BACKGROUND: Inhibition of Akt signaling is considered one of the most promising therapeutic strategies for many cancers. However, rational target-orientated approaches to cell based drug screens for anti-cancer agents have historically been compromised by the notorious absence of suitable control cells. METHODOLOGY/PRINCIPAL FINDINGS: In order to address this fundamental problem, we have developed BaFiso, a live-cell screening platform to identify specific inhibitors of this pathway. BaFiso relies on the co-culture of isogenic cell lines that have been engineered to sustain interleukin-3 independent survival of the parental Ba/F3 cells, and that are individually tagged with different fluorescent proteins. Whilst in the first of these two lines cell survival in the absence of IL-3 is dependent on the expression of activated Akt, the cells expressing constitutively-activated Stat5 signaling display IL-3 independent growth and survival in an Akt-independent manner. Small molecules can then be screened in these lines to identify inhibitors that rescue IL-3 dependence. CONCLUSIONS/SIGNIFICANCE: BaFiso measures differential cell survival using multiparametric live cell imaging and permits selective inhibitors of Akt signaling to be identified. BaFiso is a platform technology suitable for the identification of small molecule inhibitors of IL-3 mediated survival signaling.

  20. Novel Small Molecule Inhibitors of Choline Kinase Identified by Fragment-Based Drug Discovery.

    Science.gov (United States)

    Zech, Stephan G; Kohlmann, Anna; Zhou, Tianjun; Li, Feng; Squillace, Rachel M; Parillon, Lois E; Greenfield, Matthew T; Miller, David P; Qi, Jiwei; Thomas, R Mathew; Wang, Yihan; Xu, Yongjin; Miret, Juan J; Shakespeare, William C; Zhu, Xiaotian; Dalgarno, David C

    2016-01-28

    Choline kinase α (ChoKα) is an enzyme involved in the synthesis of phospholipids and thereby plays key roles in regulation of cell proliferation, oncogenic transformation, and human carcinogenesis. Since several inhibitors of ChoKα display antiproliferative activity in both cellular and animal models, this novel oncogene has recently gained interest as a promising small molecule target for cancer therapy. Here we summarize our efforts to further validate ChoKα as an oncogenic target and explore the activity of novel small molecule inhibitors of ChoKα. Starting from weakly binding fragments, we describe a structure based lead discovery approach, which resulted in novel highly potent inhibitors of ChoKα. In cancer cell lines, our lead compounds exhibit a dose-dependent decrease of phosphocholine, inhibition of cell growth, and induction of apoptosis at low micromolar concentrations. The druglike lead series presented here is optimizable for improvements in cellular potency, drug target residence time, and pharmacokinetic parameters. These inhibitors may be utilized not only to further validate ChoKα as antioncogenic target but also as novel chemical matter that may lead to antitumor agents that specifically interfere with cancer cell metabolism.

  1. Structure-based methods to predict mutational resistance to diarylpyrimidine non-nucleoside reverse transcriptase inhibitors.

    Science.gov (United States)

    Azeem, Syeda Maryam; Muwonge, Alecia N; Thakkar, Nehaben; Lam, Kristina W; Frey, Kathleen M

    2018-01-01

    Resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) is a leading cause of HIV treatment failure. Often included in antiviral therapy, NNRTIs are chemically diverse compounds that bind an allosteric pocket of enzyme target reverse transcriptase (RT). Several new NNRTIs incorporate flexibility in order to compensate for lost interactions with amino acid conferring mutations in RT. Unfortunately, even successful inhibitors such as diarylpyrimidine (DAPY) inhibitor rilpivirine are affected by mutations in RT that confer resistance. In order to aid drug design efforts, it would be efficient and cost effective to pre-evaluate NNRTI compounds in development using a structure-based computational approach. As proof of concept, we applied a residue scan and molecular dynamics strategy using RT crystal structures to predict mutations that confer resistance to DAPYs rilpivirine, etravirine, and investigational microbicide dapivirine. Our predictive values, changes in affinity and stability, are correlative with fold-resistance data for several RT mutants. Consistent with previous studies, mutation K101P is predicted to confer high-level resistance to DAPYs. These findings were further validated using structural analysis, molecular dynamics, and an enzymatic reverse transcription assay. Our results confirm that changes in affinity and stability for mutant complexes are predictive parameters of resistance as validated by experimental and clinical data. In future work, we believe that this computational approach may be useful to predict resistance mutations for inhibitors in development. Published by Elsevier Inc.

  2. Impact of Stereochemistry on Ligand Binding: X-ray Crystallographic Analysis of an Epoxide-Based HIV Protease Inhibitor.

    Science.gov (United States)

    Benedetti, Fabio; Berti, Federico; Campaner, Pietro; Fanfoni, Lidia; Demitri, Nicola; Olajuyigbe, Folasade M; De March, Matteo; Geremia, Silvano

    2014-09-11

    A new pseudopeptide epoxide inhibitor, designed for irreversible binding to HIV protease (HIV-PR), has been synthesized and characterized in solution and in the solid state. However, the crystal structure of the complex obtained by inhibitor-enzyme cocrystallization revealed that a minor isomer, with inverted configuration of the epoxide carbons, has been selected by HIV-PR during crystallization. The structural characterization of the well-ordered pseudopeptide, inserted in the catalytic channel with its epoxide group intact, provides deeper insights into inhibitor binding and HIV-PR stereoselectivity, which aids development of future epoxide-based HIV inhibitors.

  3. A Xylenol Orange-Based Screening Assay for the Substrate Specificity of Flavin-Dependent para-Phenol Oxidases

    Directory of Open Access Journals (Sweden)

    Tom A. Ewing

    2018-01-01

    Full Text Available Vanillyl alcohol oxidase (VAO and eugenol oxidase (EUGO are flavin-dependent enzymes that catalyse the oxidation of para-substituted phenols. This makes them potentially interesting biocatalysts for the conversion of lignin-derived aromatic monomers to value-added compounds. To facilitate their biocatalytic exploitation, it is important to develop methods by which variants of the enzymes can be rapidly screened for increased activity towards substrates of interest. Here, we present the development of a screening assay for the substrate specificity of para-phenol oxidases based on the detection of hydrogen peroxide using the ferric-xylenol orange complex method. The assay was used to screen the activity of VAO and EUGO towards a set of twenty-four potential substrates. This led to the identification of 4-cyclopentylphenol as a new substrate of VAO and EUGO and 4-cyclohexylphenol as a new substrate of VAO. Screening of a small library of VAO and EUGO active-site variants for alterations in their substrate specificity led to the identification of a VAO variant (T457Q with increased activity towards vanillyl alcohol (4-hydroxy-3-methoxybenzyl alcohol and a EUGO variant (V436I with increased activity towards chavicol (4-allylphenol and 4-cyclopentylphenol. This assay provides a quick and efficient method to screen the substrate specificity of para-phenol oxidases, facilitating the enzyme engineering of known para-phenol oxidases and the evaluation of the substrate specificity of novel para-phenol oxidases.

  4. A Xylenol Orange-Based Screening Assay for the Substrate Specificity of Flavin-Dependent para-Phenol Oxidases.

    Science.gov (United States)

    Ewing, Tom A; van Noord, Aster; Paul, Caroline E; van Berkel, Willem J H

    2018-01-14

    Vanillyl alcohol oxidase (VAO) and eugenol oxidase (EUGO) are flavin-dependent enzymes that catalyse the oxidation of para -substituted phenols. This makes them potentially interesting biocatalysts for the conversion of lignin-derived aromatic monomers to value-added compounds. To facilitate their biocatalytic exploitation, it is important to develop methods by which variants of the enzymes can be rapidly screened for increased activity towards substrates of interest. Here, we present the development of a screening assay for the substrate specificity of para -phenol oxidases based on the detection of hydrogen peroxide using the ferric-xylenol orange complex method. The assay was used to screen the activity of VAO and EUGO towards a set of twenty-four potential substrates. This led to the identification of 4-cyclopentylphenol as a new substrate of VAO and EUGO and 4-cyclohexylphenol as a new substrate of VAO. Screening of a small library of VAO and EUGO active-site variants for alterations in their substrate specificity led to the identification of a VAO variant (T457Q) with increased activity towards vanillyl alcohol (4-hydroxy-3-methoxybenzyl alcohol) and a EUGO variant (V436I) with increased activity towards chavicol (4-allylphenol) and 4-cyclopentylphenol. This assay provides a quick and efficient method to screen the substrate specificity of para -phenol oxidases, facilitating the enzyme engineering of known para- phenol oxidases and the evaluation of the substrate specificity of novel para -phenol oxidases.

  5. Carbon- versus sulphur-based zinc binding groups for carbonic anhydrase inhibitors?

    Science.gov (United States)

    Supuran, Claudiu T

    2018-12-01

    A set of compounds incorporating carbon-based zinc-binding groups (ZBGs), of the type PhX (X = COOH, CONH 2 , CONHNH 2 , CONHOH, CONHOMe), and the corresponding derivatives with sulphur(VI)-based ZBGs (X = SO 3 H, SO 2 NH 2 , SO 2 NHNH 2 , SO 2 NHOH, SO 2 NHOMe) were tested as inhibitors of all mammalian isoforms of carbonic anhydrase (CA, EC 4.2.1.1), CA I-XV. Three factors connected with the ZBG influenced the efficacy as CA inhibitor (CAI) of the investigated compounds: (i) the pKa of the ZBG; (ii) its geometry (tetrahedral, i.e. sulphur-based, versus trigonal, i.e. carbon-based ZBGs), and (iii) orientation of the organic scaffold induced by the nature of the ZBG. Benzenesulphonamide was the best inhibitor of all isoforms, but other ZBGs led to interesting inhibition profiles, although with an efficacy generally reduced when compared to the sulphonamide. The nature of the ZBG also influenced the CA inhibition mechanism. Most of these derivatives were zinc binders, but some of them (sulfonates, carboxylates) may interact with the enzyme by anchoring to the zinc-coordinated water molecule or by other inhibition mechanisms (occlusion of the active site entrance, out of the active site binding, etc.). Exploring structurally diverse ZBGs may lead to interesting new developments in the field of CAIs.

  6. Design and fabrication of non silicon substrate based MEMS energy harvester for arbitrary surface applications

    Energy Technology Data Exchange (ETDEWEB)

    Balpande, Suresh S., E-mail: balpandes@rknec.edu [Ph.D.. Scholar, Department of Electronics Engineering Shri Ramdeobaba College of Engineering & Management, Nagpur-13, (M.S.) (India); Pande, Rajesh S. [Professor, Department of Electronics Engineering Shri Ramdeobaba College of Engineering & Management, Nagpur-13, (M.S.) (India)

    2016-04-13

    Internet of Things (IoT) uses MEMS sensor nodes and actuators to sense and control objects through Internet. IOT deploys millions of chemical battery driven sensors at different locations which are not reliable many times because of frequent requirement of charging & battery replacement in case of underground laying, placement at harsh environmental conditions, huge count and difference between demand (24 % per year) and availability (energy density growing rate 8% per year). Energy harvester fabricated on silicon wafers have been widely used in manufacturing MEMS structures. These devices require complex fabrication processes, costly chemicals & clean room. In addition to this silicon wafer based devices are not suitable for curved surfaces like pipes, human bodies, organisms, or other arbitrary surface like clothes, structure surfaces which does not have flat and smooth surface always. Therefore, devices based on rigid silicon wafers are not suitable for these applications. Flexible structures are the key solution for this problems. Energy transduction mechanism generates power from free surrounding vibrations or impact. Sensor nodes application has been purposefully selected due to discrete power requirement at low duty cycle. Such nodes require an average power budget in the range of about 0.1 microwatt to 1 mW over a period of 3-5 seconds. Energy harvester is the best alternate source in contrast with battery for sensor node application. Novel design of Energy Harvester based on cheapest flexible non silicon substrate i.e. cellulose acetate substrate have been modeled, simulated and analyzed on COMSOL multiphysics and fabricated using sol-gel spin coating setup. Single cantilever based harvester generates 60-75 mV peak electric potential at 22Hz frequency and approximately 22 µW power at 1K-Ohm load. Cantilever array can be employed for generating higher voltage by replicating this structure. This work covers design, optimization, fabrication of

  7. Design and fabrication of non silicon substrate based MEMS energy harvester for arbitrary surface applications

    Science.gov (United States)

    Balpande, Suresh S.; Pande, Rajesh S.

    2016-04-01

    Internet of Things (IoT) uses MEMS sensor nodes and actuators to sense and control objects through Internet. IOT deploys millions of chemical battery driven sensors at different locations which are not reliable many times because of frequent requirement of charging & battery replacement in case of underground laying, placement at harsh environmental conditions, huge count and difference between demand (24 % per year) and availability (energy density growing rate 8% per year). Energy harvester fabricated on silicon wafers have been widely used in manufacturing MEMS structures. These devices require complex fabrication processes, costly chemicals & clean room. In addition to this silicon wafer based devices are not suitable for curved surfaces like pipes, human bodies, organisms, or other arbitrary surface like clothes, structure surfaces which does not have flat and smooth surface always. Therefore, devices based on rigid silicon wafers are not suitable for these applications. Flexible structures are the key solution for this problems. Energy transduction mechanism generates power from free surrounding vibrations or impact. Sensor nodes application has been purposefully selected due to discrete power requirement at low duty cycle. Such nodes require an average power budget in the range of about 0.1 microwatt to 1 mW over a period of 3-5 seconds. Energy harvester is the best alternate source in contrast with battery for sensor node application. Novel design of Energy Harvester based on cheapest flexible non silicon substrate i.e. cellulose acetate substrate have been modeled, simulated and analyzed on COMSOL multiphysics and fabricated using sol-gel spin coating setup. Single cantilever based harvester generates 60-75 mV peak electric potential at 22Hz frequency and approximately 22 µW power at 1K-Ohm load. Cantilever array can be employed for generating higher voltage by replicating this structure. This work covers design, optimization, fabrication of harvester and

  8. Design and fabrication of non silicon substrate based MEMS energy harvester for arbitrary surface applications

    International Nuclear Information System (INIS)

    Balpande, Suresh S.; Pande, Rajesh S.

    2016-01-01

    Internet of Things (IoT) uses MEMS sensor nodes and actuators to sense and control objects through Internet. IOT deploys millions of chemical battery driven sensors at different locations which are not reliable many times because of frequent requirement of charging & battery replacement in case of underground laying, placement at harsh environmental conditions, huge count and difference between demand (24 % per year) and availability (energy density growing rate 8% per year). Energy harvester fabricated on silicon wafers have been widely used in manufacturing MEMS structures. These devices require complex fabrication processes, costly chemicals & clean room. In addition to this silicon wafer based devices are not suitable for curved surfaces like pipes, human bodies, organisms, or other arbitrary surface like clothes, structure surfaces which does not have flat and smooth surface always. Therefore, devices based on rigid silicon wafers are not suitable for these applications. Flexible structures are the key solution for this problems. Energy transduction mechanism generates power from free surrounding vibrations or impact. Sensor nodes application has been purposefully selected due to discrete power requirement at low duty cycle. Such nodes require an average power budget in the range of about 0.1 microwatt to 1 mW over a period of 3-5 seconds. Energy harvester is the best alternate source in contrast with battery for sensor node application. Novel design of Energy Harvester based on cheapest flexible non silicon substrate i.e. cellulose acetate substrate have been modeled, simulated and analyzed on COMSOL multiphysics and fabricated using sol-gel spin coating setup. Single cantilever based harvester generates 60-75 mV peak electric potential at 22Hz frequency and approximately 22 µW power at 1K-Ohm load. Cantilever array can be employed for generating higher voltage by replicating this structure. This work covers design, optimization, fabrication of

  9. Photo-sensitive Ge nanocrystal based films controlled by substrate deposition temperature

    Science.gov (United States)

    Stavarache, Ionel; Maraloiu, Valentin Adrian; Negrila, Catalin; Prepelita, Petronela; Gruia, Ion; Iordache, Gheorghe

    2017-10-01

    Lowering the temperature of crystallization by deposition of thin films on a heated substrate represents the easiest way to find new means to develop and improve new working devices based on nanocrystals embedded in thin films. The improvements are strongly related with the increasing of operation speed, substantially decreasing the energy consumption and reducing unit fabrication costs of the respective semiconductor devices. This approach avoids major problems, such as those related to diffusion or difficulties in controlling nanocrystallites size, which appear during thermal treatments at high temperatures after deposition. This article reports on a significant progress given by structuring Ge nanocrystals (Ge-NCs) embedded in silicon dioxide (SiO2) thin films by heating the substrate at 400 °C during co-deposition of Ge and SiO2 by magnetron sputtering. As a proof-of-concept, a Si/Ge-NCs:SiO2 photo-sensitive structure was fabricated thereof and characterized. The structure shows superior performance on broad operation bandwidth from visible to near-infrared, as strong rectification properties in dark, significant current rise in the inversion mode when illuminated, high responsivity, high photo-detectivity of 1014 Jones, quick response and significant conversion efficiency with peak value reaching 850% at -1 V and about 1000 nm. This simple preparation approach brings an important contribution to the effort of structuring Ge nanocrystallites in SiO2 thin films at a lower temperature for the purpose of using these materials for devices in optoelectronics, solar cells and electronics on flexible substrates.

  10. Photo-sensitive Ge nanocrystal based films controlled by substrate deposition temperature

    KAUST Repository

    Stavarache, Ionel

    2017-07-21

    Lowering the temperature of crystallization by deposition of thin films on a heated substrate represents the easiest way to find new means to develop and improve new working devices based on nanocrystals embedded in thin films. The improvements are strongly related with the increasing of operation speed, substantially decreasing the energy consumption and reducing unit fabrication costs of the respective semiconductor devices. This approach avoids major problems, such as those related to diffusion or difficulties in controlling of nanocrystallites size, which appear during thermal treatments at high temperatures after deposition. It is reported here the significant progress introduced by synthesis procedure to the in-situ structuring of Ge nanocrystallites in SiO2 thin films by heating the substrate at low temperature, 400 °C during co-deposition of Ge and SiO2 by magnetron sputtering. As a proof-of-concept, a Si/Ge-NCs:SiO2 photo-sensitive structure was fabricated thereof and characterized. The structure shows superior performance on broad operation bandwidth from visible to near-infrared, as strong rectification properties in dark, significant current rise in the inversion mode when illuminated, high responsivity, high photo-detectivity of 1014 Jones, quick response and significant conversion efficiency of 850 %. This simple preparation approach brings an important contribution to the efort of structuring Ge nanocrystallites in SiO2 thin films at a lower temperature for the purpose of using these materials for devices in optoelectronics, solar cells and electronics on flexible substrates.

  11. Printing-based fabrication method using sacrificial paper substrates for flexible and wearable microfluidic devices

    Science.gov (United States)

    Chung, Daehan; Gray, Bonnie L.

    2017-11-01

    We present a simple, fast, and inexpensive new printing-based fabrication process for flexible and wearable microfluidic channels and devices. Microfluidic devices are fabricated on textiles (fabric) for applications in clothing-based wearable microfluidic sensors and systems. The wearable and flexible microfluidic devices are comprised of water-insoluable screen-printable plastisol polymer. Sheets of paper are used as sacrificial substrates for multiple layers of polymer on the fabric’s surface. Microfluidic devices can be made within a short time using simple processes and inexpensive equipment that includes a laser cutter and a thermal laminator. The fabrication process is characterized to demonstrate control of microfluidic channel thickness and width. Film thickness smaller than 100 micrometers and lateral dimensions smaller than 150 micrometers are demonstrated. A flexible microfluidic mixer is also developed on fabric and successfully tested on both flat and curved surfaces at volumetric flow rates ranging from 5.5-46 ml min-1.

  12. Performance of carbon-based hot frit substrates: I, Low pressure helium and hydrogen testing

    International Nuclear Information System (INIS)

    Barletta, R.; Adams, J.; Svandrlik, J.; Powell, J.R.

    1993-07-01

    The performance of various carbon-based materials in flowing, high-temperature helium and hydrogen is described. These materials which are candidate hot frit substrates for possible application in a PBR include various grades of graphite, carbon-carbon and vitreous carbon. Vitreous carbon showed extremely good performance in helium, while that of the various graphite grades was quite variable and, in some cases, poor. Purified grades performed better than unpurified grades, but in all cases large sample-to-sample variations in weight loss were observed. For carbon-carbon samples, the performance was intermediate. Since the weight loss in these samples was in large measure due to the loss of the densification media, improvements in the performance of carbon-carbon may be possible. With respect to the performance in hydrogen, high weight losses were observed, re-enforcing the need for coating carbon-based materials for service in a flowing hydrogen environment

  13. Fragment-Based Drug Discovery of Potent Protein Kinase C Iota Inhibitors.

    Science.gov (United States)

    Kwiatkowski, Jacek; Liu, Boping; Tee, Doris Hui Ying; Chen, Guoying; Ahmad, Nur Huda Binte; Wong, Yun Xuan; Poh, Zhi Ying; Ang, Shi Hua; Tan, Eldwin Sum Wai; Ong, Esther Hq; Nurul Dinie; Poulsen, Anders; Pendharkar, Vishal; Sangthongpitag, Kanda; Lee, May Ann; Sepramaniam, Sugunavathi; Ho, Soo Yei; Cherian, Joseph; Hill, Jeffrey; Keller, Thomas H; Hung, Alvin W

    2018-05-24

    Protein kinase C iota (PKC-ι) is an atypical kinase implicated in the promotion of different cancer types. A biochemical screen of a fragment library has identified several hits from which an azaindole-based scaffold was chosen for optimization. Driven by a structure-activity relationship and supported by molecular modeling, a weakly bound fragment was systematically grown into a potent and selective inhibitor against PKC-ι.

  14. Substrate Integrated Waveguide (SIW)-Based Wireless Temperature Sensor for Harsh Environments.

    Science.gov (United States)

    Tan, Qiulin; Guo, Yanjie; Zhang, Lei; Lu, Fei; Dong, Helei; Xiong, Jijun

    2018-05-03

    This paper presents a new wireless sensor structure based on a substrate integrated circular waveguide (SICW) for the temperature test in harsh environments. The sensor substrate material is 99% alumina ceramic, and the SICW structure is composed of upper and lower metal plates and a series of metal cylindrical sidewall vias. A rectangular aperture antenna integrated on the surface of the SICW resonator is used for electromagnetic wave transmission between the sensor and the external antenna. The resonant frequency of the temperature sensor decreases when the temperature increases, because the relative permittivity of the alumina ceramic increases with temperature. The temperature sensor presented in this paper was tested four times at a range of 30⁻1200 °C, and a broad band coplanar waveguide (CPW)-fed antenna was used as an interrogation antenna during the test process. The resonant frequency changed from 2.371 to 2.141 GHz as the temperature varied from 30 to 1200 °C, leading to a sensitivity of 0.197 MHz/°C. The quality factor of the sensor changed from 3444.6 to 35.028 when the temperature varied from 30 to 1000 °C.

  15. Global patterns and substrate-based mechanisms of the terrestrial nitrogen cycle.

    Science.gov (United States)

    Niu, Shuli; Classen, Aimée T; Dukes, Jeffrey S; Kardol, Paul; Liu, Lingli; Luo, Yiqi; Rustad, Lindsey; Sun, Jian; Tang, Jianwu; Templer, Pamela H; Thomas, R Quinn; Tian, Dashuan; Vicca, Sara; Wang, Ying-Ping; Xia, Jianyang; Zaehle, Sönke

    2016-06-01

    Nitrogen (N) deposition is impacting the services that ecosystems provide to humanity. However, the mechanisms determining impacts on the N cycle are not fully understood. To explore the mechanistic underpinnings of N impacts on N cycle processes, we reviewed and synthesised recent progress in ecosystem N research through empirical studies, conceptual analysis and model simulations. Experimental and observational studies have revealed that the stimulation of plant N uptake and soil retention generally diminishes as N loading increases, while dissolved and gaseous losses of N occur at low N availability but increase exponentially and become the dominant fate of N at high loading rates. The original N saturation hypothesis emphasises sequential N saturation from plant uptake to soil retention before N losses occur. However, biogeochemical models that simulate simultaneous competition for soil N substrates by multiple processes match the observed patterns of N losses better than models based on sequential competition. To enable better prediction of terrestrial N cycle responses to N loading, we recommend that future research identifies the response functions of different N processes to substrate availability using manipulative experiments, and incorporates the measured N saturation response functions into conceptual, theoretical and quantitative analyses. © 2016 John Wiley & Sons Ltd/CNRS.

  16. The neural substrates of procrastination: A voxel-based morphometry study.

    Science.gov (United States)

    Hu, Yue; Liu, Peiwei; Guo, Yiqun; Feng, Tingyong

    2018-03-01

    Procrastination is a pervasive phenomenon across different cultures and brings about lots of serious consequences, including performance, subjective well-being, and even public policy. However, little is known about the neural substrates of procrastination. In order to shed light upon this question, we investigated the neuroanatomical substrates of procrastination across two independent samples using voxel-based morphometry (VBM) method. The whole-brain analysis showed procrastination was positively correlated with the graymatter (GM) volume of clusters in the parahippocampal gyrus (PHG) and the orbital frontal cortex (OFC), while negatively correlated with the GM volume of clusters in the inferior frontal gyrus (IFG) and the middle frontal gyrus (MFG) in sample one (151 participants). We further conducted a verification procedure on another sample (108 participants) using region-of-interest analysis to examine the reliability of these results. Results showed procrastination can be predicted by the GM volume of the OFC and the MFG. The present findings suggest that the MFG and OFC, which are the key regions of self-control and emotion regulation, may play an important role in procrastination. Copyright © 2018 Elsevier Inc. All rights reserved.

  17. Light extraction from GaN-based LED structures on silicon-on-insulator substrates

    Energy Technology Data Exchange (ETDEWEB)

    Tripathy, S.; Teo, S.L.; Lin, V.K.X.; Chen, M.F. [Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology, and Research), 117602 (Singapore); Dadgar, A.; Krost, A. [Institut fuer Exerimentelle Physik, Otto-von Guericke Universitaet Magdeburg, Universitaetsplatz 1, 39016 Magdeburg (Germany); AZZURRO Semiconductors AG, Universitaetsplatz 1, 39016 Magdeburg (Germany); Christen, J. [Institut fuer Exerimentelle Physik, Otto-von Guericke Universitaet Magdeburg, Universitaetsplatz 1, 39016 Magdeburg (Germany)

    2010-01-15

    Nano-patterning of GaN-based devices is a promising technology in the development of high output power devices. Recent researches have been focused on the realization of two-dimensional (2D) photonic crystal (PhC) structure to improve light extraction efficiency and to control the direction of emission. In this study, we have demonstrated improved light extraction from green light emitting diode (LED) structures on thin silicon-on-insulator (SOI) substrates using surface nanopatterning. Scanning electron microscopy (SEM) is used to probe the size, shape, and etch depth of nano-patterns on the LED surfaces. Different types of nanopatterns were created by e-beam lithography and inductively coupled plasma etching. The LED structures after post processing are studied by photoluminescence (PL) measurements. The GaN nanophotonic structures formed by ICP etching led to more than five-fold increase in the intensity of the green emission. The improved light extraction is due to the combination of SOI substrate reflectivity and photonic structures on top GaN LED surfaces. (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  18. Identification of quinazoline based inhibitors of IRAK4 for the treatment of inflammation

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Graham F.; Altman, Michael D.; Andresen, Brian; Baker, James; Brubaker, Jason D.; Chen, Hongmin; Chen, Yiping; Childers, Matthew; Donofrio, Anthony; Ferguson, Heidi; Fischer, Christian; Fischmann, Thierry O.; Gibeau, Craig; Hicks, Alexander; Jin, Sue; Kattar, Sam; Kleinschek, Melanie A.; Leccese, Erica; Lesburg, Charles; Li, Chaomin; Lim, Jongwon; Liu, Duan; Maclean, John K.F.; Mansoor, Faruk; Moy, Lilly Y.; Mulrooney, Erin F.; Necheva, Antoaneta S.; Presland, Jeremy; Rakhilina, Larissa; Yang, Ruojing; Torres, Luis; Zhang-Hoover, Jie; Northrup, Alan (Merck); (Oncorus); (Theravance Biopharma); (AstraZeneca); (Blueprint Medicines)

    2017-06-01

    Interleukin-1 receptor associated kinase 4 (IRAK4) has been implicated in IL-1R and TLR based signaling. Therefore selective inhibition of the kinase activity of this protein represents an attractive target for the treatment of inflammatory diseases. Medicinal chemistry optimization of high throughput screening (HTS) hits with the help of structure based drug design led to the identification of orally-bioavailable quinazoline based IRAK4 inhibitors with excellent pharmacokinetic profile and kinase selectivity. These highly selective IRAK4 compounds show activity in vivo via oral dosing in a TLR7 driven model of inflammation.

  19. Comparison of Clot-based, Chromogenic, and Fluorescence Assays for Measurement of Factor VIII Inhibitors in the U.S. Hemophilia Inhibitor Research Study

    Science.gov (United States)

    Miller, Connie H.; Rice, Anne S.; Boylan, Brian; Shapiro, Amy D.; Lentz, Steven R.; Wicklund, Brian M.; Kelly, Fiona M.; Soucie, J. Michael

    2015-01-01

    Summary Background Detection and validation of inhibitors (antibodies) to hemophilia treatment products are important for clinical care, evaluation of product safety, and assessment of population trends. Methods Centralized monitoring for factor VIII (FVIII) inhibitors was conducted for patients in the Hemophilia Inhibitor Research Study using a previously reported modified Nijmegen-Bethesda clotting assay (NBA), a chromogenic Bethesda assay (CBA), and a novel fluorescence immunoassay (FLI). Results NBA and CBA were performed on 1005 specimens and FLI on 272 specimens. CBA was negative on 880/883 specimens (99.7%) with Nijmegen-Bethesda units (NBU)NBA and negative CBA, 58.1% were FLI-negative, 12.9% had evidence of lupus anticoagulant, and 35.5% had non-time-dependent inhibition. CBA and FLI were positive on 72.4% and 100% of 1.0–1.9 NBU specimens and 43.1% and 50.0% of 0.5–0.9 NBU specimens. FLI detected antibodies in 98.0% of CBA-positive and 81.6% of NBA-positive specimens (P=0.004). Among 21 new inhibitors detected by NBA, 5 (23.8%) with 0.7–1.3 NBU did not react in CBA or FLI. Among previously positive patients with 0.5–1.9 NBU, 7/25 (28%) were not CBA or FLI positive. FLI was positive on 36/169 NBU-negative specimens (21.3%). Conclusions FVIII specificity could not be demonstrated by CBA or FLI for 26% of inhibitors of 0.5–1.9 NBU; such results must be interpreted with caution. Low titer inhibitors detected in clot-based assays should always be repeated, with consideration given to evaluating their reactivity with FVIII using more specific assays. PMID:23601690

  20. Nitride-based Quantum-Confined Structures for Ultraviolet-Visible Optical Devices on Silicon Substrates

    KAUST Repository

    Janjua, Bilal

    2017-04-01

    III–V nitride quantum-confined structures embedded in nanowires (NWs), also known as quantum-disks-in-nanowires (Qdisks-in-NWs), have recently emerged as a new class of nanoscale materials exhibiting outstanding properties for optoelectronic devices and systems. It is promising for circumventing the technology limitation of existing planar epitaxy devices, which are bounded by the lattice-, crystal-structure-, and thermal- matching conditions. This work presents significant advances in the growth of good quality GaN, InGaN and AlGaN Qdisks-in-NWs based on careful optimization of the growth parameters, coupled with a meticulous layer structure and active region design. The NWs were grown, catalyst-free, using plasma assisted molecular beam epitaxy (PAMBE) on silicon (Si) substrates. A 2-step growth scheme was developed to achieve high areal density, dislocation free and vertically aligned NWs on Ti/Si substrates. Numerical modeling of the NWs structures, using the nextnano3 software, showed reduced polarization fields, and, in the presence of Qdisks, exhibited improved quantum-confinement; thus contributing to high carrier radiative-recombination rates. As a result, based on the growth and device structure optimization, the technologically challenging orange and yellow NWs light emitting devices (LEDs) targeting the ‘green-yellow’ gap were demonstrated on scalable, foundry compatible, and low-cost Ti coated Si substrates. The NWs work was also extended to LEDs emitting in the ultraviolet (UV) range with niche applications in environmental cleaning, UV-curing, medicine, and lighting. In this work, we used a Ti (100 nm) interlayer and Qdisks to achieve good quality AlGaN based UV-A (320 - 400 nm) device. To address the issue of UV-absorbing polymer, used in the planarization process, we developed a pendeo-epitaxy technique, for achieving an ultra-thin coalescence of the top p-GaN contact layer, for a self-planarized Qdisks-in-NWs UV-B (280 – 320 nm) LED grown

  1. Corrosion inhibitors for neutral aqueous media based on the products on sugar cane processing. 1.Furfural derivatives as inhibitors

    International Nuclear Information System (INIS)

    Ledovskikh, V.M.; Kamekho Khinnebra, Kh.Kh.

    1993-01-01

    A series of carboxy-, nitrogen- and nitroderivaties of furfural - the main product of sugar cane processing (furancasboxylic acid, 5-nitrofurancarboxylic acid and its salts, furfurine, furfurylamine) was studied as inhibitors of iron and copper, corrosion in aqueous-salt media. Nitrofuroates of sodium and ammonium, which decelerate anode process, intensity cathode one and provide the stable passive state, are considered to be the most effective

  2. Kinetics and substrate selectivity of a Triticum aestivum xylanase inhibitor (TAXI) resistant D11F/R122D variant of Bacillus subtilis XynA xylanase

    DEFF Research Database (Denmark)

    Rasmussen, Louise Enggaard; Sørensen, Jens F.; Meyer, Anne S.

    2010-01-01

    This study examined the kinetics and substrate selectivity of a GH11 Bacillus subtilis XynA xylanase (BsX) sensitive to inhibition by TAXI and an engineered variant, which is much less inhibited by TAXI (BsX(mut)). The main purpose of the work was to elucidate any influence of the structural point...

  3. Electrochemical behaviour and nanoscale characteristics of CNT-based fibers as new substrate for cell growth

    Energy Technology Data Exchange (ETDEWEB)

    Polizu, S.; Yahia, L.H. [Ecole Polytechnique de Montreal, PQ (Canada). Laboratoire d' innovation et d' analyse de la bioperformance; Savadogo, O. [Ecole Polytechnique de Montreal, Montreal, PQ (Canada). Laboratoire de nouveaux materiaux pour l' energie et l' electrochimie; Maugey, M.; Poulin, P. [Centre de Recherche Paul Pascal, CNRS, Bordeaux (France); Rouabhia, M. [Laval Univ., Quebec City, PQ (Canada). Faculty of Medicine

    2008-07-01

    This paper reported on a study in which carbon nanotube (CNT) macroscopic fibers were formulated by a newly developed non-covalent method for fabricating fibrous substrate. The covalent and noncovalent chemistry of CNTs has been widely used in the development of CNT-based biomaterials as active substrates for living cells. Time of Flight Mass Spectroscopy (TOF-SIMS) analysis was used to determine the surface characteristics of the CNT-based fibers produced by wet spinning method. The structure and texture of fibers were imaged using Low-Vacuum Scanning Electron Microscopy (LV-SEM) equipped with an Energy Dispersive Spectrometer (EDS) for microanalysis. Atomic Force Microscopy (AFM) imaging revealed the structure of fibers. Cyclic Voltametry (CV) measurements were performed to examine the electrochemical behaviour of fibers. Sulfuric acid and a cell culture medium was used as the 2 different electrolytes. The influences of environmental parameters on the electrochemical phenomena taking place were identified. The intrinsic electrochemical characteristics of fibers were revealed through measurements in acid environment. The cell culture medium simulated the physiological conditions. It was concluded that the newly developed wet spinning method is very efficient for making CNT-based fibers as electroactive biomaterials. The structural nanoscale details evidenced a good alignment of nanotubes in the thread and the critical role it plays in electrochemical interactions. The differences induced by the variation of electrolytes suggest that a relationship could be established between the fiber chemistry and the electrochemical response. This correlation has considerably potential for the design of new biomedical devices. 2 refs.

  4. Development of a novel non-radioactive cell-based method for the screening of SGLT1 and SGLT2 inhibitors using 1-NBDG.

    Science.gov (United States)

    Chang, Hung-Chi; Yang, Su-Fu; Huang, Ching-Chun; Lin, Tzung-Sheng; Liang, Pi-Hui; Lin, Chun-Jung; Hsu, Lih-Ching

    2013-08-01

    Sodium-coupled glucose co-transporters SGLT1 and SGLT2 play important roles in intestinal absorption and renal reabsorption of glucose, respectively. Blocking SGLT2 is a novel mechanism for lowering the blood glucose level by inhibiting renal glucose reabsorption and selective SGLT2 inhibitors are under development for treatment of type 2 diabetes. Furthermore, it has been reported that perturbation of SGLT1 is associated with cardiomyopathy and cancer. Therefore, both SGLT1 and SGLT2 are potential therapeutic targets. Here we report the development of a non-radioactive cell-based method for the screening of SGLT inhibitors using COS-7 cells transiently expressing human SGLT1 (hSGLT1), CHO-K1 cells stably expressing human SGLT2 (hSGLT2), and a novel fluorescent d-glucose analogue 1-NBDG as a substrate. Our data indicate that 1-NBDG can be a good replacement for the currently used isotope-labeled SGLT substrate, (14)C-AMG. The Michaelis constant of 1-NBDG transport (0.55 mM) is similar to that of d-glucose (0.51 mM) and AMG (0.40 mM) transport through hSGLT1. The IC50 values of a SGLT inhibitor phlorizin for hSGLT1 obtained using 1-NBDG and (14)C-AMG were identical (0.11 μM) in our cell-based system. The IC50 values of dapagliflozin, a well-known selective SGLT2 inhibitor, for hSGLT2 and hSGLT1 determined using 1-NBDG were 1.86 nM and 880 nM, respectively, which are comparable to the published results obtained using (14)C-AMG. Compared to (14)C-AMG, the use of 1-NBDG is cost-effective, convenient and potentially more sensitive. Taken together, a non-radioactive system using 1-NBDG has been validated as a rapid and reliable method for the screening of SGLT1 and SGLT2 inhibitors.

  5. Support effects on adsorption and catalytic activation of O2 in single atom iron catalysts with graphene-based substrates.

    Science.gov (United States)

    Gao, Zheng-Yang; Yang, Wei-Jie; Ding, Xun-Lei; Lv, Gang; Yan, Wei-Ping

    2018-03-07

    The adsorption and catalytic activation of O 2 on single atom iron catalysts with graphene-based substrates were investigated systematically by density functional theory calculation. It is found that the support effects of graphene-based substrates have a significant influence on the stability of the single atom catalysts, the adsorption configuration, the electron transfer mechanism, the adsorption energy and the energy barrier. The differences in the stable adsorption configuration of O 2 on single atom iron catalysts with different graphene-based substrates can be well understood by the symmetrical matching principle based on frontier molecular orbital analysis. There are two different mechanisms of electron transfer, in which the Fe atom acts as the electron donor in single vacancy graphene-based substrates while the Fe atom mainly acts as the bridge for electron transfer in double vacancy graphene-based substrates. The Fermi softness and work function are good descriptors of the adsorption energy and they can well reveal the relationship between electronic structure and adsorption energy. This single atom iron catalyst with single vacancy graphene modified by three nitrogen atoms is a promising non-noble metal single atom catalyst in the adsorption and catalytic oxidation of O 2 . Furthermore, the findings can lay the foundation for the further study of graphene-based support effects and provide a guideline for the development and design of new non-noble-metal single atom catalysts.

  6. Structure-Based Drug Design of Small Molecule Peptide Deformylase Inhibitors to Treat Cancer

    Directory of Open Access Journals (Sweden)

    Jian Gao

    2016-03-01

    Full Text Available Human peptide deformylase (HsPDF is an important target for anticancer drug discovery. In view of the limited HsPDF, inhibitors were reported, and high-throughput virtual screening (HTVS studies based on HsPDF for developing new PDF inhibitors remain to be reported. We reported here on diverse small molecule inhibitors with excellent anticancer activities designed based on HTVS and molecular docking studies using the crystal structure of HsPDF. The compound M7594_0037 exhibited potent anticancer activities against HeLa, A549 and MCF-7 cell lines with IC50s of 35.26, 29.63 and 24.63 μM, respectively. Molecular docking studies suggested that M7594_0037 and its three derivatives could interact with HsPDF by several conserved hydrogen bonds. Moreover, the pharmacokinetic and toxicity properties of M7594_0037 and its derivatives were predicted using the OSIRIS property explorer. Thus, M7594_0037 and its derivatives might represent a promising scaffold for the further development of novel anticancer drugs.

  7. Structure-Activity Relationship Analysis of 3-phenylcoumarin-Based Monoamine Oxidase B Inhibitors

    Science.gov (United States)

    Rauhamäki, Sanna; Postila, Pekka A.; Niinivehmas, Sanna; Kortet, Sami; Schildt, Emmi; Pasanen, Mira; Manivannan, Elangovan; Ahinko, Mira; Koskimies, Pasi; Nyberg, Niina; Huuskonen, Pasi; Multamäki, Elina; Pasanen, Markku; Juvonen, Risto O.; Raunio, Hannu; Huuskonen, Juhani; Pentikäinen, Olli T.

    2018-03-01

    Monoamine oxidase B (MAO-B) catalyzes deamination of monoamines such as neurotransmitters dopamine and norepinephrine. Accordingly, small-molecule MAO-B inhibitors potentially alleviate the symptoms of dopamine-linked neuropathologies such as depression or Parkinson’s disease. Coumarin with a functionalized 3-phenyl ring system is a promising scaffold for building potent MAO-B inhibitors. Here, a vast set of 3-phenylcoumarin derivatives was designed using virtual combinatorial chemistry or rationally de novo and synthesized using microwave chemistry. The derivatives inhibited the MAO-B at 100 nM - 1 µM. The IC50 value of the most potent derivative 1 was 56 nM. A docking-based structure-activity relationship analysis summarizes the atom-level determinants of the MAO-B inhibition by the derivatives. Finally, the cross-reactivity of the derivatives was tested against monoamine oxidase A and a specific subset of enzymes linked to estradiol metabolism, known to have coumarin-based inhibitors. Overall, the results indicate that the 3-phenylcoumarins, especially derivative 1, present unique pharmacological features worth considering in future drug development.

  8. Fragment-based discovery of novel pentacyclic triterpenoid derivatives as cholesteryl ester transfer protein inhibitors.

    Science.gov (United States)

    Chang, Yongzhi; Zhou, Shuxi; Li, Enqin; Zhao, Wenfeng; Ji, Yanpeng; Wen, Xiaoan; Sun, Hongbin; Yuan, Haoliang

    2017-01-27

    Cholesteryl Ester Transfer Protein (CETP) is an important therapeutic target for the treatment of atherosclerotic cardiovascular disease. Our molecular modeling study revealed that pentacyclic triterpenoid compounds could mimic the protein-ligand interactions of the endogenous ligand cholesteryl ester (CE) by occupying its binding site. Alignment of the docking conformations of oleanolic acid (OA), ursolic acid (UA) and the crystal conformations of known CETP inhibitor Torcetrapib in the active site proposed the applicability of fragment-based drug design (FBDD) approaches in this study. Accordingly, a series of pentacyclic triterpenoid derivatives have been designed and synthesized as novel CETP inhibitors. The most potent compound 12e (IC 50 :0.28 μM) validated our strategy for molecular design. Molecular dynamics simulations illustrated that the more stable hydrogen bond interaction of the UA derivative 12e with Ser191 and stronger hydrophobic interactions with Val198, Phe463 than those of OA derivative 12b mainly led to their significantly different CETP inhibitory activity. These novel potent CETP inhibitors based on ursane-type scaffold should deserve further investigation. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  9. A Limited Structural Modification Results in a Significantly More Efficacious Diazachrysene-Based Filovirus Inhibitor

    Directory of Open Access Journals (Sweden)

    Rekha G. Panchal

    2012-08-01

    Full Text Available Ebola (EBOV and Marburg (MARV filoviruses are highly infectious pathogens causing deadly hemorrhagic fever in humans and non-human primates. Promising vaccine candidates providing immunity against filoviruses have been reported. However, the sporadic nature and swift progression of filovirus disease underlines the need for the development of small molecule therapeutics providing immediate antiviral effects. Herein we describe a brief structural exploration of two previously reported diazachrysene (DAAC-based EBOV inhibitors. Specifically, three analogs were prepared to examine how slight substituent modifications would affect inhibitory efficacy and inhibitor-mediated toxicity during not only EBOV, but also MARV cellular infection. Of the three analogs, one was highly efficacious, providing IC50 values of 0.696 µM ± 0.13 µM and 2.76 µM ± 0.21 µM against EBOV and MARV infection, respectively, with little or no associated cellular toxicity. Overall, the structure-activity and structure-toxicity results from this study provide a framework for the future development of DAAC-based filovirus inhibitors that will be both active and non-toxic in vivo.

  10. Homology modeling of parasite histone deacetylases to guide the structure-based design of selective inhibitors.

    Science.gov (United States)

    Melesina, Jelena; Robaa, Dina; Pierce, Raymond J; Romier, Christophe; Sippl, Wolfgang

    2015-11-01

    Histone deacetylases (HDACs) are promising epigenetic targets for the treatment of various diseases, including cancer and neurodegenerative disorders. There is evidence that they can also be addressed to treat parasitic infections. Recently, the first X-ray structure of a parasite HDAC was published, Schistosoma mansoni HDAC8, giving structural insights into its inhibition. However, most of the targets from parasites of interest still lack this structural information. Therefore, we prepared homology models of relevant parasitic HDACs and compared them to human and S. mansoni HDACs. The information about known S. mansoni HDAC8 inhibitors and compounds that affect the growth of Trypanosoma, Leishmania and Plasmodium species was used to validate the models by docking and molecular dynamics studies. Our results provide analysis of structural features of parasitic HDACs and should be helpful for selecting promising candidates for biological testing and for structure-based optimisation of parasite-specific inhibitors. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Design of monodisperse and well-defined polypeptide-based polyvalent inhibitors of anthrax toxin.

    Science.gov (United States)

    Patke, Sanket; Boggara, Mohan; Maheshwari, Ronak; Srivastava, Sunit K; Arha, Manish; Douaisi, Marc; Martin, Jacob T; Harvey, Ian B; Brier, Matthew; Rosen, Tania; Mogridge, Jeremy; Kane, Ravi S

    2014-07-28

    The design of polyvalent molecules, presenting multiple copies of a specific ligand, represents a promising strategy to inhibit pathogens and toxins. The ability to control independently the valency and the spacing between ligands would be valuable for elucidating structure-activity relationships and for designing potent polyvalent molecules. To that end, we designed monodisperse polypeptide-based polyvalent inhibitors of anthrax toxin in which multiple copies of an inhibitory toxin-binding peptide were separated by flexible peptide linkers. By tuning the valency and linker length, we designed polyvalent inhibitors that were over four orders of magnitude more potent than the corresponding monovalent ligands. This strategy for the rational design of monodisperse polyvalent molecules may not only be broadly applicable for the inhibition of toxins and pathogens, but also for controlling the nanoscale organization of cellular receptors to regulate signaling and the fate of stem cells. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Design, Synthesis, and Evaluation of Novel Tyrosine-Based DNA Gyrase B Inhibitors.

    Science.gov (United States)

    Cotman, Andrej E; Trampuž, Marko; Brvar, Matjaž; Kikelj, Danijel; Ilaš, Janez; Peterlin-Mašič, Lucija; Montalvão, Sofia; Tammela, Päivi; Frlan, Rok

    2017-08-01

    The discovery and synthesis of new tyrosine-based inhibitors of DNA gyrase B (GyrB), which target its ATPase subunit, is reported. Twenty-four compounds were synthesized and evaluated for activity against DNA gyrase and DNA topoisomerase IV. The antibacterial properties of selected GyrB inhibitors were demonstrated by their activity against Staphylococcus aureus and Enterococcus faecalis in the low micromolar range. The most promising compounds, 8a and 13e, inhibited Escherichia coli and S. aureus GyrB with IC 50 values of 40 and 30 µM. The same compound also inhibited the growth of S. aureus and E. faecalis with minimal inhibitory concentrations (MIC 90 ) of 14 and 28 µg/mL, respectively. © 2017 Deutsche Pharmazeutische Gesellschaft.

  13. Design of patterned sapphire substrates for GaN-based light-emitting diodes

    International Nuclear Information System (INIS)

    Wang Hai-Yan; Lin Zhi-Ting; Han Jing-Lei; Zhong Li-Yi; Li Guo-Qiang

    2015-01-01

    A new method for patterned sapphire substrate (PSS) design is developed and proven to be reliable and cost-effective. As progress is made with LEDs’ luminous efficiency, the pattern units of PSS become more complicated, and the effect of complicated geometrical features is almost impossible to study systematically by experiments only. By employing our new method, the influence of pattern parameters can be systematically studied, and various novel patterns are designed and optimized within a reasonable time span, with great improvement in LEDs’ light extraction efficiency (LEE). Clearly, PSS pattern design with such a method deserves particular attention. We foresee that GaN-based LEDs on these newly designed PSSs will achieve more progress in the coming years. (topical review)

  14. Photodetectors based on single-walled carbon nanotubes and thiamonomethinecyanine J-aggregates on flexible substrates

    Energy Technology Data Exchange (ETDEWEB)

    Fedorov, I. V., E-mail: i-v-fedorov@mail.ru; Emel’yanov, A. V.; Romashkin, A. V.; Bobrinetskiy, I. I. [National Research University of Electronic Technology (MIET) (Russian Federation)

    2015-09-15

    The present paper is devoted to observations of the photoresistive effect in multilayer structures with a sensitive layer of J-aggregates of thiamonomethinecyanine polymethine dye and a transparent electrode of a conductive carbon-nanotube network on a flexible polyethylenenaphtalate substrate. The effect of narrow-band emission with a wavelength of 465 nm on a change in the conductivity of the fabricated structures is studied. The prepared samples are studied by atomic-force microscopy, Raman spectroscopy, and spectrophotometry methods. It is shown that these structures are photosensitive to the indicated spectral region, and the dye layer is a film of dye J-aggregates. The change in the sample conductivity upon exposure to light one hundred times exceeds the dark conductivity. In general, the principal possibility of developing a photoresistive detector based on J-aggregates of cyanine dyes on flexible supports on account of the use of transparent and conductive carbon-nanotube layers is shown.

  15. Schottky x-ray detectors based on a bulk β-Ga2O3 substrate

    Science.gov (United States)

    Lu, Xing; Zhou, Leidang; Chen, Liang; Ouyang, Xiaoping; Liu, Bo; Xu, Jun; Tang, Huili

    2018-03-01

    β-Ga2O3 Schottky barrier diodes (SBDs) have been fabricated on a bulk (100) β-Ga2O3 substrate and tested as X-ray detectors in this study. The devices exhibited good rectification properties, such as a high rectification ratio and a close-to-unity ideality factor. A high photo-to-dark current ratio exceeding 800 was achieved for X-ray detection, which was mainly attributed to the low reverse leakage current in the β-Ga2O3 SBDs. Furthermore, transient response of the β-Ga2O3 X-ray detectors was investigated, and two different detection mechanisms, photovoltaic and photoconductive, were identified. The results imply the great potential of β-Ga2O3 based devices for X-ray detection.

  16. Study of pyrolysed acid and based treated coconut coir as green photocatalyst substrate

    Science.gov (United States)

    Asim, Nilofar; Emdadi, Zeynab; Abdullah, N. A.; Mohammad, Masita; Badiei, Marzieh; Sopian, Kamaruzzaman

    2017-12-01

    This study investigates the possible contribution to sustainable development by utilizing agriculture waste materials to prepare a substrate for photo-catalysis application. The photocatalytic performance of impregnated TiO2 on acid and base- treated coconut coir (CC) and their pyrolysed form have been studied. The photocatalytic performance of impregnated TiO2 on acid treated CC improved compared to bare TiO2. However, the pyrolysed samples showed higher thermal stability and porosity compared to only treated CC, their catalytic performance was decreased. It seems that impregnated TiO2 undergo interaction with treated CC during pyrolysis. More investigations to reveal exact reason of this behavior is in progress.

  17. Recent Progress in Fabrication and Applications of Superhydrophobic Coating on Cellulose-Based Substrates

    Science.gov (United States)

    Liu, Hui; Gao, Shou-Wei; Cai, Jing-Sheng; He, Cheng-Lin; Mao, Jia-Jun; Zhu, Tian-Xue; Chen, Zhong; Huang, Jian-Ying; Meng, Kai; Zhang, Ke-Qin; Al-Deyab, Salem S.; Lai, Yue-Kun

    2016-01-01

    Multifuntional fabrics with special wettability have attracted a lot of interest in both fundamental research and industry applications over the last two decades. In this review, recent progress of various kinds of approaches and strategies to construct super-antiwetting coating on cellulose-based substrates (fabrics and paper) has been discussed in detail. We focus on the significant applications related to artificial superhydrophobic fabrics with special wettability and controllable adhesion, e.g., oil-water separation, self-cleaning, asymmetric/anisotropic wetting for microfluidic manipulation, air/liquid directional gating, and micro-template for patterning. In addition to the anti-wetting properties and promising applications, particular attention is paid to coating durability and other incorporated functionalities, e.g., air permeability, UV-shielding, photocatalytic self-cleaning, self-healing and patterned antiwetting properties. Finally, the existing difficulties and future prospects of this traditional and developing field are briefly proposed and discussed. PMID:28773253

  18. Terahertz polarizing beam splitter based on copper grating on polyimide substrate

    Science.gov (United States)

    Zhang, Mengen; Li, Xiangjun; Wang, Wentao; Liu, Jianjun; Hong, Zhi

    2012-12-01

    A terahertz polarizing beam splitter, based on a copper grating on polyimide (PI) substrate, was fabricated by the way of laser induced and non-electrolytic plating. The good polarization characteristics of the splitter in the range of 0°-180°polarization are verified experimentally using backward wave oscillator at fixed frequency of 300GHz, and the insertion losses of 0.13dB and 0.32dB are measured for the transmitted and reflected beams, respectively. The broadband transmission of TM wave of the splitter was also measured by terahertz time-domain spectroscopy, and the extinction ratio larger than 22dB is obtained in the frequency range of 0.2-1.5THz. The experiment results are in good agreement with finite element simulation results.

  19. Cysteine protease inhibition by nitrile-based inhibitors: a computational study

    Science.gov (United States)

    Quesne, Matthew G.; Ward, Richard A.; de Visser, Sam P.

    2013-01-01

    Cysteine protease enzymes are important for human physiology and catalyze key protein degradation pathways. These enzymes react via a nucleophilic reaction mechanism that involves a cysteine residue and the proton of a proximal histidine. Particularly efficient inhibitors of these enzymes are nitrile-based, however, the details of the catalytic reaction mechanism currently are poorly understood. To gain further insight into the inhibition of these molecules, we have performed a combined density functional theory and quantum mechanics/molecular mechanics study on the reaction of a nitrile-based inhibitor with the enzyme active site amino acids. We show here that small perturbations to the inhibitor structure can have dramatic effects on the catalysis and inhibition processes. Thus, we investigated a range of inhibitor templates and show that specific structural changes reduce the inhibitory efficiency by several orders of magnitude. Moreover, as the reaction takes place on a polar surface, we find strong differences between the DFT and QM/MM calculated energetics. In particular, the DFT model led to dramatic distortions from the starting structure and the convergence to a structure that would not fit the enzyme active site. In the subsequent QM/MM study we investigated the use of mechanical vs. electronic embedding on the kinetics, thermodynamics and geometries along the reaction mechanism. We find minor effects on the kinetics of the reaction but large geometric and thermodynamics differences as a result of inclusion of electronic embedding corrections. The work here highlights the importance of model choice in the investigation of this biochemical reaction mechanism. PMID:24790966

  20. Crack-free AlGaN-based UV LED on Si(111) substrate

    Energy Technology Data Exchange (ETDEWEB)

    Saengkaew, P.; Dadgar, A.; Blaesing, J.; Witte, H.; Mueller, M.; Guenther, K.M.; Fey, T.; Bastek, B.; Bertram, F.; Kurnatowski, M. von; Wieneke, M.; Hempel, T.; Veit, P.; Clos, R.; Christen, J.; Krost, A. [FNW/IEP/AHE Otto-von-Guericke-Universitaet Magdeburg (Germany)

    2010-07-01

    To achieve low-cost UV LEDs on large-diameter substrates it is a very interesting approach to grow AlGaN on low-cost Si substrates. Here, AlGaN layers and AlGaN LED structures grown on Si(111) were additionally monitored by in-situ curvature measurements. They show that with the insertion of AlN-based SL buffer layers and LT-AlN interlayers, the AlGaN layers are under compressive stress during growth enabling to compensate tensile stress after cooling. To characterize the crystalline quality, HR-XRD measurements were performed. Cross-sectional TEM to investigate dislocation propagation and annihilation. n- and p- conductivities were achieved by Si and Mg doping of the layers, respectively. By C-V and Hall-effect measurements, the maximum free-electron concentration of 2.6{sup +18} cm{sup -3} and free-hole concentration of 2.4{sup +17} cm{sup -3} by using a structure of Mg-doped GaN/Al{sub 0.1}Ga{sub 0.9}N multilayers for the latter were determined. A GaN/Al{sub 0.1}Ga{sub 0.9}N MQW structure showed near UV-luminescence around 350-360 nm. The optical and electrical properties of AlGaN-based LED samples were further characterized by I-V, EL, PL and CL measurements. The I-V measurements show forward-diode characteristics with turn-on voltage about 2.6-3.1 V.

  1. Potent inhibitors of human LAT1 (SLC7A5) transporter based on dithiazole and dithiazine compounds for development of anticancer drugs.

    Science.gov (United States)

    Napolitano, Lara; Scalise, Mariafrancesca; Koyioni, Maria; Koutentis, Panayiotis; Catto, Marco; Eberini, Ivano; Parravicini, Chiara; Palazzolo, Luca; Pisani, Leonardo; Galluccio, Michele; Console, Lara; Carotti, Angelo; Indiveri, Cesare

    2017-11-01

    The LAT1 transporter is acknowledged as a pharmacological target of tumours since it is strongly overexpressed in many human cancers. The purpose of this work was to find novel compounds exhibiting potent and prolonged inhibition of the transporter. To this aim, compounds based on dithiazole and dithiazine scaffold have been screened in the proteoliposome experimental model. Inhibition was tested on the antiport catalysed by hLAT1 as transport of extraliposomal [ 3 H]histidine in exchange with intraliposomal histidine. Out of 59 compounds tested, 8 compounds, showing an inhibition higher than 90% at 100µM concentration, were subjected to dose-response analysis. Two of them exhibited IC 50 lower than 1µM. Inhibition kinetics, performed on the two best inhibitors, indicated a mixed type of inhibition with respect to the substrate. Furthermore, inhibition of the transporter was still present after removal of the compounds from the reaction mixture, but was reversed on addition of dithioerythritol, a S-S reducing agent, indicating the formation of disulfide(s) between the compounds and the protein. Molecular docking of the two best inhibitors on the hLAT1 homology structural model, highlighted interaction with the substrate binding site and formation of a covalent bond with the residue C407. Indeed, the inhibition was impaired in the hLAT1 mutant C407A confirming the involvement of that Cys residue. Treatment of SiHa cells expressing hLAT1 at relatively high level, with the two most potent inhibitors led to cell death which was not observed after treatment with a compound exhibiting very poor inhibitory effect. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. A MAM7 peptide-based inhibitor of Staphylococcus aureus adhesion does not interfere with in vitro host cell function.

    Directory of Open Access Journals (Sweden)

    Catherine Alice Hawley

    Full Text Available Adhesion inhibitors that block the attachment of pathogens to host tissues may be used synergistically with or as an alternative to antibiotics. The wide-spread bacterial adhesin Multivalent Adhesion Molecule (MAM 7 has recently emerged as a candidate molecule for a broad-spectrum adhesion inhibitor which may be used to prevent bacterial colonization of wounds. Here we have tested if the antibacterial properties of a MAM-based inhibitor could be used to competitively inhibit adhesion of methicillin-resistant Staphylococcus aureus (MRSA to host cells. Additionally, we analyzed its effect on host cellular functions linked to the host receptor fibronectin, such as migration, adhesion and matrix formation in vitro, to evaluate potential side effects prior to advancing our studies to in vivo infection models. As controls, we used inhibitors based on well-characterized bacterial adhesin-derived peptides from F1 and FnBPA, which are known to affect host cellular functions. Inhibitors based on F1 or FnBPA blocked MRSA attachment but at the same time abrogated important cellular functions. A MAM7-based inhibitor did not interfere with host cell function while showing good efficacy against MRSA adhesion in a tissue culture model. These observations provide a possible candidate for a bacterial adhesion inhibitor that does not cause adverse effects on host cells while preventing bacterial infection.

  3. How to Achieve Better Results Using PASS-Based Virtual Screening: Case Study for Kinase Inhibitors

    Directory of Open Access Journals (Sweden)

    Pavel V. Pogodin

    2018-04-01

    Full Text Available Discovery of new pharmaceutical substances is currently boosted by the possibility of utilization of the Synthetically Accessible Virtual Inventory (SAVI library, which includes about 283 million molecules, each annotated with a proposed synthetic one-step route from commercially available starting materials. The SAVI database is well-suited for ligand-based methods of virtual screening to select molecules for experimental testing. In this study, we compare the performance of three approaches for the analysis of structure-activity relationships that differ in their criteria for selecting of “active” and “inactive” compounds included in the training sets. PASS (Prediction of Activity Spectra for Substances, which is based on a modified Naïve Bayes algorithm, was applied since it had been shown to be robust and to provide good predictions of many biological activities based on just the structural formula of a compound even if the information in the training set is incomplete. We used different subsets of kinase inhibitors for this case study because many data are currently available on this important class of drug-like molecules. Based on the subsets of kinase inhibitors extracted from the ChEMBL 20 database we performed the PASS training, and then applied the model to ChEMBL 23 compounds not yet present in ChEMBL 20 to identify novel kinase inhibitors. As one may expect, the best prediction accuracy was obtained if only the experimentally confirmed active and inactive compounds for distinct kinases in the training procedure were used. However, for some kinases, reasonable results were obtained even if we used merged training sets, in which we designated as inactives the compounds not tested against the particular kinase. Thus, depending on the availability of data for a particular biological activity, one may choose the first or the second approach for creating ligand-based computational tools to achieve the best possible results in

  4. Nelfinavir and Non-Nucleoside Reverse Transcriptase Inhibitor-Based Salvage Regimes in Heavily Hiv Pretreated Patients

    Directory of Open Access Journals (Sweden)

    Jean-Guy Baril

    2003-01-01

    Full Text Available OBJECTIVE: To assess the efficacy of nelfinavir mesylate (NFV in combination with delavirdine mesylate(DLV or efavirenz (EFV and other antiretroviral agents following virological failure on other protease inhibitor (PI-based regimens.

  5. Fragment-based discovery of potent inhibitors of the anti-apoptotic MCL-1 protein.

    Science.gov (United States)

    Petros, Andrew M; Swann, Steven L; Song, Danying; Swinger, Kerren; Park, Chang; Zhang, Haichao; Wendt, Michael D; Kunzer, Aaron R; Souers, Andrew J; Sun, Chaohong

    2014-03-15

    Apoptosis is regulated by the BCL-2 family of proteins, which is comprised of both pro-death and pro-survival members. Evasion of apoptosis is a hallmark of malignant cells. One way in which cancer cells achieve this evasion is thru overexpression of the pro-survival members of the BCL-2 family. Overexpression of MCL-1, a pro-survival protein, has been shown to be a resistance factor for Navitoclax, a potent inhibitor of BCL-2 and BCL-XL. Here we describe the use of fragment screening methods and structural biology to drive the discovery of novel MCL-1 inhibitors from two distinct structural classes. Specifically, cores derived from a biphenyl sulfonamide and salicylic acid were uncovered in an NMR-based fragment screen and elaborated using high throughput analog synthesis. This culminated in the discovery of selective and potent inhibitors of MCL-1 that may serve as promising leads for medicinal chemistry optimization efforts. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Structural characterization of human heme oxygenase-1 in complex with azole-based inhibitors.

    Science.gov (United States)

    Rahman, Mona N; Vlahakis, Jason Z; Roman, Gheorghe; Vukomanovic, Dragic; Szarek, Walter A; Nakatsu, Kanji; Jia, Zongchao

    2010-03-01

    The development of inhibitors specific for heme oxygenases (HO) aims to provide powerful tools in understanding the HO system. Based on the lead structure (2S, 4S)-2-[2-(4-chlorophenyl)ethyl]-2-[(1H-imidazol-1-yl)methyl]-4-[((4-aminophenyl)thio)methyl]-1,3-dioxolane (azalanstat, QC-1) we have synthesized structural modifications to develop novel and selective HO inhibitors. The structural study of human HO-1 (hHO-1) in complex with a select group of the inhibitors was initiated using X-ray crystallographic techniques. Comparison of the structures of four such compounds each in complex with hHO-1 revealed a common binding mode, despite having different structural fragments. The compounds bind to the distal side of heme through an azole "anchor" which coordinates with the heme iron. An expansion of the distal pocket, mainly due to distal helix flexibility, allows accommodation of the compounds without displacing heme or the critical Asp140 residue. Rather, binding displaces a catalytically critical water molecule and disrupts an ordered hydrogen-bond network involving Asp140. The presence of a triazole "anchor" may provide further stability via a hydrogen bond with the protein. A hydrophobic pocket acts to stabilize the region occupied by the phenyl or adamantanyl moieties of these compounds. Further, a secondary hydrophobic pocket is formed via "induced fit" to accommodate bulky substituents at the 4-position of the dioxolane ring. Copyright 2009 Elsevier Inc. All rights reserved.

  7. GaN-based micro-LED arrays on flexible substrates for optical cochlear implants

    International Nuclear Information System (INIS)

    Goßler, Christian; Bierbrauer, Colin; Moser, Rüdiger; Kunzer, Michael; Holc, Katarzyna; Pletschen, Wilfried; Köhler, Klaus; Wagner, Joachim; Schwarz, Ulrich T; Schwaerzle, Michael; Ruther, Patrick; Paul, Oliver; Neef, Jakob; Keppeler, Daniel; Hoch, Gerhard; Moser, Tobias

    2014-01-01

    Currently available cochlear implants are based on electrical stimulation of the spiral ganglion neurons. Optical stimulation with arrays of micro-sized light-emitting diodes (µLEDs) promises to increase the number of distinguishable frequencies. Here, the development of a flexible GaN-based micro-LED array as an optical cochlear implant is reported for application in a mouse model. The fabrication of 15 µm thin and highly flexible devices is enabled by a laser-based layer transfer process of the GaN-LEDs from sapphire to a polyimide-on-silicon carrier wafer. The fabricated 50 × 50 µm 2 LEDs are contacted via conducting paths on both p- and n-sides of the LEDs. Up to three separate channels could be addressed. The probes, composed of a linear array of the said µLEDs bonded to the flexible polyimide substrate, are peeled off the carrier wafer and attached to flexible printed circuit boards. Probes with four µLEDs and a width of 230 µm are successfully implanted in the mouse cochlea both in vitro and in vivo. The LEDs emit 60 µW at 1 mA after peel-off, corresponding to a radiant emittance of 6 mW mm −2 . (paper)

  8. Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening.

    Science.gov (United States)

    Yu, Miao; Gu, Qiong; Xu, Jun

    2018-02-01

    PI3Kα is a promising drug target for cancer chemotherapy. In this paper, we report a strategy of combing ligand-based and structure-based virtual screening to identify new PI3Kα inhibitors. First, naïve Bayesian (NB) learning models and a 3D-QSAR pharmacophore model were built based upon known PI3Kα inhibitors. Then, the SPECS library was screened by the best NB model. This resulted in virtual hits, which were validated by matching the structures against the pharmacophore models. The pharmacophore matched hits were then docked into PI3Kα crystal structures to form ligand-receptor complexes, which are further validated by the Glide-XP program to result in structural validated hits. The structural validated hits were examined by PI3Kα inhibitory assay. With this screening protocol, ten PI3Kα inhibitors with new scaffolds were discovered with IC 50 values ranging 0.44-31.25 μM. The binding affinities for the most active compounds 33 and 74 were estimated through molecular dynamics simulations and MM-PBSA analyses.

  9. Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening

    Science.gov (United States)

    Yu, Miao; Gu, Qiong; Xu, Jun

    2018-02-01

    PI3Kα is a promising drug target for cancer chemotherapy. In this paper, we report a strategy of combing ligand-based and structure-based virtual screening to identify new PI3Kα inhibitors. First, naïve Bayesian (NB) learning models and a 3D-QSAR pharmacophore model were built based upon known PI3Kα inhibitors. Then, the SPECS library was screened by the best NB model. This resulted in virtual hits, which were validated by matching the structures against the pharmacophore models. The pharmacophore matched hits were then docked into PI3Kα crystal structures to form ligand-receptor complexes, which are further validated by the Glide-XP program to result in structural validated hits. The structural validated hits were examined by PI3Kα inhibitory assay. With this screening protocol, ten PI3Kα inhibitors with new scaffolds were discovered with IC50 values ranging 0.44-31.25 μM. The binding affinities for the most active compounds 33 and 74 were estimated through molecular dynamics simulations and MM-PBSA analyses.

  10. Surface-enhanced Raman scattering (SERS)-based volatile organic compounds (VOCs) detection using plasmonic bimetallic nanogap substrate

    DEFF Research Database (Denmark)

    Wong, Chi Lok; Dinish, U. S.; Buddharaju, Kavitha Devi

    2014-01-01

    In this paper, we present surface-enhanced Raman scattering (SERS)-based volatile organic compounds (VOCs) detection with bimetallic nanogap structure substrate. Deep UV photolithography at the wavelength of 250 nm is used to pattern circular shape nanostructures. The nanogap between adjacent cir......-based VOCs detection platform for point-of-care breath analysis, homeland security, chemical sensing and environmental monitoring....

  11. Comparative of fibroblast and osteoblast cells adhesion on surface modified nanofibrous substrates based on polycaprolactone.

    Science.gov (United States)

    Sharifi, Fereshteh; Irani, Shiva; Zandi, Mojgan; Soleimani, Masoud; Atyabi, Seyed Mohammad

    2016-12-01

    One of the determinant factors for successful bioengineering is to achieve appropriate nano-topography and three-dimensional substrate. In this research, polycaprolactone (PCL) nano-fibrous mat with different roughness modified with O 2 plasma was fabricated via electrospinning. The purpose of this study was to evaluate the effect of plasma modification along with surface nano-topography of mats on the quality of human fibroblast (HDFs) and osteoblast cells (OSTs)-substrate interaction. Surface properties were studied using scanning electron microscopy (SEM), atomic force microscopy (AFM), contact angle, Fourier-transformation infrared spectroscopy. We evaluated mechanical properties of fabricated mats by tensile test. The viability and proliferation of HDFs and OSTs on the substrates were followed by 3-[4, 5-dimethylthiazol-2-yl]-2, 5-diphenyltetrazolium bromide (MTT). Mineralization of the substrate was determined by alizarin red staining method and calcium content of OSTs was determined by calcium content kit. Cells morphology was studied by SEM analysis. The results revealed that the plasma-treated electrospun nano-fibrous substrate with higher roughness was an excellent designed substrate. A bioactive topography for stimulating proliferation of HDFs and OSTs is to accelerate the latter's differentiation time. Therefore, the PCL substrate with high density and major nano-topography were considered as a bio-functional and elegant bio-substrate for tissue regeneration applications.

  12. Spherical harmonics coefficients for ligand-based virtual screening of cyclooxygenase inhibitors.

    Science.gov (United States)

    Wang, Quan; Birod, Kerstin; Angioni, Carlo; Grösch, Sabine; Geppert, Tim; Schneider, Petra; Rupp, Matthias; Schneider, Gisbert

    2011-01-01

    Molecular descriptors are essential for many applications in computational chemistry, such as ligand-based similarity searching. Spherical harmonics have previously been suggested as comprehensive descriptors of molecular structure and properties. We investigate a spherical harmonics descriptor for shape-based virtual screening. We introduce and validate a partially rotation-invariant three-dimensional molecular shape descriptor based on the norm of spherical harmonics expansion coefficients. Using this molecular representation, we parameterize molecular surfaces, i.e., isosurfaces of spatial molecular property distributions. We validate the shape descriptor in a comprehensive retrospective virtual screening experiment. In a prospective study, we virtually screen a large compound library for cyclooxygenase inhibitors, using a self-organizing map as a pre-filter and the shape descriptor for candidate prioritization. 12 compounds were tested in vitro for direct enzyme inhibition and in a whole blood assay. Active compounds containing a triazole scaffold were identified as direct cyclooxygenase-1 inhibitors. This outcome corroborates the usefulness of spherical harmonics for representation of molecular shape in virtual screening of large compound collections. The combination of pharmacophore and shape-based filtering of screening candidates proved to be a straightforward approach to finding novel bioactive chemotypes with minimal experimental effort.

  13. Synthesis of Graphene Based Membranes: Effect of Substrate Surface Properties on Monolayer Graphene Transfer.

    Science.gov (United States)

    Kafiah, Feras; Khan, Zafarullah; Ibrahim, Ahmed; Atieh, Muataz; Laoui, Tahar

    2017-01-21

    In this work, we report the transfer of graphene onto eight commercial microfiltration substrates having different pore sizes and surface characteristics. Monolayer graphene grown on copper by the chemical vapor deposition (CVD) process was transferred by the pressing method over the target substrates, followed by wet etching of copper to obtain monolayer graphene/polymer membranes. Scanning electron microscopy (SEM), atomic force microscopy (AFM), and contact angle (CA) measurements were carried out to explore the graphene layer transferability. Three factors, namely, the substrate roughness, its pore size, and its surface wetting (degree of hydrophobicity) are found to affect the conformality and coverage of the transferred graphene monolayer on the substrate surface. A good quality graphene transfer is achieved on the substrate with the following characteristics; being hydrophobic (CA > 90°), having small pore size, and low surface roughness, with a CA to RMS (root mean square) ratio higher than 2.7°/nm.

  14. Controlling droplet-based deposition uniformity of long silver nanowires by micrometer scale substrate patterning

    International Nuclear Information System (INIS)

    Basu, Nandita; Cross, Graham L W

    2015-01-01

    We report control of droplet-deposit uniformity of long silver nanowires suspended in solutions by microscopic influence of the liquid contact line. Substrates with microfabricated line patterns with a pitch far smaller than mean wire length lead to deposit thickness uniformity compared to unpatterned substrates. For high boiling-point solvents, two significant effects were observed: The substrate patterns suppressed coffee ring staining, and the wire deposits exhibited a common orientation lying perpendicular over top the lines. The latter result is completely distinct from previously reported substrate groove channeling effects. This work shows that microscopic influence of the droplet contact line geometry including the contact angle by altered substrate wetting allows significant and advantageous influence of deposition patterns of wire-like solutes as the drop dries. (paper)

  15. Structures of Trypanosoma brucei methionyl-tRNA synthetase with urea-based inhibitors provide guidance for drug design against sleeping sickness.

    Directory of Open Access Journals (Sweden)

    Cho Yeow Koh

    2014-04-01

    Full Text Available Methionyl-tRNA synthetase of Trypanosoma brucei (TbMetRS is an important target in the development of new antitrypanosomal drugs. The enzyme is essential, highly flexible and displaying a large degree of changes in protein domains and binding pockets in the presence of substrate, product and inhibitors. Targeting this protein will benefit from a profound understanding of how its structure adapts to ligand binding. A series of urea-based inhibitors (UBIs has been developed with IC50 values as low as 19 nM against the enzyme. The UBIs were shown to be orally available and permeable through the blood-brain barrier, and are therefore candidates for development of drugs for the treatment of late stage human African trypanosomiasis. Here, we expand the structural diversity of inhibitors from the previously reported collection and tested for their inhibitory effect on TbMetRS and on the growth of T. brucei cells. The binding modes and binding pockets of 14 UBIs are revealed by determination of their crystal structures in complex with TbMetRS at resolutions between 2.2 Å to 2.9 Å. The structures show binding of the UBIs through conformational selection, including occupancy of the enlarged methionine pocket and the auxiliary pocket. General principles underlying the affinity of UBIs for TbMetRS are derived from these structures, in particular the optimum way to fill the two binding pockets. The conserved auxiliary pocket might play a role in binding tRNA. In addition, a crystal structure of a ternary TbMetRS•inhibitor•AMPPCP complex indicates that the UBIs are not competing with ATP for binding, instead are interacting with ATP through hydrogen bond. This suggests a possibility that a general 'ATP-engaging' binding mode can be utilized for the design and development of inhibitors targeting tRNA synthetases of other disease-causing pathogen.

  16. 3D QSAR models built on structure-based alignments of Abl tyrosine kinase inhibitors.

    Science.gov (United States)

    Falchi, Federico; Manetti, Fabrizio; Carraro, Fabio; Naldini, Antonella; Maga, Giovanni; Crespan, Emmanuele; Schenone, Silvia; Bruno, Olga; Brullo, Chiara; Botta, Maurizio

    2009-06-01

    Quality QSAR: A combination of docking calculations and a statistical approach toward Abl inhibitors resulted in a 3D QSAR model, the analysis of which led to the identification of ligand portions important for affinity. New compounds designed on the basis of the model were found to have very good affinity for the target, providing further validation of the model itself.The X-ray crystallographic coordinates of the Abl tyrosine kinase domain in its active, inactive, and Src-like inactive conformations were used as targets to simulate the binding mode of a large series of pyrazolo[3,4-d]pyrimidines (known Abl inhibitors) by means of GOLD software. Receptor-based alignments provided by molecular docking calculations were submitted to a GRID-GOLPE protocol to generate 3D QSAR models. Analysis of the results showed that the models based on the inactive and Src-like inactive conformations had very poor statistical parameters, whereas the sole model based on the active conformation of Abl was characterized by significant internal and external predictive ability. Subsequent analysis of GOLPE PLS pseudo-coefficient contour plots of this model gave us a better understanding of the relationships between structure and affinity, providing suggestions for the next optimization process. On the basis of these results, new compounds were designed according to the hydrophobic and hydrogen bond donor and acceptor contours, and were found to have improved enzymatic and cellular activity with respect to parent compounds. Additional biological assays confirmed the important role of the selected compounds as inhibitors of cell proliferation in leukemia cells.

  17. Printing-based fabrication method using sacrificial paper substrates for flexible and wearable microfluidic devices

    International Nuclear Information System (INIS)

    Chung, Daehan; Gray, Bonnie L

    2017-01-01

    We present a simple, fast, and inexpensive new printing-based fabrication process for flexible and wearable microfluidic channels and devices. Microfluidic devices are fabricated on textiles (fabric) for applications in clothing-based wearable microfluidic sensors and systems. The wearable and flexible microfluidic devices are comprised of water-insoluable screen-printable plastisol polymer. Sheets of paper are used as sacrificial substrates for multiple layers of polymer on the fabric’s surface. Microfluidic devices can be made within a short time using simple processes and inexpensive equipment that includes a laser cutter and a thermal laminator. The fabrication process is characterized to demonstrate control of microfluidic channel thickness and width. Film thickness smaller than 100 micrometers and lateral dimensions smaller than 150 micrometers are demonstrated. A flexible microfluidic mixer is also developed on fabric and successfully tested on both flat and curved surfaces at volumetric flow rates ranging from 5.5–46 ml min −1 . (paper)

  18. Characterization and evaluation of whey protein-based biofilms as substrates for in vitro cell cultures.

    Science.gov (United States)

    Gilbert, Vanessa; Rouabhia, Mahmoud; Wang, Hongxum; Arnould, Anne-Lise; Remondetto, Gabriel; Subirade, Muriel

    2005-12-01

    Whey proteins-based biofilms were prepared using different plasticizers in order to obtain a biomaterial for the human keratinocytes and fibroblasts in vitro culture. The film properties were evaluated by Fourier Transform Infrared Spectroscopy (FTIR) technique and mechanical tests. A relationship was found between the decrease of intermolecular hydrogen bond strength and film mechanical behavior changes, expressed by a breaking stress and Young modulus values diminishing. These results allow stating that the film molecular configuration could induce dissimilarities in its mechanical properties. The films toxicity was assessed by evaluating the cutaneous cells adherence, growth, proliferation and structural stratification. Microscopic observation demonstrated that both keratinocytes and fibroblasts adhered to the biofilms. The trypan blue exclusion test showed that keratinocytes grew at a significantly high rate on all the biofilms. Structural analysis demonstrated that keratinocytes stratified when cultured on the whey protein-based biofilms and gave rise to multi-layered epidermal structures. The most organized epidermis was obtained with whey protein isolate/DEG biofilm. This structure had a well-organized basal layer under supra-basal and corneous layers. This study demonstrated that whey proteins, an inexpensive renewable resource which can be obtained readily, were non-toxic to cutaneous cells and thus they could be useful substrates for a variety of biomedical applications, including tissue engineering.

  19. Solid-support substrates for plant growth at a lunar base

    Science.gov (United States)

    Ming, D. W.; Galindo, C.; Henninger, D. L.

    1990-01-01

    Zeoponics is only in its developmental stages at the Johnson Space Center and is defined as the cultivation of plants in zeolite substrates that contain several essential plant growth cations on their exchange sites, and have minor amounts of mineral phases and/or anion-exchange resins that supply essential plant growth anions. Zeolites are hydrated aluminosilicates of alkali and alkaline earth cations with the ability to exchange most of their constituent exchange cations as well as hydrate/dehydrate without change to their structural framework. Because zeolites have extremely high cation exchange capabilities, they are very attractive media for plant growth. It is possible to partially or fully saturate plant-essential cations on zeolites. Zeoponic systems will probably have their greatest applications at planetary bases (e.g., lunar bases). Lunar raw materials will have to be located that are suited for the synthesis of zeolites and other exchange resings. Lunar 'soil' simulants have been or are being prepared for zeolite/smectite synthesis and 'soil' dissolution studies.

  20. Discovery and Optimization of Imidazopyridine-Based Inhibitors of Diacylglycerol Acyltransferase 2 (DGAT2).

    Science.gov (United States)

    Futatsugi, Kentaro; Kung, Daniel W; Orr, Suvi T M; Cabral, Shawn; Hepworth, David; Aspnes, Gary; Bader, Scott; Bian, Jianwei; Boehm, Markus; Carpino, Philip A; Coffey, Steven B; Dowling, Matthew S; Herr, Michael; Jiao, Wenhua; Lavergne, Sophie Y; Li, Qifang; Clark, Ronald W; Erion, Derek M; Kou, Kou; Lee, Kyuha; Pabst, Brandon A; Perez, Sylvie M; Purkal, Julie; Jorgensen, Csilla C; Goosen, Theunis C; Gosset, James R; Niosi, Mark; Pettersen, John C; Pfefferkorn, Jeffrey A; Ahn, Kay; Goodwin, Bryan

    2015-09-24

    The medicinal chemistry and preclinical biology of imidazopyridine-based inhibitors of diacylglycerol acyltransferase 2 (DGAT2) is described. A screening hit 1 with low lipophilic efficiency (LipE) was optimized through two key structural modifications: (1) identification of the pyrrolidine amide group for a significant LipE improvement, and (2) insertion of a sp(3)-hybridized carbon center in the core of the molecule for simultaneous improvement of N-glucuronidation metabolic liability and off-target pharmacology. The preclinical candidate 9 (PF-06424439) demonstrated excellent ADMET properties and decreased circulating and hepatic lipids when orally administered to dyslipidemic rodent models.

  1. The effects of addition of poly(vinyl) alcohol (PVA) as a green corrosion inhibitor to the phosphate conversion coating on the anticorrosion and adhesion properties of the epoxy coating on the steel substrate

    Energy Technology Data Exchange (ETDEWEB)

    Ramezanzadeh, B., E-mail: ramezanzadeh-bh@icrc.ac.ir; Vakili, H.; Amini, R.

    2015-02-01

    Highlights: • Room temperature zinc phosphate coating was applied on the surface of steel sample. • Poly(vinyl) alcohol was added to the phosphating bath as a green corrosion inhibitor. • The adhesion and anticorrosion properties of the epoxy coating were investigated. • PVA decreased the phosphate crystal size and porosity. • PVA enhanced the corrosion protection and adhesion properties of the epoxy coating. - Abstract: Steel substrates were chemically treated by room temperature zinc phosphate conversion coating. Poly(vinyl) alcohol (PVA) was added to the phosphate solution as a green corrosion inhibitor. Finally, the epoxy/polyamide coating was applied on the untreated and surface treated steel samples. The effects of PVA on the morphological properties of the phosphate coating were studied by scanning electron microscope (SEM), X-ray photoelectron spectroscopy (XPS) and contact angle measuring device. The adhesion properties of the epoxy coatings applied on the surface treated samples were investigated by pull-off and cathodic delamination tests. Also, the anticorrosion properties of the epoxy coatings were studied by electrochemical impedance spectroscopy (EIS). Results showed that addition of PVA to the phosphate coating increased the population density of the phosphate crystals and decreased the phosphate grain size. The contact angle of the steel surface treated by Zn-PVA was lower than Zn treated one. The corrosion resistance of the epoxy coating was considerably increased on the steel substrate treated by zinc phosphate conversion coating containing PVA. PVA also enhanced the adhesion properties of the epoxy coating to the steel surface and decreased the cathodic delamination significantly.

  2. Occurrence of urea-based soluble epoxide hydrolase inhibitors from the plants in the order Brassicales.

    Directory of Open Access Journals (Sweden)

    Seiya Kitamura

    Full Text Available Recently, dibenzylurea-based potent soluble epoxide hydrolase (sEH inhibitors were identified in Pentadiplandra brazzeana, a plant in the order Brassicales. In an effort to generalize the concept, we hypothesized that plants that produce benzyl glucosinolates and corresponding isothiocyanates also produce these dibenzylurea derivatives. Our overall aim here was to examine the occurrence of urea derivatives in Brassicales, hoping to find biologically active urea derivatives from plants. First, plants in the order Brassicales were analyzed for the presence of 1, 3-dibenzylurea (compound 1, showing that three additional plants in the order Brassicales produce the urea derivatives. Based on the hypothesis, three dibenzylurea derivatives with sEH inhibitory activity were isolated from maca (Lepidium meyenii roots. Topical application of one of the identified compounds (compound 3, human sEH IC50 = 222 nM effectively reduced pain in rat inflammatory pain model, and this compound was bioavailable after oral administration in mice. The biosynthetic pathway of these urea derivatives was investigated using papaya (Carica papaya seed as a model system. Finally, a small collection of plants from the Brassicales order was grown, collected, extracted and screened for sEH inhibitory activity. Results show that several plants of the Brassicales order could be potential sources of urea-based sEH inhibitors.

  3. A rhodium(III)-based inhibitor of autotaxin with antiproliferative activity.

    Science.gov (United States)

    Kang, Tian-Shu; Wang, Wanhe; Zhong, Hai-Jing; Liang, Jia-Xin; Ko, Chung-Nga; Lu, Jin-Jian; Chen, Xiu-Ping; Ma, Dik-Lung; Leung, Chung-Hang

    2017-02-01

    Cancer of the skin is by far the most common of all cancers. Melanoma accounts for only about 1% of skin cancers but causes a large majority of skin cancer deaths. Autotaxin (ATX), also known as ectonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2), regulates physiological and pathological functions of lysophosphatidic acid (LPA), and is thus an important therapeutic target. We synthesized ten metal-based complexes and a novel cyclometalated rhodium(III) complex 1 was identified as an ATX enzymatic inhibitor using multiple methods, including ATX enzymatic assay, thermal shift assay, western immunoblotting and so on. Protein thermal shift assays showed that 1 increased the melting temperature (T m ) of ATX by 3.5°C. 1 also reduced ATX-LPA mediated downstream survival signal pathway proteins such as ERK and AKT, and inhibited the activation of the transcription factor nuclear factor κB (NF-κB) and signal transducer and activator of transcription 3 (STAT3). 1 also exhibited strong anti-proliferative activity against A2058 melanoma cells (IC 50 =0.58μM). Structure-activity relationship indicated that both the rhodium(III) center and the auxiliary ligands of complex 1 are important for bioactivity. 1 represents a promising scaffold for the development of small-molecule ATX inhibitors for anti-tumor applications. To our knowledge, complex 1 is the first metal-based ATX inhibitor reported to date. Rhodium complexes will have the increased attention in therapeutic and bioanalytical applications. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Discovery of potent inhibitors of soluble epoxide hydrolase by combinatorial library design and structure-based virtual screening.

    Science.gov (United States)

    Xing, Li; McDonald, Joseph J; Kolodziej, Steve A; Kurumbail, Ravi G; Williams, Jennifer M; Warren, Chad J; O'Neal, Janet M; Skepner, Jill E; Roberds, Steven L

    2011-03-10

    Structure-based virtual screening was applied to design combinatorial libraries to discover novel and potent soluble epoxide hydrolase (sEH) inhibitors. X-ray crystal structures revealed unique interactions for a benzoxazole template in addition to the conserved hydrogen bonds with the catalytic machinery of sEH. By exploitation of the favorable binding elements, two iterations of library design based on amide coupling were employed, guided principally by the docking results of the enumerated virtual products. Biological screening of the libraries demonstrated as high as 90% hit rate, of which over two dozen compounds were single digit nanomolar sEH inhibitors by IC(50) determination. In total the library design and synthesis produced more than 300 submicromolar sEH inhibitors. In cellular systems consistent activities were demonstrated with biochemical measurements. The SAR understanding of the benzoxazole template provides valuable insights into discovery of novel sEH inhibitors as therapeutic agents.

  5. Formation of substrate-based gold nanocage chains through dealloying with nitric acid

    Directory of Open Access Journals (Sweden)

    Ziren Yan

    2015-06-01

    Full Text Available Metal nanocages have raised great interest because of their new properties and wide applications. Here, we report on the use of galvanic replacement reactions to synthesize substrate-supported Ag–Au nanocages from silver templates electrodeposited on transparent indium tin oxide (ITO film coated glass. The residual Ag in the composition was dealloyed with 10% nitric acid. It was found that chains of Au nanocages were formed on the substrate surface during dealloying. When the concentration of HNO3 increased to 20%, the structures of nanocages were damaged and formed crescent or semi-circular shapes. The transfer process on the substrate surface was discussed.

  6. Second Generation HTs Wire Based on RABiTS Substrates and MOD YBCO

    Energy Technology Data Exchange (ETDEWEB)

    Schoop, U. [American Superconductor Corporation, Westborough, MA; Rupich, Marty [American Superconductor Corporation, Westborough, MA; Thieme, C. L. H. [American Superconductor Corporation, Westborough, MA; Verebelyi, D. T. [American Superconductor Corporation, Westborough, MA; Zhang, W. [American Superconductor Corporation, Westborough, MA; Li, Xiaoping [American Superconductor Corporation, Westborough, MA; Kodenkandath, Thomas [American Superconductor Corporation, Westborough, MA; Nguyen, N. [American Superconductor Corporation, Westborough, MA; Siegal, E. E. [American Superconductor Corporation, Westborough, MA; Civale, L. [Los Alamos National Laboratory (LANL); Holesinger, T. G. [Los Alamos National Laboratory (LANL); Maiorov, B. [Los Alamos National Laboratory (LANL); Goyal, Amit [ORNL; Paranthaman, Mariappan Parans [ORNL

    2005-01-01

    The performance of Second Generation (2G) high temperature superconducting wire manufactured by continuous reel-to-reel processes is nearing the 300 A/cm-width (77 K, self field) performance threshold for commercial power cable applications. The 2G manufacturing approach under development at American Superconductor is based on the combination of the RABiTS substrate-buffer technology with metal organic deposition (MOD) of the YBCO layer. The capability of this process has been demonstrated in multiple 10 meter lengths with critical currents exceeding 250 A/cm-width with high uniformity and reproducibility. Critical currents of 380 A/cm-width have been achieved in short length samples prepared by the same basic process. The incorporation of nanoparticles ('nanodots') into the YBCO layer using the MOD process has resulted in a 2-fold improvement in the critical current at 65 K in a 3 T field. The research and development focus at ASMC is now directed toward the economical scale-up of the RABiTS/MOD process, optimization of the conductor properties for targeted applications and the use of 2G wire in initial demonstration applications.

  7. Surface modification of polymeric substrates by plasma-based ion implantation

    International Nuclear Information System (INIS)

    Okuji, S.; Sekiya, M.; Nakabayashi, M.; Endo, H.; Sakudo, N.; Nagai, K.

    2006-01-01

    Plasma-based ion implantation (PBII) as a tool for polymer modification is studied. Polymeric films have good performances for flexible use, such as food packaging or electronic devices. Compared with inorganic rigid materials, polymers generally have large permeability for gases and moisture, which causes packaged contents and devices to degrade. In order to add a barrier function, surface of polymeric films are modified by PBII. One of the advantageous features of this method over deposition is that the modified surface does not have peeling problem. Besides, micro-cracks due to mechanical stress in the modified layer can be decreased. From the standpoint of mass production, conventional ion implantation that needs low-pressure environment of less than 10 -3 Pa is not suitable for continuous large-area processing, while PBII works at rather higher pressure of several Pa. In terms of issues mentioned above, PBII is one of the most expected techniques for modification on flexible substrates. However, the mechanism how the barrier function appears by ion implantation is not well explained so far. In this study, various kinds of polymeric films, including polyethyleneterephthalate (PET), are modified by PBII and their barrier characteristics that depend on the ion dose are evaluated. In order to investigate correlations of the barrier function with implanted ions, modified surface is analyzed with X-ray photoelectron spectroscopy (XPS). It is assumed that the diffusion and sorption coefficients are changed by ion implantation, resulting in higher barrier function

  8. Novel low-temperature sintering ceramic substrate based on indialite/cordierite glass ceramics

    Science.gov (United States)

    Varghese, Jobin; Vahera, Timo; Ohsato, Hitoshi; Iwata, Makoto; Jantunen, Heli

    2017-10-01

    In this paper, a novel low-temperature sintering substrate for low temperature co-fired ceramic applications based on indialite/cordierite glass ceramics with Bi2O3 as a sintering aid showing low permittivity (εr) and ultralow dielectric loss (tan δ) is described. The fine powder of indialite was prepared by the crystallization of cordierite glass at 1000 °C/1 h. The optimized sintering temperature was 900 °C with 10 wt % Bi2O3 addition. The relative density achieved was 97%, and εr and tan δ were 6.10 and 0.0001 at 1 MHz, respectively. The composition also showed a moderately low temperature coefficient of relative permittivity of 118 ppm/°C at 1 MHz. The obtained linear coefficient of thermal expansion was 3.5 ppm/°C in the measured temperature range of 100 to 600 °C. The decreasing trend in dielectric loss, the low relative permittivity at 1 MHz, and the low thermal expansion of the newly developed composition make it an ideal choice for radio frequency applications.

  9. The effect of silver thickness on the enhancement of polymer based SERS substrates

    International Nuclear Information System (INIS)

    Schneidewind, H; Weber, K; Zeisberger, M; Hübner, U; Dellith, A; Cialla-May, D; Mattheis, R; Popp, J

    2014-01-01

    We investigated silver-covered polymer based nanogratings as substrates for surface-enhanced Raman spectroscopy (SERS), in particular with respect to the thickness of the plasmonically active silver film. In order to obtain accurate geometrical input data for the simulation process, we inspected cross sections of the gratings prepared by breaking at cryogenic temperature. We noticed a strong dependence of the simulation results on geometrical variations of the structures. Measurements revealed that an increasing silver film thickness on top of the nanogratings leads to a blue shift of the plasmonic resonance, as predicted by numerical simulations, as well as to an increased field enhancement for an excitation at 488 nm. We found a clear deviation of the experimental data compared to the simulated results for very thin silver films due to an island-like growth at a silver thickness below 20 nm. In order to investigate the SERS activity. we carried out measurements with crystal violet as a model analyte at an excitation wavelength of 488 nm. The SERS enhancement increases up to a silver thickness of about 30 nm, whereas it remains nearly constant for thicker silver films. (paper)

  10. Electrochemical Capacitors Based on Aligned Carbon Nanotubes Directly Synthesized on Tantalum Substrates

    International Nuclear Information System (INIS)

    Kim, Byung Woo; Chung, Hae Geun; Kim, Woong; Min, Byoung Koun; Kim, Hong Gon

    2010-01-01

    We demonstrate that vertically aligned carbon nanotubes can be synthesized directly on tantalum substrate via waterassisted chemical vapor deposition and evaluate their properties as electrochemical capacitors. The mean diameter of the carbon nanotubes was 7.1 ± 1.5 nm, and 70% of them had double walls. The intensity ratio of G-band to D-band in Raman spectra was as high as 5, indicating good quality of the carbon nanotubes. Owing to the alignment and low equivalent series resistance, the carbon nanotube based supercapacitors showed good rate performance. Rectangular shape of cyclic voltammogram was maintained even at the scan rate of > 1 V/s in 1 M sulfuric acid aqueous solution. Specific capacitance was well-retained (∼94%) even when the discharging current density dramatically increased up to 145 A/g. Consequently, specific power as high as 60 kW/kg was obtained from as-grown carbon nanotubes in aqueous solution. Maximum specific energy of ∼20 Wh/kg was obtained when carbon nanotubes were electrochemically oxidized and operated in organic solution. Demonstration of direct synthesis of carbon nanotubes on tantalum current collectors and their applications as supercapacitors could be an invaluable basis for fabrication of high performance carbon nanotube supercapacitors

  11. Surface modification of polymeric substrates by plasma-based ion implantation

    Science.gov (United States)

    Okuji, S.; Sekiya, M.; Nakabayashi, M.; Endo, H.; Sakudo, N.; Nagai, K.

    2006-01-01

    Plasma-based ion implantation (PBII) as a tool for polymer modification is studied. Polymeric films have good performances for flexible use, such as food packaging or electronic devices. Compared with inorganic rigid materials, polymers generally have large permeability for gases and moisture, which causes packaged contents and devices to degrade. In order to add a barrier function, surface of polymeric films are modified by PBII. One of the advantageous features of this method over deposition is that the modified surface does not have peeling problem. Besides, micro-cracks due to mechanical stress in the modified layer can be decreased. From the standpoint of mass production, conventional ion implantation that needs low-pressure environment of less than 10-3 Pa is not suitable for continuous large-area processing, while PBII works at rather higher pressure of several Pa. In terms of issues mentioned above, PBII is one of the most expected techniques for modification on flexible substrates. However, the mechanism how the barrier function appears by ion implantation is not well explained so far. In this study, various kinds of polymeric films, including polyethyleneterephthalate (PET), are modified by PBII and their barrier characteristics that depend on the ion dose are evaluated. In order to investigate correlations of the barrier function with implanted ions, modified surface is analyzed with X-ray photoelectron spectroscopy (XPS). It is assumed that the diffusion and sorption coefficients are changed by ion implantation, resulting in higher barrier function.

  12. RECOVERY OF ASPERGILLUS ENDO-GLUCANASE PRODUCED ON SOLID SUBSTRATE: A DOE BASED APPROACH

    Directory of Open Access Journals (Sweden)

    Sibabrata Mukherjee

    2014-10-01

    Full Text Available The endo-glucanase (E.C. 3.2.1.4 was produced by Aspergillus terreus adopting solid state fermentation (SSF using agro residues as main substrate. To recover the enzyme from the fermented mass, different extraction liquids were tried and 10% aqueous solution of glycerol was found to be superior. When the selected extractant was applied at different ratio to the fermented solid mass, maximum enzyme was recovered at 1:5 (w/v ratio. The other process parameters (time, temperature and mixing speed effects on the enzyme recovery were subsequently studied by response surface methodology (RSM. Box-Bhenken Design of experiment (BBDOE was exploited for the analysis of interactive effects of the independent variables. The optimization was done following the numerical approach focusing reduction in utility cost without compromising the endo-glucanse activity. Based on the predicted solution the validation experiments were carried out and finally 32 IU/g of endo-glucanase was recovered at room temperature, at a mixing speed of 100 rpm in 2.65 h which was very close to the predicted response. The optimization evidenced more than two times betterment in enzyme recovery than the un-optimized state. The model developed was found to be robust for process analysis. Repetitive extraction had revealed that maximum endo-glucanase recovery was required of two cycles of extraction at optimized conditions.

  13. Electrochemical study of galvanic corrosion inhibitors in water-based and ethylene glycol-based heat transfer circuits

    International Nuclear Information System (INIS)

    Netter, Pierre

    1981-01-01

    This research thesis reports the search for and the efficiency assessment of mixes of inhibitors for coolant circuits of motor cars. After a discussion of the general properties of water-alcohol solvents (chemical properties, acid-base equilibriums) and of parameters affecting corrosion in coolant circuits, the author proposes an overview of the main inhibitors which are used to protect these circuits against corrosion, and discusses their action mechanism and efficiency. The different methods used to study the corrosion of these circuits are described, and the advantages and drawbacks of test methods are commented. The second part proposes a synthesis of the different corrosion electromechanical mechanisms which may occur with respect to the used metallic materials and to possible galvanic couplings. The next part describes the experimental installations. The last part focuses on the different protections obtained with the different used inhibitor class in terms of results obtained by gravimetric tests and visual examination of samples, current-voltage curves in hydrodynamic regime, and galvanic corrosion tests performed in laboratory or in situ in motor cars [fr

  14. Design, synthesis, in vitro Evaluation and docking studies on dihydropyrimidine-based urease inhibitors.

    Science.gov (United States)

    Iftikhar, Fatima; Ali, Yousaf; Ahmad Kiani, Farooq; Fahad Hassan, Syed; Fatima, Tabeer; Khan, Ajmal; Niaz, Basit; Hassan, Abbas; Latif Ansari, Farzana; Rashid, Umer

    2017-10-01

    In our previous report, we have identified 3,4-dihydropyrimidine scaffold as promising class of urease inhibitor in a structure based virtual screen (SBVS) experiment. In present study, we attempted to optimize the scaffold by varying C-5 substituent. The elongation of the C-5 chain was achieved by the reaction of C-5 ester with hydrazine leading to C-5 carbohydrazides which were further used as building blocks for the synthesis of fifteen new compounds having diverse moieties. A significantly higher in vitro urease inhibitory activity with IC 50 values in submicromolar range was observed for semithiocarbazide derivatives (4a-c, 0.58-0.79µM) and isatin Schiff base derivative 5a (0.23µM). Docking analysis suggests that the synthesized compounds were anchored well in the catalytic site and extending to the entrance of binding pocket and thus restrict the mobility of the flap by interacting with its key amino acid residues. The overall results of urease inhibition have shown that these compounds can be further optimized and developed as lead urease inhibitors. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Synthesis of ceria based superhydrophobic coating on Ni20Cr substrate via cathodic electrodeposition.

    Science.gov (United States)

    Pedraza, F; Mahadik, S A; Bouchaud, B

    2015-12-21

    In this work, superhydrophobic cerium oxide coating surface (111) with dual scale texture on Ni20Cr substrate is obtained by combination of electropolishing the substrate and subsequent cathodic electrodeposition and long-term UVH surface relaxation. To form hierarchical structures of CeO2 is controllable by varying the substrate roughness, and electropolishing period. The results indicated that at the optimal condition, the surface of the cerium oxide coating showed a superhydrophobicity with a great water contact angle (151.0 ± 1.4°) with Gecko state. An interface model for electropolishing of substrate surface in cerium nitrate medium is proposed. We expect that this facile process can be readily and widely adopted for the design of superhydrophobic coating on engineering materials.

  16. Seven-Segment Organic Polymer Based Light-Emitting Devices on Plastic Substrates

    National Research Council Canada - National Science Library

    Kanicki, Jerzy

    2001-01-01

    .../A; and maximum luminous efficiency = 0.1 lm/W. The extrapolated lifetime of unpackaged OPLEDs on flexible plastic substrate of about 1160 min for initial brightness of 100 cd/m(squared) has been obtained.

  17. Comparative of fibroblast and osteoblast cells adhesion on surface modified nanofibrous substrates based on polycaprolactone

    OpenAIRE

    Sharifi, Fereshteh; Irani, Shiva; Zandi, Mojgan; Soleimani, Masoud; Atyabi, Seyed Mohammad

    2016-01-01

    One of the determinant factors for successful bioengineering is to achieve appropriate nano-topography and three-dimensional substrate. In this research, polycaprolactone (PCL) nano-fibrous mat with different roughness modified with O2 plasma was fabricated via electrospinning. The purpose of this study was to evaluate the effect of plasma modification along with surface nano-topography of mats on the quality of human fibroblast (HDFs) and osteoblast cells (OSTs)-substrate interaction. Surfac...

  18. Highly sensitive, reproducible and stable SERS substrate based on reduced graphene oxide/silver nanoparticles coated weighing paper

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Guina, E-mail: xiaoguina@shnu.edu.cn; Li, Yunxiang; Shi, Wangzhou; Shen, Leo; Chen, Qi; Huang, Lei, E-mail: leihuang@shnu.edu.cn

    2017-05-15

    Highlights: • We developed a paper-based SERS substrate by gravure and inkjet printing methods. • The S-RGO/AgNPs comoposite structure had higher SERS activity than the pure AgNPs. • The Raman enhancement factor of S-RGO/AgNPs substrate was calculated to be 10{sup 9}. • The paper-based substrate exhibited good reproducibility and long-term stability. - Abstract: Paper-based surface-enhanced Raman scattering (SERS) substrates receive a great deal of attention due to low cost and high flexibility. Herein, we developed an efficient SERS substrate by gravure printing of sulfonated reduced graphene-oxide (S-RGO) thin film and inkjet printing of silver nanoparticles (AgNPs) on weighing paper successively. Malachite green (MG) and rhodamine 6G (R6G) were chosen as probe molecules to evaluate the enhanced performance of the fabricated SERS-active substrates. It was found that the S-RGO/AgNPs composite structure possessed higher enhancement ability than the pure AgNPs. The Raman enhancement factor of S-RGO/AgNPs was calculated to be as large as 10{sup 9}. The minimum detection limit for MG and R6G was down to 10{sup −7} M with good linear responses (R{sup 2} = 0.9996, 0.9983) range from 10{sup −4} M to 10{sup −7} M. In addition, the S-RGO/AgNPs exhibited good uniformity with a relative standard deviation (RSD) of 7.90% measured by 572 points, excellent reproducibility with RSD smaller than 3.36%, and long-term stability with RSD less than 7.19%.

  19. Human pregnane X receptor is activated by dibenzazepine carbamate-based inhibitors of constitutive androstane receptor.

    Science.gov (United States)

    Jeske, Judith; Windshügel, Björn; Thasler, Wolfgang E; Schwab, Matthias; Burk, Oliver

    2017-06-01

    Unintentional activation of xenosensing nuclear receptors pregnane X receptor (PXR) and/or constitutive androstane receptor (CAR) by clinical drug use is known to produce severe side effects in patients, which may be overcome by co-administering antagonists. However, especially antagonizing CAR is hampered by the lack of specific inhibitors, which do not activate PXR. Recently, compounds based on a dibenzazepine carbamate scaffold were identified as potent CAR inhibitors. However, their potential to activate PXR was not thoroughly investigated, even if the lead compound was named "CAR inhibitor not PXR activator 1" (CINPA1). Thus, we performed a comprehensive analysis of the interaction of CINPA1 and four analogs with PXR. Cellular assays were used to investigate intra- and intermolecular interactions and transactivation activity of PXR as a function of the compounds. Modulation of PXR target gene expression was analyzed in primary human hepatocytes. Ligand binding to PXR was investigated by molecular docking and limited proteolytic digestion. We show here that CINPA1 induced the assembly of the PXR ligand-binding domain, released co-repressors from and recruited co-activators to the receptor. CINPA1 and its analogs induced the PXR-dependent activation of a CYP3A4 reporter gene and CINPA1 induced the expression of endogenous cytochrome P450 genes in primary hepatocytes, while not consistently inhibiting CAR-mediated induction. Molecular docking revealed favorable binding of CINPA1 and analogs to the PXR ligand-binding pocket, which was confirmed in vitro. Altogether, our data provide consistent evidence that compounds with a dibenzazepine carbamate scaffold, such as CINPA1 and its four analogs, bind to and activate PXR.

  20. Novel environment friendly corrosion inhibitor pigments based on naturally occurring clay minerals

    Energy Technology Data Exchange (ETDEWEB)

    Bohm, S.; McMurray, H.N.; Worsley, D.A. [University of Wales, Swansea (United Kingdom). Dept. of Materials Engineering; Powell, S.M. [University of Wales, Swansea (United Kingdom). Engineering Doktorate Centre

    2001-12-01

    Novel, ceramic, corrosion inhibitor pigments consisting of cerium (III) and calcium (II) cation exchanged bentonites have been shown to provide effective cut-edge corrosion resistance in organic coated galvanised steel. The bentonite pigments were prepared from a naturally occurring (Wyoming) bentonite with a cation-exchange-capacity of 0.7 milli-equivalents per gram. Cation exchange was carried out by repeated washing with aqueous solutions of cerium (III) chloride and calcium (II) chloride to produce bentonites containing 31500 ppm exchangeable cerium (III) and 13500 ppm exchangeable calcium (II) respectively. The resulting bentonite pigments were dispersed in a polyester-resin based primer paint system to give a pigment volume concentration of 19%. For comparison, two similar primer systems were prepared containing a commercial calcium (II) exchanged silica pigment Shieldex: 60 000 ppm calcium (II) and a strontium chromate dispersion, both with a 19% pigment volume concentration. All three primer systems were applied (5 {mu}m) to the zinc surface of galvanised 0.7 mm gauge sheet steel and overcoated with an architectural polyester topcoat (18 {mu}m). The performance of the inhibitor pigments was compared by measuring the rate of corrosion-driven organic coating delamination from the cut edge of samples during 1000 h of salt-spray testing. The calcium (II) bentonite pigment exhibited an anti-delamination performance similar to that of strontium chromate but superior to that of Shieldex. However, the cerium (III) bentonite pigment was superior in performance to both strontium chromate and Shieldex. Thus, the bentonite pigments represent promising, environmentally friendly, ion-exchange corrosion inhibitors which exhibit good anti-delamination performance by comparison with current commercial systems. (orig.)

  1. Evaluation and Optimization of Paper-Based SERS Substrate for Potential Label-Free Raman Analysis of Seminal Plasma

    Directory of Open Access Journals (Sweden)

    Zufang Huang

    2017-01-01

    Full Text Available Characterization and optimization of paper SERS substrate were performed in detail, in which morphologies and distribution of silver nanoparticles (AgNPs on the paper substrate pretreated with different concentrations of NaCl and the subsequent soaking with colloidal AgNPs for different period of time were evaluated. Our results show that both NaCl concentration and soaking time with AgNPs have a significant influence on SERS enhancement, showing that an optimal EF of 2.27 × 107 was achieved when the paper substrate was treated with 20 mM NaCl and one-hour soak with AgNPs. Moreover, seminal plasma (SP was specifically selected to evaluate the performance of paper-based SERS substrate for potential clinical detection and diagnosis. The optimization of the paper SERS substrate demonstrates potential applications in reliable on-site detection of SP and clinical diagnosis of fertility-related diseases as well.

  2. Structure-based prediction of free energy changes of binding of PTP1B inhibitors

    Science.gov (United States)

    Wang, Jing; Ling Chan, Shek; Ramnarayan, Kal

    2003-08-01

    The goals were (1) to understand the driving forces in the binding of small molecule inhibitors to the active site of PTP1B and (2) to develop a molecular mechanics-based empirical free energy function for compound potency prediction. A set of compounds with known activities was docked onto the active site. The related energy components and molecular surface areas were calculated. The bridging water molecules were identified and their contributions were considered. Linear relationships were explored between the above terms and the binding free energies of compounds derived based on experimental inhibition constants. We found that minimally three terms are required to give rise to a good correlation (0.86) with predictive power in five-group cross-validation test (q2 = 0.70). The dominant terms are the electrostatic energy and non-electrostatic energy stemming from the intra- and intermolecular interactions of solutes and from those of bridging water molecules in complexes.

  3. Anti-trypanosomal activity of non-peptidic nitrile-based cysteine protease inhibitors.

    Science.gov (United States)

    Burtoloso, Antonio C B; de Albuquerque, Sérgio; Furber, Mark; Gomes, Juliana C; Gonçalez, Cristiana; Kenny, Peter W; Leitão, Andrei; Montanari, Carlos A; Quilles, José Carlos; Ribeiro, Jean F R; Rocha, Josmar R

    2017-02-01

    The cysteine protease cruzipain is considered to be a validated target for therapeutic intervention in the treatment of Chagas disease. Anti-trypanosomal activity against the CL Brener strain of T. cruzi was observed in the 0.1 μM to 1 μM range for three nitrile-based cysteine protease inhibitors based on two scaffolds known to be associated with cathepsin K inhibition. The two compounds showing the greatest potency against the trypanosome were characterized by EC50 values (0.12 μM and 0.25 μM) that were an order of magnitude lower than the corresponding Ki values measured against cruzain, a recombinant form of cruzipain, in an enzyme inhibition assay. This implies that the anti-trypanosomal activity of these two compounds may not be explained only by the inhibition of the cruzain enzyme, thereby triggering a putative polypharmacological profile towards cysteine proteases.

  4. Effect of Schiff's Bases as Corrosion Inhibitors on Mild Steel in Sulphuric Acid

    Directory of Open Access Journals (Sweden)

    R. K. Upadhyay

    2007-01-01

    Full Text Available Mass loss and thermometric methods have been used to study the corrosion inhibitory effect of synthesised Schiff's bases viz. N-(furfurilidine – 4- methoxy aniline (SB1, N-(furfurilidine – 4- methylaniline (SB2, N-(salicylidine – 4- methoxy aniline (SB3, N-(cinnamalidine – 4 –methoxy aniline (SB4 and N-(cinnamalidine - 2-methylaniline (SB5 on mild steel in sulphuric acid solutions. Results show that both methods have good agreement with each other and inhibition efficiency depends upon the concentration of inhibitor as well as that of acid. Maximum inhibition efficiency is shown at highest concentration of Schiff's bases at the highest strength of acid.

  5. Development of a Biochar-Plant-Extract-Based Nitrification Inhibitor and Its Application in Field Conditions

    Directory of Open Access Journals (Sweden)

    Jhónatan Reyes-Escobar

    2015-10-01

    Full Text Available The global use of nitrogen (N fertilizer has increased 10-fold in the last fifty years, resulting in increased N losses via nitrate leaching to groundwater bodies or from gaseous emissions to the atmosphere. One of the biggest problems farmers face in agricultural production systems is the loss of N. In this context, novel biological nitrification inhibitors (BNI using biochar (BC as a renewable matrix to increase N use efficiency, by reducing nitrification rates, have been evaluated. The chemical and morphological characteristics of BC were analyzed and BC-BNI complexes were formulated using plant extracts from pine (Pinus radiata, eucalyptus (Eucalyptus globulus and peumo (Cryptocarya alba. In field experiments, fertilizer and treatments, based on crude plant extracts and BC-BNI complexes, were applied and the effect on nitrification was periodically monitored, and at the laboratory level, a phytotoxicity assay was performed. The biochar-peumo (BCPe complex showed the highest nitrification inhibition (66% on day 60 after application compared with the crude plant extract, suggesting that BCPe complex protects the BNI against biotic or abiotic factors, and therefore BC-BNI complexes could increase the persistence of biological nitrification inhibitors. None of the biochar complexes had toxic effect on radish plants.

  6. Wetting behaviour of lead-free Sn-based alloys on Cu and Ni substrates

    International Nuclear Information System (INIS)

    Amore, S.; Ricci, E.; Borzone, G.; Novakovic, R.

    2008-01-01

    The present work was carried out in the framework of the study of new lead-free solder alloys for technical applications in electronic devices. In the focus of this characterisation the wetting behaviour of several Sn-rich alloys belonging to the In-Sn, Au-Sn and Cu-Sn systems has been studied by measuring the contact angle variations on Cu and Ni substrates as a function of time and temperature. The interface between the alloy and the substrate has been analysed by the use of optical microscopy and scanning electron microscopy combined with energy-dispersive X-ray spectrometry in order to study the reaction between the alloy and the solid substrate and the possible formation of different compounds at the interface. A remarkable effect of the two different substrates on the behaviour of the contact angle as a function of temperature and on the morphology of the interface between the liquid solder and the solid substrate was observed for the In-Sn and Cu-Sn, while the Au-Sn system shows a very similar wetting behaviour on Cu and Ni

  7. Design and simulation of a novel GaN based resonant tunneling high electron mobility transistor on a silicon substrate

    International Nuclear Information System (INIS)

    Chowdhury, Subhra; Biswas, Dhrubes; Chattaraj, Swarnabha

    2015-01-01

    For the first time, we have introduced a novel GaN based resonant tunneling high electron mobility transistor (RTHEMT) on a silicon substrate. A monolithically integrated GaN based inverted high electron mobility transistor (HEMT) and a resonant tunneling diode (RTD) are designed and simulated using the ATLAS simulator and MATLAB in this study. The 10% Al composition in the barrier layer of the GaN based RTD structure provides a peak-to-valley current ratio of 2.66 which controls the GaN based HEMT performance. Thus the results indicate an improvement in the current–voltage characteristics of the RTHEMT by controlling the gate voltage in this structure. The introduction of silicon as a substrate is a unique step taken by us for this type of RTHEMT structure. (paper)

  8. NMR-based Structural Analysis of Threonylcarbamoyl-AMP Synthase and Its Substrate Interactions.

    Science.gov (United States)

    Harris, Kimberly A; Bobay, Benjamin G; Sarachan, Kathryn L; Sims, Alexis F; Bilbille, Yann; Deutsch, Christopher; Iwata-Reuyl, Dirk; Agris, Paul F

    2015-08-14

    The hypermodified nucleoside N(6)-threonylcarbamoyladenosine (t(6)A37) is present in many distinct tRNA species and has been found in organisms in all domains of life. This post-transcriptional modification enhances translation fidelity by stabilizing the anticodon/codon interaction in the ribosomal decoding site. The biosynthetic pathway of t(6)A37 is complex and not well understood. In bacteria, the following four proteins have been discovered to be both required and sufficient for t(6)A37 modification: TsaC, TsaD, TsaB, and TsaE. Of these, TsaC and TsaD are members of universally conserved protein families. Although TsaC has been shown to catalyze the formation of L-threonylcarbamoyl-AMP, a key intermediate in the biosynthesis of t(6)A37, the details of the enzymatic mechanism remain unsolved. Therefore, the solution structure of Escherichia coli TsaC was characterized by NMR to further study the interactions with ATP and L-threonine, both substrates of TsaC in the biosynthesis of L-threonylcarbamoyl-AMP. Several conserved amino acids were identified that create a hydrophobic binding pocket for the adenine of ATP. Additionally, two residues were found to interact with L-threonine. Both binding sites are located in a deep cavity at the center of the protein. Models derived from the NMR data and molecular modeling reveal several sites with considerable conformational flexibility in TsaC that may be important for L-threonine recognition, ATP activation, and/or protein/protein interactions. These observations further the understanding of the enzymatic reaction catalyzed by TsaC, a threonylcarbamoyl-AMP synthase, and provide structure-based insight into the mechanism of t(6)A37 biosynthesis. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Periodic array-based substrates for surface-enhanced infrared spectroscopy

    Science.gov (United States)

    Mayerhöfer, Thomas G.; Popp, Jürgen

    2018-01-01

    At the beginning of the 1980s, the first reports of surface-enhanced infrared spectroscopy (SEIRS) surfaced. Probably due to signal-enhancement factors of only 101 to 103, which are modest compared to those of surface-enhanced Raman spectroscopy (SERS), SEIRS did not reach the same significance up to date. However, taking the compared to Raman scattering much larger cross-sections of infrared absorptions and the enhancement factors together, SEIRS reaches about the same sensitivity for molecular species on a surface in terms of the cross-sections as SERS and, due to the complementary nature of both techniques, can valuably augment information gained by SERS. For the first 20 years since its discovery, SEIRS relied completely on metal island films, fabricated by either vapor or electrochemical deposition. The resulting films showed a strong variance concerning their structure, which was essentially random. Therefore, the increase in the corresponding signal-enhancement factors of these structures stagnated in the last years. In the very same years, however, the development of periodic array-based substrates helped SEIRS to gather momentum. This development was supported by technological progress concerning electromagnetic field solvers, which help to understand plasmonic properties and allow targeted design. In addition, the strong progress concerning modern fabrication methods allowed to implement these designs into practice. The aim of this contribution is to critically review the development of these engineered surfaces for SEIRS, to compare the different approaches with regard to their performance where possible, and report further gain of knowledge around and in relation to these structures.

  10. Development of antibody-based c-Met inhibitors for targeted cancer therapy

    Directory of Open Access Journals (Sweden)

    Lee D

    2015-02-01

    Full Text Available Dongheon Lee, Eun-Sil Sung, Jin-Hyung Ahn, Sungwon An, Jiwon Huh, Weon-Kyoo You Hanwha Chemical R&D Center, Biologics Business Unit, Daejeon, Republic of Korea Abstract: Signaling pathways mediated by receptor tyrosine kinases (RTKs and their ligands play important roles in the development and progression of human cancers, which makes RTK-mediated signaling pathways promising therapeutic targets in the treatment of cancer. Compared with small-molecule compounds, antibody-based therapeutics can more specifically recognize and bind to ligands and RTKs. Several antibody inhibitors of RTK-mediated signaling pathways, such as human epidermal growth factor receptor 2, vascular endothelial growth factor, epidermal growth factor receptor or vascular endothelial growth factor receptor 2, have been developed and are widely used to treat cancer patients. However, since the therapeutic options are still limited in terms of therapeutic efficacy and types of cancers that can be treated, efforts are being made to identify and evaluate novel RTK-mediated signaling pathways as targets for more efficacious cancer treatment. The hepatocyte growth factor/c-Met signaling pathway has come into the spotlight as a promising target for development of potent cancer therapeutic agents. Multiple antibody-based therapeutics targeting hepatocyte growth factor or c-Met are currently in preclinical or clinical development. This review focuses on the development of inhibitors of the hepatocyte growth factor/c-Met signaling pathway for cancer treatment, including critical issues in clinical development and future perspectives for antibody-based therapeutics. Keywords: hepatocyte growth factor, ligands, receptor tyrosine kinase, signaling pathway, therapeutic agent

  11. Structure-Based Design and Optimization of Multitarget-Directed 2H-Chromen-2-one Derivatives as Potent Inhibitors of Monoamine Oxidase B and Cholinesterases.

    Science.gov (United States)

    Farina, Roberta; Pisani, Leonardo; Catto, Marco; Nicolotti, Orazio; Gadaleta, Domenico; Denora, Nunzio; Soto-Otero, Ramon; Mendez-Alvarez, Estefania; Passos, Carolina S; Muncipinto, Giovanni; Altomare, Cosimo D; Nurisso, Alessandra; Carrupt, Pierre-Alain; Carotti, Angelo

    2015-07-23

    The multifactorial nature of Alzheimer's disease calls for the development of multitarget agents addressing key pathogenic processes. To this end, by following a docking-assisted hybridization strategy, a number of aminocoumarins were designed, prepared, and tested as monoamine oxidases (MAOs) and acetyl- and butyryl-cholinesterase (AChE and BChE) inhibitors. Highly flexible N-benzyl-N-alkyloxy coumarins 2-12 showed good inhibitory activities at MAO-B, AChE, and BChE but low selectivity. More rigid inhibitors, bearing meta- and para-xylyl linkers, displayed good inhibitory activities and high MAO-B selectivity. Compounds 21, 24, 37, and 39, the last two featuring an improved hydrophilic/lipophilic balance, exhibited excellent activity profiles with nanomolar inhibitory potency toward hMAO-B, high hMAO-B over hMAO-A selectivity and submicromolar potency at hAChE. Cell-based assays of BBB permeation, neurotoxicity, and neuroprotection supported the potential of compound 37 as a BBB-permeant neuroprotective agent against H2O2-induced oxidative stress with poor interaction as P-gp substrate and very low cytotoxicity.

  12. Discovery of novel inhibitors of Mycobacterium tuberculosis MurG: homology modelling, structure based pharmacophore, molecular docking, and molecular dynamics simulations.

    Science.gov (United States)

    Saxena, Shalini; Abdullah, Maaged; Sriram, Dharmarajan; Guruprasad, Lalitha

    2017-10-17

    MurG (Rv2153c) is a key player in the biosynthesis of the peptidoglycan layer in Mycobacterium tuberculosis (Mtb). This work is an attempt to highlight the structural and functional relationship of Mtb MurG, the three-dimensional (3D) structure of protein was constructed by homology modelling using Discovery Studio 3.5 software. The quality and consistency of generated model was assessed by PROCHECK, ProSA and ERRAT. Later, the model was optimized by molecular dynamics (MD) simulations and the optimized model complex with substrate Uridine-diphosphate-N-acetylglucosamine (UD1) facilitated us to employ structure-based virtual screening approach to obtain new hits from Asinex database using energy-optimized pharmacophore modelling (e-pharmacophore). The pharmacophore model was validated using enrichment calculations, and finally, validated model was employed for high-throughput virtual screening and molecular docking to identify novel Mtb MurG inhibitors. This study led to the identification of 10 potential compounds with good fitness, docking score, which make important interactions with the protein active site. The 25 ns MD simulations of three potential lead compounds with protein confirmed that the structure was stable and make several non-bonding interactions with amino acids, such as Leu290, Met310 and Asn167. Hence, we concluded that the identified compounds may act as new leads for the design of Mtb MurG inhibitors.

  13. Fabrication of Si-based planar type patch clamp biosensor using silicon on insulator substrate

    International Nuclear Information System (INIS)

    Zhang, Z.L.; Asano, T.; Uno, H.; Tero, R.; Suzui, M.; Nakao, S.; Kaito, T.; Shibasaki, K.; Tominaga, M.; Utsumi, Y.; Gao, Y.L.; Urisu, T.

    2008-01-01

    The aim of this paper is to fabricate the planar type patch clamp ion-channel biosensor, which is suitable for the high throughput screening, using silicon-on-insulator (SOI) substrate. The micropore with 1.2 μm diameter is formed through the top Si layer and the SiO 2 box layer of the SOI substrate by focused ion beam (FIB). Then the substrate is assembled into the microfluidic circuit. The human embryonic kidney 293 (HEK-293) cell transfected with transient receptor potential vanilloid type 1 (TRPV1) is positioned on the micropore and the whole-cell configuration is formed by the suction. Capsaicin is added to the extracellular solution as a ligand molecule, and the channel current showing the desensitization unique to TRPV1 is measured successfully

  14. The next generation CdTe technology- Substrate foil based solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Ferekides, Chris [Univ. of South Florida, Tampa, FL (United States)

    2017-03-22

    The main objective of this project was the development of one of the most promising Photovoltaic (PV) materials CdTe into a versatile, cost effective, and high throughput technology, by demonstrating substrate devices on foil substrates using high throughput fabrication conditions. The typical CdTe cell is of the superstrate configuration where the solar cell is fabricated on a glass superstrate by the sequential deposition of a TCO, n-type heterojunction partner, p-CdTe absorber, and back contact. Large glass modules are heavy and present significant challenges during manufacturing (uniform heating, etc.). If a substrate CdTe cell could be developed (the main goal of this project) a roll-to-toll high throughput technology could be developed.

  15. Fabrication of Si-based planar type patch clamp biosensor using silicon on insulator substrate

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Z.L.; Asano, T. [Graduate University for Advanced Studies, Myodaiji, Okazaki, 444-8585 (Japan); Uno, H. [Institute for Molecular Science, Myodaiji, Okazaki, 444-8585 (Japan); Tero, R. [Graduate University for Advanced Studies, Myodaiji, Okazaki, 444-8585 (Japan); Institute for Molecular Science, Myodaiji, Okazaki, 444-8585 (Japan); Suzui, M.; Nakao, S. [Institute for Molecular Science, Myodaiji, Okazaki, 444-8585 (Japan); Kaito, T. [SII NanoTechnology Inc., 36-1, Takenoshita, Oyama-cho, Sunto-gun, Shizuoka, 410-1393 (Japan); Shibasaki, K.; Tominaga, M. [Okazaki Institute for Integrative Bioscience, 5-1, Higashiyama, Myodaiji, Okazaki, 444-8787 (Japan); Utsumi, Y. [Laboratory of Advanced Science and Technology for Industry, University of Hyogo, 3-1-2, Koto, Kamigori, Ako-gun, Hyogo, 678-1205 (Japan); Gao, Y.L. [Department of Physics and Astronomy, Rochester University, Rochester, New York 14627 (United States); Urisu, T. [Graduate University for Advanced Studies, Myodaiji, Okazaki, 444-8585 (Japan); Institute for Molecular Science, Myodaiji, Okazaki, 444-8585 (Japan)], E-mail: urisu@ims.ac.jp

    2008-03-03

    The aim of this paper is to fabricate the planar type patch clamp ion-channel biosensor, which is suitable for the high throughput screening, using silicon-on-insulator (SOI) substrate. The micropore with 1.2 {mu}m diameter is formed through the top Si layer and the SiO{sub 2} box layer of the SOI substrate by focused ion beam (FIB). Then the substrate is assembled into the microfluidic circuit. The human embryonic kidney 293 (HEK-293) cell transfected with transient receptor potential vanilloid type 1 (TRPV1) is positioned on the micropore and the whole-cell configuration is formed by the suction. Capsaicin is added to the extracellular solution as a ligand molecule, and the channel current showing the desensitization unique to TRPV1 is measured successfully.

  16. Sawdust and Bark-Based Substrates for Soilless Strawberry Production: Irrigation and Electrical Conductivity Management.

    Science.gov (United States)

    Depardieu, Claire; Prémont, Valérie; Boily, Carole; Caron, Jean

    2016-01-01

    The objective of this work was to optimize a soilless growing system for producing bare-root strawberry transplants in three organic substrates. Three trials were conducted in the Quebec City area to determine the productivity potential of a peat-sawdust mixture (PS25) and an aged bark (AB) material compared to conventional coconut fiber (CF) substrate. A first experiment was carried out to define appropriate irrigation set points for each substrate that allowed optimal plant growth and fruit yields. For all substrates, wetter conditions (irrigation started at -1.0 kPa for CF; -1.5 kPa for AB and PS25, relative to -1.5 kPa for CF; -2.5 kPa for AB and PS25) enhanced plant growth and fruit production. The second trial was carried out to test the productivity potential for commercial production of the three substrates using high-tunnels. After the addition of an initial fertilizer application to PS25, we successfully established bare-root plants that gave similar fruit yields than those in CF and AB. The productivity potential of PS25 and AB were further confirmed during a third trial under greenhouse conditions. The critical factor for plant establishment in PS25 was attributed to consistent N, P and S immobilization by microorganisms, as well as the retention of other elements (Mg2+, K+) in the growth media. Taken together, our results showed that PS25 and AB are promising alternative substrates to coconut coir dust for strawberry cultivation. This paper also provides a useful guide for strawberry cultivation in Quebec, and suggests future research that might be conducted to optimize soilless systems for cold-climate strawberry production in Northern America.

  17. Sawdust and Bark-Based Substrates for Soilless Strawberry Production: Irrigation and Electrical Conductivity Management.

    Directory of Open Access Journals (Sweden)

    Claire Depardieu

    Full Text Available The objective of this work was to optimize a soilless growing system for producing bare-root strawberry transplants in three organic substrates. Three trials were conducted in the Quebec City area to determine the productivity potential of a peat-sawdust mixture (PS25 and an aged bark (AB material compared to conventional coconut fiber (CF substrate. A first experiment was carried out to define appropriate irrigation set points for each substrate that allowed optimal plant growth and fruit yields. For all substrates, wetter conditions (irrigation started at -1.0 kPa for CF; -1.5 kPa for AB and PS25, relative to -1.5 kPa for CF; -2.5 kPa for AB and PS25 enhanced plant growth and fruit production. The second trial was carried out to test the productivity potential for commercial production of the three substrates using high-tunnels. After the addition of an initial fertilizer application to PS25, we successfully established bare-root plants that gave similar fruit yields than those in CF and AB. The productivity potential of PS25 and AB were further confirmed during a third trial under greenhouse conditions. The critical factor for plant establishment in PS25 was attributed to consistent N, P and S immobilization by microorganisms, as well as the retention of other elements (Mg2+, K+ in the growth media. Taken together, our results showed that PS25 and AB are promising alternative substrates to coconut coir dust for strawberry cultivation. This paper also provides a useful guide for strawberry cultivation in Quebec, and suggests future research that might be conducted to optimize soilless systems for cold-climate strawberry production in Northern America.

  18. A carbon nanotube-based transparent conductive substrate for flexible ZnO dye-sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Du, Juan; Bittner, Florian [Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Callinstr. 3a, 30167 Hannover (Germany); Hecht, David S.; Ladous, Corinne [Unidym, 1244 Reamwood Avenue, Sunnyvale, CA (United States); Ellinger, Jan [Tesa SE, Quickbornstr. 24, 20253 Hamburg (Germany); Oekermann, Torsten, E-mail: torstensan@t-online.de [Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Callinstr. 3a, 30167 Hannover (Germany); Wark, Michael, E-mail: michael.wark@techem.ruhr-uni-bochum.de [Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Callinstr. 3a, 30167 Hannover (Germany); Laboratory of Industrial Chemistry, Ruhr University Bochum, Universitaetsstr. 150, 44801 Bochum (Germany)

    2013-03-01

    A transparent carbon nanotube (CNT)-coated polyethylenterephthalat film was used as conducting substrate for the photoanode of a flexible ZnO-based dye-sensitized solar cell (DSSC). The porous ZnO films were fabricated by an electrochemical deposition method at low temperature. Electrochemical impedance spectroscopy revealed that the CNT/ZnO interface adds to the overall impedance of the cell, leading to a higher series resistance compared to DSSCs based on substrates employing a transparent conducting oxide. Nevertheless, an overall conversion efficiency of 2.5% was obtained with porous ZnO films electrodeposited on the CNT substrate for 60 min. Thicker films led to an increased loss by recombination, which could not be compensated by faster electron transport due to the decrease of the light intensity inside the ZnO film with increasing distance from the back contact. - Highlights: ► ZnO was electrochemically deposited on carbon nanotube (CNT) coated polymer. ► Highly porous ZnO was obtained at temperatures not exceeding 70 °C. ► The porous ZnO was tested as photoanode in dye-sensitized solar cells. ► Conversion efficiency of 2.5% was found on the high resistance CNT substrates. ► Barriers formed at the CNT–ZnO interface are determined by impedance spectroscopy.

  19. A carbon nanotube-based transparent conductive substrate for flexible ZnO dye-sensitized solar cells

    International Nuclear Information System (INIS)

    Du, Juan; Bittner, Florian; Hecht, David S.; Ladous, Corinne; Ellinger, Jan; Oekermann, Torsten; Wark, Michael

    2013-01-01

    A transparent carbon nanotube (CNT)-coated polyethylenterephthalat film was used as conducting substrate for the photoanode of a flexible ZnO-based dye-sensitized solar cell (DSSC). The porous ZnO films were fabricated by an electrochemical deposition method at low temperature. Electrochemical impedance spectroscopy revealed that the CNT/ZnO interface adds to the overall impedance of the cell, leading to a higher series resistance compared to DSSCs based on substrates employing a transparent conducting oxide. Nevertheless, an overall conversion efficiency of 2.5% was obtained with porous ZnO films electrodeposited on the CNT substrate for 60 min. Thicker films led to an increased loss by recombination, which could not be compensated by faster electron transport due to the decrease of the light intensity inside the ZnO film with increasing distance from the back contact. - Highlights: ► ZnO was electrochemically deposited on carbon nanotube (CNT) coated polymer. ► Highly porous ZnO was obtained at temperatures not exceeding 70 °C. ► The porous ZnO was tested as photoanode in dye-sensitized solar cells. ► Conversion efficiency of 2.5% was found on the high resistance CNT substrates. ► Barriers formed at the CNT–ZnO interface are determined by impedance spectroscopy

  20. Stepwise O-Atom Transfer in Heme-Based Tryptophan Dioxygenase: Role of Substrate Ammonium in Epoxide Ring Opening.

    Science.gov (United States)

    Shin, Inchul; Ambler, Brett R; Wherritt, Daniel; Griffith, Wendell P; Maldonado, Amanda C; Altman, Ryan A; Liu, Aimin

    2018-03-28

    Heme-based tryptophan dioxygenases are established immunosuppressive metalloproteins with significant biomedical interest. Here, we synthesized two mechanistic probes to specifically test if the α-amino group of the substrate directly participates in a critical step of the O atom transfer during catalysis in human tryptophan 2,3-dioxygenase (TDO). Substitution of the nitrogen atom of the substrate to a carbon (probe 1) or oxygen (probe 2) slowed the catalytic step following the first O atom transfer such that transferring the second O atom becomes less likely to occur, although the dioxygenated products were observed with both probes. A monooxygenated product was also produced from probe 2 in a significant quantity. Analysis of this new product by HPLC coupled UV-vis spectroscopy, high-resolution mass spectrometry, 1 H NMR, 13 C NMR, HSQC, HMBC, and infrared (IR) spectroscopies concluded that this monooxygenated product is a furoindoline compound derived from an unstable epoxyindole intermediate. These results prove that small molecules can manipulate the stepwise O atom transfer reaction of TDO and provide a showcase for a tunable mechanism by synthetic compounds. The product analysis results corroborate the presence of a substrate-based epoxyindole intermediate during catalysis and provide the first substantial experimental evidence for the involvement of the substrate α-amino group in the epoxide ring-opening step during catalysis. This combined synthetic, biochemical, and biophysical study establishes the catalytic role of the α-amino group of the substrate during the O atom transfer reactions and thus represents a substantial advance to the mechanistic comprehension of the heme-based tryptophan dioxygenases.

  1. Imidazopyridine-Based Fatty Acid Synthase Inhibitors That Show Anti-HCV Activity and in Vivo Target Modulation.

    Science.gov (United States)

    Oslob, Johan D; Johnson, Russell J; Cai, Haiying; Feng, Shirley Q; Hu, Lily; Kosaka, Yuko; Lai, Julie; Sivaraja, Mohanram; Tep, Samnang; Yang, Hanbiao; Zaharia, Cristiana A; Evanchik, Marc J; McDowell, Robert S

    2013-01-10

    Potent imidazopyridine-based inhibitors of fatty acid synthase (FASN) are described. The compounds are shown to have antiviral (HCV replicon) activities that track with their biochemical activities. The most potent analogue (compound 19) also inhibits rat FASN and inhibits de novo palmitate synthesis in vitro (cell-based) as well as in vivo.

  2. Fragment-Based Discovery of Pyrimido[1,2-b]indazole PDE10A Inhibitors.

    Science.gov (United States)

    Chino, Ayaka; Seo, Ryushi; Amano, Yasushi; Namatame, Ichiji; Hamaguchi, Wataru; Honbou, Kazuya; Mihara, Takuma; Yamazaki, Mayako; Tomishima, Masaki; Masuda, Naoyuki

    2018-01-01

    In this study, we report the identification of potent pyrimidoindazoles as phosphodiesterase10A (PDE10A) inhibitors by using the method of fragment-based drug discovery (FBDD). The pyrazolopyridine derivative 2 was found to be a fragment hit compound which could occupy a part of the binding site of PDE10A enzyme by using the method of the X-ray co-crystal structure analysis. On the basis of the crystal structure of compound 2 and PDE10A protein, a number of compounds were synthesized and evaluated, by means of structure-activity relationship (SAR) studies, which culminated in the discovery of a novel pyrimidoindazole derivative 13 having good physicochemical properties.

  3. Evaluation of adamantane hydroxamates as botulinum neurotoxin inhibitors: synthesis, crystallography, modeling, kinetic and cellular based studies.

    Science.gov (United States)

    Šilhár, Peter; Silvaggi, Nicholas R; Pellett, Sabine; Čapková, Kateřina; Johnson, Eric A; Allen, Karen N; Janda, Kim D

    2013-03-01

    Botulinum neurotoxins (BoNTs) are the most lethal biotoxins known to mankind and are responsible for the neuroparalytic disease botulism. Current treatments for botulinum poisoning are all protein based and thus have a limited window of treatment opportunity. Inhibition of the BoNT light chain protease (LC) has emerged as a therapeutic strategy for the treatment of botulism as it may provide an effective post exposure remedy. Using a combination of crystallographic and modeling studies a series of hydroxamates derived from 1-adamantylacetohydroxamic acid (3a) were prepared. From this group of compounds, an improved potency of about 17-fold was observed for two derivatives. Detailed mechanistic studies on these structures revealed a competitive inhibition model, with a K(i)=27 nM, which makes these compounds some of the most potent small molecule, non-peptidic BoNT/A LC inhibitors reported to date. Copyright © 2012 Elsevier Ltd. All rights reserved.

  4. Structure-activity relationships of benzimidazole-based glutaminyl cyclase inhibitors featuring a heteroaryl scaffold.

    Science.gov (United States)

    Ramsbeck, Daniel; Buchholz, Mirko; Koch, Birgit; Böhme, Livia; Hoffmann, Torsten; Demuth, Hans-Ulrich; Heiser, Ulrich

    2013-09-12

    Glutaminyl cyclase (hQC) has emerged as a new potential target for the treatment of Alzheimer's disease (AD). The inhibition of hQC prevents of the formation of the Aβ3(pE)-40,42 species which were shown to be of elevated neurotoxicity and are likely to act as a seeding core, leading to an accelerated formation of Aβ-oligomers and fibrils. This work presents a new class of inhibitors of hQC, resulting from a pharmacophore-based screen. Hit molecules were identified, containing benzimidazole as the metal binding group connected to 1,3,4-oxadiazole as the central scaffold. The subsequent optimization resulted in benzimidazolyl-1,3,4-thiadiazoles and -1,2,3-triazoles with an inhibitory potency in the nanomolar range. Further investigation into the potential binding mode of the new compound classes combined molecular docking and site directed mutagenesis studies.

  5. Investigation into adamantane-based M2 inhibitors with FB-QSAR.

    Science.gov (United States)

    Wei, Hang; Wang, Cheng-Hua; Du, Qi-Shi; Meng, Jianzong; Chou, Kuo-Chen

    2009-07-01

    Because of their high resistance rate to the existing drugs, influenza A viruses have become a threat to human beings. It is known that the replication of influenza A viruses needs a pH-gated proton channel, the so-called M2 channel. Therefore, to develop effective drugs against influenza A, the most logic strategy is to inhibit the M2 channel. Recently, the atomic structure of the M2 channel was determined by NMR spectroscopy (Schnell, J.R. and Chou, J.J., Nature, 2008, 451, 591-595). The high-resolution NMR structure has provided a solid basis for structure-based drug design approaches. In this study, a benchmark dataset has been constructed that contains 34 newly-developed adamantane-based M2 inhibitors and covers considerable structural diversities and wide range of bioactivities. Based on these compounds, an in-depth analysis was performed with the newly developed fragment-based quantitative structure-activity relationship (FB-QSAR) algorithm. The results thus obtained provide useful insights for dealing with the drug-resistant problem and designing effective adamantane-based antiflu drugs.

  6. Development of Bio-Based Paint by using Methyl Esters from Palm Oil for Corrosion Inhibitor

    International Nuclear Information System (INIS)

    Mohibah Musa; Miradatul Najwa Muhd Rodhi; Najmiddin Yaakob; Ku Halim Ku Hamid; Juferi Idris

    2013-01-01

    Paint is used as a means of protection to prevent surfaces from being corroded over time. This research is focused on the development of a Bio-based paint made from palm oil methyl ester (POME) which originated from crude palm oil (CPO). New formulation paint has been developed to protect the pipeline from corrosion thus reducing the cost of the operation. Bio-based paint is made up of four components which are solvent, binder, additives, and pigment. The solvent in the bio-based paint is POME. The additives used are wetting and dispersing agent. The pigment used in the bio-based paint is TiO 2 . The formulation was developed by using a constant amount of additives and binder but varying the amount of POME at 10 ml, 15 ml, 20 ml, 25 ml and 30 ml with addition of water. The Standard Testing Methods for measuring the corrosion rate (ASTM G5-94(2011)) was carried out for each sample. In conclusion, it is proven that in the making of bio-based paint formulation for better corrosion inhibitor; the best amount of binder, additives and de-foam that should be used is 20 ml, 10 ml and 10 ml, respectively. (author)

  7. Discovery of novel selenium derivatives as Pin1 inhibitors by high-throughput screening

    International Nuclear Information System (INIS)

    Subedi, Amit; Shimizu, Takeshi; Ryo, Akihide; Sanada, Emiko; Watanabe, Nobumoto; Osada, Hiroyuki

    2016-01-01

    Peptidyl prolyl cis/trans isomerization by Pin1 regulates various oncogenic signals during cancer progression, and its inhibition through multiple approaches has established Pin1 as a therapeutic target. However, lack of simplified screening systems has limited the discovery of potent Pin1 inhibitors. We utilized phosphorylation-dependent binding of Pin1 to its specific substrate to develop a screening system for Pin1 inhibitors. Using this system, we screened a chemical library, and identified a novel selenium derivative as Pin1 inhibitor. Based on structure-activity guided chemical synthesis, we developed more potent Pin1 inhibitors that inhibited cancer cell proliferation. -- Highlights: •Novel screening for Pin1 inhibitors based on Pin1 binding is developed. •A novel selenium compound is discovered as Pin1 inhibitor. •Activity guided chemical synthesis of selenium derivatives resulted potent Pin1 inhibitors.

  8. Novel approach of fragment-based lead discovery applied to renin inhibitors.

    Science.gov (United States)

    Tawada, Michiko; Suzuki, Shinkichi; Imaeda, Yasuhiro; Oki, Hideyuki; Snell, Gyorgy; Behnke, Craig A; Kondo, Mitsuyo; Tarui, Naoki; Tanaka, Toshimasa; Kuroita, Takanobu; Tomimoto, Masaki

    2016-11-15

    A novel approach was conducted for fragment-based lead discovery and applied to renin inhibitors. The biochemical screening of a fragment library against renin provided the hit fragment which showed a characteristic interaction pattern with the target protein. The hit fragment bound only to the S1, S3, and S3 SP (S3 subpocket) sites without any interactions with the catalytic aspartate residues (Asp32 and Asp215 (pepsin numbering)). Prior to making chemical modifications to the hit fragment, we first identified its essential binding sites by utilizing the hit fragment's substructures. Second, we created a new and smaller scaffold, which better occupied the identified essential S3 and S3 SP sites, by utilizing library synthesis with high-throughput chemistry. We then revisited the S1 site and efficiently explored a good building block attaching to the scaffold with library synthesis. In the library syntheses, the binding modes of each pivotal compound were determined and confirmed by X-ray crystallography and the library was strategically designed by structure-based computational approach not only to obtain a more active compound but also to obtain informative Structure Activity Relationship (SAR). As a result, we obtained a lead compound offering synthetic accessibility as well as the improved in vitro ADMET profiles. The fragments and compounds possessing a characteristic interaction pattern provided new structural insights into renin's active site and the potential to create a new generation of renin inhibitors. In addition, we demonstrated our FBDD strategy integrating highly sensitive biochemical assay, X-ray crystallography, and high-throughput synthesis and in silico library design aimed at fragment morphing at the initial stage was effective to elucidate a pocket profile and a promising lead compound. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Positioning SGLT2 Inhibitors/Incretin-Based Therapies in the Treatment Algorithm.

    Science.gov (United States)

    Wilding, John P H; Rajeev, Surya Panicker; DeFronzo, Ralph A

    2016-08-01

    Sodium-glucose cotransporter 2 inhibitors (SGLT2i) are the most recent addition to the therapeutic options available for the treatment of type 2 diabetes and became available after the introduction of incretin-based therapies, dipeptidyl peptidase 4 inhibitors and glucagon-like peptide 1 receptor agonists (GLP-1 RAs). These agents have potential advantages with regard to their weight loss-promoting effect, low risk of hypoglycemia, reduction in blood pressure, and reduction in cardiovascular events in high-risk patients (with empagliflozin). Apart from these clinically important outcomes, they may also correct core defects present in type 2 diabetes (i.e., improvement in β-cell function and insulin sensitivity). They do, however, have some adverse effects, notably, nausea with GLP-1 RAs and genital tract infections and potential for volume depletion with SGLT2i. Whether incretin-based therapies are associated with an increased risk of pancreatitis is unclear. Most recently, diabetic ketoacidosis has been reported with SGLT2i. Therefore, a key clinical question in relation to guidelines is whether these clinical advantages, in the context of the adverse effect profile, outweigh the additional cost compared with older, more established therapies. This article reviews the therapeutic rationale for the use of these newer drugs for diabetes treatment, considers their place in current guidelines, and discusses how this may change as new data emerge about their long-term efficacy and safety from ongoing outcome trials. © 2016 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

  10. Template-based preparation of free-standing semiconducting polymeric nanorod arrays on conductive substrates.

    Science.gov (United States)

    Haberkorn, Niko; Weber, Stefan A L; Berger, Rüdiger; Theato, Patrick

    2010-06-01

    We describe the synthesis and characterization of a cross-linkable siloxane-derivatized tetraphenylbenzidine (DTMS-TPD), which was used for the fabrication of semiconducting highly ordered nanorod arrays on conductive indium tin oxide or Pt-coated substrates. The stepwise process allow fabricating of macroscopic areas of well-ordered free-standing nanorod arrays, which feature a high resistance against organic solvents, semiconducting properties and a good adhesion to the substrate. Thin films of the TPD derivate with good hole-conducting properties could be prepared by cross-linking and covalently attaching to hydroxylated substrates utilizing an initiator-free thermal curing at 160 degrees C. The nanorod arrays composed of cross-linked DTMS-TPD were fabricated by an anodic aluminum oxide (AAO) template approach. Furthermore, the nanorod arrays were investigated by a recently introduced method allowing to probe local conductivity on fragile structures. It revealed that more than 98% of the nanorods exhibit electrical conductance and consequently feature a good electrical contact to the substrate. The prepared nanorod arrays have the potential to find application in the fabrication of multilayered device architectures for building well-ordered bulk-heterojunction solar cells.

  11. A comparative study of graphene and graphite-based field effect transistor on flexible substrate

    Science.gov (United States)

    Bhatt, Kapil; Rani, Cheenu; Vaid, Monika; Kapoor, Ankit; Kumar, Pramod; Kumar, Sandeep; Shriwastawa, Shilpi; Sharma, Sandeep; Singh, Randhir; Tripathi, C. C.

    2018-06-01

    In the present era, there has been a great demand of cost-effective, biodegradable, flexible and wearable electronics which may open the gate to many applications like flexible displays, RFID tags, health monitoring devices, etc. Due to the versatile nature of plastic substrates, they have been extensively used in packaging, printing, etc. However, the fabrication of electronic devices requires specially prepared substrates with high quality surfaces, chemical compositions and solutions to the related fabrication issues along with its non-biodegradable nature. Therefore, in this report, a cost-effective, biodegradable cellulose paper as an alternative dielectric substrate material for the fabrication of flexible field effect transistor (FET) is presented. The graphite and liquid phase exfoliated graphene have been used as the material for the realisation of source, drain and channel on cellulose paper substrate for its comparative analysis. The mobility of fabricated FETs was calculated to be 83 cm2/V s (holes) and 33 cm2/V s (electrons) for graphite FET and 100 cm2/V s (holes) and 52 cm2/V s (electrons) for graphene FET, respectively. The output characteristic of the device demonstrates the linear behaviour and a comprehensive increase in conductance as a function of gate voltages. The fabricated FETs may be used for strain sensing, health care monitoring devices, human motion detection, etc.

  12. SOLVENT-BASED TO WATERBASED ADHESIVE-COATED SUBSTRATE RETROFIT - VOLUME I: COMPARATIVE ANALYSIS

    Science.gov (United States)

    This volume represents the analysis of case study facilities' experience with waterbased adhesive use and retrofit requirements. (NOTE: The coated and laminated substrate manufacturing industry was selected as part of NRMRL'S support of the 33/50 Program because of its significan...

  13. Development of Silicon-substrate Based Fabry-Perot Etalons for far-IR Astrophysics

    Science.gov (United States)

    Stacey, Gordon

    We propose to design, construct and test silicon-substrate-based (SSB) mirrors necessary for high performance Fabry-Perot interferometers (FPIs) to be used in the 25-40 um mid-IR band. These mirrors will be fabricated from silicon wafers that are anti-reflection coated (ARC) by micromachining an artificial dielectric meta-material on one side, and depositing optimized gold-metalized patterns on the other. Two mirrors with the metalized surfaces facing one-another form the Fabry-Perot cavity, also known as the FPI etalon. The exterior surfaces of the silicon mirrors are anti-reflection coated for both good transmission in the science band, and to prevent unwanted parasitic FPI cavities from forming between the four surfaces (one anti-reflection coated, one metalized for each mirror) of the FPI etalon. The mirrors will be tested within a Miniature Cryogenic Scanning Fabry-Perot (MCSF) that we have designed through support of a previous NASA grant (NNX09AB95G). This design is based on our long experience in constructing and using scanning FPI in the mid-IR to submm range, and fits within test-beds we have on hand that are suitable for both warm and cold tests. The key technologies are the ARC and tuned mirrors that are enabled by silicon nano-machining techniques. The creation of these SSB mirrors promises greatly improved performance over previous versions of mid-IR to submm-band FPIs that are based on mirrors made from free-standing metal mesh stretched over support rings. Performance is improved both structurally and in terms of sensitivity, and is measured as the product of the cavity finesse times transmission. Our electromagnetic modeling suggests that SSB mirrors will improve this product by a factor of 2 over the best free standing mesh etalons available. This translates into a factor of sqrt(2) improvement in sensitivity per etalon, or a full factor of 2 when used in a tandem (dual etalon) FPI spectrometer. The SSB improvements are due to both the stiff (~ 0

  14. Structure based protein engineering of Bacillus stearothermophilus {alpha}-amylase: toward a new substrate specificity

    Energy Technology Data Exchange (ETDEWEB)

    Rasera, Ana Claudia [Sao Paulo Univ., SP (Brazil). Inst. de Ciencias Biomedicas; Iulek, Jorge [Universidade Estadual de Ponta Grossa, PR (Brazil). Inst. de Quimica; Delboni, Luis Fernando; Barbosa, Valma Martins Barbosa [Parana Univ., Curitiba, PR (Brazil). Dept. de Bioquimica

    1997-12-31

    Full text. Structural similarity is observed in all members of {alpha}-amylase family but different products are generated during hydrolysis of starch due to different affinities for intermediate dextrins. In order to understand the structural determinants for this property and to introduce different specificity to {alpha}-amylase of Bacillus stearothermophilus we intend to solve the three dimensional structure by X-ray crystallography of the native protein by using synchrotron radiation at Brazilian National Synchrotron Light Laboratory (LNLS). Protein was over expressed in E. coli, purified and crystallization experiments were carried out by using sparse matrix Crystal Screen and Crystal Screen II from Hampton Research (Laguna Hills, CA, USA). Several condition have produced crystals with some defined characteristic: MDP seems to be important to the crystallization: the preferential pH is around 7.5 with organic buffer (HEPES); organic solvent as 2-propanol seems to be also important for the crystallization. On those condition crystals appeared as cluster of needles or small crystals with high number of nucleation. New conditions are being prepared to improve the site and quality of crystals. Data collection of native of Bacillus stearothermophilus {alpha}-amylase will e done at Protein Crystallography Station at LNLS. Crystal structure of mutated {alpha}-amylase bu site direct mutagenesis of residues suggested by the native crystal structure will be obtained. Co-crystallization of Bacillus stearothermophilus {alpha}-amylase and oligosaccharide will be carried out to identify residues involved in the binding site to plan new mutation. In another series of mutation the putative binding site residues, once identified, will be mutated to residues observed in TAKA amylase to confer different specificity to {alpha}-amylase. Based on the available TAKA amylase structure, in the primary sequence homology and in the three dimensional model of Bacillus stearothermophilus

  15. Structure based protein engineering of Bacillus stearothermophilus α-amylase: toward a new substrate specificity

    International Nuclear Information System (INIS)

    Rasera, Ana Claudia; Iulek, Jorge; Delboni, Luis Fernando; Barbosa, Valma Martins Barbosa

    1997-01-01

    Full text. Structural similarity is observed in all members of α-amylase family but different products are generated during hydrolysis of starch due to different affinities for intermediate dextrins. In order to understand the structural determinants for this property and to introduce different specificity to α-amylase of Bacillus stearothermophilus we intend to solve the three dimensional structure by X-ray crystallography of the native protein by using synchrotron radiation at Brazilian National Synchrotron Light Laboratory (LNLS). Protein was over expressed in E. coli, purified and crystallization experiments were carried out by using sparse matrix Crystal Screen and Crystal Screen II from Hampton Research (Laguna Hills, CA, USA). Several condition have produced crystals with some defined characteristic: MDP seems to be important to the crystallization: the preferential pH is around 7.5 with organic buffer (HEPES); organic solvent as 2-propanol seems to be also important for the crystallization. On those condition crystals appeared as cluster of needles or small crystals with high number of nucleation. New conditions are being prepared to improve the site and quality of crystals. Data collection of native of Bacillus stearothermophilus α-amylase will e done at Protein Crystallography Station at LNLS. Crystal structure of mutated α-amylase bu site direct mutagenesis of residues suggested by the native crystal structure will be obtained. Co-crystallization of Bacillus stearothermophilus α-amylase and oligosaccharide will be carried out to identify residues involved in the binding site to plan new mutation. In another series of mutation the putative binding site residues, once identified, will be mutated to residues observed in TAKA amylase to confer different specificity to α-amylase. Based on the available TAKA amylase structure, in the primary sequence homology and in the three dimensional model of Bacillus stearothermophilus α-amylase (using Bacillus

  16. Exploring the water-binding pocket of the type II dehydroquinase enzyme in the structure-based design of inhibitors.

    Science.gov (United States)

    Blanco, Beatriz; Sedes, Antía; Peón, Antonio; Otero, José M; van Raaij, Mark J; Thompson, Paul; Hawkins, Alastair R; González-Bello, Concepción

    2014-04-24

    Structural and computational studies to explore the WAT1 binding pocket in the structure-based design of inhibitors against the type II dehydroquinase (DHQ2) enzyme are reported. The crystal structures of DHQ2 from M. tuberculosis in complex with four of the reported compounds are described. The electrostatic interaction observed between the guanidinium group of the essential arginine and the carboxylate group of one of the inhibitors in the reported crystal structures supports the recently suggested role of this arginine as the residue that triggers the release of the product from the active site. The results of the structural and molecular dynamics simulation studies revealed that the inhibitory potency is favored by promoting interactions with WAT1 and the residues located within this pocket and, more importantly, by avoiding situations where the ligands occupy the WAT1 binding pocket. The new insights can be used to advantage in the structure-based design of inhibitors.

  17. Comparison of cell-based assays for the identification and evaluation of competitive CXCR4 inhibitors.

    Directory of Open Access Journals (Sweden)

    Anneleen Van Hout

    Full Text Available The chemokine receptor CXCR4 is activated by its unique chemokine ligand CXCL12 and regulates many physiological and developmental processes such as hematopoietic cell trafficking. CXCR4 is also one of the main co-receptors for human immunodeficiency virus (HIV entry. Dysfunction of the CXCL12/CXCR4 axis contributes to several human pathologies, including cancer and inflammatory diseases. Consequently, inhibition of CXCR4 activation is recognized as an attractive target for therapeutic intervention. In this regard, numerous agents modifying CXCR4 activity have been evaluated in in vitro experimental studies and pre-clinical models. Here, we evaluated a CXCL12 competition binding assay for its potential as a valuable initial screen for functional and competitive CXCR4 inhibitors. In total, 11 structurally diverse compounds were included in a side-by-side comparison of in vitro CXCR4 cell-based assays, such as CXCL12 competition binding, CXCL12-induced calcium signaling, CXCR4 internalization, CXCL12-guided cell migration and CXCR4-specific HIV-1 replication experiments. Our data indicated that agents that inhibit CXCL12 binding, i.e. the anti-CXCR4 peptide analogs T22, T140 and TC14012 and the small molecule antagonists AMD3100, AMD3465, AMD11070 and IT1t showed inhibitory activity with consistent relative potencies in all further applied CXCR4-related assays. Accordingly, agents exerting no or very weak receptor binding (i.e., CTCE-9908, WZ811, Me6TREN and gambogic acid showed no or very poor anti-CXCR4 inhibitory activity. Thus, CXCL12 competition binding studies were proven to be highly valuable as an initial screening assay and indicative for the pharmacological and functional profile of competitive CXCR4 antagonists, which will help the design of new potent CXCR4 inhibitors.

  18. Novel Cholinesterase Inhibitors Based on O-Aromatic N,N-Disubstituted Carbamates and Thiocarbamates

    Directory of Open Access Journals (Sweden)

    Martin Krátký

    2016-02-01

    Full Text Available Based on the presence of carbamoyl moiety, twenty salicylanilide N,N-disubstituted (thiocarbamates were investigated using Ellman’s method for their ability to inhibit acetylcholinesterase (AChE and butyrylcholinesterase (BChE. O-Aromatic (thiocarbamates exhibited weak to moderate inhibition of both cholinesterases with IC50 values within the range of 1.60 to 311.0 µM. IC50 values for BChE were mostly lower than those obtained for AChE; four derivatives showed distinct selectivity for BChE. All of the (thiocarbamates produced a stronger inhibition of AChE than rivastigmine, and five of them inhibited BChE more effectively than both established drugs rivastigmine and galantamine. In general, 5-chloro-2-hydroxy-N-[4-(trifluoromethyl-phenyl]benzamide, 2-hydroxy-N-phenylbenzamide as well as N-methyl-N-phenyl carbamate derivatives led to the more potent inhibition. O-{4-Chloro-2-[(4-chlorophenylcarbamoyl]phenyl} dimethylcarbamothioate was identified as the most effective AChE inhibitor (IC50 = 38.98 µM, while 2-(phenylcarbamoylphenyl diphenylcarbamate produced the lowest IC50 value for BChE (1.60 µM. Results from molecular docking studies suggest that carbamate compounds, especially N,N-diphenyl substituted representatives with considerable portion of aromatic moieties may work as non-covalent inhibitors displaying many interactions at peripheral anionic sites of both enzymes. Mild cytotoxicity for HepG2 cells and consequent satisfactory calculated selectivity indexes qualify several derivatives for further optimization.

  19. Discovery of Highly Selective and Nanomolar Carbamate-Based Butyrylcholinesterase Inhibitors by Rational Investigation into Their Inhibition Mode.

    Science.gov (United States)

    Sawatzky, Edgar; Wehle, Sarah; Kling, Beata; Wendrich, Jan; Bringmann, Gerhard; Sotriffer, Christoph A; Heilmann, Jörg; Decker, Michael

    2016-03-10

    Butyrylcholinesterase (BChE) is a promising target for the treatment of later stage cognitive decline in Alzheimer's disease. A set of pseudo-irreversible BChE inhibitors with high selectivity over hAChE was synthesized based on carbamates attached to tetrahydroquinazoline scaffolds with the 2-thiophenyl compound 2p as the most potent inhibitor of eqBChE (KC = 14.3 nM) and also of hBChE (KC = 19.7 nM). The inhibitors transfer the carbamate moiety onto the active site under release of the phenolic tetrahydroquinazoline scaffolds that themselves act as neuroprotectants. By combination of kinetic data with molecular docking studies, a plausible binding model was probed describing how the tetrahydroquinazoline scaffold guides the carbamate into a close position to the active site. The model explains the influence of the carrier scaffold onto the affinity of an inhibitor just before carbamate transfer. This strategy can be used to utilize the binding mode of other carbamate-based inhibitors.

  20. Characterization of nickel-based C276 alloy coatings by Plasma Transferred Arc (PTA) on different steel substrates

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, L.S.; Graf, K.; Scheid, A., E-mail: scheid@ufpr.br [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil)

    2014-07-01

    Nickel-based coatings by plasma transferred arc (PTA) for protection of components are widely applied to withstand operations under corrosion in different media. This paper characterized Nickel-based C276 alloy coatings obtained by Plasma Transferred Arc (PTA) on two different substrates, AISI 316L and API 5L X70 steels, correlating their features to hardness. Coatings were deposited utilizing three different intensity current levels, 120, 150 and 180 A and were characterized by optical, Laser confocal and scanning electron microscopy and X-ray diffraction. Vickers hardness profiles on transversal section were carried out. Produced coatings exhibited a microstructure of austenite (FCC) dendrites with interdendritic regions with carbides. Dilution levels from 4,9 to 41,5 % leaded to hardness ranging from 225 to 283 HV{sub 0,5}, showing coatings dependence on intensity current level and substrate. (author)

  1. Characterization of nickel-based C276 alloy coatings by Plasma Transferred Arc (PTA) on different steel substrates

    International Nuclear Information System (INIS)

    Ferreira, L.S.; Graf, K.; Scheid, A.

    2014-01-01

    Nickel-based coatings by plasma transferred arc (PTA) for protection of components are widely applied to withstand operations under corrosion in different media. This paper characterized Nickel-based C276 alloy coatings obtained by Plasma Transferred Arc (PTA) on two different substrates, AISI 316L and API 5L X70 steels, correlating their features to hardness. Coatings were deposited utilizing three different intensity current levels, 120, 150 and 180 A and were characterized by optical, Laser confocal and scanning electron microscopy and X-ray diffraction. Vickers hardness profiles on transversal section were carried out. Produced coatings exhibited a microstructure of austenite (FCC) dendrites with interdendritic regions with carbides. Dilution levels from 4,9 to 41,5 % leaded to hardness ranging from 225 to 283 HV_0_,_5, showing coatings dependence on intensity current level and substrate. (author)

  2. Tumor endothelium marker-8 based decoys exhibit superiority over capillary morphogenesis protein-2 based decoys as anthrax toxin inhibitors.

    Directory of Open Access Journals (Sweden)

    Chenguang Cai

    Full Text Available Anthrax toxin is the major virulence factor produced by Bacillus anthracis. The toxin consists of three protein subunits: protective antigen (PA, lethal factor, and edema factor. Inhibition of PA binding to its receptors, tumor endothelium marker-8 (TEM8 and capillary morphogenesis protein-2 (CMG2 can effectively block anthrax intoxication, which is particularly valuable when the toxin has already been overproduced at the late stage of anthrax infection, thus rendering antibiotics ineffectual. Receptor-like agonists, such as the mammalian cell-expressed von Willebrand factor type A (vWA domain of CMG2 (sCMG2, have demonstrated potency against the anthrax toxin. However, the soluble vWA domain of TEM8 (sTEM8 was ruled out as an anthrax toxin inhibitor candidate due to its inferior affinity to PA. In the present study, we report that L56A, a PA-binding-affinity-elevated mutant of sTEM8, could inhibit anthrax intoxication as effectively as sCMG2 in Fisher 344 rats. Additionally, pharmacokinetics showed that L56A and sTEM8 exhibit advantages over sCMG2 with better lung-targeting and longer plasma retention time, which may contribute to their enhanced protective ability in vivo. Our results suggest that receptor decoys based on TEM8 are promising anthrax toxin inhibitors and, together with the pharmacokinetic studies in this report, may contribute to the development of novel anthrax drugs.

  3. A facile metal-free "grafting-from" route from acrylamide-based substrate toward complex macromolecular combs

    KAUST Repository

    Zhao, Junpeng

    2013-01-01

    High-molecular-weight poly(N,N-dimethylacrylamide-co-acrylamide) was used as a model functional substrate to investigate phosphazene base (t-BuP 4)-promoted metal-free anionic graft polymerization utilizing primary amide moieties as initiating sites. The (co)polymerization of epoxides was proven to be effective, leading to macromolecular combs with side chains being single- or double-graft homopolymer, block copolymer and statistical copolymer. © 2013 The Royal Society of Chemistry.

  4. Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries.

    Science.gov (United States)

    Brylinski, Michal; Waldrop, Grover L

    2014-04-02

    As the spread of antibiotic resistant bacteria steadily increases, there is an urgent need for new antibacterial agents. Because fatty acid synthesis is only used for membrane biogenesis in bacteria, the enzymes in this pathway are attractive targets for antibacterial agent development. Acetyl-CoA carboxylase catalyzes the committed and regulated step in fatty acid synthesis. In bacteria, the enzyme is composed of three distinct protein components: biotin carboxylase, biotin carboxyl carrier protein, and carboxyltransferase. Fragment-based screening revealed that amino-oxazole inhibits biotin carboxylase activity and also exhibits antibacterial activity against Gram-negative organisms. In this report, we redesigned previously identified lead inhibitors to expand the spectrum of bacteria sensitive to the amino-oxazole derivatives by including Gram-positive species. Using 9,411 small organic building blocks, we constructed a diverse combinatorial library of 1.2×10⁸ amino-oxazole derivatives. A subset of 9×10⁶ of these compounds were subjected to structure-based virtual screening against seven biotin carboxylase isoforms using similarity-based docking by eSimDock. Potentially broad-spectrum antibiotic candidates were selected based on the consensus ranking by several scoring functions including non-linear statistical models implemented in eSimDock and traditional molecular mechanics force fields. The analysis of binding poses of the top-ranked compounds docked to biotin carboxylase isoforms suggests that: (1) binding of the amino-oxazole anchor is stabilized by a network of hydrogen bonds to residues 201, 202 and 204; (2) halogenated aromatic moieties attached to the amino-oxazole scaffold enhance interactions with a hydrophobic pocket formed by residues 157, 169, 171 and 203; and (3) larger substituents reach deeper into the binding pocket to form additional hydrogen bonds with the side chains of residues 209 and 233. These structural insights into drug

  5. Fragment Based Strategies for Discovery of Novel HIV-1 Reverse Transcriptase and Integrase Inhibitors.

    Science.gov (United States)

    Latham, Catherine F; La, Jennifer; Tinetti, Ricky N; Chalmers, David K; Tachedjian, Gilda

    2016-01-01

    Human immunodeficiency virus (HIV) remains a global health problem. While combined antiretroviral therapy has been successful in controlling the virus in patients, HIV can develop resistance to drugs used for treatment, rendering available drugs less effective and limiting treatment options. Initiatives to find novel drugs for HIV treatment are ongoing, although traditional drug design approaches often focus on known binding sites for inhibition of established drug targets like reverse transcriptase and integrase. These approaches tend towards generating more inhibitors in the same drug classes already used in the clinic. Lack of diversity in antiretroviral drug classes can result in limited treatment options, as cross-resistance can emerge to a whole drug class in patients treated with only one drug from that class. A fresh approach in the search for new HIV-1 drugs is fragment-based drug discovery (FBDD), a validated strategy for drug discovery based on using smaller libraries of low molecular weight molecules (FBDD is aimed at not only finding novel drug scaffolds, but also probing the target protein to find new, often allosteric, inhibitory binding sites. Several fragment-based strategies have been successful in identifying novel inhibitory sites or scaffolds for two proven drug targets for HIV-1, reverse transcriptase and integrase. While any FBDD-generated HIV-1 drugs have yet to enter the clinic, recent FBDD initiatives against these two well-characterised HIV-1 targets have reinvigorated antiretroviral drug discovery and the search for novel classes of HIV-1 drugs.

  6. Image-based compound profiling reveals a dual inhibitor of tyrosine kinase and microtubule polymerization.

    Science.gov (United States)

    Tanabe, Kenji

    2016-04-27

    Small-molecule compounds are widely used as biological research tools and therapeutic drugs. Therefore, uncovering novel targets of these compounds should provide insights that are valuable in both basic and clinical studies. I developed a method for image-based compound profiling by quantitating the effects of compounds on signal transduction and vesicle trafficking of epidermal growth factor receptor (EGFR). Using six signal transduction molecules and two markers of vesicle trafficking, 570 image features were obtained and subjected to multivariate analysis. Fourteen compounds that affected EGFR or its pathways were classified into four clusters, based on their phenotypic features. Surprisingly, one EGFR inhibitor (CAS 879127-07-8) was classified into the same cluster as nocodazole, a microtubule depolymerizer. In fact, this compound directly depolymerized microtubules. These results indicate that CAS 879127-07-8 could be used as a chemical probe to investigate both the EGFR pathway and microtubule dynamics. The image-based multivariate analysis developed herein has potential as a powerful tool for discovering unexpected drug properties.

  7. Substrate and Passivation Techniques for Flexible Amorphous Silicon-Based X-ray Detectors.

    Science.gov (United States)

    Marrs, Michael A; Raupp, Gregory B

    2016-07-26

    Flexible active matrix display technology has been adapted to create new flexible photo-sensing electronic devices, including flexible X-ray detectors. Monolithic integration of amorphous silicon (a-Si) PIN photodiodes on a flexible substrate poses significant challenges associated with the intrinsic film stress of amorphous silicon. This paper examines how altering device structuring and diode passivation layers can greatly improve the electrical performance and the mechanical reliability of the device, thereby eliminating one of the major weaknesses of a-Si PIN diodes in comparison to alternative photodetector technology, such as organic bulk heterojunction photodiodes and amorphous selenium. A dark current of 0.5 pA/mm² and photodiode quantum efficiency of 74% are possible with a pixelated diode structure with a silicon nitride/SU-8 bilayer passivation structure on a 20 µm-thick polyimide substrate.

  8. Nonlinear Analysis of Actuation Performance of Shape Memory Alloy Composite Film Based on Silicon Substrate

    Directory of Open Access Journals (Sweden)

    Shuangshuang Sun

    2014-01-01

    Full Text Available The mechanical model of the shape memory alloy (SMA composite film with silicon (Si substrate was established by the method of mechanics of composite materials. The coupled action between the SMA film and Si substrate under thermal loads was analyzed by combining static equilibrium equations, geometric equations, and physical equations. The material nonlinearity of SMA and the geometric nonlinearity of bending deformation were both considered. By simulating and analyzing the actuation performance of the SMA composite film during one cooling-heating thermal cycle, it is found that the final cooling temperature, boundary condition, and the thickness of SMA film have significant effects on the actuation performance of the SMA composite film. Besides, the maximum deflection of the SMA composite film is affected obviously by the geometric nonlinearity of bending deformation when the thickness of SMA film is very large.

  9. Evaluation of single and multi-threshold entropy-based algorithms for folded substrate analysis

    Directory of Open Access Journals (Sweden)

    Magdolna Apro

    2011-10-01

    Full Text Available This paper presents a detailed evaluation of two variants of Maximum Entropy image segmentation algorithm(single and multi-thresholding with respect to their performance on segmenting test images showing folded substrates.The segmentation quality was determined by evaluating values of four different measures: misclassificationerror, modified Hausdorff distance, relative foreground area error and positive-negative false detection ratio. Newnormalization methods were proposed in order to combine all parameters into a unique algorithm evaluation rating.The segmentation algorithms were tested on images obtained by three different digitalisation methods coveringfour different surface textures. In addition, the methods were also tested on three images presenting a perfect fold.The obtained results showed that Multi-Maximum Entropy algorithm is better suited for the analysis of imagesshowing folded substrates.

  10. Chemical vapor deposition of diamond onto iron based substrates. The use of barrier layers

    International Nuclear Information System (INIS)

    Weiser, P.S.; Prawer, S.

    1995-01-01

    When Fe is exposed to the plasma environment suitable for the chemical vapor deposition (CVD) of diamond, the surface is rapidly covered with a thick layer graphitic soot and C swiftly diffuses into the Fe substrate. Once the soot reaches a critical thickness, diamond films nucleate and grow on top of it. However, adhesion of the film to the substrate is poor due to the lack of structural integrity of the soot layer, A thin coating of TiN on the Fe can act to prevent diffusion and soot formation. Diamond readily grows upon the TiN via an a-C interface layer, but the a-C/TiN interface is weak and delamination occurs at this interface. In order to try and improve the adhesion, the use of a high dose Ti implant was investigated to replace the TiN coating. 7 refs., 6 figs

  11. Ductility prediction of substrate-supported metal layers based on rate-independent crystal plasticity theory

    Directory of Open Access Journals (Sweden)

    Akpama Holanyo K.

    2016-01-01

    Full Text Available In this paper, both the bifurcation theory and the initial imperfection approach are used to predict localized necking in substrate-supported metal layers. The self-consistent scale-transition scheme is used to derive the mechanical behavior of a representative volume element of the metal layer from the behavior of its microscopic constituents (the single crystals. The mechanical behavior of the elastomer substrate follows the neo-Hookean hyperelastic model. The adherence between the two layers is assumed to be perfect. Through numerical results, it is shown that the limit strains predicted by the initial imperfection approach tend towards the bifurcation predictions when the size of the geometric imperfection in the metal layer vanishes. Also, it is shown that the addition of an elastomer layer to a metal layer enhances ductility.

  12. Enhanced quantum efficiency for CsI grown on a graphite-based substrate coating

    CERN Document Server

    Friese, J; Homolka, J; Kastenmüller, A; Maier-Komor, P; Peter, M; Zeitelhack, K; Kienle, P; Körner, H J

    1999-01-01

    Quantum efficiencies (QE) in the vacuum ultraviolet (VUV) wavelength region have been measured for solid CsI layers on various substrates. The CsI films were deposited applying electron beam evaporation. The QE measurements were performed utilizing synchrotron radiation as well as light from a deuterium lamp. A GaAsP diode with a sensitivity calibration traceable to a primary radiation standard was used for normalization. For CsI layers grown on resin-stabilized graphite films a significant enhancement of QE was observed. Substrates suitable for gas detector applications and aging properties were investigated. The procedures to prepare and reproduce high quantum efficient CsI layers are described.

  13. MEMS based fabrication of high-frequency integrated inductors on Ni–Cu–Zn ferrite substrates

    Energy Technology Data Exchange (ETDEWEB)

    Anthony, Ricky, E-mail: ricky.anthony@tyndall.ie; Wang, Ningning, E-mail: ning.wang@tyndall.ie; Casey, Declan P.; Ó Mathúna, Cian; Rohan, James F.

    2016-05-15

    A surface micro-machining process is described to realize planar inductors on ferrite (Ni{sub 0.49}Zn{sub 0.33}Cu{sub 0.18} Fe{sub 2}O{sub 4}) for high-frequency applications (<30 MHz). The highly resistive nature (~10{sup 8} Ω m) of the Ni–Cu–Zn substrate allows direct conductor patterning by electroplating of Cu windings through a photoresist mold on a sputtered seed layer and eliminates the need for a dielectric layer to isolate the windings from the bottom magnetic core. Measured inductances~367 nH (DC resistance~1.16 Ω and Q-value>14 at 30 MHz) and ~244 nH (DC resistance~0.86 Ω and Q-value~18 at 30 MHz) at 1 MHz for elongated racetrack (10.75 nH/mm{sup 2}) and racetrack inductors (12.5 nH/mm{sup 2}), respectively show good agreement with simulated finite element method analysis. This device can be integrated with power management ICs PMICs for cost-effective, high-performance realization of power-supply in package (PSiP) or on-chip (PSoC). This simple process lays the foundation for fabricating closed core ferrite nano-crystalline core micro-inductors. - Graphical abstract: Material Characterization of Ni–Cu–Zn ferrite substrate and process developed for on-ferrite integrated micro-inductor fabrication. - Highlights: • High-frequency microinductors have been fabricated on Ni-Cu-Zn substrates. • High-resistive ferrite substrates assist direct conductor patterning on the surface. • Uniform inductances ~365 nH over 30 MHz frequency have been achieved. • High Q-values (>18 at 30 MHz) attained are applicable for high-frequency DC–DC conversion applications. • The described process lays the foundation for fabricating closed core ferrite nano-crystalline core.

  14. Non-conventional photocathodes based on Cu thin films deposited on Y substrate by sputtering

    Energy Technology Data Exchange (ETDEWEB)

    Perrone, A. [Department of Mathematics and Physics “E. De Giorgi”, University of Salento, 73100 Lecce (Italy); National Institute of Nuclear Physics and University of Salento, 73100 Lecce (Italy); D’Elia, M. [Department of Mathematics and Physics “E. De Giorgi”, University of Salento, 73100 Lecce (Italy); Gontad, F., E-mail: francisco.gontad@le.infn.it [Department of Mathematics and Physics “E. De Giorgi”, University of Salento, 73100 Lecce (Italy); National Institute of Nuclear Physics and University of Salento, 73100 Lecce (Italy); Di Giulio, M.; Maruccio, G. [Department of Mathematics and Physics “E. De Giorgi”, University of Salento, 73100 Lecce (Italy); Cola, A. [National Council Research, Institute for Microelectronics and Microsystems, 73100 Lecce (Italy); Stankova, N.E. [Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia (Bulgaria); Kovacheva, D.G. [Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia (Bulgaria); Broitman, E. [Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping (Sweden)

    2014-07-01

    Copper (Cu) thin films were deposited on yttrium (Y) substrate by sputtering. During the deposition, a small central area of the Y substrate was shielded to avoid the film deposition and was successively used to study its photoemissive properties. This configuration has two advantages: the cathode presents (i) the quantum efficiency and the work function of Y and (ii) high electrical compatibility when inserted into the conventional radio-frequency gun built with Cu bulk. The photocathode was investigated by scanning electron microscopy to determine surface morphology. X-ray diffraction and atomic force microscopy studies were performed to compare the structure and surface properties of the deposited film. The measured electrical resistivity value of the Cu film was similar to that of high purity Cu bulk. Film to substrate adhesion was also evaluated using the Daimler–Benz Rockwell-C adhesion test method. Finally, the photoelectron performance in terms of quantum efficiency was obtained in a high vacuum photodiode cell before and after laser cleaning procedures. A comparison with the results obtained with a twin sample prepared by pulsed laser deposition is presented and discussed.

  15. A flexible and highly sensitive nonenzymatic glucose sensor based on DVD-laser scribed graphene substrate.

    Science.gov (United States)

    Lin, Songyue; Feng, Wendou; Miao, Xiaofei; Zhang, Xiangxin; Chen, Sujing; Chen, Yuanqiang; Wang, Wei; Zhang, Yining

    2018-07-01

    Flexible and implantable glucose biosensors are emerging technologies for continuous monitoring of blood-glucose of diabetes. Developing a flexible conductive substrates with high active surface area is critical for advancing the technology. Here, we successfully fabricate a flexible and highly sensitive nonenzymatic glucose by using DVD-laser scribed graphene (LSG) as a flexible conductively substrate. Copper nanoparticles (Cu-NPs) are electrodeposited as the catalyst. The LSG/Cu-NPs sensor demonstrates excellent catalytic activity toward glucose oxidation and exhibits a linear glucose detection range from 1 μM to 4.54 mM with high sensitivity (1.518 mA mM -1 cm -2 ) and low limit of detection (0.35 μM). Moreover, the LSG/Cu-NPs sensor shows excellent reproducibility and long-term stability. It is also highly selective toward glucose oxidation under the presence of various interfering species. Excellent flexing stability is also demonstrated by the LSG/Cu-NPs sensor, which is capable of maintaining 83.9% of its initial current after being bent against a 4-mm diameter rod for 180 times. The LSG/Cu-NPs sensor shows great potential for practical application as a nonenzymatic glucose biosensor. Meanwhile, the LSG conductive substrate provides a platform for the developing next-generation flexible and potentially implantable bioelectronics and biosensors. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Virtual screening filters for the design of type II p38 MAP kinase inhibitors: a fragment based library generation approach.

    Science.gov (United States)

    Badrinarayan, Preethi; Sastry, G Narahari

    2012-04-01

    In this work, we introduce the development and application of a three-step scoring and filtering procedure for the design of type II p38 MAP kinase leads using allosteric fragments extracted from virtual screening hits. The design of the virtual screening filters is based on a thorough evaluation of docking methods, DFG-loop conformation, binding interactions and chemotype specificity of the 138 p38 MAP kinase inhibitors from Protein Data Bank bound to DFG-in and DFG-out conformations using Glide, GOLD and CDOCKER. A 40 ns molecular dynamics simulation with the apo, type I with DFG-in and type II with DFG-out forms was carried out to delineate the effects of structural variations on inhibitor binding. The designed docking-score and sub-structure filters were first tested on a dataset of 249 potent p38 MAP kinase inhibitors from seven diverse series and 18,842 kinase inhibitors from PDB, to gauge their capacity to discriminate between kinase and non-kinase inhibitors and likewise to selectively filter-in target-specific inhibitors. The designed filters were then applied in the virtual screening of a database of ten million (10⁷) compounds resulting in the identification of 100 hits. Based on their binding modes, 98 allosteric fragments were extracted from the hits and a fragment library was generated. New type II p38 MAP kinase leads were designed by tailoring the existing type I ATP site binders with allosteric fragments using a common urea linker. Target specific virtual screening filters can thus be easily developed for other kinases based on this strategy to retrieve target selective compounds. Copyright © 2012 Elsevier Inc. All rights reserved.

  17. Development of novel series and parallel sensing system based on nanostructured surface enhanced Raman scattering substrate for biomedical application

    Science.gov (United States)

    Chang, Te-Wei

    With the advance of nanofabrication, the capability of nanoscale metallic structure fabrication opens a whole new study in nanoplasmonics, which is defined as the investigation of photon-electron interaction in the vicinity of nanoscale metallic structures. The strong oscillation of free electrons at the interface between metal and surrounding dielectric material caused by propagating surface plasmon resonance (SPR) or localized surface plasmon resonance (LSPR) enables a variety of new applications in different areas, especially biological sensing techniques. One of the promising biological sensing applications by surface resonance polariton is surface enhanced Raman spectroscopy (SERS), which significantly reinforces the feeble signal of traditional Raman scattering by at least 104 times. It enables highly sensitive and precise molecule identification with the assistance of a SERS substrate. Until now, the design of new SERS substrate fabrication process is still thriving since no dominant design has emerged yet. The ideal process should be able to achieve both a high sensitivity and low cost device in a simple and reliable way. In this thesis two promising approaches for fabricating nanostructured SERS substrate are proposed: thermal dewetting technique and nanoimprint replica technique. These two techniques are demonstrated to show the capability of fabricating high performance SERS substrate in a reliable and cost efficient fashion. In addition, these two techniques have their own unique characteristics and can be integrated with other sensing techniques to build a serial or parallel sensing system. The breakthrough of a combination system with different sensing techniques overcomes the inherent limitations of SERS detection and leverages it to a whole new level of systematic sensing. The development of a sensing platform based on thermal dewetting technique is covered as the first half of this thesis. The process optimization, selection of substrate material

  18. Linagliptin, a xanthine-based dipeptidyl peptidase-4 inhibitor with an unusual profile for the treatment of type 2 diabetes

    DEFF Research Database (Denmark)

    Deacon, Carolyn F; Holst, Jens Juul

    2010-01-01

    data presented at Scientific Meetings and peer-reviewed studies published since 2007. WHAT THE READER WILL GAIN: This article reviews pharmacokinetic and pharmacodynamic characteristics of linagliptin. Linagliptin belongs to a new chemical class of dipeptidyl pepidase-4 (DPP-4) inhibitors, which...... comprise xanthine-based compounds. It is a potent, long-acting inhibitor with high selectivity for DPP-4 versus the related enzymes DPP-8 and DPP-9. The drug has modest oral availability in humans, but is absorbed rapidly to inhibit plasma DPP-4 activity by > 80% over 24 h. It is not metabolized...

  19. Optimization of TRPV6 Calcium Channel Inhibitors Using a 3D Ligand-Based Virtual Screening Method.

    OpenAIRE

    Simonin Céline; Awale Mahendra; Brand Michael; van Deursen Ruud; Schwartz Julian; Fine Michael; Kovacs Gergely; Häfliger Pascal; Gyimesi Gergely; Sithampari Abilashan; Charles Roch-Philippe; Hediger Matthias A; Reymond Jean-Louis

    2015-01-01

    Herein we report the discovery of the first potent and selective inhibitor of TRPV6 a calcium channel overexpressed in breast and prostate cancer and its use to test the effect of blocking TRPV6 mediated Ca(2+) influx on cell growth. The inhibitor was discovered through a computational method xLOS a 3D shape and pharmacophore similarity algorithm a type of ligand based virtual screening (LBVS) method described briefly here. Starting with a single weakly active seed molecule two successive rou...

  20. High-performance liquid chromatography-mass spectrometry-based acetylcholinesterase assay for the screening of inhibitors in natural extracts

    NARCIS (Netherlands)

    de Jong, C.F.; Derks, R.J.E.; Bruyneel, B.; Niessen, W.M.A.; Irth, H.

    2006-01-01

    The present paper describes a High-performance liquid chromatography-mass spectrometry (LC-MS) methodology for the screening of acetylcholinesterase (AChE) inhibitors in natural extracts. AChE activity of sample components is monitored by a post-column biochemical assay that is based on the

  1. A fluorescence polarization based screening assay for identification of small molecule inhibitors of the PICK1 PDZ domain

    DEFF Research Database (Denmark)

    Thorsen, Thor S; Madsen, Kenneth L; Dyhring, Tino

    2011-01-01

    PDZ (PSD-95/Discs-large/ZO-1 homology) domains represent putative targets in several diseases including cancer, stroke, addiction and neuropathic pain. Here we describe the application of a simple and fast screening assay based on fluorescence polarization (FP) to identify inhibitors of the PDZ...

  2. ACE inhibitors and the risk of acute pancreatitis-a population-based case-control study.

    Science.gov (United States)

    Kuoppala, Jaana; Enlund, Hannes; Pulkkinen, Jukka; Kastarinen, Helena; Jyrkkä, Johanna; Happonen, Pertti; Paajanen, Hannu

    2017-07-01

    The aim of this study was to examine the association between angiotensin converting enzyme (ACE) inhibitor use and the risk of acute pancreatitis. Information on all 4966 cases hospitalized in 2008-2010 for acute pancreatitis was retrieved from the Finnish national registers on hospital discharges and prescriptions. A total of 24 788 age and sex-matched population-based controls were randomly selected using density sampling. ACE inhibitor use between 1 January 2003 and the index date were determined by the date of hospitalization for acute pancreatitis among the cases. The incidence rate ratios of acute pancreatitis not diagnosed as biliary or alcohol-induced were modeled by conditional logistic regression and adjusted for comorbidities. A total of 1276 (26%) cases and 3946 (16%) controls had been exposed to ACE inhibitors. The use of ACE inhibitors was associated with an increased incidence rate of acute pancreatitis (odds ratio [OR] 1.76, 95% confidence interval [CI] 1.59-1.95). The increase was slightly higher among current new users (OR 1.86, 95%CI 1.65-2.09) and somewhat lower among current prevalent (OR 1.54, 95%CI 1.35-1.75) and former users (OR 1.51, 95%CI 1.31-1.74). Angiotensin converting enzyme inhibitor use seems to be associated with a moderately increased risk of acute pancreatitis. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  3. Ligand-based virtual screening and inductive learning for identification of SIRT1 inhibitors in natural products.

    Science.gov (United States)

    Sun, Yunan; Zhou, Hui; Zhu, Hongmei; Leung, Siu-wai

    2016-01-25

    Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide-dependent deacetylase, and its dysregulation can lead to ageing, diabetes, and cancer. From 346 experimentally confirmed SIRT1 inhibitors, an inhibitor structure pattern was generated by inductive logic programming (ILP) with DMax Chemistry Assistant software. The pattern contained amide, amine, and hetero-aromatic five-membered rings, each of which had a hetero-atom and an unsubstituted atom at a distance of 2. According to this pattern, a ligand-based virtual screening of 1 444 880 active compounds from Chinese herbs identified 12 compounds as inhibitors of SIRT1. Three compounds (ZINC08790006, ZINC08792229, and ZINC08792355) had high affinity (-7.3, -7.8, and -8.6 kcal/mol, respectively) for SIRT1 as estimated by molecular docking software AutoDock Vina. This study demonstrated a use of ILP and background knowledge in machine learning to facilitate virtual screening.

  4. Structure-Based Design of a Novel Series of Potent, Selective Inhibitors of the Class I Phosphatidylinositol 3-Kinases

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Adrian L.; D’Angelo, Noel D.; Bo, Yunxin Y.; Booker, Shon K.; Cee, Victor J.; Herberich, Brad; Hong, Fang-Tsao; Jackson, Claire L.M.; Lanman, Brian A.; Liu, Longbin; Nishimura, Nobuko; Pettus, Liping H.; Reed, Anthony B.; Tadesse, Seifu; Tamayo, Nuria A.; Wurz, Ryan P.; Yang, Kevin; Andrews, Kristin L.; Whittington, Douglas A.; McCarter, John D.; Miguel, Tisha San; Zalameda, Leeanne; Jiang, Jian; Subramanian, Raju; Mullady, Erin L.; Caenepeel, Sean; Freeman, Daniel J.; Wang, Ling; Zhang, Nancy; Wu, Tian; Hughes, Paul E.; Norman, Mark H. (Amgen)

    2012-09-17

    A highly selective series of inhibitors of the class I phosphatidylinositol 3-kinases (PI3Ks) has been designed and synthesized. Starting from the dual PI3K/mTOR inhibitor 5, a structure-based approach was used to improve potency and selectivity, resulting in the identification of 54 as a potent inhibitor of the class I PI3Ks with excellent selectivity over mTOR, related phosphatidylinositol kinases, and a broad panel of protein kinases. Compound 54 demonstrated a robust PD-PK relationship inhibiting the PI3K/Akt pathway in vivo in a mouse model, and it potently inhibited tumor growth in a U-87 MG xenograft model with an activated PI3K/Akt pathway.

  5. Fermentative hydrogen production from agroindustrial lignocellulosic substrates

    Science.gov (United States)

    Reginatto, Valeria; Antônio, Regina Vasconcellos

    2015-01-01

    To achieve economically competitive biological hydrogen production, it is crucial to consider inexpensive materials such as lignocellulosic substrate residues derived from agroindustrial activities. It is possible to use (1) lignocellulosic materials without any type of pretreatment, (2) lignocellulosic materials after a pretreatment step, and (3) lignocellulosic materials hydrolysates originating from a pretreatment step followed by enzymatic hydrolysis. According to the current literature data on fermentative H2 production presented in this review, thermophilic conditions produce H2 in yields approximately 75% higher than those obtained in mesophilic conditions using untreated lignocellulosic substrates. The average H2 production from pretreated material is 3.17 ± 1.79 mmol of H2/g of substrate, which is approximately 50% higher compared with the average yield achieved using untreated materials (2.17 ± 1.84 mmol of H2/g of substrate). Biological pretreatment affords the highest average yield 4.54 ± 1.78 mmol of H2/g of substrate compared with the acid and basic pretreatment - average yields of 2.94 ± 1.85 and 2.41 ± 1.52 mmol of H2/g of substrate, respectively. The average H2 yield from hydrolysates, obtained from a pretreatment step and enzymatic hydrolysis (3.78 ± 1.92 mmol of H2/g), was lower compared with the yield of substrates pretreated by biological methods only, demonstrating that it is important to avoid the formation of inhibitors generated by chemical pretreatments. Based on this review, exploring other microorganisms and optimizing the pretreatment and hydrolysis conditions can make the use of lignocellulosic substrates a sustainable way to produce H2. PMID:26273246

  6. Functional paper-based SERS substrate for rapid and sensitive detection of Sudan dyes in herbal medicine

    Science.gov (United States)

    Wu, Mianmian; Li, Pan; Zhu, Qingxia; Wu, Meiran; Li, Hao; Lu, Feng

    2018-05-01

    There has been an increasing demand for rapid and sensitive techniques for the identification of Sudan compounds that emerged as the most often illegally added fat-soluble dyes in herbal medicine. In this report, we have designed and fabricated a functionalized filter paper consisting of gold nanorods (GNRs) and mono-6-thio-cyclodextrin (HS-β-CD) as a surface-enhanced Raman spectroscopy (SERS) substrate, in which the GNR provides sufficient SERS enhancement, and the HS-β-CD with strong chemical affinity toward GNR provides the inclusion compound to capture hydrophobic molecules. Moreover, the CD-GNR were uniformly assembled on filter paper cellulose through the electrostatic adsorption and hydrogen bond, so that the CD-GNR paper-based SERS substrate (CD-GNR-paper) demonstrated higher sensitivity for the determination of Sudan III (0.1 μM) and Sudan IV (0.5 μM) than GNRs paper-based SERS substrate (GNR-paper), with high stability after the storage in the open air for 90 days. Importantly, CD-GNR-paper can effectively collect the Sudan dyes from illegally adulterated onto samples of Resina Draconis with a simple operation, further open up new exciting opportunity for SERS detection of more compounds illegally added with high sensitivity and fast signal responses.

  7. Investigations into alterntive substrate, absorber, and buffer layer processing for Cu(In,Ga)Se{sub 2}-based solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Tuttle, J.R.; Berens, T.A.; Keane, J. [National Renewable Energy Lab., Golden, CO (United States)] [and others

    1996-05-01

    High-performance Cu(In,Ga)Se{sub 2}(CIGS)-based solar cells are presently fabricated within a narrow range of processing options. In this contribution, alternative substrate, absorber, and buffer layer processing is considered. Cell performance varies considerably when alternative substrates are employed. These variations are narrowed with the addition of Na via a Na{sub 2}S compound. Sputtered and electrodeposited CIGS precursors and completed absorbers show promise as alternatives to evaporation. A recrystallization process is required to improve their quality. (In,Ga){sub y}Se buffer layers contribute to cell performance above 10. Further improvements in these alternatives will lead to combined cell performance greater than 10% in the near term.

  8. Discovery of new nanomolar inhibitors of GPa: Extension of 2-oxo-1,2-dihydropyridinyl-3-yl amide-based GPa inhibitors.

    Science.gov (United States)

    Loughlin, Wendy A; Jenkins, Ian D; Karis, N David; Healy, Peter C

    2017-02-15

    Glycogen Phosphorylase (GP) is a functionally active dimeric enzyme, which is a target for inhibition of the conversion of glycogen to glucose-1-phosphate. In this study we report the design and synthesis of 14 new pyridone derivatives, and seek to extend the SAR analysis of these compounds. The SAR revealed the minor influence of the amide group, importance of the pyridone ring both spatially around the pyridine ring and for possible π-stacking, and confirmed a preference for inclusion of 3,4-dichlorobenzyl moieties, as bookends to the pyridone scaffold. Upon exploring a dimer strategy as part of the SAR analysis, the first extended 2-oxo-dihydropyridinyl-3-yl amide nanomolar based inhibitors of GPa (IC 50  = 230 and 260 nM) were identified. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  9. Structure based classification for bile salt export pump (BSEP) inhibitors using comparative structural modeling of human BSEP

    Science.gov (United States)

    Jain, Sankalp; Grandits, Melanie; Richter, Lars; Ecker, Gerhard F.

    2017-06-01

    The bile salt export pump (BSEP) actively transports conjugated monovalent bile acids from the hepatocytes into the bile. This facilitates the formation of micelles and promotes digestion and absorption of dietary fat. Inhibition of BSEP leads to decreased bile flow and accumulation of cytotoxic bile salts in the liver. A number of compounds have been identified to interact with BSEP, which results in drug-induced cholestasis or liver injury. Therefore, in silico approaches for flagging compounds as potential BSEP inhibitors would be of high value in the early stage of the drug discovery pipeline. Up to now, due to the lack of a high-resolution X-ray structure of BSEP, in silico based identification of BSEP inhibitors focused on ligand-based approaches. In this study, we provide a homology model for BSEP, developed using the corrected mouse P-glycoprotein structure (PDB ID: 4M1M). Subsequently, the model was used for docking-based classification of a set of 1212 compounds (405 BSEP inhibitors, 807 non-inhibitors). Using the scoring function ChemScore, a prediction accuracy of 81% on the training set and 73% on two external test sets could be obtained. In addition, the applicability domain of the models was assessed based on Euclidean distance. Further, analysis of the protein-ligand interaction fingerprints revealed certain functional group-amino acid residue interactions that could play a key role for ligand binding. Though ligand-based models, due to their high speed and accuracy, remain the method of choice for classification of BSEP inhibitors, structure-assisted docking models demonstrate reasonably good prediction accuracies while additionally providing information about putative protein-ligand interactions.

  10. Understanding the Broad Substrate Repertoire of Nitroreductase Based on Its Kinetic Mechanism*

    Science.gov (United States)

    Pitsawong, Warintra; Hoben, John P.; Miller, Anne-Frances

    2014-01-01

    The oxygen-insensitive nitroreductase from Enterobacter cloacae (NR) catalyzes two-electron reduction of nitroaromatics to the corresponding nitroso compounds and, subsequently, to hydroxylamine products. NR has an unusually broad substrate repertoire, which may be related to protein dynamics (flexibility) and/or a simple non-selective kinetic mechanism. To investigate the possible role of mechanism in the broad substrate repertoire of NR, the kinetics of oxidation of NR by para-nitrobenzoic acid (p-NBA) were investigated using stopped-flow techniques at 4 °C. The results revealed a hyperbolic dependence on the p-NBA concentration with a limiting rate of 1.90 ± 0.09 s−1, indicating one-step binding before the flavin oxidation step. There is no evidence for a distinct binding step in which specificity might be enforced. The reduction of p-NBA is rate-limiting in steady-state turnover (1.7 ± 0.3 s−1). The pre-steady-state reduction kinetics of NR by NADH indicate that NADH reduces the enzyme with a rate constant of 700 ± 20 s−1 and a dissociation constant of 0.51 ± 0.04 mm. Thus, we demonstrate simple transient kinetics in both the reductive and oxidative half-reactions that help to explain the broad substrate repertoire of NR. Finally, we tested the ability of NR to reduce para-hydroxylaminobenzoic acid, demonstrating that the corresponding amine does not accumulate to significant levels even under anaerobic conditions. Thus E. cloacae NR is not a good candidate for enzymatic production of aromatic amines. PMID:24706760

  11. Effectiveness of Ritonavir-Boosted Protease Inhibitor Monotherapy in Clinical Practice Even with Previous Virological Failures to Protease Inhibitor-Based Regimens.

    Directory of Open Access Journals (Sweden)

    Luis F López-Cortés

    Full Text Available Significant controversy still exists about ritonavir-boosted protease inhibitor monotherapy (mtPI/rtv as a simplification strategy that is used up to now to treat patients that have not experienced previous virological failure (VF while on protease inhibitor (PI -based regimens. We have evaluated the effectiveness of two mtPI/rtv regimens in an actual clinical practice setting, including patients that had experienced previous VF with PI-based regimens.This retrospective study analyzed 1060 HIV-infected patients with undetectable viremia that were switched to lopinavir/ritonavir or darunavir/ritonavir monotherapy. In cases in which the patient had previously experienced VF while on a PI-based regimen, the lack of major HIV protease resistance mutations to lopinavir or darunavir, respectively, was mandatory. The primary endpoint of this study was the percentage of participants with virological suppression after 96 weeks according to intention-to-treat analysis (non-complete/missing = failure.A total of 1060 patients were analyzed, including 205 with previous VF while on PI-based regimens, 90 of whom were on complex therapies due to extensive resistance. The rates of treatment effectiveness (intention-to-treat analysis and virological efficacy (on-treatment analysis at week 96 were 79.3% (CI95, 76.8-81.8 and 91.5% (CI95, 89.6-93.4, respectively. No relationships were found between VF and earlier VF while on PI-based regimens, the presence of major or minor protease resistance mutations, the previous time on viral suppression, CD4+ T-cell nadir, and HCV-coinfection. Genotypic resistance tests were available in 49 out of the 74 patients with VFs and only four patients presented new major protease resistance mutations.Switching to mtPI/rtv achieves sustained virological control in most patients, even in those with previous VF on PI-based regimens as long as no major resistance mutations are present for the administered drug.

  12. Surface-enhanced Raman spectroscopy substrate based on Ag-coated self-assembled polystyrene spheres

    Science.gov (United States)

    Mikac, Lara; Ivanda, Mile; Gotić, Marijan; Janicki, Vesna; Zorc, Hrvoje; Janči, Tibor; Vidaček, Sanja

    2017-10-01

    The silver (Ag) films were deposited on the monodispersed polystyrene spheres that were drop-coated on hydrophilic glass substrates in order to form a self-assembled 2D monolayer. Thus prepared Ag films over polystyrene nanospheres (AgFONs) were used to record the surface-enhanced Raman scattering (SERS) spectra of rhodamine 6G (R6G) and pyridine (λex = 514.5 nm). AgFONs were prepared by depositing 120, 180 and 240 nm thick Ag layer on the 1000 nm polystyrene spheres and 80, 120, 160 and 200 nm thick Ag layer on the 350 nm spheres as well as on their mixture (350 + 1000 nm). The silver was deposited by electron beam evaporation technique. The best enhancement of the Raman signal for both test molecules was obtained using 180 nm Ag film deposited on the 1000 nm spheres and using 80 nm Ag film deposited on the 350 nm polystyrene spheres. The lowest detectable concentrations of R6G and pyridine were 10-9 mol L-1 and 1.2 × 10-3 mol L-1, respectively. This study has shown that AgFONs could be regarded as good and reproducible SERS substrate for analytical detection of various organic molecules.

  13. High-content profiling of cell responsiveness to graded substrates based on combinyatorially variant polymers.

    Science.gov (United States)

    Liu, Er; Treiser, Matthew D; Patel, Hiral; Sung, Hak-Joon; Roskov, Kristen E; Kohn, Joachim; Becker, Matthew L; Moghe, Prabhas V

    2009-08-01

    We have developed a novel approach combining high information and high throughput analysis to characterize cell adhesive responses to biomaterial substrates possessing gradients in surface topography. These gradients were fabricated by subjecting thin film blends of tyrosine-derived polycarbonates, i.e. poly(DTE carbonate) and poly(DTO carbonate) to a gradient temperature annealing protocol. Saos-2 cells engineered with a green fluorescent protein (GFP) reporter for farnesylation (GFP-f) were cultured on the gradient substrates to assess the effects of nanoscale surface topology and roughness that arise during the phase separation process on cell attachment and adhesion strength. The high throughput imaging approach allowed us to rapidly identify the "global" and "high content" structure-property relationships between cell adhesion and biomaterial properties such as polymer chemistry and topography. This study found that cell attachment and spreading increased monotonically with DTE content and were significantly elevated at the position with intermediate regions corresponding to the highest "gradient" of surface roughness, while GFP-f farnesylation intensity descriptors were sensitively altered by surface roughness, even in cells with comparable levels of spreading.

  14. Nitride-based quantum structures and devices on modified GaN substrates

    International Nuclear Information System (INIS)

    Perlin, Piotr; Leszczynski, Mike; Grzegory, Izabella; Franssen, Gijs; Targowski, Grzegorz; Krysko, Marcin; Nowak, Grzegorz; Litwin-Staszewska, Elzbieta; Piotrzkowski, Ryszard; Lucznik, Bolek; Suski, Tadek; Szeszko, Justyna; Czernecki, R.; Grzanka, Szymon; Jakiela, Rafal; Albrecht, Martin

    2009-01-01

    We have studied the properties of InGaN layers and quantum wells grown on gallium nitride substrates with intentional surface misorientation with respect to its crystalline c-axis. Misorientation varied in the range from 0 up to 2 degree. The indium content was changed by using the different growth temperature (between 750 C and 820 C) during metalorganic vapor phase epitaxy. With increasing misorientation angle the average indium content decreased significantly. This effect was accompanied by the strong increase of the emission line bandwidth suggesting more pronounced indium segregation. The results of cathodoluminescence measurements show that these effects correspond to different number of atomic steps/terraces existing on the surface of gallium nitride substrate. Very interesting result is also demonstrated concerning p-type GaN layers. With increasing misorientation, the free hole density drastically increases above 10 18 cm -3 . This improvement in p-type doping is not related to the increased Mg concentration but to the reduction in the compensating donor density. Using this advantage we demonstrate nitride light emitters with improved electrical properties. (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  15. Molecular mechanisms for synergistic effect of proteasome inhibitors with platinum-based therapy in solid tumors.

    Science.gov (United States)

    Chao, Angel; Wang, Tzu-Hao

    2016-02-01

    The successful development of the proteasome inhibitor bortezomib as an anticancer drug has improved survival in patients with multiple myeloma. With the emergence of the newly US Food and Drug Administration-approved proteasome inhibitor carfilzomib, ongoing trials are investigating this compound and other proteasome inhibitors either alone or in combination with other chemotherapy drugs. However, in solid tumors, the efficacy of proteasome inhibitors has not lived up to expectations. Results regarding the potential clinical efficacy of bortezomib combined with other agents in the treatment of solid tumors are eagerly awaited. Recent identification of the molecular mechanisms (involving apoptosis and autophagy) by which bortezomib and cisplatin can overcome chemotherapy resistance and sensitize tumor cells to anticancer therapy can provide insights into the development of novel therapeutic strategies for patients with solid malignancies. Copyright © 2016. Published by Elsevier B.V.

  16. An efficient method for synthesis of succinate-based MMP inhibitors.

    Science.gov (United States)

    Sibi, Mukund P; Hasegawa, Hikaru

    2002-10-03

    A differentially protected fumarate undergoes radical addition followed by allylstannane trapping to provide disubstituted succinates in good yields and high anti diastereoselectivity. The conversion of the succinate to a known MMP inhibitor has been accomplished. [reaction: see text

  17. Carbohydrate-Based Ice Recrystallization Inhibitors Increase Infectivity and Thermostability of Viral Vectors

    Science.gov (United States)

    Ghobadloo, Shahrokh M.; Balcerzak, Anna K.; Gargaun, Ana; Muharemagic, Darija; Mironov, Gleb G.; Capicciotti, Chantelle J.; Briard, Jennie G.; Ben, Robert N.; Berezovski, Maxim V.

    2014-07-01

    The inability of vaccines to retain sufficient thermostability has been an obstacle to global vaccination programs. To address this major limitation, we utilized carbohydrate-based ice recrystallization inhibitors (IRIs) to eliminate the cold chain and stabilize the potency of Vaccinia virus (VV), Vesicular Stomatitis virus (VSV) and Herpes virus-1 (HSV-1). The impact of these IRIs was tested on the potency of the viral vectors using a plaque forming unit assay following room temperature storage, cryopreservation with successive freeze-thaw cycles and lyophilization. Viral potency after storage with all three conditions demonstrated that N-octyl-gluconamide (NOGlc) recovered the infectivity of shelf stored VV, 5.6 Log10 PFU mL-1 during 40 days, and HSV-1, 2.7 Log10 PFU mL-1 during 9 days. Carbon-linked antifreeze glycoprotein analogue ornithine-glycine-glycine-galactose (OGG-Gal) increases the recovery of VV and VSV more than 1 Log10 PFU mL-1 after 10 freeze-thaw cycles. In VSV, cryostorage with OGG-Gal maintains high infectivity and reduces temperature-induced aggregation of viral particles by 2 times that of the control. In total, OGG-Gal and NOGlc preserve virus potency during cryostorage. Remarkably, NOGlc has potential to eliminate the cold chain and permit room temperature storage of viral vectors.

  18. Discovery of a new mitochondria permeability transition pore (mPTP) inhibitor based on gallic acid.

    Science.gov (United States)

    Teixeira, José; Oliveira, Catarina; Cagide, Fernando; Amorim, Ricardo; Garrido, Jorge; Borges, Fernanda; Oliveira, Paulo J

    2018-12-01

    Pharmacological interventions targeting mitochondria present several barriers for a complete efficacy. Therefore, a new mitochondriotropic antioxidant (AntiOxBEN 3 ) based on the dietary antioxidant gallic acid was developed. AntiOxBEN 3 accumulated several thousand-fold inside isolated rat liver mitochondria, without causing disruption of the oxidative phosphorylation apparatus, as seen by the unchanged respiratory control ratio, phosphorylation efficiency, and transmembrane electric potential. AntiOxBEN 3 showed also limited toxicity on human hepatocarcinoma cells. Moreover, AntiOxBEN 3 presented robust iron-chelation and antioxidant properties in both isolated liver mitochondria and cultured rat and human cell lines. Along with its low toxicity profile and high antioxidant activity, AntiOxBEN 3 strongly inhibited the calcium-dependent mitochondrial permeability transition pore (mPTP) opening. From our data, AntiOxBEN 3 can be considered as a lead compound for the development of a new class of mPTP inhibitors and be used as mPTP de-sensitiser for basic research or clinical applications or emerge as a therapeutic application in mitochondria dysfunction-related disorders.

  19. In silico modelling and molecular dynamics simulation studies of thiazolidine based PTP1B inhibitors.

    Science.gov (United States)

    Mahapatra, Manoj Kumar; Bera, Krishnendu; Singh, Durg Vijay; Kumar, Rajnish; Kumar, Manoj

    2018-04-01

    Protein tyrosine phosphatase 1B (PTP1B) has been identified as a negative regulator of insulin and leptin signalling pathway; hence, it can be considered as a new therapeutic target of intervention for the treatment of type 2 diabetes. Inhibition of this molecular target takes care of both diabetes and obesity, i.e. diabestiy. In order to get more information on identification and optimization of lead, pharmacophore modelling, atom-based 3D QSAR, docking and molecular dynamics studies were carried out on a set of ligands containing thiazolidine scaffold. A six-point pharmacophore model consisting of three hydrogen bond acceptor (A), one negative ionic (N) and two aromatic rings (R) with discrete geometries as pharmacophoric features were developed for a predictive 3D QSAR model. The probable binding conformation of the ligands within the active site was studied through molecular docking. The molecular interactions and the structural features responsible for PTP1B inhibition and selectivity were further supplemented by molecular dynamics simulation study for a time scale of 30 ns. The present investigation has identified some of the indispensible structural features of thiazolidine analogues which can further be explored to optimize PTP1B inhibitors.

  20. Droplet-based microfluidics for dose-response assay of enzyme inhibitors by electrochemical method.

    Science.gov (United States)

    Gu, Shuqing; Lu, Youlan; Ding, Yaping; Li, Li; Zhang, Fenfen; Wu, Qingsheng

    2013-09-24

    A simple but robust droplet-based microfluidic system was developed for dose-response enzyme inhibition assay by combining concentration gradient generation method with electrochemical detection method. A slotted-vials array and a tapered tip capillary were used for reagents introduction and concentration gradient generation, and a polydimethylsiloxane (PDMS) microfluidic chip integrated with microelectrodes was used for droplet generation and electrochemical detection. Effects of oil flow rate and surfactant on electrochemical sensing were investigated. This system was validated by measuring dose-response curves of three types of acetylcholinesterase (AChE) inhibitors, including carbamate pesticide, organophosphorus pesticide, and therapeutic drugs regulating Alzheimer's disease. Carbaryl, chlorpyrifos, and tacrine were used as model analytes, respectively, and their IC50 (half maximal inhibitory concentration) values were determined. A whole enzyme inhibition assay was completed in 6 min, and the total consumption of reagents was less than 5 μL. This microfluidic system is applicable to many biochemical reactions, such as drug screening and kinetic studies, as long as one of the reactants or products is electrochemically active. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Evidence-based support for the use of proton pump inhibitors in cancer therapy.

    Science.gov (United States)

    Fais, Stefano

    2015-11-24

    'We can only cure what we can understand first', said Otto H. Warburg, the 1931 Nobel laureate for his discovery on tumor metabolism. Unfortunately, we still don't know too much the mechanisms underlying of cancer development and progression. One of the unsolved mystery includes the strategies that cancer cells adopt to cope with an adverse microenvironment. However, we knew, from the Warburg's discovery, that through their metabolism based on sugar fermentation, cancer cells acidify their microenvironment and this progressive acidification induces a selective pressure, leading to development of very malignant cells entirely armed to survive in the hostile microenvironment generated by their own metabolism. One of the most mechanism to survive to the acidic tumor microenvironment are proton exchangers not allowing intracellular acidification through a continuous elimination of H(+) either outside the cells or within the internal vacuoles. This article wants to comment a translational process through which from the preclinical demonstration that a class of proton pump inhibitors (PPI) exploited worldwide for peptic ulcer treatment and gastroprotection are indeed chemosensitizers as well, we have got to the clinical proof of concept that PPI may well be included in new anti-cancer strategies, and with a solid background and rationale.

  2. Yeast based small molecule screen for inhibitors of SARS-CoV.

    Directory of Open Access Journals (Sweden)

    Matthew Frieman

    Full Text Available Severe acute respiratory coronavirus (SARS-CoV emerged in 2002, resulting in roughly 8000 cases worldwide and 10% mortality. The animal reservoirs for SARS-CoV precursors still exist and the likelihood of future outbreaks in the human population is high. The SARS-CoV papain-like protease (PLP is an attractive target for pharmaceutical development because it is essential for virus replication and is conserved among human coronaviruses. A yeast-based assay was established for PLP activity that relies on the ability of PLP to induce a pronounced slow-growth phenotype when expressed in S. cerevisiae. Induction of the slow-growth phenotype was shown to take place over a 60-hour time course, providing the basis for conducting a screen for small molecules that restore growth by inhibiting the function of PLP. Five chemical suppressors of the slow-growth phenotype were identified from the 2000 member NIH Diversity Set library. One of these, NSC158362, potently inhibited SARS-CoV replication in cell culture without toxic effects on cells, and it specifically inhibited SARS-CoV replication but not influenza virus replication. The effect of NSC158362 on PLP protease, deubiquitinase and anti-interferon activities was investigated but the compound did not alter these activities. Another suppressor, NSC158011, demonstrated the ability to inhibit PLP protease activity in a cell-based assay. The identification of these inhibitors demonstrated a strong functional connection between the PLP-based yeast assay, the inhibitory compounds, and SARS-CoV biology. Furthermore the data with NSC158362 suggest a novel mechanism for inhibition of SARS-CoV replication that may involve an unknown activity of PLP, or alternatively a direct effect on a cellular target that modifies or bypasses PLP function in yeast and mammalian cells.

  3. Inequity of access to ACE inhibitors in Swedish heart failure patients: a register-based study

    Science.gov (United States)

    Lindahl, Bertil; Hanning, Marianne; Westerling, Ragnar

    2016-01-01

    Background Several international studies suggest inequity in access to evidence-based heart failure (HF) care. Specifically, studies of ACE inhibitors (ACEIs) point to reduced ACEI access related to female sex, old age and socioeconomic position. Thus far, most studies have either been rather small, lacking diagnostic data, or lacking the possibility to account for several individual-based sociodemographic factors. Our aim was to investigate differences, which could reflect inequity in access to ACEIs based on sex, age, socioeconomic status or immigration status in Swedish patients with HF. Methods Individually linked register data for all Swedish adults hospitalised for HF in 2005–2010 (n=93 258) were analysed by multivariate regression models to assess the independent risk of female sex, high age, low employment status, low income level, low educational level or foreign country of birth, associated with lack of an ACEI dispensation within 1 year of hospitalisation. Adjustment for possible confounding was made for age, comorbidity, Angiotensin receptor blocker therapy, period and follow-up time. Results Analysis revealed an adjusted OR for no ACEI dispensation for women of 1.31 (95% CI 1.27 to 1.35); for the oldest patients of 2.71 (95% CI 2.53 to 2.91); and for unemployed patients of 1.59 (95% CI 1.46 to 1.73). Conclusions Access to ACEI treatment was reduced in women, older patients and unemployed patients. We conclude that access to ACEIs is inequitable among Swedish patients with HF. Future studies should include clinical data, as well as mortality outcomes in different groups. PMID:26261264

  4. Designing an orally available nontoxic p38 inhibitor with a fragment-based strategy.

    Science.gov (United States)

    Guarnieri, Frank

    2015-01-01

    The MAPK p38 became a focal point of inflammatory research when it was recognized that it played a key role in the production of the pro-inflammatory molecules TNF-alpha, IL-beta, and cyclooxygenase-2 (COX-2). The pharmaceutical industry devoted enormous efforts to creating p38 inhibitors, because blocking p38 had the potential of downregulating a group of pro-inflammatory mediators, and thus, one drug could have a cocktail effect. The market potential seemed to be clearly established (Bonafede et al., Clinicoecon Outcomes Res 6:381-388, 2014) with a multiplicity of TNF-alpha antibodies and a soluble receptor (Mewar and Wilson, Br J Pharmacol 162:785-791, 2011) already on the market, although the relationship between TNF-alpha production and p38 activation is a complicated two-way (Sabio and Davis, Semin Immunol 26:237-245, 2014) signal transduction process. With the discovery that activated p38 stabilizes (Mancini and Di Battista, Inflamm Res 60:1083-1092, 2011) COX-2 mRNA and upregulates expression of IL-beta (Bachstetter and Van Eldik, Aging Dis 1:199-211, 2010) probably in a similar manner, inhibiting p38 appeared to be a way of blocking TNF-alpha, COX-2, and IL-beta simultaneously. At Locus Pharmaceuticals we jumped on this opportunity, because we believed that our fragment-based drug discovery approach was ideally suited for making a potent small molecule p38 inhibitor that did not bind in the ATP site, but also had the solubility, lack of planarity, and low molecular weight required of a clinical candidate. Just to be clear, in our experience highly planar compounds often result in poor pharmacokinetics, because they tend to bind strongly to plasma proteins. At Locus we typically repeated assays by adding increasing amounts of plasma to check for potency degradation in the presence of blood. We found this to be a useful early indicator of pharmacokinetics and in vivo behavior. It became clear from our work and the work of others that binding to the ATP site

  5. High-performance SERS substrate based on hybrid structure of graphene oxide/AgNPs/Cu film@pyramid Si

    Science.gov (United States)

    Li, Zhe; Xu, Shi Cai; Zhang, Chao; Liu, Xiao Yun; Gao, Sai Sai; Hu, Li Tao; Guo, Jia; Ma, Yong; Jiang, Shou Zhen; Si, Hai Peng

    2016-12-01

    We present a novel surface-enhanced Raman scattering (SERS) substrate based on graphene oxide/silver nanoparticles/copper film covered silicon pyramid arrays (GO/AgNPs/PCu@Si) by a low-cost and simple method. The GO/AgNPs/PCu@Si substrate presents high sensitivity, good homogeneity and well stability with R6G molecules as a probe. The detected concentration of Rhodamine 6 G (R6G) is as low as 10-15 M. These sensitive SERS behaviors are also confirmed in theory via a commercial COMSOL software, the electric field enhancement is not only formed between the AgNPs, but also formed between the AgNPs and Cu film. And the GO/AgNPs/PCu@Si substrates also present good property on practical application for the detection of methylene blue (MB) and crystal violet (CV). This work may offer a novel and practical method to facilitate the SERS applications in areas of medicine, food safety and biotechnology.

  6. Impact of mTOR Inhibitors on Cancer Development in Kidney Transplantation Recipients: A Population-Based Study.

    Science.gov (United States)

    Kao, C-C; Liu, J-S; Lin, M-H; Hsu, C-Y; Chang, F-C; Lin, Y-C; Chen, H-H; Chen, T-W; Hsu, C-C; Wu, M-S

    2016-04-01

    The mammalian target of rapamycin (mTOR) inhibitor is an immunosuppressive drug used in kidney transplantation. Whether the mTOR inhibitor is associated with reduced risk of cancer development and mortality after kidney transplantation is controversial. We conducted a nationwide population-based study. Patients who did not have malignancy history and received kidney transplantation between 2010 and 2013 were enrolled. Recipients who had mTOR inhibitors (n = 430) for more than 30 days comprised the study group; 1720 recipients who did not have mTOR inhibitors comprised the control group. The primary outcome is the development of cancer after kidney transplantation. These patients were followed until the first-time admission with diagnosis of cancer, death, or the end of 2014. A Cox proportional-hazard model was used to determine the risk of cancer development and all-cause mortality. During the 35-month median duration of observation, there were 16 and 61 patients with cancer development in the study group and the control group, respectively. The cancer incidence was 12.8 and 12.4 per 1000 person-years. There were 10 and 135 mortality cases, with the incidence rate of 7.8 and 26.9 per 1000 person-years. After multivariable adjustment, the mTOR inhibitors users were not associated with reduced risk of new cancer development as compared with control (hazard ratio [HR], 0.86; 95% confidence interval [CI], 0.46-1.60; P = .63), nor risk of all-cause mortality (HR, 0.70; 95% CI, 0.33-1.46; P = .34). The use of mTOR inhibitors was not associated with a reduction in the risk of cancer development and all-cause mortality in kidney transplantation recipients. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Structure-based virtual screening of molecular libraries as cdk2 inhibitors

    International Nuclear Information System (INIS)

    Riaz, U.; Khaleeq, M.

    2011-01-01

    CDK2 inhibitor is an important target in multiple processes associated with tumor growth and development, including proliferation, neovascularization, and metastasis. In this study, hit identification was performed by virtual screening of commercial and in-house compound libraries. Docking studies for the hits were performed, and scoring functions were used to evaluate the docking results and to rank ligand-binding affinities. Subsequently, hit optimization for potent and selective candidate CDK2 inhibitors was performed through focused library design and docking analyses. Consequently, we report that a novel compound with an IC50 value of 89 nM, representing 2-Amino-4,6-di-(4',6'-dibromophenyl)pyrimidine 1, is highly selective for CDK2 inhibitors. The docking structure of compound 1 with CDK2 inhibitor disclosed that the NH moiety and pyrimidine ring appeared to fit tightly into the hydrophobic pocket of CDK2 inhibitor. Additionally, the pyrimidine NH forms a hydrogen bond with the carboxyl group of Asp348. These results confirm the successful application of virtual screening studies in the lead discovery process, and suggest that our novel compound can be an effective CDK2 inhibitor candidate for further lead optimization. (author)

  8. Curcumin Based Drug Screening for Inhibitors of NF kappa B in a Cell Model of Prostate Cancer Progression

    Science.gov (United States)

    2008-02-01

    identify new and structurally diverse chemical analogs of the polyphenolic phytochemical Curcumin from the Indian herb Curcuma longa (family...AD_________________ Award Number: W81XWH-07-1-0081 TITLE: Curcumin Based Drug Screening for... Curcumin Based Drug Screening for Inhibitors of NF kappa B in a Cell Model of Prostate Cancer Progression 5b. GRANT NUMBER W81XWH-07-1-0081 5c

  9. In silico-based identification of human α-enolase inhibitors to block cancer cell growth metabolically

    Science.gov (United States)

    Lung, Jrhau; Chen, Kuan-Liang; Hung, Chien-Hui; Chen, Chih-Cheng; Hung, Ming-Szu; Lin, Yu-Ching; Wu, Ching-Yuan; Lee, Kuan-Der; Shih, Neng-Yao; Tsai, Ying Huang

    2017-01-01

    Unlimited growth of cancer cells requires an extensive nutrient supply. To meet this demand, cancer cells drastically upregulate glucose uptake and metabolism compared to normal cells. This difference has made the blocking of glycolysis a fascinating strategy to treat this malignant disease. α-enolase is not only one of the most upregulated glycolytic enzymes in cancer cells, but also associates with many cellular processes or conditions important to cancer cell survival, such as cell migration, invasion, and hypoxia. Targeting α-enolase could simultaneously disturb cancer cells in multiple ways and, therefore, is a good target for anticancer drug development. In the current study, more than 22 million chemical structures meeting the criteria of Lipinski’s rule of five from the ZINC database were docked to α-enolase by virtual screening. Twenty-four chemical structures with docking scores better than that of the enolase substrate, 2-phosphoglycerate, were further screened by the absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties prediction. Four of them were classified as non-mutagenic, non-carcinogenic, and capable of oral administration where they showed steady interactions to α-enolase that were comparable, even superior, to the currently available inhibitors in molecular dynamics (MD) simulation. These compounds may be considered promising leads for further development of the α-enolase inhibitors and could help fight cancer metabolically. PMID:29180852

  10. Structure-based drug design of a highly potent CDK1,2,4,6 inhibitor with novel macrocyclic quinoxalin-2-one structure.

    Science.gov (United States)

    Kawanishi, Nobuhiko; Sugimoto, Tetsuya; Shibata, Jun; Nakamura, Kaori; Masutani, Kouta; Ikuta, Mari; Hirai, Hiroshi

    2006-10-01

    The design of a novel series of cyclin-dependent kinase (CDK) inhibitors containing a macrocyclic quinoxaline-2-one is reported. Structure-based drug design and optimization from the starting point of diarylurea 2, which we previously reported as a moderate CDK1,2,4,6 inhibitor [J. Biol.Chem.2001, 276, 27548], led to the discovery of potent CDK1,2,4,6 inhibitor that were suitable for iv administration for in vivo study.

  11. Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling

    Science.gov (United States)

    Bharatham, Kavitha; Bharatham, Nagakumar; Kwon, Yong Jung; Lee, Keun Woo

    2008-12-01

    Allosteric inhibition of protein tyrosine phosphatase 1B (PTP1B), has paved a new path to design specific inhibitors for PTP1B, which is an important drug target for the treatment of type II diabetes and obesity. The PTP1B1-282-allosteric inhibitor complex crystal structure lacks α7 (287-298) and moreover there is no available 3D structure of PTP1B1-298 in open form. As the interaction between α7 and α6-α3 helices plays a crucial role in allosteric inhibition, α7 was modeled to the PTP1B1-282 in open form complexed with an allosteric inhibitor (compound-2) and a 5 ns MD simulation was performed to investigate the relative orientation of the α7-α6-α3 helices. The simulation conformational space was statistically sampled by clustering analyses. This approach was helpful to reveal certain clues on PTP1B allosteric inhibition. The simulation was also utilized in the generation of receptor based pharmacophore models to include the conformational flexibility of the protein-inhibitor complex. Three cluster representative structures of the highly populated clusters were selected for pharmacophore model generation. The three pharmacophore models were subsequently utilized for screening databases to retrieve molecules containing the features that complement the allosteric site. The retrieved hits were filtered based on certain drug-like properties and molecular docking simulations were performed in two different conformations of protein. Thus, performing MD simulation with α7 to investigate the changes at the allosteric site, then developing receptor based pharmacophore models and finally docking the retrieved hits into two distinct conformations will be a reliable methodology in identifying PTP1B allosteric inhibitors.

  12. Virtual screening approach to identifying influenza virus neuraminidase inhibitors using molecular docking combined with machine-learning-based scoring function.

    Science.gov (United States)

    Zhang, Li; Ai, Hai-Xin; Li, Shi-Meng; Qi, Meng-Yuan; Zhao, Jian; Zhao, Qi; Liu, Hong-Sheng

    2017-10-10

    In recent years, an epidemic of the highly pathogenic avian influenza H7N9 virus has persisted in China, with a high mortality rate. To develop novel anti-influenza therapies, we have constructed a machine-learning-based scoring function (RF-NA-Score) for the effective virtual screening of lead compounds targeting the viral neuraminidase (NA) protein. RF-NA-Score is more accurate than RF-Score, with a root-mean-square error of 1.46, Pearson's correlation coefficient of 0.707, and Spearman's rank correlation coefficient of 0.707 in a 5-fold cross-validation study. The performance of RF-NA-Score in a docking-based virtual screening of NA inhibitors was evaluated with a dataset containing 281 NA inhibitors and 322 noninhibitors. Compared with other docking-rescoring virtual screening strategies, rescoring with RF-NA-Score significantly improved the efficiency of virtual screening, and a strategy that averaged the scores given by RF-NA-Score, based on the binding conformations predicted with AutoDock, AutoDock Vina, and LeDock, was shown to be the best strategy. This strategy was then applied to the virtual screening of NA inhibitors in the SPECS database. The 100 selected compounds were tested in an in vitro H7N9 NA inhibition assay, and two compounds with novel scaffolds showed moderate inhibitory activities. These results indicate that RF-NA-Score improves the efficiency of virtual screening for NA inhibitors, and can be used successfully to identify new NA inhibitor scaffolds. Scoring functions specific for other drug targets could also be established with the same method.

  13. Cancer risk and use of protease inhibitor or nonnucleoside reverse transcriptase inhibitor-based combination antiretroviral therapy: the D: A: D study

    NARCIS (Netherlands)

    Bruyand, M.; Ryom, L.; Shepherd, L.; Fatkenheuer, G.; Grulich, A.; Reiss, P.; Wit, S. de; Monforte, A.M.; Furrer, H.; Pradier, C.; Lundgren, J.; Sabin, C.; Warris, A.; et al.,

    2015-01-01

    BACKGROUND: The association between combination antiretroviral therapy (cART) and cancer risk, especially regimens containing protease inhibitors (PIs) or nonnucleoside reverse transcriptase inhibitors (NNRTIs), is unclear. METHODS: Participants were followed from the latest of D:A:D study entry or

  14. Cancer risk and use of protease inhibitor or nonnucleoside reverse transcriptase inhibitor-based combination antiretroviral therapy : the D: A: D study

    NARCIS (Netherlands)

    Bruyand, Mathias; Ryom, Lene; Shepherd, Leah; Fatkenheuer, Gerd; Grulich, Andrew; Reiss, Peter; de Wit, Stéphane; D Arminio Monforte, Antonella; Furrer, Hansjakob; Pradier, Christian; Lundgren, Jens; Sabin, Caroline; Schölvinck, Elisabeth H.

    2015-01-01

    BACKGROUND: The association between combination antiretroviral therapy (cART) and cancer risk, especially regimens containing protease inhibitors (PIs) or nonnucleoside reverse transcriptase inhibitors (NNRTIs), is unclear. METHODS: Participants were followed from the latest of D:A:D study entry or

  15. Optimisation and characterisation of tungsten thick coatings on copper based alloy substrates

    Science.gov (United States)

    Riccardi, B.; Montanari, R.; Casadei, M.; Costanza, G.; Filacchioni, G.; Moriani, A.

    2006-06-01

    Tungsten is a promising armour material for plasma facing components of nuclear fusion reactors because of its low sputter rate and favourable thermo-mechanical properties. Among all the techniques able to realise W armours, plasma spray looks particularly attractive owing to its simplicity and low cost. The present work concerns the optimisation of spraying parameters aimed at 4-5 mm thick W coating on copper-chromium-zirconium (Cu,Cr,Zr) alloy substrates. Characterisation of coatings was performed in order to assess microstructure, impurity content, density, tensile strength, adhesion strength, thermal conductivity and thermal expansion coefficient. The work performed has demonstrated the feasibility of thick W coatings on flat and curved geometries. These coatings appear as a reliable armour for medium heat flux plasma facing component.

  16. Optimisation and characterisation of tungsten thick coatings on copper based alloy substrates

    International Nuclear Information System (INIS)

    Riccardi, B.; Montanari, R.; Casadei, M.; Costanza, G.; Filacchioni, G.; Moriani, A.

    2006-01-01

    Tungsten is a promising armour material for plasma facing components of nuclear fusion reactors because of its low sputter rate and favourable thermo-mechanical properties. Among all the techniques able to realise W armours, plasma spray looks particularly attractive owing to its simplicity and low cost. The present work concerns the optimisation of spraying parameters aimed at 4-5 mm thick W coating on copper-chromium-zirconium (Cu,Cr,Zr) alloy substrates. Characterisation of coatings was performed in order to assess microstructure, impurity content, density, tensile strength, adhesion strength, thermal conductivity and thermal expansion coefficient. The work performed has demonstrated the feasibility of thick W coatings on flat and curved geometries. These coatings appear as a reliable armour for medium heat flux plasma facing component

  17. Optimisation and characterisation of tungsten thick coatings on copper based alloy substrates

    Energy Technology Data Exchange (ETDEWEB)

    Riccardi, B. [Associazione Euratom-ENEA sulla Fusione, CR Frascati, P.B. 65 00044 Frascati, Roma (Italy)]. E-mail: riccardi@frascati.enea.it; Montanari, R. [Dipartimento di Ingegneria Meccanica, Universita di Roma, Tor Vergata, 00133 Roma (Italy); Casadei, M. [Centro Sviluppo Materiali, 00100 Roma (Italy); Costanza, G. [Dipartimento di Ingegneria Meccanica, Universita di Roma, Tor Vergata, 00133 Roma (Italy); Filacchioni, G. [ENEA CR Casaccia, I-00060 S. M. di Galeria, Roma (Italy); Moriani, A. [Associazione Euratom-ENEA sulla Fusione, CR Frascati, P.B. 65 00044 Frascati, Roma (Italy)

    2006-06-30

    Tungsten is a promising armour material for plasma facing components of nuclear fusion reactors because of its low sputter rate and favourable thermo-mechanical properties. Among all the techniques able to realise W armours, plasma spray looks particularly attractive owing to its simplicity and low cost. The present work concerns the optimisation of spraying parameters aimed at 4-5 mm thick W coating on copper-chromium-zirconium (Cu,Cr,Zr) alloy substrates. Characterisation of coatings was performed in order to assess microstructure, impurity content, density, tensile strength, adhesion strength, thermal conductivity and thermal expansion coefficient. The work performed has demonstrated the feasibility of thick W coatings on flat and curved geometries. These coatings appear as a reliable armour for medium heat flux plasma facing component.

  18. Flexible Pressure Sensor with Ag Wrinkled Electrodes Based on PDMS Substrate

    Directory of Open Access Journals (Sweden)

    Jianli Cui

    2016-12-01

    Full Text Available Flexible pressure sensors are essential components of electronic skins for future attractive applications ranging from human healthcare monitoring to biomedical diagnostics, robotic skins, and prosthetic limbs. Here we report a new kind of flexible pressure sensor. The sensors are capacitive, and composed of two Ag wrinkled electrodes separated by a carbon nanotubes (CNTs/polydimethylsiloxane (PDMS composite deformable dielectric layer. Ag wrinkled electrodes were formed by vacuum deposition on top of pre-strained and relaxed PDMS substrates which were treated using an O2 plasma, a surface functionalization process, and a magnetron sputtering process. Ultimately, the developed sensor exhibits a maximum sensitivity of 19.80% kPa−1 to capacitance, great durability over 500 cycles, and rapid mechanical responses (<200 ms. We also demonstrate that our sensor can be used to effectively detect the location and distribution of finger pressure.

  19. Identifying 8-hydroxynaringenin as a suicide substrate of mushroom tyrosinase.

    Science.gov (United States)

    Chang, Te-Sheng; Lin, Meng-Yi; Lin, Hsuan-Jung

    2010-01-01

    A biotransformed metabolite of naringenin was isolated from the fermentation broth of Aspergillus oryzae, fed with naringenin, and identified as 8-hydroxynaringenin based on the mass and (1)H- and (13)C-NMR spectral data. The compound showed characteristics of both an irreversible inhibitor and a substrate of mushroom tyrosinase in preincubation and HPLC analysis. These results demonstrate that 8-hydroxynaringenin belongs to a suicide substrate of mushroom tyrosinase. The partition ratio between the compound's molecules in the formation of product and in the inactivation of the enzyme was determined to be 283 +/- 21. The present study's results, together with our previous findings, which proved that both 8-hydroxydaidzein and 8-hydroxygenistein are suicide substrates of mushroom tyrosinase, show that 7,8,4'-trihydroxyl functional groups on flavonoids' skeletons play important roles in producing suicide substrate properties toward mushroom tyrosinase.

  20. UV detectors based on epitaxial diamond films grown on single-crystal diamond substrates by vapor-phase synthesis

    International Nuclear Information System (INIS)

    Sharonov, G.V.; Petrov, S.A.; Bol'shakov, A.P.; Ral'chenko, V.G.; Kazyuchits, N.M.

    2010-01-01

    The prospects for use of CVD-technology for epitaxial growth of single-crystal diamond films of instrumental quality in UHF plasma for the production of optoelectronic devices are discussed. A technology for processing diamond single crystals that provides a perfect surface crystal structure with roughness less than 0,5 nm was developed. It was demonstrated that selective UV detectors based on synthetic single-crystal diamond substrates coated with single-crystal films can be produced. A criterion for selecting clean and structurally perfect single crystals of synthetic diamond was developed for the epitaxial growth technology. (authors)

  1. A chemical genetic screen for mTOR pathway inhibitors based on 4E-BP-dependent nuclear accumulation of eIF4E.

    Science.gov (United States)

    Livingstone, Mark; Larsson, Ola; Sukarieh, Rami; Pelletier, Jerry; Sonenberg, Nahum

    2009-12-24

    The signal transduction pathway wherein mTOR regulates cellular growth and proliferation is an active target for drug discovery. The search for new mTOR inhibitors has recently yielded a handful of promising compounds that hold therapeutic potential. This search has been limited by the lack of a high-throughput assay to monitor the phosphorylation of a direct rapamycin-sensitive mTOR substrate in cells. Here we describe a novel cell-based chemical genetic screen useful for efficiently monitoring mTOR signaling to 4E-BPs in response to stimuli. The screen is based on the nuclear accumulation of eIF4E, which occurs in a 4E-BP-dependent manner specifically upon inhibition of mTOR signaling. Using this assay in a small-scale screen, we have identified several compounds not previously known to inhibit mTOR signaling, demonstrating that this method can be adapted to larger screens. Copyright 2009 Elsevier Ltd. All rights reserved.

  2. Cholinesterase inhibitors and hospitalization for bradycardia: a population-based study.

    Directory of Open Access Journals (Sweden)

    Laura Y Park-Wyllie

    2009-09-01

    Full Text Available BACKGROUND: Cholinesterase inhibitors are commonly used to treat dementia. These drugs enhance the effects of acetylcholine, and reports suggest they may precipitate bradycardia in some patients. We aimed to examine the association between use of cholinesterase inhibitors and hospitalization for bradycardia. METHODS AND FINDINGS: We examined the health care records of more than 1.4 million older adults using a case-time-control design, allowing each individual to serve as his or her own control. Case patients were residents of Ontario, Canada, aged 67 y or older hospitalized for bradycardia between January 1, 2003 and March 31, 2008. Control patients (3:1 were not hospitalized for bradycardia, and were matched to the corresponding case on age, sex, and a disease risk index. All patients had received cholinesterase inhibitor therapy in the 9 mo preceding the index hospitalization. We identified 1,009 community-dwelling older persons hospitalized for bradycardia within 9 mo of using a cholinesterase inhibitor. Of these, 161 cases informed the matched analysis of discordant pairs. Of these, 17 (11% required a pacemaker during hospitalization, and six (4% died prior to discharge. After adjusting for temporal changes in drug utilization, hospitalization for bradycardia was associated with recent initiation of a cholinesterase inhibitor (adjusted odds ratio [OR] 2.13, 95% confidence interval [CI] 1.29-3.51. The risk was similar among individuals with pre-existing cardiac disease (adjusted OR 2.25, 95% CI 1.18-4.28 and those receiving negative chronotropic drugs (adjusted OR 2.34, 95% CI 1.16-4.71. We found no such association when we replicated the analysis using proton pump inhibitors as a neutral exposure. Despite hospitalization for bradycardia, more than half of the patients (78 of 138 cases [57%] who survived to discharge subsequently resumed cholinesterase inhibitor therapy. CONCLUSIONS: Among older patients, initiation of cholinesterase

  3. Structural insights into the binding mechanism of IDO1 with hydroxylamidine based inhibitor INCB14943

    International Nuclear Information System (INIS)

    Wu, You; Xu, Tingting; Liu, Jinsong; Ding, Ke; Xu, Jinxin

    2017-01-01

    IDO1 (indoleamine 2, 3-dioxygenase 1), a well characterized immunosuppressive enzyme, has attracted growing attention as a potential target for cancer immunotherapy. Hydroxylamidine compounds INCB024360 and INCB14943 (INCB024360 analogue) are highly effective IDO1 inhibitors. INCB024360 is undergoing clinical trials for treatment of various types of human cancer. Here, we determined the co-crystal structure of IDO1 and INCB14943, and elucidate the detailed binding mode. INCB14943 binds to heme iron in IDO1 protein through the oxime nitrogen. Further analysis also reveals that a halogen bonding interaction between the chlorine atom (3-Cl) of INCB14943 and the sulphur atom of C129 significantly improves the inhibition activity against IDO1. Comparing with the other reported inhibitors, the oxime nitrogen and halogen bond interaction are identified as the unique features of INCB14943 among the IDO1 inhibitors. Thus, our study provides novel insights into the interaction between a small molecule inhibitor INCB14943 and IDO1 protein. The structural information will facilitate future IDO1 inhibitor design. - Highlights: • This is the first co-crystal structure of IDO1 with hydroxylamidine compound. • INCB14943 binds to heme iron through oxime nitrogen instead of imidazole nitrogen. • Halogen bond interaction with C129 is another unique feature of INCB14943.

  4. In vivo evaluation of an oral delivery system for P-gp substrates based on thiolated chitosan.

    Science.gov (United States)

    Föger, Florian; Schmitz, Thierry; Bernkop-Schnürch, Andreas

    2006-08-01

    Recently, thiolated polymers, so called thiomers, have been reported to modulate drug absorption by inhibition of intestinal P-glycoprotein (P-gp). The aim of the present study was to provide a proof-of-principle for a delivery system based on thiolated chitosan in vivo in rats, using rhodamine-123 (Rho-123) as representative P-gp substrate. In vitro, the permeation enhancing effect of unmodified chitosan, chitosan-4 thiobutylamidine (Ch-TBA) and the combination of Ch-TBA with reduced glutathione (GSH) was evaluated by using freshly excised rat intestinal mucosa mounted in Ussing-type chambers. In comparison to buffer only, Rho-123 transport in presence of 0.5% (w/v) chitosan, 0.5% (w/v) Ch-TBA and the combination of 0.5% (w/v) Ch-TBA/0.5% (w/v) GSH, was 1.8-fold, 2.6-fold, 3.8-fold improved, respectively. Furthermore, enteric-coated tablets based on unmodified chitosan or Ch-TBA/GSH, were investigated in vivo. In rats, the Ch-TBA/GSH tablets increased the area under the plasma concentration time curve (AUC0-12) of Rho-123 by 217% in comparison to buffer control and by 58% in comparison to unmodified chitosan. This in vivo study showed that a delivery system based on thiolated chitosan significantly increased the oral bioavailability of P-gp substrate Rho-123.

  5. Wireless sEMG System with a Microneedle-Based High-Density Electrode Array on a Flexible Substrate.

    Science.gov (United States)

    Kim, Minjae; Gu, Gangyong; Cha, Kyoung Je; Kim, Dong Sung; Chung, Wan Kyun

    2017-12-30

    Surface electromyography (sEMG) signals reflect muscle contraction and hence, can provide information regarding a user's movement intention. High-density sEMG systems have been proposed to measure muscle activity in small areas and to estimate complex motion using spatial patterns. However, conventional systems based on wet electrodes have several limitations. For example, the electrolyte enclosed in wet electrodes restricts spatial resolution, and these conventional bulky systems limit natural movements. In this paper, a microneedle-based high-density electrode array on a circuit integrated flexible substrate for sEMG is proposed. Microneedles allow for high spatial resolution without requiring conductive substances, and flexible substrates guarantee stable skin-electrode contact. Moreover, a compact signal processing system is integrated with the electrode array. Therefore, sEMG measurements are comfortable to the user and do not interfere with the movement. The system performance was demonstrated by testing its operation and estimating motion using a Gaussian mixture model-based, simplified 2D spatial pattern.

  6. Identification of human flap endonuclease 1 (FEN1) inhibitors using a machine learning based consensus virtual screening.

    Science.gov (United States)

    Deshmukh, Amit Laxmikant; Chandra, Sharat; Singh, Deependra Kumar; Siddiqi, Mohammad Imran; Banerjee, Dibyendu

    2017-07-25

    Human Flap endonuclease1 (FEN1) is an enzyme that is indispensable for DNA replication and repair processes and inhibition of its Flap cleavage activity results in increased cellular sensitivity to DNA damaging agents (cisplatin, temozolomide, MMS, etc.), with the potential to improve cancer prognosis. Reports of the high expression levels of FEN1 in several cancer cells support the idea that FEN1 inhibitors may target cancer cells with minimum side effects to normal cells. In this study, we used large publicly available, high-throughput screening data of small molecule compounds targeted against FEN1. Two machine learning algorithms, Support Vector Machine (SVM) and Random Forest (RF), were utilized to generate four classification models from huge PubChem bioassay data containing probable FEN1 inhibitors and non-inhibitors. We also investigated the influence of randomly selected Zinc-database compounds as negative data on the outcome of classification modelling. The results show that the SVM model with inactive compounds was superior to RF with Matthews's correlation coefficient (MCC) of 0.67 for the test set. A Maybridge database containing approximately 53 000 compounds was screened and top ranking 5 compounds were selected for enzyme and cell-based in vitro screening. The compound JFD00950 was identified as a novel FEN1 inhibitor with in vitro inhibition of flap cleavage activity as well as cytotoxic activity against a colon cancer cell line, DLD-1.

  7. Guanfu base A, an antiarrhythmic alkaloid of Aconitum coreanum, Is a CYP2D6 inhibitor of human, monkey, and dog isoforms.

    Science.gov (United States)

    Sun, Jianguo; Peng, Ying; Wu, Hui; Zhang, Xueyuan; Zhong, Yunxi; Xiao, Yanan; Zhang, Fengyi; Qi, Huanhuan; Shang, Lili; Zhu, Jianping; Sun, Yue; Liu, Ke; Liu, Jinghan; A, Jiye; Ho, Rodney J Y; Wang, Guangji

    2015-05-01

    Guanfu base A (GFA) is a novel heterocyclic antiarrhythmic drug isolated from Aconitum coreanum (Lèvl.) rapaics and is currently in a phase IV clinical trial in China. However, no study has investigated the influence of GFA on cytochrome P450 (P450) drug metabolism. We characterized the potency and specificity of GFA CYP2D inhibition based on dextromethorphan O-demethylation, a CYP2D6 probe substrate of activity in human, mouse, rat, dog, and monkey liver microsomes. In addition, (+)-bufuralol 1'-hydroxylation was used as a CYP2D6 probe for the recombinant form (rCYP2D6), 2D1 (rCYP2D1), and 2D2 (rCYP2D2) activities. Results show that GFA is a potent noncompetitive inhibitor of CYP2D6, with inhibition constant Ki = 1.20 ± 0.33 μM in human liver microsomes (HLMs) and Ki = 0.37 ± 0.16 μM for the human recombinant form (rCYP2D6). GFA is also a potent competitive inhibitor of CYP2D in monkey (Ki = 0.38 ± 0.12 μM) and dog (Ki = 2.4 ± 1.3 μM) microsomes. However, GFA has no inhibitory activity on mouse or rat CYP2Ds. GFA did not exhibit any inhibition activity on human recombinant CYP1A2, 2A6, 2C8, 2C19, 3A4, or 3A5, but showed slight inhibition of 2B6 and 2E1. Preincubation of HLMs and rCYP2D6 resulted in the inactivation of the enzyme, which was attenuated by GFA or quinidine. Beagle dogs treated intravenously with dextromethorphan (2 mg/ml) after pretreatment with GFA injection showed reduced CYP2D metabolic activity, with the Cmax of dextrorphan being one-third that of the saline-treated group and area under the plasma concentration-time curve half that of the saline-treated group. This study suggests that GFA is a specific CYP2D6 inhibitor that might play a role in CYP2D6 medicated drug-drug interaction. Copyright © 2015 by The American Society for Pharmacology and Experimental Therapeutics.

  8. Ligand-based modeling of Akt3 lead to potent dual Akt1/Akt3 inhibitor.

    Science.gov (United States)

    Al-Sha'er, Mahmoud A; Taha, Mutasem O

    2018-02-13

    Akt1 and Akt3 are important serine/threonine-specific protein kinases involved in G2 phase required by cancer cells to maintain cell cycle and to prevent cell death. Accordingly, inhibitors of these kinases should have potent anti-cancer properties. This prompted us to use pharmacophore/QSAR modeling to identify optimal binding models and physicochemical descriptors that explain bioactivity variation within a set of 74 diverse Akt3 inhibitors. Two successful orthogonal pharmacophores were identified and further validated using receiver operating characteristic (ROC) curve analyses. The pharmacophoric models and associated QSAR equation were applied to screen the national cancer institute (NCI) list of compounds for new Akt3 inhibitors. Six hits showed significant experimental anti-Akt3 IC 50 values, out of which one compound exhibited dual low micromolar anti-Akt1 and anti-Akt3 inhibitory profiles. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. Identification of AI-2 Quorum Sensing Inhibitors in Vibrio harveyi Through Structure-Based Virtual Screening.

    Science.gov (United States)

    Jiang, Tianyu; Zhu, Peng; Du, Lupei; Li, Minyong

    2018-01-01

    Quorum sensing (QS) is a cell-to-cell communication system that regulates gene expression as a result of the production and perception of signal molecules called autoinducers (AIs). AI-2 is a QS autoinducer produced by both Gram-negative and Gram-positive bacteria, in which it regulates intraspecies and interspecies communication. The identification of QS inhibitors is considered a promising strategy for the development of anti-virulence drugs with reduced selective pressure for resistance. Here we describe a high-throughput virtual screening approach to identify AI-2 quorum sensing inhibitors on the basis of Vibrio harveyi LuxPQ crystal structure. Seven potent inhibitors with IC 50 values in the micromolar range were selected with no effect or low effect on V. harveyi growth rate.

  10. Exploration of mild copper-mediated coupling of organotrifluoroborates in the synthesis of thiirane-based inhibitors of matrix metalloproteinases.

    Science.gov (United States)

    Testero, Sebastian A; Bouley, Renee; Fisher, Jed F; Chang, Mayland; Mobashery, Shahriar

    2011-05-01

    The copper-mediated and non-basic oxidative cross-coupling of organotrifluoroborates with phenols was applied to elaboration of the structures of thiirane-based inhibitors of matrix metalloproteinases. By revision of the synthetic sequence to allow this cross-coupling as the final step, and taking advantage of the neutral nature of organotrifluoroborate cross-coupling, a focussed series of inhibitors showing aryloxy and alkenyloxy replacement of the phenoxy substituent was prepared. This reaction shows exceptional promise as an alternative to the classic copper-mediated but strongly basic Ullmann reaction, for the diversification of ether segments within base-labile lead structures. Copyright © 2010 Elsevier Ltd. All rights reserved.

  11. Designing of phenol-based β-carbonic anhydrase1 inhibitors through QSAR, molecular docking, and MD simulation approach.

    Science.gov (United States)

    Ahamad, Shahzaib; Hassan, Md Imtaiyaz; Dwivedi, Neeraja

    2018-05-01

    Tuberculosis (Tb) is an airborne infectious disease caused by Mycobacterium tuberculosis. Beta-carbonic anhydrase 1 ( β-CA1 ) has emerged as one of the potential targets for new antitubercular drug development. In this work, three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking, and molecular dynamics (MD) simulation approaches were performed on a series of natural and synthetic phenol-based β-CA1 inhibitors. The developed 3D-QSAR model ( r 2  = 0.94, q 2  = 0.86, and pred_r 2  = 0.74) indicated that the steric and electrostatic factors are important parameters to modulate the bioactivity of phenolic compounds. Based on this indication, we designed 72 new phenolic inhibitors, out of which two compounds (D25 and D50) effectively stabilized β-CA1 receptor and, thus, are potential candidates for new generation antitubercular drug discovery program.

  12. Preadmission Use of Platelet Inhibitors and Short-Term Stroke Mortality:A Population-Based Cohort Study

    DEFF Research Database (Denmark)

    Würtz, Morten; Schmidt, Morten; Grove, Erik Lerkevang

    2018-01-01

    Aims: The impact of preadmission antiplatelet treatment on prognosis after stroke is poorly understood. We therefore investigated whether preadmission use of aspirin and clopidogrel was associated with mortality in patients hospitalized with ischemic stroke, intracerebral hemorrhage (ICH......), or subarachnoid hemorrhage (SAH). Methods and Results: We used nationwide population-based registries to identify all first-time hospitalizations for stroke and subsequent mortality in patients treated with aspirin and clopidogrel in Denmark during 2004-2012. Based on redeemed prescriptions, we computed absolute...... 30-day mortality rates and mortality rate ratios (MRRs) for current platelet inhibitor users and non-users. We used Cox regression to control for potentially confounding factors. Among platelet inhibitor non-users, 30-day stroke mortality was 12.0% (8.8% for ischemic stroke, 29.6% for ICH, and 21...

  13. Radiolabeled hydroxamate-based matrix metalloproteinase inhibitors: How chemical modifications affect pharmacokinetics and metabolic stability

    International Nuclear Information System (INIS)

    Hugenberg, Verena; Hermann, Sven; Galla, Fabian; Schäfers, Michael

    2016-01-01

    Introduction: Dysregulated MMP expression or activation is associated with several diseases. To study MMP activity in vivo by means of PET a radiolabeled MMP inhibitor (MMPI) functioning as radiotracer has been developed by our group based on the lead structure CGS 25966. Materials and methods: Aiming at the modification of the pharmacokinetics of this lipophilic model tracer a new class of MMPIs has been discovered, consisting of additional fluorinated hydrophilic substructures, such as mini-PEG and/or 1,2,3-triazole units. To identify the best candidate for further clinical applications, radiofluorinated compounds of each subgroup have been (radio) synthesized and evaluated regarding their biodistribution behavior and their metabolic stability. Results: Radiosyntheses of different triazole based MMPIs could be realized using two step “click chemistry” procedures. Compared to lead structure [ 18 F]FEtO-CGS 25966 ([ 18 F]1e, log D(exp) = 2.02, IC 50 = 2–50 nM) all selected candidates showed increased hydrophilicities and inhibition potencies (log D(exp) = 0.23–1.25, IC 50 = 0.006–6 nM). Interestingly, despite different hydrophilicities most triazole based MMPIs showed no significant differences in their in vivo biodistribution behavior and were cleared predominantly via the hepatobiliary excretion route. Biostability and metabolism studies in vitro and in vivo revealed significant higher metabolic stability for the triazole moiety compared to the benzyl ring in the lead structure. Cleavage of ethylene glycol subunits of the mini-PEG chain led to a faster metabolism of mini-PEG containing MMPIs. Conclusion: The introduction of hydrophilic groups such as mini-PEG and 1,2,3-triazole units did not lead to a significant shift of the hepatobiliary elimination towards renal clearance. Particularly the introduction of mini-PEG chains led to an intense metabolic decomposition. Substitution of the benzyl moiety in lead structure 1e by a 1,2,3-trizole ring resulted

  14. One-carbon substrate-based biohydrogen production: microbes, mechanism, and productivity.

    Science.gov (United States)

    Rittmann, Simon K-M R; Lee, Hyun Sook; Lim, Jae Kyu; Kim, Tae Wan; Lee, Jung-Hyun; Kang, Sung Gyun

    2015-01-01

    Among four basic mechanisms for biological hydrogen (H2) production, dark fermentation has been considered to show the highest hydrogen evolution rate (HER). H2 production from one-carbon (C1) compounds such as formate and carbon monoxide (CO) is promising because formate is an efficient H2 carrier, and the utilization of CO-containing syngas or industrial waste gas may render the industrial biohydrogen production process cost-effective. A variety of microbes with the formate hydrogen lyase (FHL) system have been identified from phylogenetically diverse groups of archaea and bacteria, and numerous efforts have been undertaken to improve the HER for formate through strain optimization and bioprocess development. CO-dependent H2 production has been investigated to enhance the H2 productivity of various carboxydotrophs via an increase in CO gas-liquid mass transfer rates and the construction of genetically modified strains. Hydrogenogenic CO-conversion has been applied to syngas and by-product gas of the steel-mill process, and this low-cost feedstock has shown to be promising in the production of biomass and H2. Here, we focus on recent advances in the isolation of novel phylogenetic groups utilizing formate or CO, the remarkable genetic engineering that enhances H2 productivity, and the practical implementation of H2 production from C1 substrates. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Molten Salt-Based Growth of Bulk GaN and InN for Substrates

    Energy Technology Data Exchange (ETDEWEB)

    Waldrip, Karen Elizabeth [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Advanced Power Sources Technology Dept.; Tsao, Jeffrey Yeenien [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Energy Sciences Dept.; Kerley, Thomas M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Advanced Materials Sciences Dept.

    2006-09-01

    An atmospheric pressure approach to growth of bulk group III-nitrides is outlined. Native III-nitride substrates for optoelectronic and high power, high frequency electronics are desirable to enhance performance and reliability of these devices; currently, these materials are available in research quantities only for GaN, and are unavailable in the case of InN. The thermodynamics and kinetics of the reactions associated with traditional crystal growth techniques place these activities on the extreme edges of experimental physics. The technique described herein relies on the production of the nitride precursor (N3-) by chemical and/or electrochemical methods in a molten halide salt. This nitride ion is then reacted with group III metals in such a manner as to form the bulk nitride material. The work performed during the period of funding (July 2004-September 2005) focused on the initial measurement of the solubility of GaN in molten LiCl as a function of temperature, the construction of electrochemical cells, the modification of a commercial glove box (required for handling very hygroscopic LiCl), and on securing intellectual property for the technique.

  16. Low-cost flexible supercapacitors based on laser reduced graphene oxide supported on polyethylene terephthalate substrate

    Science.gov (United States)

    Ghoniem, Engy; Mori, Shinsuke; Abdel-Moniem, Ahmed

    2016-08-01

    A controlled high powered CO2 laser system is used to reduce and pattern graphene oxide (GO) film supported onto a flexible polyethylene terephthalate (PET) substrate. The laser reduced graphene oxide (rGO) film is characterized and evaluated electrochemically in the absence and presence of an overlying anodicaly deposited thin film of pseuodcapactive MnO2 as electrodes for supercapacitor applications using aqueous electrolyte. The laser treatment of the GO film leads to an overlapped structure of defective multi-layer rGO sheets with an electrical conductivity of 273 S m-1. The rGO and MnO2/rGO electrodes exhibit specific capacitance in the range of 82-107 and 172-368 Fg-1 at applied current range of 0.1-1.0 mA cm-2 and retain 98 and 95% of their initial capacitances after 2000 cycles at a current density of 1.0 mA cm-2, respectively. Also, the rGO is assigned as an electrode material for flexible conventionally stacked and interdigitated in-plane supercapacitor structures using gel electrolyte. Three electrode architectures of 2, 4, and 6 sub-electrodes are studied for the interdigital in-plane design. The device with interdigital 6 sub-electrodes architecture I-PS(6) delivers power density of 537.1 Wcm-3 and an energy density of 0.45 mWh cm-3.

  17. Dinuclear ru-aqua complexes for selective epoxidation catalysis based on supramolecular substrate orientation effects

    KAUST Repository

    Di Giovanni, Carlo; Poater, Albert; Benet-Buchholz, Jordi; Cavallo, Luigi; Solà , Miquel; Llobet, Antoni A.

    2014-01-01

    Ru-aqua complex {[RuII(trpy)(H2O)] 2(μ-pyr-dc)}+ is a powerful epoxidation catalyst for a wide range of linear and cyclic alkenes. High turnover numbers (TNs), up to 17000, and turnover frequencies (TOF), up to 24120 h-1 (6.7 s -1), have been obtained using PhIO as oxidant. This species presents an outstanding stereospecificity for both cis and trans olefins towards the formation of their corresponding cis and trans epoxides. In addition, it shows different reactivity to cis and trans olefins due to a substrate orientation supramolecular effect transmitted by its ligand scaffold. This effect together with the impressive reaction rates are rationalized using electrochemical techniques and DFT calculations. A new Ru-aqua complex that behaves as a powerful epoxidation catalyst for a wide range of linear and cyclic alkenes is reported. High turnover numbers and frequencies are obtained by using PhIO as oxidant. The complex shows an outstanding stereospecificity for both cis and trans olefins towards the formation of their corresponding cis and trans epoxides (see figure). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Self-assembly nanoparticle based tripetaloid structure arrays as surface-enhanced Raman scattering substrates

    International Nuclear Information System (INIS)

    Sun Mingrui; Qian Chuang; Wu Wengang; Yu Wenxuan; Wang Yifei; Mao Haiyang

    2012-01-01

    This paper reports a novel highly ordered tripetaloid structure array (TPSA) which performs very well as an active surface-enhanced Raman scattering (SERS) substrate. The TPSA is easily fabricated by anisotropic etching of a self-assembly silica-nanoparticle bilayer and a subsequent metal deposition step, with notable uniformity and reproducibility. Electromagnetic simulation indicates that the narrow inter-gaps and edge protrusions in the TPSA act as hot spots. In addition, the peak electromagnetic field intensity in the inter-gaps changes slightly and periodically as the polarization of the incident light varies from 0° to 360°. SERS experiments show that the SERS enhancement factor (EF) of a Au-film-covered TPSA is 12 times higher than that of regular Au-film-over-nanoparticles, and not sensitive to the polarization of the incident light. The spatially averaged EF of the TPSA is as high as 5.7 × 10 6 , and the local EF of its hot spots is much higher. (paper)

  19. Lead toxicity thresholds in 17 Chinese soils based on substrate-induced nitrification assay.

    Science.gov (United States)

    Li, Ji; Huang, Yizong; Hu, Ying; Jin, Shulan; Bao, Qiongli; Wang, Fei; Xiang, Meng; Xie, Huiting

    2016-06-01

    The influence of soil properties on toxicity threshold values for Pb toward soil microbial processes is poorly recognized. The impact of leaching on the Pb threshold has not been assessed systematically. Lead toxicity was screened in 17 Chinese soils using a substrate-induced nitrification (SIN) assay under both leached and unleached conditions. The effective concentration of added Pb causing 50% inhibition (EC50) ranged from 185 to >2515mg/kg soil for leached soil and 130 to >2490mg/kg soil for unleached soil. These results represented >13- and >19-fold variations among leached and unleached soils, respectively. Leaching significantly reduced Pb toxicity for 70% of both alkaline and acidic soils tested, with an average leaching factor of 3.0. Soil pH and CEC were the two most useful predictors of Pb toxicity in soils, explaining over 90% of variance in the unleached EC50 value. The relationships established in the present study predicted Pb toxicity within a factor of two of measured values. These relationships between Pb toxicity and soil properties could be used to establish site-specific guidance on Pb toxicity thresholds. Copyright © 2016. Published by Elsevier B.V.

  20. Dinuclear ru-aqua complexes for selective epoxidation catalysis based on supramolecular substrate orientation effects

    KAUST Repository

    Di Giovanni, Carlo

    2014-03-03

    Ru-aqua complex {[RuII(trpy)(H2O)] 2(μ-pyr-dc)}+ is a powerful epoxidation catalyst for a wide range of linear and cyclic alkenes. High turnover numbers (TNs), up to 17000, and turnover frequencies (TOF), up to 24120 h-1 (6.7 s -1), have been obtained using PhIO as oxidant. This species presents an outstanding stereospecificity for both cis and trans olefins towards the formation of their corresponding cis and trans epoxides. In addition, it shows different reactivity to cis and trans olefins due to a substrate orientation supramolecular effect transmitted by its ligand scaffold. This effect together with the impressive reaction rates are rationalized using electrochemical techniques and DFT calculations. A new Ru-aqua complex that behaves as a powerful epoxidation catalyst for a wide range of linear and cyclic alkenes is reported. High turnover numbers and frequencies are obtained by using PhIO as oxidant. The complex shows an outstanding stereospecificity for both cis and trans olefins towards the formation of their corresponding cis and trans epoxides (see figure). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Fabrication of transparent superhydrophobic silica-based film on a glass substrate

    Science.gov (United States)

    Wang, Shing-Dar; Luo, Shih-Shiang

    2012-05-01

    Tetraethoxysilane (TEOS) was hydrolyzed in an acidic environment and then reacted with hexamethyldisilazane (HMDS) to obtain a superhydrophobic transparent film on a glass substrate. The molar ratios of water and ethanol to TEOS, the pH value of the acidic (or basic) water that is used to hydrolyze TEOS, the heat treatment conditions and other factors were investigated systematically to optimize the transmission through, and the contact angle of water on the film. HMDS (total amount of HMDS/TEOS = 2) was divided into 20 parts, which were added into the sol successively to prevent the sudden production of a large quantity of NH3 in a small area of the sol. The optical and hydrophobic properties of the sol gel continued to change after it had been prepared. The conditions that TEOS was hydrolyzed with acidic water at pH 1.2 at 70 °C and the sol gel was aged at 20 °C for 48 h realized transmission of 90.9% and a water contact angle of 154.3°. No additional surface chemistry modification was needed.

  2. Caprylate Salts Based on Amines as Volatile Corrosion Inhibitors for Metallic Zinc: Theoretical and Experimental Studies

    Science.gov (United States)

    Valente, Marco A. G.; Teixeira, Deiver A.; Azevedo, David L.; Feliciano, Gustavo T.; Benedetti, Assis V.; Fugivara, Cecílio S.

    2017-01-01

    The interaction of volatile corrosion inhibitors (VCI), caprylate salt derivatives from amines, with zinc metallic surfaces is assessed by density functional theory (DFT) computer simulations, electrochemical impedance (EIS) measurements and humid chamber tests. The results obtained by the different methods were compared, and linear correlations were obtained between theoretical and experimental data. The correlations between experimental and theoretical results showed that the molecular size is the determining factor in the inhibition efficiency. The models used and experimental results indicated that dicyclohexylamine caprylate is the most efficient inhibitor. PMID:28620602

  3. The TosMIC approach to 3-(oxazol-5-yl) indoles: application to the synthesis of indole-based IMPDH inhibitors.

    Science.gov (United States)

    Dhar, T G Murali; Shen, Zhongqi; Fleener, Catherine A; Rouleau, Katherine A; Barrish, Joel C; Hollenbaugh, Diane L; Iwanowicz, Edwin J

    2002-11-18

    A modified approach to the synthesis of 3-(oxazolyl-5-yl) indoles is reported. This method was applied to the synthesis of series of novel indole based inhibitors of inosine monophosphate dehydrogenase (IMPDH). The synthesis and the structure-activity relationships (SARs), derived from in vitro studies, for this new series of inhibitors is given.

  4. Quinolone-based IMPDH inhibitors: introduction of basic residues on ring D and SAR of the corresponding mono, di and benzofused analogues.

    Science.gov (United States)

    Dhar, T G Murali; Watterson, Scott H; Chen, Ping; Shen, Zhongqi; Gu, Henry H; Norris, Derek; Carlsen, Marianne; Haslow, Kristin D; Pitts, William J; Guo, Junqing; Chorba, John; Fleener, Catherine A; Rouleau, Katherine A; Townsend, Robert; Hollenbaugh, Diane; Iwanowicz, Edwin J

    2003-02-10

    The synthesis and the structure-activity relationships (SAR) of analogues derived from the introduction of basic residues on ring D of quinolone-based inhibitors of IMPDH are described. This led to the identification of compound 27 as a potent inhibitor of IMPDH with significantly improved aqueous solubility over the lead compound 1.

  5. CMV and BKPyV Infections in Renal Transplant Recipients Receiving an mTOR Inhibitor-Based Regimen Versus a CNI-Based Regimen: A Systematic Review and Meta-Analysis of Randomized, Controlled Trials.

    Science.gov (United States)

    Mallat, Samir G; Tanios, Bassem Y; Itani, Houssam S; Lotfi, Tamara; McMullan, Ciaran; Gabardi, Steven; Akl, Elie A; Azzi, Jamil R

    2017-08-07

    The objective of this meta-analysis is to compare the incidences of cytomegalovirus and BK polyoma virus infections in renal transplant recipients receiving a mammalian target of rapamycin inhibitor (mTOR)-based regimen compared with a calcineurin inhibitor-based regimen. We conducted a comprehensive search for randomized, controlled trials up to January of 2016 addressing our objective. Other outcomes included acute rejection, graft loss, serious adverse events, proteinuria, wound-healing complications, and eGFR. Two review authors selected eligible studies, abstracted data, and assessed risk of bias. We assessed quality of evidence using the Grading of Recommendations Assessment, Development and Evaluation methodology. We included 28 randomized, controlled trials with 6211 participants classified into comparison 1: mTOR inhibitor versus calcineurin inhibitor and comparison 2: mTOR inhibitor plus reduced dose of calcineurin inhibitor versus regular dose of calcineurin inhibitor. Results showed decreased incidence of cytomegalovirus infection in mTOR inhibitor-based group in both comparison 1 (risk ratio, 0.54; 95% confidence interval, 0.41 to 0.72), with high quality of evidence, and comparison 2 (risk ratio, 0.43; 95% confidence interval, 0.24 to 0.80), with moderate quality of evidence. The available evidence neither confirmed nor ruled out a reduction of BK polyoma virus infection in mTOR inhibitor-based group in both comparisons. Secondary outcomes revealed more serious adverse events and acute rejections in mTOR inhibitor-based group in comparison 1 and no difference in comparison 2. There was no difference in graft loss in both comparisons. eGFR was higher in the mTOR inhibitor-based group in comparison 1 (mean difference =4.07 ml/min per 1.73 m 2 ; 95% confidence interval, 1.34 to 6.80) and similar to the calcineurin inhibitor-based group in comparison 2. More proteinuria and wound-healing complications occurred in the mTOR inhibitor-based groups. We found

  6. Pharmacophore-Based Repositioning of Approved Drugs as Novel Staphylococcus aureus NorA Efflux Pump Inhibitors.

    Science.gov (United States)

    Astolfi, Andrea; Felicetti, Tommaso; Iraci, Nunzio; Manfroni, Giuseppe; Massari, Serena; Pietrella, Donatella; Tabarrini, Oriana; Kaatz, Glenn W; Barreca, Maria L; Sabatini, Stefano; Cecchetti, Violetta

    2017-02-23

    An intriguing opportunity to address antimicrobial resistance is represented by the inhibition of efflux pumps. Focusing on NorA, the most important efflux pump of Staphylococcus aureus, an efflux pump inhibitors (EPIs) library was used for ligand-based pharmacophore modeling studies. By exploitation of the obtained models, an in silico drug repositioning approach allowed for the identification of novel and potent NorA EPIs.

  7. Imidazopyridine-based inhibitors of glycogen synthase kinase 3: synthesis and evaluation of amide isostere replacements of the carboxamide scaffold.

    Science.gov (United States)

    Yngve, Ulrika; Söderman, Peter; Svensson, Mats; Rosqvist, Susanne; Arvidsson, Per I

    2012-11-01

    In this study, we explored the effect of bioisostere replacement in a series of glycogen synthase kinase 3 (GSK3) inhibitors based on the imidazopyridine core. The synthesis and biological evaluation of a number of novel sulfonamide, 1,2,4-oxadiazole, and thiazole derivates as amide bioisosteres, as well as a computational rationalization of the obtained results are reported. Copyright © 2012 Verlag Helvetica Chimica Acta AG, Zürich.

  8. Unprecedented Binding Mode of Hydroxamate-Based Inhibitors of Glutamate Carboxypeptidase II: Structural Characterization and Biological Activity

    Czech Academy of Sciences Publication Activity Database

    Nováková, Zora; Wozniak, K.; Jančařík, Andrej; Rais, R.; Wu, Y.; Pavlíček, Jiří; Ferraris, D.; Havlínová, Barbora; Ptáček, Jakub; Vávra, Jan; Hin, N.; Rojas, C.; Majer, Pavel; Slusher, B. S.; Tsukamoto, T.; Bařinka, Cyril

    2016-01-01

    Roč. 59, č. 10 (2016), s. 4539-4550 ISSN 0022-2623 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0109; GA ČR GAP301/12/1513 Institutional support: RVO:86652036 ; RVO:61388963 Keywords : LINKED ACIDIC DIPEPTIDASE * N-ACETYLASPARTYLGLUTAMATE NAAG * THIOL-BASED INHIBITORS Subject RIV: FR - Pharmacology ; Medidal Chemistry ; CC - Organic Chemistry (UOCHB-X) Impact factor: 6.259, year: 2016

  9. Offshore Substrate

    Data.gov (United States)

    California Natural Resource Agency — This shapefile displays the distribution of substrate types from Pt. Arena to Pt. Sal in central/northern California. Originally this data consisted of seven paper...

  10. Effect of Peptides' Binding on the Antimicrobial Activity and Biocompatibility of Protein-Based Substrates

    Science.gov (United States)

    Kaisersberger Vincek, Maja

    This work reveals the effect of coupling approach (chemical by using carbodiimide chemistry and grafting-to vs. grafting-from synthesis routes, and enzymatic by using transglutaminase) of a hydrophilic epsilon-poly-L-lysine (epsilonPL) and an amphiphilic oligo-acyl-lysyl (OAK) derivative (K-7alpha 12-OH) to wool fibers and gelatine (GEL) macromolecules, respectively, and substrates antibacterial activity against Gram-negative E. coli and Gram-positive S. aureus bacteria after 1-24 h of exposure, as well as their cytotoxicity. Different spectroscopic (ultraviolet-visible, infrared, fluorescence and electron paramagnetic resonance) and separation techniques (size-exclusion chromatography and capillary zone electrophoresis) as well as zeta potential and potentiometric titration analysis, were performed to confirm the covalent coupling of epsilonPL/OAK, and to determine the amount and orientation of its immobilisation. The highest and kinetically the fastest level of bacterial reduction was achieved with wool/GEL functionalised with epsilonPL/OAK by chemical grafting-to approach. This effect correlated with both the highest grafting yield and conformationally the highly-flexible (brush-like) orientation linkage of epsilonPL/OAK, implicating on the highest amount of accessible amino groups interacting with bacterial membrane. However, OAK's amphipathic structure, the cationic charge and the hydrophobic moieties, resulted to relatively high reduction of S. aureus for grafting-from and the enzymatic coupling approaches using OAK-functionalised GEL. The epsilonPL/OAK-functionalised GEL did not induce toxicity in human osteoblast cells, even at 25-fold higher concentration than bacterial minimum inhibitory (MIC) concentration of epsilonPL/OAK, supporting their potential usage in biomedical applications. It was also shown that non-ionic surfactant adsorbs strongly onto the wool surface during the process of washing, thereby blocking the functional sites of immobilized

  11. Wax inhibitor based on ethylene vinyl acetate with methyl methacrylate and diethanolamine for crude oil pipeline

    Science.gov (United States)

    Anisuzzaman, S. M.; Abang, S.; Bono, A.; Krishnaiah, D.; Karali, R.; Safuan, M. K.

    2017-06-01

    Wax precipitation and deposition is one of the most significant flow assurance challenges in the production system of the crude oil. Wax inhibitors are developed as a preventive strategy to avoid an absolute wax deposition. Wax inhibitors are polymers which can be known as pour point depressants as they impede the wax crystals formation, growth, and deposition. In this study three formulations of wax inhibitors were prepared, ethylene vinyl acetate, ethylene vinyl acetate co-methyl methacrylate (EVA co-MMA) and ethylene vinyl acetate co-diethanolamine (EVA co-DEA) and the comparison of their efficiencies in terms of cloud point¸ pour point, performance inhibition efficiency (%PIE) and viscosity were evaluated. The cloud point and pour point for both EVA and EVA co-MMA were similar, 15°C and 10-5°C, respectively. Whereas, the cloud point and pour point for EVA co-DEA were better, 10°C and 10-5°C respectively. In conclusion, EVA co-DEA had shown the best % PIE (28.42%) which indicates highest percentage reduction of wax deposit as compared to the other two inhibitors.

  12. Simple, mammalian cell-based assay for identification of inhibitors of the Erk MAP kinase pathway

    Czech Academy of Sciences Publication Activity Database

    Krejčí, Pavel; Pejchalová, K.; Wilcox, W.R.

    2007-01-01

    Roč. 25, č. 4 (2007), s. 391-395 ISSN 0167-6997 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : Erk * inhibitor * FGFR3 Subject RIV: BO - Biophysics Impact factor: 2.806, year: 2007

  13. Fragment-based lead discovery of small molecule inhibitors for the EPHA4 receptor tyrosine kinase

    NARCIS (Netherlands)

    van Linden, O.P.J.; Farenc, C; Zoutman, W.H.; Hameetman, L; Wijtmans, M.; Leurs, R.; Tensen, C.P.; Siegal, G.; de Esch, I.J.P.

    2011-01-01

    The in silico identification, optimization and crystallographic characterization of a 6,7,8,9-tetrahydro-3H-pyrazolo[3,4-c]isoquinolin-1-amine scaffold as an inhibitor for the EPHA4 receptor tyrosine kinase is described. A database containing commercially available compounds was subjected to an in

  14. Design of Highly Potent Urea-Based, Exosite-Binding Inhibitors Selective for Glutamate Carboxypeptidase II

    Czech Academy of Sciences Publication Activity Database

    Tykvart, Jan; Schimer, Jiří; Jančařík, Andrej; Bařinková, Jitka; Navrátil, Václav; Starková, Jana; Šrámková, Karolína; Konvalinka, Jan; Majer, Pavel; Šácha, Pavel

    2015-01-01

    Roč. 58, č. 10 (2015), s. 4357-4363 ISSN 0022-2623 R&D Projects: GA ČR GBP208/12/G016; GA MŠk LO1302 Institutional support: RVO:61388963 Keywords : GCPII selective inhibitors * GCPIII * GCPII Subject RIV: CE - Biochemistry Impact factor: 5.589, year: 2015

  15. Mechanism-based PK/PD modeling of selective serotonin reuptake inhibitors

    NARCIS (Netherlands)

    Geldof, Marian

    2007-01-01

    The main objective of the investigations was to explore the PK/PD correlations of fluvoxamine, as a prototype for the Selective Serotonin Reuptake Inhibitors (SSRIs). In the various investigations, a spectrum of different biomarkers was used, each reflecting a specific process on the causal path

  16. Structure-Based Optimization of Arylamides as Inhibitors of Soluble Epoxide Hydrolase

    Energy Technology Data Exchange (ETDEWEB)

    Eldrup, Anne B.; Soleymanzadeh, Fariba; Taylor, Steven J.; Muegge, Ingo; Farrow, Neil A.; Joseph, David; McKellop, Keith; Man, Chuk C.; Kukulka, Alison; De Lombaert, Stephane; (Boehringer)

    2009-11-04

    Inhibition of soluble epoxide hydrolase (sEH) is hypothesized to lead to an increase in circulating levels of epoxyeicosatrienoic acids, resulting in the potentiation of their in vivo pharmacological properties. As part of an effort to identify inhibitors of sEH with high and sustained plasma exposure, we recently performed a high throughput screen of our compound collection. The screen identified N-(3,3-diphenyl-propyl)-nicotinamide as a potent inhibitor of sEH. Further profiling of this lead revealed short metabolic half-lives in microsomes and rapid clearance in the rat. Consistent with these observations, the determination of the in vitro metabolic profile of N-(3,3-diphenyl-propyl)-nicotinamide in rat liver microsomes revealed extensive oxidative metabolism and a propensity for metabolite switching. Lead optimization, guided by the analysis of the solid-state costructure of N-(3,3-diphenyl-propyl)-nicotinamide bound to human sEH, led to the identification of a class of potent and selective inhibitors. An inhibitor from this class displayed an attractive in vitro metabolic profile and high and sustained plasma exposure in the rat after oral administration.

  17. Synthesis and Biological Evaluation of a Chitobiose-Based Peptide N-Glycanase Inhibitor Library

    NARCIS (Netherlands)

    Witte, Martin D.; Horst, Danielle; Wiertz, Emmanuel J.H.J.; Marel, Gijsbert A. van der; Overkleeft, Herman S.

    2009-01-01

    Peptide N-glycanase (PNGase), the enzyme responsible for the deglycosylation of N-linked glycoproteins, has an active site related to that of cysteine proteases. Chitiobiose was equipped with electrophilic traps often used in cysteine protease inhibitors, and the resulting compounds were evaluated

  18. Mechanism-based Categorization of Aromatase Inhibitors: A Potential Discovery and Screening Tool

    Science.gov (United States)

    Cytochrome P450 aromatase is a key steroidogenic enzyme that converts androgens to estrogens in vertebrates. There is much interest in aromatase inhibitors (AIs) because a number of environmental contaminants can act as AIs, thereby disrupting endocrine function in humans and wil...

  19. Discovery of Peptide-based Inhibitors against Dendrotoxin B from Black Mamba through Phage Display Screening

    DEFF Research Database (Denmark)

    O. Cob, Saioa; Munk, Andreas; Laustsen, Andreas Hougaard

    The black mamba (Dendroaspis polylepis) is Africa’s most feared snake due to its potent, rapidacting venom and its speed of attack. The most abundant toxins in D. polylepis venom are the Kunitz-type proteinase inhibitors, dendrotoxins, which are unique for mamba. Dendrotoxinsare poorly neutralized...

  20. Structure-based drug design of selective 5´-nucleotidases inhibitors

    Czech Academy of Sciences Publication Activity Database

    Pachl, Petr; Brynda, Jiří; Rosenberg, Ivan; Fábry, Milan; Řezáčová, Pavlína

    2011-01-01

    Roč. 18, č. 1 (2011), s. 33-34 ISSN 1211-5894. [Discussions in Structural Molecular Biology /9./. 24.03.2011-26.03.2011, Nové Hrady] Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50520701 Keywords : inhibitor design * nucleotidase * Xray crystalography Subject RIV: EB - Genetics ; Molecular Biology

  1. Critical Data-Based Re-Evaluation of Minocycline as a Putative Specific Microglia Inhibitor

    NARCIS (Netherlands)

    Moller, Thomas; Bard, Frederique; Bhattacharya, Anindya; Biber, Knut; Campbell, Brian; Dale, Elena; Eder, Claudia; Gan, Li; Garden, Gwenn A.; Hughes, Zoe A.; Pearse, Damien D.; Staal, Roland G. W.; Sayed, Faten A.; Wes, Paul D.; Boddeke, Hendrikus W. G. M.

    2016-01-01

    Minocycline, a second generation broad-spectrum antibiotic, has been frequently postulated to be a "microglia inhibitor." A considerable number of publications have used minocycline as a tool and concluded, after achieving a pharmacological effect, that the effect must be due to "inhibition" of

  2. Identification of Early Intermediates of Caspase Activation Using Selective Inhibitors and Activity-Based Probes

    NARCIS (Netherlands)

    Berger, Alicia B.; Witte, Martin D.; Denault, Jean-Bernard; Sadaghiani, Amir Masoud; Sexton, Kelly M.B.; Salvesen, Guy S.; Bogyo, Matthew

    2006-01-01

    Caspases are cysteine proteases that are key effectors in apoptotic cell death. Currently, there is a lack of tools that can be used to monitor the regulation of specific caspases in the context of distinct apoptotic programs. We describe the development of highly selective inhibitors and active

  3. Rational design of a carboxylic esterase RhEst1 based on computational analysis of substrate binding.

    Science.gov (United States)

    Chen, Qi; Luan, Zheng-Jiao; Yu, Hui-Lei; Cheng, Xiaolin; Xu, Jian-He

    2015-11-01

    A new carboxylic esterase RhEst1 which catalyzes the hydrolysis of (S)-(+)-2,2-dimethylcyclopropanecarboxylate (S-DmCpCe), the key chiral building block of cilastatin, was identified and subsequently crystallized in our previous work. Mutant RhEst1A147I/V148F/G254A was found to show a 5-fold increase in the catalytic activity. In this work, molecular dynamic simulations were performed to elucidate the molecular determinant of the enzyme activity. Our simulations show that the substrate binds much more strongly in the A147I/V148F/G254A mutant than in wild type, with more hydrogen bonds formed between the substrate and the catalytic triad and the oxyanion hole. The OH group of the catalytic residue Ser101 in the mutant is better positioned to initiate the nucleophilic attack on S-DmCpCe. Interestingly, the "170-179" loop which is involved in shaping the catalytic sites and facilitating the product release shows remarkable dynamic differences in the two systems. Based on the simulation results, six residues were identified as potential "hot-spots" for further experimental testing. Consequently, the G126S and R133L mutants show higher catalytic efficiency as compared with the wild type. This work provides molecular-level insights into the substrate binding mechanism of carboxylic esterase RhEst1, facilitating future experimental efforts toward developing more efficient RhEst1 variants for industrial applications. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Sensor Substrate Development

    Data.gov (United States)

    National Aeronautics and Space Administration — Novel substrates, such as aerogels and porous, low density ceramics may increase the sensitivities of chemical reaction-based sensors for toxic vapors. These sensors...

  5. Vertically integrated logic circuits constructed using ZnO-nanowire-based field-effect transistors on plastic substrates.

    Science.gov (United States)

    Kang, Jeongmin; Moon, Taeho; Jeon, Youngin; Kim, Hoyoung; Kim, Sangsig

    2013-05-01

    ZnO-nanowire-based logic circuits were constructed by the vertical integration of multilayered field-effect transistors (FETs) on plastic substrates. ZnO nanowires with an average diameter of -100 nm were synthesized by thermal chemical vapor deposition for use as the channel material in FETs. The ZnO-based FETs exhibited a high I(ON)/I(OFF) of > 10(6), with the characteristic of n-type depletion modes. For vertically integrated logic circuits, three multilayer FETs were sequentially prepared. The stacked FETs were connected in series via electrodes, and C-PVPs were used for the layer-isolation material. The NOT and NAND gates exhibited large logic-swing values of -93%. These results demonstrate the feasibility of three dimensional flexible logic circuits.

  6. On-chip microfluidic systems for determination of L-glutamate based on enzymatic recycling of substrate

    DEFF Research Database (Denmark)

    Laiwattanapaisal, W.; Yakovleva, J.; Bengtsson, Martin

    2009-01-01

    Two microfluidic systems have been developed for specific analysis of L-glutamate in food based on substrate recycling fluorescence detection. L-glutamate dehydrogenase and a novel enzyme, D-phenylglycine aminotransferase, were covalently immobilized on (i) the surface of silicon microchips....... The reaction was accompanied by reduction of nicotinamide adenine dinucleotide (NAD(+)) to NADH, which was monitored by fluorescence detection (epsilon(ex)=340 nm, epsilon(em)=460 nm). First, the microchip-based system, L-glutamate was detected within a range of 3.1-50.0 mM. Second, to be automatically......). In the case of SIA, the beads were introduced and removed from the microchip automatically. The immobilized beads could be stored in a 20% glycerol and 0.5 mM ethylenediaminetetraacetic acid solution maintained at a pH of 7.0 using a phosphate buffer for at least 15 days with 72% of the activity remaining...

  7. Electrocatalytic oxidation of organic substrates with molecular oxygen using tetradentate ruthenium(III)-Schiff base complexes as catalysts

    International Nuclear Information System (INIS)

    Ourari, Ali; Khelafi, Mostefa; Aggoun, Djouhra; Jutand, Anny; Amatore, Christian

    2012-01-01

    Three complexes Ru(III)ClL n involving different tetradentate Schiff base ligands L n (see L 1 , L 2 and L 3 in ) were used as catalysts in the oxidation of cyclooctene and tetraline in the presence of molecular dioxygen associated with benzoic anhydride. The efficiency of this oxidation reaction was tested in the presence of two apical bases: 1- or 2-methylimidazole. All complexes exhibit a quasi-reversible redox system. The electrolysis experiments were carried out at controlled potential for each complex, using different substrates such as cyclooctene and tetraline. The oxidized products are cyclooctene oxide (turnover 6.7), a mixture of 1-tetralol and 1-tetralone (turnover 7.6) respectively.

  8. Entomopathogenic fungi-based mechanisms for improved Fe nutrition in sorghum plants grown on calcareous substrates.

    Directory of Open Access Journals (Sweden)

    Silvia Raya-Díaz

    Full Text Available Although entomopathogenic fungi (EPF are best known for their ability to protect crops against insect pests, they may have other beneficial effects on their host plants. These effects, which include promoting plant growth and conferring resistance against abiotic stresses, have been examined in recent years to acquire a better understanding of them. The primary purposes of the present study were (i to ascertain in vitro whether three different strains of EPF (viz., Metarhizium, Beauveria and Isaria would increase the Fe bioavailability in calcareous or non-calcareous media containing various Fe sources (ferrihydrite, hematite and goethite and (ii to assess the influence of the EPF inoculation method (seed dressing, soil treatment or leaf spraying on the extent of the endophytic colonization of sorghum and the improvement in the Fe nutrition of pot-grown sorghum plants on an artificial calcareous substrate. All the EPFs studied were found to increase the Fe availability during the in vitro assay. The most efficient EPF was M. brunneum EAMa 01/58-Su, which lowered the pH of the calcareous medium, suggesting that it used a different strategy (organic acid release than the other two fungi that raised the pH of the non-calcareous medium. The three methods used to inoculate sorghum plants with B. bassiana and M. brunneum in the pot experiment led to differences in re-isolation from plant tissues and in the plant height. These three inoculation methods increased the leaf chlorophyll content of young leaves when the Fe deficiency symptoms were most apparent in the control plants (without fungal inoculation as well as the Fe content of the above-ground biomass in the plants at the end of the experiment. The total root lengths and fine roots were also increased in response to fungal applications with the three inoculation methods. However, the soil treatment was the most efficient method; thus, its effect on the leaf chlorophyll content was the most

  9. Identification of potent orally active factor Xa inhibitors based on conjugation strategy and application of predictable fragment recommender system.

    Science.gov (United States)

    Ishihara, Tsukasa; Koga, Yuji; Iwatsuki, Yoshiyuki; Hirayama, Fukushi

    2015-01-15

    Anticoagulant agents have emerged as a promising class of therapeutic drugs for the treatment and prevention of arterial and venous thrombosis. We investigated a series of novel orally active factor Xa inhibitors designed using our previously reported conjugation strategy to boost oral anticoagulant effect. Structural optimization of anthranilamide derivative 3 as a lead compound with installation of phenolic hydroxyl group and extensive exploration of the P1 binding element led to the identification of 5-chloro-N-(5-chloro-2-pyridyl)-3-hydroxy-2-{[4-(4-methyl-1,4-diazepan-1-yl)benzoyl]amino}benzamide (33, AS1468240) as a potent factor Xa inhibitor with significant oral anticoagulant activity. We also reported a newly developed Free-Wilson-like fragment recommender system based on the integration of R-group decomposition with collaborative filtering for the structural optimization process. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Development of a Rapid Fluorescence-Based High-Throughput Screening Assay to Identify Novel Kynurenine 3-Monooxygenase Inhibitor Scaffolds.

    Science.gov (United States)

    Jacobs, K R; Guillemin, G J; Lovejoy, D B

    2018-02-01

    Kynurenine 3-monooxygenase (KMO) is a well-validated therapeutic target for the treatment of neurodegenerative diseases, including Alzheimer's disease (AD) and Huntington's disease (HD). This work reports a facile fluorescence-based KMO assay optimized for high-throughput screening (HTS) that achieves a throughput approximately 20-fold higher than the fastest KMO assay currently reported. The screen was run with excellent performance (average Z' value of 0.80) from 110,000 compounds across 341 plates and exceeded all statistical parameters used to describe a robust HTS assay. A subset of molecules was selected for validation by ultra-high-performance liquid chromatography, resulting in the confirmation of a novel hit with an IC 50 comparable to that of the well-described KMO inhibitor Ro-61-8048. A medicinal chemistry program is currently underway to further develop our novel KMO inhibitor scaffolds.

  11. Oligosaccharide substrate preferences of human extracellular sulfatase Sulf2 using liquid chromatography-mass spectrometry based glycomics approaches.

    Directory of Open Access Journals (Sweden)

    Yu Huang

    Full Text Available Sulfs are extracellular endosulfatases that selectively remove the 6-O-sulfate groups from cell surface heparan sulfate (HS chain. By altering the sulfation at these particular sites, Sulfs function to remodel HS chains. As a result of the remodeling activity, HSulf2 regulates a multitude of cell-signaling events that depend on interactions between proteins and HS. Previous efforts to characterize the substrate specificity of human Sulfs (HSulfs focused on the analysis of HS disaccharides and synthetic repeating units. In this study, we characterized the substrate preferences of human HSulf2 using HS oligosaccharides with various lengths and sulfation degrees from several naturally occurring HS sources by applying liquid chromatography mass spectrometry based glycomics methods. The results showed that HSulf2 preferentially digests highly sulfated HS oligosaccharides with zero acetyl groups and this preference is length dependent. In terms of length of oligosaccharides, HSulf2 digestion induced more sulfation decrease on DP6 (DP: degree of polymerization compared to DP2, DP4 and DP8. In addition, the HSulf2 preferentially digests the oligosaccharide domain located at the non-reducing end (NRE of the HS and heparin chain. In addition, the HSulf2 digestion products were altered only for specific isomers. HSulf2 treated NRE oligosaccharides also showed greater decrease in cell proliferation than those from internal domains of the HS chain. After further chromatographic separation, we identified the three most preferred unsaturated hexasaccharide for HSulf2.

  12. Air-void embedded GaN-based light-emitting diodes grown on laser drilling patterned sapphire substrates

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Hao; Li, Yufeng; Wang, Shuai; Feng, Lungang; Xiong, Han; Yun, Feng, E-mail: fyun2010@mail.xjtu.edu.cn [Key Laboratory of Physical Electronics and Devices of Ministry of Education and Shaanxi Provincial Key Laboratory of Photonics and Information Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 (China); Solid-State Lighting Engineering Research Center, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 (China); Su, Xilin [Shaanxi Supernova Lighting Technology Co., Ltd., Xi’an, Shaanxi 710075 (China)

    2016-07-15

    Air-void structure was introduced in GaN-based blue light-emitting diodes (LED) with one-step growth on periodic laser drilling patterned sapphire substrate, which free of any photolithography or wet/dry etching process. The influence of filling factors (FF) of air-void on crystal quality and optical performance were investigate. Transmission electron microscopy images and micro-Raman spectroscopy indicated that the dislocation was bended and the partially compressed strain was released. When FF was 55.43%, compared with the LED structure grown on flat sapphire substrate, the incorporation of air-void was observed to reduce the compressed stress of ∼20% and the luminance intensity has improved by 128%. Together with the simulated reflection intensity enhancement by finite difference time-domain (FDTD) method, we attribute the enhanced optical performance to the combined contribution of strong back-side light reflection of air-void and better GaN epitaxial quality. This approach provides a simple replacement to the conventional air-void embedded LED process.

  13. Development of High-Performance eSWIR HgCdTe-Based Focal-Plane Arrays on Silicon Substrates

    Science.gov (United States)

    Park, J. H.; Pepping, J.; Mukhortova, A.; Ketharanathan, S.; Kodama, R.; Zhao, J.; Hansel, D.; Velicu, S.; Aqariden, F.

    2016-09-01

    We report the development of high-performance and low-cost extended short-wavelength infrared (eSWIR) focal-plane arrays (FPAs) fabricated from molecular beam epitaxial (MBE)-grown HgCdTe on Si-based substrates. High-quality n-type eSWIR HgCdTe (cutoff wavelength ˜2.68 μm at 77 K, electron carrier concentration 5.82 × 1015 cm-3) layers were grown on CdTe/Si substrates by MBE. High degrees of uniformity in composition and thickness were demonstrated over three-inch areas, and low surface defect densities (voids 9.56 × 101 cm-2, micro-defects 1.67 × 103 cm-2) were measured. This material was used to fabricate 320 × 256 format, 30 μm pitch FPAs with a planar device architecture using arsenic implantation to achieve p-type doping. The dark current density of test devices showed good uniformity between 190 K and room temperature, and high-quality eSWIR imaging from hybridized FPAs was obtained with a median dark current density of 2.63 × 10-7 A/cm2 at 193 K with a standard deviation of 1.67 × 10-7 A/cm2.

  14. A study of graphene films synthesized on nickel substrates: existence and origin of small-base-area peaks

    International Nuclear Information System (INIS)

    Kahng, Yung Ho; Choe, Minhyeok; Jo, Gunho; Park, Woojin; Yoon, Jongwon; Hong, Woong-Ki; Lee, Byoung Hun; Lee, Takhee; Lee, Sangchul; Cho, Chun Hum

    2011-01-01

    Large-area graphene films, synthesized by the chemical vapor deposition (CVD) method, have the potential to be used as electrodes. However, the electrical properties of CVD-synthesized graphene films fall short of the best results obtained for graphene films prepared by other methods. Therefore, it is important to understand the reason why these electrical properties are inferior to improve the applicability of CVD-grown graphene films. Here, we show that CVD-grown graphene films on nickel substrates contain many small-base-area (SBA) peaks that scatter conducting electrons, thereby decreasing the Hall mobility of charges in the films. These SBA peaks were induced by small peaks on the nickel surface and are likely composed of amorphous carbon. The formation of these SBA peaks on graphene films was successfully suppressed by controlling the surface morphology of the nickel substrate. These findings may be useful for the development of a CVD synthesis method that is capable of producing better quality graphene films with large areas.

  15. Design and production of a 2.5 kWe insulated metal substrate-based densely packed CPV assembly

    Science.gov (United States)

    Micheli, Leonardo; Sarmah, Nabin; Luo, Xichun; Reddy, K. S.; Mallick, Tapas K.

    2014-09-01

    The original design of a new 144-cell concentrating photovoltaic assembly is presented in this paper. It is conceived to work under 500 suns and to generate about 2.5 kWe. An insulated metal substrate was selected as baseplate, in order to get the best compromise between costs and thermal performances. It is based on a 2mm thick aluminum plate, which is in charge of removing the heat as quick as possible. The copper pattern and thickness has been designed accordingly to the IPC Generic Standard on Printed Board Design and to the restrictions of fit a reflective 125x primary optics and a 4x secondary refractive optics. The original outline of the conductive copper layer has been developed to minimize Joule losses by reducing the number of interconnections between the cells in series. Multijunction solar cells and Schottky bypass diodes have been soldered onto the board as surface mounted components. All the fabrication processes are described. This board represents a novelty for the innovative pattern of the conductive layer, which can be easily adapted to be coupled with different optics geometries and to allocate a different number of cells. The use of an IMS as baseplate will give an experimental contribution to the debate about the exploitability of this kind of substrates in CPV. This board is being characterized indoor and outdoor: the results will be used to improve the design and the reliability of the future receivers.

  16. Density functional theory and quantum mechanics/molecular mechanics study of cysteine protease inhibition by nitrile-based inhibitors.

    Directory of Open Access Journals (Sweden)

    Sam P De Visser

    2013-12-01

    Full Text Available Cysteine protease enzymes are important for human physiology and catalyze key protein degradation pathways. These enzymes react via a nucleophilic reaction mechanism that involves a cysteine residue and the proton of a proximal histidine. Particularly efficient inhibitors of these enzymes are nitrile-based, however, the details of the catalytic reaction mechanism currently are poorly understood. To gain further insight into the inhibition of these molecules, we have performed a combined density functional theory and quantum mechanics/molecular mechanics study on the reaction of a nitrile-based inhibitor with the enzyme active site amino acids. We show here that small perturbations to the inhibitor structure can have dramatic effects on the catalysis and inhibition processes. Thus, we investigated a range of inhibitor templates and show that specific structural changes reduce the inhibitory efficiency by several orders of magnitude. Moreover, as the reaction takes place on a polar surface, we find strong differences between the DFT and QM/MM calculated energetics. In particular, the DFT model led to dramatic distortions from the starting structure and the convergence to a structure that would not fit the enzyme active site. In the subsequent QM/MM study we investigated the use of mechanical versus electronic embedding on the kinetics, thermodynamics and geometries along the reaction mechanism. We find minor effects on the kinetics of the reaction but large geometric and thermodynamics differences as a result of inclusion of electronic embedding corrections. The work here highlights the importance of model choice in the investigation of this biochemical reaction mechanism.

  17. [Screen potential CYP450 2E1 inhibitors from Chinese herbal medicine based on support vector regression and molecular docking method].

    Science.gov (United States)

    Chen, Xi; Lu, Fang; Jiang, Lu-di; Cai, Yi-Lian; Li, Gong-Yu; Zhang, Yan-Ling

    2016-07-01

    Inhibition of cytochrome P450 (CYP450) enzymes is the most common reasons for drug interactions, so the study on early prediction of CYPs inhibitors can help to decrease the incidence of adverse reactions caused by drug interactions.CYP450 2E1(CYP2E1), as a key role in drug metabolism process, has broad spectrum of drug metabolism substrate. In this study, 32 CYP2E1 inhibitors were collected for the construction of support vector regression (SVR) model. The test set data were used to verify CYP2E1 quantitative models and obtain the optimal prediction model of CYP2E1 inhibitor. Meanwhile, one molecular docking program, CDOCKER, was utilized to analyze the interaction pattern between positive compounds and active pocket to establish the optimal screening model of CYP2E1 inhibitors.SVR model and molecular docking prediction model were combined to screen traditional Chinese medicine database (TCMD), which could improve the calculation efficiency and prediction accuracy. 6 376 traditional Chinese medicine (TCM) compounds predicted by SVR model were obtained, and in further verification by using molecular docking model, 247 TCM compounds with potential inhibitory activities against CYP2E1 were finally retained. Some of them have been verified by experiments. The results demonstrated that this study could provide guidance for the virtual screening of CYP450 inhibitors and the prediction of CYPs-mediated DDIs, and also provide references for clinical rational drug use. Copyright© by the Chinese Pharmaceutical Association.

  18. Linear Discriminant Analysis for the in Silico Discovery of Mechanism-Based Reversible Covalent Inhibitors of a Serine Protease: Application of Hydration Thermodynamics Analysis and Semi-empirical Molecular Orbital Calculation.

    Science.gov (United States)

    Masuda, Yosuke; Yoshida, Tomoki; Yamaotsu, Noriyuki; Hirono, Shuichi

    2018-01-01

    We recently reported that the Gibbs free energy of hydrolytic water molecules (ΔG wat ) in acyl-trypsin intermediates calculated by hydration thermodynamics analysis could be a useful metric for estimating the catalytic rate constants (k cat ) of mechanism-based reversible covalent inhibitors. For thorough evaluation, the proposed method was tested with an increased number of covalent ligands that have no corresponding crystal structures. After modeling acyl-trypsin intermediate structures using flexible molecular superposition, ΔG wat values were calculated according to the proposed method. The orbital energies of antibonding π* molecular orbitals (MOs) of carbonyl C=O in covalently modified catalytic serine (E orb ) were also calculated by semi-empirical MO calculations. Then, linear discriminant analysis (LDA) was performed to build a model that can discriminate covalent inhibitor candidates from substrate-like ligands using ΔG wat and E orb . The model was built using a training set (10 compounds) and then validated by a test set (4 compounds). As a result, the training set and test set ligands were perfectly discriminated by the model. Hydrolysis was slower when (1) the hydrolytic water molecule has lower ΔG wat ; (2) the covalent ligand presents higher E orb (higher reaction barrier). Results also showed that the entropic term of hydrolytic water molecule (-TΔS wat ) could be used for estimating k cat and for covalent inhibitor optimization; when the rotational freedom of the hydrolytic water molecule is limited, the chance for favorable interaction with the electrophilic acyl group would also be limited. The method proposed in this study would be useful for screening and optimizing the mechanism-based reversible covalent inhibitors.

  19. Evaluation of novel arginine based inhibitors of DDAH and investigations into radical hydroacylation of vinyl sulfonates

    OpenAIRE

    Khanom, N.

    2010-01-01

    The thesis is in two main sections. In the first section, studies on methylarginine processing enzymes are presented. Dimethyalrginine dimethylaminohydrolase (DDAH) is a class of enzymes involved in the metabolism of methylarginines ADMA and L-NMMA, which indirectly regulate physiological nitric oxide levels. It is desirable to inhibit excess NO in pathological situations, and the arginine mimetic L-257 is a DDAH inhibitor which reduces levels of NO. Synthesis of ester analo...

  20. Structure-Aided Design of Novel Inhibitors of HIV Protease Based on a Benzodiazepine Scaffold

    Czech Academy of Sciences Publication Activity Database

    Schimer, Jiří; Cígler, Petr; Veselý, J.; Grantz Šašková, Klára; Lepšík, Martin; Brynda, Jiří; Řezáčová, Pavlína; Kožíšek, Milan; Císařová, I.; Oberwinkler, H.; Kraeusslich, H. G.; Konvalinka, Jan

    2012-01-01

    Roč. 55, č. 22 (2012), s. 10130-10135 ISSN 0022-2623 R&D Projects: GA ČR GBP208/12/G016; GA ČR GAP207/11/1798 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50520514 Keywords : HIV protease inhibitor * rational drug design * 1,4-benzodiazepines Subject RIV: CE - Biochemistry Impact factor: 5.614, year: 2012

  1. Design and screening of ASIC inhibitors based on aromatic diamidines for combating neurological disorders.

    Science.gov (United States)

    Chen, Xuanmao; Orser, Beverley A; MacDonald, John F

    2010-12-01

    Acid sensing ion channels (ASICs) are implicated in various brain functions including learning and memory and are involved in a number of neurological disorders such as pain, ischemic stroke, depression, and multiple sclerosis. We have recently defined ASICs as one of receptor targets of aromatic diamidines in neurons. Aromatic diamidines are DNA-binding agents and have long been used in the treatment of leishmaniasis, trypanosomiasis, pneumocystis pneumonia and babesiosis. Moreover, some aromatic diamidines are used as skin-care and baby products and others have potential to suppress tumor growth or to combat malaria. A large number of aromatic diamidines or analogs have been synthesized. Many efforts are being made to optimize the therapeutic spectrum of aromatic diamidines, i.e. to reduce toxicity, increase oral bioavailability and enhance their penetration of the blood-brain barrier. Aromatic diamidines therefore provide a shortcut of screening for selective ASIC inhibitors with therapeutic potential. Intriguingly nafamostat, a protease inhibitor for treating acute pancreatitis, also inhibits ASIC activities. Aromatic diamidines and nafamostat have many similarities although they belong to distinct classes of medicinal agents for curing different diseases. Here we delineate background, clinical application and drug development of aromatic diamidines that could facilitate the screening for selective ASIC inhibitors for research purposes. Further studies may lead to a drug with therapeutic value and extend the therapeutic scope of aromatic diamidines to combat neurological diseases. Copyright © 2010 Elsevier B.V. All rights reserved.

  2. Therapies based on inhibitors of the epidermal growth factor receptor: enclosing the future

    International Nuclear Information System (INIS)

    Diaz, Arlhee; Lage, Agustin

    2007-01-01

    The Epidermal Growth Factor Receptor (EGFR) is considered an important target for rational drug design due to its key role in numerous tumors. Potential contribution of EGFR-related signaling pathways to promote tumorigenic processes, including cell proliferation, angiogenesis, and resistance to apoptosis has been well established. Two classes of anti-EGFR agents in late-stage clinical testing include monoclonal antibodies against extracellular EGFR domain (Cetuximab, Nimotuzumab) and small molecules tyrosine kinase inhibitors, which inhibit the receptor enzyme activity (Gefitinib, Erlotinib). A considerable body of evidence has emerged since its introduction in the treatment of cancer patients. However, important questions such as reliable surrogate markers to predict response to the treatment, or optimal sequence and combination of these agents with conventional therapies remain to be addressed. Identify and validate predictive factors to select patients likely to respond to EGFR inhibitors, such as mutations that confer resistance versus those associated with sensitivity is required. A better understanding of molecular mechanisms associated with antitumor activity will useful to predict the interaction of these agents with other therapies in order to avoid antagonisms or overlapping effects resulting in no adding effects. Finally, the benefits derived from EGFR inhibitors as first-line therapy in selected populations, and the optimal doses and ways to delivery to the tumor site resulting in optimal target modulation should be established by the ongoing investigation. (Author)

  3. Ligand and Structure-Based Approaches for the Identification of Peptide Deformylase Inhibitors as Antibacterial Drugs.

    Science.gov (United States)

    Gao, Jian; Liang, Li; Zhu, Yasheng; Qiu, Shengzhi; Wang, Tao; Zhang, Ling

    2016-07-15

    Peptide deformylase (PDF) is a metalloprotease catalyzing the removal of a formyl group from newly synthesized proteins, which makes it an important antibacterial drug target. Given the importance of PDF inhibitors like actinonin in antibacterial drug discovery, several reported potent PDF inhibitors were used to develop pharmacophore models using the Galahad module of Sybyl 7.1 software. Generated pharmacophore models were composed of two donor atom centers, four acceptor atom centers and two hydrophobic groups. Model-1 was screened against the Zinc database and several compounds were retrieved as hits. Compounds with Qfit values of more than 60 were employed to perform a molecular docking study with the receptor Escherichia coli PDF, then compounds with docking score values of more than 6 were used to predict the in silico pharmacokinetic and toxicity risk via OSIRIS property explorer. Two known PDF inhibitors were also used to perform a molecular docking study with E. coli PDF as reference molecules. The results of the molecular docking study were validated by reproducing the crystal structure of actinonin. Molecular docking and in silico pharmacokinetic and toxicity prediction studies suggested that ZINC08740166 has a relatively high docking score of 7.44 and a drug score of 0.78.

  4. Inhibitors for human glutaminyl cyclase by structure based design and bioisosteric replacement.

    Science.gov (United States)

    Buchholz, Mirko; Hamann, Antje; Aust, Susanne; Brandt, Wolfgang; Böhme, Livia; Hoffmann, Torsten; Schilling, Stephan; Demuth, Hans-Ulrich; Heiser, Ulrich

    2009-11-26

    The inhibition of human glutaminyl cyclase (hQC) has come into focus as a new potential approach for the treatment of Alzheimer's disease. The hallmark of this principle is the prevention of the formation of Abeta(3,11(pE)-40,42), as these Abeta-species were shown to be of elevated neurotoxicity and likely to act as a seeding core leading to an accelerated formation of Abeta-oligomers and fibrils. Starting from 1-(3-(1H-imidazol-1-yl)propyl)-3-(3,4-dimethoxyphenyl)thiourea, bioisosteric replacements led to the development of new classes of inhibitors. The optimization of the metal-binding group was achieved by homology modeling and afforded a first insight into the probable binding mode of the inhibitors in the hQC active site. The efficacy assessment of the hQC inhibitors was performed in cell culture, directly monitoring the inhibition of Abeta(3,11(pE)-40,42) formation.

  5. The effect of chemical anti-inhibitors on fibrinolytic enzymes and inhibitors

    DEFF Research Database (Denmark)

    Sidelmann, Johannes Jakobsen; Jespersen, J; Kluft, C

    1997-01-01

    proteases. We studied the influence of chemical anti-inhibitors (chloramine T, flufenamate, sodium lauryl sulfate, and methylamine) on fibrinolytic serine proteases and fibrinolytic enzyme inhibitors using the physiological substrate fibrin as plasmin substrate. Low concentrations of chloramine T (0.01 mmol......%) and plasminogen activators (apparent recovery > 200%). Sodium lauryl sulfate eliminates the major fibrinolytic enzyme inhibitors, but increases the activity of plasmin (apparent recovery > 200%) and plasminogen activator, urokinase type (apparent recovery 130%). Methylamine affects only plasmin inhibition. We...

  6. Seedlings of Jasminum mesnyi Hance produced in substrates based on composted sewage sludge

    OpenAIRE

    Scheer, Maurício B.; Carneiro, Charles; Bressan, Otávio A.; Santos, Kaline G. dos

    2012-01-01

    Entre as alternativas de disposição de resíduos urbanos está o reaproveitamento do lodo de esgoto no cultivo de plantas ornamentais e florestais. Objetivou-se, com este trabalho, avaliar o crescimento de Jasminum mesnyi (jasmim amarelo) em substratos à base de lodo de esgoto aeróbio compostado com resíduos de podas de árvores trituradas, com diferentes níveis de fertilizante e comparar o desempenho em relação às mudas produzidas em substrato comercial à base de casca de Pinus compostada e ver...

  7. The nucleation of HCl and Cl{sub 2}-based HVPE GaN on mis-oriented sapphire substrates

    Energy Technology Data Exchange (ETDEWEB)

    Bohnen, Tim; Dreumel, Gerbe W.G. van; Enckevort, Willem J.P. van; Ashraf, Hina; Jong, Aryan E.F. de; Hageman, Paul R.; Vlieg, Elias [IMM, Radboud University, Nijmegen (Netherlands); Weyher, Jan L. [Institute of High Pressure Physics, Polish Academy of Sciences, Warsaw (Poland)

    2010-07-15

    The nucleation of both classic HCl-based and novel Cl{sub 2{sup -}} based HVPE GaN on mis-oriented sapphire substrates was investigated. The use of Cl{sub 2}in HVPE increases the growth rate by a factor of 4-5 and strongly reduces the parasitic deposition, allowing for the growth of much thicker wafers than HCl-based HVPE. Morphological SEM surface studies of the HCl-based HVPE sample surface show that at 600 C a nanocrystalline layer is deposited on the sapphire. During the subsequent annealing phase, the morphology changes to a {mu}m-sized island structure. During overgrowth at 1080 C, the islands coalesce. Small voids or pinholes are then formed in between the coalescing GaN islands. These pinholes lead to numerous pits on the surface of the GaN at thicknesses of 5 {mu}m. The pits disappear during continued overgrowth and can no longer be found on the surface, when the GaN film reaches a thickness of 45 {mu}m. This particular coalescence mechanism also applies to Cl{sub 2}-based HVPE GaN on sapphire (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  8. Epitaxial growth and properties of AlGaN-based UV-LEDs on Si(111) substrates

    Energy Technology Data Exchange (ETDEWEB)

    Saengkaew, Phannee

    2010-07-08

    An increasing demand for bright and efficient ultraviolet light emitting diodes (UVLEDs) is generated by numerous applications such as biochemical sensors, purification and sterilization, and solid-state white lighting. Al{sub x}Ga{sub 1-x}N is a promising material to develop UVLEDs due to the direct wide-bandgap material for emission wavelengths in the UV range and the capability of n- and p-type doping. To develop UV-LEDs on Si substrates is very interesting for low-cost UV-light sources since the Si substrate is available at low cost, in large-diameter size enabling the integration with well-known Si electronics. This work presents the first crack-free AlGaN-based UV-LEDs on Si(111) substrates by MOVPE growth. This AlGaN-based UV-LED on Si(111) substrate consists of Al{sub 0.1}Ga{sub 0.9}N:Si layers on LT-AlN/HT-AlN SL buffer layers and an active layer of GaN/Al{sub 0.1}Ga{sub 0.9}N MQWs followed by Mg-doped (GaN/Al{sub 0.1}Ga{sub 0.9}N) superlattices and GaN:Mg cap layers. It yields a {proportional_to}350 nm UV electroluminescence at room temperature and a turn-on voltage in a range of 2.6-3.1 V by current-voltage (I-V) measurements. The novel LT-AlN/HT-AlN superlattice buffer layers efficiently improve the crystalline quality of Al{sub x}Ga{sub 1-x}N layers and compensate a thermal tensile strain in Al{sub x}Ga{sub 1-x}N layers after cooling as observed by in-situ curvature measurements. The dislocation density could be reduced from 8.4 x 10{sup 10} cm{sup -2} in the AlN-based SLs to 1.8 x 10{sup 10} cm{sup -2} in the Al{sub 0.1}Ga{sub 0.9}N layers as determined by cross-sectional transmission electron microscopy (TEM) measurements. Crack-free Al{sub x}Ga{sub 1-x}N layers grown on these LT-AlN/HT-AlN superlattices with 0.05{<=}x{<=} 0.65 are achieved on Si substrates with good crystalline, optical, and electrical properties. The best crystalline quality of Al{sub 0.1}Ga{sub 0.9}N is obtained with {omega}-FWHMs of the (0002) and (10-10) reflections of

  9. Advances in maskless and mask-based optical lithography on plastic flexible substrates

    NARCIS (Netherlands)

    Barbu, I.; Ivan, M.G.; Giesen, P.; Moosdijk, M. van de; Meinders, E.R.

    2009-01-01

    Organic flexible electronics is an emerging technology with huge potential growth in the future which is likely to open up a complete new series of potential applications such as flexible OLED-based displays, urban commercial signage, and flexible electronic paper. The transistor is the fundamental

  10. Nitride-based Quantum-Confined Structures for Ultraviolet-Visible Optical Devices on Silicon Substrates

    KAUST Repository

    Janjua, Bilal

    2017-01-01

    quality GaN, InGaN and AlGaN Qdisks-in-NWs based on careful optimization of the growth parameters, coupled with a meticulous layer structure and active region design. The NWs were grown, catalyst-free, using plasma assisted molecular beam epitaxy (PAMBE

  11. Elasticity-based patterning of red blood cells on undulated lipid membranes supported on porous topographic substrates.

    Science.gov (United States)

    Lee, Sang-Wook; Jeong, Cherlhyun; Lee, Sin-Doo

    2009-03-26

    We describe elasticity-based patterning of human red blood cells (RBCs) into a microarray form on supported lipid membranes (SLMs) prepared on a solid substrate having two types of topographic patterns, porous and flat regions. The underlying concept is to precisely control the interplay between adhesion and the bending rigidity of the RBCs that interact with the SLMs. Attachment of the RBCs on highly undulated SLMs formed on the porous region is not energetically favorable, since membrane bending of the RBCs costs a high curvature elastic energy which exceeds adhesion. The RBCs are thus selectively confined within relatively flat regions of the SLMs without causing considerable elastic distortions. It was found that the population of the RBCs in a single corral is linearly proportional to the area of one element in our microarray.

  12. Characteristics of InGaN-Based Light-Emitting Diodes on Patterned Sapphire Substrates with Various Pattern Heights

    Directory of Open Access Journals (Sweden)

    Sheng-Fu Yu

    2012-01-01

    Full Text Available The optical and electrical characteristics of InGaN-based blue light-emitting diodes (LEDs grown on patterned sapphire substrates (PSSs with different pattern heights and on planar sapphire by atmospheric-pressure metal-organic chemical vapor deposition were investigated. Compared with planar sapphire, it was found that the LED electroluminescence intensity is significantly enhanced on PSSs with pattern heights of 0.5 (21%, 1.1 (57%, 1.5 (81%, and 1.9 (91% μm at an injected current of 20 mA. The increased light intensity exhibits the same trend in a TracePro simulation. In addition, it was also found that the level of leakage current depends on the density of V-shape defects, which were measured by scanning electron microscopy.

  13. Discovery of Novel Inhibitors of Indoleamine 2,3-Dioxygenase 1 Through Structure-Based Virtual Screening

    Directory of Open Access Journals (Sweden)

    Guoqing Zhang

    2018-03-01

    Full Text Available Indoleamine 2,3-dioxygenase 1 (IDO1 is an intracellular monomeric heme-containing enzyme that catalyzes the first and the rate limiting step in catabolism of tryptophan via the kynurenine (KYN pathway, which plays a significant role in the proliferation and differentiation of T cells. IDO1 has been proven to be an attractive target for anticancer therapy and chronic viral infections. In the present study, a class of IDO1 inhibitors with novel scaffolds were identified by virtual screening and biochemical validation, in which the compound DC-I028 shows moderate IDO1 inhibitory activity with an IC50 of 21.61 μM on enzymatic level and 89.11 μM on HeLa cell. In the following hit expansion stage, DC-I02806, an analog of DC-I028, showed better inhibitory activity with IC50 about 18 μM on both enzymatic level and cellular level. The structure–activity relationship (SAR of DC-I028 and its analogs was then discussed based on the molecular docking result. The novel IDO1 inhibitors of DC-I028 and its analogs may provide useful clues for IDO1 inhibitor development.

  14. Discovery of Novel Inhibitors of Indoleamine 2,3-Dioxygenase 1 Through Structure-Based Virtual Screening

    Science.gov (United States)

    Zhang, Guoqing; Xing, Jing; Wang, Yulan; Wang, Lihao; Ye, Yan; Lu, Dong; Zhao, Jihui; Luo, Xiaomin; Zheng, Mingyue; Yan, Shiying

    2018-01-01

    Indoleamine 2,3-dioxygenase 1 (IDO1) is an intracellular monomeric heme-containing enzyme that catalyzes the first and the rate limiting step in catabolism of tryptophan via the kynurenine (KYN) pathway, which plays a significant role in the proliferation and differentiation of T cells. IDO1 has been proven to be an attractive target for anticancer therapy and chronic viral infections. In the present study, a class of IDO1 inhibitors with novel scaffolds were identified by virtual screening and biochemical validation, in which the compound DC-I028 shows moderate IDO1 inhibitory activity with an IC50 of 21.61 μM on enzymatic level and 89.11 μM on HeLa cell. In the following hit expansion stage, DC-I02806, an analog of DC-I028, showed better inhibitory activity with IC50 about 18 μM on both enzymatic level and cellular level. The structure–activity relationship (SAR) of DC-I028 and its analogs was then discussed based on the molecular docking result. The novel IDO1 inhibitors of DC-I028 and its analogs may provide useful clues for IDO1 inhibitor development. PMID:29651242

  15. A cell-based high-throughput protocol to screen entry inhibitors of highly pathogenic viruses with Traditional Chinese Medicines.

    Science.gov (United States)

    Yang, Yong; Cheng, Han; Yan, Hui; Wang, Peng-Zhan; Rong, Rong; Zhang, Ying-Ying; Zhang, Cheng-Bo; Du, Rui-Kun; Rong, Li-Jun

    2017-05-01

    Emerging viruses such as Ebola virus (EBOV), Lassa virus (LASV), and avian influenza virus H5N1 (AIV) are global health concerns. Since there is very limited options (either vaccine or specific therapy) approved for humans against these viruses, there is an urgent need to develop prophylactic and therapeutic treatments. Previously we reported a high-throughput screening (HTS) protocol to identify entry inhibitors for three highly pathogenic viruses (EBOV, LASV, and AIV) using a human immunodeficiency virus-based pseudotyping platform which allows us to perform the screening in a BSL-2 facility. In this report, we have adopted this screening protocol to evaluate traditional Chinese Medicines (TCMs) in an effort to discover entry inhibitors against these viruses. Here we show that extracts of the following Chinese medicinal herbs exhibit potent anti-Ebola viral activities: Gardenia jasminoides Ellis, Citrus aurantium L., Viola yedoensis Makino, Prunella vulgaris L., Coix lacryma-jobi L. var. mayuen (Roman.) Stapf, Pinellia ternata (Thunb.) Breit., and Morus alba L. This study represents a proof-of-principle investigation supporting the suitability of this assay for rapid screening TCMs and identifying putative entry inhibitors for these viruses. J. Med. Virol. 89:908-916, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  16. Study of New Thiazole Based Pyridine Derivatives as Potential Corrosion Inhibitors for Mild Steel: Theoretical and Experimental Approach

    Directory of Open Access Journals (Sweden)

    T. K. Chaitra

    2016-01-01

    Full Text Available Three new thiazole based pyridine derivatives 5-(4-methoxy-phenyl-thiazole-2-carboxylic acid pyridin-2-ylmethylene-hydrazide (2-MTPH, 5-(4-methoxy-phenyl-thiazole-2-carboxylic acid pyridin-3-ylmethylene-hydrazide (3-MTPH, and 5-(4-methoxy-phenyl-thiazole-2-carboxylic acid pyridin-4-ylmethylene-hydrazide (4-MTPH were synthesized and characterized. Corrosion inhibition performance of the prepared compounds on mild steel in 0.5 M HCl was studied using gravimetric, potentiodynamic polarisation, and electrochemical impedance techniques. Inhibition efficiency has direct relation with concentration and inverse relation with temperature. Thermodynamic parameters for dissolution and adsorption process were evaluated. Polarisation study reveals that compounds act as both anodic and cathodic inhibitors with emphasis on the former. Impedance study shows that decrease in charge transfer resistance is responsible for effective protection of steel surface by inhibitors. The film formed on the mild steel was investigated using FTIR, SEM, and EDX spectroscopy. Quantum chemical parameters like EHOMO, ELUMO, ΔE, hardness, softness, and ionisation potential were calculated. Higher value of EHOMO and lower value of ΔE indicate the better inhibition efficiency of the compounds. Lower ionisation potential of inhibitors indicates higher reactivity and lower chemical stability.

  17. Development of a microarray-based assay for efficient testing of new HSP70/DnaK inhibitors.

    Science.gov (United States)

    Mohammadi-Ostad-Kalayeh, Sona; Hrupins, Vjaceslavs; Helmsen, Sabine; Ahlbrecht, Christin; Stahl, Frank; Scheper, Thomas; Preller, Matthias; Surup, Frank; Stadler, Marc; Kirschning, Andreas; Zeilinger, Carsten

    2017-12-15

    A facile method for testing ATP binding in a highly miniaturized microarray environment using human HSP70 and DnaK from Mycobacterium tuberculosis as biological targets is reported. Supported by molecular modelling studies we demonstrate that the position of the fluorescence label on ATP has a strong influence on the binding to human HSP70. Importantly, the label has to be positioned on the adenine ring and not to the terminal phosphate group. Unlabelled ATP displaced bound Cy5-ATP from HSP70 in the micromolar range. The affinity of a well-known HSP70 inhibitor VER155008 for the ATP binding site in HSP70 was determined, with a EC 50 in the micromolar range, whereas reblastin, a HSP90-inhibitor, did not compete for ATP in the presence of HSP70. The applicability of the method was demonstrated by screening a small compound library of natural products. This unraveled that terphenyls rickenyl A and D, recently isolated from cultures of the fungus Hypoxylon rickii, are inhibitors of HSP70. They compete with ATP for the chaperone in the range of 29 µM (Rickenyl D) and 49 µM (Rickenyl A). Furthermore, the microarray-based test system enabled protein-protein interaction analysis using full-length HSP70 and HSP90 proteins. The labelled full-length human HSP90 binds with a half-maximal affinity of 5.5 µg/ml (∼40 µM) to HSP70. The data also demonstrate that the microarray test has potency for many applications from inhibitor screening to target-oriented interaction studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. An Explanation to Individual Knowledge and Behavior Based on Empirical Substrates

    OpenAIRE

    Zhao, Liang; Zhu, Xian Chen

    2008-01-01

    Using recent findings from modern empirical disciplines and mainly building on F.A.Hayek’s thoughts, the paper gives a definition of knowledge in accord with the Austrian School’s tradition, and basing on the definition, it sums up three behavior assumptions and a framework on explaining individual behavior and expounds ideas on hierarchical knowledge and its change in real situations. By this way, the paper believes that the Austrian School can be greatly advanced with the help of modern emp...

  19. Microwave sintering of poly-ether-ether-ketone (PEEK) based coatings deposited on metallic substrate

    International Nuclear Information System (INIS)

    Zhang, G.; Leparoux, S.; Liao, H.; Coddet, C.

    2006-01-01

    In this paper, the feasibility of microwave (MW) sintering PEEK (poly-ether-ether-ketone) based coatings was investigated. Three coatings were studied: pure PEEK, micron-SiC and nano-SiC particles filled (wt.10%) PEEK coatings. The results indicate that, for the two composite coatings, the SiC particles distributed in the polymer matrix, as a good MW susceptor, could be heated preferentially by MW radiation. Consequently, the polymer matrix was heated by these particles

  20. Computational Studies of Difference in Binding Modes of Peptide and Non-Peptide Inhibitors to MDM2/MDMX Based on Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Yuxin Zhang

    2012-02-01

    Full Text Available Inhibition of p53-MDM2/MDMX interaction is considered to be a promising strategy for anticancer drug design to activate wild-type p53 in tumors. We carry out molecular dynamics (MD simulations to study the binding mechanisms of peptide and non-peptide inhibitors to MDM2/MDMX. The rank of binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA method agrees with one of the experimental values. The results suggest that van der Waals energy drives two kinds of inhibitors to MDM2/MDMX. We also find that the peptide inhibitors can produce more interaction contacts with MDM2/MDMX than the non-peptide inhibitors. Binding mode predictions based on the inhibitor-residue interactions show that the π–π, CH–π and CH–CH interactions dominated by shape complimentarity, govern the binding of the inhibitors in the hydrophobic cleft of MDM2/MDMX. Our studies confirm the residue Tyr99 in MDMX can generate a steric clash with the inhibitors due to energy and structure. This finding may theoretically provide help to develop potent dual-specific or MDMX inhibitors.

  1. Gas Diffusivity-Based Design and Characterization of Greenhouse Growth Substrates

    DEFF Research Database (Denmark)

    Deepagoda Thuduwe Kankanamge Kelum, Chamindu; Møldrup, Per; Tuller, Markus

    2013-01-01

    combinations thereof, are commonly used as growth media, detailed and comparable physical characterization is key to identify the best performing media. In this study, five potential growth media and two mixtures thereof were characterized based on soil gas diffusivity (Dp/Do, where Dp and Do are gas diffusion...... coefficients in soil air and free air, respectively) and an operationally defined critical window of diffusivity (CWD) representing the interval of air-filled porosity between critical air filled porosity where Dp/Do ≈ 0.02 and interaggregate porosity. The Dp measurements were conducted with 100-cm3 samples...

  2. Neural substrates of motor and cognitive dysfunctions in SCA2 patients: A network based statistics analysis

    Directory of Open Access Journals (Sweden)

    G. Olivito

    2017-01-01

    In the present study, the network-based statistics (NBS approach was used to assess differences in functional connectivity between specific cerebellar and cerebral “nodes” in SCA2 patients. Altered inter-nodal connectivity was found between more posterior regions in the cerebellum and regions in the cerebral cortex clearly related to cognition and emotion. Furthermore, more anterior cerebellar lobules showed altered inter-nodal connectivity with motor and somatosensory cerebral regions. The present data suggest that in SCA2 a cerebellar dysfunction affects long-distance cerebral regions and that the clinical symptoms may be specifically related with connectivity changes between motor and non-motor cerebello-cortical nodes.

  3. Si Substrate-Based Meta materials for Ultra broadband Perfect Absorption in Visible Regime

    International Nuclear Information System (INIS)

    Han, Q.; Jin, L.; Fu, Y.; Yu, W.; Yu, W.

    2014-01-01

    We report the broadband efficient light absorbing property of a structure of quadrangular frustum pyramid array in visible regime. The structure can absorb light efficiently with an average absorptivity of 0.98 over the whole visible waveband. In addition, it is found that this kind of super light absorbing can maintain an average of 0.9 for a wide incident angle range. The perfect absorbing property of the meta material-based nano ring array is attributed to the effect of the Fabry-Perot resonance. The structure is possible to be used as a type of Si photonics devices in future photonic circuits

  4. Neural substrates of social facilitation effects on incentive-based performance

    Science.gov (United States)

    Chib, Vikram S; Adachi, Ryo; O’Doherty, John P

    2018-01-01

    Abstract Throughout our lives we must perform tasks while being observed by others. Previous studies have shown that the presence of an audience can cause increases in an individual’s performance as compared to when they are not being observed—a phenomenon called ‘social facilitation’. However, the neural mechanisms underlying this effect, in the context of skilled-task performance for monetary incentives, are not well understood. We used functional magnetic resonance imaging to monitor brain activity while healthy human participants performed a skilled-task during conditions in which they were paid based on their performance and observed and not observed by an audience. We found that during social facilitation, social signals represented in the dorsomedial prefrontal cortex (dmPFC) enhanced reward value computations in ventromedial prefrontal cortex (vmPFC). We also found that functional connectivity between dmPFC and ventral striatum was enhanced when participants exhibited social facilitation effects, indicative of a means by which social signals serve to modulate brain regions involved in regulating behavioral motivation. These findings illustrate how neural processing of social judgments gives rise to the enhanced motivational state that results in social facilitation of incentive-based performance. PMID:29648653

  5. Structural Bioinformatics-Based Prediction of Exceptional Selectivity of p38 MAP Kinase Inhibitor PH-797804

    Energy Technology Data Exchange (ETDEWEB)

    Xing, Li; Shieh, Huey S.; Selness, Shaun R.; Devraj, Rajesh V.; Walker, John K.; Devadas, Balekudru; Hope, Heidi R.; Compton, Robert P.; Schindler, John F.; Hirsch, Jeffrey L.; Benson, Alan G.; Kurumbail, Ravi G.; Stegeman, Roderick A.; Williams, Jennifer M.; Broadus, Richard M.; Walden, Zara; Monahan, Joseph B.; Pfizer

    2009-07-24

    PH-797804 is a diarylpyridinone inhibitor of p38{alpha} mitogen-activated protein (MAP) kinase derived from a racemic mixture as the more potent atropisomer (aS), first proposed by molecular modeling and subsequently confirmed by experiments. On the basis of structural comparison with a different biaryl pyrazole template and supported by dozens of high-resolution crystal structures of p38{alpha} inhibitor complexes, PH-797804 is predicted to possess a high level of specificity across the broad human kinase genome. We used a structural bioinformatics approach to identify two selectivity elements encoded by the TXXXG sequence motif on the p38{alpha} kinase hinge: (i) Thr106 that serves as the gatekeeper to the buried hydrophobic pocket occupied by 2,4-difluorophenyl of PH-797804 and (ii) the bidentate hydrogen bonds formed by the pyridinone moiety with the kinase hinge requiring an induced 180{sup o} rotation of the Met109-Gly110 peptide bond. The peptide flip occurs in p38{alpha} kinase due to the critical glycine residue marked by its conformational flexibility. Kinome-wide sequence mining revealed rare presentation of the selectivity motif. Corroboratively, PH-797804 exhibited exceptionally high specificity against MAP kinases and the related kinases. No cross-reactivity was observed in large panels of kinase screens (selectivity ratio of >500-fold). In cellular assays, PH-797804 demonstrated superior potency and selectivity consistent with the biochemical measurements. PH-797804 has met safety criteria in human phase I studies and is under clinical development for several inflammatory conditions. Understanding the rationale for selectivity at the molecular level helps elucidate the biological function and design of specific p38{alpha} kinase inhibitors.

  6. SOL-GEL SILICA-BASED Ag–Ca–P COATINGS WITH AGRESSIVE PRETREATMENT OF TITANIUM SUBSTRATE

    Directory of Open Access Journals (Sweden)

    ELENA BORSHCHEVA

    2011-12-01

    Full Text Available The aim of the experiment was the obtaining of thin silica coatings on titanium by sol-gel method, using mechanical (SiC - paper No.180 and chemical (leaching in HF pretreatments of the titanium substrates. The solutions were based on TEOS. For the sol-gel dipping process 4 different solutions were prepared: silica, silica with AgNO3 and silica + AgNO3 with brushite (CaHPO4·2H2O or monetite (CaHPO4 powders. The solutions were aged for 7 and 14 days at laboratory temperature. After sol-gel dip-coating process the samples were dried and fired. The adhesion of fired coatings was measured by tape test according to ASTM procedure and the bioactivity of the coatings was tested using in vitro test. The surfaces of the samples after firing, tape test and in vitro test were observed with the optical and electron microscopes. The firing results showed that silica-silver coatings did not change, brushite sol-gel coatings have cracked and the monetite sol-gel coatings have cracked also, but less than brushite ones. In spite of coating´s crackings, the square’s frames made on the surfaces were without any breakdowns after tape tests and the adhesion of all coatings was very good, classified by the highest grade 5. The results of in vitro tests showed that all coatings interacted with simulated body fluid (SBF. After exposition in SBF the new layer formed on substrates. In case of 7 days aged coatings containing brushite the new layer was uniform and compact. In case of 7 days aged coatings containing monetite the new layer was formed by crystals aggregated tightly together. The monetite and brushite coatings prepared from 14 days aged sol were the same as previous ones, but they were thicker. X-ray analyses after in vitro test confirmed dellaite, titanate and hydroxyapatite phases.

  7. Rapid and direct spectrophotometric method for kinetics studies and routine assay of peroxidase based on aniline diazo substrates.

    Science.gov (United States)

    Mirazizi, Fatemeh; Bahrami, Azita; Haghbeen, Kamahldin; Shahbani Zahiri, Hossein; Bakavoli, Mehdi; Legge, Raymond L

    2016-12-01

    Peroxidases are ubiquitous enzymes that play an important role in living organisms. Current spectrophotometrically based peroxidase assay methods are based on the production of chromophoric substances at the end of the enzymatic reaction. The ambiguity regarding the formation and identity of the final chromophoric product and its possible reactions with other molecules have raised concerns about the accuracy of these methods. This can be of serious concern in inhibition studies. A novel spectrophotometric assay for peroxidase, based on direct measurement of a soluble aniline diazo substrate, is introduced. In addition to the routine assays, this method can be used in comprehensive kinetics studies. 4-[(4-Sulfophenyl)azo]aniline (λmax = 390 nm, ɛ = 32 880 M(-1) cm(-1) at pH 4.5 to 9) was introduced for routine assay of peroxidase. This compound is commercially available and is indexed as a food dye. Using this method, a detection limit of 0.05 nmol mL(-1) was achieved for peroxidase.

  8. An fMRI paradigm based on Williams inhibition test to study the neural substrates of attention and inhibitory control.

    Science.gov (United States)

    Dores, Artemisa R; Barbosa, Fernando; Carvalho, Irene P; Almeida, Isabel; Guerreiro, Sandra; da Rocha, Benedita Martins; Cunha, Gil; Castelo Branco, Miguel; de Sousa, Liliana; Castro Caldas, Alexandre

    2017-12-01

    The purpose of this study is to present an fMRI paradigm, based on the Williams inhibition test (WIT), to study attentional and inhibitory control and their neuroanatomical substrates. We present an index of the validity of the proposed paradigm and test whether the experimental task discriminates the behavioral performances of healthy participants from those of individuals with acquired brain injury. Stroop and Simon tests present similarities with WIT, but this latter is more demanding. We analyze the BOLD signal in 10 healthy participants performing the WIT. The dorsolateral prefrontal cortex, the inferior prefrontal cortex, the anterior cingulate cortex, and the posterior cingulate cortex were defined for specified region of interest analysis. We additionally compare behavioral data (hits, errors, reaction times) of the healthy participants with those of eight acquired brain injury patients. Data were analyzed with GLM-based random effects and Mann-Whitney tests. Results show the involvement of the defined regions and indicate that the WIT is sensitive to brain lesions. This WIT-based block design paradigm can be used as a research methodology for behavioral and neuroimaging studies of the attentional and inhibitory components of executive functions.

  9. Blue electroluminescence nanodevice prototype based on vertical ZnO nanowire/polymer film on silicon substrate

    International Nuclear Information System (INIS)

    He Ying; Wang Junan; Chen Xiaoban; Zhang Wenfei; Zeng Xuyu; Gu Qiuwen

    2010-01-01

    We present a polymer-complexing soft template technique to construct the ZnO-nanowire/polymer light emitting device prototype that exhibits blue electrically driven emission with a relatively low-threshold voltage at room temperature in ambient atmosphere, and the ZnO-nanowire-based LED's emission wavelength is easily tuned by controlling the applied-excitation voltage. The nearly vertically aligned ZnO-nanowires with polymer film were used as emissive layers in the devices. The method uses polymer as binder in the LED device and dispersion medium in the luminescence layer, which stabilizes the quasi-arrays of ZnO nanowires embedding in a thin polymer film on silicon substrate and passivates the surface of ZnO nanocrystals, to prevent the quenching of luminescence. Additionally, the measurements of electrical properties showed that ZnO-nanowire/polymer film could significantly improve the conductivity of the film, which could be attributed to an increase in both Hall mobility and carrier concentration. The results indicated that the novel technique is a low-cost process for ZnO-based UV or blue light emission and reduces the requirement for achieving robust p-doping of ZnO film. It suggests that such ZnO-nanowire/polymer-based LEDs will be suitable for the electro-optical application.

  10. Disposable urea biosensor based on nanoporous ZnO film fabricated from omissible polymeric substrate

    International Nuclear Information System (INIS)

    Rahmanian, Reza; Mozaffari, Sayed Ahmad; Abedi, Mohammad

    2015-01-01

    In the present study, a facile and simple fabrication method of a semiconductor based urea biosensor was reported via three steps: (i) producing a ZnO–PVA composite film by means of a polymer assisted electrodeposition of zinc oxide (ZnO) on the F-doped SnO 2 conducting glass (FTO) using water soluble polyvinyl alcohol (PVA), (ii) obtaining a nanoporous ZnO film by PVA omission via a subsequent post-treatment by annealing of the ZnO–PVA film, and (iii) preparation of a FTO/ZnO/Urs biosensor by exploiting a nanoporous ZnO film as an efficient and excellent platform area for electrostatic immobilization of urease enzyme (Urs) which was forced by the difference in their isoelectric point (IEP). The characterization techniques focused on the analysis of the ZnO–PVA film surfaces before and after annealing, which had a prominent effect on the porosity of the prepared ZnO film. The surface characterization of the nanostructured ZnO film by a field emission-scanning electron microscopy (FE–SEM), exhibited a film surface area as an effective bio-sensing matrix for enzyme immobilization. The structural characterization and monitoring of the biosensor fabrication was performed using UV–Vis, Fourier Transform Infrared (FT-IR), Raman Spectroscopy, Thermogravimetric Analysis (TGA), Cyclic Voltammetry (CV), and Electrochemical Impedance Spectroscopy (EIS) techniques. The impedimetric results of the FTO/ZnO/Urs biosensor showed a high sensitivity for urea detection within 8.0–110.0 mg dL −1 with the limit of detection as 5.0 mg dL −1 . - Highlights: • Novel disposable impedimetric urea biosensor fabrication based on ZnO–nanoporous transducer • Exploiting omissible PVA polymer as a simple strategy for ZnO–nanoporous film preparation • ZnO–nanoporous film as a good pore framework with large surface area/volume for enzyme immobilization • Application of impedimetric measurement for urea monitoring due to its rapidity, sensitivity, and repeatability

  11. Disposable urea biosensor based on nanoporous ZnO film fabricated from omissible polymeric substrate

    Energy Technology Data Exchange (ETDEWEB)

    Rahmanian, Reza; Mozaffari, Sayed Ahmad, E-mail: mozaffari@irost.ir; Abedi, Mohammad

    2015-12-01

    In the present study, a facile and simple fabrication method of a semiconductor based urea biosensor was reported via three steps: (i) producing a ZnO–PVA composite film by means of a polymer assisted electrodeposition of zinc oxide (ZnO) on the F-doped SnO{sub 2} conducting glass (FTO) using water soluble polyvinyl alcohol (PVA), (ii) obtaining a nanoporous ZnO film by PVA omission via a subsequent post-treatment by annealing of the ZnO–PVA film, and (iii) preparation of a FTO/ZnO/Urs biosensor by exploiting a nanoporous ZnO film as an efficient and excellent platform area for electrostatic immobilization of urease enzyme (Urs) which was forced by the difference in their isoelectric point (IEP). The characterization techniques focused on the analysis of the ZnO–PVA film surfaces before and after annealing, which had a prominent effect on the porosity of the prepared ZnO film. The surface characterization of the nanostructured ZnO film by a field emission-scanning electron microscopy (FE–SEM), exhibited a film surface area as an effective bio-sensing matrix for enzyme immobilization. The structural characterization and monitoring of the biosensor fabrication was performed using UV–Vis, Fourier Transform Infrared (FT-IR), Raman Spectroscopy, Thermogravimetric Analysis (TGA), Cyclic Voltammetry (CV), and Electrochemical Impedance Spectroscopy (EIS) techniques. The impedimetric results of the FTO/ZnO/Urs biosensor showed a high sensitivity for urea detection within 8.0–110.0 mg dL{sup −1} with the limit of detection as 5.0 mg dL{sup −1}. - Highlights: • Novel disposable impedimetric urea biosensor fabrication based on ZnO–nanoporous transducer • Exploiting omissible PVA polymer as a simple strategy for ZnO–nanoporous film preparation • ZnO–nanoporous film as a good pore framework with large surface area/volume for enzyme immobilization • Application of impedimetric measurement for urea monitoring due to its rapidity, sensitivity, and

  12. Incretin-based treatment of type 2 diabetes: glucagon-like peptide-1 receptor agonists and dipeptidyl peptidase-4 inhibitors

    DEFF Research Database (Denmark)

    Deacon, Carolyn F

    2007-01-01

    Incretins are gut peptides that potentiate nutrient-stimulated insulin secretion following meal ingestion. Activities of the dominant incretins, glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic peptide, include glucose-dependent stimulation of insulin secretion and, in preclin...... and liraglutide) and DPP-4 inhibitors that act to increase concentrations of endogenous intact incretins (e.g. sitagliptin and vildagliptin). Clinical trials of these incretin-based therapies have shown them to be effective in improving glycaemic control in patients with T2DM....

  13. Probing protein phosphatase substrate binding

    DEFF Research Database (Denmark)

    Højlys-Larsen, Kim B.; Sørensen, Kasper Kildegaard; Jensen, Knud Jørgen

    2012-01-01

    Proteomics and high throughput analysis for systems biology can benefit significantly from solid-phase chemical tools for affinity pull-down of proteins from complex mixtures. Here we report the application of solid-phase synthesis of phosphopeptides for pull-down and analysis of the affinity...... profile of the integrin-linked kinase associated phosphatase (ILKAP), a member of the protein phosphatase 2C (PP2C) family. Phosphatases can potentially dephosphorylate these phosphopeptide substrates but, interestingly, performing the binding studies at 4 °C allowed efficient binding to phosphopeptides......, without the need for phosphopeptide mimics or phosphatase inhibitors. As no proven ILKAP substrates were available, we selected phosphopeptide substrates among known PP2Cδ substrates including the protein kinases: p38, ATM, Chk1, Chk2 and RSK2 and synthesized directly on PEGA solid supports through a BAL...

  14. Stable Au–C bonds to the substrate for fullerene-based nanostructures

    Directory of Open Access Journals (Sweden)

    Taras Chutora

    2017-05-01

    Full Text Available We report on the formation of fullerene-derived nanostructures on Au(111 at room temperature and under UHV conditions. After low-energy ion sputtering of fullerene films deposited on Au(111, bright spots appear at the herringbone corner sites when measured using a scanning tunneling microscope. These features are stable at room temperature against diffusion on the surface. We carry out DFT calculations of fullerene molecules having one missing carbon atom to simulate the vacancies in the molecules resulting from the sputtering process. These modified fullerenes have an adsorption energy on the Au(111 surface that is 1.6 eV higher than that of C60 molecules. This increased binding energy arises from the saturation by the Au surface of the bonds around the molecular vacancy defect. We therefore interpret the observed features as adsorbed fullerene-derived molecules with C vacancies. This provides a pathway for the formation of fullerene-based nanostructures on Au at room temperature.

  15. Enhanced electrical conductivity in Xe ion irradiated CNT based transparent conducting electrode on PET substrate

    Science.gov (United States)

    Surbhi; Sharma, Vikas; Singh, Satyavir; Garg, Priyanka; Asokan, K.; Sachdev, Kanupriya

    2018-02-01

    An investigation of MWCNT-based hybrid electrode films with improved electrical conductivity after Xe ion irradiation is reported. A multilayer hybrid structure of Ag-MWCNT layer embedded in between two ZnO layers was fabricated and evaluated, pre and post 100 keV Xe ion irradiation, for their performance as Transparent Conducting Electrode in terms of their optical and electrical properties. X-ray diffraction pattern exhibits highly c-axis oriented ZnO films with a small variation in lattice parameters with an increase in ion fluence. There is no significant change in the surface roughness of these films. Raman spectra were used to confirm the presence of CNT. The pristine multilayer films exhibit an average transmittance of ˜70% in the entire visible region and the transmittance increases with Xe ion fluence. A significant enhancement in electrical conductivity post-Xe ion irradiation viz from 1.14 × 10-7 Ω-1 cm-1 (pristine) to 7.04 × 103 Ω-1 cm-1 is seen which is due to the high connectivity in the top layer with Ag-CNT hybrid layer facilitating the smooth transfer of electrons.

  16. Neuron Stimulation Device Integrated with Silicon Nanowire-Based Photodetection Circuit on a Flexible Substrate

    Directory of Open Access Journals (Sweden)

    Suk Won Jung

    2016-12-01

    Full Text Available This paper proposes a neural stimulation device integrated with a silicon nanowire (SiNW-based photodetection circuit for the activation of neurons with light. The proposed device is comprised of a voltage divider and a current driver in which SiNWs are used as photodetector and field-effect transistors; it has the functions of detecting light, generating a stimulation signal in proportion to the light intensity, and transmitting the signal to a micro electrode. To show the applicability of the proposed neural stimulation device as a high-resolution retinal prosthesis system, a high-density neural stimulation device with a unit cell size of 110 × 110 μ m and a resolution of 32 × 32 was fabricated on a flexible film with a thickness of approximately 50 μm. Its effectiveness as a retinal stimulation device was then evaluated using a unit cell in an in vitro animal experiment involving the retinal tissue of retinal Degeneration 1 (rd1 mice. Experiments wherein stimulation pulses were applied to the retinal tissues successfully demonstrate that the number of spikes in neural response signals increases in proportion to light intensity.

  17. A comparative analysis of property of lychee polyphenoloxidase using endogenous and exogenous substrates.

    Science.gov (United States)

    Sun, Jian; Shi, John; Zhao, Mouming; Xue, Sophia Jun; Ren, Jiaoyan; Jiang, Yueming

    2008-06-01

    Lychee polyphenoloxidase (PPO) was extracted and partially purified using ammonium sulphate precipitation and dialysis. The comparative analysis of PPO property was performed using its endogenous substrate (-)-epicatechin and exogenous substrate catechol. The pH optima for activity and activation temperature profiles of lychee PPO were very different when the enzyme reacted with endogenous and exogenous substrates. The addition of ethylenediaminetetraacetic acid disodium salt into the endogenous or exogenous substrate-enzyme system exhibited the same lowest inhibition of the PPO activity. However, l-cysteine was most effective in inhibiting enzymatic activity in the endogenous substrate-enzyme system while ascorbic acid was the best inhibitor in the exogenous substrate-enzyme system. Fe(2+) greatly accelerated the enzymatic reaction between endogenous substrate and PPO, but Cu(2+) exerted the same effect on the reaction between exogenous substrate and PPO. Based on the kinetic analysis, lychee PPO could strongly bind endogenous substrate but it possessed a higher catalytic efficiency to exogenous substrate. Copyright © 2007 Elsevier Ltd. All rights reserved.

  18. Structure-activity relationship study of oxindole-based inhibitors of cyclin-dependent kinases based on least-squares support vector machines

    International Nuclear Information System (INIS)

    Li Jiazhong; Liu Huanxiang; Yao Xiaojun; Liu Mancang; Hu Zhide; Fan Botao

    2007-01-01

    The least-squares support vector machines (LS-SVMs), as an effective modified algorithm of support vector machine, was used to build structure-activity relationship (SAR) models to classify the oxindole-based inhibitors of cyclin-dependent kinases (CDKs) based on their activity. Each compound was depicted by the structural descriptors that encode constitutional, topological, geometrical, electrostatic and quantum-chemical features. The forward-step-wise linear discriminate analysis method was used to search the descriptor space and select the structural descriptors responsible for activity. The linear discriminant analysis (LDA) and nonlinear LS-SVMs method were employed to build classification models, and the best results were obtained by the LS-SVMs method with prediction accuracy of 100% on the test set and 90.91% for CDK1 and CDK2, respectively, as well as that of LDA models 95.45% and 86.36