WorldWideScience

Sample records for groove binding drugs

  1. Antineoplastic DNA-binding compounds: intercalating and minor groove binding drugs.

    Science.gov (United States)

    Mišković, Katarina; Bujak, Maro; Baus Lončar, Mirela; Glavaš-Obrovac, Ljubica

    2013-12-01

    DNA intercalating and minor groove binding compounds are new weapons in the battle against malignant diseases. These antineoplastic agents target the DNA molecule and interfere with the cell cycle leading to rapidly proliferating cell death. They are mainly derivates of a naturally occurring organic compound derived from a microorganism or plant. Intercalators usually act as topoisomerase I and/or II poisons, while the mechanisms of DNA minor groove binders are a combination of several steps including topoisomerase poisoning. This paper gives an overview of some of the developed DNA intercalating and minor groove binding compounds, as well as an explanation of their chemical structures, origins, and application in chemotherapy.

  2. Minor-Groove Binding Drugs: Where Is the Second Hoechst 33258 Molecule?

    KAUST Repository

    Fornander, Louise H.

    2013-05-16

    Hoechst 33258 binds with high affinity into the minor groove of AT-rich sequences of double-helical DNA. Despite extensive studies of this and analogous DNA binding molecules, there still remains uncertainty concerning the interactions when multiple ligand molecules are accommodated within close distance. Albeit not of direct concern for most biomedical applications, which are at low drug concentrations, interaction studies for higher drug binding are important as they can give fundamental insight into binding mechanisms and specificity, including drug self-stacking interactions that can provide base-sequence specificity. Using circular dichroism (CD), isothermal titration calorimetry (ITC), and proton nuclear magnetic resonance (1H NMR), we examine the binding of Hoechst 33258 to three oligonucleotide duplexes containing AT regions of different lengths: [d(CGCGAATTCGCG)]2 (A2T2), [d(CGCAAATTTGCG)]2 (A3T 3), and [d(CGAAAATTTTCG)]2 (A4T4). We find similar binding geometries in the minor groove for all oligonucleotides when the ligand-to-duplex ratio is less than 1:1. At higher ratios, a second ligand can be accommodated in the minor groove of A4T4 but not A2T2 or A3T3. We conclude that the binding of the second Hoechst to A4T4 is not cooperative and that the molecules are sitting with a small separation apart, one after the other, and not in a sandwich structure as previously proposed. © 2013 American Chemical Society.

  3. Binding to the DNA Minor Groove by Heterocyclic Dications: From AT Specific Monomers to GC Recognition with Dimers

    Science.gov (United States)

    Nanjunda, Rupesh; Wilson, W. David

    2012-01-01

    Compounds that bind in the DNA minor groove have provided critical information on DNA molecular recognition, they have found extensive uses in biotechnology and they are providing clinically useful drugs against diseases as diverse as cancer and sleeping sickness. This review focuses on the development of clinically useful heterocyclic diamidine minor groove binders. These compounds have shown us that the classical model for minor groove binding in AT DNA sequences must be expanded in several ways: compounds with nonstandard shapes can bind strongly to the groove, water can be directly incorporated into the minor groove complex in an interfacial interaction, and the compounds can form cooperative stacked dimers to recognize GC and mixed AT/GC base pair sequences. PMID:23255206

  4. Studies on a Novel Minor-groove Targeting Artificial Nuclease: Synthesis and DNA Binding Behavior

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Nucleases play an important role in molecular biology, for example, in DNA sequencing. Synthetic polyamide conjugates can be considered as a novel tool for the selective inhibition of gene expressions and also as potential drugs in anticancer or antiviral chemotherapy. In this article, the synthesis of a novel minor-groove targeting artificial nuclease, an oligopyrrol-containing compound, has been reported. It was found that this novel compound can bind DNA in AT-rich minor groove with high affinity and site specificity. DNA binding behavior was determined by using UV-Vis and CD. It is indicated that compound 6 can enhance the Tm of DNA from 80. 4 C to 84. 4 ℃ and that it possesses a high binding constant value(Kb = 3.05×104 L/mol).

  5. In and out of the minor groove: interaction of an AT-rich DNA with the drug CD27

    Energy Technology Data Exchange (ETDEWEB)

    Acosta-Reyes, Francisco J. [Universitat Politécnica de Catalunya, Diagonal 647, 08028 Barcelona (Spain); Dardonville, Christophe [Instituto de Química Médica, IQM–CSIC, Juan de la Cierva 3, 28006 Madrid (Spain); Koning, Harry P. de; Natto, Manal [University of Glasgow, 120 University Place, Glasgow G12 8TA, Scotland (United Kingdom); Subirana, Juan A.; Campos, J. Lourdes, E-mail: lourdes.campos@upc.edu [Universitat Politécnica de Catalunya, Diagonal 647, 08028 Barcelona (Spain)

    2014-06-01

    New features of an antiprotozoal DNA minor-groove binding drug, which acts as a cross-linking agent, are presented. It also fills the minor groove of DNA completely and prevents the access of proteins. These features are also expected for other minor-groove binding drugs when associated with suitable DNA targets. The DNA of several pathogens is very rich in AT base pairs. Typical examples include the malaria parasite Plasmodium falciparum and the causative agents of trichomoniasis and trypanosomiases. This fact has prompted studies of drugs which interact with the minor groove of DNA, some of which are used in medical practice. Previous studies have been performed almost exclusively with the AATT sequence. New features should be uncovered through the study of different DNA sequences. In this paper, the crystal structure of the complex of the DNA duplex d(AAAATTTT){sub 2} with the dicationic drug 4, 4′-bis(imidazolinylamino)diphenylamine (CD27) is presented. The drug binds to the minor groove of DNA as expected, but it shows two new features that have not previously been described: (i) the drugs protrude from the DNA and interact with neighbouring molecules, so that they may act as cross-linking agents, and (ii) the drugs completely cover the whole minor groove of DNA and displace bound water. Thus, they may prevent the access to DNA of proteins such as AT-hook proteins. These features are also expected for other minor-groove binding drugs when associated with all-AT DNA. These findings allow a better understanding of this family of compounds and will help in the development of new, more effective drugs. New data on the biological interaction of CD27 with the causative agent of trichomoniasis, Trichomonas vaginalis, are also reported.

  6. NMR studies of DNA oligomers and their interactions with minor groove binding ligands

    Energy Technology Data Exchange (ETDEWEB)

    Fagan, Patricia A. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1996-05-01

    The cationic peptide ligands distamycin and netropsin bind noncovalently to the minor groove of DNA. The binding site, orientation, stoichiometry, and qualitative affinity of distamycin binding to several short DNA oligomers were investigated by NMR spectroscopy. The oligomers studied contain A,T-rich or I,C-rich binding sites, where I = 2-desaminodeoxyguanosine. I•C base pairs are functional analogs of A•T base pairs in the minor groove. The different behaviors exhibited by distamycin and netropsin binding to various DNA sequences suggested that these ligands are sensitive probes of DNA structure. For sites of five or more base pairs, distamycin can form 1:1 or 2:1 ligand:DNA complexes. Cooperativity in distamycin binding is low in sites such as AAAAA which has narrow minor grooves, and is higher in sites with wider minor grooves such as ATATAT. The distamycin binding and base pair opening lifetimes of I,C-containing DNA oligomers suggest that the I,C minor groove is structurally different from the A,T minor groove. Molecules which direct chemistry to a specific DNA sequence could be used as antiviral compounds, diagnostic probes, or molecular biology tools. The author studied two ligands in which reactive groups were tethered to a distamycin to increase the sequence specificity of the reactive agent.

  7. Different thermodynamic signatures for DNA minor groove binding with changes in salt concentration and temperature.

    Science.gov (United States)

    Wang, Shuo; Kumar, Arvind; Aston, Karl; Nguyen, Binh; Bashkin, James K; Boykin, David W; Wilson, W David

    2013-10-04

    The effects of salt concentration and temperature on the thermodynamics of DNA minor groove binding have quite different signatures: binding enthalpy is salt concentration independent but temperature dependent. Conversely, binding free energy is salt dependent but essentially temperature independent through enthalpy-entropy compensation.

  8. Different Thermodynamic Signatures for DNA Minor Groove Binding with Changes in Salt Concentration and Temperature

    OpenAIRE

    2013-01-01

    The effects of salt concentration and temperature on the thermodynamics of DNA minor groove binding have quite different signatures: binding enthalpy is salt concentration independent but temperature dependent. Conversely, binding free energy is salt dependent but essentially temperature independent through enthalpy-entropy compensation.

  9. Zooming into the binding groove of HLA molecules : which positions and which substitutions change peptide binding most?

    NARCIS (Netherlands)

    van Deutekom, Hanneke W M; Kesmir, C.

    2015-01-01

    Human leukocyte antigen (HLA) genes are the most polymorphic genes in the human genome. Almost all polymorphic residues are located in the peptide-binding groove, resulting in different peptide-binding preferences. Whether a single amino acid change can alter the peptide-binding repertoire of an HLA

  10. Minor Groove Binding between Norfloxacin and DNA Duplexes in Solution: A Molecular Dynamics Study

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Molecular dynamics were used to investigate the interaction between norfloxacin and DNA duplex. The results showed that norfloxacin was situated in the minor groove of DNA,binding to the TCGA region of d [ATATCGATAT] 2. Specific hydrogen bonds were formed between norfloxacin and guanine base of DNA during the 2 ns MD, which may be the reason for the preferentiality of quinolone antibacterial towards the guanine base of DNA duplex.

  11. DAPI binding to the DNA minor groove: a continuum solvent analysis.

    Science.gov (United States)

    De Castro, L F Pineda; Zacharias, M

    2002-01-01

    A continuum solvent model based on the generalized Born (GB) or finite-difference Poisson-Boltzmann (FDPB) approaches has been employed to compare the binding of 4'-6-diamidine-2-phenyl indole (DAPI) to the minor groove of various DNA sequences. Qualitative agreement between the results of GB and FDPB approaches as well as between calculated and experimentally observed trends regarding the sequence specificity of DAPI binding to B-DNA was obtained. Calculated binding energies were decomposed into various contributions to solvation and DNA-ligand interaction. DNA conformational adaptation was found to make a favorable contribution to the calculated total interaction energy but did not change the DAPI binding affinity ranking of different DNA sequences. The calculations indicate that closed complex formation is mainly driven by nonpolar contributions and was found to be disfavored electrostatically due to a desolvation penalty that outbalances the attractive Coulomb interaction. The calculated penalty was larger for DAPI binding to GC-rich sequences compared with AT-rich target sequences and generally larger for the FDPB vs the GB continuum model. A radial interaction profile for DAPI at different distances from the DNA minor groove revealed an electrostatic energy minimum a few Angstroms farther away from the closed binding geometry. The calculated electrostatic interaction up to this distance is attractive and it may stabilize a nonspecific binding arrangement.

  12. DNA minor groove binding of small molecules: Experimental and computational evidence

    Indian Academy of Sciences (India)

    Prateek Pandya; Md Maidul Islam; G Suresh Kumar; B Jayaram; Surat Kumar

    2010-03-01

    Eight indole derivatives were studied for their DNA binding ability using fluorescence quenching and molecular docking methods. These indole compounds have structural moieties similar as in few indole alkaloids. Experimental and theoretical studies have suggested that indole derivatives bind in the minor groove of DNA. Thermodynamic profiles of DNA complexes of indole derivatives were obtained from computational methods. The complexes were largely stabilized by H-bonding and van der Waal’s forces with positive entropy values. Indole derivatives were found to possess some Purine (Pu) - Pyrimidine (Py) specificity with DNA sequences. The results obtained from experimental and computational methods showed good agreement with each other, supported by their correlation constant values.

  13. A structural insight into major groove directed binding of nitrosourea derivative nimustine with DNA: a spectroscopic study.

    Directory of Open Access Journals (Sweden)

    Shweta Agarwal

    Full Text Available Nitrosourea therapeutics occupies a definite place in cancer therapy but its exact mechanism of action has yet to be established. Nimustine, a chloroethyl nitrosourea derivative, is used to treat various types of malignancy including gliomas. The present work focuses on the understanding of nimustine interaction with DNA to delineate its mechanism at molecular level. Attenuated total reflection-Fourier transform infrared (ATR-FTIR has been used to determine the binding sites of nimustine on DNA. Circular dichroism (CD spectroscopy has been used to confirm conformational variations in DNA molecule upon nimustine-DNA interaction. Thermodynamic parameters of nimustine-DNA reaction have been calculated by isothermal titration calorimetry. Results of the present study demonstrate that nimustine is not a simple alkylating agent rather it causes major grove-directed-alkylation. Spectroscopic data suggest binding of nimustine with nitrogenous bases guanine (C6 = O6 and thymine (C4 = O4 in DNA major groove. CD spectra of nimustine-DNA complexes point toward the perturbation of native B-conformation of DNA and its partial transition into C-form. Thermodynamically, nimustine-DNA interaction is an entropy driven endothermic reaction, which suggests hydrophobic interaction of nimustine in DNA-major groove pocket. Spectral results suggest base binding and local conformational changes in DNA upon nimustine interaction. Investigation of drug-DNA interaction is an essential part of rational drug designing that also provides information about the drug's action at molecular level. Results, demonstrated here, may contribute in the development of new nitrosourea therapeutics with better efficacy and fewer side effects.

  14. Deciphering the groove binding modes of tau-fluvalinate and flumethrin with calf thymus DNA

    Science.gov (United States)

    Tao, Mo; Zhang, Guowen; Pan, Junhui; Xiong, Chunhong

    2016-02-01

    Tau-fluvalinate (TFL) and flumethrin (FL), widely used in agriculture and a class of synthetic pyrethroid pesticides with a similar structure, may cause a potential security risk. Herein, the modes of binding in vitro of TFL and FL with calf thymus DNA (ctDNA) were characterized by fluorescence, UV-vis absorption, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy with the aid of viscosity measurements, melting analyses and molecular docking studies. The fluorescence titration indicated that both TFL and FL bound to ctDNA forming complexes through hydrogen bonding and van der Waals forces. The binding constants of TFL and FL with ctDNA were in the range of 104 L mol- 1, and FL exhibited a higher binding propensity than TFL. The iodide quenching effect, single/double-stranded DNA effects, and ctDNA melting and viscosity measurements demonstrated that the binding of both TFL and FL to ctDNA was groove mode. The FT-IR analyses suggested the A-T region of the minor groove of ctDNA as the preferential binding for TFL and FL, which was confirmed by the displacement assays with Hoechst 33258 probe, and the molecular docking visualized the specific binding. The changes in CD spectra indicated that both FL and TFL induced the perturbation on the base stacking and helicity of B-DNA, but the disturbance caused by FL was more obvious. Gel electrophoresis analyses indicated that both TFL and FL did not cause significant DNA cleavage. This study provides novel insights into the binding properties of TFL/FL with ctDNA and its toxic mechanisms.

  15. Deciphering the groove binding modes of tau-fluvalinate and flumethrin with calf thymus DNA.

    Science.gov (United States)

    Tao, Mo; Zhang, Guowen; Pan, Junhui; Xiong, Chunhong

    2016-02-15

    Tau-fluvalinate (TFL) and flumethrin (FL), widely used in agriculture and a class of synthetic pyrethroid pesticides with a similar structure, may cause a potential security risk. Herein, the modes of binding in vitro of TFL and FL with calf thymus DNA (ctDNA) were characterized by fluorescence, UV-vis absorption, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy with the aid of viscosity measurements, melting analyses and molecular docking studies. The fluorescence titration indicated that both TFL and FL bound to ctDNA forming complexes through hydrogen bonding and van der Waals forces. The binding constants of TFL and FL with ctDNA were in the range of 10(4)Lmol(-1), and FL exhibited a higher binding propensity than TFL. The iodide quenching effect, single/double-stranded DNA effects, and ctDNA melting and viscosity measurements demonstrated that the binding of both TFL and FL to ctDNA was groove mode. The FT-IR analyses suggested the A-T region of the minor groove of ctDNA as the preferential binding for TFL and FL, which was confirmed by the displacement assays with Hoechst 33258 probe, and the molecular docking visualized the specific binding. The changes in CD spectra indicated that both FL and TFL induced the perturbation on the base stacking and helicity of B-DNA, but the disturbance caused by FL was more obvious. Gel electrophoresis analyses indicated that both TFL and FL did not cause significant DNA cleavage. This study provides novel insights into the binding properties of TFL/FL with ctDNA and its toxic mechanisms.

  16. From intercalation to groove binding: switching the DNA-binding mode of isostructural transition-metal complexes.

    Science.gov (United States)

    Ahmad, Haslina; Wragg, Ashley; Cullen, Will; Wombwell, Claire; Meijer, Anthony J H M; Thomas, Jim A

    2014-03-10

    The interaction with duplex DNA of a small library of structurally related complexes that all contain a d6-metal ion coordinated to either the 2,2′:4,4′′:4′,4′′′-quaterpyridyl ligand or its methylated derivative are reported. This library is made up of a mixture of newly synthesised and previously reported systems. Despite their structural similarities the complexes display an almost 20-fold variation in binding affinities. Although effects due to the overall charge of the complexes are apparent, the differences in binding characteristics are deeper than this; indeed, in a number of cases, changes in overall charge have little effect on binding affinity. Intriguingly, despite interacting with DNA through unfused ring systems, although two of the complexes studied are groove binders, the majority are non-classical intercalators. A rationale for these effects has been obtained through a combination of experimental and computational studies.

  17. Molecular Probing of the HPV-16 E6 Protein Alpha Helix Binding Groove with Small Molecule Inhibitors.

    Directory of Open Access Journals (Sweden)

    Anne Rietz

    Full Text Available The human papillomavirus (HPV HPV E6 protein has emerged as a central oncoprotein in HPV-associated cancers in which sustained expression is required for tumor progression. A majority of the E6 protein interactions within the human proteome use an alpha-helix groove interface for binding. The UBE3A/E6AP HECT domain ubiquitin ligase binds E6 at this helix-groove interface. This enables formation of a trimeric complex with p53, resulting in destruction of this tumor suppressor. While recent x-ray crystal structures are useful, examples of small molecule probes that can modulate protein interactions at this interface are limited. To develop insights useful for potential structure-based design of ligands for HPV E6, a series of 2,6-disubstituted benzopyranones were prepared and tested as competitive antagonists of E6-E6AP helix-groove interactions. These small molecule probes were used in both binding and functional assays to evaluate recognition features of the E6 protein. Evidence for an ionic functional group interaction within the helix groove was implicated by the structure-activity among the highest affinity ligands. The molecular topographies of these protein-ligand interactions were evaluated by comparing the binding and activities of single amino acid E6 mutants with the results of molecular dynamic simulations. A group of arginine residues that form a rim-cap over the E6 helix groove offer compensatory roles in binding and recognition of the small molecule probes. The flexibility and impact on the overall helix-groove shape dictated by these residues offer new insights for structure-based targeting of HPV E6.

  18. Troxerutin, a natural flavonoid binds to DNA minor groove and enhances cancer cell killing in response to radiation.

    Science.gov (United States)

    Panat, Niranjan A; Singh, Beena G; Maurya, Dharmendra K; Sandur, Santosh K; Ghaskadbi, Saroj S

    2016-05-05

    Troxerutin, a flavonoid best known for its radioprotective and antioxidant properties is of considerable interest of study due to its broad pharmacological activities. The present study on troxerutin highlights its abilities to bind DNA and enhance cancer cell killing in response to radiation. Troxerutin showed strong binding with calf thymus DNA in vitro. Troxerutin-DNA interaction was confirmed by CD spectropolarimetry. The mode of binding of troxerutin to DNA was assessed by competing troxerutin with EtBr or DAPI, known DNA intercalator and a minor groove binder, respectively. DAPI fluorescence was drastically reduced with linear increase in troxerutin concentration suggesting possible binding of troxerutin to DNA minor groove. Further, computational studies of docking of troxerutin molecule on mammalian DNA also indicated possible troxerutin-DNA interaction at minor groove of DNA. Troxerutin was found to mainly localize in the nucleus of prostate cancer cells. It induced cytotoxicity in radioresistant (DU145) and sensitive (PC3) prostate cancer cells. When troxerutin pre-treated DU145 and PC3 cells were exposed to γ-radiation, cytotoxicity as estimated by MTT assay, was found to be further enhanced. In addition, the % subG1 population detected by propidium iodide staining also showed similar response when combined with radiation. A similar trend was observed in terms of ROS generation and DNA damage in DU145 cells when troxerutin and radiation were combined. DNA binding at minor groove by troxerutin may have contributed to strand breaks leading to increased radiation induced cell death.

  19. A monofunctional platinum complex coordinated to a rhodium metalloinsertor selectively binds mismatched DNA in the minor groove.

    Science.gov (United States)

    Weidmann, Alyson G; Barton, Jacqueline K

    2015-10-05

    We report the synthesis and characterization of a bimetallic complex derived from a new family of potent and selective metalloinsertors containing an unusual Rh-O axial coordination. This complex incorporates a monofunctional platinum center containing only one labile site for coordination to DNA, rather than two, and coordinates DNA nonclassically through adduct formation in the minor groove. This conjugate displays bifunctional, interdependent binding of mismatched DNA via metalloinsertion at a mismatch as well as covalent platinum binding. DNA sequencing experiments revealed that the preferred site of platinum coordination is not the traditional N7-guanine site in the major groove, but rather N3-adenine in the minor groove. The complex also displays enhanced cytotoxicity in mismatch repair-deficient and mismatch repair-proficient human colorectal carcinoma cell lines compared to the chemotherapeutic cisplatin, and it triggers cell death via an apoptotic pathway, rather than the necrotic pathway induced by rhodium metalloinsertors.

  20. Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove.

    Science.gov (United States)

    McMurtrey, Curtis; Trolle, Thomas; Sansom, Tiffany; Remesh, Soumya G; Kaever, Thomas; Bardet, Wilfried; Jackson, Kenneth; McLeod, Rima; Sette, Alessandro; Nielsen, Morten; Zajonc, Dirk M; Blader, Ira J; Peters, Bjoern; Hildebrand, William

    2016-01-29

    HLA class I presentation of pathogen-derived peptide ligands is essential for CD8+ T-cell recognition of Toxoplasma gondii infected cells. Currently, little data exist pertaining to peptides that are presented after T. gondii infection. Herein we purify HLA-A*02:01 complexes from T. gondii infected cells and characterize the peptide ligands using LCMS. We identify 195 T. gondii encoded ligands originating from both secreted and cytoplasmic proteins. Surprisingly, T. gondii ligands are significantly longer than uninfected host ligands, and these longer pathogen-derived peptides maintain a canonical N-terminal binding core yet exhibit a C-terminal extension of 1-30 amino acids. Structural analysis demonstrates that binding of extended peptides opens the HLA class I F' pocket, allowing the C-terminal extension to protrude through one end of the binding groove. In summary, we demonstrate that unrealized structural flexibility makes MHC class I receptive to parasite-derived ligands that exhibit unique C-terminal peptide extensions.

  1. Unusually strong binding to the DNA minor groove by a highly twisted benzimidazole diphenylether: induced fit and bound water.

    Science.gov (United States)

    Tanious, Farial A; Laine, William; Peixoto, Paul; Bailly, Christian; Goodwin, Kristie D; Lewis, Mark A; Long, Eric C; Georgiadis, Millie M; Tidwell, Richard R; Wilson, W David

    2007-06-12

    RT29 is a dicationic diamidine derivative that does not obey the classical "rules" for shape and functional group placement that are expected to result in strong binding and specific recognition of the DNA minor groove. The compound contains a benzimidazole diphenyl ether core that is flanked by the amidine cations. The diphenyl ether is highly twisted and gives the entire compound too much curvature to fit well to the shape of the minor groove. DNase I footprinting, fluorescence intercalator displacement studies, and circular dichroism spectra, however, indicate that the compound is an AT specific minor groove binding agent. Even more surprisingly, quantitative biosensor-surface plasmon resonance and isothermal titration calorimetric results indicate that the compound binds with exceptional strength to certain AT sequences in DNA with a large negative enthalpy of binding. Crystallographic results for the DNA complex of RT29 compared to calculated results for the free compound show that the compound undergoes significant conformational changes to enhance its minor groove interactions. In addition, a water molecule is incorporated directly into the complex to complete the compound-DNA interface, and it forms an essential link between the compound and base pair edges at the floor of the minor groove. The calculated DeltaCp value for complex formation is substantially less than the experimentally observed value, which supports the idea of water being an intrinsic part of the complex with a major contribution to the DeltaCp value. Both the induced fit conformational changes of the compound and the bound water are essential for strong binding to DNA by RT29.

  2. Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove

    DEFF Research Database (Denmark)

    McMurtrey, Curtis; Trolle, Thomas; Sansom, Tiffany

    2016-01-01

    N-terminal binding core yet exhibit a C-terminal extension of 1-30 amino acids. Structural analysis demonstrates that binding of extended peptides opens the HLA class I F' pocket, allowing the C-terminal extension to protrude through one end of the binding groove. In summary, we demonstrate...... cells and characterize the peptide ligands using LCMS. We identify 195 T. gondii encoded ligands originating from both secreted and cytoplasmic proteins. Surprisingly, T. gondii ligands are significantly longer than uninfected host ligands, and these longer pathogen derived peptides maintain a canonical...

  3. Chronic beryllium disease, HLA-DPB1, and the DP peptide binding groove.

    Science.gov (United States)

    Silveira, Lori J; McCanlies, Erin C; Fingerlin, Tasha E; Van Dyke, Michael V; Mroz, Margaret M; Strand, Matthew; Fontenot, Andrew P; Bowerman, Natalie; Dabelea, Dana M; Schuler, Christine R; Weston, Ainsley; Maier, Lisa A

    2012-10-15

    Multiple epidemiologic studies demonstrate associations between chronic beryllium disease (CBD), beryllium sensitization (BeS), and HLA-DPB1 alleles with a glutamic acid residue at position 69 (E69). Results suggest that the less-frequent E69 variants (non-*0201/*0202 alleles) might be associated with greater risk of CBD. In this study, we sought to define specific E69-carrying alleles and their amino acid sequences in the DP peptide binding groove, as well as their relationship to CBD and BeS risk, using the largest case control study to date. We enrolled 502 BeS/CBD subjects and 653 beryllium-exposed controls from three beryllium industries who gave informed consent for participation. Non-Hispanic white cases and controls were frequency-matched by industry. HLA-DPB1 genotypes were determined using sequence-specific primer PCR. The E69 alleles were tested for association with disease individually and grouped by amino acid structure using logistic regression. The results show that CBD cases were more likely than controls to carry a non-*02 E69 allele than an *02 E69, with odds ratios (95% confidence interval) ranging from 3.1 (2.1-4.5) to 3.9 (2.6-5.9) (p < 0.0001). Polymorphic amino acids at positions 84 and 11 were associated with CBD: DD versus GG, 2.8 (1.8-4.6), p < 0.0001; GD versus GG, 2.1 (1.5-2.8), p < 0.0001; LL versus GG, 3.2 (1.8-5.6), p < 0.0001; GL versus GG, 2.8 (2.1-3.8), p < 0.0001. Similar results were found within the BeS group and CBD/BeS combined group. We conclude that the less frequent E69 alleles confer more risk for CBD than does *0201. Recent studies examining how the composition and structure of the binding pockets influence peptide binding in MHC genes, as well of studies showing the topology of the TCR to likely bind DPB1 preferentially, give plausible biological rationale for these findings.

  4. Binding of resveratrol to the minor groove of DNA sequences with AATT and TTAA segments induces differential stability.

    Science.gov (United States)

    Nair, Maya S; D'Mello, Samar; Pant, Rashmi; Poluri, Krishna Mohan

    2017-05-01

    Interactions of a natural stilbene compound, resveratrol with two DNA sequences containing AATT/TTAA segments have been studied. Resveratrol is found to interact with both the sequences. The mode of interaction has been studied using absorption, steady state fluorescence and circular dichroism spectroscopic techniques. UV-visible absorption and fluorescence studies provided the information regarding the binding constants and the stoichiometry of binding, whereas circular dichroism studies depicted the structural changes in DNA upon resveratrol binding. Our results evidenced that, though resveratrol showed similar affinity to both the sequences, the mode of interactions was different. The binding constants of resveratrol to AATT/TTAA sequences were found to be 7.55×10(5)M(-1) and 5.42×10(5)M(-1) respectively. Spectroscopic data evidenced for a groove binding interaction. Melting studies showed that the binding of resveratrol induces differential stability to the DNA sequences d(CGTTAACG)2 and d(CGAATTCG)2. Fluorescence data showed a stoichiometry of 1:1 for d(CGAATTCG)2-resveratrol complex and 1:4 for d(CGTTAACG)2-resveratrol complex. Molecular docking studies demonstrated that resveratrol binds to the minor groove region of both the sequences to form stable complexes with varied atomic contacts to the DNA bases or backbone. Both the complexes are stabilized by hydrogen bond formation. Our results evidenced that modulation of DNA sequence within the same bases can greatly alter the binding geometry and stability of the complex upon binding to small molecule inhibitor compounds like resveratrol. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. NMR structure of dual site binding of mitoxantrone dimer to opposite grooves of parallel stranded G-quadruplex [d-(TTGGGGT)]4.

    Science.gov (United States)

    Pradeep, Tarikere Palakshan; Barthwal, Ritu

    2016-01-01

    The formation of complex between anti-cancer drug mitoxantrone (MTX) and tetra-molecular parallel G-quadruplex DNA [d-(TTGGGGT)]4 has been studied by solution state one and two dimensional NMR spectroscopy. Mitoxantrone forms a head-to-tail dimer and binds at two opposite grooves of the G-quadruplex. The Job's method of continuous variation and thermal melting studies independently ascertain binding stoichiometry of 4:1 in mitoxantrone:DNA complex. The existence of only four guanine NH peaks corresponding to the four G-quartets during the course of titration shows that C4 symmetry of G-quadruplex is intact upon binding of mitoxantrone. The specific inter molecular short distance contacts between protons of two mitoxantrone molecules of dimer, that is, ring A protons with ring C and side chain methylene protons, confirms the formation of mitoxantrone head-to-tail dimer. The observed 38 Nuclear Overhauser Enhancement (NOE) cross peaks between MTX and G-quadruplex DNA indicate formation of a well-defined complex. The three dimensional structure of 4:1 mitoxantrone:[d-(TTGGGGT)]4 complex computed by using experimental distance restraints followed by restrained Molecular Dynamics (rMD) simulations envisages the critical knowledge of specific molecular interactions within ligand-G-quadruplex complex. The findings are of direct interest in development of anti-cancer therapeutic drug based on G-quadruplex stabilization, resulting in telomerase inhibition.

  6. Successful treatment of osseous lesion associated with palatoradicular groove using local drug delivery and guided tissue regeneration: A report of two cases

    Directory of Open Access Journals (Sweden)

    Jayaprakash S Gadagi

    2012-01-01

    Full Text Available Developmental grooves are not rare and often appear on maxillary lateral and central incisors and are an important predisposing factor to localized periodontal disease. Various techniques have been adopted to eliminate the groove and regenerate lost periodontium. This report of two cases describes the technique of using the local drug delivery system with chlorehexidine and the guided tissue regeneration (GTR to control the disease progression and regeneration.

  7. Successful treatment of osseous lesion associated with palatoradicular groove using local drug delivery and guided tissue regeneration: A report of two cases

    OpenAIRE

    Jayaprakash S Gadagi; Sugumari Elavarasu; Divya Ananda; Thamaraiselvan Murugan

    2012-01-01

    Developmental grooves are not rare and often appear on maxillary lateral and central incisors and are an important predisposing factor to localized periodontal disease. Various techniques have been adopted to eliminate the groove and regenerate lost periodontium. This report of two cases describes the technique of using the local drug delivery system with chlorehexidine and the guided tissue regeneration (GTR) to control the disease progression and regeneration.

  8. DNA-binding study of anticancer drug cytarabine by spectroscopic and molecular docking techniques.

    Science.gov (United States)

    Shahabadi, Nahid; Falsafi, Monireh; Maghsudi, Maryam

    2017-01-02

    The interaction of anticancer drug cytarabine with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multispectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove-binding mode, while the binding constant of UV-vis and the number of binding sites were 4.0 ± 0.2 × 10(4) L mol(-1) and 1.39, respectively. The fluorimetric studies showed that the reaction between the drugs with CT-DNA is exothermic. Circular dichroism spectroscopy was employed to measure the conformational change of DNA in the presence of cytarabine. Furthermore, the drug induces detectable changes in its viscosity for DNA interaction. The molecular modeling results illustrated that cytarabine strongly binds to groove of DNA by relative binding energy of docked structure -20.61 KJ mol(-1). This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the interaction of small molecular pollutants and drugs with biomacromolecules for clarifying the molecular mechanism of toxicity or side effect in vivo.

  9. Behavior of solvent-exposed hydrophobic groove in the anti-apoptotic Bcl-XL protein: clues for its ability to bind diverse BH3 ligands from MD simulations.

    Directory of Open Access Journals (Sweden)

    Dilraj Lama

    Full Text Available Bcl-XL is a member of Bcl-2 family of proteins involved in the regulation of intrinsic pathway of apoptosis. Its overexpression in many human cancers makes it an important target for anti-cancer drugs. Bcl-XL interacts with the BH3 domain of several pro-apoptotic Bcl-2 partners. This helical bundle protein has a pronounced hydrophobic groove which acts as a binding region for the BH3 domains. Eight independent molecular dynamics simulations of the apo/holo forms of Bcl-XL were carried out to investigate the behavior of solvent-exposed hydrophobic groove. The simulations used either a twin-range cut-off or particle mesh Ewald (PME scheme to treat long-range interactions. Destabilization of the BH3 domain-containing helix H2 was observed in all four twin-range cut-off simulations. Most of the other major helices remained stable. The unwinding of H2 can be related to the ability of Bcl-XL to bind diverse BH3 ligands. The loss of helical character can also be linked to the formation of homo- or hetero-dimers in Bcl-2 proteins. Several experimental studies have suggested that exposure of BH3 domain is a crucial event before they form dimers. Thus unwinding of H2 seems to be functionally very important. The four PME simulations, however, revealed a stable helix H2. It is possible that the H2 unfolding might occur in PME simulations at longer time scales. Hydrophobic residues in the hydrophobic groove are involved in stable interactions among themselves. The solvent accessible surface areas of bulky hydrophobic residues in the groove are significantly buried by the loop LB connecting the helix H2 and subsequent helix. These observations help to understand how the hydrophobic patch in Bcl-XL remains stable in the solvent-exposed state. We suggest that both the destabilization of helix H2 and the conformational heterogeneity of loop LB are important factors for binding of diverse ligands in the hydrophobic groove of Bcl-XL.

  10. Drug binding properties of neonatal albumin

    DEFF Research Database (Denmark)

    Brodersen, R; Honoré, B

    1989-01-01

    Neonatal and adult albumin was isolated by gel chromatography on Sephacryl S-300, from adult and umbilical cord serum, respectively. Binding of monoacetyl-diamino-diphenyl sulfone, warfarin, sulfamethizole, and diazepam was studied by means of equilibrium dialysis and the binding data were analyzed...... by the method of several acceptable fitted curves. It was found that the binding affinity to neonatal albumin is less than to adult albumin for monoacetyl-diamino-diphenyl sulfone and warfarin. Sulfamethizole binding to the neonatal protein is similarly reduced when more than one molecule of the drug is bound...

  11. Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove

    Energy Technology Data Exchange (ETDEWEB)

    Ivanova, Marina E.; Fletcher, Georgina C.; O’Reilly, Nicola; Purkiss, Andrew G.; Thompson, Barry J. [Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY (United Kingdom); McDonald, Neil Q., E-mail: neil.mcdonald@cancer.org.uk [Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY (United Kingdom); Birkbeck College, University of London, Malet Street, London WC1E 7HX (United Kingdom)

    2015-03-01

    This study characterizes the interaction between the carboxy-terminal (ERLI) motif of the essential polarity protein Crb and the Pals1/Stardust PDZ-domain protein. Structures of human Pals1 PDZ with and without a Crb peptide are described, explaining the highly conserved nature of the ERLI motif and revealing a sterically blocked peptide-binding groove in the absence of ligand. Many components of epithelial polarity protein complexes possess PDZ domains that are required for protein interaction and recruitment to the apical plasma membrane. Apical localization of the Crumbs (Crb) transmembrane protein requires a PDZ-mediated interaction with Pals1 (protein-associated with Lin7, Stardust, MPP5), a member of the p55 family of membrane-associated guanylate kinases (MAGUKs). This study describes the molecular interaction between the Crb carboxy-terminal motif (ERLI), which is required for Drosophila cell polarity, and the Pals1 PDZ domain using crystallography and fluorescence polarization. Only the last four Crb residues contribute to Pals1 PDZ-domain binding affinity, with specificity contributed by conserved charged interactions. Comparison of the Crb-bound Pals1 PDZ structure with an apo Pals1 structure reveals a key Phe side chain that gates access to the PDZ peptide-binding groove. Removal of this side chain enhances the binding affinity by more than fivefold, suggesting that access of Crb to Pals1 may be regulated by intradomain contacts or by protein–protein interaction.

  12. Sensitive detection of African swine fever virus using real-time PCR with a 5' conjugated minor groove binding probe

    DEFF Research Database (Denmark)

    McKillan, John; McMenamy, Michael; Hjertner, Bernt;

    2010-01-01

    The design of a 5′ conjugated minor groove binder (MGB) probe real-time PCR assay is described for the rapid, sensitive and specific detection of African swine fever virus (ASFV) DNA. The assay is designed against the 9GL region and is capable of detecting 20 copies of a DNA standard. It does...

  13. The rem Mutations in the ATP-Binding Groove of the Rad3/XPD Helicase Lead to Xeroderma pigmentosum-Cockayne Syndrome-Like Phenotypes

    Science.gov (United States)

    Montelone, Beth A.; Aguilera, Andrés

    2014-01-01

    The eukaryotic TFIIH complex is involved in Nucleotide Excision Repair and transcription initiation. We analyzed three yeast mutations of the Rad3/XPD helicase of TFIIH known as rem (recombination and mutation phenotypes). We found that, in these mutants, incomplete NER reactions lead to replication fork breaking and the subsequent engagement of the homologous recombination machinery to restore them. Nevertheless, the penetrance varies among mutants, giving rise to a phenotype gradient. Interestingly, the mutations analyzed reside at the ATP-binding groove of Rad3 and in vivo experiments reveal a gain of DNA affinity upon damage of the mutant Rad3 proteins. Since mutations at the ATP-binding groove of XPD in humans are present in the Xeroderma pigmentosum-Cockayne Syndrome (XP-CS), we recreated rem mutations in human cells, and found that these are XP-CS-like. We propose that the balance between the loss of helicase activity and the gain of DNA affinity controls the capacity of TFIIH to open DNA during NER, and its persistence at both DNA lesions and promoters. This conditions NER efficiency and transcription resumption after damage, which in human cells would explain the XP-CS phenotype, opening new perspectives to understand the molecular basis of the role of XPD in human disease. PMID:25500814

  14. Anticancer drug mithramycin interacts with core histones: An additional mode of action of the DNA groove binder

    Directory of Open Access Journals (Sweden)

    Amrita Banerjee

    2014-01-01

    Full Text Available Mithramycin (MTR is a clinically approved DNA-binding antitumor antibiotic currently in Phase 2 clinical trials at National Institutes of Health for treatment of osteosarcoma. In view of the resurgence in the studies of this generic antibiotic as a human medicine, we have examined the binding properties of MTR with the integral component of chromatin – histone proteins – as a part of our broad objective to classify DNA-binding molecules in terms of their ability to bind chromosomal DNA alone (single binding mode or both histones and chromosomal DNA (dual binding mode. The present report shows that besides DNA, MTR also binds to core histones present in chromatin and thus possesses the property of dual binding in the chromatin context. In contrast to the MTR–DNA interaction, association of MTR with histones does not require obligatory presence of bivalent metal ion like Mg2+. As a consequence of its ability to interact with core histones, MTR inhibits histone H3 acetylation at lysine 18, an important signature of active chromatin, in vitro and ex vivo. Reanalysis of microarray data of Ewing sarcoma cell lines shows that upon MTR treatment there is a significant down regulation of genes, possibly implicating a repression of H3K18Ac-enriched genes apart from DNA-binding transcription factors. Association of MTR with core histones and its ability to alter post-translational modification of histone H3 clearly indicates an additional mode of action of this anticancer drug that could be implicated in novel therapeutic strategies.

  15. Binding studies of the antidiabetic drug, metformin to calf thymus DNA using multispectroscopic methods

    Science.gov (United States)

    Shahabadi, Nahid; Heidari, Leila

    2012-11-01

    Interaction between antidiabetic drug, Metformin and calf thymus DNA (CT-DNA) in (50 mM Tris-HCl) buffer were studied by UV-Visible absorption, fluorescence, CD spectroscopy and viscosity measurements. In fluorimetric studies, the enthalpy and entropy of the reaction between the drug and CT-DNA showed that the reaction is exothermic (ΔH = -35.4522 kJ mol-1; ΔS = -49.9523 J mol-1 K-1). The competitive binding studies showed that the drug could release Hoechst 33258 completely. The complex showed absorption hyperchromism in its UV-Vis spectrum with DNA. The calculated binding constant, Kb, obtained from UV-Vis absorption studies was 8.3 × 104 M-1. Moreover, the changes in the CD spectra in the presence of the drug show stabilization of the right-handed B form of CT-DNA. Finally, viscosity measurements revealed that the binding of the complex with CT-DNA could be surface binding, mainly due to groove binding.

  16. Role of minor groove width and hydration pattern on amsacrine interaction with DNA.

    Directory of Open Access Journals (Sweden)

    Deepak K Jangir

    Full Text Available Amsacrine is an anilinoacridine derivative anticancer drug, used to treat a wide variety of malignancies. In cells, amsacrine poisons topoisomerase 2 by stabilizing DNA-drug-enzyme ternary complex. Presence of amsacrine increases the steady-state concentration of these ternary complexes which in turn hampers DNA replication and results in subsequent cell death. Due to reversible binding and rapid slip-out of amsacrine from DNA duplex, structural data is not available on amsacrine-DNA complexes. In the present work, we designed five oligonucleotide duplexes, differing in their minor groove widths and hydration pattern, and examined their binding with amsacrine using attenuated total reflection Fourier transform infrared (ATR-FTIR spectroscopy. Complexes of amsacrine with calf thymus DNA were also evaluated for a comparison. Our results demonstrate for the first time that amsacrine is not a simple intercalator; rather mixed type of DNA binding (intercalation and minor groove takes place between amsacrine and DNA. Further, this binding is highly sensitive towards the geometries and hydration patterns of different minor grooves present in the DNA. This study shows that ligand binding to DNA could be very sensitive to DNA base composition and DNA groove structures. Results demonstrated here could have implication for understanding cytotoxic mechanism of aminoacridine based anticancer drugs and provide directions to modify these drugs for better efficacy and few side-effects.

  17. Programmable oligomers targeting 5'-GGGG-3' in the minor groove of DNA and NF-kappaB binding inhibition.

    Science.gov (United States)

    Chenoweth, David M; Poposki, Julie A; Marques, Michael A; Dervan, Peter B

    2007-01-15

    A series of hairpin oligomers containing benzimidazole (Bi) and imidazopyridine (Ip) rings were synthesized and screened to target 5'-WGGGGW-3', a core sequence in the DNA-binding site of NF-kappaB, a prolific transcription factor important in biology and disease. Five Bi and Ip containing oligomers bound to the 5'-WGGGGW-3' site with high affinity. One of the oligomers (Im-Im-Im-Im-gamma-Py-Bi-Py-Bi-beta-Dp) was able to inhibit DNA binding by the transcription factor NF-kappaB.

  18. RNA targeting by DNA binding drugs: structural, conformational and energetic aspects of the binding of quinacrine and DAPI to A-form and H(L)-form of poly(rC).poly(rG).

    Science.gov (United States)

    Sinha, Rangana; Hossain, Maidul; Kumar, Gopinatha Suresh

    2007-12-01

    A key step in the rational design of new RNA binding small molecules necessitates a complete elucidation of the molecular aspects of the binding of existing molecules to RNA structures. This work focuses towards the understanding of the interaction of a DNA intercalator, quinacrine and a minor groove binder 4',6-diamidino-2-phenylindole (DAPI) with the right handed Watson-Crick base paired A-form and the left-handed Hoogsteen base paired H(L)-form of poly(rC).poly(rG) evaluated by multifaceted spectroscopic and viscometric techniques. The energetics of their interaction has also been elucidated by isothermal titration calorimetry. Results of this study converge to suggest that (i) quinacrine intercalates to both A-form and H(L)-form of poly(rC).poly(rG); (ii) DAPI shows both intercalative and groove-binding modes to the A-form of the RNA but binds by intercalative mode to the H(L)-form. Isothermal calorimetric patterns of quinacrine binding to both the forms of RNA and of DAPI binding to the H(L)-form are indicative of single binding while the binding of DAPI to the A-form reveals two kinds of binding. The binding of both the drugs to both conformations of RNA is exothermic; while the binding of quinacrine to both conformations and DAPI to the A-form (first site) is entropy driven, the binding of DAPI to the second site of A-form and H(L)-conformation is enthalpy driven. Temperature dependence of the binding enthalpy revealed that the RNA-ligand interaction reactions are accompanied by small heat capacity changes that are nonetheless significant. We conclude that the binding affinity characteristics and energetics of interaction of these DNA binding molecules to the RNA conformations are significantly different and may serve as data for the development of effective structure selective RNA-based antiviral drugs.

  19. Experimental DNA-binding and computer modelling studies on an analogue of the anti-tumor drug amsacrine.

    Science.gov (United States)

    Abraham, Z H; Agbandje, M; Neidle, S; Acheson, R M

    1988-12-01

    The DNA-binding properties of the anti-cancer drug amsacrine and a 9-aminoacridine analogue substituted at the 4 position with a 4-methanesulphonanilido-group, have been examined by means of unwinding, melting and equilibrium binding experiments. These find that the latter compound is at least as effective as a DNA-binder and intercalator as amsacrine itself. Molecular modelling and energetic calculations have confirmed this, and have produced plausible intercalation geometries. These show that there are subtle differences in the low-energy minor groove arrangements adopted by the substituents of the two drugs. Speculation is advanced that these differences may be relevant to the marked differences in cytotoxicity shown by the two compounds.

  20. Stereoselective binding of chiral drugs to plasma proteins

    Institute of Scientific and Technical Information of China (English)

    Qi SHEN; Lu WANG; Hui ZHOU; Hui-di JIANG; Lu-shan YU; Su ZENG

    2013-01-01

    Chiral drugs show distinct biochemical and pharmacological behaviors in the human body.The binding of chiral drugs to plasma proteins usually exhibits stereoselectivity,which has a far-reaching influence on their pharmacological activities and pharmacokinetic profiles.In this review,the stereoselective binding of chiral drugs to human serum albumin (HSA),α1-acid glycoprotein (AGP)and lipoprotein,three most important proteins in human plasma,are detailed.Furthermore,the application of AGP variants and recombinant fragments of HSA for studying enantiomer binding properties is also discussed.Apart from the stereoselectivity of enantiomer-protein binding,enantiomer-enantiomer interactions that may induce allosteric effects are also described.Additionally,the techniques and methods used to determine drug-protein binding parameters are briefly reviewed.

  1. Substrate and drug binding sites in LeuT.

    Science.gov (United States)

    Nyola, Ajeeta; Karpowich, Nathan K; Zhen, Juan; Marden, Jennifer; Reith, Maarten E; Wang, Da-Neng

    2010-08-01

    LeuT is a member of the neurotransmitter/sodium symporter family, which includes the neuronal transporters for serotonin, norepinephrine, and dopamine. The original crystal structure of LeuT shows a primary leucine-binding site at the center of the protein. LeuT is inhibited by different classes of antidepressants that act as potent inhibitors of the serotonin transporter. The newly determined crystal structures of LeuT-antidepressant complexes provide opportunities to probe drug binding in the serotonin transporter, of which the exact position remains controversial. Structure of a LeuT-tryptophan complex shows an overlapping binding site with the primary substrate site. A secondary substrate binding site was recently identified, where the binding of a leucine triggers the cytoplasmic release of the primary substrate. This two binding site model presents opportunities for a better understanding of drug binding and the mechanism of inhibition for mammalian transporters.

  2. Chitosan drug binding by ionic interaction.

    Science.gov (United States)

    Boonsongrit, Yaowalak; Mitrevej, Ampol; Mueller, Bernd W

    2006-04-01

    Three model drugs (insulin, diclofenac sodium, and salicylic acid) with different pI or pKa were used to prepare drug-chitosan micro/nanoparticles by ionic interaction. Physicochemical properties and entrapment efficiencies were determined. The amount of drug entrapped in the formulation influences zeta potential and surface charge of the micro/nanoparticles. A high entrapment efficiency of the micro/nanoparticles could be obtained by careful control of formulation pH. The maximum entrapment efficiency did not occur in the highest ionization range of the model drugs. The high burst release of drugs from chitosan micro/nanoparticles was observed regardless of the pH of dissolution media. It can be concluded that the ionic interaction between drug and chitosan is low and too weak to control the drug release.

  3. Structure and localisation of drug binding sites on neurotransmitter transporters.

    Science.gov (United States)

    Ravna, Aina W; Sylte, Ingebrigt; Dahl, Svein G

    2009-10-01

    The dopamine (DAT), serotontin (SERT) and noradrenalin (NET) transporters are molecular targets for different classes of psychotropic drugs. The crystal structure of Aquifex aeolicus LeuT(Aa) was used as a template for molecular modeling of DAT, SERT and NET, and two putative drug binding sites (pocket 1 and 2) in each transporter were identified. Cocaine was docked into binding pocket 1 of DAT, corresponding to the leucine binding site in LeuT(Aa), which involved transmembrane helices (TMHs) 1, 3, 6 and 8. Clomipramine was docked into binding pocket 2 of DAT, involving TMHs 1, 3, 6, 10 and 11, and extracellular loops 4 and 6, corresponding to the clomipramine binding site in a crystal structure of a LeuT(Aa)-clomipramine complex. The structures of the proposed cocaine- and tricyclic antidepressant-binding sites may be of particular interest for the design of novel DAT interacting ligands.

  4. Quantifying drug-protein binding in vivo.

    Energy Technology Data Exchange (ETDEWEB)

    Buchholz, B; Bench, G; Keating III, G; Palmblad, M; Vogel, J; Grant, P G; Hillegonds, D

    2004-02-17

    Accelerator mass spectrometry (AMS) provides precise quantitation of isotope labeled compounds that are bound to biological macromolecules such as DNA or proteins. The sensitivity is high enough to allow for sub-pharmacological (''micro-'') dosing to determine macromolecular targets without inducing toxicities or altering the system under study, whether it is healthy or diseased. We demonstrated an application of AMS in quantifying the physiologic effects of one dosed chemical compound upon the binding level of another compound in vivo at sub-toxic doses [4].We are using tissues left from this study to develop protocols for quantifying specific binding to isolated and identified proteins. We also developed a new technique to quantify nanogram to milligram amounts of isolated protein at precisions that are comparable to those for quantifying the bound compound by AMS.

  5. Pancreatic groove cancer

    Science.gov (United States)

    Ku, Yuan-Hao; Chen, Shih-Chin; Shyr, Bor-Uei; Lee, Rheun-Chuan; Shyr, Yi-Ming; Wang, Shin-E.

    2017-01-01

    Abstract Pancreatic groove cancer is very rare and can be indistinguishable from groove pancreatitis. This study is to clarify the characteristics, clinical features, managements, and survival outcomes of this rare tumor. Brief descriptions were made for each case of pancreatic groove cancer encountered at our institute. Individualized data of pancreatic groove cancer cases described in the literature were extracted and added to our database to expand the study sample size for a more complete analysis. A total of 33 patients with pancreatic groove cancer were included for analysis, including 4 cases from our institute. The median tumor size was 2.7 cm. The most common symptom was nausea or vomiting (89%), followed by jaundice (67%). Duodenal stenosis was noted by endoscopy in 96% of patients. The histopathological examination revealed well differentiated tumor in 43%. Perineural invasion was noted in 90%, and lymphovascular invasion and lymph node involvement in 83%. Overall 1-year survival rate was 93.3%, and 3- or 5-year survival rate was 62.2%, with a median survival of 11.0 months. Survival outcome for the well-differentiated tumors was better than those of the moderate/poorly differentiated ones. Early involvement of duodenum causing vomiting is often the initial presentation, but obstructive jaundice does not always happen until the disease progresses. Tumor differentiation is a prognostic factor for survival outcome. The possibility of pancreatic groove cancer should be carefully excluded before making the diagnosis of groove pancreatitis for any questionable case. PMID:28079795

  6. The enigmatic drug binding site for sodium channel inhibitors.

    Science.gov (United States)

    Mike, Arpad; Lukacs, Peter

    2010-11-01

    Local anesthetics have been in clinical use since 1884, and different aspects of the local anesthetic binding site have been studied in enormous detail. In spite of all these efforts, some of the most fundamental questions--such as which exact residues constitute the binding site, how many binding sites exist, do local anesthetics share their binding site(s) with other sodium channel inhibitors, and what are the mechanisms of inhibition--are still largely unanswered. We review accumulated data on the "local anesthetic receptor"and discuss controversial points, such as possible mechanisms of inhibition, the possibility of additional binding sites, the orientation of S6 helices, and the internal vs. external position of the anticonvulsant binding site. We describe the four following specific groups of functionally important residues: i) conserved asparagines six residues below the hinge residues; we propose that they are oriented toward the external surface of S6 helices, and have a critical role in the coupling of voltage sensors to gating, ii) residues lining the inner vestibule and constructing the "orthodox" binding site, iii) residues around the outer vestibule, which have been proposed to constitute an alternative external binding site, and iv) residues determining external access for quaternary amine inhibitors, such as QX314. We conclude that sodium channel inhibitors must be heterogenous in terms of binding sites and inhibition mechanisms, and propose that this heterogeneity should be taken into consideration during drug development.

  7. Studies of interaction between a new synthesized minor-groove targeting artificial nuclease and DNA

    Science.gov (United States)

    Yin, Qiang; Zhang, Zhen; Zhao, Yu-Fen

    2007-04-01

    Nuclease plays an important role in molecular biology, such as DNA sequencing. Synthetic polyamide conjugates can be considered as new tool in the selective inhibition of gene expression and as potential drugs in anticancer or antiviral chemotherapy. In this paper, a new synthesized minor-groove targeting artificial nuclease, oligopyrrol-containing peptide, was reported. It was found that this new compound can bind DNA in AT-riched minor groove with high affinity and site specificity. DNA binding behavior was determined by UV-vis and circular dichroism (CD) methods. It was indicated that compound 6 can enhance the Tm of oligomer DNA from 51.8 to 63.5 °C and possesses large binding constant ( Kb = 8.83 × 10 4 L/mol).

  8. Molecular Mechanisms of Pharmaceutical Drug Binding into Calsequestrin

    Directory of Open Access Journals (Sweden)

    ChulHee Kang

    2012-11-01

    Full Text Available Calsequestrin (CASQ is a major Ca2+-storage/buffer protein present in the sarcoplasmic reticulum of both skeletal (CASQ1 and cardiac (CASQ2 muscles. CASQ has significant affinity for a number of pharmaceutical drugs with known muscular toxicities. Our approach, with in silico molecular docking, single crystal X-ray diffraction, and isothermal titration calorimetry (ITC, identified three distinct binding pockets on the surface of CASQ2, which overlap with 2-methyl-2,4-pentanediol (MPD binding sites observed in the crystal structure. Those three receptor sites based on canine CASQ1 crystal structure gave a high correlation (R2 = 0.80 to our ITC data. Daunomycin, doxorubicin, thioridazine, and trifluoperazine showed strong affinity to the S1 site, which is a central cavity formed between three domains of CASQ2. Some of the moderate-affinity drugs and some high-affinity drugs like amlodipine and verapamil displayed their binding into S2 sites, which are the thioredoxin-like fold present in each CASQ domain. Docking predictions combined with dissociation constants imply that presence of large aromatic cores and less flexible functional groups determines the strength of binding affinity to CASQ. In addition, the predicted binding pockets for both caffeine and epigallocatechin overlapped with the S1 and S2 sites, suggesting competitive inhibition by these natural compounds as a plausible explanation for their antagonistic effects on cardiotoxic side effects.

  9. Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip?

    Science.gov (United States)

    Geschwindner, Stefan; Ulander, Johan; Johansson, Patrik

    2015-08-27

    The use of ligand binding thermodynamics has been proposed as a potential success factor to accelerate drug discovery. However, despite the intuitive appeal of optimizing binding enthalpy, a number of factors complicate routine use of thermodynamic data. On a macroscopic level, a range of experimental parameters including temperature and buffer choice significantly influence the observed thermodynamic signatures. On a microscopic level, solute effects, structural flexibility, and cooperativity lead to nonlinear changes in enthalpy. This multifactorial character hides essential enthalpy contributions of intermolecular contacts, making them experimentally nonobservable. In this perspective, we present three case studies, reflect on some key factors affecting thermodynamic signatures, and investigate their relation to the hydrophobic effect, enthalpy-entropy compensation, lipophilic ligand efficiency, and promiscuity. The studies highlight that enthalpy and entropy cannot be used as direct end points but can together with calculations increase our understanding of ligand binding and identify interesting outliers that do not behave as expected.

  10. Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins.

    Science.gov (United States)

    Poornima, C S; Dean, P M

    1995-12-01

    Water molecules are known to play an important rôle in mediating protein-ligand interactions. If water molecules are conserved at the ligand-binding sites of homologous proteins, such a finding may suggest the structural importance of water molecules in ligand binding. Structurally conserved water molecules change the conventional definition of 'binding sites' by changing the shape and complementarity of these sites. Such conserved water molecules can be important for site-directed ligand/drug design. Therefore, five different sets of homologous protein/protein-ligand complexes have been examined to identify the conserved water molecules at the ligand-binding sites. Our analysis reveals that there are as many as 16 conserved water molecules at the FAD binding site of glutathione reductase between the crystal structures obtained from human and E. coli. In the remaining four sets of high-resolution crystal structures, 2-4 water molecules have been found to be conserved at the ligand-binding sites. The majority of these conserved water molecules are either bound in deep grooves at the protein-ligand interface or completely buried in cavities between the protein and the ligand. All these water molecules, conserved between the protein/protein-ligand complexes from different species, have identical or similar apolar and polar interactions in a given set. The site residues interacting with the conserved water molecules at the ligand-binding sites have been found to be highly conserved among proteins from different species; they are more conserved compared to the other site residues interacting with the ligand. These water molecules, in general, make multiple polar contacts with protein-site residues.

  11. Groove / Solar energy cataloque; Groove aurinkoenergian yritysluettelo

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2013-06-01

    According to Tekes, renewable energy offer Finnish companies opportunities for renewal and international growth. Especially in the field of solar energy, development is fast and the market is growing rapidly. The purpose of this catalogue is to provide information about organizations active in the field of solar energy so that different players can find each other more easily. Information is provided about organizations active both on the supply side (solar energy solution and service providers) and demand side (cities, construction contractors, real estate owners) as well as research teams at universities and research centers. We hope that this catalogue will help different actors to find each other both nationally and internationally so that good development and demonstration projects in the field of solar energy can get started. Tekes participates for instance in Solar Eranet, a joint effort of several funding organizations in Europe support transnational solar projects. This catalogue is provided by Tekes program Groove - Growth from renewables. Tekes' programmes and initiatives are topical entities targeted at financial and expert service areas. Within the programmes and initiatives, businesses and public research units can develop new know-how, build networks and have an impact on the development of their field. (orig.)

  12. Fluoroquinolone-gyrase-DNA complexes: two modes of drug binding.

    Science.gov (United States)

    Mustaev, Arkady; Malik, Muhammad; Zhao, Xilin; Kurepina, Natalia; Luan, Gan; Oppegard, Lisa M; Hiasa, Hiroshi; Marks, Kevin R; Kerns, Robert J; Berger, James M; Drlica, Karl

    2014-05-02

    DNA gyrase and topoisomerase IV control bacterial DNA topology by breaking DNA, passing duplex DNA through the break, and then resealing the break. This process is subject to reversible corruption by fluoroquinolones, antibacterials that form drug-enzyme-DNA complexes in which the DNA is broken. The complexes, called cleaved complexes because of the presence of DNA breaks, have been crystallized and found to have the fluoroquinolone C-7 ring system facing the GyrB/ParE subunits. As expected from x-ray crystallography, a thiol-reactive, C-7-modified chloroacetyl derivative of ciprofloxacin (Cip-AcCl) formed cross-linked cleaved complexes with mutant GyrB-Cys(466) gyrase as evidenced by resistance to reversal by both EDTA and thermal treatments. Surprisingly, cross-linking was also readily seen with complexes formed by mutant GyrA-G81C gyrase, thereby revealing a novel drug-gyrase interaction not observed in crystal structures. The cross-link between fluoroquinolone and GyrA-G81C gyrase correlated with exceptional bacteriostatic activity for Cip-AcCl with a quinolone-resistant GyrA-G81C variant of Escherichia coli and its Mycobacterium smegmatis equivalent (GyrA-G89C). Cip-AcCl-mediated, irreversible inhibition of DNA replication provided further evidence for a GyrA-drug cross-link. Collectively these data establish the existence of interactions between the fluoroquinolone C-7 ring and both GyrA and GyrB. Because the GyrA-Gly(81) and GyrB-Glu(466) residues are far apart (17 Å) in the crystal structure of cleaved complexes, two modes of quinolone binding must exist. The presence of two binding modes raises the possibility that multiple quinolone-enzyme-DNA complexes can form, a discovery that opens new avenues for exploring and exploiting relationships between drug structure and activity with type II DNA topoisomerases.

  13. Programmable Oligomers Targeting 5′-GGGG-3′ in the Minor Groove of DNA and NF-κB Binding Inhibition

    Science.gov (United States)

    Chenoweth, David M.; Poposki, Julie A.; Marques, Michael A.; Dervan, Peter B.

    2009-01-01

    A series of hairpin oligomers containing benzimidazole (Bi) and imidazopyridine (Ip) rings were synthesized and screened to target 5′-WGGGGW-3′, a core sequence in the DNA binding site of NF-κB, a prolific transcription factor important in biology and disease. Five Bi and Ip containing oligomers bound to the 5′-WGGGGW-3′ site with high affinity. One of the oligomers (Im-Im-Im-Im-γ-PyBi-PyBi-β-Dp) was able to inhibit DNA binding by the transcription factor NF-κB. PMID:17095230

  14. Cooperative binding of drugs on human serum albumin

    Science.gov (United States)

    Varela, L. M.; Pérez-Rodríguez, M.; García, M.

    In order to explain the adsorption isotherms of the amphiphilic penicillins nafcillin and cloxacillin onto human serum albumin (HSA), a cooperative multilayer adsorption model is introduced, combining the Brunauer-Emmet-Teller (BET) adsorption isotherm with an amphiphilic ionic adsorbate, whose chemical potential is derived from Guggenheim's theory. The non-cooperative model has been previously proved to qualitatively predict the measured adsorption maxima of these drugs [Varela, L. M., García, M., Pérez-Rodríguez, M., Taboada, P., Ruso, J. M., and Mosquera, V., 2001, J. chem. Phys., 114, 7682]. The surface interactions among adsorbed drug molecules are modelled in a mean-field fashion, so the chemical potential of the adsorbate is assumed to include a term proportional to the surface coverage, the constant of proportionality being the lateral interaction energy between bound molecules. The interaction energies obtained from the empirical binding isotherms are of the order of tenths of the thermal energy, therefore suggesting the principal role of van der Waals forces in the binding process.

  15. 3-D Image Analysis of Fluorescent Drug Binding

    Directory of Open Access Journals (Sweden)

    M. Raquel Miquel

    2005-01-01

    Full Text Available Fluorescent ligands provide the means of studying receptors in whole tissues using confocal laser scanning microscopy and have advantages over antibody- or non-fluorescence-based method. Confocal microscopy provides large volumes of images to be measured. Histogram analysis of 3-D image volumes is proposed as a method of graphically displaying large amounts of volumetric image data to be quickly analyzed and compared. The fluorescent ligand BODIPY FL-prazosin (QAPB was used in mouse aorta. Histogram analysis reports the amount of ligand-receptor binding under different conditions and the technique is sensitive enough to detect changes in receptor availability after antagonist incubation or genetic manipulations. QAPB binding was concentration dependent, causing concentration-related rightward shifts in the histogram. In the presence of 10 μM phenoxybenzamine (blocking agent, the QAPB (50 nM histogram overlaps the autofluorescence curve. The histogram obtained for the 1D knockout aorta lay to the left of that of control and 1B knockout aorta, indicating a reduction in 1D receptors. We have shown, for the first time, that it is possible to graphically display binding of a fluorescent drug to a biological tissue. Although our application is specific to adrenergic receptors, the general method could be applied to any volumetric, fluorescence-image-based assay.

  16. Mechanistic models enable the rational use of in vitro drug-target binding kinetics for better drug effects in patients.

    NARCIS (Netherlands)

    Witte, W.E.; Wong, Y.C.; Nederpelt, I.; Heitman, L.H.; Danhof, M.; Graaf, van der P.H.; Gilissen, R.A.; de, Lange E.C.

    2016-01-01

    INTRODUCTION Drug-target binding kinetics are major determinants of the time course of drug action for several drugs, as clearly described for the irreversible binders omeprazole and aspirin. This supports the increasing interest to incorporate newly developed high-throughput assays for drug-target

  17. Target-mediated drug disposition model for drugs with two binding sites that bind to a target with one binding site.

    Science.gov (United States)

    Gibiansky, Leonid; Gibiansky, Ekaterina

    2017-07-19

    The paper extended the TMDD model to drugs with two identical binding sites (2-1 TMDD). The quasi-steady-state (2-1 QSS), quasi-equilibrium (2-1 QE), irreversible binding (2-1 IB), and Michaelis-Menten (2-1 MM) approximations of the model were derived. Using simulations, the 2-1 QSS approximation was compared with the full 2-1 TMDD model. As expected and similarly to the standard TMDD for monoclonal antibodies (mAb), 2-1 QSS predictions were nearly identical to 2-1 TMDD predictions, except for times of fast changes following initiation of dosing, when equilibrium has not yet been reached. To illustrate properties of new equations and approximations, several variations of population PK data for mAbs with soluble (slow elimination of the complex) or membrane-bound (fast elimination of the complex) targets were simulated from a full 2-1 TMDD model and fitted to 2-1 TMDD models, to its approximations, and to the standard (1-1) QSS model. For a mAb with a soluble target, it was demonstrated that the 2-1 QSS model provided nearly identical description of the observed (simulated) free drug and total target concentrations, although there was some minor bias in predictions of unobserved free target concentrations. The standard QSS approximation also provided a good description of the observed data, but was not able to distinguish between free drug concentrations (with no target attached and both binding site free) and partially bound drug concentrations (with one of the binding sites occupied by the target). For a mAb with a membrane-bound target, the 2-1 MM approximation adequately described the data. The 2-1 QSS approximation converged 10 times faster than the full 2-1 TMDD, and its run time was comparable with the standard QSS model.

  18. Experimental and computational studies on the effects of valganciclovir as an antiviral drug on calf thymus DNA.

    Science.gov (United States)

    Shahabadi, Nahid; Pourfoulad, Mehdi; Moghadam, Neda Hosseinpour

    2017-01-02

    DNA-binding properties of an antiviral drug, valganciclovir (valcyte) was studied by using emission, absorption, circular dichroism, viscosity, differential pulse voltammetry, fluorescence techniques, and computational studies. The drug bound to calf thymus DNA (ct-DNA) in a groove-binding mode. The calculated binding constant of UV-vis, Ka, is comparable to groove-binding drugs. Competitive fluorimetric studies with Hoechst 33258 showed that valcyte could displace the DNA-bound Hoechst 33258. The drug could not displace intercalated methylene blue from DNA double helix. Furthermore, the induced detectable changes in the CD spectrum of ct-DNA as well as changes in its viscosity confirm the groove-binding mode. In addition, an integrated molecular docking was employed to further investigate the binding interactions between valcyte and calf thymus DNA.

  19. Predicting the multi-modal binding propensity of small molecules: towards an understanding of drug promiscuity.

    Science.gov (United States)

    Park, Keunwan; Lee, Soyoung; Ahn, Hee-Sung; Kim, Dongsup

    2009-08-01

    Drug promiscuity is one of the key issues in current drug development. Many famous drugs have turned out to behave unexpectedly due to their propensity to bind to multiple targets. One of the primary reasons for this promiscuity is that drugs bind to multiple distinctive target environments, a feature that we call multi-modal binding. Accordingly, investigations into whether multi-modal binding propensities can be predicted, and if so, whether the features determining this behavior can be found, would be an important advance. In this study, we have developed a structure-based classifier that predicts whether small molecules will bind to multiple distinct binding sites. The binding sites for all ligands in the Protein Data Bank (PDB) were clustered by binding site similarity, and the ligands that bind to many dissimilar binding sites were identified as multi-modal binding ligands. The mono-binding ligands were also collected, and the classifiers were built using various machine-learning algorithms. A 10-fold cross-validation procedure showed 70-85% accuracy depending on the choice of machine-learning algorithm, and the different definitions used to identify multi-modal binding ligands. In addition, a quantified importance measurement for global and local descriptors was also provided, which suggests that the local features are more likely to have an effect on multi-modal binding than the global ones. The interpretable global and local descriptors were also ranked by their importance. To test the classifier on real examples, several test sets including well-known promiscuous drugs were collected by a literature and database search. Despite the difficulty in constructing appropriate testable sets, the classifier showed reasonable results that were consistent with existing information on drug behavior. Finally, a test on natural enzyme substrates and artificial drugs suggests that the natural compounds tend to exhibit a broader range of multi-modal binding than the

  20. Room to Groove?

    DEFF Research Database (Denmark)

    Seabrooke, Leonard

    . As long as they stay within the parameters of legitimate financial practice to signal institutional isomorphism, the `groove', creditors may well allow borrowers room for change in self-determined ways. This paper maps out the historical and conceptual terrain concerning civilizing ideas about...... the legitimacy of financial practices within global capital markets, and investigates relationships between Western `civilizers' and Emerging Market Economies during the last two periods of financial globalization, the late-nineteenth/ early-twentieth centuries and the late-twentieth century.......The use of a `standard of civilization', a preferred form of socio-political organization, in global capital markets presents both constraints and opportunities for creditors and borrowers. When imposed, civilizing standards may change how a borrower would prefer to conduct their affairs. Creditors...

  1. Netropsin . dG-dG-dA-dA-dT-dT-dC-dC complex. Antibiotic binding at adenine . thymine base pairs in the minor groove of the self-complementary octanucleotide duplex.

    Science.gov (United States)

    Patel, D J

    1979-09-01

    The structure of the netropsin . dG-dG-dA-dA-dT-dT-dC-dC complex (one antibiotic molecule/self-complementary octanucleodide duplex) and its dynamics as a function of temperature have been monitored by the nuclear magnetic resonances of the Watson-Crick protons, the nonexchangeable base and sugar protons and the backbone phosphates. The antibiotic forms a complex with the nucleic acid duplex at the dA . dT-containing tetranucleotide segment dA-dA-dT-dT, with slow migration amongst potential binding sites at low temperature. The downfield shifts in the exchangeable protons of netropsin on complex formation demonstrate the contributions of hydrogen-bonding interactions between the antibiotic and the nucleic acid to the stability of the complex. Complex formation results in changes in the glycosidic torsion angles of both thymidine residues and one deoxyadenosine residue as monitored by chemical shift changes in the thymine C-6 and adenine C-8 protons. The close proximity of the pyrrole rings of the antibiotic and the base-pair edges in the minor groove is manifested in the downfield shifts (0.3--0.5 ppm) of the pyrrole C-3 protons of netropsin and one adenine C-2 proton and one thymine N-3 base-pair proton on complex formation. The internucleotide phosphates of the octanucleotide undergo 31P chemical shift changes on addition of netropsin and these may reflect, in part, contributions from electrostatic interactions between the charged ends of the antibiotic and the backbone phosphates of the nucleic acid.

  2. Recent developments in sequence selective minor groove DNA effectors.

    Science.gov (United States)

    Reddy, B S; Sharma, S K; Lown, J W

    2001-04-01

    DNA is a well characterized intracellular target but its large size and sequential nature make it an elusive target for selective drug action. Binding of low molecular weight ligands to DNA causes a wide variety of potential biological responses. In this respect the main consideration is given to recent developments in DNA sequence selective binding agents bearing conjugated effectors because of their potential application in diagnosis and treatment of cancers as well as in molecular biology. Recent progress in the development of cross linked lexitropsin oligopeptides and hairpins, which bind selectively to the minor groove of duplex DNA, is discussed. Bis-distamycins and related lexitropsins show inhibitory activity against HIV-1 and HIV-2 integrases at low nanomolar concentrations. Benzoyl nitrogen mustard analogs of lexitropsins are active against a variety of tumor models. Certain of the bis-benzimidazoles show altered DNA sequence preference and bind to DNA at 5'CG and TG sequences rather than at the preferred AT sites of the parent drug. A comparison of bifunctional bizelesin with monoalkylating adozelesin shows that it appears to have an increased sequence selectivity such that monoalkylating compounds react at more than one site but bizelesin reacts only at sites where there are two suitably positioned alkylation sites. Adozelesin, bizelesin and carzelesin are far more potent as cytotoxic agents than cisplatin or doxorubicin. A new class of 1,2,9,9a-tetrahydrocyclo-propa[c]benz[e]indole-4-one (CBI) analogs i.e., CBI-lexitropsin conjugates arising from the latter leads are also discussed.A number of cyclopropylpyrroloindole (CPI) and CBI-lexitropsin conjugates related to CC-1065 alkylate at the N3 position of adenine in the minor groove of DNA in a sequence specific manner, and also show cytotoxicities in the femtomolar range. The cross linking efficiency of PBD dimers is much greater than that of other cross linkers including cisplatin, and melphalan. A new

  3. On the role of specific drug binding in modelling arterial eluting stents

    OpenAIRE

    McGinty, Sean; Pontrelli, Giuseppe

    2016-01-01

    In this paper we consider drug binding in the arterial wall following\\ud delivery by a drug-eluting stent. Whilst it is now generally accepted that a\\ud non-linear saturable reversible binding model is required to properly describe\\ud the binding process, the precise form of the binding model varies between authors.\\ud Our particular interest in this manuscript is in assessing to what extent\\ud modelling specific and non-specific binding in the arterial wall as separate\\ud phases is important...

  4. Drug-drug interactions related to altered absorption and plasma protein binding: theoretical and regulatory considerations, and an industry perspective.

    Science.gov (United States)

    Hochman, Jerome; Tang, Cuyue; Prueksaritanont, Thomayant

    2015-03-01

    Drug-drug interactions (DDIs) related to altered drug absorption and plasma protein binding have received much less attention from regulatory agencies relative to DDIs mediated via drug metabolizing enzymes and transporters. In this review, a number of theoretical bases and regulatory framework are presented for these DDI aspects. Also presented is an industry perspective on how to approach these issues in support of drug development. Overall, with the exception of highly permeable and highly soluble (BCS 1) drugs, DDIs related to drug-induced changes in gastrointestinal (GI) physiology can be substantial, thus warranting more attentions. For a better understanding of absorption-associated DDI potential in a clinical setting, mechanistic studies should be conducted based on holistic integration of the pharmaceutical profiles (e.g., pH-dependent solubility) and pharmacological properties (e.g., GI physiology and therapeutic margin) of drug candidates. Although majority of DDI events related to altered plasma protein binding are not expected to be of clinical significance, exceptions exist for a subset of compounds with certain pharmacokinetic and pharmacological properties. Knowledge of the identity of binding proteins and the binding extent in various clinical setting (including disease states) can be valuable in aiding clinical DDI data interpretations, and ensuring safe and effective use of new drugs.

  5. Replacing a piece of loop-structure in the substrate-binding groove of Aspergillus usamii β-mannanase, AuMan5A, to improve its enzymatic properties by rational design.

    Science.gov (United States)

    Dong, Yun Hai; Li, Jian Fang; Hu, Die; Yin, Xin; Wang, Chun Juan; Tang, Shi Han; Wu, Min Chen

    2016-05-01

    To perfect the enzymatic properties of AuMan5A, a mesophilic glycoside hydrolase (GH) family 5 β-mannanase from Aspergillus usamii, its loop-structure substitution was carried out by rational design and followed by megaprimer PCR. Based on the structural analysis and enzymatic property comparison of various β-mannanases, a piece of loop-structure with seven amino acids between two β-strands (βD and βE) in the substrate-binding groove, named "Loop DE," was speculated to be correlative to the thermostability and catalytic efficiency of GH family 5 β-mannanases. Therefore, three AuMan5A's mutants, AuMan5A-Af, AuMan5A-An, and AuMan5A-Th, were designed by substituting a Loop DE sequence ((316)KSPDGGN(322)) of AuMan5A with the corresponding sequences of other three family 5 β-mannanases, respectively. Then, the mutant-encoding genes, Auman5A-Af, Auman5A-An, and Auman5A-Th, were constructed as designed theoretically and then expressed in Pichia pastoris GS115. The expressed recombinant AuMan5A-Af (re-AuMan5A-Af) displayed the temperature optimum (T opt) of 75 °C, T m value of 76.6 °C and half-life (t 1/2) of 480 min at 70 °C, which were 10 and 12.1 °C higher and 48-fold longer than those of re-AuMan5A, respectively. Its catalytic efficiency (k cat/K m) was 12.7-fold that of re-AuMan5A. What is more, the site-directed mutagenesis of D320G in AuMan5A-Af was performed. The T opt and t 1/2 of expressed re-AuMan5A-Af(D320G) decreased to 70 °C and 40 min, respectively, while its k cat/K m was only 35 % of that of re-AuMan5A-Af. These results demonstrated that the mutation of G320 (in AuMan5A) into D320 (in AuMan5A-Af) through Loop DE substitution was mainly responsible for the thermostability and catalytic efficiency improvement of AuMan5A-Af.

  6. The influence of drug distribution and drug-target binding on target occupancy: The rate-limiting step approximation.

    Science.gov (United States)

    de Witte, W E A; Vauquelin, G; van der Graaf, P H; de Lange, E C M

    2017-05-12

    The influence of drug-target binding kinetics on target occupancy can be influenced by drug distribution and diffusion around the target, often referred to as "rebinding" or "diffusion-limited binding". This gives rise to a decreased decline of the drug-target complex concentration as a result of a locally higher drug concentration that arises around the target, which leads to prolonged target exposure to the drug. This phenomenon has been approximated by the steady-state approximation, assuming a steady-state concentration around the target. Recently, a rate-limiting step approximation of drug distribution and drug-target binding has been published. However, a comparison between both approaches has not been made so far. In this study, the rate-limiting step approximation has been rewritten into the same mathematical format as the steady-state approximation in order to compare the performance of both approaches for the investigation of the influence of drug-target binding kinetics on target occupancy. While both approximations clearly indicated the importance of kon and high target concentrations, it was shown that the rate-limiting step approximation is more accurate than the steady-state approximation, especially when dissociation is fast compared to association and distribution out of the binding compartment. It is therefore concluded that the new rate-limiting step approximation is to be preferred for assessing the influence of binding kinetics on local target site concentrations and target occupancy. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  7. Binding thermodynamics discriminates fragments from druglike compounds: a thermodynamic description of fragment-based drug discovery.

    Science.gov (United States)

    Williams, Glyn; Ferenczy, György G; Ulander, Johan; Keserű, György M

    2016-12-01

    Small is beautiful - reducing the size and complexity of chemical starting points for drug design allows better sampling of chemical space, reveals the most energetically important interactions within protein-binding sites and can lead to improvements in the physicochemical properties of the final drug. The impact of fragment-based drug discovery (FBDD) on recent drug discovery projects and our improved knowledge of the structural and thermodynamic details of ligand binding has prompted us to explore the relationships between ligand-binding thermodynamics and FBDD. Information on binding thermodynamics can give insights into the contributions to protein-ligand interactions and could therefore be used to prioritise compounds with a high degree of specificity in forming key interactions.

  8. Bioanalysis for plasma protein binding studies in drug discovery and drug development: views and recommendations of the European Bioanalysis Forum.

    Science.gov (United States)

    Buscher, Brigitte; Laakso, Sirpa; Mascher, Hermann; Pusecker, Klaus; Doig, Mira; Dillen, Lieve; Wagner-Redeker, Winfried; Pfeifer, Thomas; Delrat, Pascal; Timmerman, Philip

    2014-03-01

    Plasma protein binding (PPB) is an important parameter for a drug's efficacy and safety that needs to be investigated during each drug-development program. Even though regulatory guidance exists to study the extent of PPB before initiating clinical studies, there are no detailed instructions on how to perform and validate such studies. To explore how PPB studies involving bioanalysis are currently executed in the industry, the European Bioanalysis Forum (EBF) has conducted three surveys among their member companies: PPB studies in drug discovery (Part I); in vitro PPB studies in drug development (Part II); and in vivo PPB studies in drug development. This paper reflects the outcome of the three surveys, which, together with the team discussions, formed the basis of the EBF recommendation. The EBF recommends a tiered approach to the design of PPB studies and the bioanalysis of PPB samples: 'PPB screening' experiments in (early) drug discovery versus qualified/validated procedures in drug development.

  9. Microdialysis-liquid chromatographic study on competitive binding of drugs to protein

    Institute of Scientific and Technical Information of China (English)

    汪海林; 邹汉法; 张玉奎

    1997-01-01

    A new method to determine the interaction between drug and protein has been developed by utilizing the technique of microdialysis sampling with the ketoprofen and the human serum albumin (HSA) as the model of drug and protein.Two kinds of binding sites of HSA to ketoprofen have been observed.The binding constants and number of binding sites obtained by the Scatchard equation are 0.799,3.18×106 mol-1 L and 2.15,2.01×105 mol-1 L,respectively The displacement binding of drugs to HSA has also been studied.The strong displacement of competitive binding of ibuprofen with ketoprofen to HSA was observed,which means that the primary binding site of HSA to ketoprofen and that to ibuprofen are the same.However,only a weaker displacement of warfarin for the association of ketoprofen with HSA was observed,which may suggest that the primary binding site of HSA to ketoprofen is different from that to warfarin.Such a displacement effect for competitive binding of drugs to HSA was explained by the displacement model i

  10. Shared peptide binding of HLA Class I and II alleles associate with cutaneous nevirapine hypersensitivity and identify novel risk alleles

    DEFF Research Database (Denmark)

    Pavlos, Rebecca; McKinnon, Elizabeth J.; Ostrov, David A.

    2017-01-01

    Genes of the human leukocyte antigen (HLA) system encode cell-surface proteins involved in regulation of immune responses, and the way drugs interact with the HLA peptide binding groove is important in the immunopathogenesis of T-cell mediated drug hypersensitivity syndromes. Nevirapine (NVP), is...

  11. Comparative modelling of human β tubulin isotypes and implications for drug binding

    Science.gov (United States)

    Torin Huzil, J.; Ludueña, Richard F.; Tuszynski, Jack

    2006-02-01

    The protein tubulin is a target for several anti-mitotic drugs, which affect microtubule dynamics, ultimately leading to cell cycle arrest and apoptosis. Many of these drugs, including the taxanes and Vinca alkaloids, are currently used clinically in the treatment of several types of cancer. Another tubulin binding drug, colchicine, although too toxic to be used as a chemotherapeutic agent, is commonly used for the treatment of gout. The main disadvantage that all of these drugs share is that they bind tubulin indiscriminately, leading to the death of both cancerous and healthy cells. However, the broad cellular distribution of several tubulin isotypes provides a platform upon which to construct novel chemotherapeutic drugs that could differentiate between different cell types, reducing the undesirable side effects associated with current chemotherapeutic treatments. Here, we report an analysis of ten human β tubulin isotypes and discuss differences within each of the previously characterized paclitaxel, colchicine and vinblastine binding sites.

  12. Rational use of plasma protein and tissue binding data in drug design.

    Science.gov (United States)

    Liu, Xingrong; Wright, Matthew; Hop, Cornelis E C A

    2014-10-23

    It is a commonly accepted assumption that only unbound drug molecules are available to interact with their targets. Therefore, one of the objectives in drug design is to optimize the compound structure to increase in vivo unbound drug concentration. In this review, theoretical analyses and experimental observations are presented to illustrate that low plasma protein binding does not necessarily lead to high in vivo unbound plasma concentration. Similarly, low brain tissue binding does not lead to high in vivo unbound brain tissue concentration. Instead, low intrinsic clearance leads to high in vivo unbound plasma concentration, and low efflux transport activity at the blood-brain barrier leads to high unbound brain concentration. Plasma protein and brain tissue binding are very important parameters in understanding pharmacokinetics, pharmacodynamics, and toxicities of drugs, but these parameters should not be targeted for optimization in drug design.

  13. Structure of a pheromone receptor-associated MHC molecule with an open and empty groove.

    Directory of Open Access Journals (Sweden)

    2005-08-01

    Full Text Available Neurons in the murine vomeronasal organ (VNO express a family of class Ib major histocompatibility complex (MHC proteins (M10s that interact with the V2R class of VNO receptors. This interaction may play a direct role in the detection of pheromonal cues that initiate reproductive and territorial behaviors. The crystal structure of M10.5, an M10 family member, is similar to that of classical MHC molecules. However, the M10.5 counterpart of the MHC peptide-binding groove is open and unoccupied, revealing the first structure of an empty class I MHC molecule. Similar to empty MHC molecules, but unlike peptide-filled MHC proteins and non-peptide-binding MHC homologs, M10.5 is thermally unstable, suggesting that its groove is normally occupied. However, M10.5 does not bind endogenous peptides when expressed in mammalian cells or when offered a mixture of class I-binding peptides. The F pocket side of the M10.5 groove is open, suggesting that ligands larger than 8-10-mer class I-binding peptides could fit by extending out of the groove. Moreover, variable residues point up from the groove helices, rather than toward the groove as in classical MHC structures. These data suggest that M10s are unlikely to provide specific recognition of class I MHC-binding peptides, but are consistent with binding to other ligands, including proteins such as the V2Rs.

  14. Structure of a Pheromone Receptor-Associated Mhc Molecule With An Open And Empty Groove

    Energy Technology Data Exchange (ETDEWEB)

    Olson, R.; Huey-Tubman, K.E.; Dulac, C.; Bjorkman, P.J.; /Caltech /Harvard U.

    2006-10-06

    Neurons in the murine vomeronasal organ (VNO) express a family of class Ib major histocompatibility complex (MHC) proteins (M10s) that interact with the V2R class of VNO receptors. This interaction may play a direct role in the detection of pheromonal cues that initiate reproductive and territorial behaviors. The crystal structure of M10.5, an M10 family member, is similar to that of classical MHC molecules. However, the M10.5 counterpart of the MHC peptide-binding groove is open and unoccupied, revealing the first structure of an empty class I MHC molecule. Similar to empty MHC molecules, but unlike peptide-filled MHC proteins and non-peptide-binding MHC homologs, M10.5 is thermally unstable, suggesting that its groove is normally occupied. However, M10.5 does not bind endogenous peptides when expressed in mammalian cells or when offered a mixture of class I-binding peptides. The F pocket side of the M10.5 groove is open, suggesting that ligands larger than 8-10-mer class I-binding peptides could fit by extending out of the groove. Moreover, variable residues point up from the groove helices, rather than toward the groove as in classical MHC structures. These data suggest that M10s are unlikely to provide specific recognition of class I MHC-binding peptides, but are consistent with binding to other ligands, including proteins such as the V2Rs.

  15. The role of water in the thermodynamics of drug binding to cyclodextrin

    Energy Technology Data Exchange (ETDEWEB)

    Todorova, Niya A. [Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850 (United States); Schwarz, Frederick P. [Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850 (United States)]. E-mail: fred@carb.nist.gov

    2007-07-15

    The thermodynamic parameters, {delta}{sub B} G {sup 0}, {delta}{sub B} H {sup 0}, {delta}{sub B} S {sup 0}, and {delta}{sub B} C {sub p}, of the drugs flurbiprofen (FLP), nabumetone (NAB), and naproxen (NPX) binding to {beta}-cyclodextrin ({beta}CD) and to {gamma}-cyclodextrin ({gamma}CD) in 0.10 M sodium phosphate buffer were determined from isothermal titration calorimetry (ITC) measurements over the temperature range from 293.15 K to 313.15 K. The heat capacity changes for the binding reactions ranged from -(362 {+-} 48) J . mol{sup -1} . K{sup -1} for FLP and -(238 {+-} 90) J . mol{sup -1} . K{sup -1} for NAB binding in the {beta}CD cavity to 0 for FLP and -(25.1 {+-} 9.2) J . mol{sup -1} . K{sup -1} for NPX binding in the larger {gamma}CD cavity, implying that the structure of water is reorganized in the {beta}CD binding reactions but not reorganized in the {gamma}CD binding reactions. Comparison of the fluorescence enhancements of FLP and NAB upon transferring from the aqueous buffer to isopropanol with the maximum fluorescence enhancements observed for their {beta}CD binding reactions indicated that some localized water was retained in the FLP-{beta}CD complex and almost none in the NAB-{beta}CD complex. No fluorescence change occurs with drug binding in the larger {gamma}CD cavity, indicating the retention of the bulk water environment in the drug-{gamma}CD complex. Since the specific drug binding interactions are essentially the same for {beta}CD and {gamma}CD, these differences in the retention of bulk water may account for the enthalpically driven nature of the {beta}CD binding reactions and the entropically driven nature of the {gamma}CD binding reactions.

  16. A spectroscopic investigations of anticancer drugs binding to bovine serum albumin

    Science.gov (United States)

    Bakkialakshmi, S.; Chandrakala, D.

    2012-03-01

    The binding of anticancer drugs (i) Uracil (U), (ii) 5-Fluorouracil (5FU) and (iii) 5-Chlorouracil (5ClU), to bovine serum albumin (BSA) at two levels of temperature was studied by the fluorescence of quenching method. UV/Vis, time-resolved fluorescence, Fourier transform infrared spectroscopy (FTIR), proton nuclear magnetic resonance (1H NMR) and scanning electron microscope (SEM) analyses were also made. Binding constants (Ka) and binding sites (n) at various levels of temperature were calculated. The obtained binding sites were found to be equal to one for all the three quenchers (U, 5FU and 5ClU) at two different temperature levels. Thermodynamic parameters ΔH, ΔG and ΔS have been calculated and were presented in tables. Change in FTIR absorption intensity shows strong binding of anticancer drugs to BSA. Changes in chemical shifts of NMR and fluorescence lifetimes of the drugs indicate the presence of interaction and binding of BSA to anticancer drugs. 1H NMR spectra and SEM photographs also conform this binding.

  17. Lysozyme binding ability toward psychoactive stimulant drugs: Modulatory effect of colloidal metal nanoparticles.

    Science.gov (United States)

    Sonu, Vikash K; Islam, Mullah Muhaiminul; Rohman, Mostofa Ataur; Mitra, Sivaprasad

    2016-10-01

    The interaction and binding behavior of the well-known psychoactive stimulant drugs theophylline (THP) and theobromine (THB) with lysozyme (LYS) was monitored by in-vitro fluorescence titration and molecular docking calculations under physiological condition. The quenching of protein fluorescence on addition of the drugs is due to the formation of protein-drug complex in the ground state in both the cases. However, the binding interaction is almost three orders of magnitude stronger in THP, which involves mostly hydrogen bonding interaction in comparison with THB where hydrophobic binding plays the predominant role. The mechanism of fluorescence quenching (static type) remains same also in presence of gold and silver nanoparticles (NPs); however, the binding capacity of LYS with the drugs changes drastically in comparison with that in aqueous buffer medium. While the binding affinity of LYS to THB increases ca. 100 times in presence of both the NPs, it is seen to decrease drastically (by almost 1000 fold) for THP. This significant modulation in binding behavior indicates that the drug transportation capacity of LYS can be controlled significantly with the formation protein-NP noncovalent assembly system as an efficient delivery channel.

  18. Discovery of Grooves on Gaspra

    Science.gov (United States)

    Veverka, J.; Thomas, P.; Simonelli, D.; Belton, M.J.S.; Carr, M.; Chapman, C.; Davies, M.E.; Greeley, R.; Greenberg, R.; Head, J.; Klaasen, K.; Johnson, T.V.; Morrison, D.; Neukum, G.

    1994-01-01

    We report the discovery of grooves in Galileo high-resolution images of Gaspra. These features, previously seen only on Mars' satellite Phobos, are most likely related to severe impacts. Grooves on Gaspra occur as linear and pitted depressions, typically 100-200 m wide, 0.8 to 2.5 km long, and 10-20 m deep. Most occur in two major groups, one of which trends approximately parallel to the asteroid's long axis, but is offset by some 15??; the other is approximately perpendicular to this trend. The first of these directions falls along a family of planes which parallel three extensive flat facets identified by Thomas et al., Icarus 107. The occurrence of grooves on Gaspra is consistent with other indications (irregular shape, cratering record) that this asteroid has evolved through a violent collisional history. The bodywide congruence of major groove directions and other structural elements suggests that present-day Gaspra is a globally coherent body. ?? 1994 Academic Press. All rights reserved.

  19. Species-dependent stereoselective drug binding to albumin: a circular dichroism study.

    Science.gov (United States)

    Pistolozzi, Marco; Bertucci, Carlo

    2008-03-01

    Drug binding to albumins from different mammalian species was investigated to disclose evidence of species-dependent stereoselectivity in drug-binding processes and affinities. This aspect is important for evaluating the reliability of extrapolating distribution data among species. The circular dichroism (CD) signal induced by drug binding to the albumins [human serum albumin (HSA), bovine serum albumin (BSA), rat serum albumin (RSA), and dog serum albumin (DSA)] were measured and analyzed. The binding of selected drugs and metabolites to HSA significantly differed from the binding to the other albumins in terms of affinity and conformation of the bound ligands. In particular, phenylbutazone, a marker of site one on HSA, showed a higher affinity for binding to BSA with respect to RSA, HSA, and DSA, respectively. In the case of diazepam, a marker of site two on HSA, the affinity decreased in order from HSA to DSA, RSA, and BSA. The induced CD spectra were similar in terms of energy and band signs, suggesting almost the same conformation for the bound drug to the different albumins. Stereoselectivity was high for the binding of ketoprofen to HSA and RSA. A different sign was observed for the CD spectra induced by the drug to the two albumins because of the prevalence of a different conformation of the bound drug. Interestingly, the same induced CD spectra were obtained using either the racemic form or the (S)-enantiomer. Finally, significant differences were observed in the affinity of bilirubin, being highest for BSA, then decreasing for RSA, HSA, and DSA. A more complex conformational equilibrium was observed for bound bilirubin.

  20. The minimum scale of grooving on faults

    NARCIS (Netherlands)

    Candela, T.; Brodsky, E.E.

    2016-01-01

    At the field scale, nearly all fault surfaces contain grooves generated as one side of the fault slips past the other. Grooves are so common that they are one of the key indicators of principal slip surfaces. Here, we show that at sufficiently small scales, grooves do not exist on fault surfaces. A

  1. The minimum scale of grooving on faults

    NARCIS (Netherlands)

    Candela, T.; Brodsky, E.E.

    2016-01-01

    At the field scale, nearly all fault surfaces contain grooves generated as one side of the fault slips past the other. Grooves are so common that they are one of the key indicators of principal slip surfaces. Here, we show that at sufficiently small scales, grooves do not exist on fault surfaces. A

  2. Structure of P-Glycoprotein Reveals a Molecular Basis for Poly-Specific Drug Binding

    Energy Technology Data Exchange (ETDEWEB)

    Aller, Stephen G.; Yu, Jodie; Ward, Andrew; Weng, Yue; Chittaboina, Srinivas; Zhuo, Rupeng; Harrell, Patina M.; Trinh, Yenphuong T.; Zhang, Qinghai; Urbatsch, Ina L.; Chang, Geoffrey; (Scripps); (TTU)

    2009-04-22

    P-glycoprotein (P-gp) detoxifies cells by exporting hundreds of chemically unrelated toxins but has been implicated in multidrug resistance (MDR) in the treatment of cancers. Substrate promiscuity is a hallmark of P-gp activity, thus a structural description of poly-specific drug-binding is important for the rational design of anticancer drugs and MDR inhibitors. The x-ray structure of apo P-gp at 3.8 angstroms reveals an internal cavity of -6000 angstroms cubed with a 30 angstrom separation of the two nucleotide-binding domains. Two additional P-gp structures with cyclic peptide inhibitors demonstrate distinct drug-binding sites in the internal cavity capable of stereoselectivity that is based on hydrophobic and aromatic interactions. Apo and drug-bound P-gp structures have portals open to the cytoplasm and the inner leaflet of the lipid bilayer for drug entry. The inward-facing conformation represents an initial stage of the transport cycle that is competent for drug binding.

  3. Evaporation from open microchannel grooves.

    Science.gov (United States)

    Kachel, Sibylle; Zhou, Ying; Scharfer, Philip; Vrančić, Christian; Petrich, Wolfgang; Schabel, Wilhelm

    2014-02-21

    The evaporation of water from open u-shaped microchannel grooves was investigated with particular emphasis on the roles of channel width and air flow conditions. Given the small dimensions of the microchannels, all measurements were conducted in a range where convection and diffusion are of equal importance and known correlations for the calculation of mass transfer coefficients cannot be applied. The evaporation rates were measured using a new optical method and a gravimetric method. Both measurement methods yielded mass transfer coefficients that are in agreement with each other. The observed relation between mass transfer coefficient, air velocity and channel width vastly differs from the predictions obtained from macroscopic structures. With respect to diagnostic devices we conclude that analyte concentration in an open microchannel groove strongly increases even within short times due to the evaporation process and we show that wider channels are more favourable in terms of minimizing the relative evaporation rate.

  4. Piperine Decreases Binding of Drugs to Human Plasma and Increases Uptake by Brain Microvascular Endothelial Cells.

    Science.gov (United States)

    Dubey, Raghvendra K; Leeners, Brigitte; Imthurn, Bruno; Merki-Feld, Gabriele Susanne; Rosselli, Marinella

    2017-09-26

    We previously reported that piperine, an active alkaloidal principal of black and long peppers, enhances drug bioavailability by inhibiting drug metabolism. Another mechanism influencing drug availability/uptake is its free fraction. Since piperine is highly lipophilic, we hypothesize that it could also interact with drugs through binding displacement and influence their bioavailability. Accordingly, using equilibrium dialysis, we investigated whether piperine alters the binding of model drug ligands, that is flunitrazepam, diazepam, warfarin, salicylic acid, propranolol, lidocaine, and disopyramide to human plasma (n = 4). Since alterations in binding influence drug disposition, we also studied the effects of piperine on the uptake of plasma bound (3) H-propranolol and (14) C-warfarin by cultured bovine brain microvascular endothelial cells (BMECs). Piperine (1-1000 μM) increased the free fraction (fu) of both albumin and alpha-acid glycoprotein bound drugs in a concentration-dependent manner (p < 0.01). Moreover, piperine (10 μM) increased the uptake of (3) H-propranolol and (14) C-warfarin by BMECs (p < 0.01). In conclusion, our findings provide the first evidence that piperine displaces plasma bound drugs from both albumin and alpha-acid glycoprotein and facilitates drug uptake across biological membranes (e.g. BMEC). Moreover, it is feasible that piperine may similarly facilitate the transport of drugs into tissues, in vivo, and alter both pharmacokinetics and pharmacodynamics of administered drugs. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  5. Interactions Between Sirolimus and Anti-Inflammatory Drugs: Competitive Binding for Human Serum Albumin

    Science.gov (United States)

    Khodaei, Arash; Bolandnazar, Soheila; Valizadeh, Hadi; Hasani, Leila; Zakeri-Milani, Parvin

    2016-01-01

    Purpose: The aim of the present study was investigating the effects of three anti-inflammatory drugs, on Sirolimus protein biding. The binding site of Sirolimus on human serum albumin (HSA) was also determined. Methods: Six different concentrations of Sirolimus were separately exposed to HSA at pH 7.4 and 37°C. Ultrafiltration method was used for separating free drug; then free drug concentrations were measured by HPLC. Finally, Sirolimus protein binding parameters was calculated using Scatchard plots. The same processes were conducted in the presence of NSAIDs at lower concentration of albumin and different pH conditions. To characterize the binding site of Sirolimus on albumin, the free concentration of warfarin sodium and Diazepam, site I and II specific probes, bound to albumin were measured upon the addition of increasing Sirolimus concentrations. Results: Based on the obtained results presence of Diclofenac, Piroxicam and Naproxen, could significantly decrease the percentage of Sirolimus protein binding. The Binding reduction was the most in the presence of Piroxicam. Sirolimus-NSAIDs interactions were increased in higher pH values and also in lower albumin concentrations. Probe displacement study showed that Sirolimus may mainly bind to site I on albumin molecule. Conclusion: More considerations in co-administration of NSAIDs and Sirolimus is recommended. PMID:27478785

  6. Biocompatible medical implant materials with binding sites for a biodegradable drug-delivery system

    Directory of Open Access Journals (Sweden)

    Al-Dubai H

    2011-10-01

    Full Text Available Haifa Al-Dubai1, Gisela Pittner1, Fritz Pittner1, Franz Gabor21Max F Perutz Laboratories, Department of Biochemistry, University of Vienna, Vienna, Austria; 2Department of Pharmaceutical Technology and Biopharmaceutics, Faculty of Life Sciences, University of Vienna, Vienna, AustriaAbstract: Feasibility studies have been carried out for development of a biocompatible coating of medical implant materials allowing the binding of biodegradable drug-delivery systems in a way that their reloading might be possible. These novel coatings, able to bind biodegradable nanoparticles, may serve in the long run as drug carriers to mediate local pharmacological activity. After biodegradation of the nanoparticles, the binding sites could be reloaded with fresh drug-delivering particles. As a suitable receptor system for the nanoparticles, antibodies are anchored. The design of the receptor is of great importance as any bio- or chemorecognitive interaction with other components circulating in the blood has to be avoided. Furthermore, the binding between receptor and the particles has to be strong enough to keep them tightly bound during their lifetime, but on the other hand allow reloading after final degradation of the particles. The nanoparticles suggested as a drug-delivery system for medical implants can be loaded with different pharmaceuticals such as antibiotics, growth factors, or immunosuppressives. This concept may enable the changing of medication, even after implantation of the medical device, if afforded by patients’ needs.Keywords: antibody immobilization, biocompatible coating, chitosan nanoparticles, drug targeting, medical device

  7. Drug binding to human serum albumin: abridged review of results obtained with high-performance liquid chromatography and circular dichroism.

    Science.gov (United States)

    Ascoli, Giorgio A; Domenici, Enrico; Bertucci, Carlo

    2006-09-01

    The drug binding to plasma and tissue proteins are fundamental factors in determining the overall pharmacological activity of a drug. Human serum albumin (HSA), together with alpha1-acid glycoprotein (AGP), are the most important plasma proteins, which act as drug carriers, with drug pharmacokinetic implications, resulting in important clinical impacts for drugs that have a relatively narrow therapeutic index. This review focuses on the combination of biochromatography and circular dichroism as an effective approach for the characterization of albumin binding sites and their enantioselectivity. Furthermore, their applications to the study of changes in the binding properties of the protein arising by the reversible or covalent binding of drugs are discussed, and examples of physiological relevance reported. Perspectives of these studies reside in supporting the development of new drugs, which require miniaturization to facilitate the screening of classes of compounds for their binding to the target protein, and a deeper characterization of the mechanisms involved in the molecular recognition processes.

  8. Single water entropy: hydrophobic crossover and application to drug binding.

    Science.gov (United States)

    Sasikala, Wilbee D; Mukherjee, Arnab

    2014-09-11

    Entropy of water plays an important role in both chemical and biological processes e.g. hydrophobic effect, molecular recognition etc. Here we use a new approach to calculate translational and rotational entropy of the individual water molecules around different hydrophobic and charged solutes. We show that for small hydrophobic solutes, the translational and rotational entropies of each water molecule increase as a function of its distance from the solute reaching finally to a constant bulk value. As the size of the solute increases (0.746 nm), the behavior of the translational entropy is opposite; water molecules closest to the solute have higher entropy that reduces with distance from the solute. This indicates that there is a crossover in translational entropy of water molecules around hydrophobic solutes from negative to positive values as the size of the solute is increased. Rotational entropy of water molecules around hydrophobic solutes for all sizes increases with distance from the solute, indicating the absence of crossover in rotational entropy. This makes the crossover in total entropy (translation + rotation) of water molecule happen at much larger size (>1.5 nm) for hydrophobic solutes. Translational entropy of single water molecule scales logarithmically (Str(QH) = C + kB ln V), with the volume V obtained from the ellipsoid of inertia. We further discuss the origin of higher entropy of water around water and show the possibility of recovering the entropy loss of some hypothetical solutes. The results obtained are helpful to understand water entropy behavior around various hydrophobic and charged environments within biomolecules. Finally, we show how our approach can be used to calculate the entropy of the individual water molecules in a protein cavity that may be replaced during ligand binding.

  9. Competitive binding of fluoroquinolone antibiotics and some other drugs to human serum albumin: a luminescence spectroscopic study.

    Science.gov (United States)

    Seedher, Neelam; Agarwal, Pooja

    2013-01-01

    Co-administration of several drugs in multidrug therapy may alter the binding of each to human serum albumin (HSA) and hence their pharmacological activity. Thirty-two frequently prescribed drug combinations, consisting of four fluoroquinolone antibiotics and eight competing drugs, have been studied using fluorescence and circular dichroism spectroscopic techniques. Competitive binding studies on the drug combinations are not available in the literature. In most cases, the presence of competing drug decreased the binding affinity of fluoroquinolone, resulting in an increase in the concentration of free pharmacologically active drug. The competitive binding mechanism involved could be interpreted in terms of the site specificity of the binding and competing drugs. For levofloxacin, the change in the binding affinity was small because in the presence of site II-specific competing drugs, levofloxacin mainly occupied site I. A competitive interference mechanism was operative for sparfloxacin, whereas competitive interference as well as site-to-site displacement of competing drugs was observed in the case of ciprofloxacin hydrochloride. For enrofloxacin, a different behavior was observed for different combinations; site-to-site displacement and conformational changes as well as independent binding has been observed for various drug combinations. Circular dichroism spectral studies showed that competitive binding did not cause any major structural changes in the HSA molecule. Copyright © 2013 John Wiley & Sons, Ltd.

  10. Quantitative predictions of binding free energy changes in drug-resistant influenza neuraminidase.

    Directory of Open Access Journals (Sweden)

    Daniel R Ripoll

    Full Text Available Quantitatively predicting changes in drug sensitivity associated with residue mutations is a major challenge in structural biology. By expanding the limits of free energy calculations, we successfully identified mutations in influenza neuraminidase (NA that confer drug resistance to two antiviral drugs, zanamivir and oseltamivir. We augmented molecular dynamics (MD with Hamiltonian Replica Exchange and calculated binding free energy changes for H274Y, N294S, and Y252H mutants. Based on experimental data, our calculations achieved high accuracy and precision compared with results from established computational methods. Analysis of 15 micros of aggregated MD trajectories provided insights into the molecular mechanisms underlying drug resistance that are at odds with current interpretations of the crystallographic data. Contrary to the notion that resistance is caused by mutant-induced changes in hydrophobicity of the binding pocket, our simulations showed that drug resistance mutations in NA led to subtle rearrangements in the protein structure and its dynamics that together alter the active-site electrostatic environment and modulate inhibitor binding. Importantly, different mutations confer resistance through different conformational changes, suggesting that a generalized mechanism for NA drug resistance is unlikely.

  11. Development of Drug Loaded Nanoparticles Binding to Hydroxyapatite Based on a Bisphosphonate Modified Nonionic Surfactant

    Directory of Open Access Journals (Sweden)

    Jiabin Zhang

    2015-01-01

    Full Text Available This study aimed at development of drug loaded nanoparticles which could bind to hydroxyapatite (HA to construct drug or growth factor releasing bone graft substitutes. To this end, the terminal hydroxyl group of a nonionic surfactant Brij 78 (polyoxyethylene (20 stearyl ether was first modified with pamidronate (Pa. Using Pa-Brij 78 as both a surfactant and an affinity ligand to HA, three different Pa surface functionalized nanoparticles were prepared, named as solid lipid nanoparticles (Pa-SNPs, nanoemulsions (Pa-NEMs, and PLGA nanoparticles (Pa-PNPs. A model drug curcumin was successfully encapsulated in the three nanoparticles. The sizes of Pa-NEM and Pa-PNP were around 150 nm and the size of Pa-SNP was around 90 nm with polydispersity indexes (PDIs less than 0.20. Drug encapsulation efficiencies of the three nanoparticles were all greater than 85%. Furthermore, the order of binding affinity of the nanoparticles to HA was Pa-PNP>Pa-NEM=Pa-SNP. After lyophilization, the sizes of the three nanoparticles were increased about 0.5–2.0-fold but their binding affinities to HA were almost the same as the fresh prepared nanoparticles. In conclusion, a Pa-modified Brij 78 was synthesized and used for fabrication of a series of drug loaded nanoparticles to construct drug-eluting HA-based bone graft substitutes.

  12. HIV-1 binding and neutralizing antibodies of injecting drug users

    Directory of Open Access Journals (Sweden)

    Ouverney E.P.

    2005-01-01

    Full Text Available Previous studies have demonstrated a stronger seroreactivity against some synthetic peptides responsible for inducing neutralizing antibodies in injecting drug users (IDU compared to that of individuals sexually infected with HIV-1 (S, but the effectiveness in terms of the neutralizing ability of these antibodies has not been evaluated. Our objective was to study the humoral immune response of IDU by determining the specificity of their antibodies and the presence of neutralizing antibodies. The neutralization capacity against the HIV-1 isolate MN (genotype B, the primary HIV-1 isolate 95BRRJ021 (genotype F, and the seroreactivity with peptides known to induce neutralizing antibodies, from the V2 and V3 loops of different HIV-1 subtypes, were analyzed. Seroreactivity indicates that IDU plasma are more likely to recognize a broader range of peptides than S plasma, with significantly higher titers, especially of V3 peptides. Similar neutralization frequencies of the MN isolate were observed in plasma of the IDU (16/47 and S (20/60 groups in the 1:10 dilution. The neutralization of the 95BRRJ021 isolate was more frequently observed for plasma from the S group (15/23 than from the IDU group (15/47, P = 0.0108. No correlation between neutralization and seroreactivity with the peptides tested was observed. These results suggest that an important factor responsible for the extensive and broad humoral immune response observed in IDU is their infection route. There was very little difference in neutralizing antibody response between the IDU and S groups despite their differences in seroreactivity and health status.

  13. In vivo receptor binding of opioid drugs at the mu site

    Energy Technology Data Exchange (ETDEWEB)

    Rosenbaum, J.S.; Holford, N.H.; Sadee, W.

    1985-06-01

    The in vivo receptor binding of a series of opioid drugs was investigated in intact rats after s.c. administration of (/sup 3/H)etorphine tracer, which selectively binds to mu sites in vivo. Receptor binding was determined by a membrane filtration assay immediately after sacrifice of the animals and brain homogenization. Coadministration of unlabeled opioid drugs together with tracer led to a dose-dependent decrease of in vivo tracer binding. Estimates of the doses required to occupy 50% of the mu sites in vivo established the following potency rank order: diprenorphine, naloxone, buprenorphine, etorphine, levallorphan, cyclazocine, sufentanil, nalorphine, ethylketocyclazocine, ketocyclazocine, pentazocine, morphine. In vivo-in vitro differences among the relative receptor binding potencies were only partially accounted for by differences in their access to the brain and the regulatory effects of Na+ and GTP, which are expected to reduce agonist affinities in vivo. The relationship among mu receptor occupancy in vivo and pharmacological effects of the opioid drugs is described.

  14. Induced circular dichroism as a tool to investigate the binding of drugs to carrier proteins: Classic approaches and new trends.

    Science.gov (United States)

    Tedesco, Daniele; Bertucci, Carlo

    2015-09-10

    Induced circular dichroism (ICD) is a spectroscopic phenomenon that provides versatile and useful methods for characterizing the structural and dynamic properties of the binding of drugs to target proteins. The understanding of biorecognition processes at the molecular level is essential to discover and validate new pharmacological targets, and to design and develop new potent and selective drugs. The present article reviews the main applications of ICD to drug binding studies on serum carrier proteins, going from the classic approaches for the derivation of drug binding parameters and the identification of binding sites, to an overview of the emerging trends for the characterization of binding modes by means of quantum chemical (QC) techniques. The advantages and limits of the ICD methods for the determination of binding parameters are critically reviewed; the capability to investigate the binding interactions of drugs and metabolites to their target proteins is also underlined, as well as the possibility of characterizing the binding sites to obtain a complete picture of the binding mechanism and dynamics. The new applications of ICD methods to identify stereoselective binding modes of drug/protein complexes are then reviewed with relevant examples. The combined application of experimental ICD spectroscopy and QC calculations is shown to identify qualitatively the bound conformations of ligands to target proteins even in the absence of a detailed structure of the binding sites, either obtained from experimental X-ray crystallography and NMR measurements or from computational models of the complex. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Metabolism of ATP-binding cassette drug transporter inhibitors: complicating factor for multidrug resistance.

    NARCIS (Netherlands)

    Cnubben, N.H.; Wortelboer, H.M.; Zanden, J.J. van; Rietjens, I.M.; Bladeren, P.J. van

    2005-01-01

    Membrane transport proteins belonging to the ATP-binding cassette (ABC) family of transport proteins play a central role in the defence of organisms against toxic compounds, including anticancer drugs. However, for compounds that are designed to display a toxic effect, this defence system diminishes

  16. Study on the drug resistance and the binding mode of HIV-1 integrase with LCA inhibitor

    Institute of Scientific and Technical Information of China (English)

    HU; JianPing; CHANG; Shan; CHEN; WeiZu; WANG; CunXin

    2007-01-01

    Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the lifecycle of this virus and also an important target for the study of anti-HIV drugs. The binding mode of the wild type IN core domain and its G140S mutant with L-Chicoric acid (LCA) inhibitor were investigated by using multiple conformation molecular docking and molecular dynamics (MD) simulation. Based on the binding modes, the drug resistance mechanism was explored for the G140S mutant of IN with LCA. The results indicate that the binding site of the G140S mutant of IN core domain with LCA is different from that of the core domain of the wild type IN, which leads to the partial loss of inhibition potency of LCA. The flexibility of the IN functional loop region and the interactions between Mg2+ ion and the three key residues (i.e., D64, D116, E152) stimulate the biological operation of IN. The drug resistance also lies in several other important effects, such as the repulsion between LCA and E152 in the G140S mutant core domain, the weakening of K159 binding with LCA and Y143 pointing to the pocket of the G140S mutant. All of the above simulation results agree well with experimental data, which provide us with some helpful information for designing the drug of anti-HIV based on the structure of IN.

  17. Detection, characterization, and screening of heme-binding molecules by mass spectrometry for malaria drug discovery

    NARCIS (Netherlands)

    Munoz-Durango, K.; Maciuk, A.; Harfouche, A.; Torijano-Gutierrez, S.; Jullian, J.C.; Quintin, J.; Spelman, K.; Mouray, E.; Grellier, P.; Figadere, B.

    2012-01-01

    Drug screening for antimalarials uses heme biocrystallization inhibition methods as an alternative to parasite cultures, but they involve complex processes and cannot detect artemisinin-like molecules. The described method detects heme-binding compounds by mass spectrometry, using dissociation of th

  18. Oligomycin frames a common drug-binding site in the ATP synthase

    Energy Technology Data Exchange (ETDEWEB)

    Symersky, Jindrich; Osowski, Daniel; Walters, D. Eric; Mueller, David M. (Rosalind)

    2015-12-01

    We report the high-resolution (1.9 {angstrom}) crystal structure of oligomycin bound to the subunit c10 ring of the yeast mitochondrial ATP synthase. Oligomycin binds to the surface of the c10 ring making contact with two neighboring molecules at a position that explains the inhibitory effect on ATP synthesis. The carboxyl side chain of Glu59, which is essential for proton translocation, forms an H-bond with oligomycin via a bridging water molecule but is otherwise shielded from the aqueous environment. The remaining contacts between oligomycin and subunit c are primarily hydrophobic. The amino acid residues that form the oligomycin-binding site are 100% conserved between human and yeast but are widely different from those in bacterial homologs, thus explaining the differential sensitivity to oligomycin. Prior genetics studies suggest that the oligomycin-binding site overlaps with the binding site of other antibiotics, including those effective against Mycobacterium tuberculosis, and thereby frames a common 'drug-binding site.' We anticipate that this drug-binding site will serve as an effective target for new antibiotics developed by rational design.

  19. Differential diagnosis of groove pancreatic carcinomas vs. groove pancreatitis: Usefulness of the portal venous phase

    Energy Technology Data Exchange (ETDEWEB)

    Ishigami, Kousei, E-mail: Ishigamikousei@aol.co [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582 (Japan); Tajima, Tsuyoshi; Nishie, Akihiro; Kakihara, Daisuke [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582 (Japan); Fujita, Nobuhiro [Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Asayama, Yoshiki; Ushijima, Yasuhiro; Irie, Hiroyuki [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582 (Japan); Nakamura, Masafumi; Takahata, Shunichi [Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Ito, Tetsuhide [Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Honda, Hiroshi [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582 (Japan)

    2010-06-15

    Purpose: To clarify if the portal venous phase is helpful for the differential diagnosis of groove pancreatic carcinomas and groove pancreatitis. Materials and methods: MDCT and MRI of groove pancreatic carcinomas (n = 7) and groove pancreatitis (n = 15) were retrospectively reviewed by two radiologists independently. The signal intensity on T2-weighted images was subjectively assessed. The presence or absence of common bile duct (CBD) and main pancreatic duct (MPD) strictures, calcifications, and cystic lesions was evaluated. Additionally, the appearance of groove pancreatic carcinoma and that of groove pancreatitis in the portal venous phase on dynamic MDCT and MRI were compared. Results: There were no significant differences in the signal intensity on T2-weighted images and in the presence or absence of CBD and MPD strictures, calcifications, and cystic lesions between groove pancreatic carcinomas and groove pancreatitis. However, patchy focal enhancement in the portal venous phase was more commonly observed in groove pancreatitis than groove pancreatic carcinoma (Reviewers 1 and 2: 14/15 [93.3%] vs. 1/7 [14.3%], P < 0.0001). In addition, peripheral enhancement was only seen in groove pancreatic carcinomas (Reviewer 1: 4/7 [57.1%] vs. 0/15 [0%], P < 0.005, and Reviewer 2: 3/7 [42.9%] vs. 0/15 [0%], P < 0.05). Conclusion: The portal venous phase may be helpful for the differential diagnosis of groove pancreatic carcinomas and groove pancreatitis.

  20. EO-199, a specific antagonist of antiarrhythmic drugs: Assessment by binding experiments and in vivo studies

    Energy Technology Data Exchange (ETDEWEB)

    Oppenheimer, E.; Harel, G.; Lipinsky, D.; Sarne, Y. (Tel-Aviv Univ. (Israel))

    1991-01-01

    EO-199, a demethylated analog of the novel class I antiarrhythmic drug EO-122 was found to antagonize the antiarrhythmic activity of EO-122 and that of procainamide (Class I{sub A}). EO-199 did not block significantly the activity of a class I{sub B} antiarrhythmic agent, lidocaine. EO-199 also displaced the specific binding of ({sup 3}H)EO-122 to rate heart membranes similarly to procainamide whereas lidocaine did not. The correlation between binding experiments and pharmacological effects points to a possible subclassification of these drugs; the two chemical analogs EO-199 and EO-122, as well as procainamide (I{sub A}) but not lidocaine (I{sub B}), compete at the same site or the same state of the sodium channel. The availability of a specific antagonist might be useful for studying the mechanism of action of antiarrhythmic drugs as well as an antidote in cases of antiarrhythmics overdose intoxication.

  1. Laser grooving of surface cracks on hot work tool steel

    Directory of Open Access Journals (Sweden)

    D. Klobčar

    2011-10-01

    Full Text Available The paper presents the analysis of laser grooving of 1.2343 tool steel hardened to 46 HRC. The effect of laser power and grooving speed on groove shape (i.e. depth and width, the material removal rate and the purity of produced groove as a measure of groove quality was investigated and analyzed using response surface methodology. Optimal parameters of laser grooving were found, which enables pure grooves suitable for laser welding.

  2. Insights into the binding of the drugs diclofenac sodium and cefotaxime sodium to serum albumin: calorimetry and spectroscopy.

    Science.gov (United States)

    Sharma, Ruchika; Choudhary, Sinjan; Kishore, Nand

    2012-08-15

    Understanding physical chemistry underlying drug-protein interactions is essential to devise guidelines for the synthesis of target oriented drugs. Binding of a non-steroidal anti-inflammatory drug, diclofenac sodium (DCF) and an antibiotic drug, cefotaxime sodium (CFT) belonging to the family of cephalosporins with bovine serum albumin (BSA) has been examined using a combination of isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC), steady state and time resolved fluorescence and circular dichroism spectroscopies. Binding affinity of both DCF and CFT with BSA is observed to be of the order of 10(4)M(-1), with the binding profiles fitting well to the single set of binding site model. The disagreement between calorimetric and van't Hoff enthalpies indicates non-adherence to a two-state binding process which could be attributed to changes in the conformation of the protein upon ligand binding as well as with increase in the temperature. Circular dichroism and the fluorescence results, however, do not show any major conformational changes upon binding of these drugs to BSA, and hence the discrepancy could be due to temperature induced conformational changes in the protein. The results of ionic strength dependence and binding in the presence of anionic, cationic and non-ionic surfactants indicate, involvement of more that a single type of interaction in the binding process. The ITC results for the binding of these drugs to BSA in presence of each other indicate that the binding sites for the two drugs are different, and therefore binding of one is not influenced by the other. The DSC results provide quantitative information on the effect of these drugs on the stability of serum albumin. The combined calorimetric and spectroscopic approach has provided a detailed analysis including thermodynamics of the binding of DCF and CFT with BSA qualitatively and quantitatively.

  3. Binding of the Lactococcal Drug Dependent Transcriptional Regulator LmrR to Its Ligands and Responsive Promoter Regions.

    Directory of Open Access Journals (Sweden)

    Jan Pieter van der Berg

    Full Text Available The heterodimeric ABC transporter LmrCD from Lactococcus lactis is able to extrude several different toxic compounds from the cell, fulfilling a role in the intrinsic and induced drug resistance. The expression of the lmrCD genes is regulated by the multi-drug binding repressor LmrR, which also binds to its own promoter to autoregulate its own expression. Previously, we reported the crystal structure of LmrR in the presence and absence of the drugs Hoechst 33342 and daunomycin. Analysis of the mechanism how drugs control the repressor activity of LmrR is impeded by the fact that these drugs also bind to DNA. Here we identified, using X-ray crystallography and fluorescence, that riboflavin binds into the drug binding cavity of LmrR, adopting a similar binding mode as Hoechst 33342 and daunomycin. Microscale thermophoresis was employed to quantify the binding affinity of LmrR to its responsive promoter regions and to evaluate the cognate site of LmrR in the lmrCD promoter region. Riboflavin reduces the binding affinity of LmrR for the promoter regions. Our results support a model wherein drug binding to LmrR relieves the LmrR dependent repression of the lmrCD genes.

  4. A quantitative model for the in vivo assessment of drug binding sites with positron emission tomography

    Energy Technology Data Exchange (ETDEWEB)

    Mintun, M.A.; Raichle, M.E.; Kilbourn, M.R.; Wooten, G.F.; Welch, M.J.

    1984-03-01

    We propose an in vivo method for use with positron emission tomography (PET) that results in a quantitative characterization of neuroleptic binding sites using radiolabeled spiperone. The data are analyzed using a mathematical model that describes transport, nonspecific binding, and specific binding in the brain. The model demonstrates that the receptor quantities Bmax (i.e., the number of binding sites) and KD-1 (i.e., the binding affinity) are not separably ascertainable with tracer methodology in human subjects. We have, therefore, introduced a new term, the binding potential, equivalent to the product BmaxKD-1, which reflects the capacity of a given tissue, or region of a tissue, for ligand-binding site interaction. The procedure for obtaining these measurements is illustrated with data from sequential PET scans of baboons after intravenous injection of carrier-added (18F)spiperone. From these data we estimate the brain tissue nonspecific binding of spiperone to be in the range of 94.2 to 95.3%, and the regional brain spiperone permeability (measured as the permeability-surface area product) to be in the range of 0.025 to 0.036 cm3/(s X ml). The binding potential of the striatum ranged from 17.4 to 21.6; these in vivo estimates compare favorably to in vitro values in the literature. To our knowledge this represents the first direct evidence that PET can be used to characterize quantitatively, locally and in vivo, drug binding sites in brain. The ability to make such measurements with PET should permit the detailed investigation of diseases thought to result from disorders of receptor function.

  5. Binding of the Lactococcal Drug Dependent Transcriptional Regulator LmrR to Its Ligands and Responsive Promoter Regions

    NARCIS (Netherlands)

    van der Berg, Jan Pieter; Madoori, Pramod Kumar; Komarudin, Amalina Ghaisani; Thunnissen, Andy-Mark; Driessen, Arnold J M

    2015-01-01

    The heterodimeric ABC transporter LmrCD from Lactococcus lactis is able to extrude several different toxic compounds from the cell, fulfilling a role in the intrinsic and induced drug resistance. The expression of the lmrCD genes is regulated by the multi-drug binding repressor LmrR, which also bind

  6. Structural similarity between binding sites in influenza sialidase and isocitrate dehydrogenase: implications for an alternative approach to rational drug design.

    OpenAIRE

    Poirrette, A. R.; Artymiuk, P. J.; Grindley, H. M.; Rice, D.W.; Willett, P.

    1994-01-01

    Using searching techniques based on algorithms derived from graph theory, we have established a similarity between a 3-dimensional cluster of side chains implicated in drug binding in influenza sialidase and side chains involved in isocitrate binding in Escherichia coli isocitrate dehydrogenase. The possible implications of the use of such comparative methods in drug design are discussed.

  7. Genome-wide characterisation of the binding repertoire of small molecule drugs

    Directory of Open Access Journals (Sweden)

    Makowski Lee

    2003-11-01

    Full Text Available Abstract Most, if not all, drugs interact with multiple proteins. One or more of these interactions are responsible for carrying out the primary therapeutic effects of the drug. Others are involved in the transport or metabolic processing of the drug or in the mediation of side effects. Still others may be responsible for activities that correspond to alternate therapeutic applications. The potential clinical impact of a drug and its cost of development are affected by the sum of all these interactions. The drug development process includes the identification and characterisation of a drug's clinically relevant interactions. This characterisation is presently accomplished by a combination of experimental laboratory techniques and clinical trials, with increasing numbers of patient participants. Efficient methods for the identification of all the molecular targets of a drug prior to clinical trials could greatly expedite the drug development process. Combinatorial peptide and cDNA phage display have the potential for achieving a complete characterisation of the binding repertoire of a small molecule. This paper will discuss the current state of phage display technology, as applied to the identification of novel receptors for small molecules, using a successful application with the drug Taxol™ as an example of the technical and theoretical benefits and pitfalls of this method.

  8. Influence of musical groove on postural sway.

    Science.gov (United States)

    Ross, Jessica M; Warlaumont, Anne S; Abney, Drew H; Rigoli, Lillian M; Balasubramaniam, Ramesh

    2016-03-01

    Timescales of postural fluctuation reflect underlying neuromuscular processes in balance control that are influenced by sensory information and the performance of concurrent cognitive and motor tasks. An open question is how postural fluctuations entrain to complex environmental rhythms, such as in music, which also vary on multiple timescales. Musical groove describes the property of music that encourages auditory-motor synchronization and is used to study voluntary motor entrainment to rhythmic sounds. The influence of groove on balance control mechanisms remains unexplored. We recorded fluctuations in center of pressure (CoP) of standing participants (N = 40) listening to low and high groove music and during quiet stance. We found an effect of musical groove on radial sway variability, with the least amount of variability in the high groove condition. In addition, we observed that groove influenced postural sway entrainment at various temporal scales. For example, with increasing levels of groove, we observed more entrainment to shorter, local timescale rhythmic musical occurrences. In contrast, we observed more entrainment to longer, global timescale features of the music, such as periodicity, with decreasing levels of groove. Finally, musical experience influenced the amount of postural variability and entrainment at local and global timescales. We conclude that groove in music and musical experience can influence the neural mechanisms that govern balance control, and discuss implications of our findings in terms of multiscale sensorimotor coupling. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  9. Differential binding of prohibitin-2 to estrogen receptor α and to drug-resistant ERα mutants

    Energy Technology Data Exchange (ETDEWEB)

    Chigira, Takeru, E-mail: 8120661875@mail.ecc.u-tokyo.ac.jp [Department of Chemistry and Biotechnology, School of Engineering, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 (Japan); Nagatoishi, Satoru, E-mail: nagatoishi@bioeng.t.u-tokyo.ac.jp [Department of Bioengineering, School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 (Japan); Tsumoto, Kouhei, E-mail: tsumoto@bioeng.t.u-tokyo.ac.jp [Department of Chemistry and Biotechnology, School of Engineering, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 (Japan); Department of Bioengineering, School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 (Japan)

    2015-08-07

    Endocrine resistance is one of the most challenging problems in estrogen receptor alpha (ERα)-positive breast cancer. The transcriptional activity of ERα is controlled by several coregulators, including prohibitin-2 (PHB2). Because of its ability to repress the transcriptional activity of activated ERα, PHB2 is a promising antiproliferative agent. In this study, were analyzed the interaction of PHB2 with ERα and three mutants (Y537S, D538G, and E380Q) that are frequently associated with a lack of sensitivity to hormonal treatments, to help advance novel drug discovery. PHB2 bound to ERα wild-type (WT), Y537S, and D538G, but did not bind to E380Q. The binding thermodynamics of Y537S and D538G to PHB2 were favorably altered entropically compared with those of WT to PHB2. Our results show that PHB2 binds to the ligand binding domain of ERα with a conformational change in the helix 12 of ERα. - Highlights: • Molten globule-likeness of an ERα repressor Prohibitin-2 (PHB2) is identified. • The thermodynamics is validated for the interaction between ERα and PHB2. • PHB2 binds to Y537S and D538G mutants of ERα commonly found in breast cancer. • ERα WT and mutants showed different thermodynamic parameters in the binding to PHB2. • ERα binds to PHB2 with conformational change involving packing of helix 12.

  10. Ligands recognizing the minor groove of DNA: development and applications.

    Science.gov (United States)

    Wemmer, D E

    Polyamide ligands comprised of pyrrole, imidazole and hydroxypyrrole rings have been developed over the past decade which can be used to target many different, predetermined DNA sequences through recognition of functional groups in the minor groove. The design principles for these ligands are described with a description of the characterization of their binding. Variations containing linked recognition modules have been described which allow high affinity and specificity recognition of DNA sequences of over 15 base pairs. Recent applications of these ligands in affecting biological response through competition with proteins for DNA binding sites are reviewed. Copyright 2001 John Wiley & Sons, Inc.

  11. Structure-based drug design enables conversion of a DFG-in binding CSF-1R kinase inhibitor to a DFG-out binding mode.

    Science.gov (United States)

    Meyers, Marvin J; Pelc, Matthew; Kamtekar, Satwik; Day, Jacqueline; Poda, Gennadiy I; Hall, Molly K; Michener, Marshall L; Reitz, Beverly A; Mathis, Karl J; Pierce, Betsy S; Parikh, Mihir D; Mischke, Deborah A; Long, Scott A; Parlow, John J; Anderson, David R; Thorarensen, Atli

    2010-03-01

    The work described herein demonstrates the utility of structure-based drug design (SBDD) in shifting the binding mode of an HTS hit from a DFG-in to a DFG-out binding mode resulting in a class of novel potent CSF-1R kinase inhibitors suitable for lead development.

  12. Structure-based drug design enables conversion of a DFG-in binding CSF-1R kinase inhibitor to a DFG-out binding mode

    Energy Technology Data Exchange (ETDEWEB)

    Meyers, Marvin J.; Pelc, Matthew; Kamtekar, Satwik; Day, Jacqueline; Poda, Gennadiy I.; Hall, Molly K.; Michener, Marshall L.; Reitz, Beverly A.; Mathis, Karl J.; Pierce, Betsy S.; Parikh, Mihir D.; Mischke, Deborah A.; Long, Scott A.; Parlow, John J.; Anderson, David R.; Thorarensen, Atli (Pfizer)

    2010-08-11

    The work described herein demonstrates the utility of structure-based drug design (SBDD) in shifting the binding mode of an HTS hit from a DFG-in to a DFG-out binding mode resulting in a class of novel potent CSF-1R kinase inhibitors suitable for lead development.

  13. Interactions between Human Liver Fatty Acid Binding Protein and Peroxisome Proliferator Activated Receptor Selective Drugs

    Directory of Open Access Journals (Sweden)

    Tony Velkov

    2013-01-01

    Full Text Available Fatty acid binding proteins (FABPs act as intracellular shuttles for fatty acids as well as lipophilic xenobiotics to the nucleus, where these ligands are released to a group of nuclear receptors called the peroxisome proliferator activated receptors (PPARs. PPAR mediated gene activation is ultimately involved in maintenance of cellular homeostasis through the transcriptional regulation of metabolic enzymes and transporters that target the activating ligand. Here we show that liver- (L- FABP displays a high binding affinity for PPAR subtype selective drugs. NMR chemical shift perturbation mapping and proteolytic protection experiments show that the binding of the PPAR subtype selective drugs produces conformational changes that stabilize the portal region of L-FABP. NMR chemical shift perturbation studies also revealed that L-FABP can form a complex with the PPAR ligand binding domain (LBD of PPARα. This protein-protein interaction may represent a mechanism for facilitating the activation of PPAR transcriptional activity via the direct channeling of ligands between the binding pocket of L-FABP and the PPARαLBD. The role of L-FABP in the delivery of ligands directly to PPARα via this channeling mechanism has important implications for regulatory pathways that mediate xenobiotic responses and host protection in tissues such as the small intestine and the liver where L-FABP is highly expressed.

  14. Binding of benzodiazepine drugs to bovine serum albumin: A second derivative spectrophotometric study

    Science.gov (United States)

    Omran, Ahmed A.; El-Sayed, Abdel-Aziz; Shehata, Ahmed

    2011-12-01

    The binding constants ( K values) of three benzodiazepine drugs to bovine serum albumin were determined by a second derivative spectrophotometric method. Despite the sample and reference samples were prepared in the same way to maintain the same albumin content in each sample and reference pair, the absorption spectra show that the baseline compensation was incomplete because of the strong background signals caused by bovine serum albumin. Accordingly, further quantitative spectral information could not be obtained from these absorption spectra. On the other hand, the calculated second derivative spectra clearly show isosbestic points indicating the complete removal of the residual background signal effects. Using the derivative intensity differences (Δ D values) of the studied benzodiazepine drugs before and after the addition of albumin, the binding constants were calculated and obtained with R.S.D. of less than 8%. The interactions of drugs with bovine serum albumin were investigated using Scatchard's plot. In addition, the consistency between the fractions of bound benzodiazepine calculated from the obtained K values and the experimental values were established. The results indicate that the second derivative method can be advantageously applicable to the determination of binding constants of drugs to serum albumin without prior separation. Moreover, the validity of the proposed method was confirmed.

  15. Binding of several anti-tumor drugs to bovine serum albumin: Fluorescence study

    Energy Technology Data Exchange (ETDEWEB)

    Bi Shuyun [College of Chemistry, Changchun Normal University, Changchun 130032 (China)], E-mail: sy_bi@sina.com; Sun Yantao [College of Chemistry, Jilin University, Changchun 130023 (China); College of Chemistry, Jilin Normal University, Siping 136000 (China); Qiao Chunyu; Zhang Hanqi [College of Chemistry, Jilin University, Changchun 130023 (China); Liu Chunming [College of Chemistry, Changchun Normal University, Changchun 130032 (China)

    2009-05-15

    The interactions of mitomycin C (MMC), fluorouracil (FU), mercaptopurine (MP) and doxorubicin hydrochloride (DXR) with bovine serum albumin (BSA) were studied by spectroscopic method. Quenching of fluorescence of serum albumin by these drugs was found to be a static quenching process. The binding constants (K{sub A}) were 9.66x10{sup 3}, 2.08x10{sup 3}, 8.20x10{sup 2} and 7.50x10{sup 3} L mol{sup -1} for MMC-, FU-, MP- and DXR-BSA, respectively, at pH 7.4 Britton-Robinson buffer at 28 deg. C. The thermodynamic functions such as enthalpy change ({delta}H), entropy change ({delta}S) and Gibbs free-energy change ({delta}G) for the reactions were also calculated according to the thermodynamic equations. The main forces in the interactions of these drugs with BSA were evaluated. It was found that the interactions of MMC and FU with BSA were exothermic processes and those of MP and DXR with BSA were endothermic. In addition, the binding sites on BSA for the four drugs were probed by the changes of binding properties of these drugs with BSA in the presence of two important site markers such as ibuprofen and indomethacin. Based on the Foester theory of non-radiation energy transfer, the binding distances between the drugs and tryptophane were calculated and they were 3.00, 1.14, 2.85, and 2.79 nm for MMC, FU, MP and DXR, respectively.

  16. Evolutionary trace analysis of eukaryotic DNA topoisomerase I superfamily: Identification of novel antitumor drug binding site

    Institute of Scientific and Technical Information of China (English)

    SONG; Yunlong; QI; Yunpeng; ZHANG; Wannian; SHENG; Chunqu

    2005-01-01

    The studies of novel inhibitors of DNA topoisomerase I (Topo I) have already become very promising in cancer chemotherapy. Identifying the new drug-binding residues is playing an important role in the design and optimization of Topo I inhibitors. The designed compounds may have novel scaffolds, thus will be helpful to overcome the toxicities of current camptothecin (CPT) drugs and may provide a solution to cross resistance with these drugs. Multiple sequence alignments were performed on eukaryotic DNA topoisomerase I superfamily and thus the evolutionary tree was constructed. The Evolutionary Trace method was applied to identify functionally important residues of human Topo I. It has been demonstrated that class-specific hydrophobic residues Ala351, Met428, Pro431 are located around the 7,9-position of CPT, indicating suitable substitution of hydrophobic group on CPT will increase antitumor activity. The conservative residue Lys436 in the superfamily is of particular interest and new CPT derivatives designed based on this residue may greatly increase water solubility of such drugs. It has also been demonstrated that the residues Asn352 and Arg364 were conservative in the superfamily, whose mutation will render CPT resistance. As our molecular docking studies demonstrated they did not make any direct interaction with CPT, they are important drug-binding site residues for future design of novel non-camptothecin lead compounds. This work provided a strong basis for the design and synthesis of novel highly potent CPT derivatives and virtual screening for novel lead compounds.

  17. Structure-Based Drug Discovery for Prion Disease Using a Novel Binding Simulation

    Directory of Open Access Journals (Sweden)

    Daisuke Ishibashi

    2016-07-01

    Full Text Available The accumulation of abnormal prion protein (PrPSc converted from the normal cellular isoform of PrP (PrPC is assumed to induce pathogenesis in prion diseases. Therefore, drug discovery studies for these diseases have focused on the protein conversion process. We used a structure-based drug discovery algorithm (termed Nagasaki University Docking Engine: NUDE that ran on an intensive supercomputer with a graphic-processing unit to identify several compounds with anti-prion effects. Among the candidates showing a high-binding score, the compounds exhibited direct interaction with recombinant PrP in vitro, and drastically reduced PrPSc and protein-aggresomes in the prion-infected cells. The fragment molecular orbital calculation showed that the van der Waals interaction played a key role in PrPC binding as the intermolecular interaction mode. Furthermore, PrPSc accumulation and microgliosis were significantly reduced in the brains of treated mice, suggesting that the drug candidates provided protection from prion disease, although further in vivo tests are needed to confirm these findings. This NUDE-based structure-based drug discovery for normal protein structures is likely useful for the development of drugs to treat other conformational disorders, such as Alzheimer's disease.

  18. Thermal Bridge Effects in Window Grooves

    DEFF Research Database (Denmark)

    Rose, Jørgen

    1997-01-01

    In this report thermal bridge effects in window grooves are analyzed. The analysis is performed using different thicknesses of the window groove insulation, to evaluate what the optimal solution is.All analysis in the report is performed using both 2- and 3-dimensional numerical analysis....

  19. Gratings in plasmonic V-groove waveguides

    DEFF Research Database (Denmark)

    Smith, Cameron; Cuesta, Irene Fernandez; Kristensen, Anders

    2011-01-01

    We introduce visible light optical gratings to surface plasmon V-groove waveguides. Gradient e-beam dosage onto silicon stamp enables structuring V-grooves of varying depth. Nanoimprint lithography maintains a Λ=265 nm corrugation for gold surface devices....

  20. Gratings in plasmonic V-groove waveguides

    DEFF Research Database (Denmark)

    Smith, Cameron; Cuesta, Irene Fernandez; Kristensen, Anders

    2011-01-01

    We introduce visible light optical gratings to surface plasmon V-groove waveguides. Gradient e-beam dosage onto silicon stamp enables structuring V-grooves of varying depth. Nanoimprint lithography maintains a Λ=265 nm corrugation for gold surface devices....

  1. Interpretation of Ocular Melanin Drug Binding Assays. Alternatives to the Model of Multiple Classes of Independent Sites.

    Science.gov (United States)

    Manzanares, José A; Rimpelä, Anna-Kaisa; Urtti, Arto

    2016-04-04

    Melanin has a high binding affinity for a wide range of drugs. The determination of the melanin binding capacity and its binding affinity are important, e.g., in the determination of the ocular drug distribution, the prediction of drug effects in the eye, and the trans-scleral drug delivery. The binding parameters estimated from a given data set vary significantly when using different isotherms or different nonlinear fitting methods. In this work, the commonly used bi-Langmuir isotherm, which assumes two classes of independent sites, is confronted with the Sips isotherm. Direct, log-log, and Scatchard plots are used, and the interpretation of the binding curves in the latter is critically analyzed. In addition to the goodness of fit, the emphasis is placed on the physical meaning of the binding parameters. The bi-Langmuir model imposes a bimodal distribution of binding energies for the sites on the melanin granules, but the actual distribution is most likely continuous and unimodal, as assumed by the Sips isotherm. Hence, the latter describes more accurately the distribution of binding energies and also the experimental results of melanin binding to drugs and metal ions. Simulations are used to show that the existence of two classes of sites cannot be confirmed on the sole basis of the shape of the binding curve in the Scatchard plot, and that serious doubts may appear on the meaning of the binding parameters of the bi-Langmuir model. Experimental results of melanin binding to chloroquine and metoprolol are used to illustrate the importance of the choice of the binding isotherm and of the method used to evaluate the binding parameters.

  2. Carrageenans as a New Source of Drugs with Metal Binding Properties

    Directory of Open Access Journals (Sweden)

    Yuri S. Khotimchenko

    2010-04-01

    Full Text Available Carrageenans are abundant and safe non-starch polysaccharides exerting their biological effects in living organisms. Apart from their known pro-inflammation properties and some pharmacological activity, carrageenans can also strongly bind and hold metal ions. This property can be used for creation of the new drugs for elimination of metals from the body or targeted delivery of these metal ions for healing purposes. Metal binding activity of different carrageenans in aqueous solutions containing Y3+ or Pb2+ ions was studied in a batch sorption system. The metal uptake by carrageenans is not affected by the change of the pH within the range from 2.0 to 6.0. The rates and binding capacities of carrageenans regarding metal ions were evaluated. The Langmuir, Freundlich and BET sorption models were applied to describe the isotherms and constants, and the sorption isothermal data could be explained well by the Langmuir equation. The results obtained through the study suggest that κ-, ι-, and λ-carrageenans are favorable sorbents. The largest amount of Y3+ and Pb2+ ions are bound by i-carrageenan. Therefore, it can be concluded that this type of polysaccharide is the more appropriate substance for elaboration of the drugs with high selective metal binding properties.

  3. Nanomechanical detection of antibiotic-mucopeptide binding in a model for superbug drug resistance

    Science.gov (United States)

    Ndieyira, Joseph Wafula; Watari, Moyu; Barrera, Alejandra Donoso; Zhou, Dejian; Vögtli, Manuel; Batchelor, Matthew; Cooper, Matthew A.; Strunz, Torsten; Horton, Mike A.; Abell, Chris; Rayment, Trevor; Aeppli, Gabriel; McKendry, Rachel A.

    2008-11-01

    The alarming growth of the antibiotic-resistant superbugs methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) is driving the development of new technologies to investigate antibiotics and their modes of action. We report the label-free detection of vancomycin binding to bacterial cell wall precursor analogues (mucopeptides) on cantilever arrays, with 10 nM sensitivity and at clinically relevant concentrations in blood serum. Differential measurements have quantified binding constants for vancomycin-sensitive and vancomycin-resistant mucopeptide analogues. Moreover, by systematically modifying the mucopeptide density we gain new insights into the origin of surface stress. We propose that stress is a product of a local chemical binding factor and a geometrical factor describing the mechanical connectivity of regions activated by local binding in terms of a percolation process. Our findings place BioMEMS devices in a new class of percolative systems. The percolation concept will underpin the design of devices and coatings to significantly lower the drug detection limit and may also have an impact on our understanding of antibiotic drug action in bacteria.

  4. Microcirculation within grooved substrates regulates cell positioning and cell docking inside microfluidic channels.

    Science.gov (United States)

    Manbachi, Amir; Shrivastava, Shamit; Cioffi, Margherita; Chung, Bong Geun; Moretti, Matteo; Demirci, Utkan; Yliperttula, Marjo; Khademhosseini, Ali

    2008-05-01

    Immobilization of cells inside microfluidic devices is a promising approach for enabling studies related to drug screening and cell biology. Despite extensive studies in using grooved substrates for immobilizing cells inside channels, a systematic study of the effects of various parameters that influence cell docking and retention within grooved substrates has not been performed. We demonstrate using computational simulations that the fluid dynamic environment within microgrooves significantly varies with groove width, generating microcirculation areas in smaller microgrooves. Wall shear stress simulation predicted that shear stresses were in the opposite direction in smaller grooves (25 and 50 microm wide) in comparison to those in wider grooves (75 and 100 microm wide). To validate the simulations, cells were seeded within microfluidic devices, where microgrooves of different widths were aligned perpendicularly to the direction of the flow. Experimental results showed that, as predicted, the inversion of the local direction of shear stress within the smaller grooves resulted in alignment of cells on two opposite sides of the grooves under the same flow conditions. Also, the amplitude of shear stress within microgrooved channels significantly influenced cell retainment in the channels. Therefore, our studies suggest that microscale shear stresses greatly influence cellular docking, immobilization, and retention in fluidic systems and should be considered for the design of cell-based microdevices.

  5. Molecular Model of Anticonvulsant Drug Binding to the Voltage-Gated Sodium Channel Inner Pore

    Science.gov (United States)

    Lipkind, Gregory M.

    2010-01-01

    The tricyclic anticonvulsant drugs phenytoin, carbamazepine, and lamotrigine block neuronal voltage-gated Na+ channels, and their binding sites to domain IV-S6 in the channel's inner pore overlap with those of local anesthetic drugs. These anticonvulsants are neutral, in contrast to the mostly positively charged local anesthetics, but their open/inactivated-state blocking affinities are similar. Using a model of the open pore of the Na+ channel that we developed by homology with the crystal structures of potassium channels, we have docked these three anticonvulsants with residues identified by mutagenesis as important for their binding energy. The three drugs show a common pharmacophore, including an aromatic ring that has an aromatic-aromatic interaction with Tyr-1771 of NaV1.2 and a polar amide or imide that interacts with the aromatic ring of Phe-1764 by a low-energy amino-aromatic hydrogen bond. The second aromatic ring is nearly at a right angle to the pharmacophore and fills the pore lumen, probably interacting with the other S6 segments and physically occluding the inner pore to block Na+ permeation. Hydrophobic interactions with this second aromatic ring may contribute an important component to binding for anticonvulsants, which compensates energetically for the absence of positive charge in their structures. Voltage dependence of block, their important therapeutic property, results from their interaction with Phe-1764, which connects them to the voltage sensors. Their use dependence is modest and this results from being neutral, with a fast drug off-rate after repolarization, allowing a normal action potential rate in the presence of the drugs. PMID:20643904

  6. A Novel Design of Grooved Fibers for Fiber-Optic Localized Plasmon Resonance Biosensors

    Directory of Open Access Journals (Sweden)

    Lai-Kwan Chau

    2009-08-01

    Full Text Available Bio-molecular recognition is detected by the unique optical properties of self-assembled gold nanoparticles on the unclad portions of an optical fiber whose surfaces have been modified with a receptor. To enhance the performance of the sensing platform, the sensing element is integrated with a microfluidic chip to reduce sample and reagent volume, to shorten response time and analysis time, as well as to increase sensitivity. The main purpose of the present study is to design grooves on the optical fiber for the FO-LPR microfluidic chip and investigate the effect of the groove geometry on the biochemical binding kinetics through simulations. The optical fiber is designed and termed as U-type or D-type based on the shape of the grooves. The numerical results indicate that the design of the D-type fiber exhibits efficient performance on biochemical binding. The grooves designed on the optical fiber also induce chaotic advection to enhance the mixing in the microchannel. The mixing patterns indicate that D-type grooves enhance the mixing more effectively than U-type grooves. D-type fiber with six grooves is the optimum design according to the numerical results. The experimental results show that the D-type fiber could sustain larger elongation than the U-type fiber. Furthermore, this study successfully demonstrates the feasibility of fabricating the grooved optical fibers by the femtosecond laser, and making a transmission-based FO-LPR probe for chemical sensing. The sensor resolution of the sensor implementing the D-type fiber modified by gold nanoparticles was 4.1 × 10-7 RIU, which is much more sensitive than that of U-type optical fiber (1.8 × 10-3 RIU.

  7. DNA Binding Proteins and Drug Delivery Vehicles: Tales of Elephants and Snakes.

    Science.gov (United States)

    Karpel, Richard L

    2015-01-01

    We compare the DNA-interactive properties of bacteriophage T4 gene 32 protein (gp32) with those of crotamine, a component of the venom of the South American rattlesnake. Gene 32 protein is a classical single-stranded DNA binding protein that has served as a model for this class of proteins. We discuss its biological functions, structure, binding specificities, and how it controls its own expression. In addition, we delineate the roles of the structural domains of gp32 and how they regulate the protein's various activities. Crotamine, a component of the venom of the South American rattlesnake, is probably not a DNA binding protein in nature, but clearly shows significant DNA binding in vitro. Crotamine has been shown to selectively disrupt rapidly dividing cells and this specificity has been demonstrated for crotamine-facilitated delivery of plasmid DNA Thus, crotamine, or a variant of the protein, could have important clinical and/or diagnostic roles. Understanding its DNA binding properties may therefore lead to more effective drug delivery vehicles.

  8. A Cell-Based Pharmacokinetics Assay for Evaluating Tubulin-Binding Drugs

    Science.gov (United States)

    Wang, Yuwei; Liu, Jihua; Zhang, Jun; Wang, Liping; Chan, Jonathon; Wang, Hai; Jin, Yi; Yu, Lei; Grainger, David W.; Ying, Wenbin

    2014-01-01

    Increasing evidence reveals that traditional pharmacokinetics parameters based on plasma drug concentrations are insufficient to reliably demonstrate accurate pharmacological effects of drugs in target organs or cells in vivo. This underscores the increasing need to improve the types and qualities of cellular pharmacokinetic information for drug preclinical screening and clinical efficacy assessments. Here we report a whole cell-based method to assess drugs that disturb microtubule dynamics to better understand different formulation-mediated intracellular drug release profiles. As proof of concept for this approach, we compared the well-known taxane class of anti-microtubule drugs based on paclitaxel (PTX), including clinically familiar albumin nanoparticle-based Abraxane™, and a polymer nanoparticle-based degradable paclitaxel carrier, poly(L-glutamic acid)-paclitaxel conjugate (PGA-PTX, also known as CT-2103) versus control PTX. This in vitro cell-based evaluation of PTX efficacy includes determining the cellular kinetics of tubulin polymerization, relative populations of cells under G2 mitotic arrest, cell proliferation and total cell viability. For these taxane tubulin-binding compounds, the kinetics of cell microtubule stabilization directly correlate with G2 arrest and cell proliferation, reflecting the kinetics and amounts of intracellular PTX release. Each individual cell-based dose-response experiment correlates with published, key therapeutic parameters and taken together, provide a comprehensive understanding of drug intracellular pharmacokinetics at both cellular and molecular levels. This whole cell-based evaluating method is convenient, quantitative and cost-effective for evaluating new formulations designed to optimize cellular pharmacokinetics for drugs perturbing tubulin polymerization as well as assisting in explaining drug mechanisms of action at cellular levels. PMID:24688312

  9. A cell-based pharmacokinetics assay for evaluating tubulin-binding drugs.

    Science.gov (United States)

    Wang, Yuwei; Liu, Jihua; Zhang, Jun; Wang, Liping; Chan, Jonathon; Wang, Hai; Jin, Yi; Yu, Lei; Grainger, David W; Ying, Wenbin

    2014-01-01

    Increasing evidence reveals that traditional pharmacokinetics parameters based on plasma drug concentrations are insufficient to reliably demonstrate accurate pharmacological effects of drugs in target organs or cells in vivo. This underscores the increasing need to improve the types and qualities of cellular pharmacokinetic information for drug preclinical screening and clinical efficacy assessments. Here we report a whole cell-based method to assess drugs that disturb microtubule dynamics to better understand different formulation-mediated intracellular drug release profiles. As proof of concept for this approach, we compared the well-known taxane class of anti-microtubule drugs based on paclitaxel (PTX), including clinically familiar albumin nanoparticle-based Abraxane™, and a polymer nanoparticle-based degradable paclitaxel carrier, poly(L-glutamic acid)-paclitaxel conjugate (PGA-PTX, also known as CT-2103) versus control PTX. This in vitro cell-based evaluation of PTX efficacy includes determining the cellular kinetics of tubulin polymerization, relative populations of cells under G2 mitotic arrest, cell proliferation and total cell viability. For these taxane tubulin-binding compounds, the kinetics of cell microtubule stabilization directly correlate with G2 arrest and cell proliferation, reflecting the kinetics and amounts of intracellular PTX release. Each individual cell-based dose-response experiment correlates with published, key therapeutic parameters and taken together, provide a comprehensive understanding of drug intracellular pharmacokinetics at both cellular and molecular levels. This whole cell-based evaluating method is convenient, quantitative and cost-effective for evaluating new formulations designed to optimize cellular pharmacokinetics for drugs perturbing tubulin polymerization as well as assisting in explaining drug mechanisms of action at cellular levels.

  10. Experimental and molecular docking studies on DNA binding interaction of adefovir dipivoxil: Advances toward treatment of hepatitis B virus infections

    Science.gov (United States)

    Shahabadi, Nahid; Falsafi, Monireh

    The toxic interaction of adefovir dipivoxil with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multi-spectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove binding mode. The binding constant of UV-visible and the number of binding sites were 3.33 ± 0.2 × 104 L mol-1and 0.99, respectively. The fluorimetric studies showed that the reaction between the drug and CT-DNA is exothermic (ΔH = 34.4 kJ mol-1; ΔS = 184.32 J mol-1 K-1). Circular dichroism spectroscopy (CD) was employed to measure the conformational change of CT-DNA in the presence of adefovir dipivoxil, which verified the groove binding mode. Furthermore, the drug induces detectable changes in its viscosity. The molecular modeling results illustrated that adefovir strongly binds to groove of DNA by relative binding energy of docked structure -16.83 kJ mol-1. This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the toxic interaction of small molecular pollutants and drugs with bio macromolecules, which contributes to clarify the molecular mechanism of toxicity or side effect in vivo.

  11. Diagnostics and Treatment of Palatal Radicular Grooves

    Institute of Scientific and Technical Information of China (English)

    James Deschner; Birgit Rath; Wang Zheng; Ding Yi

    2006-01-01

    The palatal radicular groove represents a developmental anomaly that mainly affects the maxillary incisor teeth. This anomaly is probably caused by an infolding of the enamel organ and Hertwig's epithelial root sheath during odontogenesis. The groove often originates in the central fossa or cingulum and continues towards the root apex for various distances. The anatomical defect can act as a funnel for plaque and, therefore, result in extensive bone and attachment loss. A complete lack of closure of the calcified tissues along the groove, that is a direct communication between pulp and periodontium, rarely occurs. However, accessory canals between the pulp cavity and periodontal tissues frequently exist along the groove and are main entrances of infectious material into the pulp cavity, facilitating the development of endodontic lesions. Grooves can also complicate restorative therapy or interfere with the accessibility for scaling and root planing. Patients usually present with pain and gingival inflammation in the maxillary incisor region. Bleeding on probing and increased pocket depths are strictly confined to the area of the groove in an otherwise periodontally healthy patient. Radiographs may show a parapulpal line that represents the radiographic image of the groove. Treatment of the anomaly by scaling and root planing alone or in combination with procedures such as odontoplasty, flap surgery, application of an enamel matrix derivative or guided tissue regeneration can be successful. A short case report of a patient treated successfully with an enamel matrix derivative for localized attachment loss due to this anomaly is presented.

  12. Metallomics for drug development: serum protein binding and analysis of an anticancer tris(8-quinolinolato)gallium(III) drug using inductively coupled plasma mass spectrometry.

    Science.gov (United States)

    Ossipov, Konstantin; Foteeva, Lidia S; Seregina, Irina F; Perevalov, Sergei A; Timerbaev, Andrei R; Bolshov, Mikhail A

    2013-06-27

    The application of an inductively coupled plasma mass spectrometry (ICP-MS) assay for quantifying in vitro binding of a gallium-based anticancer drug, tris(8-quinolinolato)gallium(III), to serum albumin and transferrin and in human serum is described. The distribution of the drug between the protein-rich and protein-free fractions was assessed via ICP-MS measurement of total gallium in ultrafiltrates. Comparative kinetic studies revealed that the drug exhibits a different reactivity toward individual proteins. While the maximum possible binding to albumin (~10%) occurs practically immediately, interaction with transferrin has a step-like character and the equilibrium state (with more than 50% binding) is reached for about 48 h. Drug transformation into the bound form in serum, also very fast, results in almost quantitative binding (~95%). The relative affinity of protein-drug binding was characterized in terms of the association constants ranging from 10(3) to 10(4)M(-1). In order to further promote clinical testing of the gallium drug, the ICP-MS method was applied for direct quantification of gallium in human serum spiked with the drug. The detection limit for gallium was found to be as low as 20 ng L(-1). The repeatability was better than 8% (as RSD) and the achieved recoveries were in the range 99-103%.

  13. Spectroscopic study of drug-binding characteristics of unmodified and pNPA-based acetylated human serum albumin: Does esterase activity affect microenvironment of drug binding sites on the protein?

    Energy Technology Data Exchange (ETDEWEB)

    Moradi, Nastaran [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Faculty of Pharmaceutical Sciences, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Ashrafi-Kooshk, Mohammad Reza [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Ghobadi, Sirous [Department of Biology, Faculty of Sciences, Razi University, Kermanshah (Iran, Islamic Republic of); Shahlaei, Mohsen [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Faculty of Pharmaceutical Sciences, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Khodarahmi, Reza, E-mail: rkhodarahmi@mbrc.ac.ir [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Faculty of Pharmaceutical Sciences, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of)

    2015-04-15

    Human serum albumin (HSA) is the most prominent extracellular protein in blood plasma. There are several binding sites on the protein which provide accommodation for structurally-unrelated endogenous and exogenous ligands and a wide variety of drugs. “Esterase-like” activity (hydrolysis of p-nitrophenyl esters) by the protein has been also reported. In the current study, we set out to investigate the interaction of indomethacin and ibuprofen with the unmodified and modified HSA (pNPA-modified HSA) using various spectroscopic techniques. Fluorescence data showed that 1:1 binding of drug to HSA is associated with quenching of the protein intrinsic fluorescence. Decrease of protein surface hydrophobicity (PSH), alteration in drug binding affinity and change of the protein stability, after esterase-like activity and permanent acetylation of HSA, were also documented. Analysis of the quenching and thermodynamic parameters indicated that forces involved in drug–HSA interactions change upon the protein modification. - Highlights: • Binding propensity of indomethacin extremely decreased upon the protein acetylation. • There is no ibuprofen binding after protein acetylation. • Protein stability changes upon drug binding as well as protein acetylation. • Drug pharmacokinetics may be influenced under co-administration of HSA-modifier drugs.

  14. The new generation drug candidate molecules: Spectral, electrochemical, DNA-binding and anticancer activity properties

    Science.gov (United States)

    Gölcü, Ayşegül; Muslu, Harun; Kılıçaslan, Derya; Çeşme, Mustafa; Eren, Özge; Ataş, Fatma; Demirtaş, İbrahim

    2016-09-01

    The new generation drug candidate molecules [Cu(5-Fu)2Cl2H2O] (NGDCM1) and [Zn(5-Fu)2(CH3COO)2] (NGDCM2) were obtained from the reaction of copper(II) and zinc(II) salts with the anticancer drug 5-fluoracil (5-Fu). These compounds have been characterized by spectroscopic and analytical techniques. Thermal behavior of the compounds were also investigated. The electrochemical properties of the compounds have been investigated by cyclic voltammetry (CV) using glassy carbon electrode. The biological activity of the NGDCM1 and NGDCM2 has been evaluated by examining their ability to bind to fish sperm double strand DNA (FSdsDNA) with UV spectroscopy. UV studies of the interaction of the 5-Fu and metal derivatives with FSdsDNA have shown that these compounds can bind to FSdsDNA. The binding constants of the compounds with FSdsDNA have also been calculated. Thermal decomposition of the compounds lead to the formation of CuO and ZnO as final products. The effect of proliferation 5-Fu, NGDCM1 and NGDCM2 were examined on the HeLa cells using real-time cell analyzer with three different concentrations.

  15. Molecular Docking of 3-Methylindole-containing Drugs Binding into CYP3A4

    Institute of Scientific and Technical Information of China (English)

    MENG Xuan-yu; LI Zhuo; NIU Rui-juan; ZHANG Hong-xing; ZHENG Qing-chuan

    2012-01-01

    Drugs SPD-304(6,7-dimethyl-3- { [methyl-(2-{methyl-[ 1-(3-trifluoromethyl-phenyl)- 1H-indol-3-ylmethyl]-amino}-ethyl)-amino]-methyl}-chromen-4-one) and zafirlukast contain a common structural element of 3-substituted indole moiety which closely relates to a dehydrogenated reaction catalyzed by cytochrome P450s(CYPs).It was reported that the dehydrogenation can produce a reactive electrophilic intermediate which cause toxicities and inactivate CYPs. Drug L-745,870(3-{[4-(4-chlorophenyl)piperazin-l-yl]-methyl}-1H-pyrrolo-2,3-β-pyridine) might have similar effect since it contains the same structural element.We used molecular docking approach combined with molecular dynamics(MD) simulation to model three-dimensional(3D) complex structures of SPD-304,zafirlukast and L-745,870 into CYP3A4,respectively.The results show that these three drugs can stably bind into the active site and the 3-methylene carbons of the drugs keep a reasonable reactive distance from the heme iron.The complex structure of SPD-304-CYP3A4 is in agreement with experimental data.For zafirlukast,the calculation results indicate that 3-methylene carbon might be the dehydrogenation reaction site.Docking model of L-745,870-CYP3A4 shows a potential possibility of L-745,870 dehydrogenated by CYP3A4 at 3-methylene carbon which is in agreement with experiment in vivo.In addition,residues in the phenylalanine cluster as well as S119 and R212 play a critical role in the ligands binding based on our calculations.The docking models could provide some clues to understand the metabolic mechanism of the drugs by CYP3A4.

  16. Liposomal Tumor Targeting in Drug Delivery Utilizing MMP-2- and MMP-9-Binding Ligands

    Directory of Open Access Journals (Sweden)

    Oula Penate Medina

    2011-01-01

    Full Text Available Nanotechnology offers an alternative to conventional treatment options by enabling different drug delivery and controlled-release delivery strategies. Liposomes being especially biodegradable and in most cases essentially nontoxic offer a versatile platform for several different delivery approaches that can potentially enhance the delivery and targeting of therapies to tumors. Liposomes penetrate tumors spontaneously as a result of fenestrated blood vessels within tumors, leading to known enhanced permeability and subsequent drug retention effects. In addition, liposomes can be used to carry radioactive moieties, such as radiotracers, which can be bound at multiple locations within liposomes, making them attractive carriers for molecular imaging applications. Phage display is a technique that can deliver various high-affinity and selectivity peptides to different targets. In this study, gelatinase-binding peptides, found by phage display, were attached to liposomes by covalent peptide-PEG-PE anchor creating a targeted drug delivery vehicle. Gelatinases as extracellular targets for tumor targeting offer a viable alternative for tumor targeting. Our findings show that targeted drug delivery is more efficient than non-targeted drug delivery.

  17. Advances and applications of binding affinity prediction methods in drug discovery.

    Science.gov (United States)

    Parenti, Marco Daniele; Rastelli, Giulio

    2012-01-01

    Nowadays, the improvement of R&D productivity is the primary commitment in pharmaceutical research, both in big pharma and smaller biotech companies. To reduce costs, to speed up the discovery process and to increase the chance of success, advanced methods of rational drug design are very helpful, as demonstrated by several successful applications. Among these, computational methods able to predict the binding affinity of small molecules to specific biological targets are of special interest because they can accelerate the discovery of new hit compounds. Here we provide an overview of the most widely used methods in the field of binding affinity prediction, as well as of our own work in developing BEAR, an innovative methodology specifically devised to overtake some limitations in existing approaches. The BEAR method was successfully validated against different biological targets, and proved its efficacy in retrieving active compounds from virtual screening campaigns. The results obtained so far indicate that BEAR may become a leading tool in the drug discovery pipeline. We primarily discuss advantages and drawbacks of each technique and show relevant examples and applications in drug discovery.

  18. A short update on the structure of drug binding sites on neurotransmitter transporters

    Directory of Open Access Journals (Sweden)

    Gabrielsen Mari

    2011-12-01

    Full Text Available Abstract Background The dopamine (DAT, noradrenalin (NET and serotonin (SERT transporters are molecular targets for different classes of psychotropic drugs. Cocaine and the SSRI (S-citalopram block neurotransmitter reuptake competitively, but while cocaine is a non-selective reuptake inhibitor, (S-citalopram is a selective SERT inhibitor. Findings Here we present comparisons of the binding sites and the electrostatic potential surfaces (EPS of DAT, NET and SERT homology models based on two different LeuTAa templates; with a substrate (leucine in an occluded conformation (PDB id 2a65, and with an inhibitor (tryptophan in an open-to-out conformation (PDB id 3f3a. In the occluded homology models, two conserved aromatic amino acids (tyrosine and phenylalanine formed a gate between the putative binding pockets, and this contact was interrupted in the open to out conformation. The EPS of DAT and NET were generally negative in the vestibular area, whereas the EPS of the vestibular area of SERT was more neutral. Conclusions The findings presented here contribute as an update on the structure of the binding sites of DAT, NET and SERT. The updated models, which have larger ligand binding site areas than models based on other templates, may serve as improved tools for virtual ligand screening.

  19. Zinc complexes of the antibacterial drug oxolinic acid: structure and DNA-binding properties.

    Science.gov (United States)

    Tarushi, Alketa; Psomas, George; Raptopoulou, Catherine P; Kessissoglou, Dimitris P

    2009-06-01

    The neutral mononuclear zinc complexes with the quinolone antibacterial drug oxolinic acid in the absence or presence of a nitrogen donor heterocyclic ligand 2,2'-bipyridine or 1,10-phenanthroline have been synthesized and characterized. The experimental data suggest that oxolinic acid is on deprotonated mode acting as a bidentate ligand coordinated to the metal ion through the ketone and one carboxylato oxygen atoms. The crystal structures of (chloro)(oxolinato)(2,2'-bipyridine)zinc(II), 2, and bis(oxolinato)(1,10-phenanthroline)zinc(II), 3, have been determined with X-ray crystallography. The biological activity of the complexes has been evaluated by examining their ability to bind to calf-thymus DNA (CT DNA) with UV and fluorescence spectroscopies. UV studies of the interaction of the complexes with DNA have shown that they can bind to CT DNA and the DNA-binding constants have been calculated. Competitive studies with ethidium bromide (EB) have shown that complex 3 exhibits the ability to displace the DNA-bound EB indicating that it binds to DNA in strong competition with EB.

  20. A Combinatorial Approach to Biophysically Characterise Chemokine-Glycan Binding Affinities for Drug Development

    Directory of Open Access Journals (Sweden)

    Tanja Gerlza

    2014-07-01

    Full Text Available Chemokine binding to glycosaminoglycans (GAGs is recognised to be an important step in inflammation and other pathological disorders like tumor growth and metastasis. Although different ways and strategies to interfere with these interactions are being pursued, no major breakthrough in the development of glycan-targeting drugs has been reported so far. We have engineered CXCL8 towards a dominant-negative form of this chemokine (dnCXCL8 which was shown to be highly active in various inflammatory animal models due to its inability to bind/activate the cognate CXCL8 GPC receptors on neutrophils in combination with its significantly increased GAG-binding affinity [1]. For the development of GAG-targeting chemokine-based biopharmaceuticals, we have established a repertoire of methods which allow the quantification of protein-GAG interactions. Isothermal fluorescence titration (IFT, surface plasmon resonance (SPR, isothermal titration calorimetry (ITC, and a novel ELISA-like competition assay (ELICO have been used to determine Kd and IC50 values for CXCL8 and dnCXCL8 interacting with heparin and heparan sulfate (HS, the proto-typical members of the GAG family. Although the different methods gave different absolute affinities for the four protein-ligand pairs, the relative increase in GAG-binding affinity of dnCXCL8 compared to the wild type chemokine was found by all methods. In combination, these biophysical methods allow to discriminate between unspecific and specific protein-GAG interactions.

  1. Drug-binding energetics of human α-1-acid glycoprotein assessed by isothermal titration calorimetry and molecular docking simulations

    Science.gov (United States)

    Huang, Johnny X.; Cooper, Matthew A.; Baker, Mark A.; Azad, Mohammad A.K.; Nation, Roger L.; Li, Jian; Velkov, Tony

    2012-01-01

    This study utilizes sensitive, modern isothermal titration calorimetric (ITC) methods to characterize the microscopic thermodynamic parameters that drive the binding of basic drugs to α-1-acid glycoprotein (AGP) and thereby rationalize the thermodynamic data in relation to docking models and crystallographic structures of the drug-AGP complexes. The binding of basic compounds from the tricyclic antidepressant series, together with miaserine, chlorpromazine, disopyramide and cimetidine all displayed an exothermically driven binding interaction with AGP. The impact of protonation/deprotonation events, ionic strength, temperature and the individual selectivity of the A and F1*S AGP variants on drug-binding thermodynamics were characterized. A correlation plot of the thermodynamic parameters for all of the test compounds revealed enthalpy-entropy compensation is in effect. The exothermic binding energetics of the test compounds were driven by a combination of favorable (negative) enthalpic (ΔH°) and favorable (positive) entropic (ΔS°) contributions to the Gibbs free energy (ΔG°). Collectively, the data imply that the free energies that drive drug binding to AGP and its relationship to drug-serum residency evolve from the complex interplay of enthalpic and entropic forces from interactions with explicit combinations of hydrophobic and polar side-chain sub-domains within the multi-lobed AGP ligand binding cavity. PMID:23192962

  2. Level Set Modeling of Transient Electromigration Grooving

    OpenAIRE

    Khenner, M.; Averbuch, A.; Israeli, M.; Nathan, M; Glickman, E.

    2000-01-01

    A numerical investigation of grain-boundary (GB) grooving by means of the Level Set (LS) method is carried out. GB grooving is emerging as a key element of electromigration drift in polycrystalline microelectronic interconnects, as evidenced by a number of recent studies. The purpose of the present study is to provide an efficient numerical simulation, allowing a parametric study of the effect of key physical parameters (GB and surface diffusivities, grain size, current density, etc) on the e...

  3. Effectiveness of transverse grooves in rigid pavement

    Science.gov (United States)

    Gurney, G. F.; Bryden, J. E.

    1982-10-01

    Transverse grooves were installed at 11 intersection approaches on worn rigid pavement to reduce a high rate of wet road accidents. In most cases, accident reductions were experienced only at intersections with multiple negative operational characteristics, including higher approach speeds, limited sight distances, and frequent vehicle stopping for turns or stop signs. Intersections with no more than one negative characteristic generally did not benefit from grooving.

  4. Spectroscopic and molecular docking studies on the interaction of the drug olanzapine with calf thymus DNA

    Science.gov (United States)

    Shahabadi, Nahid; Bagheri, Somayeh

    2015-02-01

    The present study investigated the binding interaction between olanzapine and calf thymus DNA (ct-DNA) using emission, absorption, circular dichroism, viscosity measurements and molecular modeling. Thermodynamic parameters (ΔH < 0 and ΔS < 0) indicated that hydrogen bond and van der Waals play main roles in the binding of the drug to ct-DNA. Spectrophotometric studies of the interaction of olanzapine with DNA have shown that it could bind to ct-DNA (Kb = 2 × 103 M-1). The binding constant is comparable to standard groove binding drugs. Competitive fluorimetric studies with Hoechst 33258 have shown that olanzapine exhibits the ability to displace the DNA-bound Hoechst 33258 indicating that binds strongly in minor groove of DNA helix. Furthermore, the drug induces detectable changes in the CD spectrum of ct-DNA as well as changes in its viscosity. All of the experimental results prove that the groove binding must be predominant. The results obtained from experimental data were in good agreement with molecular modeling studies.

  5. Groove model of tibia-femoral osteoarthritis in the rat.

    Science.gov (United States)

    de Visser, Huub M; Weinans, Harrie; Coeleveld, Katja; van Rijen, Mattie H P; Lafeber, Floris P J G; Mastbergen, Simon C

    2017-03-01

    Several experimental models of osteoarthritis in rats are used to study the pathophysiology of osteoarthritis. Many mechanically induced models have the limitation that permanent joint instability is induced by, for example, ligament transection or meniscal damage. This permanent instability will counteract the potential beneficial effects of therapy. The groove model of osteoarthritis uses a one-time trigger, surgically induced cartilage damage on the femoral condyles, and has been validated for the canine tibia-femoral compartment. The present study evaluates this model for the rat knee joint. The articular cartilage of the weight bearing surface of both femoral condyles and trochlea were damaged (grooved) without damaging the underlying subchondral bone. Severity of joint degeneration was histologically assessed, in addition to patella cartilage damage, and subchondral bone characteristics by means of (contrast-enhanced) micro-CT. Mild histological degeneration of the surgically untouched tibial plateau cartilage was observed in addition to damage of the femoral condyles, without clear synovial tissue inflammation. Contrast enhanced micro-CT demonstrated proteoglycan loss of the surgically untouched patella cartilage. Besides, a more sclerotic structure of the subchondral bone was observed. The tibia-femoral groove model in a rat results in mild knee joint degeneration, without permanent joint instability and joint inflammation. This makes the rat groove model a useful model to study the onset and progression of post-traumatic non-inflammatory osteoarthritis, creating a relatively sensitive model to study disease modifying osteoarthritic drugs. © 2016 The Authors. Journal of Orthopaedic Research published by Wiley Periodicals, Inc. on behalf of the Orthopaedic Research Society. J Orthop Res 35:496-505, 2017.

  6. In vitro binding studies of drugs to hair: influence of melanin and lipids on cocaine binding to Caucasoid and Africoid hair.

    Science.gov (United States)

    Joseph, R E; Su, T P; Cone, E J

    1996-10-01

    Although the mechanism(s) of drug deposition in hair are unknown, there is evidence that suggests that the amount and type of melanin present are major factors in determining how much drug enters hair after exposure. The role of other hair components, such as lipids, has received less attention. We used in vitro binding techniques to evaluate the binding of radiolabeled cocaine to different types of treated and untreated hair specimens. Divided male and female Caucasoid (black/brown and blond colored) and Africoid (black colored) hair specimens (N = 7) were exhaustively extracted to remove lipid components (lipid-extracted hair). Separate portions were bleached to denature or alter melanin content. Experiments with radiolabeled cocaine were performed on untreated, lipid-extracted, and bleached portions of hair from different groups. Cocaine binding was significantly higher (p hair compared with other groups. The amount of drug binding was similar among female Africoid and male and female, black/brown Caucasoid specimens. The lowest amount of binding was observed with blond, female Caucasoid specimens. Binding experiments also revealed that specific cocaine binding generally did not differ significantly between lipid-extracted hair and untreated hair, but bleaching of most hair specimens resulted in significant (p hair. In separate experiments with cocaine-treated hair specimens, digested samples were evaluated to determine if removal of the insoluble melanin fraction from soluble hair components provided a means of normalization of drug content and elimination of color bias. Removal of the insoluble melanin fraction was not effective in removal of significant amounts of cocaine, which indicated that the digestion process released bound cocaine into the digest solution. Overall, these experiments suggested that lipids in hair play a minor role in drug binding, whereas melanin functions as a major binding site for cocaine. Natural (ethnic) or artificial (bleaching

  7. Structures of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding Pocket And Transcription Activation Through Tyrosine Expulsion

    Energy Technology Data Exchange (ETDEWEB)

    Newberry, K.J.; Huffman, J.L.; Miller, M.C.; Vazquez-Laslop, N.; Neyfakh, A.A.; Brennan, R.G.

    2009-05-22

    BmrR is a member of the MerR family and a multidrug binding transcription factor that up-regulates the expression of the bmr multidrug efflux transporter gene in response to myriad lipophilic cationic compounds. The structural mechanism by which BmrR binds these chemically and structurally different drugs and subsequently activates transcription is poorly understood. Here, we describe the crystal structures of BmrR bound to rhodamine 6G (R6G) or berberine (Ber) and cognate DNA. These structures reveal each drug stacks against multiple aromatic residues with their positive charges most proximal to the carboxylate group of Glu-253 and that, unlike other multidrug binding pockets, that of BmrR is rigid. Substitution of Glu-253 with either alanine (E253A) or glutamine (E253Q) results in unpredictable binding affinities for R6G, Ber, and tetraphenylphosphonium. Moreover, these drug binding studies reveal that the negative charge of Glu-253 is not important for high affinity binding to Ber and tetraphenylphosphonium but plays a more significant, but unpredictable, role in R6G binding. In vitro transcription data show that E253A and E253Q are constitutively active, and structures of the drug-free E253A-DNA and E253Q-DNA complexes support a transcription activation mechanism requiring the expulsion of Tyr-152 from the multidrug binding pocket. In sum, these data delineate the mechanism by which BmrR binds lipophilic, monovalent cationic compounds and suggest the importance of the redundant negative electrostatic nature of this rigid drug binding pocket that can be used to discriminate against molecules that are not substrates of the Bmr multidrug efflux pump.

  8. Gap and channeled plasmons in tapered grooves: a review

    DEFF Research Database (Denmark)

    Smith, C. L. C.; Stenger, Nicolas; Kristensen, Anders

    2015-01-01

    ) that are confined laterally between the tapered groove sidewalls and propagate either along the groove axis or normal to the planar surface, and channeled plasmon polaritons (CPPs) that occupy the tapered groove profile and propagate exclusively along the groove axis. Both GSPs and CPPs exhibit an assortment...

  9. Receptor binding peptides for target-selective delivery of nanoparticles encapsulated drugs

    Directory of Open Access Journals (Sweden)

    Accardo A

    2014-03-01

    Full Text Available Antonella Accardo,1 Luigi Aloj,2 Michela Aurilio,2 Giancarlo Morelli,1 Diego Tesauro11Centro interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPeB, Department of Pharmacy and Istituto di Biostrutture e Bioimmagini - Consiglio Nazionale delle Ricerche (IBB CNR, University of Naples “Federico II”, 2Department of Nuclear Medicine, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione “G. Pascale”, Napoli, ItalyAbstract: Active targeting by means of drug encapsulated nanoparticles decorated with targeting bioactive moieties represents the next frontier in drug delivery; it reduces drug side effects and increases the therapeutic index. Peptides, based on their chemical and biological properties, could have a prevalent role to direct drug encapsulated nanoparticles, such as liposomes, micelles, or hard nanoparticles, toward the tumor tissues. A considerable number of molecular targets for peptides are either exclusively expressed or overexpressed on both cancer vasculature and cancer cells. They can be classified into three wide categories: integrins; growth factor receptors (GFRs; and G-protein coupled receptors (GPCRs. Therapeutic agents based on nanovectors decorated with peptides targeting membrane receptors belonging to the GPCR family overexpressed by cancer cells are reviewed in this article. The most studied targeting membrane receptors are considered: somatostatin receptors; cholecystokinin receptors; receptors associated with the Bombesin like peptides family; luteinizing hormone-releasing hormone receptors; and neurotensin receptors. Nanovectors of different sizes and shapes (micelles, liposomes, or hard nanoparticles loaded with doxorubicin or other cytotoxic drugs and externally functionalized with natural or synthetic peptides are able to target the overexpressed receptors and are described based on their formulation and in vitro and in vivo behaviors.Keywords: receptors binding peptides, drug delivery

  10. Effect of bioceramic functional groups on drug binding and release kinetics

    Science.gov (United States)

    Trujillo, Christopher

    Bioceramics have been studied extensively as drug delivery systems (DDS). Those studies have aimed to tailor the drug binding and release kinetics to successfully treat infections and other diseases. This research suggests that the drug binding and release kinetics are predominantly driven by the functional groups available on the surface of a bioceramic. The goal of the present study is to explain the role of silicate and phosphate functional groups in drug binding to and release kinetics from bioceramics. alpha-cristobalite (Cris; SiO2) particles (90-150 microm) were prepared and doped with 0 microg (P-0), 39.1 microg (P-39.1), 78.2 microg (P-78.2), 165.5 microg (P-165.5) or 331 microg (P-331) of P 2O5 per gram Cris, using 85% orthophosphoric (H3PO 4) acid and thermal treatment. The material structure was analyzed using X-ray diffraction (XRD) with Rietveld Refinement and Fourier Transform Infrared (FTIR) spectroscopy with Gaussian fitting. XRD demonstrated an increase from sample P-0 (170.5373 A3) to P-331 (170.6466 A 3) in the unit cell volume as the P2O5 concentration increased in the material confirming phosphate silicate substitution in Cris. Moreover, FTIR showed the characteristic bands of phosphate functional groups of nu4 PO4/O-P-O bending, P-O-P stretching, P-O-P bending, P=O stretching, and P-O-H bending in doped Cris indicating phosphate incorporation in the silicate structure. Furthermore, FTIR showed that the nu4 PO4/O-P-O bending band around 557.6 cm-1 and P=O stretching band around 1343.9 cm-1 increased in area for samples P-39.1 to P-331 from 3.5 to 10.5 and from 10.1 to 22.4, respectively due to phosphate doping. In conjunction with the increase of the nu4 PO4/O-P-O bending band and P=O stretching band, a decrease in area of the O-Si-O bending bands around 488.1 and 629.8 cm-1 was noticed for samples P-39.1 to P-331 from 5 to 2 and from 11.8 to 5.4, respectively. Furthermore, Cris samples (200 mg, n=5 for each sample) were immersed separately in

  11. Crystallographic analysis of TPP riboswitch binding by small-molecule ligands discovered through fragment-based drug discovery approaches.

    Science.gov (United States)

    Warner, Katherine Deigan; Ferré-D'Amaré, Adrian R

    2014-01-01

    Riboswitches are structured mRNA elements that regulate gene expression in response to metabolite or second-messenger binding and are promising targets for drug discovery. Fragment-based drug discovery methods have identified weakly binding small molecule "fragments" that bind a thiamine pyrophosphate (TPP) riboswitch. However, these fragments require substantial chemical elaboration into more potent, drug-like molecules. Structure determination of the fragments bound to the riboswitch is the necessary next step. In this chapter, we describe the methods for co-crystallization and structure determination of fragment-bound TPP riboswitch structures. We focus on considerations for screening crystallization conditions across multiple crystal forms and provide guidance for building the fragment into the refined crystallographic model. These methods are broadly applicable for crystallographic analyses of any small molecules that bind structured RNAs.

  12. Development of New Drugs for an Old Target — The Penicillin Binding Proteins

    Directory of Open Access Journals (Sweden)

    André Luxen

    2012-10-01

    Full Text Available The widespread use of β-lactam antibiotics has led to the worldwide appearance of drug-resistant strains. Bacteria have developed resistance to β-lactams by two main mechanisms: the production of β-lactamases, sometimes accompanied by a decrease of outer membrane permeability, and the production of low-affinity, drug resistant Penicillin Binding Proteins (PBPs. PBPs remain attractive targets for developing new antibiotic agents because they catalyse the last steps of the biosynthesis of peptidoglycan, which is unique to bacteria, and lies outside the cytoplasmic membrane. Here we summarize the “current state of the art” of non-β-lactam inhibitors of PBPs, which have being developed in an attempt to counter the emergence of β-lactam resistance. These molecules are not susceptible to hydrolysis by β-lactamases and thus present a real alternative to β-lactams. We present transition state analogs such as boronic acids, which can covalently bind to the active serine residue in the catalytic site. Molecules containing ring structures different from the β-lactam-ring like lactivicin are able to acylate the active serine residue. High throughput screening methods, in combination with virtual screening methods and structure based design, have allowed the development of new molecules. Some of these novel inhibitors are active against major pathogens, including methicillin-resistant Staphylococcus aureus (MRSA and thus open avenues new for the discovery of novel antibiotics.

  13. New metal based drugs: Spectral, electrochemical, DNA-binding, surface morphology and anticancer activity properties

    Science.gov (United States)

    Çeşme, Mustafa; Gölcü, Aysegul; Demirtaş, Ibrahim

    2015-01-01

    The NSAID piroxicam (PRX) drug was used for complex formation reactions with Cu(II), Zn(II) and Pt(II) metal salts have been synthesized. Then, these complexes have been characterized by spectroscopic and analytical techniques. Thermal behavior of the complexes were also investigated. The electrochemical properties of all complexes have been investigated by cyclic voltammetry (CV) using glassy carbon electrode. The biological activity of the complexes has been evaluated by examining their ability to bind to fish sperm double strand DNA (FSFSdsDNA) with UV spectroscopy. UV studies of the interaction of the PRX and its complexes with FSdsDNA have shown that these compounds can bind to FSdsDNA. The binding constants of the compounds with FSdsDNA have also been calculated. The morphology of the FSdsDNA, PRX, metal ions and metal complexes has been investigated by scanning electron microscopy (SEM). To get the SEM images, the interaction of compounds with FSdsDNA has been studied by means of differential pulse voltammetry (DPV) at FSdsDNA modified pencil graphite electrode (PGE). The decrease in intensity of the guanine oxidation signals has been used as an indicator for the interaction mechanism. The effect of proliferation PRX and complexes were examined on the HeLA and C6 cells using real-time cell analyzer with four different concentrations.

  14. Concerted intercalation and minor groove recognition of DNA by a homodimeric thiazole orange dye

    DEFF Research Database (Denmark)

    Bunkenborg, Jakob; Gadjev, N I; Deligeorgiev, T

    2000-01-01

    The thiazole orange dye TOTO binds to double-stranded DNA (dsDNA) by a sequence selective bis-intercalation. Each chromophore is sandwiched between two base pairs in a (5'-CpT-3'):(5'-ApG-3') site, and the linker spans two base pairs in the minor groove. We have used one- and two-dimensional NMR...

  15. Determination of the cationic amphiphilic drug-DNA binding mode and DNA-assisted fluorescence resonance energy transfer amplification.

    Science.gov (United States)

    Yaseen, Zahid; Banday, Abdul Rouf; Hussain, Mohammed Aamir; Tabish, Mohammad; Kabir-ud-Din

    2014-03-25

    Understanding the mechanism of drug-DNA binding is crucial for predicting the potential genotoxicity of drugs. Agarose gel electrophoresis, absorption, steady state fluorescence, and circular dichroism have been used in exploring the interaction of cationic amphiphilic drugs (CADs) such as amitriptyline hydrochloride (AMT), imipramine hydrochloride (IMP), and promethazine hydrochloride (PMT) with calf thymus or pUC19 DNA. Agarose gel electrophoresis assay, along with absorption and steady state fluorescence studies, reveal interaction between the CADs and DNA. A comparative study of the drugs with respect to the effect of urea, iodide induced quenching, and ethidium bromide (EB) exclusion assay reflects binding of CADs to the DNA primarily in an intercalative fashion. Circular dichroism data also support the intercalative mode of binding. Besides quenching, there is fluorescence exchange energy transfer (FRET) in between CADs and EB using DNA as a template.

  16. The antiviral drug acyclovir is a slow-binding inhibitor of (D)-amino acid oxidase.

    Science.gov (United States)

    Katane, Masumi; Matsuda, Satsuki; Saitoh, Yasuaki; Sekine, Masae; Furuchi, Takemitsu; Koyama, Nobuhiro; Nakagome, Izumi; Tomoda, Hiroshi; Hirono, Shuichi; Homma, Hiroshi

    2013-08-20

    d-Amino acid oxidase (DAO) is a degradative enzyme that is stereospecific for d-amino acids, including d-serine and d-alanine, which are believed to be coagonists of the N-methyl-d-aspartate (NMDA) receptor. To identify a new class of DAO inhibitor(s) that can be used to elucidate the molecular details of the active site environment of DAO, manifold biologically active compounds of microbial origin and pre-existing drugs were screened for their ability to inhibit DAO activity, and several compounds were identified as candidates. One of these compounds, acyclovir (ACV), a well-known antiviral drug used for the treatment of herpesvirus infections, was characterized and evaluated as a novel DAO inhibitor in vitro. Analysis showed that ACV acts on DAO as a reversible slow-binding inhibitor, and interestingly, the time required to achieve equilibrium between DAO, ACV, and the DAO/ACV complex was highly dependent on temperature. The binding mechanism of ACV to DAO was investigated in detail by several approaches, including kinetic analysis, structural modeling of DAO complexed with ACV, and site-specific mutagenesis of an active site residue postulated to be involved in the binding of ACV. The results confirm that ACV is a novel, active site-directed inhibitor of DAO that can be a valuable tool for investigating the structure-function relationships of DAO, including the molecular details of the active site environment of DAO. In particular, it appears that ACV can serve as an active site probe to study the structural basis of temperature-induced conformational changes of DAO.

  17. Drug binding and mobility relating to the thermal fluctuation in fluid lipid membranes

    Science.gov (United States)

    Okamura, Emiko; Yoshii, Noriyuki

    2008-12-01

    Drug binding and mobility in fluid lipid bilayer membranes are quantified in situ by using the multinuclear solution NMR combined with the pulsed-field-gradient technique. One-dimensional and pulsed-field-gradient F19 and H1 NMR signals of an anticancer drug, 5-fluorouracil (5FU) are analyzed at 283-313 K in the presence of large unilamellar vesicles (LUVs) of egg phosphatidylcholine (EPC) as model cell membranes. The simultaneous observation of the membrane-bound and free 5FU signals enables to quantify in what amount of 5FU is bound to the membrane and how fast 5FU is moving within the membrane in relation to the thermal fluctuation of the soft, fluid environment. It is shown that the mobility of membrane-bound 5FU is slowed down by almost two orders of magnitude and similar to the lipid movement in the membrane, the movement closely related to the intramembrane fluidity. The mobility of 5FU and EPC is, however, not similar at 313 K; the 5FU movement is enhanced in the membrane as a result of the loose binding of 5FU in the lipid matrices. The membrane-bound fraction of 5FU is ˜0.1 and almost unaltered over the temperature range examined. It is also independent of the 5FU concentration from 2 to 30 mM with respect to the 40-50 mM LUV. The free energy of the 5FU binding is estimated at -4 to -2 kJ/mol, the magnitude always close to the thermal fluctuation, 2.4-2.6 kJ/mol.

  18. Ligand- and drug-binding studies of membrane proteins revealed through circular dichroism spectroscopy.

    Science.gov (United States)

    Siligardi, Giuliano; Hussain, Rohanah; Patching, Simon G; Phillips-Jones, Mary K

    2014-01-01

    A great number of membrane proteins have proven difficult to crystallise for use in X-ray crystallographic structural determination or too complex for NMR structural studies. Circular dichroism (CD) is a fast and relatively easy spectroscopic technique to study protein conformational behaviour. In this review examples of the applications of CD and synchrotron radiation CD (SRCD) to membrane protein ligand binding interaction studies are discussed. The availability of SRCD has been an important advancement in recent progress, most particularly because it can be used to extend the spectral region in the far-UV region (important for increasing the accuracy of secondary structure estimations) and for working with membrane proteins available in only small quantities for which SRCD has facilitated molecular recognition studies. Such studies have been accomplished by probing in the near-UV region the local tertiary structure of aromatic amino acid residues upon addition of chiral or non-chiral ligands using long pathlength cells of small volume capacity. In particular, this review describes the most recent use of the technique in the following areas: to obtain quantitative data on ligand binding (exemplified by the FsrC membrane sensor kinase receptor); to distinguish between functionally similar drugs that exhibit different mechanisms of action towards membrane proteins (exemplified by secretory phospholipase A2); and to identify suitable detergent conditions to observe membrane protein-ligand interactions using stabilised proteins (exemplified by the antiseptic transporter SugE). Finally, the importance of characterising in solution the conformational behaviour and ligand binding properties of proteins in both far- and near-UV regions is discussed. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding. © 2013.

  19. Micro Groove for Trapping of Flowing Cell

    Directory of Open Access Journals (Sweden)

    Yusuke Takahashi

    2015-06-01

    Full Text Available Micro grooves have been designed to trap a biological cell, which flows through a micro channel in vitro. Each micro groove of a rectangular shape (0.002 mm depth, 0.025 mm width and 0.2 mm length has been fabricated on the surface of the polydimethylsiloxane (PDMS disk with the photolithography technique. Variation has been made on the angle between the longitudinal direction of the groove and the flow direction: zero, 0.79, or 1.57 rad. A rectangular flow channel (0.1 mm depth x 5 mm width x 30 mm length has been constructed with a silicone film of 0.1 mm thick, which has been sandwiched by two transparent PDMS disks. Two types of biological cells were used in the test alternatively: C2C12 (mouse myoblast cell line originated with cross-striated muscle of C3H mouse, or 3T3-L1 (mouse fat precursor cells. A constant flow (2.8 x 10-11 m3/s of a suspension of cells was introduced with a syringe pump. The behavior of cells moving over the micro grooves was observed with an inverted phase contrast microscope. The results show that the cell is trapped with the micro grooves under the wall shear rate of 3 s-1 for a few seconds and that the trapped interval depends on the kind of cells.

  20. Biophysical Approaches Facilitate Computational Drug Discovery for ATP-Binding Cassette Proteins

    Science.gov (United States)

    Molinski, Steven V.; Bozóky, Zoltán; Iram, Surtaj H.

    2017-01-01

    Although membrane proteins represent most therapeutically relevant drug targets, the availability of atomic resolution structures for this class of proteins has been limited. Structural characterization has been hampered by the biophysical nature of these polytopic transporters, receptors, and channels, and recent innovations to in vitro techniques aim to mitigate these challenges. One such class of membrane proteins, the ATP-binding cassette (ABC) superfamily, are broadly expressed throughout the human body, required for normal physiology and disease-causing when mutated, yet lacks sufficient structural representation in the Protein Data Bank. However, recent improvements to biophysical techniques (e.g., cryo-electron microscopy) have allowed for previously “hard-to-study” ABC proteins to be characterized at high resolution, providing insight into molecular mechanisms-of-action as well as revealing novel druggable sites for therapy design. These new advances provide ample opportunity for computational methods (e.g., virtual screening, molecular dynamics simulations, and structure-based drug design) to catalyze the discovery of novel small molecule therapeutics that can be easily translated from computer to bench and subsequently to the patient's bedside. In this review, we explore the utility of recent advances in biophysical methods coupled with well-established in silico techniques towards drug development for diseases caused by dysfunctional ABC proteins. PMID:28409029

  1. Computational Assay of H7N9 Influenza Neuraminidase Reveals R292K Mutation Reduces Drug Binding Affinity

    Science.gov (United States)

    Woods, Christopher J.; Malaisree, Maturos; Long, Ben; McIntosh-Smith, Simon; Mulholland, Adrian J.

    2013-12-01

    The emergence of a novel H7N9 avian influenza that infects humans is a serious cause for concern. Of the genome sequences of H7N9 neuraminidase available, one contains a substitution of arginine to lysine at position 292, suggesting a potential for reduced drug binding efficacy. We have performed molecular dynamics simulations of oseltamivir, zanamivir and peramivir bound to H7N9, H7N9-R292K, and a structurally related H11N9 neuraminidase. They show that H7N9 neuraminidase is structurally homologous to H11N9, binding the drugs in identical modes. The simulations reveal that the R292K mutation disrupts drug binding in H7N9 in a comparable manner to that observed experimentally for H11N9-R292K. Absolute binding free energy calculations with the WaterSwap method confirm a reduction in binding affinity. This indicates that the efficacy of antiviral drugs against H7N9-R292K will be reduced. Simulations can assist in predicting disruption of binding caused by mutations in neuraminidase, thereby providing a computational `assay.'

  2. New modulated design and synthesis of chiral CuII/SnIV bimetallic potential anticancer drug entity: In vitro DNA binding and pBR322 DNA cleavage activity

    Science.gov (United States)

    Tabassum, Sartaj; Sharma, Girish Chandra; Arjmand, Farukh

    2012-05-01

    A new chiral ligand scaffold L derived from (R)-2-amino-2-phenyl ethanol and diethyl oxalate was isolated and thoroughly characterized by various spectroscopic methods. The ligand L was allowed to react with CuCl2·2H2O and NiCl2·6H2O to achieve monometallic complexes 1 and 2, respectively. Subsequently modulation of 1 and 2 was carried out in the presence of SnCl4·5H2O to obtain heterobimetallic potential drug candidates 3 and 4 possessing (CuII/SnIV and NiII/SnIV) metallic cores, respectively and characterized by elemental analysis and spectroscopic data including 1H, 13C and 119Sn NMR in case of 3 and 4. In vitro DNA binding studies revealed that complex 3 avidly binds to DNA as quantified by Kb and Ksv values. Complex 3 exhibits a remarkable DNA cleavage activity (concentration dependent) with pBR322 DNA and the cleavage activity of 3 was significantly enhanced in the presence of activators and follows the order H2O2 > Asc > MPA > GSH. Complex 3 cleave pBR322 DNA via hydrolytic pathway and accessible to major groove of DNA.

  3. Effect of anticonvulsant drugs on (/sup 35/S)t-butylbicyclophosphorothionate binding in vitro and ex vivo

    Energy Technology Data Exchange (ETDEWEB)

    Pitkaenen, A.; Riekkinen, P.J.; Saano, V.; Tuomisto, L.

    1987-01-01

    Using several concentrations of eight anticonvulsant drugs in clinical use (carbamazepine, clonazepam, phenytoin, phenobarbital, ethosuximide, primidone, sodium valproate, and D,L-..gamma..-vinyl GABA), we studied their abilities in vitro to displace (/sup 35/S)t-butylbicyclophosphorothionate (/sup 35/S-TBPS) from its binding site in a homogenate of rat brain. Thereafter ethosuximide (150 mg/kg), phenobarbital (30 mg/kg), clonazepam (0.3 mg/kg), or phenytoin (100 mg/kg) was injected intraperitoneally into rats for 16-20 days; and the effect of drug administration on /sup 35/S-TBPS binding was studied in the cortex and hippocampus ex vivo. Phenobarbital (100 ..mu..M, P<0.001), ethosuximide (500 ..mu..M, P<0.001), and phenytoin (40 ..mu..M, P<0.001) decreased the specific /sup 35/S-TBPS binding in vitro by 10-16%. After drug administration of phenobarbital (concentration in plasma 168 ..mu..M), the number of binding sites decreased and the binding affinity (p<0.05) in the cortex increased. Other anticonvulsants did not modulate /sup 35/S-TBPS binding in vitro at the concentration analogous to therapeutic plasma levels or ex vivo at the dose used. These results suggest that the use of phenobarbital may modulate the TBPS binding site, but the role of the present findings in the anticonvulsant action of phenobarbital needs to be further studied.

  4. Drug binding to the inactivated state is necessary but not sufficient for high-affinity binding to human ether-à-go-go-related gene channels.

    Science.gov (United States)

    Perrin, Mark J; Kuchel, Philip W; Campbell, Terence J; Vandenberg, Jamie I

    2008-11-01

    Drug block of the human ether-à-go-go-related gene K(+) channel (hERG) is the most common cause of acquired long QT syndrome, a disorder of cardiac repolarization that may result in ventricular tachycardia and sudden cardiac death. We investigated the open versus inactivated state dependence of drug block by using hERG mutants N588K and N588E, which shift the voltage dependence of inactivation compared with wild-type but in which the mutated residue is remote from the drug-binding pocket in the channel pore. Four high-affinity drugs (cisapride, dofetilide, terfenadine, and astemizole) demonstrated lower affinity for the inactivation-deficient N588K mutant hERG channel compared with N588E and wild-type hERG. Three of four low-affinity drugs (erythromycin, perhexiline, and quinidine) demonstrated no preference for N588E over N588K channels, whereas dl-sotalol was an example of a low-affinity state-dependent blocker. All five state-dependent blockers showed an even lower affinity for S620T mutant hERG (no inactivation) compared with N588K mutant hERG (greatly reduced inactivation). Computer modeling indicates that the reduced affinity for S620T compared with N588K and wild-type channels can be explained by the relative kinetics of drug block and unblock compared with the kinetics of inactivation and recovery from inactivation. We were also able to calculate, for the first time, the relative affinities for the inactivated versus the open state, which for the drugs tested here ranged from 4- to 70-fold. Our results show that preferential binding to the inactivated state is necessary but not sufficient for high-affinity binding to hERG channels.

  5. Musical groove modulates motor cortex excitability: a TMS investigation.

    Science.gov (United States)

    Stupacher, Jan; Hove, Michael J; Novembre, Giacomo; Schütz-Bosbach, Simone; Keller, Peter E

    2013-07-01

    Groove is often described as a musical quality that can induce movement in a listener. This study examines the effects of listening to groove music on corticospinal excitability. Musicians and non-musicians listened to high-groove music, low-groove music, and spectrally matched noise, while receiving single-pulse transcranial magnetic stimulation (TMS) over the primary motor cortex either on-beat or off-beat. We examined changes in the amplitude of the motor-evoked potentials (MEPs), recorded from hand and arm muscles, as an index of activity within the motor system. Musicians and non-musicians rated groove similarly. MEP results showed that high-groove music modulated corticospinal excitability, whereas no difference occurred between low-groove music and noise. More specifically, musicians' MEPs were larger with high-groove than low-groove music, and this effect was especially pronounced for on-beat compared to off-beat pulses. These results indicate that high-groove music increasingly engages the motor system, and the temporal modulation of corticospinal excitability with the beat could stem from tight auditory-motor links in musicians. Conversely, non-musicians' MEPs were smaller for high-groove than low-groove music, and there was no effect of on- versus off-beat pulses, potentially stemming from suppression of overt movement. In sum, high-groove music engages the motor system, and previous training modulates how listening to music with a strong groove activates the motor system.

  6. Profiling of drug binding proteins by monolithic affinity chromatography in combination with liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Zhang, Xuepei; Wang, Tongdan; Zhang, Hanzhi; Han, Bing; Wang, Lishun; Kang, Jingwu

    2014-09-12

    A new approach for proteome-wide profiling drug binding proteins by using monolithic capillary affinity chromatography in combination with HPLC-MS/MS is reported. Two immunosuppresive drugs, namely FK506 and cyclosporin A, were utilized as the experimental models for proof-of-concept. The monolithic capillary affinity columns were prepared through a single-step copolymerization of the drug derivatives with glycidyl methacrylate and ethylene dimethacrylate. The capillary chromatography with the affinity monolithic column facilitates the purification of the drug binding proteins from the cell lysate. By combining the capillary affinity column purification and the shot-gun proteomic analysis, totally 33 FK506- and 32 CsA-binding proteins including all the literature reported target proteins of these two drugs were identified. Among them, two proteins, namely voltage-dependent anion-selective channel protein 1 and serine/threonine-protein phosphatase PGAM5 were verified by using the recombinant proteins. The result supports that the monolithic capillary affinity chromatography is likely to become a valuable tool for profiling of binding proteins of small molecular drugs as well as bioactive compounds.

  7. Mixed convection in a baffled grooved channel

    Indian Academy of Sciences (India)

    Aayush K Sharma; Pallab S Mahapatra; Nirmal K Manna; Koushik Ghosh

    2015-05-01

    In the present numerical work, flow structure and heat transfer characteristics are investigated in a baffled grooved channel, differentially heated from the sides. The baffle is placed vertically downward from the top wall of grooved channel geometry, with the motive of diverting outside forced flow towards the inside of the square cavity. In-house CFD code based on finite volume method has been used to solve the 2D equations of continuity, momentum and energy. The effect of change in baffle position and height is investigated in the range of Richardson numbers 0.1 to 10. For the present study, external flow from both left and right of the grooved channel are considered. A remarkable enhancement of heat transfer is observed in presence of baffle. The study has also pointed out that for optimal performance, the position and height of the baffle need to be adjusted depending on the direction of external flow.

  8. Resistance Patterns Associated with HCV NS5A Inhibitors Provide Limited Insight into Drug Binding

    Directory of Open Access Journals (Sweden)

    Moheshwarnath Issur

    2014-11-01

    Full Text Available Direct-acting antivirals (DAAs have significantly improved the treatment of infection with the hepatitis C virus. A promising class of novel antiviral agents targets the HCV NS5A protein. The high potency and broad genotypic coverage are favorable properties. NS5A inhibitors are currently assessed in advanced clinical trials in combination with viral polymerase inhibitors and/or viral protease inhibitors. However, the clinical use of NS5A inhibitors is also associated with new challenges. HCV variants with decreased susceptibility to these drugs can emerge and compromise therapy. In this review, we discuss resistance patterns in NS5A with focus prevalence and implications for inhibitor binding.

  9. A Case of Right Atrioventricular Groove Paraganglioma

    Institute of Scientific and Technical Information of China (English)

    Yi ZHANG; Tie-cheng PAN

    2009-01-01

    @@ Cardiac paraganglioma is an extremely rare clinical en-tities of the heart. The usual investigations for pheochro-mocytoma are necessary, however the most useful, spe-cific to primary cardiac tumors, are coronary angiogra-phy and echocardiography. While complete surgical ex-cision is the standard treatment of mainstay. We report a case of a 55-year-old woman with cardiac paraganglioma located in fight atriaoventricular groove of the heart. As we know, this is the first case that cardiac paraganglioma located in fight atriaoventricular groove of the heart in English literature.

  10. Graphene Plasmons in Triangular Wedges and Grooves

    DEFF Research Database (Denmark)

    Gonçalves, P. A. D.; Dias, E. J. C.; Xiao, Sanshui

    2016-01-01

    and electric-field distributions. We have found that the dispersion of wedge/groove graphene plasmons follows the same functional dependence as their flat-graphene plasmon counterparts, but now scaled by a (purely) geometric factor in which all the information about the system’s geometry is contained. We...... and tunability of graphene plasmons guided along the apex of a graphene-covered dielectric wedge or groove. In particular, we present a quasi-analytic model to describe the plasmonic eigenmodes in such a system, including the complete determination of their spectrum and corresponding induced potential...

  11. Rectangular-to-circular groove waveguide junction

    Institute of Scientific and Technical Information of China (English)

    CUI; Licheng; (崔立成); YANG; Hongsheng; (杨鸿生)

    2003-01-01

    Mode matching method is used to analyze the scattering characteristics of the rectangular-to-circular groove waveguide junction. Firstly, the scattering matrix equation is obtained by matching the electromagnetic fields at the boundary of the junction. The scattering coefficients can be obtained from the equation. Secondly the scattering characteristics of the iris with rectangular window positioned in circular groove waveguide are briefly analyzed. Thirdly, the convergent problem is discussed and the numerical results are given. At last experiment is made and good agreement is found between the calculated results and the measured results.

  12. Binding of the neuroleptic drug, gabapentin, to bovine serum albumin: Insights from experimental and computational studies

    Energy Technology Data Exchange (ETDEWEB)

    Jalali, Fahimeh, E-mail: fahimehjalali@yahoo.com [Department of Chemistry, Razi University, 67346 Kermanshah (Iran, Islamic Republic of); Dorraji, Parisa S. [Department of Chemistry, Razi University, 67346 Kermanshah (Iran, Islamic Republic of); Mahdiuni, Hamid [Department of Biology, Razi University, 67346 Kermanshah (Iran, Islamic Republic of)

    2014-04-15

    The interaction between antiepileptic drug, gabapentin (GP), and bovin serum albumin (BSA) was studied by spectroscopic and computational methods. The native fluorescence of BSA was quenched by GP. Stern–Volmer quenching constant was calculated at different temperatures which suggested a static mechanism. The association constant (K{sub a}) was calculated from fluorescence quenching studies, which increased with temperature rising. GP competed well with warfarine for hydrophobic subdomain IIA (Sudlow's site I) on the protein. Enthalpy and entropy changes during the interaction of GP with BSA were obtained using van't Hoff plot, which showed an entropy-driven process and involvement of hydrophobic forces (ΔH>0 and ΔS>0). Synchronous fluorescence measurements of BSA solution in the presence of GP showed a considerable blue shift when Δλ=15 nm, therefore, GP interacts with tyrosine-rich sites on BSA. Optimized docked model of BSA–GP mixture confirmed the experimental results. -- Highlights: • Interaction of gabapentin and bovine serum albumin (BSA) is investigated by spectroscopic techniques. • Gabapentin can quench the fluorescence of BSA through a static quenching procedure. • The binding of gabapentin to BSA is driven mainly by hydrophobic interactions. • Subdomain IIA (Sudlow's site I) of BSA is found to be the main binding site for gabapentin. • Molecular docking modeling confirmed the experimental results.

  13. The pleuromutilin drugs tiamulin and valnemulin bind to the RNA at the peptidyl transferase centre on the ribosome

    DEFF Research Database (Denmark)

    Poulsen, S M; Karlsson, M; Johansson, L B

    2001-01-01

    The pleuromutilin antibiotic derivatives, tiamulin and valnemulin, inhibit protein synthesis by binding to the 50S ribosomal subunit of bacteria. The action and binding site of tiamulin and valnemulin was further characterized on Escherichia coli ribosomes. It was revealed that these drugs...... results that tiamulin and valnemulin interact with the rRNA in the peptidyl transferase slot on the ribosomes in which they prevent the correct positioning of the CCA-ends of tRNAs for peptide transfer....

  14. Multivariate Analysis of Side Effects of Drug Molecules Based on Knowledge of Protein Bindings and ProteinProtein Interactions.

    Science.gov (United States)

    Hasegawa, Kiyoshi; Funatsu, Kimito

    2014-12-01

    Here, we examined the relationships between 969 side effects associated with 658 drugs and their 1368 human protein targets using our hybrid approaches. Firstly, L-shaped PLS (LPLS) was used to construct a multivariate model of side effects and protein bindings of drug molecules. LPLS is an extension of standard PLS regression, where, in addition to the response matrix Y and the regressor matrix X, an extra data matrix Z is constructed that summarizes the background information of X. X and Y are matrices comprising drugs-target proteins, and drugs-side effects, respectively. The Z matrix is the proteinprotein interaction data. From the loading plot of Y, we could identify two remarkable side effects (urinary incontinence and increased salivation) From the corresponding loading plot of X, the responsible protein targets causing each side effect could be estimated (sodium channels and gamma-aminobutyric acid (GABA) receptors). The loading plot of the Z matrix indicated that the GABA receptors interact with each other and they heavily influence the side effect of increased salivation. Secondly, Bayesian classifier methods were separately applied to the cases of the two side effects. That is, the Bayesian classifier method was used to classify drug molecules as binding or not binding to the responsible protein targets associated with each side effect. Using atom-coloring techniques, it was possible to estimate which fragments on the drug molecule might cause the specific side effects. This information is valuable for drug design to avoid specific side effects.

  15. Genetically encoded photocrosslinkers locate the high-affinity binding site of antidepressant drugs in the human serotonin transporter

    DEFF Research Database (Denmark)

    Rannversson, Hafsteinn; Andersen, Jacob; Hall, Lena Sørensen;

    2016-01-01

    Despite the well-established role of the human serotonin transporter (hSERT) in the treatment of depression, the molecular details of antidepressant drug binding are still not fully understood. Here we utilize amber codon suppression in a membrane-bound transporter protein to encode photocrosslin......Despite the well-established role of the human serotonin transporter (hSERT) in the treatment of depression, the molecular details of antidepressant drug binding are still not fully understood. Here we utilize amber codon suppression in a membrane-bound transporter protein to encode...

  16. Role of phospholipids in drug-LDL bindings as studied by high-performance frontal analysis/capillary electrophoresis.

    Science.gov (United States)

    Kuroda, Yukihiro; Watanabe, Yoshinori; Shibukawa, Akimasa; Nakagawa, Terumichi

    2003-01-15

    The binding study between basic drugs ((S)-verapamil (VER) and (S)-propranolol (PRO)) and phospholipid liposomes was performed by using high-performance frontal analysis/capillary electrophoresis (HPFA/CE) in order to investigate the effect of oxidative modification of low-density lipoprotein (LDL) upon drug-binding affinity from molecule-based viewpoint. 1-Palmitoyl-2-oleoyl-phosphatidylcholine (POPC, 16:0, 18:1), 1-palmitoyl-2-linoleoyl-phosphatidylcholine (PLPC, 16:0, 18:2), dilauloyl-phosphatidylcholine (DLaPC, 12:0, 12:0), 1-palmitoyl-2-oleoyl-phosphatidyl-glycerol (POPG, 16:0, 18:1), and 1-palmitoyl-sn-glycero-3-phosphocholine (monoPPC, 16:0) were used to prepare the model liposomes. At physiological pH (pH 7.4), the model liposome prepared from POPG+POPC had negative net charges, while the total net charge of the other model liposomes (POPC liposome, PLPC liposome, DLaPC liposome, and monoPPC+POPC liposome) was zero. The drug and the model liposome mixed solutions were subjected to HPFA/CE, and the total binding affinities (nK) were calculated. The nK values of VER and PRO to POPG+POPC liposome were more than six and 10 times higher than those of other liposomes, respectively. On the other hand, the nK values of the model drugs to POPC liposome, PLPC liposome, DLaPC liposome and monoPPC+POPC liposome showed small differences less than twice. These results indicate that the electrostatic interaction plays an important effect on drug-liposome binding, and suggest that the increase in the negative charge of LDL phospholipids gives more significant effect on the drug-binding affinity of the basic drugs than the acyl-chain structure.

  17. Appraisal of transverse nasal groove: A study

    Directory of Open Access Journals (Sweden)

    Belagola D Sathyanarayana

    2012-01-01

    Full Text Available Background: Transverse nasal groove is a condition of cosmetic concern which awaits due recognition and has been widely described as a shallow groove that extends transversely over the dorsum of nose. However, we observed variations in the clinical presentations of this entity, hitherto undescribed in literature. Aims: We conducted a clinicoepidemiological study of transverse nasal lesions in patients attending our outpatient department. Methods: We conducted a prospective observational study. We screened all patients attending our out-patient department for presence of transverse nasal lesions, signs of any dermatosis and associated other skin conditions. Results: One hundred patients were recruited in the study. Females (80% predominated over males. Most patients were of 15-45 years age group (70%. Majority of the transverse nasal lesions were classical transverse nasal groove (39% and others included transverse nasal line (28%, strip (28%, ridge (4% and loop (1%. Seborrhoeic diathesis was the most common condition associated with transverse nasal lesion. Conclusions: Occurrence of transverse nasal line, strip, ridge and loop, in addition to classical transverse nasal groove implies that latter is actually a subset of transverse nasal lesions. Common association of this entity with seborrheic dermatitis, seborrhea and dandruff raises a possibility of whether transverse nasal lesion is a manifestation of seborrheic diathesis.

  18. Optimization of Grooved Micromixer for Microengineering Technologies

    DEFF Research Database (Denmark)

    Sabotin, I.; Tristo, G.; Bissacco, Giuliano

    2013-01-01

    Due to the absence of turbulent flow and the slow diffusion process, mixing of solutions at micro-scale is a difficult task. This paper describes the optimization route towards the efficient design of a bottom grooved micromixer. Based on thoroughly discussed mixing mechanisms, the optimization w...

  19. Crystal Structure of an Integron Gene Cassette-Associated Protein from Vibrio cholerae Identifies a Cationic Drug-Binding Module

    Energy Technology Data Exchange (ETDEWEB)

    Deshpande, Chandrika N.; Harrop, Stephen J.; Boucher, Yan; Hassan, Karl A.; Di Leo, Rosa; Xu, Xiaohui; Cui, Hong; Savchenko, Alexei; Chang, Changsoo; Labbate, Maurizio; Paulsen, Ian T.; Stokes, H.W.; Curmi, Paul M.G.; Mabbutt, Bridget C. (MIT); (UT-Australia); (Macquarie); (Toronto); (New South)

    2012-02-15

    The direct isolation of integron gene cassettes from cultivated and environmental microbial sources allows an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. A structural approach is being exploited to investigate the modularity and function of novel integron gene cassettes. We report the 1.8 {angstrom} crystal structure of Cass2, an integron-associated protein derived from an environmental V. cholerae. The structure defines a monomeric beta-barrel protein with a fold related to the effector-binding portion of AraC/XylS transcription activators. The closest homologs of Cass2 are multi-drug binding proteins, such as BmrR. Consistent with this, a binding pocket made up of hydrophobic residues and a single glutamate side chain is evident in Cass2, occupied in the crystal form by polyethylene glycol. Fluorescence assays demonstrate that Cass2 is capable of binding cationic drug compounds with submicromolar affinity. The Cass2 module possesses a protein interaction surface proximal to its drug-binding cavity with features homologous to those seen in multi-domain transcriptional regulators. Genetic analysis identifies Cass2 to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and closely-related species. We propose that the Cass2 family not only has capacity to form functional transcription regulator complexes, but represents possible evolutionary precursors to multi-domain regulators associated with cationic drug compounds.

  20. Crystal structure of an integron gene cassette-associated protein from Vibrio cholerae identifies a cationic drug-binding module.

    Directory of Open Access Journals (Sweden)

    Chandrika N Deshpande

    Full Text Available The direct isolation of integron gene cassettes from cultivated and environmental microbial sources allows an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. A structural approach is being exploited to investigate the modularity and function of novel integron gene cassettes.We report the 1.8 Å crystal structure of Cass2, an integron-associated protein derived from an environmental V. cholerae. The structure defines a monomeric beta-barrel protein with a fold related to the effector-binding portion of AraC/XylS transcription activators. The closest homologs of Cass2 are multi-drug binding proteins, such as BmrR. Consistent with this, a binding pocket made up of hydrophobic residues and a single glutamate side chain is evident in Cass2, occupied in the crystal form by polyethylene glycol. Fluorescence assays demonstrate that Cass2 is capable of binding cationic drug compounds with submicromolar affinity. The Cass2 module possesses a protein interaction surface proximal to its drug-binding cavity with features homologous to those seen in multi-domain transcriptional regulators.Genetic analysis identifies Cass2 to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and closely-related species. We propose that the Cass2 family not only has capacity to form functional transcription regulator complexes, but represents possible evolutionary precursors to multi-domain regulators associated with cationic drug compounds.

  1. Estimation of Drug Binding to Brain Tissue: Methodology and in Vivo Application of a Distribution Assay in Brain Polar Lipids.

    Science.gov (United States)

    Belli, Sara; Assmus, Frauke; Wagner, Bjoern; Honer, Michael; Fischer, Holger; Schuler, Franz; Alvarez-Sánchez, Rubén

    2015-12-01

    The unbound drug concentration-effect relationship in brain is a key aspect in CNS drug discovery and development. In this work, we describe an in vitro high-throughput distribution assay between an aqueous buffer and a microemulsion of porcine brain polar lipids (BPL). The derived distribution coefficient LogDBPL was applied to the prediction of unbound drug concentrations in brain (Cu,b) and nonspecific binding to brain tissue. The in vivo relevance of the new assay was assessed for a large set of proprietary drug candidates and CNS drugs by (1) comparing observed compound concentrations in rat CSF with Cu,b calculated using the LogDBPL assay in combination with total drug brain concentrations, (2) comparing Cu,b derived from LogDBPL and total drug brain concentrations to Cu,b estimated using in vitro P-glycoprotein efflux ratio data and unbound drug plasma levels, and (3) comparing tissue nonspecific binding data from human brain autoradiography studies for 17 PET tracer candidates to distribution in BPL. In summary, the LogDBPL assay provides a predicted drug fraction unbound in brain tissue that is nearly identical to brain homogenate equilibrium dialysis with an estimation of in vivo Cu,b that is superior to LogD in octanol. LogDBPL complements the approach for predicting Cu,b based on in vitro P-glycoprotein efflux ratio and in vivo unbound plasma concentration and stands as a fast and cost-effective tool for nonspecific brain binding optimization of PET ligand candidates.

  2. Revealing kinetics and state-dependent binding properties of IKur-targeting drugs that maximize atrial fibrillation selectivity

    Science.gov (United States)

    Ellinwood, Nicholas; Dobrev, Dobromir; Morotti, Stefano; Grandi, Eleonora

    2017-09-01

    The KV1.5 potassium channel, which underlies the ultra-rapid delayed-rectifier current (IKur) and is predominantly expressed in atria vs. ventricles, has emerged as a promising target to treat atrial fibrillation (AF). However, while numerous KV1.5-selective compounds have been screened, characterized, and tested in various animal models of AF, evidence of antiarrhythmic efficacy in humans is still lacking. Moreover, current guidelines for pre-clinical assessment of candidate drugs heavily rely on steady-state concentration-response curves or IC50 values, which can overlook adverse cardiotoxic effects. We sought to investigate the effects of kinetics and state-dependent binding of IKur-targeting drugs on atrial electrophysiology in silico and reveal the ideal properties of IKur blockers that maximize anti-AF efficacy and minimize pro-arrhythmic risk. To this aim, we developed a new Markov model of IKur that describes KV1.5 gating based on experimental voltage-clamp data in atrial myocytes from patient right-atrial samples in normal sinus rhythm. We extended the IKur formulation to account for state-specificity and kinetics of KV1.5-drug interactions and incorporated it into our human atrial cell model. We simulated 1- and 3-Hz pacing protocols in drug-free conditions and with a [drug] equal to the IC50 value. The effects of binding and unbinding kinetics were determined by examining permutations of the forward (kon) and reverse (koff) binding rates to the closed, open, and inactivated states of the KV1.5 channel. We identified a subset of ideal drugs exhibiting anti-AF electrophysiological parameter changes at fast pacing rates (effective refractory period prolongation), while having little effect on normal sinus rhythm (limited action potential prolongation). Our results highlight that accurately accounting for channel interactions with drugs, including kinetics and state-dependent binding, is critical for developing safer and more effective pharmacological anti

  3. Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus.

    Science.gov (United States)

    Khurana, Ekta; Devane, Russell H; Dal Peraro, Matteo; Klein, Michael L

    2011-02-01

    The M2 protein of influenza A virus performs the crucial function of transporting protons to the interior of virions enclosed in the endosome. Adamantane drugs, amantadine (AMN) and rimantidine (RMN), block the proton conduction in some strains, and have been used for the treatment and prophylaxis of influenza A infections. The structures of the transmembrane (TM) region of M2 that have been solved in micelles using NMR (residues 23-60) (Schnell and Chou, 2008) and by X-ray crystallography (residues 22-46) (Stouffer et al., 2008) suggest different drug binding sites: external and internal for RMN and AMN, respectively. We have used molecular dynamics (MD) simulations to investigate the nature of the binding site and binding mode of adamantane drugs on the membrane-bound tetrameric M2-TM peptide bundles using as initial conformations the low-pH AMN-bound crystal structure, a high-pH model derived from the drug-free crystal structure, and the high-pH NMR structure. The MD simulations indicate that under both low- and high-pH conditions, AMN is stable inside the tetrameric bundle, spanning the region between residues Val27 to Gly34. At low pH the polar group of AMN is oriented toward the His37 gate, while under high-pH conditions its orientation exhibits large fluctuations. The present MD simulations also suggest that AMN and RMN molecules do not show strong affinity to the external binding sites.

  4. Vacuum Infusion Molding Process (Part 2 VIMP Based on Grooves)

    Institute of Scientific and Technical Information of China (English)

    ZHU Ying-dan; DENG Jing-lan; WANG Ji-hui; TAN Hua

    2003-01-01

    The optimal parameters for flow grooves and supply grooves were determined by a series of experiments , and the influences of various molding conditions on the mold filling process were analyzed. Furthermore ,the whole VIMP procedure based on grooves was introduced in detail taking the manufacture of a sandwich panel as an example.

  5. Elucidation of binding mechanism and identification of binding site for an anti HIV drug, stavudine on human blood proteins.

    Science.gov (United States)

    Sandhya, B; Hegde, Ashwini H; Seetharamappa, J

    2013-05-01

    The binding of stavudine (STV) to two human blood proteins [human hemoglobin (HHb) and human serum albumin (HSA)] was studied in vitro under simulated physiological conditions by spectroscopic methods viz., fluorescence, UV absorption, resonance light scattering, synchronous fluorescence, circular dichroism (CD) and three-dimensional fluorescence. The binding parameters of STV-blood protein were determined from fluorescence quenching studies. Stern-Volmer plots indicated the presence of static quenching mechanism in the interaction of STV with blood proteins. The values of n close to unity indicated that one molecule of STV bound to one molecule of blood protein. The binding process was found to be spontaneous. Analysis of thermodynamic parameters revealed the presence of hydrogen bond and van der Waals forces between protein and STV. Displacement experiments indicated the binding of STV to Sudlow's site I on HSA. Secondary structures of blood proteins have undergone changes upon interaction with STV as evident from the reduction of α-helices (from 46.11% in free HHb to 38.34% in STV-HHb, and from 66.44% in free HSA to 52.26% in STV-HSA). Further, the alterations in secondary structures of proteins in the presence of STV were confirmed by synchronous and 3D-fluorescence spectral data. The distance between the blood protein (donor) and acceptor (STV) was found to be 5.211 and 5.402 nm for STV-HHb and STV-HSA, respectively based on Föster's non-radiative energy transfer theory. Effect of some metal ions was also investigated. The fraction of STV bound to HSA was found to be 87.8%.

  6. Repositioning of Tyrosine Kinase Inhibitors as Antagonists of ATP-Binding Cassette Transporters in Anticancer Drug Resistance

    Directory of Open Access Journals (Sweden)

    Yi-Jun Wang

    2014-09-01

    Full Text Available The phenomenon of multidrug resistance (MDR has attenuated the efficacy of anticancer drugs and the possibility of successful cancer chemotherapy. ATP-binding cassette (ABC transporters play an essential role in mediating MDR in cancer cells by increasing efflux of drugs from cancer cells, hence reducing the intracellular accumulation of chemotherapeutic drugs. Interestingly, small-molecule tyrosine kinase inhibitors (TKIs, such as AST1306, lapatinib, linsitinib, masitinib, motesanib, nilotinib, telatinib and WHI-P154, have been found to have the capability to overcome anticancer drug resistance by inhibiting ABC transporters in recent years. This review will focus on some of the latest and clinical developments with ABC transporters, TKIs and anticancer drug resistance.

  7. Atomic modelling and systematic mutagenesis identify residues in multiple drug binding sites that are essential for drug resistance in the major Candida transporter Cdr1.

    Science.gov (United States)

    Nim, Shweta; Lobato, Lucia Gonzalez; Moreno, Alexis; Chaptal, Vincent; Rawal, Manpreet Kaur; Falson, Pierre; Prasad, Rajendra

    2016-11-01

    The ABC (ATP-Binding Cassette) transporter Cdr1 (Candida drug resistance 1) protein (Cdr1p) of Candida albicans, shows promiscuity towards the substrate it exports and plays a major role in antifungal resistance. It has two transmembrane domains (TMDs) comprising of six transmembrane helices (TMH) that envisage and confer the substrate specificity and two nucleotide binding domains (NBDs), interconnected by extracellular loops (ECLs) and intracellular loops (ICLs) Cdr1p. This study explores the diverse substrate specificity spectrum to get a deeper insight into the structural and functional features of Cdr1p. By screening with the variety of compounds towards an in-house TMH 252 mutant library of Cdr1p, we establish new substrates of Cdr1p. The localization of substrate-susceptible mutants in an ABCG5/G8 homology model highlights the common and specific binding pockets inside the membrane domain, where rhodamines and tetrazoliums mainly engage the N-moiety of Cdr1p, binding between TMH 2, 11 and surrounded by TMH 1, 5. Whereas, tin chlorides involve both N and C moieties located at the interface of TMH 2, 11, 1 and 5. Further, screening of the in house TMH mutant library of Cdr1p displays the TMH12 interaction with tetrazolium chloride, trimethyltin chloride and a Ca(2+) ionophore, A23187. In silico localization reveals a binding site at the TMH 12, 9 and 10 interface, which is widely exposed to the lipid interface. Together, for the first time, our study shows the molecular localization of Cdr1p substrates-binding sites and demonstrates the participation of TMH12 in a peripheral drug binding site.

  8. Solar cell with doped groove regions separated by ridges

    Energy Technology Data Exchange (ETDEWEB)

    Molesa, Steven Edward; Pass, Thomas; Kraft, Steve

    2017-01-31

    Solar cells with doped groove regions separated by ridges and methods of fabricating solar cells are described. In an example, a solar cell includes a substrate having a surface with a plurality of grooves and ridges. A first doped region of a first conductivity type is disposed in a first of the grooves. A second doped region of a second conductivity type, opposite the first conductivity type, is disposed in a second of the grooves. The first and second grooves are separated by one of the ridges.

  9. Impact of linker and conjugation chemistry on antigen binding, Fc receptor binding and thermal stability of model antibody-drug conjugates.

    Science.gov (United States)

    Acchione, Mauro; Kwon, Hyewon; Jochheim, Claudia M; Atkins, William M

    2012-01-01

    Antibody-drug conjugates (ADCs) with biotin as a model cargo tethered to IgG1 mAbs via different linkers and conjugation methods were prepared and tested for thermostability and ability to bind target antigen and Fc receptor. Most conjugates demonstrated decreased thermostability relative to unconjugated antibody, based on DSC, with carbohydrate and amine coupled ADCs showing the least effect compared with thiol coupled conjugates. A strong correlation between biotin-load and loss of stability is observed with thiol conjugation to one IgG scaffold, but the stability of a second IgG scaffold is relatively insensitive to biotin load. The same correlation for amine coupling was less significant. Binding of antibody to antigen and Fc receptor was investigated using surface plasmon resonance. None of the conjugates exhibited altered antigen affinity. Fc receptor FcγIIb (CD32b) interactions were investigated using captured antibody conjugate. Protein G and Protein A, known inhibitors of Fc receptor (FcR) binding to IgG, were also used to extend the analysis of the impact of conjugation on Fc receptor binding. H10NPEG4 was the only conjugate to show significant negative impact to FcR binding, which is likely due to higher biotin-load compared with the other ADCs. The ADC aHISNLC and aHISTPEG8 demonstrated some loss in affinity for FcR, but to much lower extent. The general insensitivity of target binding and effector function of the IgG1 platform to conjugation highlight their utility. The observed changes in thermostability require consideration for the choice of conjugation chemistry, depending on the system being pursued and particular application of the conjugate.

  10. Graphene Plasmons in Triangular Wedges and Grooves

    CERN Document Server

    Gonçalves, P A D; Xiao, Sanshui; Vasilevskiy, M I; Mortensen, N Asger; Peres, N M R

    2016-01-01

    The ability to effectively guide electromagnetic radiation below the diffraction limit is of the utmost importance in the prospect of all-optical plasmonic circuitry. Here, we propose an alternative solution to conventional metal-based plasmonics by exploiting the deep subwavelength confinement and tunability of graphene plasmons guided along the apex of a graphene-covered dielectric wedge or groove. In particular, we present a quasi-analytic model to describe the plasmonic eigenmodes in such a system, including the complete determination of their spectrum and corresponding induced potential and electric field distributions. We have found that the dispersion of wedge/groove graphene plasmons follows the same functional dependence as their flat-graphene plasmons counterparts, but now scaled by a (purely) geometric factor in which all the information about the system's geometry is contained. We believe our results pave the way for the development of novel custom-tailored photonic devices for subwavelength waveg...

  11. Grooving corrosion of seam welded oil pipelines

    Directory of Open Access Journals (Sweden)

    Mohamed Hanafy El-Sayed

    2014-10-01

    Full Text Available 24” pipeline carrying oil was failed in the form of longitudinal crack at the 6 O’clock position resulting in oil spill. The failed pipe was investigated to reveal the main cause of its failure. The procedure of investigation was built on studying the intact pipe, rupture area, parent material, and intact weld. Results of chemical analysis, mechanical properties, and microstructure of the pipe material were confirmed with the specified standard. Cracks were originated from weld defected sites, initiated by grooving corrosion, propagated by inertia at the normal designed pressure condition, and stopped when stress relief is attained. It is recommended to use high quality ERW pipe, with its seam weld line positioned around the 12 O’clock during installation, to minimize and decelerate grooving corrosion. It is also important to perform regular or routine inspection, on suitable intervals, determined by past experience.

  12. Diamond grooving of rapidly solidified optical aluminium

    Science.gov (United States)

    Abou-El-Hossein, Khaled; Hsu, Wei-Yao; Ghobashy, Sameh; Cheng, Yuan-Chieh; Mkoko, Zwelinzima

    2015-10-01

    Traditional optical aluminium grades such as Al 6061 are intensively used for making optical components for applications ranging from mould insert fabrication to laser machine making. However, because of their irregular microstructure and relative inhomogeneity of material properties at micro scale, traditional optical aluminium may exhibit some difficulties when ultra-high precision diamond turned. Inhomogeneity and micro-variation in the material properties combined with uneven and coarse microstructure may cause unacceptable surface finish and accelerated tool wear, especially in grooving operation when the diamond tool edge is fully immersed in the material surface. Recently, new grades of optical aluminium that are featured by their ultra-fine microstructure and improved material properties have been developed to overcome the problem of high tool wear rates. The new aluminium grades have been developed using rapid solidification process which results in extremely small grain sizes combined with improved mechanical properties. The current study is concerned with investigating the performance of single-point diamond turning when grooving two grades of rapidly solidified aluminium (RSA) grades: RSA905 which is a high-alloyed aluminium grade and RSA443 which has a high silicon content. In this study, two series of experiments employed to create radial microgrooves on the two RSA grades. The surface roughness obtained on the groove surface is measured when different combinations of cutting parameters are used. Cutting speed is varied while feed rate and depth of cut were kept constant. The results show that groove surface roughness produced on RSA443 is higher than that obtained on RSA905. Also, the paper reports on the effect of cutting speed on surface roughness for each RSA grade.

  13. Simplification of vector ray tracing by the groove function.

    Science.gov (United States)

    Hu, Zhongwen; Liu, Zuping; Wang, Qiuping

    2005-01-01

    Tracing rays through arbitrary diffraction gratings (including holographic gratings of the second generation fabricated on a curved substrate) by the vector form is somewhat complicated. Vector ray tracing utilizes the local groove density, the calculation of which highly depends on how the grooves are generated. Characterizing a grating by its groove function, available for almost arbitrary gratings, is much simpler than doing so by its groove density, essentially being a vector. Applying the concept of Riemann geometry, we give an expression of the groove density by the groove function. The groove function description of a grating can thus be incorporated into vector ray tracing, which is beneficial especially at the design stage. A unified explicit grating ray-tracing formalism is given as well.

  14. Evaluation of drug-muscarinic receptor affinities using cell membrane chromatography and radioligand binding assay in guinea pig jejunum membrane

    Institute of Scientific and Technical Information of China (English)

    Bing-xiang YUAN; Jin HOU; Lang-chong HE; Guang-de YANG

    2005-01-01

    Aim: To study if cell membrane chromatography (CMC) could reflect drug-receptor interaction and evaluate the affinity and competitive binding to muscarinic acetylcholine receptor (mAChR). Methods: The cell membrane stationary phase(CMSP) was prepared by immobilizing guinea pig jejunum cell membrane on the surface of a silica carrier, and was used for the rapid on-line chromatographic evaluation of ligand binding affinities to mAChR. The affinity to mAChR was also evaluated from radioligand binding assays (RBA) using the same jejunum membrane preparation. Results: The capacity factor (k') profiles in guinea pig jejunum CMSP were: (-)QNB (15.4)>(+)QNB (11.5)>atropine (5.35)>pirenzepine(5.26)>4-DAMP (4.45)>AF-DX 116 (4.18)>pilocarpine (3.93)>acetylcholine(1.31). These results compared with the affinity rank orders obtained from radioligand binding assays indicated that there wasa positive correlation (r2=0.8525, P<0.0001) between both data sets. Conclusion: The CMC method can be used to evaluate drug-receptor affinities for drug candidates.

  15. In vitro screening of psychoactive drugs by [(35)S]GTPgammaS binding in rat brain membranes.

    Science.gov (United States)

    Nonaka, Ryouichi; Nagai, Fumiko; Ogata, Akio; Satoh, Kanako

    2007-12-01

    We constructed a reproducible, simple, and small-scale determination method of the psychoactive drugs that acted directly on the monoamine receptor by measuring the activation of [(35)S]guanosine-5'-O-(3-thio)-triphosphate binding to guanine nucleotide-binding proteins (G proteins). This method can simultaneously measure the effects of three monoamines, namely dopamine (DA), serotonin (5-HT), and norepinephrine (NE), in rat brain membranes using a 96-well microplate. Activation of D(1) and D(2) receptors in striatal membranes by DA as well as 5-HT and NEalpha(2) receptors in cortical membranes could be measured. Of 12 tested phenethylamines, 2,5-dimethoxy-4-chlorophenethylamine (2C-C), 2,5-dimethoxy-4-ethylphenethylamine (2C-E), and 2,5-dimethoxy-4-iodophenethylamine (2C-I) stimulated G protein binding. The other phenethylamines did not affect G protein binding. All 7 tryptamines tested stimulated G protein binding with the following rank order of potency; 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT)>5-methoxy-N,N-diallyltryptamine (5-MeO-DALT)>5-methoxy-alpha-methyltryptamine (5-MeO-AMT)>or=5-methoxy-N,N-methylisopropyltryptamine (5-MeO-MIPT)>5-methoxy-N,N-diisopropyltryptamine (5-MeO-DIPT)>N,N-dipropyltryptamine (DPT)>or=alpha-methyltryptamine (AMT). This assay system was able to designate psychoactive drugs as prohibited substances in accordance with criteria set forth by the Tokyo Metropolitan government.

  16. Minor groove binder distamycin remodels chromatin but inhibits transcription.

    Directory of Open Access Journals (Sweden)

    Parijat Majumder

    Full Text Available The condensed structure of chromatin limits access of cellular machinery towards template DNA. This in turn represses essential processes like transcription, replication, repair and recombination. The repression is alleviated by a variety of energy dependent processes, collectively known as "chromatin remodeling". In a eukaryotic cell, a fine balance between condensed and de-condensed states of chromatin helps to maintain an optimum level of gene expression. DNA binding small molecules have the potential to perturb such equilibrium. We present herein the study of an oligopeptide antibiotic distamycin, which binds to the minor groove of B-DNA. Chromatin mobility assays and circular dichroism spectroscopy have been employed to study the effect of distamycin on chromatosomes, isolated from the liver of Sprague-Dawley rats. Our results show that distamycin is capable of remodeling both chromatosomes and reconstituted nucleosomes, and the remodeling takes place in an ATP-independent manner. Binding of distamycin to the linker and nucleosomal DNA culminates in eviction of the linker histone and the formation of a population of off-centered nucleosomes. This hints at a possible corkscrew type motion of the DNA with respect to the histone octamer. Our results indicate that distamycin in spite of remodeling chromatin, inhibits transcription from both DNA and chromatin templates. Therefore, the DNA that is made accessible due to remodeling is either structurally incompetent for transcription, or bound distamycin poses a roadblock for the transcription machinery to advance.

  17. Molecular Dynamics of Rab7::REP1::GGTase-II Ternary Complex and Identification of Their Putative Drug Binding Sites.

    Science.gov (United States)

    Sindhu, Meenakshi; Saini, Vandana; Piplani, Sakshi; Kumar, A

    2013-01-01

    The structure-function correlation of membrane proteins have been a difficult task, particularly in context to transient protein complexes. The molecular simulation of ternary complex of Rab7::REP1::GGTase-II was carried out to understand the basic structural events occurring during the prenylation event of Rab proteins, using the software YASARA. The study suggested that the C-terminus of Rab7 has to be in completely extended conformation during prenylation to reach the active site of RabGGTase-II. Also, attempt was made to find putative drug binding sites on the ternary complex of Rab7::REP1::GGTase-II using Q-SiteFinder programme. The comprehensive consensus probe generated by the program revealed a total of 10 major pockets as putative drug binding sites on Rab7::REP:: GGTase-II ternary complex. These pockets were found on REP protein and GGTase protein subunits. The Rab7 was found to be devoid of any putative drug binding sites in the ternary complex. The phylogenetic analysis of 60 Rab proteins of human was carried out using PHYLIP and study indicated the close phylogenetic relationship between Rab7 and Rab9 proteins of human and hence with further in silico study, the present observations can be extrapolated to Rab9 proteins. The study paves a good platform for further experimental verifications of the findings and other in silico studies like identifying the potential drug targets by searching the putative drug binding sites, generating pharmacophoric pattern, searching or constructing suitable ligand and docking studies.

  18. Entrapment of alpha1-acid glycoprotein in high-performance affinity columns for drug-protein binding studies.

    Science.gov (United States)

    Bi, Cong; Jackson, Abby; Vargas-Badilla, John; Li, Rong; Rada, Giana; Anguizola, Jeanethe; Pfaunmiller, Erika; Hage, David S

    2016-05-15

    A slurry-based method was developed for the entrapment of alpha1-acid glycoprotein (AGP) for use in high-performance affinity chromatography to study drug interactions with this serum protein. Entrapment was achieved based on the physical containment of AGP in hydrazide-activated porous silica supports and by using mildly oxidized glycogen as a capping agent. The conditions needed for this process were examined and optimized. When this type of AGP column was used in binding studies, the association equilibrium constant (Ka) measured by frontal analysis at pH 7.4 and 37°C for carbamazepine with AGP was found to be 1.0 (±0.5)×10(5)M(-1), which agreed with a previously reported value of 1.0 (±0.1)×10(5)M(-1). Binding studies based on zonal elution were conducted for several other drugs with such columns, giving equilibrium constants that were consistent with literature values. An entrapped AGP column was also used in combination with a column containing entrapped HSA in a screening assay format to compare the binding of various drugs to AGP and HSA. These results also agreed with previous data that have been reported in literature for both of these proteins. The same entrapment method could be extended to other proteins and to the investigation of additional types of drug-protein interactions. Potential applications include the rapid quantitative analysis of biological interactions and the high-throughput screening of drug candidates for their binding to a given protein.

  19. The novel antiepileptic drug levetiracetam (ucb L059) appears to act via a specific binding site in CNS membranes.

    Science.gov (United States)

    Noyer, M; Gillard, M; Matagne, A; Hénichart, J P; Wülfert, E

    1995-11-14

    Levetiracetam ((S)-alpha-ethyl-2-oxo-pyrrolidine acetamide, ucb L059) is a novel potential antiepileptic agent presently in clinical development with unknown mechanism of action. The finding that its anticonvulsant activity is highly stereoselective (Gower et al., 1992) led us to investigate the presence of specific binding sites for [3H]levetiracetam in rat central nervous system (CNS). Binding assays, performed on crude membranes, revealed the existence of a reversible, saturable and stereoselective specific binding site. Results obtained in hippocampal membranes suggest that [3H]levetiracetam labels a single class of binding sites (nH = 0.92 +/- 0.06) with modest affinity (Kd = 780 +/- 115 nM) and with a high binding capacity (Bmax = 9.1 +/- 1.2 pmol/mg protein). Similar Kd and Bmax values were obtained in other brain regions (cortex, cerebellum and striatum). ucb L060, the (R) enantiomer of levetiracetam, displayed about 1000 times less affinity for these sites. The binding of [3H]levetiracetam is confined to the synaptic plasma membranes in the central nervous system since no specific binding was observed in a range of peripheral tissues including heart, kidneys, spleen, pancreas, adrenals, lungs and liver. The commonly used antiepileptic drugs carbamazepine, phenytoin, valproate, phenobarbital and clonazepam, as well as the convulsant agent t-butylbicyclophosphorothionate (TBPS), picrotoxin and bicuculline did not displace [3H]levetiracetam binding. However, ethosuximide (pKi = 3.5 +/- 0.1), pentobarbital (pKi = 3.8 +/- 0.1), pentylenetetrazole (pKi = 4.1 +/- 0.1) and bemegride (pKi = 5.0 +/- 0.1) competed with [3H]levetiracetam with pKi values comparable to active drug concentrations observed in vivo. Structurally related compounds, including piracetam and aniracetam, also displaced [3H]levetiracetam binding. (S) Stereoisomer homologues of levetiracetam demonstrated a rank order of affinity for [3H]levetiracetam binding in correlation with their

  20. Increment in Drug Loading on an Antibody-Drug Conjugate Increases Its Binding to the Human Neonatal Fc Receptor in Vitro.

    Science.gov (United States)

    Brachet, Guillaume; Respaud, Renaud; Arnoult, Christophe; Henriquet, Corinne; Dhommée, Christine; Viaud-Massuard, Marie-Claude; Heuze-Vourc'h, Nathalie; Joubert, Nicolas; Pugnière, Martine; Gouilleux-Gruart, Valérie

    2016-04-04

    Antibody-drug conjugates, such as brentuximab vedotin (BTXv), are an innovative category of monoclonal antibodies. BTXv is bioconjugated via the chemical reduction of cysteine residues involved in disulfide bonds. Species of BTXv containing zero, two, four, six, or eight vedotin molecules per antibody coexist in the stock solution. We investigated the influence of drug loading on the binding of the antibody to FcRn, a major determinant of antibody pharmacokinetics in humans. We developed a hydrophobic interaction chromatography (HIC) method for separating the different species present in the stock solution of BTXv, and we purified and characterized the collected species before use. We assessed the binding of these different species to FcRn in a cellular assay based on flow cytometry and surface plasmon resonance. HIC separated the different species of BTXv and allowed their collection at adequate levels of purity. Physicochemical characterization showed that species with higher levels of drug loading tended to form more aggregates. FcRn binding assays showed that the most conjugated species, particularly those with saturated loading, interacted more strongly than unconjugated BTXv with the FcRn.

  1. Simple and Rapid Hollow Fiber Liquid Phase Microextraction Followed by High Performance Liquid Chromatography Method for Determination of Drug-protein Binding

    Institute of Scientific and Technical Information of China (English)

    XI Guo-chen; HU Shuang; BAI Xiao-hong

    2011-01-01

    A method was established using hollow fiber-liquid phase microextraction(HF-LPME) followed by high performance liquid chromatography(HPLC) to determine the concentration of the free(unbound) drug in the solution of the drug and protein.Measurements of drug-protein binding ratios and free drug concentrations were then analyzed with the Klotz equation to determine the equilibrium binding constant and number of binding sites for drug-protein interaction.The optimized method allows one to perform the efficient extraction and separation of free drug from protein-bound drug,protein,and other interfering substances.This approach was used to characterize the binding of the anticholinergic drugs atropine sulfate and scopolamine hydrobromide to proteins in human plasma and bovine serum albumin(BSA).The results demonstrate the utility of HF-LPME method for measuring free drug concentrations in protein-drug mixtures and determining the protein binding parameters of a pharmacologically important class of drugs.

  2. Substrate Binding Mode and its Implication on Drug Design for Botulinum Neurotoxin A

    Energy Technology Data Exchange (ETDEWEB)

    Kumaran, D.; Rawat, R; Ahmed, A; Swaminathan, S

    2008-01-01

    The seven antigenically distinct serotypes of Clostridium botulinum neurotoxins, the causative agents of botulism, block the neurotransmitter release by specifically cleaving one of the three SNARE proteins and induce flaccid paralysis. The Centers for Disease Control and Prevention (CDC) has declared them as Category A biowarfare agents. The most potent among them, botulinum neurotoxin type A (BoNT/A), cleaves its substrate synaptosome-associated protein of 25 kDa (SNAP-25). An efficient drug for botulism can be developed only with the knowledge of interactions between the substrate and enzyme at the active site. Here, we report the crystal structures of the catalytic domain of BoNT/A with its uncleavable SNAP-25 peptide 197QRATKM202 and its variant 197RRATKM202 to 1.5 A and 1.6 A, respectively. This is the first time the structure of an uncleavable substrate bound to an active botulinum neurotoxin is reported and it has helped in unequivocally defining S1 to S5? sites. These substrate peptides make interactions with the enzyme predominantly by the residues from 160, 200, 250 and 370 loops. Most notably, the amino nitrogen and carbonyl oxygen of P1 residue (Gln197) chelate the zinc ion and replace the nucleophilic water. The P1?-Arg198, occupies the S1? site formed by Arg363, Thr220, Asp370, Thr215, Ile161, Phe163 and Phe194. The S2? subsite is formed by Arg363, Asn368 and Asp370, while S3? subsite is formed by Tyr251, Leu256, Val258, Tyr366, Phe369 and Asn388. P4?-Lys201 makes hydrogen bond with Gln162. P5?-Met202 binds in the hydrophobic pocket formed by the residues from the 250 and 200 loop. Knowledge of interactions between the enzyme and substrate peptide from these complex structures should form the basis for design of potent inhibitors for this neurotoxin.

  3. Substrate binding mode and its implication on drug design for botulinum neurotoxin A.

    Directory of Open Access Journals (Sweden)

    Desigan Kumaran

    Full Text Available The seven antigenically distinct serotypes of Clostridium botulinum neurotoxins, the causative agents of botulism, block the neurotransmitter release by specifically cleaving one of the three SNARE proteins and induce flaccid paralysis. The Centers for Disease Control and Prevention (CDC has declared them as Category A biowarfare agents. The most potent among them, botulinum neurotoxin type A (BoNT/A, cleaves its substrate synaptosome-associated protein of 25 kDa (SNAP-25. An efficient drug for botulism can be developed only with the knowledge of interactions between the substrate and enzyme at the active site. Here, we report the crystal structures of the catalytic domain of BoNT/A with its uncleavable SNAP-25 peptide (197QRATKM(202 and its variant (197RRATKM(202 to 1.5 A and 1.6 A, respectively. This is the first time the structure of an uncleavable substrate bound to an active botulinum neurotoxin is reported and it has helped in unequivocally defining S1 to S5' sites. These substrate peptides make interactions with the enzyme predominantly by the residues from 160, 200, 250 and 370 loops. Most notably, the amino nitrogen and carbonyl oxygen of P1 residue (Gln197 chelate the zinc ion and replace the nucleophilic water. The P1'-Arg198, occupies the S1' site formed by Arg363, Thr220, Asp370, Thr215, Ile161, Phe163 and Phe194. The S2' subsite is formed by Arg363, Asn368 and Asp370, while S3' subsite is formed by Tyr251, Leu256, Val258, Tyr366, Phe369 and Asn388. P4'-Lys201 makes hydrogen bond with Gln162. P5'-Met202 binds in the hydrophobic pocket formed by the residues from the 250 and 200 loop. Knowledge of interactions between the enzyme and substrate peptide from these complex structures should form the basis for design of potent inhibitors for this neurotoxin.

  4. Effect of DNA groove binder distamycin A upon chromatin structure.

    Directory of Open Access Journals (Sweden)

    Parijat Majumder

    Full Text Available BACKGROUND: Distamycin A is a prototype minor groove binder, which binds to B-form DNA, preferentially at A/T rich sites. Extensive work in the past few decades has characterized the binding at the level of double stranded DNA. However, effect of the same on physiological DNA, i.e. DNA complexed in chromatin, has not been well studied. Here we elucidate from a structural perspective, the interaction of distamycin with soluble chromatin, isolated from Sprague-Dawley rat. METHODOLOGY/PRINCIPAL FINDINGS: Chromatin is a hierarchical assemblage of DNA and protein. Therefore, in order to characterize the interaction of the same with distamycin, we have classified the system into various levels, according to the requirements of the method adopted, and the information to be obtained. Isothermal titration calorimetry has been employed to characterize the binding at the levels of chromatin, chromatosome and chromosomal DNA. Thermodynamic parameters obtained thereof, identify enthalpy as the driving force for the association, with comparable binding affinity and free energy for chromatin and chromosomal DNA. Reaction enthalpies at different temperatures were utilized to evaluate the change in specific heat capacity (ΔCp, which, in turn, indicated a possible binding associated structural change. Ligand induced structural alterations have been monitored by two complementary methods--dynamic light scattering, and transmission electron microscopy. They indicate compaction of chromatin. Using transmission electron microscopy, we have visualized the effect of distamycin upon chromatin architecture at di- and trinucleosome levels. Our results elucidate the simultaneous involvement of linker bending and internucleosomal angle contraction in compaction process induced by distamycin. CONCLUSIONS/SIGNIFICANCE: We summarize here, for the first time, the thermodynamic parameters for the interaction of distamycin with soluble chromatin, and elucidate its effect on

  5. Spectral characterization of the binding and conformational changes of serum albumins upon interaction with an anticancer drug, anastrozole

    Science.gov (United States)

    Punith, Reeta; Seetharamappa, J.

    2012-06-01

    The present study employed different optical spectroscopic techniques viz., fluorescence, FTIR, circular dichroism (CD) and UV-vis absorption spectroscopy to investigate the mechanism of interaction of an anticancer drug, anastrozole (AZ) with transport proteins viz., bovine serum albumin (BSA) and human serum albumin (HSA). The drug, AZ quenched the intrinsic fluorescence of protein and the analysis of results revealed the presence of dynamic quenching mechanism. The binding characteristics of drug-protein were computed. The thermodynamic parameters, enthalpy change (ΔH°) and entropy change (ΔS°) were calculated to be +92.99 kJ/mol and +159.18 J/mol/K for AZ-BSA and, +99.43 kJ/mol and +159.19 J/mol/K for AZ-HSA, respectively. These results indicated that the hydrophobic forces stabilized the interaction between the drug and protein. CD, FTIR, absorption, synchronous and 3D fluorescence results indicated that the binding of AZ to protein induced structural perturbation in both serum albumins. The distance, r between the drug and protein was calculated based on the theory of Förster's resonance energy transfer and found to be 5.9 and 6.24 nm, respectively for AZ-BSA and AZ-HSA.

  6. The influence of intramolecular sulfur-lone pair interactions on small-molecule drug design and receptor binding.

    Science.gov (United States)

    Hudson, B M; Nguyen, E; Tantillo, D J

    2016-04-28

    Sulfur-lone pair interactions are important conformational control elements in sulfur-containing heterocycles that abound in pharmaceuticals, natural products, agrochemicals, polymers and other important classes of organic molecules. Nonetheless, the role of intramolecular sulfur-lone pair interactions in the binding of small molecules to receptors is often overlooked. Here we analyze the magnitudes and origins of these interactions for a variety of biologically relevant small molecules using quantum chemical and automated docking calculations. In most cases examined in this study, the lowest energy conformation of the small molecule displays a sulfur-lone pair close contact. However, docking studies, both published and new, often predict that conformations without sulfur-lone pair contacts have the best binding affinity for their respective receptors. This is a serious problem. Since many of these predicted bound conformations are not actually energetically accessible, pursuing design (e.g., drug design) around these binding modes necessarily will lead, serendipity aside, to dead end designs. Our results constitute a caution that one best not neglect these interactions when predicting the binding affinities of potential ligands (drugs or not) for hosts (enzymes, receptors, DNA, RNA, synthetic hosts). Moreover, a better understanding and awareness of sulfur-lone pair interactions should facilitate the rational modulation of host-guest interactions involving sulfur-containing molecules.

  7. Characterization of the Effect of Drug-Drug Interaction on Protein Binding in Concurrent Administration of Sulfamethoxazol and Diclofenac Sodium Using Bovine Serum Albumin

    Science.gov (United States)

    Hossain, Md Kamal; Khatun, Amina; Rahman, Mahmudur; Akter, Md Nahid; Chowdhury, Sadia Afreen; Alam, SM Mahbubul

    2016-01-01

    Purpose: This project was aimed to determine the effect of concurrent administration of sulfamethoxazole and diclofenac sodium. Methods: Equilibrium dialysis method was adopted to study different protein binding aspects of sulfamethoxazole and diclofenac sodium. Results: Sulfamethoxazole showed two types of association constants; high affinity constant 29.0±0.20×106 M-1 with lower number of binding sites of 0.7±1 and low affinity constant 1.13±0.20×106 M-1 with higher number of binding sites of 3.45±1 at pH 7.4 and 40 °C temperature. Diclofenac sodium showed high affinity constant 33.66±0.20×106 M-1 with lower number of binding sites of 1.01±1 and low affinity constant 1.72±0.20×106 M-1 with higher number of binding sites of 6.40±1 at the same condition. Site specific probe displacement data implied that site-I, warfarin sodium site, was the high affinity site, while site-II, diazepam site, was the low affinity site for these drugs. During concurrent administration, sulfamethoxazole increased the free concentration of diclofenac sodium from 17.5±0.14% to 70.0±0.014% in absence and from 22.5±0.07% to 83.0±0.014% in presence of site-I specific probe. Diclofenac sodium also increased the free concentration of sulfamethoxazole from 2.8±0.07% to 52.0±0.14% and from 8.5±0.014% to 64.4±0.07% in absence and presence of site-I specific probe respectively. Conclusion: The study revealed that the concurrent administration of sulfamethoxazole and diclofenac sodium may result drug concentration alteration in blood. PMID:28101466

  8. Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs

    DEFF Research Database (Denmark)

    van Beest, M; Dooijes, D; van De Wetering, M

    2000-01-01

    Sequence-specific high mobility group (HMG) box factors bind and bend DNA via interactions in the minor groove. Three-dimensional NMR analyses have provided the structural basis for this interaction. The cognate HMG domain DNA motif is generally believed to span 6-8 bases. However, alignment...

  9. Use of Capillary Electrophoresis in the Study of Interaction between dsDNA and Drug Molecules

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Two 17-mer dsDNA with different sequence characteristics were designed to investigate the binding characteristics of berberine, an anticancer drug with uncertain binding mode, and Hoechst 33258, a model DNA minor groove binder, with dsDNA, respectively by the capillary zone electrophoresis (CZE). Kenndler model analysis revealed that Hoechst 33258 exhibited intermediate affinity with dsDNA, while there was only low affinity and some weak binding preference for AATT-containing to GGCC-containing dsDNA for berberine.

  10. Subvertical grooves of interproximal facets in Neandertal posterior teeth.

    Science.gov (United States)

    Villa, G; Giacobini, G

    1995-01-01

    Subvertical grooves, located on the interproximal facets of most Neandertal posterior teeth, are less frequently noted on the teeth of other hominids, including modern humans. These grooves, 0.1-0.5 mm in width, are strictly localized within the facet area. Scanning electron microscopic (SEM) examination of grooves present on Neandertal teeth from Caverna delle Fate (Liguria, Italy) and Genay (Côte d'Or, France) demonstrated that they were produced during the life of these individuals. Characteristics of the groove surface suggest an erosion-abrasion mechanism of formation. These grooves, which developed in parts of the dentition exposed to marked stress, originated in areas characterized by changes in the orientation of enamel prism bundles (i.e., Hunter-Schreger bands). Observations carried out on modern human molars showed a subvertical disposition of these bands near interproximal ridges facilitating subvertical microfractures. Possible correlations between enamel structure, masticatory stress, and interproximal groove formation in Neandertals are discussed.

  11. Evidence for differences in the binding of drugs to the two main genetic variants of human alpha 1-acid glycoprotein.

    Science.gov (United States)

    Herve, F; Gomas, E; Duche, J C; Tillement, J P

    1993-09-01

    1. Human alpha 1-acid glycoprotein (AAG), a plasma transport protein, has three main genetic variants. F1. S and A. Native commercial AAG (a mixture of almost equal proportions of these three variants) has been separated by chromatography into variants which correspond to the proteins of the two genes which code for AAG in humans: the A variant and a mixture of the F1 and S variants (60% F1 and 40% S). Their binding properties towards imipramine, warfarin and mifepristone were studied by equilibrium dialysis. 2. The F1S variant mixture strongly bound warfarin and mifepristone with an affinity of 1.89 and 2.06 x 10(6) l mol-1, respectively, but had a low affinity for imipramine. Conversely, the A variant strongly bound imipramine with an affinity of 0.98 x 10(6) l mol-1. The low degree of binding of warfarin and mifepristone to the A variant sample was explained by the presence of protein contaminants in this sample. These results indicate specific drug transport roles for each variant, with respect to its separate genetic origin. 3. Control binding experiments performed with (unfractionated) commercial AAG and with AAG isolated from individuals with either the F1/A or S/A phenotypes, agreed with these findings. The results for the binding of warfarin and mifepristone by the AAG samples were similar to those obtained with the F1S mixture: the mean high-affinity association constant of the AAG samples for each drug was of the same order as that of the F1S mixture: the decrease in the number of binding sites of the AAG samples, as compared with the F1S mixture, was explained by the smaller proportion of variants F1 and/or S in these samples. Conversely, results of the imipramine binding study with the AAG samples concurred with those for the binding of this basic drug by the A variant, with respect to the proportion of the A variant in these samples.

  12. The multi-functional drug tropisetron binds APP and normalizes cognition in a murine Alzheimer's model.

    Science.gov (United States)

    Spilman, Patricia; Descamps, Olivier; Gorostiza, Olivia; Peters-Libeu, Clare; Poksay, Karen S; Matalis, Alexander; Campagna, Jesus; Patent, Alexander; Rao, Rammohan; John, Varghese; Bredesen, Dale E

    2014-03-10

    Tropisetron was identified in a screen for candidates that increase the ratio of the trophic, neurite-extending peptide sAPPα to the anti-trophic, neurite-retractive peptide Aβ, thus reversing this imbalance in Alzheimer's disease (AD). We describe here a hierarchical screening approach to identify such drug candidates, moving from cell lines to primary mouse hippocampal neuronal cultures to in vivo studies. By screening a clinical compound library in the primary assay using CHO-7W cells stably transfected with human APPwt, we identified tropisetron as a candidate that consistently increased sAPPα. Secondary assay testing in neuronal cultures from J20 (PDAPP, huAPP(Swe/Ind)) mice showed that tropisetron consistently increased the sAPPα/Aβ 1-42 ratio. In in vivo studies in J20 mice, tropisetron improved the sAPPα/Aβ ratio along with spatial and working memory in mice, and was effective both during the symptomatic, pre-plaque phase (5-6 months) and in the late plaque phase (14 months). This ameliorative effect occurred at a dose of 0.5mg/kg/d (mkd), translating to a human-equivalent dose of 5mg/day, the current dose for treatment of postoperative nausea and vomiting (PONV). Although tropisetron is a 5-HT3 receptor antagonist and an α7nAChR partial agonist, we found that it also binds to the ectodomain of APP. Direct comparison of tropisetron to the current AD therapeutics memantine (Namenda) and donepezil (Aricept), using similar doses for each, revealed that tropisetron induced greater improvements in memory and the sAPPα/Aβ1-42 ratio. The improvements observed with tropisetron in the J20 AD mouse model, and its known safety profile, suggest that it may be suitable for transition to human trials as a candidate therapeutic for mild cognitive impairment (MCI) and AD, and therefore it has been approved for testing in clinical trials beginning in 2014. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Binding and inhibition of drug transport proteins by heparin: a potential drug transporter modulator capable of reducing multidrug resistance in human cancer cells.

    Science.gov (United States)

    Chen, Yunliang; Scully, Michael; Petralia, Gloria; Kakkar, Ajay

    2014-01-01

    A major problem in cancer treatment is the development of resistance to chemotherapeutic agents, multidrug resistance (MDR), associated with increased activity of transmembrane drug transporter proteins which impair cytotoxic treatment by rapidly removing the drugs from the targeted cells. Previously, it has been shown that heparin treatment of cancer patients undergoing chemotherapy increases survival. In order to determine whether heparin is capable reducing MDR and increasing the potency of chemotherapeutic drugs, the cytoxicity of a number of agents toward four cancer cell lines (a human enriched breast cancer stem cell line, two human breast cancer cell lines, MCF-7 and MDA-MB-231, and a human lung cancer cell line A549) was tested in the presence or absence of heparin. Results demonstrated that heparin increased the cytotoxicity of a range of chemotherapeutic agents. This effect was associated with the ability of heparin to bind to several of the drug transport proteins of the ABC and non ABC transporter systems. Among the ABC system, heparin treatment caused significant inhibition of the ATPase activity of ABCG2 and ABCC1, and of the efflux function observed as enhanced intracellular accumulation of specific substrates. Doxorubicin cytoxicity, which was enhanced by heparin treatment of MCF-7 cells, was found to be under the control of one of the major non-ABC transporter proteins, lung resistance protein (LRP). LRP was also shown to be a heparin-binding protein. These findings indicate that heparin has a potential role in the clinic as a drug transporter modulator to reduce multidrug resistance in cancer patients.

  14. Dual-phase CT findings of groove pancreatitis

    Energy Technology Data Exchange (ETDEWEB)

    Zaheer, Atif, E-mail: azaheer1@jhmi.edu [The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD 21231 (United States); Pancreatitis Center, Division of Gastroenterology, Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21231 (United States); Haider, Maera, E-mail: mhaider3@jhmi.edu [The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD 21231 (United States); Kawamoto, Satomi, E-mail: skawamo1@jhmi.edu [The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD 21231 (United States); Hruban, Ralph H., E-mail: rhruban1@jhmi.edu [Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD 21231 (United States); Fishman, Elliot K., E-mail: efishma1@jhmi.edu [The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD 21231 (United States)

    2014-08-15

    Purpose: Groove pancreatitis is a rare focal form of chronic pancreatitis that occurs in the pancreaticoduodenal groove between the major and minor papillae, duodenum and pancreatic head. Radiologic appearance and clinical presentation can result in suspicion of malignancy rendering pancreaticoduodenectomy inevitable. This study reports dual phase CT findings in a series of 12 patients with pathology proven groove pancreatitis. Materials and methods: Retrospective review of preoperative CT findings in 12 patients with histologically proven groove pancreatitis after pancreaticoduodenectomy. Size, location, attenuation, presence of mass or cystic components in the pancreas, groove and duodenum, calcifications, duodenal stenosis and ductal changes were recorded. Clinical data, laboratory values, endoscopic ultrasonographic and histopathological findings were collected. Results: Soft tissue thickening in the groove was seen in all patients. Pancreatic head, groove and duodenum were all involved in 75% patients. A discrete lesion in the pancreatic head was seen in half of the patients, most of which appeared hypodense on both arterial and venous phases. Cystic changes in pancreatic head were seen in 75% patients. Duodenal involvement was seen in 92% patients including wall thickening and cyst formation. The main pancreatic duct was dilated in 7 patients, with an abrupt cut off in 3 and a smooth tapering stricture in 4. Five patients had evidence of chronic pancreatitis with parenchymal calcifications. Conclusion: Presence of mass or soft tissue thickening in the groove with cystic duodenal thickening is highly suggestive of groove pancreatitis. Recognizing common radiological features may help in diagnosis and reduce suspicion of malignancy.

  15. Grooved roll for a high speed twin roll caster

    OpenAIRE

    T. Haga; HIROOKA, K.; H. Watari; S. Kumai

    2008-01-01

    Purpose: Purpose of this paper is investigation of the effect of roll-surface on the strip-surface. Improvement ofsmall cracks on the strip-surface was tried and effect of groove at the roll surface on the strip surface was shown.Design/methodology/approach: Method used in the present study was high speed twin roll caster withgrooved roll. Two kinds of grooves were used: one was parallel groove and the other was cross groove machinedby knurling and bite attached to a lathe.Findings: Findings ...

  16. Sensorimotor coupling in music and the psychology of the groove.

    Science.gov (United States)

    Janata, Petr; Tomic, Stefan T; Haberman, Jason M

    2012-02-01

    The urge to move in response to music, combined with the positive affect associated with the coupling of sensory and motor processes while engaging with music (referred to as sensorimotor coupling) in a seemingly effortless way, is commonly described as the feeling of being in the groove. Here, we systematically explore this compelling phenomenon in a population of young adults. We utilize multiple levels of analysis, comprising phenomenological, behavioral, and computational techniques. Specifically, we show (a) that the concept of the groove is widely appreciated and understood in terms of a pleasurable drive toward action, (b) that a broad range of musical excerpts can be appraised reliably for the degree of perceived groove, (c) that the degree of experienced groove is inversely related to experienced difficulty of bimanual sensorimotor coupling under tapping regimes with varying levels of expressive constraint, (d) that high-groove stimuli elicit spontaneous rhythmic movements, and (e) that quantifiable measures of the quality of sensorimotor coupling predict the degree of experienced groove. Our results complement traditional discourse regarding the groove, which has tended to take the psychological phenomenon for granted and has focused instead on the musical and especially the rhythmic qualities of particular genres of music that lead to the perception of groove. We conclude that groove can be treated as a psychological construct and model system that allows for experimental exploration of the relationship between sensorimotor coupling with music and emotion.

  17. Wetting morphologies and their transitions in grooved substrates

    Energy Technology Data Exchange (ETDEWEB)

    Seemann, Ralf; Bommer, Stefan; Herrmann, Carsten; Michler, Dominik [Experimental Physics, Saarland University, D-66123 Saarbruecken (Germany); Brinkmann, Martin; Herminghaus, Stephan; Khare, Krishnacharya; Kostourou, Konstantina; Gurevich, Evgeny [Max Planck Institute for Dynamics and Self-Organization, D-37073 Goettingen (Germany); Law, Bruce M; McBride, Sean, E-mail: r.seemann@physik.uni-saarland.de [Department of Physics, Kansas State University, Manhattan, KS 66506 (United States)

    2011-05-11

    When exposed to a partially wetting liquid, many natural and artificial surfaces equipped with complex topographies display a rich variety of liquid interfacial morphologies. In the present article, we focus on a few simple paradigmatic surface topographies and elaborate on the statics and dynamics of the resulting wetting morphologies. It is demonstrated that the spectrum of wetting morphologies increases with increasing complexity of the groove structure. On elastically deformable substrates, additional structures in the liquid morphologies can be observed, which are caused by deformations of the groove geometry in the presence of capillary forces. The emergence of certain liquid morphologies in grooves can be actively controlled by changes in wettability and geometry. For electrically conducting solid substrates, the apparent contact angle can be varied by electrowetting. This allows, depending on groove geometry, a reversible or irreversible transport of liquid along surface grooves. In the case of irreversible liquid transport in triangular grooves, the dynamics of the emerging instability is sensitive to the apparent hydrodynamic slip at the substrate. On elastic substrates, the geometry can be varied in a straightforward manner by stretching or relaxing the sample. The imbibition velocity in deformable grooves is significantly reduced compared to solid grooves, which is a result of the microscopic deformation of the elastic groove material close to the three phase contact line.

  18. Laminar streak enhancement using streamwise grooves

    Science.gov (United States)

    Martel, Carlos; Martín, Juan Ángel

    2011-11-01

    Laminar streak promotion in a flat plate boundary layer results in an increase of the stability of the Tollmien-Schlichting waves with respect to that of the 2D Blasius profile. This stabilization delays the laminar-turbulent transition, increasing the laminar phase of the flow. The stabilization effect is stronger for higher streak amplitudes, and therefore simple ways of generating high amplitude stable streaks are sought to be used as boundary layer flow control methods. In a recent experiment [Tallamelli & Franson,AIAA 2010-4291] high amplitude stable steady streaks have been produced using Miniature Vortex Generators (MGVs), where one array of MGVs is used to excite the streak and a second array is used downstream to enhance their amplitude. In this presentation we numerically explore the possibility of enhancing the streaks using a different passive mechanism: streamwise grooves carved in the plate. We will present some numerical simulations for different values of the spanwise period of the streaks and of the grooves, and we will show the combinations that provide maximum streak amplitude.

  19. Nanomechanical detection of antibiotic-mucopeptide binding in a model for superbug drug resistance

    CERN Document Server

    Ndieyira, J W; Barrera, A Donoso; Zhou, D; Vögtli, M; Batchelor, M; Cooper, M A; Strunz, T; Horton, M A; Abell, C; Rayment, T; Aeppli, G; Mckendry, R A; 10.1038/nnano.2008.275

    2008-01-01

    The alarming growth of the antibiotic-resistant superbugs methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) is driving the development of new technologies to investigate antibiotics and their modes of action. We report the label-free detection of vancomycin binding to bacterial cell wall precursor analogues (mucopeptides) on cantilever arrays, with 10 nM sensitivity and at clinically relevant concentrations in blood serum. Differential measurements quantified binding constants for vancomycin-sensitive and vancomycin-resistant mucopeptide analogues. Moreover, by systematically modifying the mucopeptide density we gain new insights into the origin of surface stress. We propose that stress is a product of a local chemical binding factor and a geometrical factor describing the mechanical connectivity of regions affected by local binding in terms of a percolation process. Our findings place BioMEMS devices in a new class of percolative systems. The percolation concept w...

  20. Blockade of the BAK hydrophobic groove by inhibitory phosphorylation regulates commitment to apoptosis.

    Directory of Open Access Journals (Sweden)

    Abul Azad

    Full Text Available The BCL-2 family protein BAK is a key regulator of mitochondrial apoptosis. BAK activation first involves N-terminal conformational changes that lead to the transient exposure of the BAK BH3 domain that then inserts into a hydrophobic groove on another BAK molecule to form symmetric dimers. We showed recently that post-translational modifications are important in the regulation of BAK conformational change and multimerization, with dephosphorylation at tyrosine 108 constituting an initial step in the BAK activation process. We now show that dephosphorylation of serine 117 (S117, located in the BAK hydrophobic groove, is also critical for BAK activation to proceed to completion. Phosphorylation of BAK at S117 has two important regulatory functions: first, it occludes the binding of BH3-containing peptides that bind to BAK causing activation and cytochrome c release from mitochondria; second, it prevents BAK-BH3:BAK-Groove interactions that nucleate dimer formation for subsequent multimerization. Hence, BH3-mediated BAK conformational change and subsequent BAK multimerization for cytochrome c release and cell death is intimately linked to, and dependent on, dephosphorylation at S117. Our study reveals important novel mechanistic and structural insights into the temporal sequence of events governing the process of BAK activation in commitment to cell death and how they are regulated.

  1. Intracellular binding of the anti-inflammatory drug niflumic acid in the liver.

    Science.gov (United States)

    Kelmer-Bracht, A M; Ishii-Iwamoto, E L; Bracht, A

    1995-09-01

    Intracellular binding of niflumic acid in the perfused rat liver was analyzed according to the model of Scatchard. The data for the binding isotherm were obtained from previously published indicator dilution experiments. The intracellular bound niflumic acid was calculated as the difference between total concentration and the concentration of the free form. The intracellular concentration of the free form was inferred from the concentration of the free form in the extracellular space under the assumption of equilibrative distribution. A Scatchard model with two classes of binding sites fits very well to the experimental curve. The high affinity class has a dissociation constant of 26.10 +/- 0.69 microM and a maximal binding capacity of 2.21 +/- 0.03 micromol (ml intracellular space)(-1); the low affinity class has a dissociation constant of 721.90 +/- 229.0 microM and a maximal binding capacity of 5.96 +/- 0.67 micromol (ml intracellular space)(-1). Probably, under in vivo conditions, the binding capacity in the cellular space exceeds that of the extracellular space. This phenomenon explains, partly at least, the high intracellular concentrations of niflumic acid found under in vivo conditions.

  2. Molecular dynamics of Mycobacterium tuberculosis KasA: implications for inhibitor and substrate binding and consequences for drug design

    Science.gov (United States)

    Schaefer, Benjamin; Kisker, Caroline; Sotriffer, Christoph A.

    2011-11-01

    Inhibition of the production of fatty acids as essential components of the mycobacterial cell wall has been an established way of fighting tuberculosis for decades. However, increasing resistances and an outdated medical treatment call for the validation of new targets involved in this crucial pathway. In this regard, the β-ketoacyl ACP synthase KasA is a promising enzyme. In this study, three molecular dynamics simulations based on the wildtype crystal structures of inhibitor bound and unbound KasA were performed in order to investigate the flexibility and conformational space of this target. We present an exhaustive analysis of the binding-site flexibility and representative pocket conformations that may serve as new starting points for structure-based drug design. We also revealed a mechanism which may account for the comparatively low binding affinity of thiolactomycin. Furthermore, we examined the behavior of water molecules within the binding pocket and provide recommendations how to handle them in the drug design process. Finally, we analyzed the dynamics of a channel that accommodates the long-chain fatty acid substrates and, thereby, propose a mechanism of substrate access to this channel and how products are most likely released.

  3. Analysis of chiral non-steroidal anti-inflammatory drugs flurbiprofen, ketoprofen and etodolac binding with HSA

    Institute of Scientific and Technical Information of China (English)

    Chang-Chuan Guo; Yi-Hong Tang; Hai-Hong Hu; Lu-Shan Yu; Hui-Di Jiang; Su Zeng

    2011-01-01

    The protein binding of non-steroidal anti-inflammatory drugs flurbiprofen, ketoprofen and etodolac with human serum albumin (HSA) was investigated using indirect chiral high performance liquid chromatography (HPLC) and ultrafiltration techniques. S-(-)-1-(1-naphthyl)- ethylamine (S-NEA) was utilized as chiral derivatization reagent and pre-column derivatization RP-HPLC method was established for the separation and assay of the three pairs of enantiomer. The method had good linear relationship over the investigated concentration range without interference. The average extraction efficiency was higher than 85% in different systems, and the intra-day and inter-day precisions were less than 15%. In serum albumin, the protein binding of etodolac enantiomers showed significant stereoselectivity that the affinity of S-enantiomer was stronger than R-enantiomer, and the stereoselectivity ratio reached 6.06; Flurbiprofen had only weak stereoselectivity in HSA, and ketoprofen had no stereoselectivity at all. Scatchard curves showed that all the three chiral drugs had two types of binding sites in HSA.

  4. Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context.

    Science.gov (United States)

    Homeyer, Nadine; Stoll, Friederike; Hillisch, Alexander; Gohlke, Holger

    2014-08-12

    Correctly ranking compounds according to their computed relative binding affinities will be of great value for decision making in the lead optimization phase of industrial drug discovery. However, the performance of existing computationally demanding binding free energy calculation methods in this context is largely unknown. We analyzed the performance of the molecular mechanics continuum solvent, the linear interaction energy (LIE), and the thermodynamic integration (TI) approach for three sets of compounds from industrial lead optimization projects. The data sets pose challenges typical for this early stage of drug discovery. None of the methods was sufficiently predictive when applied out of the box without considering these challenges. Detailed investigations of failures revealed critical points that are essential for good binding free energy predictions. When data set-specific features were considered accordingly, predictions valuable for lead optimization could be obtained for all approaches but LIE. Our findings lead to clear recommendations for when to use which of the above approaches. Our findings also stress the important role of expert knowledge in this process, not least for estimating the accuracy of prediction results by TI, using indicators such as the size and chemical structure of exchanged groups and the statistical error in the predictions. Such knowledge will be invaluable when it comes to the question which of the TI results can be trusted for decision making.

  5. Study on the interaction of the drug mesalamine with calf thymus DNA using molecular docking and spectroscopic techniques.

    Science.gov (United States)

    Shahabadi, Nahid; Fili, Soraya Moradi; Kheirdoosh, Fahimeh

    2013-11-05

    The interaction of CT-DNA with the drug mesalamine (5-ASA) at physiological pH has been investigated by absorption, emission, circular dichroism (CD), cyclic voltammetry (CV), viscosity studies and molecular modeling. Thermodynamic parameters (ΔH>0 and ΔS<0) indicated that hydrogen bond and van der Waals play main roles in the binding of 5-ASA to CT-DNA. Ethidium bromide (EB) displacement studies revealed that 5-ASA did not have any effect on ethidium bromide (EB) bound DNA which is indicative of groove binding. The results obtained from experimental and molecular modeling showed that 5-ASA is a minor groove binder of DNA and preferentially binds to GC rich regions.

  6. Binding site prediction within Ebola virus VP40 protein:clue for further drug development

    Institute of Scientific and Technical Information of China (English)

    Viroj; Wiwanitkit

    2014-01-01

    To the editor.The emerging African Ebola virus infection in 2014 is the global concernl I].To manage this deadly infection,there arestill no effective drugs and vaccines.Searching for new drug is the urgent requirement for successful control of the disease.Based on the new finding,it is noted that Ebola virus VP40

  7. Human immunodeficiency virus drug development assisted with AlGaN/GaN high electron mobility transistors and binding-site models

    Science.gov (United States)

    Kang, Yen-Wen; Lee, Geng-Yen; Chyi, Jen-Inn; Hsu, Chen-Pin; Hsu, You-Ren; Hsu, Chia-Hsien; Huang, Yu-Fen; Sun, Yuh-Chang; Chen, Chih-Chen; Chun Hung, Sheng; Ren, Fan; Andrew Yeh, J.; Wang, Yu-Lin

    2013-04-01

    Human immunodeficiency virus (HIV) Reverse Transcriptase (RT)-immobilized AlGaN/GaN high electron mobility transistors (HEMTs) and binding-site models were used to find out the dissociation constants of the HIV RT-inhibitor complex and the number of the binding sites on RT for the inhibitor, Efavirenz. One binding site on the RT for the inhibitor is predicted and the dissociation constant extracted from the binding-site model is 0.212 nM. The AlGaN/GaN HEMTs and the binding-site-models are demonstrated to be good tools to assist drug developments by elucidating the dissociation constants and the number of binding sites, which can largely reduce the cost and time for drug developments.

  8. Characterization of the binding of metoprolol tartrate and guaifenesin drugs to human serum albumin and human hemoglobin proteins by fluorescence and circular dichroism spectroscopy.

    Science.gov (United States)

    Duman, Osman; Tunç, Sibel; Kancı Bozoğlan, Bahar

    2013-07-01

    The interactions of metoprolol tartrate (MPT) and guaifenesin (GF) drugs with human serum albumin (HSA) and human hemoglobin (HMG) proteins at pH 7.4 were studied by fluorescence and circular dichroism (CD) spectroscopy. Drugs quenched the fluorescence spectra of HSA and HMG proteins through a static quenching mechanism. For each protein-drug system, the values of Stern-Volmer quenching constant, bimolecular quenching constant, binding constant and number of binding site on the protein molecules were determined at 288.15, 298.15, 310.15 and 318.15 K. It was found that the binding constants of HSA-MPT and HSA-GF systems were smaller than those of HMG-MPT and HMG-GF systems. For both drugs, the affinity of HMG was much higher than that of HSA. An increase in temperature caused a negative effect on the binding reactions. The number of binding site on blood proteins for MPT and GF drugs was approximately one. Thermodynamic parameters showed that MPT interacted with HSA through electrostatic attraction forces. However, hydrogen bonds and van der Waals forces were the main interaction forces in the formation of HSA-GF, HMG-MPT and HMG-GF complexes. The binding processes between protein and drug molecules were exothermic and spontaneous owing to negative ∆H and ∆G values, respectively. The values of binding distance between protein and drug molecules were calculated from Förster resonance energy transfer theory. It was found from CD analysis that the bindings of MPT and GF drugs to HSA and HMG proteins altered the secondary structure of HSA and HMG proteins.

  9. DNA interaction studies of a platinum (II) complex containing an antiviral drug, ribavirin: the effect of metal on DNA binding.

    Science.gov (United States)

    Shahabadi, Nahid; Mirzaei kalar, Zeinab; Moghadam, Neda Hosseinpour

    2012-10-01

    The water-soluble Pt (II) complex, [PtCl (DMSO)(N(4)N(7)-ribavirin)]· H(2)O (ribavirin is an antiviral drug) has been synthesized and characterized by physico-chemical and spectroscopic methods. The binding interactions of this complex with calf thymus DNA (CT-DNA) were investigated using fluorimetry, spectrophotometry, circular dichroism and viscosimetry. The complex binds to CT-DNA in an intercalative mode. The calculated binding constant, K(b), was 7.2×10(5) M(-1). In fluorimetric studies, the enthalpy (ΔH0) changes of the reaction between the Pt (II) complex with CT-DNA showed hydrophobic interaction. In addition, CD study showed stabilization of the right-handed B form of CT-DNA. All these results prove that the complex interacts with CT-DNA via intercalative mode of binding. In comparison with the previous study of the DNA interaction with ribavirin, these results show that platinum complex has greater affinity to CT-DNA.

  10. Energy-dependent reduced drug binding as a mechanism of Vinca alkaloid resistance in human leukemic lymphoblasts.

    Science.gov (United States)

    Beck, W T; Cirtain, M C; Lefko, J L

    1983-11-01

    We studied the accumulation of [3H]vinblastine (VLB) by lines of CCRF-CEM cultured human leukemic lymphoblasts that were either sensitive or resistant to the drug. Neither cell line metabolized VLB, nor selectively retained any radioactive impurities. There was an apparent "instantaneous" accumulation of VLB by cells of both lines, resulting in cell to medium ratios greater than 1.0 within 1 sec after drug addition. Experiments between 0 and 60 sec revealed that the presumed undirectional initial rate of VLB accumulation by resistant cells, termed CEM/VLB100, was about one-half that of sensitive CEM cells. In experiments carried out over 60 min, the VLB-resistant cells accumulated considerably less [3H]VLB than did the sensitive cells. Drug accumulation by both cell lines was temperature-sensitive, since incubation of cells at 4 degrees resulted in only minimal uptake beyond that observed at zero time. CEM/VLB100 cells retained less drug than did CEM cells, apparently because of a larger fraction of readily releasable VLB compared with CEM cells. The accumulation of VLB by either cell line was related in part to cellular levels of ATP. Although depletion of ATP was associated with decreased accumulation of VLB by CEM cells, it was related to enhanced drug accumulation by CEM/VLB100 cells. Restoration of ATP levels to near control values by addition of glucose also had opposite effects on the two cell lines, causing further accumulation of VLB by the sensitive line but leading to apparent drug efflux from the resistant line. Potentially competing substrates (VM-26, colchicine, daunorubicin, and doxorubicin) failed to block this glucose-mediated release of VLB from the CEM/VLB100 cells. In experiments with energy-depleted CEM/VLB100 cells preloaded with VLB and then incubated in drug-free medium, initial drug loss was shown to be independent of cellular metabolism, being roughly the same for both metabolically intact and metabolically depleted cells. Glucose (energy

  11. Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire

    DEFF Research Database (Denmark)

    Ostrov, David A; Grant, Barry J; Pompeu, Yuri A;

    2012-01-01

    studies have identified strong linkages between drug hypersensitivity reactions to several drugs and specific HLA alleles. One of the strongest such genetic associations found has been for the antiviral drug abacavir, which causes severe adverse reactions exclusively in patients expressing the HLA...... molecular variant B*57:01. Abacavir adverse reactions were recently shown to be driven by drug-specific activation of cytokine-producing, cytotoxic CD8(+) T cells that required HLA-B*57:01 molecules for their function; however, the mechanism by which abacavir induces this pathologic T-cell response remains...... unclear. Here we show that abacavir can bind within the F pocket of the peptide-binding groove of HLA-B*57:01, thereby altering its specificity. This provides an explanation for HLA-linked idiosyncratic adverse drug reactions, namely that drugs can alter the repertoire of self-peptides presented to T...

  12. Optics of a single ultrasharp groove in metal

    DEFF Research Database (Denmark)

    Søndergaard, Thomas; Bozhevolnyi, Sergey

    2016-01-01

    Optical properties of a single ultrasharp groove of subwavelength width cut in an otherwise flat metal surface are examined theoretically. We calculate optical extinction, scattering, and absorption cross-section spectra for a wide range of groove profiles, establishing several fundamental trends...

  13. Effective slippage on superhydrophobic trapezoidal grooves

    CERN Document Server

    Zhou, Jiajia; Schmid, Friederike; Vinogradova, Olga I

    2013-01-01

    We study the effective slippage on superhydrophobic grooves with trapezoidal cross-sections of various geometries (including the limiting cases of triangles and rectangular stripes), by using two complementary approaches. First, dissipative particle dynamics (DPD) simulations of a flow past such surfaces have been performed to validate an expression [E.S.Asmolov and O.I.Vinogradova, J. Fluid Mech. \\textbf{706}, 108 (2012)] that relates the eigenvalues of the effective slip-length tensor for one-dimensional textures. Second, we propose theoretical estimates for the effective slip length and calculate it numerically by solving the Stokes equation based on a collocation method. The comparison between the two approaches shows that they are in excellent agreement. Our results demonstrate that the effective slippage depends strongly on the area-averaged slip, the amplitude of the roughness, and on the fraction of solid in contact with the liquid. To interpret these results, we analyze flow singularities near slippi...

  14. Olfactory groove meningiomas: approaches and complications.

    Science.gov (United States)

    Aguiar, Paulo Henrique Pires de; Tahara, Adriana; Almeida, Antonio Nogueira; Simm, Renata; Silva, Arnaldo Neves da; Maldaun, Marcos Vinicius Calfatt; Panagopoulos, Alexandros Theodoros; Zicarelli, Carlos Alexandre; Silva, Pedro Gabriel

    2009-09-01

    Olfactory groove meningiomas (OGM) account for 4.5% of all intracranial meningiomas. We report 21 patients with OGMs. Tumors were operated on using three surgical approaches: bifrontal (7 patients), fronto-pterional (11 patients) and fronto-orbital (3 patients). Total tumor removal (Simpson Grade 1) was achieved in 13 patients and Simpson II in 8 patients. Perioperative mortality was 4.76%. The average size of the OGM was 4.3+/-1.1cm. The overall recurrence rate was 19%. We preferred to use the pterional approach, which provides quick access to the tumor with less brain exposure. It also allows complete drainage of cisternal cerebrospinal fluid, providing a good level of brain relaxation during surgery. However, for long, thin tumors, hemostasis can be difficult using this approach.

  15. Crystallization of Poly(3-hexylthiophene Nanofiber in a Narrow Groove

    Directory of Open Access Journals (Sweden)

    Satoshi Kushi

    2016-06-01

    Full Text Available Whisker-type poly(3-hexylthiophene-2,5-diyl (P3HT nanofibers were aligned by restricting their growth direction using an approximately 100–1000 nm wide narrow groove fabricated by thermal nanoimprinting. In grooves made of an amorphous fluoropolymer (CYTOP™ with widths of less than 1500 nm, the nanofibers oriented uniaxially perpendicular to the groove and their length was limited to the width of the groove. This result indicates that the nucleation of nanofibers tends to be selectively promoted near the interface of CYTOP™ with fluoro-groups, and nanofiber growth perpendicular to the wall is promoted because P3HT molecules are supplied more frequently from the center of the groove. Furthermore, the orientation induced anisotropic conductivity, and the conductivity parallel to the oriented nanofibers was more than an order of magnitude higher than that perpendicular to the oriented nanofibers.

  16. Forming method of axial micro grooves inside copper heat pipe

    Institute of Scientific and Technical Information of China (English)

    LI Yong; XIAO Hui; LIAN Bin; TANG Yong; ZENG Zhi-xin

    2008-01-01

    The high-speed oil-filled ball spinning and drawing process was put forward to manufacture the axially grooved heat pipe with highly efficient heat-transfer performance, and the forming mechanism of micro-grooves inside the pipe was investigated. The key factors influencing the configurations of micro-grooves were analyzed. When the spinning depth varies between 0.4 mm and 0.5 mm, drawing speed varies from 200 mm/min to 450 mm/min, rotary speed is beyond 6 000 r/min and working temperature is less than 50 ℃, the grooved tubes are formed with high quality and efficiency. The ball spinning process uses full oil-filling method to set up the steady dynamic oil-film that reduces the drawing force and improves the surface quality of grooved copper tube.

  17. Accurate analysis of arbitrarily-shaped helical groove waveguide

    Institute of Scientific and Technical Information of China (English)

    Liu Hong-Tao; Wei Yan-Yu; Gong Yu-Bin; Yue Ling-Na; Wang Wen-Xiang

    2006-01-01

    This paper presents a theory on accurately analysing the dispersion relation and the interaction impedance of electromagnetic waves propagating through a helical groove waveguide with arbitrary groove shape, in which the complex groove profile is synthesized by a series of rectangular steps. By introducing the influence of high-order evanescent modes on the connection of any two neighbouring steps by an equivalent susceptance under a modified admittance matching condition, the assumption of the neglecting discontinuity capacitance in previously published analysis is avoided, and the accurate dispersion equation is obtained by means of a combination of field-matching method and admittancematching technique. The validity of this theory is proved by comparison between the measurements and the numerical calculations for two kinds of helical groove waveguides with different groove shapes.

  18. SIMULATION AND EXPERIMENT OF BUBBLY FLOW INSIDE THROTTLING GROOVE

    Institute of Scientific and Technical Information of China (English)

    FU Xin; DU Xuewen; ZOU Jun; YANG Huayong; JI Hong

    2007-01-01

    The relationship between pressure distribution and cavitation (noise) inside throttling groove is investigated by numerical simulation and experimental method. A valve pocket with several transducers is performed to detect the pressure distributions inside the valve chamber, and the results fit quite well with the computational fluid dynamics(CFD) analysis. High-speed imaging techniques are employed to investigate the cavitation mechanisms, in particular bubble inception and cluster formation near the throttling groove. A spectrum analyzer is used to measure the sound pressure level of noise generated by the bubble flow. It is found that the pressure distributions inside the groove are sensitive to the valve port configuration and back pressure. The pressure distribution determines the bubble size and number passing through the valve grooves and the sound pressure level of noise induced by collapsing bubbles. The inlet pressure mainly affects the saturation degree of bubbly flow inside the groove and the intensity of sound pressure level accordingly.

  19. Characteristics of Multiplexed Grooved Nozzles for High Flow Rate Electrospray

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kyoung Tae; Kim, Woo Jin; Kim, Sang Soo [Korea Advanced Institute of Science and Technology, Daejeon (Korea, Republic of)

    2007-10-15

    The electrospray operated in the cone-jet mode can generate highly charged micro droplets in an almost uniform size at flow rates. Therefore, the multiplexing system which can retain the characteristics of the cone-jet mode is inevitable for the electrospray application. This experiment reports the multiplexed grooved nozzle system with the extractor. The effects of the grooves and the extractor on the performance of the electrospray were evaluated through experiments. Using the grooved nozzle, the stable cone-jet mode can be achieved at the each groove in the grooved mode. Furthermore, the number of nozzles per unit area is increased by the extractor. The multiplexing density is 12 jets per cm{sup 2} at 30 mm distance from the nozzle tip to the ground plate. The multiplexing system for the high flow rate electrospray is realized with the extractor which can diminish the space charge effect without sacrificing characteristics of the cone-jet mode.

  20. Interactions of human P-glycoprotein transport substrates and inhibitors at the drug binding domain: Functional and molecular docking analyses.

    Science.gov (United States)

    Kadioglu, Onat; Saeed, Mohamed E M; Valoti, Massimo; Frosini, Maria; Sgaragli, Giampietro; Efferth, Thomas

    2016-03-15

    Rhodamine 123 (R123) transport substrate sensitizes P-glycoprotein (P-gp) to inhibition by compound 2c (cis-cis) N,N-bis(cyclohexanolamine)aryl ester isomer in a concentration-dependent manner in human MDR1-gene transfected mouse T-lymphoma L5178 cells as shown previously. By contrast, epirubicin (EPI) concentration changes left unaltered 2c IC50 values of EPI efflux. To clarify this discrepancy, defined molecular docking (DMD) analyses of 12 N,N-bis(cyclohexanolamine)aryl esters, the highly flexible aryl ester analog 4, and several P-gp substrate/non-substrate inhibitors were performed on human P-gp drug- or nucleotide-binding domains (DBD or NBD). DMD measurements yielded lowest binding energy (LBE, kcal/mol) values (mean ± SD) ranging from -11.8 ± 0.54 (valspodar) to -3.98 ± 0.01 (4). Lys234, Ser952 and Tyr953 residues formed H-bonds with most of the compounds. Only 2c docked also at ATP binding site (LBE value of -6.9 ± 0.30 kcal/mol). Inhibition of P-gp-mediated R123 efflux by 12 N,N-bis(cyclohexanolamine)aryl esters and 4 significantly correlated with LBE values. DMD analysis of EPI, (3)H-1EPI, (3)H-2EPI, (14)C-1EPI, (14)C-2EPI, R123 and 2c before and after previous docking of each of them indicated that pre-docking of either 2c or EPI significantly reduced LBE of both EPI and R123, and that of both (3)H-2EPI and (14)C-2EPI, respectively. Since the clusters of DBD amino acid residues interacting with EPI were different, if EPI docked alone or after pre-docking of EPI or 2c, the existence of alternative secondary binding site for EPI on P-gp is credible. In conclusion, 2c may allocate the drug-binding pocket and reduce strong binding of EPI and R123 in agreement with P-gp inhibition experiments, where 2c reduced efflux of EPI and R123.

  1. Plant lectins, from ancient sugar-binding proteins to emerging anti-cancer drugs in apoptosis and autophagy.

    Science.gov (United States)

    Jiang, Q-L; Zhang, S; Tian, M; Zhang, S-Y; Xie, T; Chen, D-Y; Chen, Y-J; He, J; Liu, J; Ouyang, L; Jiang, X

    2015-02-01

    Ubiquitously distributed in different plant species, plant lectins are highly diverse carbohydrate-binding proteins of non-immune origin. They have interesting pharmacological activities and currently are of great interest to thousands of people working on biomedical research in cancer-related problems. It has been widely accepted that plant lectins affect both apoptosis and autophagy by modulating representative signalling pathways involved in Bcl-2 family, caspase family, p53, PI3K/Akt, ERK, BNIP3, Ras-Raf and ATG families, in cancer. Plant lectins may have a role as potential new anti-tumour agents in cancer drug discovery. Thus, here we summarize these findings on pathway- involved plant lectins, to provide a comprehensive perspective for further elucidating their potential role as novel anti-cancer drugs, with respect to both apoptosis and autophagy in cancer pathogenesis, and future therapy.

  2. Binding of the Multimodal Antidepressant Drug Vortioxetine to the Human Serotonin Transporter

    DEFF Research Database (Denmark)

    Andersen, Jacob; Ladefoged, Lucy Kate; Wang, Danyang

    2015-01-01

    SERT. X-ray crystal structures of the bacterial amino acid transporter LeuT and the Drosophila melanogaster dopamine transporter were used to build homology models of hSERT. Comparative modeling and ligand docking suggest that vortioxetine can adopt several distinct binding modes within the central...

  3. Characterization of EPPIN's semenogelin I binding site: a contraceptive drug target.

    Science.gov (United States)

    Silva, Erick J R; Hamil, Katherine G; Richardson, Richard T; O'Rand, Michael G

    2012-09-01

    Epididymal protease inhibitor (EPPIN) is found on the surface of spermatozoa and works as a central hub for a sperm surface protein complex (EPPIN protein complex [EPC]) that inhibits sperm motility on the binding of semenogelin I (SEMG1) during ejaculation. Here, we identify EPPIN's amino acids involved in the interactions within the EPC and demonstrate that EPPIN's sequence C102-P133 contains the major binding site for SEMG1. Within the same region, the sequence F117-P133 binds the EPC-associated protein lactotransferrin (LTF). We show that residues Cys102, Tyr107, and Phe117 in the EPPIN C-terminus are required for SEMG1 binding. Additionally, residues Tyr107 and Phe117 are critically involved in the interaction between EPPIN and LTF. Our findings demonstrate that EPPIN is a key player in the protein-protein interactions within the EPC. Target identification is an important step toward the development of a novel male contraceptive, and the functionality of EPPIN's residues Cys102, Tyr107, and Phe117 offers novel opportunities for contraceptive compounds that inhibit sperm motility by targeting this region of the molecule.

  4. Probing the equatorial groove of the hookworm protein and vaccine candidate antigen, Na-ASP-2.

    Science.gov (United States)

    Mason, Lyndel; Tribolet, Leon; Simon, Anne; von Gnielinski, Natascha; Nienaber, Lisa; Taylor, Paul; Willis, Charlene; Jones, Malcolm K; Sternberg, Paul W; Gasser, Robin B; Loukas, Alex; Hofmann, Andreas

    2014-05-01

    Hookworm activation-associated secreted proteins can be structurally classified into at least three different groups. The hallmark feature of Group 1 activation-associated secreted proteins is a prominent equatorial groove, which is inferred to form a ligand binding site. Furthermore, a conserved tandem histidine motif is located in the centre of the groove and believed to provide or support a yet to be determined catalytic activity. Here, we report three-dimensional crystal structures of Na-ASP-2, an L3-secreted activation-associated secreted protein from the human hookworm Necator americanus, which demonstrate transition metal binding ability of the conserved tandem histidine motif. We further identified moderate phosphohydrolase activity of recombinant Na-ASP-2, which relates to the tandem histidine motif. By panning a random 12-mer peptide phage library, we identified a peptide with high similarity to the human calcium-activated potassium channel SK3, and confirm binding of the synthetic peptide to recombinant Na-ASP-2 by differential scanning fluorimetry. Potential binding modes of the peptide to Na-ASP-2 were studied by molecular dynamics simulations which clearly identify a preferred topology of the Na-ASP-2:SK3 peptide complex. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. How does fatty acid influence anti-thyroid drugs binding and specificity toward protein human serum albumin? A blind docking simulation study

    Indian Academy of Sciences (India)

    Bijan K Paul; Nikhil Guchhait

    2014-11-01

    This study reports an AutoDock-based blind docking simulation investigation to characterize the binding interaction of a series of anti-thyroid drugs (2-mercapto-1-methylimidazole (MMI), 2-thiouracil (TU), 6-methyl-2-thiouracil (MTU), 6--propyl-2-thiouracil (PTU) with a model plasma protein Human SerumAlbumin (HSA) in the presence and absence of fatty acid (FA). The drug-protein binding efficiency is characterized in terms of binding free energy and the association constant (Ka, which is estimated as the reciprocal of the inhibition constant, Ki) of the drugs to the transport protein. The study also unveils the substantial impact of the presence of fatty acid (FA) on the binding interaction process. It is shown that in the presence of FA the drug-protein binding efficiency is markedly enhanced (except for MTU) and the binding location is changed. Hydrogen bonding interaction appears to play a governing role in the process of FA-induced modifications of binding efficiency and location.

  6. Repurposing metformin: an old drug with new tricks in its binding pockets.

    Science.gov (United States)

    Pryor, Rosina; Cabreiro, Filipe

    2015-11-01

    Improvements in healthcare and nutrition have generated remarkable increases in life expectancy worldwide. This is one of the greatest achievements of the modern world yet it also presents a grave challenge: as more people survive into later life, more also experience the diseases of old age, including type 2 diabetes (T2D), cardiovascular disease (CVD) and cancer. Developing new ways to improve health in the elderly is therefore a top priority for biomedical research. Although our understanding of the molecular basis of these morbidities has advanced rapidly, effective novel treatments are still lacking. Alternative drug development strategies are now being explored, such as the repurposing of existing drugs used to treat other diseases. This can save a considerable amount of time and money since the pharmacokinetics, pharmacodynamics and safety profiles of these drugs are already established, effectively enabling preclinical studies to be bypassed. Metformin is one such drug currently being investigated for novel applications. The present review provides a thorough and detailed account of our current understanding of the molecular pharmacology and signalling mechanisms underlying biguanide-protein interactions. It also focuses on the key role of the microbiota in regulating age-associated morbidities and a potential role for metformin to modulate its function. Research in this area holds the key to solving many of the mysteries of our current understanding of drug action and concerted effects to provide sustained and long-life health.

  7. Identifying New Drug Targets for Potent Phospholipase D Inhibitors: Combining Sequence Alignment, Molecular Docking, and Enzyme Activity/Binding Assays.

    Science.gov (United States)

    Djakpa, Helene; Kulkarni, Aditya; Barrows-Murphy, Scheneque; Miller, Greg; Zhou, Weihong; Cho, Hyejin; Török, Béla; Stieglitz, Kimberly

    2016-05-01

    Phospholipase D enzymes cleave phospholipid substrates generating choline and phosphatidic acid. Phospholipase D from Streptomyces chromofuscus is a non-HKD (histidine, lysine, and aspartic acid) phospholipase D as the enzyme is more similar to members of the diverse family of metallo-phosphodiesterase/phosphatase enzymes than phospholipase D enzymes with active site HKD repeats. A highly efficient library of phospholipase D inhibitors based on 1,3-disubstituted-4-amino-pyrazolopyrimidine core structure was utilized to evaluate the inhibition of purified S. chromofuscus phospholipase D. The molecules exhibited inhibition of phospholipase D activity (IC50 ) in the nanomolar range with monomeric substrate diC4 PC and micromolar range with phospholipid micelles and vesicles. Binding studies with vesicle substrate and phospholipase D strongly indicate that these inhibitors directly block enzyme vesicle binding. Following these compelling results as a starting point, sequence searches and alignments with S. chromofuscus phospholipase D have identified potential new drug targets. Using AutoDock, inhibitors were docked into the enzymes selected from sequence searches and alignments (when 3D co-ordinates were available) and results analyzed to develop next-generation inhibitors for new targets. In vitro enzyme activity assays with several human phosphatases demonstrated that the predictive protocol was accurate. The strategy of combining sequence comparison, docking, and high-throughput screening assays has helped to identify new drug targets and provided some insight into how to make potential inhibitors more specific to desired targets.

  8. E-selectin binding peptide-polymer-drug conjugates and their selective cytotoxicity against vascular endothelial cells.

    Science.gov (United States)

    Shamay, Yosi; Paulin, Denise; Ashkenasy, Gonen; David, Ayelet

    2009-11-01

    The hypothesis that E-selectin on activated endothelial cells could be exploited to selectively target drug delivery systems to tumor vasculature was investigated. HPMA copolymer-doxorubicin (DOX) conjugates displaying the high affinity E-selectin binding peptide (Esbp, primary sequence DITWDQLWDLMK) as targeting ligand were synthesized and tested for their cytotoxicity and intracellular fate in human immortalized vascular endothelial cells (IVECs). The targeted copolymers displaying multiple copies of Esbp are bound to surface-associated E-selectin with affinity at the low nano-molar range, three orders of magnitude stronger than the free Esbp. In addition, the binding affinity of the HPMA-Esbp copolymers to E-selectin expressing IVECs was found to be 10-fold superior relative to non-targeted copolymers. Once bound, E-selectin facilitated rapid internalization and lysosomal trafficking of the copolymers. This lysosomotropism of HPMA-Esbp-bound DOX copolymers was then correlated with a 150-fold higher cytotoxicity relative to non-targeted HPMA-DOX conjugates. These findings strongly support the emerging role of E-selectin as a viable target for controlled drug delivery in cancer therapy.

  9. Recent Advances in Nucleic Acid Binding Aspects of Berberine Analogs and Implications for Drug Design.

    Science.gov (United States)

    Bhowmik, Debipreeta; Kumar, Gopinatha Suresh

    2016-01-01

    Berberine is one of the most widely known alkaloids belonging to the protoberberine group exhibiting myriad therapeutic properties. The anticancer potency of berberine appears to derive from its multiple actions including strong interaction with nucleic acids exhibiting adenine-thymine base pair specificity, inhibition of the enzymes topoisomerases and telomerases, and stabilizing the quadruplex structures. It was realized that the development of berberine as a potential anticancer agent necessitates enhancing its nucleic acid binding efficacy through appropriate structural modifications. More recently a number of such approaches have been attempted in various laboratories with great success. Several derivatives have been synthesized mostly with substitutions at the 8, 9 and 13 positions of the isoquinoline chromophore, and studied for enhanced nucleic acid binding activity. In this article, we present an up to date review of the details of the interaction of berberine and several of its important synthetic 8, 9 and 13 substituted derivatives with various nucleic acid structures reported recently. These studies provide interesting knowledge on the mode, mechanism, sequence and structural specificity of the binding of berberine derivatives and correlate structural and energetic aspects of the interaction providing better understanding of the structure- activity relations for designing and development of berberine based therapeutic agents with higher efficacy and therapeutic potential.

  10. The FNIP co-chaperones decelerate the Hsp90 chaperone cycle and enhance drug binding

    Science.gov (United States)

    Woodford, Mark R.; Dunn, Diana M.; Blanden, Adam R.; Capriotti, Dante; Loiselle, David; Prodromou, Chrisostomos; Panaretou, Barry; Hughes, Philip F.; Smith, Aaron; Ackerman, Wendi; Haystead, Timothy A.; Loh, Stewart N.; Bourboulia, Dimitra; Schmidt, Laura S.; Marston Linehan, W.; Bratslavsky, Gennady; Mollapour, Mehdi

    2016-01-01

    Heat shock protein-90 (Hsp90) is an essential molecular chaperone in eukaryotes involved in maintaining the stability and activity of numerous signalling proteins, also known as clients. Hsp90 ATPase activity is essential for its chaperone function and it is regulated by co-chaperones. Here we show that the tumour suppressor FLCN is an Hsp90 client protein and its binding partners FNIP1/FNIP2 function as co-chaperones. FNIPs decelerate the chaperone cycle, facilitating FLCN interaction with Hsp90, consequently ensuring FLCN stability. FNIPs compete with the activating co-chaperone Aha1 for binding to Hsp90, thereby providing a reciprocal regulatory mechanism for chaperoning of client proteins. Lastly, downregulation of FNIPs desensitizes cancer cells to Hsp90 inhibitors, whereas FNIPs overexpression in renal tumours compared with adjacent normal tissues correlates with enhanced binding of Hsp90 to its inhibitors. Our findings suggest that FNIPs expression can potentially serve as a predictive indicator of tumour response to Hsp90 inhibitors. PMID:27353360

  11. Electrospinning of Grooved Polystyrene Fibers: Effect of Solvent Systems

    Science.gov (United States)

    Liu, Wanjun; Huang, Chen; Jin, Xiangyu

    2015-05-01

    Secondary surface texture is of great significance to morphological variety and further expands the application areas of electrospun nanofibers. This paper presents the possibility of directly electrospinning grooved polystyrene (PS) fibers using both single and binary solvent systems. Solvents were classified as low boiling point solvent (LBPS): dichloromethane (DCM), acetone (ACE), and tetrahydrofuran (THF); high boiling point solvent (HBPS): N, N-dimethylformamide (DMF) and cyclohexanone (CYCo); and non-solvent (NS): 1-butanol (BuOH). By the systematic selection and combination of these solvents at given parameters, we found that single solvent systems produced non-grooved fibers. LBPS/DMF solvent systems resulted in fibers with different grooved textures, while LBPS/CYCo led to fibers with double grooved texture. Grooved fibers can also be fabricated from LBPS/LBPS, NS/LBPS, and NS/HBPS systems under specific conditions. The results indicated that the difference of evaporation rate (DER) between the two solvents played a key role in the formation of grooved texture. The formation of this unique texture should be attributed to three separate mechanisms, namely void-based elongation, wrinkle-based elongation, and collapsed jet-based elongation. Our findings can serve as guidelines for the preparation of ultrafine fibers with grooved secondary texture.

  12. Low dose tubulin-binding drugs rescue peroxisome trafficking deficit in patient-derived stem cells in Hereditary Spastic Paraplegia

    Directory of Open Access Journals (Sweden)

    Yongjun Fan

    2014-05-01

    Full Text Available Hereditary Spastic Paraplegia (HSP is a genetically heterogeneous group of disorders, diagnosed by progressive gait disturbances with muscle weakness and spasticity, for which there are no treatments targeted at the underlying pathophysiology. Mutations in spastin are a common cause of HSP. Spastin is a microtubule-severing protein whose mutation in mouse causes defective axonal transport. In human patient-derived olfactory neurosphere-derived (ONS cells, spastin mutations lead to lower levels of acetylated α-tubulin, a marker of stabilised microtubules, and to slower speed of peroxisome trafficking. Here we screened multiple concentrations of four tubulin-binding drugs for their ability to rescue levels of acetylated α-tubulin in patient-derived ONS cells. Drug doses that restored acetylated α-tubulin to levels in control-derived ONS cells were then selected for their ability to rescue peroxisome trafficking deficits. Automated microscopic screening identified very low doses of the four drugs (0.5 nM taxol, 0.5 nM vinblastine, 2 nM epothilone D, 10 µM noscapine that rescued acetylated α-tubulin in patient-derived ONS cells. These same doses rescued peroxisome trafficking deficits, restoring peroxisome speeds to untreated control cell levels. These results demonstrate a novel approach for drug screening based on high throughput automated microscopy for acetylated α-tubulin followed by functional validation of microtubule-based peroxisome transport. From a clinical perspective, all the drugs tested are used clinically, but at much higher doses. Importantly, epothilone D and noscapine can enter the central nervous system, making them potential candidates for future clinical trials.

  13. Grooved Fuel Rings for Nuclear Thermal Rocket Engines

    Science.gov (United States)

    Emrich, William

    2009-01-01

    An alternative design concept for nuclear thermal rocket engines for interplanetary spacecraft calls for the use of grooved-ring fuel elements. Beyond spacecraft rocket engines, this concept also has potential for the design of terrestrial and spacecraft nuclear electric-power plants. The grooved ring fuel design attempts to retain the best features of the particle bed fuel element while eliminating most of its design deficiencies. In the grooved ring design, the hydrogen propellant enters the fuel element in a manner similar to that of the Particle Bed Reactor (PBR) fuel element.

  14. Anterior Interhemispheric Approach for Olfactory Groove Meningioma

    Directory of Open Access Journals (Sweden)

    Imam Hidayat

    2016-09-01

    Full Text Available Objective: To evaluate the surgical technique with bifrontal interhemispheric approach for total removal of tumor in olfactory groove meningioma (OGM. Methods: This study described a case of a 38-year-old woman with bilateral blindness, anosmia, and behaviour changes. Imaging studies show a tumor mass in midfrontal base. Surgery using a bifrontal interhemispheric approach was performed and total removal was achieved and postoperative computed tomography (CT scan was performed to confirm the result. Histopathological findings established a diagnosis of meningioma. Results: A coronal skin incision behind the hairline was utilized. The scalp was elevated, taking care to reserve the vascularized pericranium medial to the linea temporalis of each side, and preserving the 2 supraorbital nerves. Eight burr holes were used, with the two initial holes made on each side of the orbitotemporal region, and the other four holes at the midline. A bifrontal craniotomy was performed. The tumor was first detached from its attachment with bipolar cautery and debulked. During this step, the main tumor feeder arteries from the anterior and posterior ethmoidal artery were interrupted, and the tumor devascularized. Total tumor removal through surgical intervention was achieved and confirmed by head CT-scan postoperatively. Conclusions: This case report supports the suitability of the bifrontal interhemispheric approach for OGM resection with additional radiation therapy.

  15. Probing kinetic drug binding mechanism in voltage-gated sodium ion channel: open state versus inactive state blockers.

    Science.gov (United States)

    Pal, Krishnendu; Gangopadhyay, Gautam

    2015-01-01

    The kinetics and nonequilibrium thermodynamics of open state and inactive state drug binding mechanisms have been studied here using different voltage protocols in sodium ion channel. We have found that for constant voltage protocol, open state block is more efficient in blocking ionic current than inactive state block. Kinetic effect comes through peak current for mexiletine as an open state blocker and in the tail part for lidocaine as an inactive state blocker. Although the inactivation of sodium channel is a free energy driven process, however, the two different kinds of drug affect the inactivation process in a different way as seen from thermodynamic analysis. In presence of open state drug block, the process initially for a long time remains entropy driven and then becomes free energy driven. However in presence of inactive state block, the process remains entirely entropy driven until the equilibrium is attained. For oscillating voltage protocol, the inactive state blocking is more efficient in damping the oscillation of ionic current. From the pulse train analysis it is found that inactive state blocking is less effective in restoring normal repolarisation and blocks peak ionic current. Pulse train protocol also shows that all the inactive states behave differently as one inactive state responds instantly to the test pulse in an opposite manner from the other two states.

  16. Implications of nanoscale based drug delivery systems in delivery and targeting tubulin binding agent, noscapine in cancer cells.

    Science.gov (United States)

    Chandra, Ramesh; Madan, Jitender; Singh, Prashant; Chandra, Ankush; Kumar, Pradeep; Tomar, Vartika; Dass, Sujata K

    2012-12-01

    Noscapine, a tubulin binding anticancer agent undergoing Phase I/II clinical trials, inhibits tumor growth in nude mice bearing human xenografts of breast, lung, ovarian, brain, and prostrate origin. The analogues of noscapine like 9-bromonoscapine (EM011) are 5 to 10-fold more active than parent compound, noscapine. Noscapinoids inhibit the proliferation of cancer cells that are resistant to paclitaxel and epothilone. Noscapine also potentiated the anticancer activity of doxorubicin in a synergistic manner against triple negative breast cancer (TNBC). However, physicochemical and pharmacokinetic (ED50˜300-600 mg/kg bodyweight) limitations of noscapine present hurdle in development of commercial anticancer formulations. Therefore, objectives of the present review are to summarize the chemotherapeutic potential of noscapine and implications of nanoscale based drug delivery systems in enhancing the therapeutic efficacy of noscapine in cancer cells. We have constructed noscapine-enveloped gelatin nanoparticles, NPs and poly (ethylene glycol) grafted gelatin NPs as well as inclusion complex of noscapine in β-cyclodextrin (β-CD) and evaluated their physicochemical characteristics. The Fe3O4 NPs were also used to incorporate noscapine in its polymeric nanomatrix system where molecular weight of the polymer governed the encapsulation efficiency of drug. The enhanced noscapine delivery using μPAR-targeted optical-MR imaging trackable NPs offer a great potential for image directed targeted delivery of noscapine. Human Serum Albumin NPs (150-300 nm) as efficient noscapine drug delivery systems have also been developed for potential use in breast cancer.

  17. Inhibitory effect of membrane-binding drugs on excision repair of DNA damage in UV-irradiated Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Todo, T.; Yonei, S. (Kyoto Univ. (Japan). Lab. of Radiation Biology)

    1983-04-01

    The effects of procaine and lidocaine on DNA-repair processes were investigated in UV-irradiated cells of E. coli with different DNA-repair capacities. The cells were irradiated with various doses of UV and then incubated at 37/sup 0/C in M9 buffer (liquid-holding) or in EM9 medium in the presence or absence of membrane-binding drugs. The results obtained are as follows. (1) In strains H/r30 (wild-type for DNA repair) and NG30 (recA/sup -/), the increase in survival with increase in time of liquid-holding was almost completely inhibited by the addition of procaine and lidocaine. The same trends were observable under conditions of post-irradiation incubation in EM9 medium, more efficiently in recA/sup -/ strain than in the wild-type strain. (2) The addition of these drugs gave an apparent enhancement of the frequency of UV-induced mutation to arginine prototrophy, corresponding to a decrease in survival. (3) There were negligible effects of the drugs on survival and mutation in the excision-repair-defective strain, Hs30 (uvrB/sup -/). (4) The removal of thymine dimers from DNA was actually reduced by the addition of procaine.

  18. A strategy for increasing the brain uptake of a radioligand in animals: use of a drug that inhibits plasma protein binding

    Energy Technology Data Exchange (ETDEWEB)

    Haradahira, Terushi E-mail: terushi@nirs.go.jp; Zhang, Ming-Rong; Maeda, Jun; Okauchi, Takashi; Kawabe, Kouichi; Kida, Takayo; Suzuki, Kazutoshi; Suhara, Tetsuya

    2000-05-01

    A positron-emitter labeled radioligand for the glycine-binding site of the N-methyl-D-aspartate (NMDA) receptor, [{sup 11}C]L-703,717, was examined for its ability to penetrate the brain in animals by simultaneous use with drugs having high-affinity separate binding sites on human serum albumin. [{sup 11}C]L-703,717 has poor blood-brain barrier (BBB) permeability because it binds tightly to plasma proteins. Co-injection of warfarin (50-200 mg/kg), a drug that binds to albumin and resembles L-703,717 in structure, dose-dependently enhanced the penetration by [{sup 11}C]L-703,717 in mice, resulting in a five-fold increase in the brain radioactivity at 1 min after the injection. Drugs structurally unrelated to L-703,717, salicylate, phenol red, and L-tryptophan, were less effective or ineffective in increasing the uptake of [{sup 11}C]L-703,717. These results suggest that the simultaneous use of a drug that inhibits the binding of a radioligand to plasma proteins is a useful way to overcome the poor BBB permeability of the radioligand triggered by its tight binding to plasma proteins. In brain distribution studies in rodents, it was found that, after the increase in brain uptake with warfarin, much of the glycine site antagonist accumulates in the cerebellum but its pharmacological specificity did not match the glycine site of NMDA receptors.

  19. Modeling the Effects of Drug Binding on the Dynamic Instability of Microtubules

    CERN Document Server

    Hinow, Peter; Lopus, Manu; Jordan, Mary Ann; Tuszynski, Jack A

    2010-01-01

    We propose a stochastic model that accounts for the growth, catastrophe and rescue processes of steady state microtubules assembled from MAP-free tubulin. Both experimentally and theoretically we study the perturbation of microtubule dynamic instability by S-methyl-D-DM1, a synthetic derivative of the microtubule-targeted agent maytansine and a potential anticancer agent. We find that to be an effective suppressor of microtubule dynamics a drug must primarily suppress the loss of GDP tubulin from the microtubule tip.

  20. Glutathione selectively modulates the binding of platinum drugs to human copper chaperone Cox17.

    Science.gov (United States)

    Zhao, Linhong; Wang, Zhen; Wu, Han; Xi, Zhaoyong; Liu, Yangzhong

    2015-12-01

    The copper chaperone Cox17 (cytochrome c oxidase copper chaperone) has been shown to facilitate the delivery of cisplatin to mitochondria, which contributes to the overall cytotoxicity of the drug [Zhao et al. (2014) Chem. Commun. 50: , 2667-2669]. Kinetic data indicate that Cox17 has reactivity similar to glutathione (GSH), the most abundant thiol-rich molecule in the cytoplasm. In the present study, we found that GSH significantly modulates the reaction of platinum complexes with Cox17. GSH enhances the reactivity of three anti-cancer drugs (cisplatin, carboplatin and oxaliplatin) to Cox17, but suppresses the reaction of transplatin. Surprisingly, the pre-formed cisplatin-GSH adducts are highly reactive to Cox17; over 90% platinum transfers from GSH to Cox17. On the other hand, transplatin-GSH adducts are inert to Cox17. These different effects are consistent with the drug activity of these platinum complexes. In addition, GSH attenuates the protein aggregation of Cox17 induced by platination. These results indicate that the platinum-protein interactions could be substantially influenced by the cellular environment.

  1. Atomic Level Rendering of DNA-Drug Encounter

    Science.gov (United States)

    Lucas, Maria F.; Cabeza de Vaca, Israel; Takahashi, Ryoji; Rubio-Martínez, Jaime; Guallar, Víctor

    2014-01-01

    Computer simulations have been demonstrated to be important for unraveling atomic mechanisms in biological systems. In this study, we show how combining unbiased molecular dynamic simulations with appropriate analysis tools can successfully describe metal-based drug interactions with DNA. To elucidate the noncovalent affinity of cisplatin’s family to DNA, we performed extensive all-atom molecular dynamics simulations (3.7 μs total simulation length). The results show that the parent drug, cisplatin, has less affinity to form noncovalent adducts in the major groove than its aquo complexes. Furthermore, the relative position in which the drugs enter the major groove is dependent on the compound’s net charge. Based on the simulations, we estimated noncovalent binding free energies through the use of Markov state models. In addition, and to overcome the lack of experimental information, we employed two additional methods: Molecular Mechanics Poisson-Boltzmann Surface Area (MMPB-SA) and steered molecular dynamics with the Jarzynski estimator, with an overall good agreement between the three methods. All complexes show interaction energies below 3 kcal/mol with DNA but the charged hydrolysis products have slightly more favorable binding free energies than the parent drug. Moreover, this study sets the precedent for future unbiased DNA-ligand simulations of more complex binders. PMID:24461017

  2. Water participation in molecular recognition and protein-ligand association: Probing the drug binding site "Sudlow I" in human serum albumin

    Science.gov (United States)

    Al-Lawatia, Najla; Steinbrecher, Thomas; Abou-Zied, Osama K.

    2012-03-01

    Human serum albumin (HSA) plays an important role in the transport and disposition of endogenous and exogenous ligands present in blood. Its capacity to reversibly bind a large variety of drugs results in its prevailing role in drug pharmacokinetics and pharmacodynamics. In this work, we used 7-hydroxyquinoline (7HQ) as a probe to study the binding nature of one of the major drug binding sites of HSA (Sudlow I) and to reveal the local environment around the probe in the binding site. The interaction between 7HQ and HSA at a physiological pH of 7.2 was investigated using steady-state and lifetime spectroscopic measurements, molecular docking and molecular dynamics (MD) simulations methods. The fluorescence results indicate a selective interaction between 7HQ and the Trp214 residue. The reduction in both the intensity and lifetime of the Trp214 fluorescence upon probe binding indicates the dominant role of static quenching. Molecular docking and MD simulations show that 7HQ binds in Sudlow site I close to Trp214, confirming the experimental results, and pinpoint the dominant role of hydrophobic interaction in the binding site. Electrostatic interactions were also found to be important in which two water molecules form strong hydrogen bonds with the polar groups of 7HQ. Detection of water in the binding site agrees with the absorption and fluorescence results that show the formation of a zwitterion tautomer of 7HQ. The unique spectral signatures of 7HQ in water make this molecule a potential probe for detecting the presence of water in nanocavities of proteins. Interaction of 7HQ with water in the binding site shows that water molecules can be crucial for molecular recognition and association in protein binding sites.

  3. Fractures of the proximal humerus involving the intertubercular groove

    Energy Technology Data Exchange (ETDEWEB)

    Ahovuo, J.; Paavolainen, P.; Bjoerkenheim, J.M. (Helsinki Univ. Central Hospital (Finland). Dept. of Radiology; Helsinki Univ. Central Hospital (Finland). Div. of Traumatology and Orthopaedic Surgery)

    The purpose of this study was to analyse the involvement of the gliding surface of the biceps tendon in fractures of the proximal humerus. Fifteen patients had a fracture of the proximal humerus verified with antero-posterior and axillary radiographs. Tangential radiographs of the intertubercular groove, obtained from the shoulder joint, showed involvement of the intertubercular groove in 13 patients (87%), which could not be shown with other projections. Groove radiographs revealed in 3 patients a dislocation of the fragments of the greater tuberosity large enough to require surgical treatment, but which had not been found using conventional techniques. Therefore, a groove radiograph should be used to precise fractures of the proximal humerus. (orig.).

  4. Heat transfer and thermal stress analysis in grooved tubes

    Indian Academy of Sciences (India)

    Veysel Özceyhan; Necdet Altuntop

    2005-08-01

    Heat transfer and thermal stresses, induced by temperature differencesin the internally grooved tubes of heat transfer equipment, have been analysed numerically. The analysis has been conducted for four different kinds of internally grooved tubes and three different mean inlet water velocities. Constant temperature was applied from the external surface of the tube. Energy and governing flow equations were solved using finite difference scheme. Finite element method (FEM) was used to compute the thermal stress fields. Grooving effects on the thermal stress ratio have been discussed. As a result, maximum thermal stress occurs in the case of $p = d$ for all water inlet velocities. The maximum thermal stress ratio positions inside the tube have been indicated as MX for all investigated cases. In the light of the thermal stress values, various designs can be applied to reduce thermal stress in grooved tubes.

  5. Analysis Groove Characteristics of Friction Dishes in Wet Speeding Clutch

    Institute of Scientific and Technical Information of China (English)

    HongYue; LiuJin; JinShiliang

    2004-01-01

    The impacts of different groove shapes, numbers, and angle of friction dish on transmitting torque, speed, push pressure in wet speeding clutch are discussed in this paper. Since the wet speeed governing clutch works within hydrodynamic lubrication mixture lubrication. boundary, lubrication and contact situation, the oils combining with a-hydrocarbon or polyester are getting widely used as lubricant.The power-law fluid model with Patir-Cheng average flow model, GT asperity contact model and oil film inertia are applied for average Reynolds equation setting, In order to investigate the relationship between average push pressure within hydrodynamic lubrication and mixture lubrication, average transmitting torque and output speed, the numeral calculation and analysis are presented. According to calculation, it is found that the groove shape, groove angle and groove numbers affect the average transfer torque and push pressure with the speed rate.

  6. Interproximal grooving in the Atapuerca-SH hominid dentitions.

    Science.gov (United States)

    Bermúdez de Castro, J M; Arsuaga, J L; Pérez, P J

    1997-03-01

    The dental sample recovered from the Sima de los Huesos (SH) Middle Pleistocene cave site of the Sierra de Atapuerca (Spain) includes 296 specimens. Interproximal wear grooves have been observed in 20 maxillary and mandibular posterior teeth belonging to at least five of the 32 individuals identified so far in the SH hypodigm. Interproximal grooving affected only the adults, and at an age between 25 and 40 years. The appearance, morphology, and location pattern of the SH wear grooves are similar to those reported in other fossil hominids and in more recent human populations. Two alternative proposals, the toothpicking and the fiber or sinew processing hypotheses, compete for explaining the formation of this anomalous wear. The characteristics observed in the wear grooves of the SH teeth are compatible only with the habitual probing of interdental spaces by means of hard and inflexible objects. Dietary grit may also have contributed to the abrasion of the root walls during the motion of the dental probes.

  7. Femtosecond laser-induced blazed periodic grooves on metals.

    Science.gov (United States)

    Hwang, Taek Yong; Guo, Chunlei

    2011-07-01

    In this Letter, we generate laser-induced periodic surface structures (LIPSSs) on platinum following femtosecond laser pulse irradiation. For the first time to our knowledge, we study the morphological profile of LIPSSs over a broad incident angular range, and find that the morphological profile of LIPSSs depends significantly on the incident angle of the laser beam. We show that LIPSS grooves become more asymmetric at a larger incident angle, and the morphological profile of LIPSSs formed at an incident angle over 55° eventually resembles that of a blazed grating. Our study suggests that the formation of the blazed groove structures is attributed to the selective ablation of grooves through the asymmetric periodic surface heating following femtosecond pulse irradiation. The blazed grooves are useful for controlling the diffraction efficiency of LIPSSs.

  8. Measurement and analysis of grain boundary grooving by volume diffusion

    Science.gov (United States)

    Hardy, S. C.; Mcfadden, G. B.; Coriell, S. R.; Voorhees, P. W.; Sekerka, R. F.

    1991-01-01

    Experimental measurements of isothermal grain boundary grooving by volume diffusion are carried out for Sn bicrystals in the Sn-Pb system near the eutectic temperature. The dimensions of the groove increase with a temporal exponent of 1/3, and measurement of the associated rate constant allows the determination of the product of the liquid diffusion coefficient D and the capillarity length Gamma associated with the interfacial free energy of the crystal-melt interface. The small-slope theory of Mullins is generalized to the entire range of dihedral angles by using a boundary integral formulation of the associated free boundary problem, and excellent agreement with experimental groove shapes is obtained. By using the diffusivity measured by Jordon and Hunt, the present measured values of Gamma are found to agree to within 5 percent with the values obtained from experiments by Gunduz and Hunt on grain boundary grooving in a temperature gradient.

  9. Groove shape characteristics of echelle gratings with high diffraction efficiency

    Science.gov (United States)

    Zhang, Shanwen; Mi, Xiaotao; Zhang, Qian; Jirigalantu; Feng, Shulong; Yu, Haili; Qi, Xiangdong

    2017-03-01

    The groove shape characteristics of echelle gratings with high diffraction efficiency are investigated. Using the coordinate transformation method (C method), an r-2 aluminum echelle with 79 grooves/mm is optimized through rigorous numerical simulations and shows high diffraction efficiency of 76-81% in the high Littrow orders. A grating is found to be essentially an echelle if it contains a series of reflective facets with a specific tilt angle that are located far from the nonworking facet of the grating and have a deep groove depth; any groove shape that meets these conditions can be called an echelle grating. The underlying mechanism is analyzed phenomenologically using electromagnetic theory. The universal model proposed here, which represents a new cognitive understanding of the concept of the echelle, is ready for use in manufacturing applications and offers a new perspective for the fabrication of these gratings.

  10. [Developmental radicular groove as a cause of endodontic failure].

    Science.gov (United States)

    Fabra Campos, H; Millet Part, J

    1989-01-01

    A clinical case of apical injury on an upper lateral incisor with endodontical and surgical failures in its treatment is presented. Extraction of the incisor and its study at the stereoscopic microscope showed the existence of a developmental groove running from the cingulum to the end of the root, establishing a communication between the crevice and the apical part of the tooth. Bacterial infection through the groove could provide an explanation for treatment failure.

  11. Surface reproduction of elastomeric materials: viscosity and groove shape effects

    OpenAIRE

    Mahmood, N.; Abu Kasim, N.H.; Azuddin, M.; Kasim, N.L. Abu

    2010-01-01

    Objective: To evaluate the effect of viscosity and type of grooves on surface detail reproduction of elastomeric impression materials. Methods: Express putty/light-, Impregum medium- and heavy/light-bodied and Aquasil medium- and putty/light-bodied elastomeric impression materials were chosen for this study. Five impressions were made using a cylindrical aluminum reference block with U- and V- shaped grooves and to produce 35 master dies. Each master die was immersed in distilled water at 370...

  12. Polymer scaffolds with preferential parallel grooves enhance nerve regeneration.

    Science.gov (United States)

    Mobasseri, Atefeh; Faroni, Alessandro; Minogue, Ben M; Downes, Sandra; Terenghi, Giorgio; Reid, Adam J

    2015-03-01

    We have modified the surface topography of poly ɛ-caprolactone (PCL) and polylactic acid (PLA) blended films to improve cell proliferation and to guide the regeneration of peripheral nerves. Films with differing shaped grooves were made using patterned silicon templates, sloped walls (SL), V-shaped (V), and square-shaped (SQ), and compared with nongrooved surfaces with micropits. The solvent cast films were tested in vitro using adult adipose-derived stem cells differentiated to Schwann cell-like cells. Cell attachment, proliferation, and cell orientation were all improved on the grooved surfaces, with SL grooves giving the best results. We present in vivo data on Sprague-Dawley rat sciatic nerve injury with a 10-mm gap, evaluating nerve regeneration at 3 weeks across a polymer nerve conduit modified with intraluminal grooves (SL, V, and SQ) and differing wall thicknesses (70, 100, 120, and 210 μm). The SL-grooved nerve conduit showed a significant improvement over the other topographical-shaped grooves, while increasing the conduit wall thickness saw no positive effect on the biological response of the regenerating nerve. Furthermore, the preferred SL-grooved conduit (C) with 70 μm wall thickness was compared with the current clinical gold standard of autologous nerve graft (Ag) in the rat 10-mm sciatic nerve gap model. At 3 weeks postsurgery, all nerve gaps across both groups were bridged with regenerated nerve fibers. At 16 weeks, features of regenerated axons were comparable between the autograft (Ag) and conduit (C) groups. End organ assessments of muscle weight, electromyography, and skin reinnervation were also similar between the groups. The comparable experimental outcome between conduit and autograft, suggests that the PCL/PLA conduit with inner lumen microstructured grooves could be used as a potential alternative treatment for peripheral nerve repair.

  13. Droplet impact on regular micro-grooved surfaces

    Institute of Scientific and Technical Information of China (English)

    Hu Hai-Bao; Huang Su-He; Chen Li-Bin

    2013-01-01

    We have investigated experimentally the process of a droplet impact on a regular micro-grooved surface.The target surfaces are patterned such that micro-scale spokes radiate from the center,concentric circles,and parallel lines on the polishing copper plate,using Quasi-LIGA molding technology.The dynamic behavior of water droplets impacting on these structured surfaces is examined using a high-speed camera,including the drop impact processes,the maximum spreading diameters,and the lengths and numbers of fingers at different values of Weber number.Experimental results validate that the spreading processes are arrested on all target surfaces at low velocity.Also,the experimental results at higher impact velocity demonstrate that the spreading process is conducted on the surface parallel to the micro-grooves,but is arrested in the direction perpendicular to the micro-grooves.Besides,the lengths of fingers increase observably,even when they are ejected out as tiny droplets along the groove direction,at the same time the drop recoil velocity is reduced by micro-grooves which are parallel to the spreading direction,but not by micro-grooves which are vertical to the spreading direction.

  14. Photoexcited triplet state provides a quantitative measure of intercalating drug-DNA binding energies

    Science.gov (United States)

    Maki, August H.; Alfredson, T. V.; Waring, M. J.

    1992-04-01

    A linear correlation between spectroscopic and thermodynamic properties of systems is rarely encountered. In triplet state ODMR studies of various DNA complexes of echinomycin, a quinoxaline-containing cyclic depsipeptide bis-intercalating antibiotic, and its biosynthesized quinoline analogs, such correlations are observed. The zero field splitting D-parameter of the intercalated quinoxaline or quinoline residue varies linearly with the free energy of drug-DNA complexing. From previous work, the DNA sequence specificity of echinomycin analogs is known to be influenced by the identity of the intercalating residue (e.g., quinoxaline vs. quinoline). The present results strongly suggest that the DNA sequence-specificity of these drugs is controlled largely by the intercalated residue, and that the energetics of the peptide- DNA interaction, although considerable, are relatively sequence independent. These conclusions run counter to the generally accepted idea that DNA recognition by sequence- seeking proteins is controlled by specific hydrogen bonding interactions. The high degree of N-methylation of the echinomycin peptide portion severely restricts these interactions, however. A simple theoretical model is presented to support the experimentally observed linear correlation between (Delta) D and (Delta) G.

  15. ATP-binding cassette transporter controls leaf surface secretion of anticancer drug components in Catharanthus roseus.

    Science.gov (United States)

    Yu, Fang; De Luca, Vincenzo

    2013-09-24

    The Madagascar periwinkle (Catharanthus roseus) is highly specialized for the biosynthesis of many different monoterpenoid indole alkaloids (MIAs), many of which have powerful biological activities. Such MIAs include the commercially important chemotherapy drugs vinblastine, vincristine, and other synthetic derivatives that are derived from the coupling of catharanthine and vindoline. However, previous studies have shown that biosynthesis of these MIAs involves extensive movement of metabolites between specialized internal leaf cells and the leaf epidermis that require the involvement of unknown secretory processes for mobilizing catharanthine to the leaf surface and vindoline to internal leaf cells. Spatial separation of vindoline and catharanthine provides a clear explanation for the low levels of dimers that accumulate in intact plants. The present work describes the molecular cloning and functional identification of a unique catharanthine transporter (CrTPT2) that is expressed predominantly in the epidermis of young leaves. CrTPT2 gene expression is activated by treatment with catharanthine, and its in planta silencing redistributes catharanthine to increase the levels of catharanthine-vindoline drug dimers in the leaves. Phylogenetic analysis shows that CrTPT2 is closely related to a key transporter involved in cuticle assembly in plants and that may be unique to MIA-producing plant species, where it mediates secretion of alkaloids to the plant surface.

  16. Isothermal titration calorimetry for drug design: Precision of the enthalpy and binding constant measurements and comparison of the instruments.

    Science.gov (United States)

    Linkuvienė, Vaida; Krainer, Georg; Chen, Wen-Yih; Matulis, Daumantas

    2016-12-15

    Isothermal titration calorimetry (ITC) is one of the most robust label- and immobilization-free techniques used to measure protein - small molecule interactions in drug design for the simultaneous determination of the binding affinity (ΔG) and the enthalpy (ΔH), both of which are important parameters for structure-thermodynamics correlations. It is important to evaluate the precision of the method and of various ITC instrument models by performing a single well-characterized reaction. The binding between carbonic anhydrase II and acetazolamide was measured by four ITC instruments - PEAQ-ITC, iTC200, VP-ITC, and MCS-ITC and the standard deviation of ΔG and ΔH was determined. Furthermore, the limit of an approach to reduce the protein concentration was studied for a high-affinity reaction (Kd = 0.3 nM), too tight to be measured by direct (non-displacement) ITC. Chemical validation of the enthalpy measurements is discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Subchronic treatment with antiepileptic drugs modifies pentylenetetrazol-induced seizures in mice: Its correlation with benzodiazepine receptor binding

    Directory of Open Access Journals (Sweden)

    Luisa Rocha

    2008-06-01

    Full Text Available Luisa RochaPharmacobiology Department, Center for Research and Advanced Studies, Calz, Tenorios, MéxicoAbstract: Experiments using male CD1 mice were carried out to investigate the effects of subchronic (daily administration for 8 days pretreatments with drugs enhancing GABAergic transmission (diazepam, 10 mg/kg, ip; gabapentin, 100 mg/kg, po; or vigabatrin, 500 mg/kg, po on pentylenetetrazol (PTZ-induced seizures, 24 h after the last injection. Subchronic administration of diazepam reduced latencies to clonus, tonic extension and death induced by PTZ. Subchronic vigabatrin produced enhanced latency to the first clonus but faster occurrence of tonic extension and death induced by PTZ. Subchronic gabapentin did not modify PTZ-induced seizures. Autoradiography experiments revealed reduced benzodiazepine receptor binding in several brain areas after subchronic treatment with diazepam or gabapentin, whereas subchronic vigabatrin did not induce significant receptor changes. The present results indicate differential effects induced by the subchronic administration of diazepam, vigabatrin, and gabapentin on the susceptibility to PTZ-induced seizures, benzodiazepine receptor binding, or both.Keywords: diazepam, gabapentin, vigabatrin, pentylenetetrazol, benzodiazepine receptors

  18. An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design.

    Science.gov (United States)

    Ballante, Flavio; Marshall, Garland R

    2016-01-25

    Molecular docking is a widely used technique in drug design to predict the binding pose of a candidate compound in a defined therapeutic target. Numerous docking protocols are available, each characterized by different search methods and scoring functions, thus providing variable predictive capability on a same ligand-protein system. To validate a docking protocol, it is necessary to determine a priori the ability to reproduce the experimental binding pose (i.e., by determining the docking accuracy (DA)) in order to select the most appropriate docking procedure and thus estimate the rate of success in docking novel compounds. As common docking programs use generally different root-mean-square deviation (RMSD) formulas, scoring functions, and format results, it is both difficult and time-consuming to consistently determine and compare their predictive capabilities in order to identify the best protocol to use for the target of interest and to extrapolate the binding poses (i.e., best-docked (BD), best-cluster (BC), and best-fit (BF) poses) when applying a given docking program over thousands/millions of molecules during virtual screening. To reduce this difficulty, two new procedures called Clusterizer and DockAccessor have been developed and implemented for use with some common and "free-for-academics" programs such as AutoDock4, AutoDock4(Zn), AutoDock Vina, DOCK, MpSDockZn, PLANTS, and Surflex-Dock to automatically extrapolate BD, BC, and BF poses as well as to perform consistent cluster and DA analyses. Clusterizer and DockAccessor (code available over the Internet) represent two novel tools to collect computationally determined poses and detect the most predictive docking approach. Herein an application to human lysine deacetylase (hKDAC) inhibitors is illustrated.

  19. 2D IR spectroscopy reveals the role of water in the binding of channel-blocking drugs to the influenza M2 channel

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Ayanjeet, E-mail: ayanjeet@sas.upenn.edu, E-mail: gai@sas.upenn.edu; Gai, Feng, E-mail: ayanjeet@sas.upenn.edu, E-mail: gai@sas.upenn.edu; Hochstrasser, Robin M. [Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (United States); Wang, Jun; DeGrado, William F. [Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143 (United States); Moroz, Yurii S.; Korendovych, Ivan V. [Department of Chemistry, Syracuse University, Syracuse, New York 13244 (United States); Zanni, Martin [Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706 (United States)

    2014-06-21

    Water is an integral part of the homotetrameric M2 proton channel of the influenza A virus, which not only assists proton conduction but could also play an important role in stabilizing channel-blocking drugs. Herein, we employ two dimensional infrared (2D IR) spectroscopy and site-specific IR probes, i.e., the amide I bands arising from isotopically labeled Ala30 and Gly34 residues, to probe how binding of either rimantadine or 7,7-spiran amine affects the water dynamics inside the M2 channel. Our results show, at neutral pH where the channel is non-conducting, that drug binding leads to a significant increase in the mobility of the channel water. A similar trend is also observed at pH 5.0 although the difference becomes smaller. Taken together, these results indicate that the channel water facilitates drug binding by increasing its entropy. Furthermore, the 2D IR spectral signatures obtained for both probes under different conditions collectively support a binding mechanism whereby amantadine-like drugs dock in the channel with their ammonium moiety pointing toward the histidine residues and interacting with a nearby water cluster, as predicted by molecular dynamics simulations. We believe these findings have important implications for designing new anti-influenza drugs.

  20. Analyzing binding data.

    Science.gov (United States)

    Motulsky, Harvey J; Neubig, Richard R

    2010-07-01

    Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and accessibility of these binding sites for various drugs. This unit explains how to design and analyze such experiments.

  1. Impact of hyperlipidemia on plasma protein binding and hepatic drug transporter and metabolic enzyme regulation in a rat model of gestational diabetes.

    Science.gov (United States)

    Anger, Gregory J; Piquette-Miller, Micheline

    2010-07-01

    It is currently unknown whether gestational diabetes mellitus (GDM), a prevalent obstetrical complication, compounds the changes in drug disposition that occur naturally in pregnancy. Hyperlipidemia occurs in GDM. Using a rat model of GDM, we determined whether excess lipids compete with drugs for plasma protein binding. Because lipids activate nuclear receptors that regulate drug transporters and metabolic enzymes, we used proteome analysis to determine whether hyperlipidemia indirectly leads to the dysregulation of these proteins in the liver. GDM was induced on gestational day 6 (GD6) via streptozotocin injection. Controls received either vehicle alone or streptozotocin with subsequent insulin treatment. Liver and plasma were collected on GD20. Glyburide and saquinavir protein binding was determined by ultrafiltration, and an established solvent method was used for plasma delipidation. Proteomics analysis was performed by using isobaric tags for relative and absolute quantitation methodology with membrane-enriched hepatic protein samples. Relative to controls, GDM rat plasma contained more cholesterol and triglycerides. Plasma protein binding of glyburide and saquinavir was decreased in GDM. Delipidation normalized protein binding in GDM plasma. Proteins linked to lipid metabolism were strongly affected in the GDM proteomics data set, with prohyperlipidemic and antihyperlipidemic changes observed, and formed networks that implicated several nuclear receptors. Up-regulation of drug transporters and metabolic enzymes was observed (e.g., multidrug resistance 1/2, CYP2A1, CYP2B9, and CYP2D3). In this study, GDM-induced hyperlipidemia decreased protein binding and was associated with drug transporter and metabolic enzyme up-regulation in the liver. Both of these findings could change drug disposition in affected pregnancies, compounding changes associated with pregnancy itself.

  2. Performance optimization of grooved slippers for aero hydraulic pumps

    Institute of Scientific and Technical Information of China (English)

    Chen Juan; Ma Jiming; Li Jia; Fu Yongling

    2016-01-01

    A computational fluid dynamics (CFD) simulation method based on 3-D Navier–Stokes equation and Arbitrary Lagrangian–Eulerian (ALE) method is presented to analyze the grooved slip-per performance of piston pump. The moving domain of grooved slipper is transformed into a fixed reference domain by the ALE method, which makes it convenient to take the effects of rotate speed, body force, temperature, and oil viscosity into account. A geometric model to express the complex structure, which covers the orifice of piston and slipper, vented groove and the oil film, is constructed. Corresponding to different oil film thicknesses calculated in light of hydrostatic equilibrium theory and boundary conditions, a set of simulations is conducted in COMSOL to analyze the pump characteristics and effects of geometry (groove width and radius, orifice size) on these characteristics. Furthermore, the mechanics and hydraulics analyses are employed to validate the CFD model, and there is an excellent agreement between simulation and analytical results. The simulation results show that the sealing land radius, orifice size and groove width all dramatically affect the slipper behavior, and an optimum tradeoff among these factors is conducive to optimizing the pump design.

  3. Performance optimization of grooved slippers for aero hydraulic pumps

    Directory of Open Access Journals (Sweden)

    Juan Chen

    2016-06-01

    Full Text Available A computational fluid dynamics (CFD simulation method based on 3-D Navier–Stokes equation and Arbitrary Lagrangian–Eulerian (ALE method is presented to analyze the grooved slipper performance of piston pump. The moving domain of grooved slipper is transformed into a fixed reference domain by the ALE method, which makes it convenient to take the effects of rotate speed, body force, temperature, and oil viscosity into account. A geometric model to express the complex structure, which covers the orifice of piston and slipper, vented groove and the oil film, is constructed. Corresponding to different oil film thicknesses calculated in light of hydrostatic equilibrium theory and boundary conditions, a set of simulations is conducted in COMSOL to analyze the pump characteristics and effects of geometry (groove width and radius, orifice size on these characteristics. Furthermore, the mechanics and hydraulics analyses are employed to validate the CFD model, and there is an excellent agreement between simulation and analytical results. The simulation results show that the sealing land radius, orifice size and groove width all dramatically affect the slipper behavior, and an optimum tradeoff among these factors is conducive to optimizing the pump design.

  4. Continuous blood fractionation using an array of slanted grooves

    Science.gov (United States)

    Bernate, Jorge A.; Chengxun, Liu; Lagae, Liesbet; Drazer, German

    2011-11-01

    Blood is a complex fluid having different specialized biological functions and containing a plethora of clinical information. The separation of different blood components is a crucial step in many research and clinical applications. In this work we take advantage of the flow characteristics in microfluidic devices in which the bottom surface is patterned with slanted rectangular grooves to continuously fractionate blood. We exploit the flow in the vicinity of the patterned surface when the dimensions of the grooves are much smaller than the dimensions of the main channel. In these devices, we observed that the grooves act as open channels guiding flow along them with the flow over them being in the direction of the main channel. We present experiments in which the different blood components are deflected laterally to a different extent by the flow along the grooves depending on their sedimentation velocity, which allows their continuous fractionation. In particular, the heavier red blood cells experience the largest deflection while the lighter white blood cells deflect the least, allowing their passive and minimally invasive isolation. In addition, this fluidic platform can also be used to separate magnetically labeled circulating cancer cells which can be retained in the flow along the grooves using a sufficiently strong magnetic force.

  5. Control of Mycosphaerella graminicola on wheat seedlings by medical drugs known to modulate the activity of ATP-binding cassette transporters

    NARCIS (Netherlands)

    Roohparvar, R.; Huser, A.; Zwiers, L.H.; Waard, de M.A.

    2007-01-01

    Medical drugs known to modulate the activity of human ATP-binding cassette (ABC) transporter proteins (modulators) were tested for the ability to potentiate the activity of the azole fungicide cyproconazole against in vitro growth of Mycosphaerella graminicola and to control disease development due

  6. Investigation of β-lactam antibacterial drugs, β-lactamases, and penicillin-binding proteins with fluorescence polarization and anisotropy: a review

    Science.gov (United States)

    Shapiro, Adam B.

    2016-06-01

    This review covers the uses of fluorescence polarization and anisotropy for the investigation of bacterial penicillin binding proteins (PBPs), which are the targets of β-lactam antibacterial drugs (penicillins, cephalosporins, carbapenems, and monobactams), and of the β-lactamase enzymes that destroy these drugs and help to render bacterial pathogens resistant to them. Fluorescence polarization and anisotropy-based methods for quantitation of β-lactam drugs are also reviewed. A particular emphasis is on methods for quantitative measurement of the interactions of β-lactams and other inhibitors with PBPs and β-lactamases.

  7. On-column entrapment of alpha1-acid glycoprotein for studies of drug-protein binding by high-performance affinity chromatography.

    Science.gov (United States)

    Anguizola, Jeanethe; Bi, Cong; Koke, Michelle; Jackson, Abby; Hage, David S

    2016-08-01

    An on-column approach for protein entrapment was developed to immobilize alpha1-acid glycoprotein (AGP) for drug-protein binding studies based on high-performance affinity chromatography. Soluble AGP was physically entrapped by using microcolumns that contained hydrazide-activated porous silica and by employing mildly oxidized glycogen as a capping agent. Three on-column entrapment methods were evaluated and compared to a previous slurry-based entrapment method. The final selected method was used to prepare 1.0 cm × 2.1 mm I.D. affinity microcolumns that contained up to 21 (±4) μg AGP and that could be used over the course of more than 150 sample applications. Frontal analysis and zonal elution studies were performed on these affinity microcolumns to examine the binding of various drugs with the entrapped AGP. Site-selective competition studies were also conducted for these drugs. The results showed good agreement with previous observations for these drug-protein systems and with binding constants that have been reported in the literature. The entrapment method developed in this study should be useful for future work in the area of personalized medicine and in the high-throughput screening of drug interactions with AGP or other proteins. Graphical abstract On-column protein entrapment using a hydrazide-activated support and oxidized glycogen as a capping agent.

  8. A physiologically based pharmacokinetic model to predict the pharmacokinetics of highly protein-bound drugs and the impact of errors in plasma protein binding.

    Science.gov (United States)

    Ye, Min; Nagar, Swati; Korzekwa, Ken

    2016-04-01

    Predicting the pharmacokinetics of highly protein-bound drugs is difficult. Also, since historical plasma protein binding data were often collected using unbuffered plasma, the resulting inaccurate binding data could contribute to incorrect predictions. This study uses a generic physiologically based pharmacokinetic (PBPK) model to predict human plasma concentration-time profiles for 22 highly protein-bound drugs. Tissue distribution was estimated from in vitro drug lipophilicity data, plasma protein binding and the blood: plasma ratio. Clearance was predicted with a well-stirred liver model. Underestimated hepatic clearance for acidic and neutral compounds was corrected by an empirical scaling factor. Predicted values (pharmacokinetic parameters, plasma concentration-time profile) were compared with observed data to evaluate the model accuracy. Of the 22 drugs, less than a 2-fold error was obtained for the terminal elimination half-life (t1/2 , 100% of drugs), peak plasma concentration (Cmax , 100%), area under the plasma concentration-time curve (AUC0-t , 95.4%), clearance (CLh , 95.4%), mean residence time (MRT, 95.4%) and steady state volume (Vss , 90.9%). The impact of fup errors on CLh and Vss prediction was evaluated. Errors in fup resulted in proportional errors in clearance prediction for low-clearance compounds, and in Vss prediction for high-volume neutral drugs. For high-volume basic drugs, errors in fup did not propagate to errors in Vss prediction. This is due to the cancellation of errors in the calculations for tissue partitioning of basic drugs. Overall, plasma profiles were well simulated with the present PBPK model. Copyright © 2016 John Wiley & Sons, Ltd.

  9. Mechanisms of rectangular groove-induced multiple-microdroplet coalescences

    Science.gov (United States)

    Shen, Feng; Li, Yi; Wang, Guiren; Liu, Zhaomiao

    2017-01-01

    The mechanism of microdroplet coalescence is a fundamental issue for droplet-based microfluidics. We developed an asymmetric expansion (a rectangular groove) along one side of a microchannel to achieve multiple-microdroplet trapping, collision, and coalescence. Compared with reported symmetric expansions, this asymmetric groove could easily trap microdroplets and control two or three microdroplet coalescences precisely without a requirement for temporal and spatial synchronization. To reveal the mechanisms of multiple-droplet coalescences in a groove, we observed five different coalescence patterns under different flow conditions. Moreover, we characterized the flow behavior quantitatively by simulating the velocity vector fields in both the microdroplets and continuous phase, finding good agreement with experiments. Finally, a map of coalescence forms with different capillary numbers (0.001droplet-based microfluidic devices.

  10. The experimental and numerical investigation of a grooved vapor chamber

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Ming [Key Laboratory of Enhanced Heat Transfer and Energy Conservation, Ministry of Education and Key Laboratory of Heat Transfer and Energy Conversion, Beijing Education Commission, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100022 (China); Liu Zhongliang [Key Laboratory of Enhanced Heat Transfer and Energy Conservation, Ministry of Education and Key Laboratory of Heat Transfer and Energy Conversion, Beijing Education Commission, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100022 (China)], E-mail: liuzhl@bjut.edu.cn; Ma Guoyuan [Key Laboratory of Enhanced Heat Transfer and Energy Conservation, Ministry of Education and Key Laboratory of Heat Transfer and Energy Conversion, Beijing Education Commission, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100022 (China)

    2009-02-15

    An effective thermal spreader can achieve more uniform heat flux distribution and thus enhance heat dissipation of heat sinks. Vapor chamber is one of highly effective thermal spreaders. In this paper, a novel grooved vapor chamber was designed. The grooved structure of the vapor chamber can improve its axial and radial heat transfer and also can form the capillary loop between condensation and evaporation surfaces. The effect of heat flux, filling amount and gravity to the performance of this vapor chamber is studied by experiment. From experiment, we also obtained the best filling amount of this grooved vapor chamber. By comparing the thermal resistance of a solid copper plate with that of the vapor chamber, it is suggested that the critical heat flux condition should be maintained to use vapor chamber as efficient thermal spreaders for electronics cooling. A two-dimensional heat and mass transfer model for the grooved vapor chamber is developed. The numerical simulation results show the thickness distribution of liquid film in the grooves is not uniform. The temperature and velocity field in vapor chamber are obtained. The thickness of the liquid film in groove is mainly influenced by pressure of vapor and liquid beside liquid-vapor interface. The thin liquid film in heat source region can enhance the performance of vapor chamber, but if the starting point of liquid film is backward beyond the heat source region, the vapor chamber will dry out easily. The optimal filling ratio should maintain steady thin liquid film in heat source region of vapor chamber. The vapor condenses on whole condensation surface, so that the condensation surface achieves great uniform temperature distribution. By comparing the experimental results with numerical simulation results, the reliability of the numerical model can be verified.

  11. Biopartitioning micellar chromatography with sodium dodecyl sulfate as a pseudo α(1)-acid glycoprotein to the prediction of protein-drug binding.

    Science.gov (United States)

    Hadjmohammadi, Mohammadreza; Salary, Mina

    2013-01-01

    A simple and fast method is of urgent need to measure protein-drug binding affinity in order to meet the rapid development of new drugs. Biopartitioning micellar chromatography (BMC), a mode of micellar liquid chromatography (MLC) using micellar mobile phases in adequate experimental conditions, can be useful as an in vitro system in mimicking the drug-protein interactions. In this study, sodium dodecyl sulfate-micellar liquid chromatography (SDS-MLC) was used for the prediction of protein-drug binding based on the similar property of SDS micelles to α(1)-acid glycoprotein (AGP). The relationships between the BMC retention data of a heterogeneous set of 14 basic and neutral drugs and their plasma protein binding parameter were studied and the predictive ability of models was evaluated. Modeling of logk(BMC) of these compounds was established by multiple linear regression (MLR) and second-order polynomial models obtained in two different concentrations (0.07 and 0.09M) of SDS. The developed MLR models were characterized by both the descriptive and predictive ability (R(2)=0.882, R(CV)(2)=0.832 and R(2)=0.840, R(CV)(2)=0.765 for 0.07 and 0.09M SDS, respectively). The p values <0.01 also indicated that the relationships between the protein-drug binding and the logk(BMC) values were statistically significant at the 99% confidence level. The standard error of estimation showed the standard deviation of the regression to be 11.89 and 13.87 for 0.07 and 0.09M, respectively. The application of the developed model to a prediction set demonstrated that the model was also reliable with good predictive accuracy. The external and internal validation results showed that the predicted values were in good agreement with the experimental value.

  12. Analysis of drug-protein binding using on-line immunoextraction and high-performance affinity microcolumns: Studies with normal and glycated human serum albumin.

    Science.gov (United States)

    Matsuda, Ryan; Jobe, Donald; Beyersdorf, Jared; Hage, David S

    2015-10-16

    A method combining on-line immunoextraction microcolumns with high-performance affinity chromatography (HPAC) was developed and tested for use in examining drug-protein interactions with normal or modified proteins. Normal human serum albumin (HSA) and glycated HSA were used as model proteins for this work. High-performance immunoextraction microcolumns with sizes of 1.0-2.0 cm × 2.1mm i.d. and containing anti-HSA polyclonal antibodies were developed and tested for their ability to bind normal HSA or glycated HSA. These microcolumns were able to extract up to 82-93% for either type of protein at 0.05-0.10 mL/min and had a binding capacity of 0.34-0.42 nmol HSA for a 1.0 cm × 2.1mm i.d. microcolumn. The immunoextraction microcolumns and their adsorbed proteins were tested for use in various approaches for drug binding studies. Frontal analysis was used with the adsorbed HSA/glycated HSA to measure the overall affinities of these proteins for the drugs warfarin and gliclazide, giving comparable values to those obtained previously using similar protein preparations that had been covalently immobilized within HPAC columns. Zonal elution competition studies with gliclazide were next performed to examine the specific interactions of this drug at Sudlow sites I and II of the adsorbed proteins. These results were also comparable to those noted in prior work with covalently immobilized samples of normal HSA or glycated HSA. These experiments indicated that drug-protein binding studies can be carried out by using on-line immunoextraction microcolumns with HPAC. The same method could be used in the future with clinical samples and other drugs or proteins of interest in pharmaceutical studies or biomedical research.

  13. V-groove plasmonic waveguides fabricated by nanoimprint lithography

    DEFF Research Database (Denmark)

    Fernandez-Cuesta, I.; Nielsen, R.B.; Boltasseva, Alexandra

    2007-01-01

    Propagation of channel plasmon-polariton modes in the bottom of a metal V groove has been recently demonstrated. It provides a unique way of manipulating light at nanometer length scale. In this work, we present a method based on nanoimprint lithography that allows parallel fabrication of integra......Propagation of channel plasmon-polariton modes in the bottom of a metal V groove has been recently demonstrated. It provides a unique way of manipulating light at nanometer length scale. In this work, we present a method based on nanoimprint lithography that allows parallel fabrication...

  14. Evaluation of the binding of the radiolabeled antidepressant drug, {sup 18}F-fluoxetine in the rodent brain: an in vitro and in vivo study

    Energy Technology Data Exchange (ETDEWEB)

    Mukherjee, Jogeshwar E-mail: jogeshwar_mukherjee@ketthealth.com; Das, Malay K.; Yang Zhiying; Lew, Robert

    1998-10-01

    We have developed {sup 18}F-fluoxetine as a radiotracer analog of the antidepressant drug fluoxetine (Prozac). In vitro saturation experiments of {sup 18}F-fluoxetine were carried out on rat midbrain tissue and citalopram was used for measuring nonspecific binding. A saturation curve for the binding of {sup 18}F-fluoxetine was not obtained. Even when fluoxetine (10 {mu}M) was used for measurements of nonspecific binding, a saturation curve was difficult to obtain. Other compounds, such as deprenyl, clorgyline, amphetamine, and reserpine were also not able to reduce the binding of {sup 18}F-fluoxetine. Ex vivo autoradiographic experiments with {sup 18}F-fluoxetine did not reveal any specific uptake in various brain regions. In vivo administration of {sup 18}F-fluoxetine in rats showed similar uptake in all the brain regions with little regional selectivity. A subcellular analysis of rat brain tissue after intravenous (IV) administration of {sup 18}F-fluoxetine indicated significant amounts of binding in mitochondria and synaptosomes. In summary, in vitro experiments with {sup 18}F-fluoxetine indicate little specific binding. Binding to the serotonin transporter was not identifiable. High nonspecific binding of the tracer resulting from its subcellular nature in the brain masks the ability to detect binding to the serotonin uptake sites in vivo. These findings indicate that a large portion of the binding of {sup 18}F-fluoxetine in rat brains is subcellular and clears slowly out of the cells. Other sites, such as monoamine oxidase, may also play a significant role in the action of fluoxetine.

  15. Association of Methotrexate with Native and PEGylated PAMAM-G4 Dendrimers: Effect of the PEGylation Degree on the Drug-Loading Capacity and Preferential Binding Sites.

    Science.gov (United States)

    Barraza, Luis F; Jiménez, Verónica A; Alderete, Joel B

    2017-01-12

    PEGylated PAMAM dendrimers (PEG-PAMAM) have been extensively studied as versatile vehicles for drug delivery. Nevertheless, little information has been reported regarding the effect of the PEGylation degree on the drug-loading properties of these systems, aimed at maximizing their performance as drug carrier nanocarrriers. In this work, fully atomistic molecular dynamics (MD) simulations were employed to examine the association of methotrexate (MTX) with native and diversely PEGylated PAMAM-G4 dendrimers, using 2 kDa PEG chains with substitution degrees from 25 to 100% and 100:1 drug:dendrimer ratios to mimic experimental conditions of drug excess in saturated solution. MD results regarding complex stoichiometries and preferential binding sites were compared to experimental data retrieved from aqueous solubility profiles and 2D-NOESY experiments showing an outstanding level of agreement. The maximum theoretical drug loading capacity was achieved by the system with 34% PEGylation (42:1) through the simultaneous complexation of MTX within internal PAMAM-G4 branches and external PEG chains. On the other hand, higher PEGylation degrees were found to be detrimental for drug complexation due to PEG chains crowding on the dendrimer surface. These results provide valuable information to design more efficient PAMAM-based drug nanocarriers and explain the positive effect that partial PEGylation exerts on the drug-loading capacity of PAMAM-G4 over native and fully PEGylated systems.

  16. Study on the interaction of the antiviral drug, zidovudine with DNA using neutral red (NR) and methylene blue (MB) dyes

    Energy Technology Data Exchange (ETDEWEB)

    Shahabadi, Nahid, E-mail: nahidshahabadi@yahoo.com [Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah (Iran, Islamic Republic of); Moghadam, Neda Hossein pour [Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah (Iran, Islamic Republic of)

    2013-02-15

    The interaction between the drug, zidovudine and calf thymus DNA (CT-DNA) in physiological buffer (pH 7.4) was investigated using neutral red (NR) and methylene blue (MB) dyes as a spectral probes by UV-vis absorption and fluorescence spectroscopy, as well as circular dichroism (CD) spectroscopy. The experimental results showed that the conformational changes in DNA helix induced by zidovudine are the reason for the fluorescence quenching of the DNA-NR system. In addition, by increasing zidovudine to DNA-MB solution, the fluorescence has no change. From the experimental results, it was found that zidovudine can cause structural changes on CT-DNA and bind with DNA via groove binding mode. At the same time, the paper proved that conformational changes of DNA can also lead to the fluorescence decrease of DNA-probe systems. - Highlights: Black-Right-Pointing-Pointer Search for new molecular structures which exhibit effective antitumor activities among popular drugs. Black-Right-Pointing-Pointer The DRUG can bind to DNA via groove binding mode. Black-Right-Pointing-Pointer Several spectroscopic techniques have been used in this research.

  17. SALL4, a stem cell factor, affects the side population by regulation of the ATP-binding cassette drug transport genes.

    Directory of Open Access Journals (Sweden)

    Ha-Won Jeong

    Full Text Available Our previous work shows that the stem cell factor SALL4 plays a central role in embryonic and leukemic stem cells. In this study, we report that SALL4 expression was higher in drug resistant primary acute myeloid leukemic patients than those from drug-responsive cases. In addition, while overexpression of SALL4 led to drug resistance in cell lines, cells with decreased SALL4 expression were more sensitive to drug treatments than the parental cells. This led to our investigation of the implication of SALL4 in drug resistance and its role in side population (SP cancer stem cells. SALL4 expression was higher in SP cells compared to non-SP cells by 2-4 fold in various malignant hematopoietic cell lines. Knocking down of SALL4 in isolated SP cells resulted in a reduction of SP cells, indicating that SALL4 is required for their self-renewal. The SP phenotype is known to be mediated by members of the ATP-binding cassette (ABC drug transport protein family, such as ABCG2 and ABCA3. Using chromatin-immunoprecipitation (ChIP, quantitative reverse transcription polymerase chain reaction (qRT-PCR and electrophoretic mobility shift assay(EMSA, we demonstrated that SALL4 was able to bind to the promoter region of ABCA3 and activate its expression while regulating the expression of ABCG2 indirectly. Furthermore, SALL4 expression was positively correlated to those of ABCG2 and ABCA3 in primary leukemic patient samples. Taken together, our results suggest a novel role for SALL4 in drug sensitivity, at least in part through the maintenance of SP cells, and therefore may be responsible for drug-resistance in leukemia. We are the first to demonstrate a direct link between stem cell factor SALL4, SP and drug resistance in leukemia.

  18. Computational Studies of a Mechanism for Binding and Drug Resistance in the Wild Type and Four Mutations of HIV-1 Protease with a GRL-0519 Inhibitor

    Directory of Open Access Journals (Sweden)

    Guodong Hu

    2016-05-01

    Full Text Available Drug resistance of mutations in HIV-1 protease (PR is the most severe challenge to the long-term efficacy of HIV-1 PR inhibitor in highly active antiretroviral therapy. To elucidate the molecular mechanism of drug resistance associated with mutations (D30N, I50V, I54M, and V82A and inhibitor (GRL-0519 complexes, we have performed five molecular dynamics (MD simulations and calculated the binding free energies using the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA method. The ranking of calculated binding free energies is in accordance with the experimental data. The free energy spectra of each residue and inhibitor interaction for all complexes show a similar binding model. Analysis based on the MD trajectories and contribution of each residues show that groups R2 and R3 mainly contribute van der Waals energies, while groups R1 and R4 contribute electrostatic interaction by hydrogen bonds. The drug resistance of D30N can be attributed to the decline in binding affinity of residues 28 and 29. The size of Val50 is smaller than Ile50 causes the residue to move, especially in chain A. The stable hydrophobic core, including the side chain of Ile54 in the wild type (WT complex, became unstable in I54M because the side chain of Met54 is flexible with two alternative conformations. The binding affinity of Ala82 in V82A decreases relative to Val82 in WT. The present study could provide important guidance for the design of a potent new drug resisting the mutation inhibitors.

  19. Novel nootropic drug sunifiram enhances hippocampal synaptic efficacy via glycine-binding site of N-methyl-D-aspartate receptor.

    Science.gov (United States)

    Moriguchi, Shigeki; Tanaka, Tomoya; Narahashi, Toshio; Fukunaga, Kohji

    2013-10-01

    Sunifiram is a novel pyrrolidone nootropic drug structurally related to piracetam, which was developed for neurodegenerative disorder like Alzheimer's disease. Sunifiram is known to enhance cognitive function in some behavioral experiments such as Morris water maze task. To address question whether sunifiram affects N-methyl-D-aspartate receptor (NMDAR)-dependent synaptic function in the hippocampal CA1 region, we assessed the effects of sunifiram on NMDAR-dependent long-term potentiation (LTP) by electrophysiology and on phosphorylation of synaptic proteins by immunoblotting analysis. In mouse hippocampal slices, sunifiram at 10-100 nM significantly enhanced LTP in a bell-shaped dose-response relationship which peaked at 10 nM. The enhancement of LTP by sunifiram treatment was inhibited by 7-chloro-kynurenic acid (7-ClKN), an antagonist for glycine-binding site of NMDAR, but not by ifenprodil, an inhibitor for polyamine site of NMDAR. The enhancement of LTP by sunifilam was associated with an increase in phosphorylation of α-amino-3-hydroxy-5-methylisozazole-4-propionate receptor (AMPAR) through activation of calcium/calmodulin-dependent protein kinase II (CaMKII) and an increase in phosphorylation of NMDAR through activation of protein kinase Cα (PKCα). Sunifiram treatments at 1-1000 nM increased the slope of field excitatory postsynaptic potentials (fEPSPs) in a dose-dependent manner. The enhancement was associated with an increase in phosphorylation of AMPAR receptor through activation of CaMKII. Interestingly, under the basal condition, sunifiram treatments increased PKCα (Ser-657) and Src family (Tyr-416) activities with the same bell-shaped dose-response curve as that of LTP peaking at 10 nM. The increase in phosphorylation of PKCα (Ser-657) and Src (Tyr-416) induced by sunifiram was inhibited by 7-ClKN treatment. The LTP enhancement by sunifiram was significantly inhibited by PP2, a Src family inhibitor. Finally, when pretreated with a high

  20. Structural, conformational and thermodynamic aspects of groove-directed-intercalation of flavopiridol into DNA.

    Science.gov (United States)

    Ray, Bhumika; Agarwal, Shweta; Lohani, Neelam; Rajeswari, Moganty R; Mehrotra, Ranjana

    2016-11-01

    Certain plant-derived alkaloids and flavonoids have shown propitious cytotoxic acitvity against different types of cancer, having deoxyribose nucleic acid (DNA) as their main cellular target. Flavopiridol, a semi-synthetic derivative of rohitukine (a natural compound isolated from Dysoxylum binectariferum plant), has attained much attention owing to its anticancer potential against various haematological malignancies and solid tumours. This work focuses on investigating interaction between flavopiridol and DNA at molecular level in order to decipher its underlying mechanism of action, which is not well understood. To define direct influence of flavopiridol on the structural, conformational and thermodynamic aspects of DNA, various spectroscopic and calorimetric techniques have been used. ATR-FTIR and SERS spectral outcomes indicate a novel insight into groove-directed-intercalation of flavopiridol into DNA via direct binding with nitrogenous bases guanine (C6=O6) and thymine (C2=O2) in DNA groove together with slight external binding to its sugar-phosphate backbone. Circular dichroism spectral analysis of flavopiridol-DNA complexes suggests perturbation in native B-conformation of DNA and its transition into C-form, which may be localized up to a few base pairs of DNA. UV-visible spectroscopic results illustrate dual binding mode of flavopiridol when interacts with DNA having association constant, Ka = 1.18 × 10(4) M(-1). This suggests moderate type of interaction between flavopiridol and DNA. Further, UV melting analysis also supports spectroscopic outcomes. Thermodynamically, flavopiridol-DNA complexation is an enthalpy-driven exothermic process. These conclusions drawn from this study could be helpful in unveiling mechanism of cytoxicity induced by flavopiridol that can be further applied in the development of flavonoid-based new chemotherapeutics with more specificity and better efficacy.

  1. Identification and Evaluation of Novel Drug Targets against the Human Fungal Pathogen Aspergillus fumigatus with Elaboration on the Possible Role of RNA-Binding Protein

    Science.gov (United States)

    Malekzadeh, Saeid; Sardari, Soroush; Azerang, Parisa; Khorasanizadeh, Dorsa; Amiri, Solmaz Agha; Azizi, Mohammad; Mohajerani, Nazanin; Khalaj, Vahid

    2017-01-01

    Bakground: Aspergillus fumigatus is an airborne opportunistic fungal pathogen that can cause fatal infections in immunocompromised patients. Although the current anti-fungal therapies are relatively efficient, some issues such as drug toxicity, drug interactions, and the emergence of drug-resistant fungi have promoted the intense research toward finding the novel drug targets. Methods: In search of new antifungal drug targets, we have used a bioinformatics approach to identify novel drug targets. We compared the whole proteome of this organism with yeast Saccharomyces cerevisiae to come up with 153 specific proteins. Further screening of these proteins revealed 50 potential molecular targets in A. fumigatus. Amongst them, RNA-binding protein (RBP) was selected for further examination. The aspergillus fumigatus RBP (AfuRBP), as a peptidylprolyl isomerase, was evaluated by homology modeling and bioinformatics tools. RBP-deficient mutant strains of A. fumigatus were generated and characterized. Furthermore, the susceptibility of these strains to known peptidylprolyl isomerase inhibitors was assessed. Results: AfuRBP-deficient mutants demonstrated a normal growth phenotype. MIC assay results using inhibitors of peptidylprolyl isomerase confirmed a higher sensitivity of these mutants compared to the wild type. Conclusion: Our bioinformatics approach revealed a number of fungal-specific proteins that may be considered as new targets for drug discovery purposes. Peptidylprolyl isomerase, as a possible drug target, was evaluated against two potential inhibitors, and the promising results were investigated mechanistically. Future studies would confirm the impact of such target on the antifungal discovery investigations PMID:28000798

  2. Groove Pancreatitis: A Case Report and Review of Literature

    Directory of Open Access Journals (Sweden)

    Vallath Balakrishnan

    2007-09-01

    Full Text Available Context Groove pancreatitis is a rare type of segmental pancreatitis characterized by fibrous scars of the anatomic space between the dorsocranial part of the head of the pancreas, the duodenum, and the common bile duct. Case report A 40-year-old man, with a past history of chronic alcohol consumption presented with epigastric pain radiating to the back and intermittent vomiting and a weight loss of 9 kg. A CT of the abdomen revealed swelling of the pancreatic head, a hypodense mass and duodenal wall thickening with luminal narrowing. Peripancreatic fluid and dense strands were also seen. Upper gastrointestinal endoscopy revealed an edematous, shiny, reddish raised mucosa having a polypoid appearance with narrowing of the second portion of the duodenum. Histological examination of the duodenal biopsy specimens showed preservation of the crypt-villus ratio, and the submucosa showed Brunner gland hyperplasia. These findings appeared consistent with the diagnosis of groove pancreatitis. Presently, the patient is on conservative medical management with analgesics, proton pump inhibitors and a pancreatic enzyme supplement. Conclusions Groove pancreatitis often masquerades as pancreatic head carcinoma. This condition should be kept in mind when making the differential diagnosis between pancreatic masses and duodenal stenosis. In all cases of focal pancreatitis involving the head or uncinate process of the pancreas with involvement of the adjacent duodenum, the possibility of groove pancreatitis should be considered.

  3. Computational analysis of frictional drag over transverse grooved ...

    African Journals Online (AJOL)

    user

    ... gaining interest as it plays important role in aircraft and submarine fuel efficiencies and noise ..... for the flow to relax, the flow reaches the last groove with less energy caused by the ... freestream velocity of air, mm ... wall shear stress, N/m2 ...

  4. Tailoring channeled plasmon polaritons in metallic V-grooves

    DEFF Research Database (Denmark)

    Smith, Cameron; Thilsted, Anil Haraksingh; Marie, Rodolphe

    2013-01-01

    of propagating plasmons to optimize the trade-off between lateral confinement and loss [2]. Accordingly, the traits of CPPs in metallic V-grooves suggest their widespread implementation, with applications ranging from ultracompact photonic circuitry [3] to lab-on-a-chip sensing. Current CPP research focuses...

  5. Syncopation, body-movement and pleasure in groove music.

    Science.gov (United States)

    Witek, Maria A G; Clarke, Eric F; Wallentin, Mikkel; Kringelbach, Morten L; Vuust, Peter

    2014-01-01

    Moving to music is an essential human pleasure particularly related to musical groove. Structurally, music associated with groove is often characterised by rhythmic complexity in the form of syncopation, frequently observed in musical styles such as funk, hip-hop and electronic dance music. Structural complexity has been related to positive affect in music more broadly, but the function of syncopation in eliciting pleasure and body-movement in groove is unknown. Here we report results from a web-based survey which investigated the relationship between syncopation and ratings of wanting to move and experienced pleasure. Participants heard funk drum-breaks with varying degrees of syncopation and audio entropy, and rated the extent to which the drum-breaks made them want to move and how much pleasure they experienced. While entropy was found to be a poor predictor of wanting to move and pleasure, the results showed that medium degrees of syncopation elicited the most desire to move and the most pleasure, particularly for participants who enjoy dancing to music. Hence, there is an inverted U-shaped relationship between syncopation, body-movement and pleasure, and syncopation seems to be an important structural factor in embodied and affective responses to groove.

  6. Steady progression of osteoarthritic features in the canine groove model

    NARCIS (Netherlands)

    Marijnissen, A.C.A.; Roermund, P.M. van; Verzijl, N.; Tekoppele, J.M.; Bijlsma, J.W.J.; Lafeber, F.P.J.G.

    2002-01-01

    Objective: Recently we described a canine model of osteoarthritis (OA), the groove model with features of OA at 10 weeks after induction, identical to those seen in the canine anterior cruciate ligament transection (ACLT) model. This new model depends on cartilage damage accompanied by transient int

  7. Syncopation, body-movement and pleasure in groove music.

    Directory of Open Access Journals (Sweden)

    Maria A G Witek

    Full Text Available Moving to music is an essential human pleasure particularly related to musical groove. Structurally, music associated with groove is often characterised by rhythmic complexity in the form of syncopation, frequently observed in musical styles such as funk, hip-hop and electronic dance music. Structural complexity has been related to positive affect in music more broadly, but the function of syncopation in eliciting pleasure and body-movement in groove is unknown. Here we report results from a web-based survey which investigated the relationship between syncopation and ratings of wanting to move and experienced pleasure. Participants heard funk drum-breaks with varying degrees of syncopation and audio entropy, and rated the extent to which the drum-breaks made them want to move and how much pleasure they experienced. While entropy was found to be a poor predictor of wanting to move and pleasure, the results showed that medium degrees of syncopation elicited the most desire to move and the most pleasure, particularly for participants who enjoy dancing to music. Hence, there is an inverted U-shaped relationship between syncopation, body-movement and pleasure, and syncopation seems to be an important structural factor in embodied and affective responses to groove.

  8. Novel scaffold design with multi-grooved PLA fibers

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Sangwon; King, Martin W [Fiber and Polymer Science, North Carolina State University, Raleigh, NC (United States); Gamcsik, Mike P, E-mail: martin_king@ncsu.edu [Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina Chapel Hill, NC (United States)

    2011-08-15

    A novel prototype nonwoven textile structure containing polylactide (PLA) multigrooved fibers has been proposed as a possible scaffold material for superior cell attachment and proliferation. Grooved cross-sectional fibers with larger surface area were obtained by a bi-component spinning system and the complete removal of the sacrificial component was confirmed by Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM) and x-ray photon spectroscopy (XPS) analysis. These PLA nonwoven scaffolds containing the grooved fibers exhibited enhanced wettability, greater flexibility and tensile properties, and a larger surface area compared to a traditional PLA nonwoven fabric containing round fibers. To evaluate cellular attachment on the two types of PLA nonwoven scaffolds, NIH 3T3 fibroblasts were cultured for up to 12 days. It was evident that the initial cellular attachment was superior on the scaffold with grooved fibers, which was confirmed by MTT viability assay (p < 0.01) and SEM analysis. In the future, by modulating the size of the grooves on the fibers, such a scaffold material with a large surface area could serve as an alternative matrix for culturing different types of cells.

  9. Steady progression of osteoarthritic features in the canine groove model

    NARCIS (Netherlands)

    Marijnissen, A.C.A.; Roermund, P.M. van; Verzijl, N.; Tekoppele, J.M.; Bijlsma, J.W.J.; Lafeber, F.P.J.G.

    2002-01-01

    Objective: Recently we described a canine model of osteoarthritis (OA), the groove model with features of OA at 10 weeks after induction, identical to those seen in the canine anterior cruciate ligament transection (ACLT) model. This new model depends on cartilage damage accompanied by transient int

  10. The multi-functional drug tropisetron binds APP and normalizes cognition in a murine Alzheimer’s model

    Science.gov (United States)

    Spilman, Patricia; Descamps, Olivier; Gorostiza, Olivia; Peters-Libeu, Clare; Poksay, Karen S.; Matalis, Alexander; Patent, Alexander; Rao, Rammohan; John, Varghese; Bredesen, Dale E.

    2014-01-01

    Tropisetron was identified in a screen for candidates that increase the ratio of the trophic, neurite-extending peptide sAPPα to the anti-trophic, neurite-retractive peptide Aβ, thus reversing this imbalance in Alzheimer’s disease (AD). We describe a hierarchical screening approach to identify such drug candidates, moving from cell lines to hippocampal neuronal cultures to in vivo studies. By screening a clinical compound library in the primary assay using CHO-7W cells stably transfected with human APPwt, we identified tropisetron as a candidate that consistently increased sAPPα. Secondary assay testing in neuronal cultures from J20 (PDAPP, huAPPSwe/Ind) mice showed that tropisetron consistently increased the sAPPα/Aβ 1-42 ratio. In in vivo studies in J20 mice, tropisetron improved the sAPPα/Aβ ratio along with spatial and working memory in mice, and was effective both during the symptomatic, pre-plaque phase (5-6 months) and in the late plaque phase (14 months). This ameliorative effect occurred at a dose of 0.5 mg/kg/d (mkd), translating to a human-equivalent dose of 5 mg/day, the current dose for treatment of postoperative nausea and vomiting (PONV). Although tropisetron is a 5-HT3 antagonist and an α7nAChR partial agonist, we found that it also binds to the ectodomain of APP. Direct comparison of tropisetron to the current AD therapeutics memantine (Namenda) and donepezil (Aricept), using similar doses for each, revealed that tropisetron induced greater improvements in memory and sAPPα/Aβ1-42. The improvements observed with tropisetron in the J20 AD mouse model, and its known safety profile, suggest that it may be suitable for transition to human trials as a candidate therapeutic for mild cognitive impairment (MCI) and AD, and therefore it has been approved for testing in clinical trials to begin in 2014. PMID:24389031

  11. Groove pancreatitis: A rare form of chronic pancreatitis

    Directory of Open Access Journals (Sweden)

    Bharivi Jani

    2015-01-01

    Full Text Available Context: Groove pancreatitis is a rare form of chronic pancreatitis affecting the "groove" of the pancreas among the pancreatic head, duodenum, and common bile duct. The exact cause is unknown, although there are associations with long-term alcohol abuse, smoking, peptic ulcer disease, heterotopic pancreas, gastric resection, biliary disease, and anatomical or functional obstruction of the minor papilla. The diagnosis can be challenging. Endoscopic ultrasound (EUS and magnetic resonance cholangiopancreatography are the preferred imaging modalities. The treatment of choice is conservative although surgical intervention can sometimes be required. Case Report: A 57-year-old male with a history of human immunodeficiency virus and hepatitis B presented with 4 days of epigastric pain. Abdominal exam revealed absent bowel sounds and epigastric tenderness. He had a creatinine of 1.72 mg/dL, potassium of 2.9 mmol/L, and a normal lipase level of 86 U/L. Liver enzymes and total bilirubin were normal. Computed tomography abdomen showed high-grade obstruction of the second portion of the duodenum without any obvious mass. An esophagogastroduodenoscopy showed a mass at the duodenal bulb causing luminal narrowing, with biopsies negative for malignancy. Magnetic resonance imaging revealed a mass in the region of the pancreatic head and descending duodenum. EUS revealed a 3 cm mass in the region of pancreatic head with irregular borders and no vascular invasion. Fine needle aspiration (FNA was nondiagnostic. The patient then underwent a Whipple′s procedure. Pathology of these specimens was negative for malignancy but was consistent with para-duodenal or groove pancreatitis. Conclusion: The low incidence of groove pancreatitis is partly due to lack of familiarity with the disease. Groove pancreatitis should be considered in the differential for patients presenting with pancreatic head lesions and no cholestatic jaundice, especially when a duodenal obstruction

  12. Grandivittin as a natural minor groove binder extracted from Ferulago macrocarpa to ct-DNA, experimental and in silico analysis.

    Science.gov (United States)

    Ahmadi, F; Valadbeigi, S; Sajjadi, S E; Shokoohinia, Y; Azizian, H; Taheripak, G

    2016-10-25

    Ferulago macrocarpa (Fenzl) Boiss., is an endemic medicinal herb of Iran. In this study a dihydrofuranocoumarin called grandivittin (GRA) was separate and purified from Ferulago macrocarpa (Fenzl) Boiss, and characterized by (1)H NMR and Mass spectroscopic methods. The electrochemical behavior of GRA was evaluated by cyclic voltammetry (CV). The interaction of GRA with calf thymus double strand deoxyribonucleic acid (ct-DNA), was evaluated by CV, differential pulse voltammetry (DPV), fluorescence, UV-Vis, FT-IR and molecular modeling methods. The thermodynamic parameters of GRA-DNA complex were measured and reported as: ΔH = 15.04 kJ mol(-1), ΔS = 105.54 J mol(-1) and ΔG = -15.62 kJ mol(-1). Docking simulation was performed to investigate the probable binding mode of GRA to various DNA, too. The polymerase extension study was performed using real-time PCR to confirm the inhibitory effect of GRA on polymerase extension activity as a mirror of binding to ct-DNA. However, all data showed that the grooves binding especially minor groove between GRA and ct-DNA is more predominant rather than other binding modes.

  13. Realization and characterization of high precision micro grooves on green ceramic

    DEFF Research Database (Denmark)

    Bissacco, Giuliano; Andrijasevic, Daniela; Hansen, Hans Nørgaard

    2006-01-01

    rectangular feature underneath. For manufacturing of the grooves a grooving process was chosen and a tool was manufactured by micro electro discharge milling. The accuracy of the tool was evaluated by means of a SEM. Grooves were measured using a stylus profilometer. The results showed that the required...

  14. Evaluation of Drug Interaction in Binding to Protein by High Performance Liquid Chromatography%高效液相色谱法研究与蛋白结合中的药物相互作用

    Institute of Scientific and Technical Information of China (English)

    李发美; 郭兴杰; 乔明曦; 熊志立; 周大炜

    2004-01-01

    Drugs in the body are bound to metabolizing enzymes, targets/receptors and transport proteins in certain extent. The binding of drugs to targets or receptors is mainly specific and responsible for its pharmacological and therapeutic effects. The metabolizing of drugs by enzyme involves both

  15. Spectroscopic and nano-molecular modeling investigation on the binary and ternary bindings of colchicine and lomefloxacin to Human serum albumin with the viewpoint of multi-drug therapy

    Energy Technology Data Exchange (ETDEWEB)

    Chamani, J., E-mail: Chamani@ibb.ut.ac.i [Department of Biology, Faculty of Sciences, Islamic Azad University-Mashhad Branch, Mashhad (Iran, Islamic Republic of); Asoodeh, A. [Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad (Iran, Islamic Republic of); Homayoni-Tabrizi, M. [Department of Biology, Faculty of Sciences, Islamic Azad University-Mashhad Branch, Mashhad (Iran, Islamic Republic of); Amiri Tehranizadeh, Z.; Baratian, A.; Saberi, M.R. [Medical Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad (Iran, Islamic Republic of); Gharanfoli, M. [Department of Development Biology, Culture and Science University, Tehran (Iran, Islamic Republic of)

    2010-12-15

    Combination of several drugs is often necessary especially during long-term therapy. The competitive binding drugs can cause a decrease in the amount of drug bound to protein and increase the biological active fraction of the drug. The aim of this study is to analyze the interactions of Lomefloxacin (LMF) and Colchicine (COL) with human serum albumin (HSA) and to evaluate the mechanism of simultaneous binding of LMF and COL to protein. Fluorescence analysis was used to estimate the effect of drugs on the protein fluorescence and to define the binding and quenching properties of drugs-HSA complexes. The binding sites for LMF and COL were identified in tertiary structure of HSA with the use of spectrofluorescence analysis. The analysis of fluorescence quenching of HSA in the binary and ternary systems show that LMF does not affect the complex formed between COL and HSA. On the contrary, COL decreases the interaction between LMF and HSA. The results of synchronous fluorescence, resonance light scattering and circular dichroism spectra of binary and ternary systems show that binding of LMF and COL to HSA can induce micro-environmental and conformational changes in HSA. The simultaneous presence of LMF and COL in binding to HSA should be taken into account in the multi-drug therapy, and necessity of using a monitoring therapy owning to the possible increase of the uncontrolled toxic effects. Molecular modeling of the possible binding sites of LMF and COL in binary and ternary systems to HSA confirms the spectroscopic results.

  16. An investigation of the photophysical properties of minor groove bound and intercalated DAPI through quantum-mechanical and spectroscopic tools.

    Science.gov (United States)

    Biancardi, Alessandro; Biver, Tarita; Secco, Fernando; Mennucci, Benedetta

    2013-04-07

    The fluorescent probe 4',6-diamidino-2-phenylindole (DAPI) is a dye known to interact with polynucleotides in a non-univocal manner, both intercalation and minor groove binding modes being possible, and to specifically change its photophysical properties according to the different environments. To investigate this behavior, quantum-mechanical calculations using time-dependent density functional theory (TDDFT), coupled with polarizable continuum and/or atomistic models, were performed in combination with spectroscopic measurements of the probe in the different environments, ranging from a homogeneous solution to the minor groove or intercalation pockets of double stranded nucleic acids. According to our simulation, the electronic transition involves a displacement of the electron charge towards the external amidine groups and this feature makes the absorption energies very environment-sensitive while a much smaller sensitivity is seen in the fluorescence energies. Moreover, the calculations show that the DAPI molecule, when minor groove bound to the nucleic acid, presents both a reduced geometrical flexibility because of the rigid DNA pocket and a reduced polarization due to the very "apolar" microenvironment. All these effects can be used to better understand the observed enhancement of the fluorescence, which makes it an excellent marker for DNA.

  17. Unravelling the interaction of pirenzepine, a gastrointestinal disorder drug, with calf thymus DNA: An in vitro and molecular modelling study.

    Science.gov (United States)

    Rahman, Yusra; Afrin, Shumaila; Husain, Mohammed Amir; Sarwar, Tarique; Ali, Abad; Shamsuzzaman; Tabish, Mohammad

    2017-07-01

    Pirenzepine is an anti-ulcer agent which belongs to the anti-cholinergic group of gastrointestinal disorder drugs and functions as an M1 receptor selective antagonist. Drug-DNA interaction studies are of great significance as it helps in the development of new therapeutic drugs. It provides a deeper understanding into the mechanism through which therapeutic drugs control gene expression. Interaction of pirenzepine with calf-thymus DNA (Ct-DNA) was determined via a series of biophysical techniques. UV-visible absorption and fluorescence spectroscopy confirmed the formation of pirenzepine-Ct-DNA complex. The values of binding constant from various experiments were calculated to be in the order of 10(3) M(-1) which is consistent with the groove binding mode. Various spectrofluorimetric experiments like competitive displacement of well known dyes with drug, iodide quenching experiments and the effect of Ct-DNA denaturation in presence of drug confirmed the binding of pirenzepine to the groove of Ct-DNA. The binding mode was further established by viscometric, circular dichroic and molecular modelling studies. Thermodynamic parameters obtained from isothermal titration calorimetric studies suggest that the interaction of pirenzepine with Ct-DNA is enthalpically driven. The value of TΔS and ΔH calculated from calorimetric studies were found to be 4.3 kcal mol(-1) and -2.54 kcal mol(-1) respectively, indicating that pirenzepine-Ct-DNA complex is mainly stabilized by hydrophobic interaction and hydrogen bonding. The binding energy calculated was -7.5 kcal mol(-1) from modelling studies which was approximately similar to that obtained by isothermal titration calorimetric studies. Moreover, the role of electrostatic interaction in the binding of pirenzepine to Ct-DNA cannot be precluded. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Definition of the G protein-coupled receptor transmembrane bundle binding pocket and calculation of receptor similarities for drug design

    DEFF Research Database (Denmark)

    Gloriam, David Erik Immanuel; Foord, Steven M; Blaney, Frank E

    2009-01-01

    Recent advances in structural biology for G-protein-coupled receptors (GPCRs) have provided new opportunities to improve the definition of the transmembrane binding pocket. Here a reference set of 44 residue positions accessible for ligand binding was defined through detailed analysis of all curr...

  19. Resistance of full veneer metal crowns with different forms of axial grooves

    Science.gov (United States)

    Hidayat, A. S.; Masulili, C.; Indrasari, M.

    2017-08-01

    Dental crowns or bridges can occasionally come loose or separate from the tooth during chewing, particularly when they are situated on small, short, and conical teeth. The main cause of this separation is a lack of retention and resistance to the tooth. There are several methods available to increase the retention and resistance of the crown during both inlay and onlay preparation, including parallelism, groove preparation, crown build-up, and surface roughness. The aim of this study was to determine the differences in resistance of full veneer metal crowns with various forms of groove preparation. The study involved the compressive strength testing of a total of 24 specimens, namely six specimens without groove preparation, six specimens with box-shaped grooves, six specimens with V-shaped grooves, and six specimens with half round grooves. The mean values of the metal crowns that separated from the teeth during testing were 27.97 ± 1.08 kgF for the crowns with box-shaped grooves, 6.15 ± 0.22 kgF for those with V-shaped grooves, 1.77 ± 0.12 kgF for those with half round grooves, and 0.95 ± 0.13 kgF for those without grooves. This study found that the resistance is best in crowns with box-shaped grooves, followed by those with V-shaped grooves, half round grooves, and those without groove. When clinicians are working on short and conical molar teeth, it is therefore recommended that box-shaped grooves are used to increase the resistance of the crown.

  20. Design, synthesis and DNA-binding study of some novel morpholine linked thiazolidinone derivatives

    Science.gov (United States)

    War, Javeed Ahmad; Srivastava, Santosh Kumar; Srivastava, Savitri Devi

    2017-02-01

    The emergence of multiple drug resistance amongst bacterial strains resulted in many clinical drugs to be ineffective. Being vulnerable to bacterial infections any lack in the development of new antimicrobial drugs could pose a serious threat to public health. Here we report design and synthesis of a novel class of morpholine linked thiazolidinone hybrid molecules. The compounds were characterized by FT-IR, NMR and HRMS techniques. Susceptibility tests showed that most of the synthesized molecules were highly active against multiple bacterial strains. Compound 3f displayed MIC values which were better than the standard drug for most of the tested strains. DNA being a well defined target for many antimicrobial drugs was probed as possible target for these synthetic molecules. DNA-binding study of 3f with sm-DNA was probed through UV-vis absorption, fluorescence quenching, gel electrophoresis and molecular docking techniques. The studies revealed that compound 3f has strong affinity towards DNA and binds at the minor groove. The docking studies revealed that the compound 3f shows preferential binding towards A/T residues.

  1. A computational analysis of the binding mode of closantel as inhibitor of the Onchocerca volvulus chitinase: insights on macrofilaricidal drug design

    Science.gov (United States)

    Segura-Cabrera, Aldo; Bocanegra-García, Virgilio; Lizarazo-Ortega, Cristian; Guo, Xianwu; Correa-Basurto, José; Rodríguez-Pérez, Mario A.

    2011-12-01

    Onchocerciasis is a leading cause of blindness with at least 37 million people infected and more than 120 million people at risk of contracting the disease; most (99%) of this population, threatened by infection, live in Africa. The drug of choice for mass treatment is the microfilaricidal Mectizan® (ivermectin); it does not kill the adult stages of the parasite at the standard dose which is a single annual dose aimed at disease control. However, multiple treatments a year with ivermectin have effects on adult worms. The discovery of new therapeutic targets and drugs directed towards the killing of the adult parasites are thus urgently needed. The chitinase of filarial nematodes is a new drug target due to its essential function in the metabolism and molting of the parasite. Closantel is a potent and specific inhibitor of chitinase of Onchocerca volvulus (OvCHT1) and other filarial chitinases. However, the binding mode and specificity of closantel towards OvCHT1 remain unknown. In the absence of a crystallographic structure of OvCHT1, we developed a homology model of OvCHT1 using the currently available X-ray structures of human chitinases as templates. Energy minimization and molecular dynamics (MD) simulation of the model led to a high quality of 3D structure of OvCHIT1. A flexible docking study using closantel as the ligand on the binding site of OvCHIT1 and human chitinases was performed and demonstrated the differences in the closantel binding mode between OvCHIT1 and human chitinase. Furthermore, molecular dynamics simulations and free-energy calculation were employed to determine and compare the detailed binding mode of closantel with OvCHT1 and the structure of human chitinase. This comparative study allowed identification of structural features and properties responsible for differences in the computationally predicted closantel binding modes. The homology model and the closantel binding mode reported herein might help guide the rational development of

  2. Competition between low-dose aspirin and other NSAIDs for COX-1 binding and its clinical consequences for the drugs' antiplatelet effects.

    Science.gov (United States)

    Stepensky, David; Rimon, Gilad

    2015-01-01

    NSAIDs are frequently used in modern medicine to inhibit the COX enzymes and induce analgesic, antipyretic, anti-inflammatory, and antiplatelet effects. Concomitant treatment with two or more NSAIDs can lead to their competition for binding and inhibition of the COX enzymes and altered time course of the pharmacological effects. The competition between the low-dose aspirin and other NSAIDs for binding to COX-1 is described, including the recent findings on the differences in the interaction of NSAIDs with the individual COX-1 subunits, and the clinical consequences of this drug-drug interaction. The major pharmacokinetic (PK) and pharmacodynamic (PD) factors that govern the interaction of low-dose aspirin with other NSAIDs are explained, along with the approaches for prediction of the magnitude of this interaction using mechanism-based PK-PD modeling. Concomitant administration of other NSAIDs can diminish the antiplatelet effects of low-dose aspirin, increase the risk of thromboembolic effects (heart attacks and strokes), and lead to patient morbidity and mortality. The healthcare providers and the patients are seldom aware to this clinical problem and its consequences. Despite this drug interaction, low-dose aspirin possesses high clinical safety and it is not expected to be replaced by the recently approved drugs.

  3. Binding and Release between Polymeric Carrier and Protein Drug: pH-Mediated Interplay of Coulomb Forces, Hydrogen Bonding, van der Waals Interactions, and Entropy.

    Science.gov (United States)

    De Luca, Sergio; Chen, Fan; Seal, Prasenjit; Stenzel, Martina H; Smith, Sean C

    2017-10-02

    The accelerating search for new types of drugs and delivery strategies poses challenge to understanding the mechanism of delivery. To this end, a detailed atomistic picture of binding between the drug and carrier is quintessential. Although many studies focus on the electrostatics of drug-vector interactions, it has also been pointed out that entropic factors relating to water and counterions can play an important role. By carrying out extensive molecular dynamics simulations and subsequently validating with experiments, we shed light herein on the binding in aqueous solution between a protein drug and polymeric carrier. We examined the complexation between the polymer poly(ethylene glycol) methyl ether acrylate-b-poly(carboxyethyl acrylate (PEGMEA-b-PCEA) and the protein egg white lysozyme, a system that acts as a model for polymer-vector/protein-drug delivery systems. The complexation has been visualized and characterized using contact maps and hydrogen bonding analyses for five independent simulations of the complex, each running over 100 ns. Binding at physiological pH is, as expected, mediated by Coulombic attraction between the positively charged protein and negatively charged carboxylate groups on the polymer. However, we find that consideration of electrostatics alone is insufficient to explain the complexation behavior at low pH. Intracomplex hydrogen bonds, van der Waals interactions, as well as water-water interactions dictate that the polymer does not release the protein at pH 4.8 or indeed at pH 3.2 even though the Coulombic attractions are largely removed as carboxylate groups on the polymer become titrated. Experiments in aqueous solution carried out at pH 7.0, 4.5, and 3.0 confirm the veracity of the computed binding behavior. Overall, these combined simulation and experimental results illustrate that coulomb interactions need to be complemented with consideration of other entropic forces, mediated by van der Waals interactions and hydrogen bonding

  4. Determining Favorable Binding Configurations of the Anti-Cancer Drug Ellipticine to the KV11.1 Potassium Channel V-VI Transmembrane Domain Through Autodock Simulations

    Science.gov (United States)

    Lipscomb, Dawn; Gentile, Saverio; Brancaleon, Lorenzo

    2011-10-01

    Ellipticines such as 9-methoxy-N-2-methylellipticinium acetate (MMEA) and 9-hydroxy-N-2-methylellipticinium acetate (NMEA, Celiptium ) are antineoplastic drugs that exert their selective cytotoxicity against leukemia and endometrial carcinoma. Ellipticine's action is also related to severe physical side effects, but the link between undesired effects and pharmacological application is not well understood. We investigated the binding of Ellipticine derivatives with the Kv11.1 potassium ion channel using Autodock and revealed that hydroxyellipticinium derivatives provide binding configurations with Kv11.1, but the energy, location and estimated dissociation constant varied. The binding energy is as follows: Chloroceliptium (-6.60 kcal/mol) > Celiptium (- 6.37 kcal/mol) > Methoxyceliptium (- 6.20 kcal/mol) > Datelliptium (-6.08 kcal/mol). Autodock simulations demonstrate that binding affinity is high at opposing ends of the channel and low within the channel interior. These favorable binding configurations suggest that Ellipticine derivatives may bridge among end subunits of the channel and potentially inhibit the flow of ions.

  5. Curcumin binds in silico to anti-cancer drug target enzyme MMP-3 (human stromelysin-1) with affinity comparable to two known inhibitors of the enzyme.

    Science.gov (United States)

    Jerah, Ahmed; Hobani, Yahya; Kumar, B Vinod; Bidwai, Anil

    2015-01-01

    In silico interaction of curcumin with the enzyme MMP-3 (human stromelysin-1) was studied by molecular docking using AutoDock 4.2 as the docking software application. AutoDock 4.2 software serves as a valid and acceptable docking application to study the interactions of small compounds with proteins. Interactions of curcumin with MMP-3 were compared to those of two known inhibitors of the enzyme, PBSA and MPPT. The calculated free energy of binding (ΔG binding) shows that curcumin binds with affinity comparable to or better than the two known inhibitors. Binding interactions of curcumin with active site residues of the enzyme are also predicted. Curcumin appears to bind in an extendended conformation making extensive VDW contacts in the active site of the enzyme. Hydrogen bonding and pi-pi interactions with key active site residues is also observed. Thus, curcumin can be considered as a good lead compound in the development of new inhibitors of MMP-3 which is a potential target of anticancer drugs. The results of these studies can serve as a starting point for further computational and experimental studies.

  6. Visualization of high-throughput and label-free antibody-polypeptide binding for drug screening based on microarrays and surface plasmon resonance imaging

    Science.gov (United States)

    Chen, Shengyi; Deng, Tao; Wang, Tongzhou; Wang, Jia; Li, Xin; Li, Qiang; Huang, Guoliang

    2012-01-01

    This work presents a visualization method for the high-throughput monitoring of antibody-polypeptide binding by integrating a microarray chip with surface plasmon resonance imaging (SPRi). A prism-coupled SPRi system with smart images processing software and a 5×5 polypeptide microarray was developed. The modeling analysis was performed to optimize the system and the materials of prism and chip, looking for the optimal incident wavelength and angle of incidence for dynamic SPRi detection in solution. The system can dynamically monitor 25 tunnels of biomolecule interactions in solution without secondary tag reactants. In addition, this system can determine the specific profile of antibody-polypeptide binding in each tunnel and yield a visual three-dimensional histogram of dynamic combinations in all microarray tunnels. Furthermore, the detection limit of the label-free antibody-polypeptide binding reached 1 pg/μL in a one-step binding test, and an ultrasensitive detection of 10 fg/μL was obtained using three-step cascade binding. Using the peptide microarray, the amount of sample and reagents used was reduced to 80 nL per tunnel, and 20×20 tunnels of biomolecule interactions could be analyzed in parallel in a 7 mm×7 mm microreaction cells. This device and method offer a potential platform for high-throughput and label-free dynamic monitoring multiple biomolecule interactions for drug discovery and basic biomedical research.

  7. Dance, Music, Meter and Groove: A Forgotten Partnership.

    Science.gov (United States)

    Fitch, W Tecumseh

    2016-01-01

    I argue that core aspects of musical rhythm, especially "groove" and syncopation, can only be fully understood in the context of their origins in the participatory social experience of dance. Musical meter is first considered in the context of bodily movement. I then offer an interpretation of the pervasive but somewhat puzzling phenomenon of syncopation in terms of acoustic emphasis on certain offbeat components of the accompanying dance style. The reasons for the historical tendency of many musical styles to divorce themselves from their dance-based roots are also briefly considered. To the extent that musical rhythms only make sense in the context of bodily movement, researchers interested in ecologically valid approaches to music cognition should make a more concerted effort to extend their analyses to dance, particularly if we hope to understand the cognitive constraints underlying rhythmic aspects of music like meter and groove.

  8. Dance, Music, Meter and Groove: A Forgotten Partnership

    Directory of Open Access Journals (Sweden)

    W Tecumseh eFitch

    2016-03-01

    Full Text Available I argue that core aspects of musical rhythm, especially groove and syncopation, can only be fully understood in the context of their origins in the participatory social experience of dance. Musical meter is first considered in the context of bodily movement. I then offer an interpretation of the pervasive but somewhat puzzling phenomenon of syncopation in terms of acoustic emphasis on certain offbeat components of the accompanying dance style. The reasons for the historical tendency of many musical styles to divorce themselves from their dance-based roots are also briefly considered. To the extent that musical rhythms only make sense in the context of bodily movement, researchers interested in ecologically valid approaches to music cognition should make a more concerted effort to extend their analyses to dance, particularly if we hope to understand the cognitive constraints underlying rhythmic aspects of music like meter and groove.

  9. Scattering by a groove in an impedance plane

    Science.gov (United States)

    Bindiganavale, Sunil; Volakis, John L.

    1993-09-01

    An analysis of two-dimensional scattering from a narrow groove in an impedance plane is presented. The groove is represented by a impedance surface and the problem reduces to that of scattering from an impedance strip in an otherwise uniform impedance plane. On the basis of this model, appropriate integral equations are constructed using a form of the impedance plane Green's functions involving rapidly convergent integrals. The integral equations are solved by introducing a single basis representation of the equivalent current on the narrow impedance insert. Both transverse electric (TE) and transverse magnetic (TM) polarizations are treated. The resulting solution is validated by comparison with results from the standard boundary integral method (BIM) and a high frequency solution. It is found that the presented solution for narrow impedance inserts can be used in conjunction with the high frequency solution for the characterization of impedance inserts of any given width.

  10. Dynamic multileaf collimation without `tongue-and-groove' underdosage effects

    Science.gov (United States)

    van Santvoort, J. P. C.; Heijmen, B. J. M.

    1996-10-01

    In all commercially available multileaf collimators, a `tongue-and-groove' - or similar - construction is used for reduction of leakage radiation between adjacent leaves. These constructions can cause serious underdosages in intensity-modulated photon beams. A method for leaf trajectory calculation for dynamic multileaf collimation, which fully avoids these underdosage effects, is presented. The method is based on pairwise synchronizations of trajectories of adjacent leaf pairs, such that the delivered beam intensity in each `tongue-and-groove' region is always equal to the smallest of the two prescribed intensities for the two corresponding leaf pairs. The effectiveness of the method has been proven for a large number of intensity-modulated fields, using the dynamic multileaf collimation mode of our MM50 Racetrack Microtron. Compared to dynamic multileaf collimation without synchronization, beam-on times are always equal or longer. For the cases that we studied, the beam-on time was typically increased by 5 to 15%.

  11. Dynamic multileaf collimation without 'tongue-and-groove' underdosage effects.

    Science.gov (United States)

    van Santvoort, J P; Heijmen, B J

    1996-10-01

    In all commercially available multileaf collimators, a 'tongue-and-groove'--or similar--construction is used for reduction of leakage radiation between adjacent leaves. These constructions can cause serious underdosages in intensity-modulated photon beams. A method for leaf trajectory calculation for dynamic multileaf collimation, which fully avoids these underdosage effects, is presented. The method is based on pairwise synchronizations of trajectories of adjacent leaf pairs, such that the delivered beam intensity in each 'tongue-and-groove' region is always equal to the smallest of the two prescribed intensities for the two corresponding leaf pairs. The effectiveness of the method has been proven for a large number of intensity-modulated fields, using the dynamic multileaf collimation mode of our MM50 Racetrack Microtron. Compared to dynamic multileaf collimation without synchronization, beam-on times are always equal or longer. For the cases that we studied, the beam-on time was typically increased by 5 to 15%.

  12. Channel plasmon polariton propagation in nanoimprinted V-groove waveguides

    DEFF Research Database (Denmark)

    Nielsen, Rasmus Bundgaard; Fernandez-Cuesta, I.; Boltasseva, Alexandra;

    2008-01-01

    We present the results of optical characterization of metal V-groove waveguides using scanning near-field microscopy, showing broadband transmission with subwavelength confinement and propagation lengths exceeding 100 mu m. An updated fabrication method using a combination of UV and nanoimprint l...... lithography is presented. The developed approach is mass-production compatible, adaptable to different designs, and offers wafer-scale parallel fabrication of plasmonic components based on profiled metal surfaces....

  13. Experimental investigations on an axial grooved cryogenic heat pipe

    Directory of Open Access Journals (Sweden)

    Senthil Kumar Muniappan

    2012-01-01

    Full Text Available This paper deals with development and studies of a trapezoidal axial grooved nitrogen heat pipe. A special liquid nitrogen cryostat has been designed and developed for evaluating the performance of heat pipe where the condenser portion is connected to the cold sink externally. Experiments have been performed on the heat pipe as well as on an equivalent diameter copper rod at different heat loads. The steady state performance of the heat pipe is compared with that of copper rod.

  14. V-groove gratings on silicon for infrared beam splitting.

    Science.gov (United States)

    Rajkumar, N; McMullin, J N

    1995-05-10

    Infrared beam-splitting transmission gratings that utilize anisotropically etched v-grooves on silicon wafers are proposed. With scalar diffraction theory to find the amplitudes of the different diffraction orders, a numerical search is used to find optimum designs for 1:3, 1:5, and 1:7 splitters with efficiencies greater than 70% with a standard deviation in intensity of no more than 7%.

  15. Grooved organogel surfaces towards anisotropic sliding of water droplets.

    Science.gov (United States)

    Zhang, Pengchao; Liu, Hongliang; Meng, Jingxin; Yang, Gao; Liu, Xueli; Wang, Shutao; Jiang, Lei

    2014-05-21

    Periodic micro-grooved organogel surfaces can easily realize the anisotropic sliding of water droplets attributing to the formed slippery water/oil/solid interface. Different from the existing anisotropic surfaces, this novel surface provides a versatile candidate for the anisotropic sliding of water droplets and might present a promising way for the easy manipulation of liquid droplets for water collection, liquid-directional transportation, and microfluidics.

  16. HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove.

    Science.gov (United States)

    Filbin, Megan E; Kieft, Jeffrey S

    2011-07-01

    Hepatitis C virus (HCV) uses a structured internal ribosome entry site (IRES) RNA to recruit the translation machinery to the viral RNA and begin protein synthesis without the ribosomal scanning process required for canonical translation initiation. Different IRES structural domains are used in this process, which begins with direct binding of the 40S ribosomal subunit to the IRES RNA and involves specific manipulation of the translational machinery. We have found that upon initial 40S subunit binding, the stem-loop domain of the IRES that contains the start codon unwinds and adopts a stable configuration within the subunit's decoding groove. This configuration depends on the sequence and structure of a different stem-loop domain (domain IIb) located far from the start codon in sequence, but spatially proximal in the IRES•40S complex. Mutation of domain IIb results in misconfiguration of the HCV RNA in the decoding groove that includes changes in the placement of the AUG start codon, and a substantial decrease in the ability of the IRES to initiate translation. Our results show that two distal regions of the IRES are structurally communicating at the initial step of 40S subunit binding and suggest that this is an important step in driving protein synthesis.

  17. CHARACTERISTCS OF FLUID FILM IN OPTIMIZED SPIRAL GROOVE MECHANICAL SEAL

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In order to investigate the sealing performance variation resulted from the thermal deformation of the end faces, the equations to calculate the fluid film pressure distribution, the bearing force and the leakage rate are derived, for the fluid film both in parallel gap and in wedgy gap. The geometrical parameters of the sealing members are optimized by means of heat transfer analysis and complex method. The analysis results indicate that the shallow spiral grooves can generate hydrodynamic pressure while the rotating ring rotates and the bearing force of the fluid film in spiral groove end faces is much larger than that in the flat end faces. The deformation increases the bearing force of the fluid film in flat end faces, but it decreases the hydrodynamic pressure of the fluid film in spiral groove end faces. The gap dimensions which determine the characteristics of the fluid film is obtained by coupling analysis of the frictional heat and the thermal deformation in consideration of the equilibrium condition of the bearing force and the closing force. For different gap dimensions, the relationship between the closing force and the leakage rate is also investigated, based on which the leakage rate can be controlled by adjusting the closing force.

  18. Thermal Characteristics of Grooved Heat pipe with Hybrid Nanofluids

    Directory of Open Access Journals (Sweden)

    W S Han

    2011-01-01

    Full Text Available In the present study, the specially designed grooved heat pipe charged with nanofluids was investigated in terms of various parameters such as heat transfer rate(50∼300W with 50 W interval, volume concentration(0.005%, 0.05%, 0.1%, and hybrid combinations, inclination(5°, 45°, 90°, cooling water temperature (1℃, 10℃, and 20℃, surface state, transient state and so on. Hybrid nanofluids with different volume concentration ratios with Ag-H2O and Al2O3-H2O were used as working fluids on a grooved heat pipe(GHP. Comparing with the pure water system, nanofluidic and hybrid nanofluidic system shows greater overall thermal resistance with increasing nano-particle concentration. Also hybrid nanofluids make the system deteriorate in terms of thermal resistance. The post nanofluid experimental data regarding GHP show that the heat transfer performance is similar to the results of nanofluid system. The thermal performance of a grooved heat pipe with nanofluids and hybrid nanofluids were varied with driving parameters but they led to worse system performance.

  19. Repair welding process of friction stir welding groove defect

    Institute of Scientific and Technical Information of China (English)

    LIU Hui-jie; ZHANG Hui-jie

    2009-01-01

    The groove defect formed in the friction stir welding dramatically deteriorates weld appearances and mechanical properties of the joints owing to its larger size and penetration. Therefore, the friction stir repair welding was utilized to remove such a groove defect, and the focus was placed on the mechanical properties and microstructural characteristics of the repair joints so as to obtain an optimum repair welding process. The experimental results indicate that the groove defect can be removed by friction stir repair welding, and the offset repair welding process is superior to the symmetrical repair welding process. In the symmetrical repair welding process, a large number of fine cavity defects and an obvious aggregation of hard-brittle phase Al2Cu occur, accordingly the mechanical properties of the repair joint are weakened, and the fracture feature of repair joint is partially brittle and partially plastic. A good-quality repair joint can be obtained by the offset repair welding process, and the repair joint is fractured near the interface between the weld nugget zone and thermal-mechanically affected zone.

  20. The flow past a cactus-inspired grooved cylinder

    Science.gov (United States)

    El-Makdah, Adnan M.; Oweis, Ghanem F.

    2013-02-01

    The star-shaped cross section of giant cylindrical cactus plants is thought to be aerodynamically favorable for protection against toppling by strong winds. Particle image velocimetry is used to investigate the flow details within the surface grooves and in the immediate wake of a cactus-inspired model cylinder with eight longitudinal grooves, at biologically relevant Reynolds numbers between 50 × 103 and 170 × 103. The wake flow is analyzed and compared to a similarly sized circular cylinder. At the lowest Re tested, the wakes from the two geometries are similar. At higher Re, the cactus wake exhibits superior behavior as seen from the mean and turbulent velocities, suggesting that the flow mechanisms are Re dependent. The flow within the surface grooves reveals counter rotating rollers, while the geometrical ridges act as vortex generators known to help with the surface flow attachment. Lastly, a simplistic analysis is described to recover, qualitatively, certain time-dependent flow features from the randomly acquired PIV realizations.

  1. Parasitic capacitance characteristics of deep submicrometre grooved gate MOSFETs

    Science.gov (United States)

    Sreelal, S.; Lau, C. K.; Samudra, G. S.

    2002-03-01

    Grooved gate metal-oxide-semiconductor field-effect transistors (MOSFETs) are known to alleviate many of the short channel and hot carrier effects that arise when MOSFET devices are scaled down to very short channel lengths. However, they exhibit much higher parasitic capacitance with stronger bias dependence when compared to conventional planar devices. In this paper, we present a model for gate-to-drain and gate-to-source capacitance characteristics of a deep submicrometre grooved gate MOSFET. Both the intrinsic and extrinsic parts of the capacitance are modelled separately. In particular, the model presents a novel but simple way to account for the accumulation layer formation in the source/drain region of MOSFETs due to the application of the gate voltage. The results are compared with those obtained from a two-dimensional device simulator. The close match between the modelled and simulated data establishes the validity of the model. The model is then used to account for the superiority of capacitance characteristics of planar device structures and to arrive at optimization guidelines for grooved gate devices to match these characteristics.

  2. Novel drug design for Chagas disease via targeting Trypanosoma cruzi tubulin: Homology modeling and binding pocket prediction on Trypanosoma cruzi tubulin polymerization inhibition by naphthoquinone derivatives.

    Science.gov (United States)

    Ogindo, Charles O; Khraiwesh, Mozna H; George, Matthew; Brandy, Yakini; Brandy, Nailah; Gugssa, Ayele; Ashraf, Mohammad; Abbas, Muneer; Southerland, William M; Lee, Clarence M; Bakare, Oladapo; Fang, Yayin

    2016-08-15

    Chagas disease, also called American trypanosomiasis, is a parasitic disease caused by Trypanosoma cruzi (T. cruzi). Recent findings have underscored the abundance of the causative organism, (T. cruzi), especially in the southern tier states of the US and the risk burden for the rural farming communities there. Due to a lack of safe and effective drugs, there is an urgent need for novel therapeutic options for treating Chagas disease. We report here our first scientific effort to pursue a novel drug design for treating Chagas disease via the targeting of T. cruzi tubulin. First, the anti T. cruzi tubulin activities of five naphthoquinone derivatives were determined and correlated to their anti-trypanosomal activities. The correlation between the ligand activities against the T. cruzi organism and their tubulin inhibitory activities was very strong with a Pearson's r value of 0.88 (P value homology model of T. cruzi tubulin dimer was generated and the putative binding site of naphthoquinone derivatives was predicted. The correlation coefficient for ligand anti-tubulin activities and their binding energies at the putative pocket was found to be r=0.79, a high correlation efficiency that was not replicated in contiguous candidate pockets. The homology model of T. cruzi tubulin and the identification of its putative binding site lay a solid ground for further structure based drug design, including molecular docking and pharmacophore analysis. This study presents a new opportunity for designing potent and selective drugs for Chagas disease. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  3. Albumin binding of anti-inflammatory drugs. Utility of a site-oriented versus a stoichiometric analysis

    DEFF Research Database (Denmark)

    Honoré, B; Brodersen, R

    1984-01-01

    Binding equilibria of 12 nonsteroidal, anti-inflammatory substances, salicylic acid, diflunisal, phenylbutazone, azapropazone, fenbufen, biphenylacetic acid, naproxen, flurbiprofen, ibuprofin, diclofenac, indomethacin, and benoxaprofen, to defatted human serum albumin has been investigated at 37...

  4. Antipsychotic drug binding in the substantia nigra: an examination of high metoclopramide binding in the brains of normal, Alzheimer's disease, Huntington's disease, and Multiple Sclerosis patients, and its relation to tardive dyskinesia.

    Science.gov (United States)

    Chen, Sheng; Seeman, Philip; Liu, Fang

    2011-02-01

    This project was done in order to determine why the annual incidence of metoclopramide-associated tardive dyskinesia is much higher than that for the commonly used antipsychotics. To test the hypothesis that metoclopramide tardive dyskinesia may be associated with high concentrations of metoclopramide in the substantia nigra under clinical conditions, the nonspecific binding of tritiated antipsychotics to the dissected melaninized regions of postmortem human substantia nigra was measured. The nonspecific binding at 1 nM [³H]ligand was 7.3, 4.2, 2.6, 0.91 and 0.66 fmoles/mg for [³H]haloperidol, [³H]clozapine, [³H]raclopride, [³H]metoclopramide, and [³H]olanzapine, respectively. After adjusting these values for the known free concentrations of these drugs in plasma or spinal fluid, the amounts that would be bound under clinical conditions would be 231, 113, 15, 11, and 3.4 fmoles/mg for metoclopramide, clozapine, raclopride, haloperidol, and olanzapine, respectively. Using rat striatum as baseline to define antipsychotic binding to nonnigral tissue, the excess amount of binding to the Alzheimer nigral tissue under clinical conditions would be 209, 19, 0, 3.4 and 0.8 fmole/mg for metoclopramide, clozapine, raclopride, haloperidol, and olanzapine, respectively, with a similar pattern for nigral tissues from Huntington and Multiple Sclerosis patients. The high accumulation of metoclopramide is sufficiently high to cause nigral nerve cell membrane damage by metoclopramide's detergent-like action, possibly explaining metoclopramide's toxic ability to elicit early tardive dyskinesia. In addition, the nonspecific binding of metoclopramide was much higher in Alzheimer-diseased substantia nigra, consistent with the fact that older individuals are relatively more vulnerable to metoclopramide tardive dyskinesia.

  5. Putative cholesterol-binding sites in human immunodeficiency virus (HIV) coreceptors CXCR4 and CCR5.

    Science.gov (United States)

    Zhukovsky, Mikhail A; Lee, Po-Hsien; Ott, Albrecht; Helms, Volkhard

    2013-04-01

    Using molecular docking, we identified a cholesterol-binding site in the groove between transmembrane helices 1 and 7 near the inner membrane-water interface of the G protein-coupled receptor CXCR4, a coreceptor for HIV entry into cells. In this docking pose, the amino group of lysine K67 establishes a hydrogen bond with the hydroxyl group of cholesterol, whereas tyrosine Y302 stacks with cholesterol by its aromatic side chain, and a number of residues form hydrophobic contacts with cholesterol. Sequence alignment showed that a similar putative cholesterol-binding site is also present in CCR5, another HIV coreceptor. We suggest that the interaction of cholesterol with these putative cholesterol-binding sites in CXCR4 and CCR5 is responsible for the presence of these receptors in lipid rafts, for the effect of cholesterol on their conformational stability and function, and for the role that cell cholesterol plays in the cell entry of HIV strains that use these membrane proteins as coreceptors. We propose that mutations of residues that are involved in cholesterol binding will make CXCR4 and CCR5 insensitive to membrane cholesterol content. Cholesterol-binding sites in HIV coreceptors are potential targets for steroid drugs that bind to CXCR4 and CCR5 with higher binding affinity than cholesterol, but do not stabilize the native conformation of these proteins.

  6. Nanoparticle Fullerene (C60) demonstrated stable binding with antibacterial potential towards probable targets of drug resistant Salmonella typhi - a computational perspective and in vitro investigation.

    Science.gov (United States)

    Skariyachan, Sinosh; Parveen, Asma; Garka, Shruti

    2016-11-23

    Salmonella typhi, a Gram negative bacterium, has become multidrug resistant (MDR) to wide classes of antibacterials which necessitate an alarming precaution. This study focuses on the binding potential and therapeutic insight of Nano-Fullerene C60 towards virulent targets of Salmonella typhi by computational prediction and preliminary in vitro assays. The clinical isolates of Salmonella typhi were collected and antibiotic susceptibility profiles were assessed. The drug targets of pathogen were selected by rigorous literature survey and gene network analysis by various metabolic network resources. Based on this study, 20 targets were screened and the 3D structures of few drug targets were retrieved from PDB and others were computationally predicted. The structures of nanoleads such as Fullerene C60, ZnO and CuO were retrieved from drug databases. The binding potential of these nanoleads towards all selected targets were predicted by molecular docking. The best docked conformations were screened and concept was investigated by preliminary bioassays. This study revealed that most of the isolates of Salmonella typhi were found to be MDR (p Salmonella typhi.

  7. Investigation of the complex structure, comparative DNA-binding and DNA cleavage of two water-soluble mono-nuclear lanthanum(III) complexes and cytotoxic activity of chitosan-coated magnetic nanoparticles as drug delivery for the complexes

    Science.gov (United States)

    Asadi, Zahra; Nasrollahi, Neda; Karbalaei-Heidari, Hamidreza; Eigner, Vaclav; Dusek, Michal; Mobaraki, Nabiallah; Pournejati, Roya

    2017-05-01

    Two water-soluble mono-nuclear macrocyclic lanthanum(III) complexes of 2,6-diformyl-4-methylphenol with 1,3-diamino-2-propanol (C1) or 1,3-propylenediamine (C2) were synthesized and characterized by UV-Vis, FT-IR, 13C and 1H NMR spectroscopy and elemental analysis. C1 complex was structurally characterized by single-crystal X-ray diffraction, which revealed that the complex was mononuclear and ten-coordinated. The coordination sites around lanthanum(III) were occupied with a five-dentate ligand, two bidentate nitrates, and one water molecule. The interaction of complexes with DNA was studied in buffered aqueous solution at pH 7.4. UV-Vis absorption spectroscopy, emission spectroscopy, circular dichroism (CD) and viscometric measurements provided clear evidence of the intercalation mechanism of binding. The obtained intrinsic binding constants (Kb) 9.3 × 103 and 1.2 × 103 M- 1 for C1 and C2, respectively confirmed that C1 is better intercalator than C2. The DNA docking studies suggested that the complexes bind with DNA in a groove binding mode with the binding affinity of C1 > C2. Moreover, agarose gel electrophoresis study of the DNA-complex for both compounds revealed that the C1 intercalation cause ethidium bromide replacement in a competitive manner which confirms the suggested mechanism of binding. Finally, the anticancer experiments for the treated cancerous cell lines with both synthesized compounds show that these hydrophilic molecules need a suitable carrier to pass through the hydrophobic nature of cell membrane efficiently.

  8. In silico inspired design and synthesis of a novel tubulin-binding anti-cancer drug: folate conjugated noscapine (Targetin)

    Science.gov (United States)

    Naik, Pradeep K.; Lopus, Manu; Aneja, Ritu; Vangapandu, Surya N.; Joshi, Harish C.

    2012-02-01

    Our screen for tubulin-binding small molecules that do not depolymerize bulk cellular microtubules, but based upon structural features of well known microtubule-depolymerizing colchicine and podophyllotoxin, revealed tubulin binding anti-cancer property of noscapine (Ye et al. in Proc Natl Acad Sci USA 95:2280-2286, 1998). Guided by molecular modelling calculations and structure-activity relationships we conjugated at C9 of noscapine, a folate group—a ligand for cellular folate receptor alpha (FRα). FRα is over-expressed on some solid tumours such as ovarian epithelial cancers. Molecular docking experiments predicted that a folate conjugated noscapine (Targetin) accommodated well inside the binding cavity (docking score -11.295 kcal/mol) at the interface between α- and β-tubulin. The bulky folate moiety of Targetin is extended toward lumen of microtubules. The binding free energy (Δ G bind) computed based on molecular mechanics energy minimization was -221.01 kcal/mol that revealed favourable interaction of Targetin with the receptor. Chemical synthesis, tubulin-binding experiments, and anti-cancer activity in vitro corroborate fully well with the molecular modelling experiments. Targetin binds tubulin with a dissociation constant ( K d value) of 149 ± 3.0 μM and decreases the transition frequencies between growth and shortening phases of microtubule assembly dynamics at concentrations that do not alter the total polymer mass. Cancer cells in general were more sensitive to Targetin compared with the founding compound noscapine (IC50 in the range of 15-40 μM). Quite strikingly, ovarian cancer cells (SKOV3 and A2780), known to overexpress FRα, were much more sensitive to targetin (IC50 in the range of 0.3-1.5 μM).

  9. In silico inspired design and synthesis of a novel tubulin-binding anti-cancer drug: folate conjugated noscapine (Targetin).

    Science.gov (United States)

    Naik, Pradeep K; Lopus, Manu; Aneja, Ritu; Vangapandu, Surya N; Joshi, Harish C

    2012-02-01

    Our screen for tubulin-binding small molecules that do not depolymerize bulk cellular microtubules, but based upon structural features of well known microtubule-depolymerizing colchicine and podophyllotoxin, revealed tubulin binding anti-cancer property of noscapine (Ye et al. in Proc Natl Acad Sci USA 95:2280-2286, 1998). Guided by molecular modelling calculations and structure-activity relationships we conjugated at C9 of noscapine, a folate group-a ligand for cellular folate receptor alpha (FRα). FRα is over-expressed on some solid tumours such as ovarian epithelial cancers. Molecular docking experiments predicted that a folate conjugated noscapine (Targetin) accommodated well inside the binding cavity (docking score -11.295 kcal/mol) at the interface between α- and β-tubulin. The bulky folate moiety of Targetin is extended toward lumen of microtubules. The binding free energy (ΔG (bind)) computed based on molecular mechanics energy minimization was -221.01 kcal/mol that revealed favourable interaction of Targetin with the receptor. Chemical synthesis, tubulin-binding experiments, and anti-cancer activity in vitro corroborate fully well with the molecular modelling experiments. Targetin binds tubulin with a dissociation constant (K (d) value) of 149 ± 3.0 μM and decreases the transition frequencies between growth and shortening phases of microtubule assembly dynamics at concentrations that do not alter the total polymer mass. Cancer cells in general were more sensitive to Targetin compared with the founding compound noscapine (IC(50) in the range of 15-40 μM). Quite strikingly, ovarian cancer cells (SKOV3 and A2780), known to overexpress FRα, were much more sensitive to targetin (IC(50) in the range of 0.3-1.5 μM).

  10. Binding of the immunomodulatory drug Bz-423 to mitochondrial FoF1-ATP synthase in living cells by FRET acceptor photobleaching

    Science.gov (United States)

    Starke, Ilka; Johnson, Kathryn M.; Petersen, Jan; Gräber, Peter; Opipari, Anthony W.; Glick, Gary D.; Börsch, Michael

    2016-03-01

    Bz-423 is a promising new drug for treatment of autoimmune diseases. This small molecule binds to subunit OSCP of the mitochondrial enzyme FoF1-ATP synthase and modulates its catalytic activities. We investigate the binding of Bz-423 to mitochondria in living cells and how subunit rotation in FoF1-ATP synthase, i.e. the mechanochemical mechanism of this enzyme, is affected by Bz-423. Therefore, the enzyme was marked selectively by genetic fusion with the fluorescent protein EGFP to the C terminus of subunit γ. Imaging the threedimensional arrangement of mitochondria in living yeast cells was possible at superresolution using structured illumination microscopy, SIM. We measured uptake and binding of a Cy5-labeled Bz-423 derivative to mitochondrial FoF1-ATP synthase in living yeast cells using FRET acceptor photobleaching microscopy. Our data confirmed the binding of Cy5-labeled Bz-423 to the top of the F1 domain of the enzyme in mitochondria of living Saccharomyces cerevisiae cells.

  11. Spectroscopic and molecular modeling study on the separate and simultaneous bindings of alprazolam and fluoxetine hydrochloride to human serum albumin (HSA): With the aim of the drug interactions probing

    Science.gov (United States)

    Dangkoob, Faeze; Housaindokht, Mohmmad Reza; Asoodeh, Ahmad; Rajabi, Omid; Rouhbakhsh Zaeri, Zeinab; Verdian Doghaei, Asma

    2015-02-01

    The objective of the present research is to study the interaction of separate and simultaneous of alprazolam (ALP) and fluoxetine hydrochloride (FLX) with human serum albumin (HSA) in phosphate buffer (pH 7.4) using different kinds of spectroscopic, cyclic voltammetry and molecular modeling techniques. The absorbance spectra of protein, drugs and protein-drug showed complex formation between the drugs and HSA. Fluorescence analysis demonstrated that ALP and FLX could quench the fluorescence spectrum of HSA and demonstrated the conformational change of HSA in the presence of both drugs. Also, fluorescence quenching mechanism of HSA-drug complexes both separately and simultaneously was suggested as static quenching. The analysis of UV absorption data and the fluorescence quenching of HSA in the binary and ternary systems showed that FLX decreased the binding affinity between ALP and HSA. On the contrary, ALP increased the binding affinity of FLX and HSA. The results of synchronous fluorescence and three-dimensional fluorescence spectra indicated that the binding of drugs to HSA would modify the microenvironment around the Trp and Tyr residues and the conformation of HSA. The distances between Trp residue and the binding sites of the drugs were estimated according to the Förster theory, and it was demonstrated that non-radiative energy transfer from HSA to the drugs occurred with a high probability. Moreover, according to CV measurements, the decrease of peak current in the cyclic voltammogram of the both drugs in the presence of HSA revealed that they interacted with albumin and binding constants were calculated for binary systems which were in agreement with the binding constants obtained from UV absorption and fluorescence spectroscopy. The prediction of the best binding sites of ALP and FLX in binary and ternary systems in molecular modeling approach was done using of Gibbs free energy.

  12. Tailoring the grooved texture of electrospun polystyrene nanofibers by controlling the solvent system and relative humidity

    Science.gov (United States)

    2014-01-01

    In this study, we have successfully fabricated electrospun polystyrene (PS) nanofibers having a diameter of 326 ± 50 nm with a parallel grooved texture using a mixed solvent of tetrahydrofuran (THF) and N,N-dimethylformamide (DMF). We discovered that solvent system, solution concentration, and relative humidity were the three key factors to the formation of grooved texture and the diameter of nanofibers. We demonstrated that grooved nanofibers with desired properties (e.g., different numbers of grooves, widths between two adjacent grooves, and depths of grooves) could be electrospun under certain conditions. When THF/DMF ratio was higher than 2:1, the formation mechanism of single grooved texture should be attributed to the formation of voids on the jet surface at the early stage of electrospinning and subsequent elongation and solidification of the voids into a line surface structure. When THF/DMF ratio was 1:1, the formation mechanism of grooved texture should be ascribed to the formation of wrinkled surface on the jet surface at the early stage of electrospinning and subsequent elongation into a grooved texture. Such findings can serve as guidelines for the preparation of grooved nanofibers with desired secondary morphology. PMID:25114643

  13. Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing.

    Science.gov (United States)

    Lawrenz, Morgan; Baron, Riccardo; Wang, Yi; McCammon, J Andrew

    2012-01-01

    The Independent-Trajectory Thermodynamic Integration (IT-TI) approach for free energy calculation with distributed computing is described. IT-TI utilizes diverse conformational sampling obtained from multiple, independent simulations to obtain more reliable free energy estimates compared to single TI predictions. The latter may significantly under- or over-estimate the binding free energy due to finite sampling. We exemplify the advantages of the IT-TI approach using two distinct cases of protein-ligand binding. In both cases, IT-TI yields distributions of absolute binding free energy estimates that are remarkably centered on the target experimental values. Alternative protocols for the practical and general application of IT-TI calculations are investigated. We highlight a protocol that maximizes predictive power and computational efficiency.

  14. Binding of (/sup 3/H)ethyl-. beta. -carboline-3-carboxylate to brain benzodiazepine receptors. Effect of drugs and anions

    Energy Technology Data Exchange (ETDEWEB)

    Williams, E.F.; Paul, S.M.; Rice, K.C.; Skolnick, P. (National Institutes of Health, Bethesda, MD (USA)); Cain, M. (Wisconsin Univ., Milwaukee (USA). Dept. of Chemistry)

    1981-09-28

    It is reported that in contrast to the changes in affinity of (/sup 3/H)benzodiazepines elicited by halide ions, barbiturates, and pyrazolopyridines, the apparent affinity of ..beta..-(/sup 3/H)CCE (ethyl-..beta..-carboline-3-carboxylate) is unaffected by these agents. Furthermore, Scatchard analysis of ..beta..-(/sup 3/H)CCE binding to cerebral cortical and cerebellar membranes revealed a significantly greater number of binding sites than was observed with either (/sup 3/H)diazepam or (/sup 3/H)flunitazepam, suggesting that at low concentrations benzodiazepines selectively label a subpopulation of the receptors labelled with ..beta..-(/sup 3/H)CCE. Alternatively, ..beta..-(/sup 3/H)CCE may bind to sites that are distinct from those labelled with (/sup 3/H)-benzodiazepines.

  15. Measurement of binding of basic drugs to acidic phospholipids using surface plasmon resonance and incorporation of the data into mechanistic tissue composition equations to predict steady-state volume of distribution.

    Science.gov (United States)

    Small, Helen; Gardner, Iain; Jones, Hannah M; Davis, John; Rowland, Malcolm

    2011-10-01

    Acidic phospholipid binding plays an important role in determining the tissue distribution of basic drugs. This article describes the use of surface plasmon resonance to measure binding affinity (K(D)) of three basic drugs to phosphatidylserine, a major tissue acidic phospholipid. The data are incorporated into mechanistic tissue composition equations to allow prediction of the steady-state volume of distribution (V(ss)). The prediction accuracy of V(ss) using this approach is compared with the original methodology described by Rodgers et al. (J Pharm Sci 94:1259-1276), in which the binding to acidic phospholipids is calculated from the blood/plasma concentration ratio (BPR). The compounds used in this study [amlodipine, propranolol, and 3-dimethylaminomethyl-4-(4-methylsulfanyl-phenoxy)-benzenesulfonamide (UK-390957)] showed higher affinity binding to phosphatidylserine than to phosphatidylcholine. When the binding affinity to phosphatidylserine was incorporated into mechanistic tissue composition equations, the V(ss) was more accurately predicted for all three compounds by using the surface plasmon resonance measurement than by using the BPR to estimate acidic phospholipid binding affinity. The difference was particularly marked for UK-390957, a sulfonamide that has a high BPR due to binding to carbonic anhydrase. The novel approach described in this article allows the binding affinity of drugs to an acidic phospholipid (phosphatidylserine) to be measured directly and demonstrates the utility of the binding data in the prediction of V(ss).

  16. Phenylacetic acids and the structurally related non-steroidal anti-inflammatory drug diclofenac bind to specific gamma-hydroxybutyric acid sites in rat brain

    DEFF Research Database (Denmark)

    Wellendorph, Petrine; Høg, Signe; Skonberg, Christian

    2009-01-01

    with a twofold higher affinity than GHB. Measuring the affinities of structurally related NSAIDs for the [(3)H]NCS-382 site identified diclofenac, a clinically relevant NSAID (Voltaren, Diclon) of the phenylacetic acid (PAA) type, as a GHB ligand (K(i) value of 5.1 microM). Other non-NSAID PAAs also exhibited...... affinities similar to GHB. Our data raise the interesting possibility that the widely used over-the-counter drug compound, diclofenac, might affect GHB binding at relevant clinical dosages. Furthermore, the identification of PAAs as GHB ligands supplies new information about the structural preferences...

  17. Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with an Unusual Mode of Binding

    Energy Technology Data Exchange (ETDEWEB)

    Sidote,D.; Barbieri, C.; Wu, T.; Stock, A.

    2008-01-01

    The LytTR domain is a DNA-binding motif found within the AlgR/AgrA/LytR family of transcription factors that regulate virulence factor and toxin gene expression in pathogenic bacteria. This previously uncharacterized domain lacks sequence similarity with proteins of known structure. The crystal structure of the DNA-binding domain of Staphylococcus aureus AgrA complexed with a DNA pentadecamer duplex has been determined at 1.6 Angstroms resolution. The structure establishes a 10-stranded {beta} fold for the LytTR domain and reveals its mode of interaction with DNA. Residues within loop regions of AgrA contact two successive major grooves and the intervening minor groove on one face of the oligonucleotide duplex, inducing a substantial bend in the DNA. Loss of DNA binding upon substitution of key interacting residues in AgrA supports the observed binding mode. This mode of protein-DNA interaction provides a potential target for future antimicrobial drug design.

  18. Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with a Novel Mode of Binding

    Science.gov (United States)

    Sidote, David J.; Barbieri, Christopher M.; Wu, Ti; Stock, Ann M.

    2008-01-01

    SUMMARY The LytTR domain is a DNA-binding motif found within the AlgR/AgrA/LytR family of transcription factors that regulate virulence factor and toxin gene expression in pathogenic bacteria. This previously uncharacterized domain lacks sequence similarity with proteins of known structure. The crystal structure of the DNA-binding domain of Staphylococcus aureus AgrA complexed with a DNA pentadecamer duplex has been determined at 1.6 Å resolution. The structure establishes a 10-stranded β fold for the LytTR domain and reveals a novel mode of interaction with DNA. Residues within loop regions of AgrA contact two successive major grooves and the intervening minor groove on one face of the oligonucleotide duplex, inducing a substantial bend in the DNA. Loss of DNA-binding upon substitution of key interacting residues in AgrA supports the observed binding mode. This novel mode of protein-DNA interacton provides a potential target for future antimicrobial drug design. PMID:18462677

  19. Structure of the Staphylococcus aureus AgrA LytTR domain bound to DNA reveals a beta fold with an unusual mode of binding.

    Science.gov (United States)

    Sidote, David J; Barbieri, Christopher M; Wu, Ti; Stock, Ann M

    2008-05-01

    The LytTR domain is a DNA-binding motif found within the AlgR/AgrA/LytR family of transcription factors that regulate virulence factor and toxin gene expression in pathogenic bacteria. This previously uncharacterized domain lacks sequence similarity with proteins of known structure. The crystal structure of the DNA-binding domain of Staphylococcus aureus AgrA complexed with a DNA pentadecamer duplex has been determined at 1.6 A resolution. The structure establishes a 10-stranded beta fold for the LytTR domain and reveals its mode of interaction with DNA. Residues within loop regions of AgrA contact two successive major grooves and the intervening minor groove on one face of the oligonucleotide duplex, inducing a substantial bend in the DNA. Loss of DNA binding upon substitution of key interacting residues in AgrA supports the observed binding mode. This mode of protein-DNA interaction provides a potential target for future antimicrobial drug design.

  20. Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design.

    Directory of Open Access Journals (Sweden)

    Arun Chandramohan

    2016-06-01

    Full Text Available A key question in mapping dynamics of protein-ligand interactions is to distinguish changes at binding sites from those associated with long range conformational changes upon binding at distal sites. This assumes a greater challenge when considering the interactions of low affinity ligands (dissociation constants, KD, in the μM range or lower. Amide hydrogen deuterium Exchange mass spectrometry (HDXMS is a robust method that can provide both structural insights and dynamics information on both high affinity and transient protein-ligand interactions. In this study, an application of HDXMS for probing the dynamics of low affinity ligands to proteins is described using the N-terminal ATPase domain of Hsp90. Comparison of Hsp90 dynamics between high affinity natural inhibitors (KD ~ nM and fragment compounds reveal that HDXMS is highly sensitive in mapping the interactions of both high and low affinity ligands. HDXMS reports on changes that reflect both orthosteric effects and allosteric changes accompanying binding. Orthosteric sites can be identified by overlaying HDXMS onto structural information of protein-ligand complexes. Regions distal to orthosteric sites indicate long range conformational changes with implications for allostery. HDXMS, thus finds powerful utility as a high throughput method for compound library screening to identify binding sites and describe allostery with important implications for fragment-based ligand discovery (FBLD.

  1. Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design

    Science.gov (United States)

    Larsson, Andreas; Nordlund, Paer; Jansson, Anna; Anand, Ganesh S.

    2016-01-01

    A key question in mapping dynamics of protein-ligand interactions is to distinguish changes at binding sites from those associated with long range conformational changes upon binding at distal sites. This assumes a greater challenge when considering the interactions of low affinity ligands (dissociation constants, KD, in the μM range or lower). Amide hydrogen deuterium Exchange mass spectrometry (HDXMS) is a robust method that can provide both structural insights and dynamics information on both high affinity and transient protein-ligand interactions. In this study, an application of HDXMS for probing the dynamics of low affinity ligands to proteins is described using the N-terminal ATPase domain of Hsp90. Comparison of Hsp90 dynamics between high affinity natural inhibitors (KD ~ nM) and fragment compounds reveal that HDXMS is highly sensitive in mapping the interactions of both high and low affinity ligands. HDXMS reports on changes that reflect both orthosteric effects and allosteric changes accompanying binding. Orthosteric sites can be identified by overlaying HDXMS onto structural information of protein-ligand complexes. Regions distal to orthosteric sites indicate long range conformational changes with implications for allostery. HDXMS, thus finds powerful utility as a high throughput method for compound library screening to identify binding sites and describe allostery with important implications for fragment-based ligand discovery (FBLD). PMID:27253209

  2. Different types of copper complexes with the quinolone antimicrobial drugs ofloxacin and norfloxacin: structure, DNA- and albumin-binding.

    Science.gov (United States)

    Živec, Petra; Perdih, Franc; Turel, Iztok; Giester, Gerald; Psomas, George

    2012-12-01

    Three novel copper(II) complexes with the second-generation quinolone antibacterial agents norfloxacin (nfH) and ofloxacin (ofloH) have been synthesized resulting in the complexes [Cu(nfH)(phen)Cl]Cl·5H(2)O (1·5H(2)O), [Cu(nfH)(2)]Cl(2)·6H(2)O (2·6H(2)O) and [Cu(II)(ofloH)(2)][(Cu(I)Cl(2))(2)] (3), respectively. The crystal structures of the complexes have been determined by X-ray crystallography revealing that the quinolones act as bidentate ligands coordinated to Cu(II) atom through the pyridone oxygen and a carboxylato oxygen. UV study of the interaction of the quinolones and the complexes with calf-thymus DNA (CT DNA) has shown that they can bind to CT DNA with [Cu(II)(ofloxacin)(2)][(Cu(I)Cl(2))(2)] exhibiting the highest binding constant to CT DNA. The cyclic voltammograms of the complexes in the presence of CT DNA solution have shown that the interaction of the complexes with CT DNA is mainly through electrostatic binding. DNA solution viscosity measurements have shown that the interaction of the compounds with CT DNA by classical intercalation may be ruled out. Competitive studies with ethidium bromide (EB) indicate that the complexes can partially displace the DNA-bound EB suggesting low to moderate competition with EB. Norfloxacin, ofloxacin and their copper complexes exhibit good binding propensity to human or bovine serum albumin protein having relatively high binding constant values. Copyright © 2012 Elsevier Inc. All rights reserved.

  3. Subpixel accuracy for extracting groove center based on corner detection

    Institute of Scientific and Technical Information of China (English)

    Liu Suyi; Wang Guorong; Shi Yonghua

    2006-01-01

    Subpixel accuracy for V-groove center in robot welding is researched and a software measure to increase the accuracy of seam tracking by laser is presented.LOG( Laplacian of Gaussian ) operator is adopted to detect image edge.Vgroove center is extracted by corner detection of extremum curvature.Subpixel position is obtained by Lagarange polynomial interpolation algorithm.Experiment results show that the method is brief and applied, and is sufficient for the real time of robot welding by laser sensors.

  4. Coronary sinus and atrioventricular groove avulsion after motor vehicle crash

    Directory of Open Access Journals (Sweden)

    Bradley M Dennis

    2014-01-01

    Full Text Available Simultaneous cardiac and pericardial rupture from blunt chest trauma is a highly lethal combination with rarely reported survival. We report of a case of young patient with a right atrioventricular groove injury, pericardial rupture and a unique description of a coronary sinus avulsion following blunt chest trauma. Rapid recognition of this injury is crucial to patient survival, but traditional diagnostic adjuncts such as ultrasound, echocardiography and computed tomography are often unhelpful. Successful repair of these injuries requires high suspicion of injury, early cardiac surgery involvement of and possible even placement of the patient on cardiopulmonary bypass.

  5. Revamping Grooving Process for Sustainability using Fuzzy Expert System

    Directory of Open Access Journals (Sweden)

    Iqba Asif

    2016-01-01

    Full Text Available The article presents an application of a fuzzy expert system for renovating a metal cutting process to cope with the sustainability requirements. The work seeks a sustainable balance between energy consumption, productivity and tool damage. Cylindrical grooving experiments were performed to generate data related to quantification of the effects of material hardness, cutting speed, width of cut and feed rate on the aforementioned sustainability measures. A fuzzy knowledge-base was developed that suggests the most suitable adjustments of the controlled variables that would lead to achievement of various combinations of the objectives.

  6. Syncopation affects free body-movement in musical groove

    DEFF Research Database (Denmark)

    Witek, Maria A. G.; Popescu, Tudor; Clarke, Eric F

    2016-01-01

    One of the most immediate and overt ways in which people respond to music is by moving their bodies to the beat. However, the extent to which the rhythmic complexity of groove-specifically its syncopation-contributes to how people spontaneously move to music is largely unexplored. Here, we measured...... on the body-part. We demonstrate that while people do not move or synchronise much to rhythms with high syncopation when dancing spontaneously to music, the relationship between rhythmic complexity and synchronisation is less linear than in simple finger-tapping studies....

  7. Deep-groove nickel gratings for solar thermal absorbers

    Science.gov (United States)

    Ahmad, N.; Núñez-Sánchez, S.; Pugh, J. R.; Cryan, M. J.

    2016-10-01

    This paper presents measured and modelled optical absorptance and reflectance for deep-groove nickel nano-gratings in the 450-950 nm wavelength range. The structures have been fabricated using focused ion beam etching and characterised using Fourier spectroscopy and the field distributions on the gratings have been studied using finite difference time domain modelling. Realistic grating structures have been modelled based on focused ion beam cross sections and these results are in good agreement between measured and modelled results. The roles of surface plasmon polaritons and slot modes are highlighted in the strong broadband absorbance that can be achieved with these structures.

  8. Optimization design of main parameters for double spiral grooves face seal

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The optimization design of the parameters, such as the groove depth, groove number, ratio of the groove width to the land width, and spiral angle of a new kind of double spiral grooves face seal, which works under the condition of high velocity, high sealing pressure and ultra-low temperature, is presented under the assump-tion of fixed closure force by finite element analysis method. The results show that the stiffness of the maximum film can be obtained when the ratio of the groove width to the land width is 0.5 and the spiral angle is about 75 degrees, when the influence of the groove number on the sealing performance is not obvious.

  9. Optimization design of main parameters for double spiral grooves face seal

    Institute of Scientific and Technical Information of China (English)

    LIU Zhong; LIU Ying; LIU XiangFeng

    2007-01-01

    The optimization design of the parameters, such as the groove depth, groove number, ratio of the groove width to the land width, and spiral angle of a new kind of double spiral grooves face seal, which works under the condition of high velocity, high sealing pressure and ultra-low temperature, is presented under the assumption of fixed closure force by finite element analysis method. The results show that the stiffness of the maximum film can be obtained when the ratio of the groove width to the land width is 0.5 and the spiral angle is about 75 degrees, when the influence of the groove number on the sealing performance is not obvious.

  10. A review of interproximal wear grooves on fossil hominin teeth with new evidence from Olduvai Gorge.

    Science.gov (United States)

    Ungar, P S; Grine, F E; Teaford, M F; Pérez-Pérez, A

    2001-04-01

    Interproximal (approximal) grooves at the cementum-enamel junction of premolar and molar teeth have been observed in a broad range of human ancestors and related extinct species from 1.84 million years ago to the present. Many hypotheses have been presented to explain the aetiology of these grooves, though their form and positioning are most consistent with tooth-picking behaviours. This paper reviews occurrences of interproximal grooves in the cheek teeth of modern and fossil humans, evaluates hypotheses on their cause, and reports on a previously undescribed groove found in OH 60, a molar tooth from Olduvai Gorge. This specimen is among the earliest to show such grooving, and is most likely attributable to Homo erectus. It is concluded that, because interproximal grooves have been observed only on Homo teeth, they probably reflect a behaviour or behaviours unique to that genus.

  11. New insight into the molecular mechanisms of the biological effects of DNA minor groove binders.

    Directory of Open Access Journals (Sweden)

    Xinbo Zhang

    Full Text Available BACKGROUND: Bisbenzimides, or Hoechst 33258 (H258, and its derivative Hoechst 33342 (H342 are archetypal molecules for designing minor groove binders, and widely used as tools for staining DNA and analyzing side population cells. They are supravital DNA minor groove binders with AT selectivity. H342 and H258 share similar biological effects based on the similarity of their chemical structures, but also have their unique biological effects. For example, H342, but not H258, is a potent apoptotic inducer and both H342 and H258 can induce transgene overexpression in in vitro studies. However, the molecular mechanisms by which Hoechst dyes induce apoptosis and enhance transgene overexpression are unclear. METHODOLOGY/PRINCIPAL FINDINGS: To determine the molecular mechanisms underlying different biological effects between H342 and H258, microarray technique coupled with bioinformatics analyses and multiple other techniques has been utilized to detect differential global gene expression profiles, Hoechst dye-specific gene expression signatures, and changes in cell morphology and levels of apoptosis-associated proteins in malignant mesothelioma cells. H342-induced apoptosis occurs in a dose-dependent fashion and is associated with morphological changes, caspase-3 activation, cytochrome c mitochondrial translocation, and cleavage of apoptosis-associated proteins. The antagonistic effect of H258 on H342-induced apoptosis indicates a pharmacokinetic basis for the two dyes' different biological effects. Differential global gene expression profiles induced by H258 and H342 are accompanied by unique gene expression signatures determined by DNA microarray and bioinformatics software, indicating a genetic basis for their different biological effects. CONCLUSIONS/SIGNIFICANCE: A unique gene expression signature associated with H342-induced apoptosis provides a new avenue to predict and classify the therapeutic class of minor groove binders in the drug

  12. Kinetics of thermal grooving during low temperature recrystallization of pure aluminum

    DEFF Research Database (Denmark)

    Zhang, Yubin; Godfrey, Andy; Juul Jensen, Dorte

    2013-01-01

    The migration of a recrystallization boundary in pure aluminum was followed during in situ annealing in a scanning electron microscope. The microstructure was characterized using the electron channeling contrast technique, and a typical stop-go grain boundary motion was observed during annealing...... time. The kinetics of thermal grooving are determined. Effects of the surface oxidation layer on the formation of thermal grooving as well as the overall influence of grooves on boundary migration are discussed. © (2013) Trans Tech Publications, Switzerland....

  13. Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site

    Science.gov (United States)

    Oguievetskaia, Ksenia; Martin-Chanas, Laetitia; Vorotyntsev, Artem; Doppelt-Azeroual, Olivia; Brotel, Xavier; Adcock, Stewart A.; de Brevern, Alexandre G.; Delfaud, Francois; Moriaud, Fabrice

    2009-08-01

    Eg5, a mitotic kinesin exclusively involved in the formation and function of the mitotic spindle has attracted interest as an anticancer drug target. Eg5 is co-crystallized with several inhibitors bound to its allosteric binding pocket. Each of these occupies a pocket formed by loop 5/helix α2 (L5/α2). Recently designed inhibitors additionally occupy a hydrophobic pocket of this site. The goal of the present study was to explore this hydrophobic pocket with our MED-SuMo fragment-based protocol, and thus discover novel chemical structures that might bind as inhibitors. The MED-SuMo software is able to compare and superimpose similar interaction surfaces upon the whole protein data bank (PDB). In a fragment-based protocol, MED-SuMo retrieves MED-Portions that encode protein-fragment binding sites and are derived from cross-mining protein-ligand structures with libraries of small molecules. Furthermore we have excluded intra-family MED-Portions derived from Eg5 ligands that occupy the hydrophobic pocket and predicted new potential ligands by hybridization that would fill simultaneously both pockets. Some of the latter having original scaffolds and substituents in the hydrophobic pocket are identified in libraries of synthetically accessible molecules by the MED-Search software.

  14. High-Throughput Melanin-Binding Affinity and In Silico Methods to Aid in the Prediction of Drug Exposure in Ocular Tissue.

    Science.gov (United States)

    Reilly, John; Williams, Sarah L; Forster, Cornelia J; Kansara, Viral; End, Peter; Serrano-Wu, Michael H

    2015-12-01

    Drugs possessing the ability to bind to melanin-rich tissue, such as the eye, are linked with higher ocular exposure, and therefore have the potential to affect the efficacy and safety profiles of therapeutics. A high-throughput melanin chromatographic affinity assay has been developed and validated, which has allowed the rapid melanin affinity assessment for a large number of compounds. Melanin affinity of compounds can be quickly assigned as low, medium, or high melanin binders. A high-throughput chromatographic method has been developed and fully validated to assess melanin affinity of pharmaceuticals and has been useful in predicting ocular tissue distribution in vivo studies. The high-throughput experimental approach has also allowed for a specific training set of 263 molecules for a quantitative structure-affinity relationships (QSAR) method to be developed, which has also been shown to be a predictor of ocular tissue exposure. Previous studies have reported the development of in silico QSAR models based on training sets of relatively small and mostly similar compounds; this model covers a broader range of melanin-binding affinities than what has been previously published and identified several physiochemical descriptors to be considered in the design of compounds where melanin-binding modulation is desired.

  15. HEAT TRANSFER ENHANCEMENT AND PRESSURE DROP OF GROOVED ANNULUS OF DOUBLE PIPE HEAT EXCHANGER

    Directory of Open Access Journals (Sweden)

    Putu Wijaya Sunu

    2017-05-01

    Full Text Available This investigation was performed to experimentally investigate the enhancement of heat transfer and the friction of an annulus in a double pipe heat exchanger system with rectangular grooves in the turbulent flow regime. The shell is made of acrylic and its diameter is 28 mm. The tube is made of aluminium and its diameter is 20 mm. Grooves were incised in the annulus room with a circumferential pattern, with a groove space of 2 mm, a distance between the grooves of 8mm and a groove height of 0.3 mm. The experiments consist of temperature and pressure measurement and a flow visualization. Throughout the investigation, the cold fluid flowed in the annulus room. The Reynold number of cold fluid varied from about 31981 to 43601 in a counter flow condition. The volume flow rate of hot fluid remains constant with Reynold number about 30904. Result showed the effect of grooves, which are applied in the annulus room. The grooves induce the pressure drop, the pressure drop in the grooved annulus was greater by about 15.88% to 16.72% than the one in the smooth annulus. The total heat transfer enhancement is of 1.09–1.11. Moreover, the use of grooves in the annulus of the heat exchanger not only increase the heat transfer process, but also increase the pressure drop, which is related to the friction factor.

  16. Space qualification of high capacity grooved heat pipes

    Energy Technology Data Exchange (ETDEWEB)

    Dubois, M.; Mullender, B.; Druart, J. [SABCA, Societe Anomyme Belgel de Construction Aeronautique (Belgium); Supper, W.; Beddows, A. [ESTEC-The (Netherlands)

    1996-12-31

    Based on the thermal requirements of the future telecommunication satellites, the development of a High Capacity Grooved Heat Pipe (HPG), was contracted by ESA to SABCA leading to an aluminium extruded heat pipe (outer diameter of 25 mm) based on a multi re-entrant grooves design. After an intensive acceptance test campaign whose results showed a good confidence in the design and the fulfillment of the required specifications of heat transport and on tilt capability (experimental maximum heat transport capability of 1500 Watt metres for a vapour temperature of 20 deg C), similar heat pipes have been developed with various outer diameters (11 mm, 15 mm and 20 mm) and with various shapes (circular outer shapes, integrated saddles). Several of these heat pipes were tested during two parabolic flight campaigns, by varying the heat loads during the micro-gravity periods. This HGP heat pipe family is now being submitted to a space qualification program according to ESA standards (ESA PSS-49), both in straight and bent configuration. Within this qualification, the heat pipes are submitted to an extended test campaign including environmental (random/sinus vibration, constant acceleration) and thermal tests (thermal performance, thermal cycle, thermal soak, ageing). (authors) 9 refs.

  17. Capillary Contact Angle in a Completely Wet Groove

    Science.gov (United States)

    Parry, A. O.; Malijevský, A.; Rascón, C.

    2014-10-01

    We consider the phase equilibria of a fluid confined in a deep capillary groove of width L with identical side walls and a bottom made of a different material. All walls are completely wet by the liquid. Using density functional theory and interfacial models, we show that the meniscus separating liquid and gas phases at two phase capillary coexistence meets the bottom capped end of the groove at a capillary contact angle θcap(L) which depends on the difference between the Hamaker constants. If the bottom wall has a weaker wall-fluid attraction than the side walls, then θcap>0 even though all the isolated walls are themselves completely wet. This alters the capillary condensation transition which is now first order; this would be continuous in a capped capillary made wholly of either type of material. We show that the capillary contact angle θcap(L) vanishes in two limits, corresponding to different capillary wetting transitions. These occur as the width (i) becomes macroscopically large, and (ii) is reduced to a microscopic value determined by the difference in Hamaker constants. This second wetting transition is characterized by large scale fluctuations and essential critical singularities arising from marginal interfacial interactions.

  18. Separate and simultaneous binding effects of aspirin and amlodipine to human serum albumin based on fluorescence spectroscopic and molecular modeling characterizations: A mechanistic insight for determining usage drugs doses

    Energy Technology Data Exchange (ETDEWEB)

    Abdollahpour, Nooshin [Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad (Iran, Islamic Republic of); Asoodeh, Ahmad [Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad (Iran, Islamic Republic of); Saberi, Mohammad Reza [Department of Medical Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad (Iran, Islamic Republic of); Chamani, JamshidKhan, E-mail: chamani@ibb.ut.ac.ir [Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad (Iran, Islamic Republic of)

    2011-09-15

    The binding of aspirin (ASA) and amlodipine (AML) to human serum albumin (HSA) in aqueous solution was investigated by multiple techniques such as fluorescence quenching, resonance light scattering (RLS), three-dimensional fluorescence spectroscopy, FT-IR and zeta-potential measurements in an aqueous solution at pH=7.4. For the protein-ligand association reaction, fluorescence measurements can give important clues as to the binding of ligands to proteins, e.g., the binding mechanism, binding mode, binding constants, binding sites, etc. Fluorescence spectroscopy showed that ASA and AML could quench the HSA fluorescence spectra, and this quenching effect became more significant when both ASA and AML coexisted. The results pointed at the interaction between HSA and both drugs as ternary systems decreasing the binding constant and binding stability of the HSA-drug complex as a binary system. Therefore, by reducing the amount of drugs transported to their targets, the free drug concentration of the target would be reduced, lowering the efficacy of the drugs. It was demonstrated that there exists antagonistic behavior between the two drugs when it comes to binding of HSA. Furthermore, the fluorescence results also showed that the quenching mechanism of HSA-drug complexes as binary and ternary systems is a static procedure. The number of binding sites of HSA-ASA, (HSA-AML)ASA, HSA-AML and (HSA-ASA) AML were 1.31, 0.92, 1 and 0.93, respectively. Due to the existence of the antagonistic action between ASA and AML, the binding distance r was reduced. The results of synchronous fluorescence and three-dimensional fluorescence spectra showed that the antagonistic action between ASA and AML would alter the micro-environment around Trp and Tyr residues. Moreover, the simultaneous presence of ASA and AML during binding to HSA should be taken into account in multidrug therapy, as it induces the necessity of a monitoring therapy owing to the possible increase of uncontrolled toxic

  19. In silico optimization of pharmacokinetic properties and receptor binding affinity simultaneously: a 'parallel progression approach to drug design' applied to β-blockers.

    Science.gov (United States)

    Advani, Poonam; Joseph, Blessy; Ambre, Premlata; Pissurlenkar, Raghuvir; Khedkar, Vijay; Iyer, Krishna; Gabhe, Satish; Iyer, Radhakrishnan P; Coutinho, Evans

    2016-01-01

    The present work exploits the potential of in silico approaches for minimizing attrition of leads in the later stages of drug development. We propose a theoretical approach, wherein 'parallel' information is generated to simultaneously optimize the pharmacokinetics (PK) and pharmacodynamics (PD) of lead candidates. β-blockers, though in use for many years, have suboptimal PKs; hence are an ideal test series for the 'parallel progression approach'. This approach utilizes molecular modeling tools viz. hologram quantitative structure activity relationships, homology modeling, docking, predictive metabolism, and toxicity models. Validated models have been developed for PK parameters such as volume of distribution (log Vd) and clearance (log Cl), which together influence the half-life (t1/2) of a drug. Simultaneously, models for PD in terms of inhibition constant pKi have been developed. Thus, PK and PD properties of β-blockers were concurrently analyzed and after iterative cycling, modifications were proposed that lead to compounds with optimized PK and PD. We report some of the resultant re-engineered β-blockers with improved half-lives and pKi values comparable with marketed β-blockers. These were further analyzed by the docking studies to evaluate their binding poses. Finally, metabolic and toxicological assessment of these molecules was done through in silico methods. The strategy proposed herein has potential universal applicability, and can be used in any drug discovery scenario; provided that the data used is consistent in terms of experimental conditions, endpoints, and methods employed. Thus the 'parallel progression approach' helps to simultaneously fine-tune various properties of the drug and would be an invaluable tool during the drug development process.

  20. In vitro resistance selections for Plasmodium falciparum dihydroorotate dehydrogenase inhibitors give mutants with multiple point mutations in the drug-binding site and altered growth.

    Science.gov (United States)

    Ross, Leila S; Gamo, Francisco Javier; Lafuente-Monasterio, Maria José; Singh, Onkar M P; Rowland, Paul; Wiegand, Roger C; Wirth, Dyann F

    2014-06-27

    Malaria is a preventable and treatable disease; yet half of the world's population lives at risk of infection, and an estimated 660,000 people die of malaria-related causes every year. Rising drug resistance threatens to make malaria untreatable, necessitating both the discovery of new antimalarial agents and the development of strategies to identify and suppress the emergence and spread of drug resistance. We focused on in-development dihydroorotate dehydrogenase (DHODH) inhibitors. Characterizing resistance pathways for antimalarial agents not yet in clinical use will increase our understanding of the potential for resistance. We identified resistance mechanisms of Plasmodium falciparum (Pf) DHODH inhibitors via in vitro resistance selections. We found 11 point mutations in the PfDHODH target. Target gene amplification and unknown mechanisms also contributed to resistance, albeit to a lesser extent. These mutant parasites were often hypersensitive to other PfDHODH inhibitors, which immediately suggested a novel combination therapy approach to preventing resistance. Indeed, a combination of wild-type and mutant-type selective inhibitors led to resistance far less often than either drug alone. The effects of point mutations in PfDHODH were corroborated with purified recombinant wild-type and mutant-type PfDHODH proteins, which showed the same trends in drug response as the cognate cell lines. Comparative growth assays demonstrated that two mutant parasites grew less robustly than their wild-type parent, and the purified protein of those mutants showed a decrease in catalytic efficiency, thereby suggesting a reason for the diminished growth rate. Co-crystallography of PfDHODH with three inhibitors suggested that hydrophobic interactions are important for drug binding and selectivity.

  1. Interaction of coumarin with calf thymus DNA: deciphering the mode of binding by in vitro studies.

    Science.gov (United States)

    Sarwar, Tarique; Rehman, Sayeed Ur; Husain, Mohammed Amir; Ishqi, Hassan Mubarak; Tabish, Mohammad

    2015-02-01

    DNA is the major target for a wide range of therapeutic substances. Thus, there has been considerable interest in the binding studies of small molecules with DNA. Interaction between small molecules and DNA provides a structural guideline in rational drug designing and in the synthesis of new and improved drugs with enhanced selective activity and greater clinical efficacy. Plant derived polyphenolic compounds have a large number of biological and pharmacological properties. Coumarin is a polyphenolic compound which has been extensively studied for its diverse pharmacological properties. However, its mode of interaction with DNA has not been elucidated. In the present study, we have attempted to ascertain the mode of binding of coumarin with calf thymus DNA (Ct-DNA) through various biophysical techniques. Analysis of UV-visible absorbance spectra and fluorescence spectra indicates the formation of complex between coumarin and Ct-DNA. Several other experiments such as effect of ionic strength, iodide induced quenching, competitive binding assay with ethidium bromide, acridine orange and Hoechst 33258 reflected that coumarin possibly binds to the minor groove of the Ct-DNA. These observations were further supported by CD spectral analysis, viscosity measurements, DNA melting studies and in silico molecular docking.

  2. Antiproliferative activity of bicyclic benzimidazole nucleosides: synthesis, DNA-binding and cell cycle analysis.

    Science.gov (United States)

    Sontakke, Vyankat A; Lawande, Pravin P; Kate, Anup N; Khan, Ayesha; Joshi, Rakesh; Kumbhar, Anupa A; Shinde, Vaishali S

    2016-04-26

    An efficient route was developed for synthesis of bicyclic benzimidazole nucleosides from readily available d-glucose. The key reactions were Vörbruggen glycosylation and ring closing metathesis (RCM). Primarily, to understand the mode of DNA binding, we performed a molecular docking study and the binding was found to be in the minor groove region. Based on the proposed binding model, UV-visible and fluorescence spectroscopic techniques using calf thymus DNA (CT-DNA) demonstrated a non-intercalative mode of binding. Antiproliferative activity of nucleosides was tested against MCF-7 and MDA-MB-231 breast cancer cell lines and found to be active at low micromolar concentrations. Compounds and displayed significant antiproliferative activity as compared to and with the reference anticancer drug, doxorubicin. Cell cycle analysis showed that nucleoside induced cell cycle arrest at the S-phase. Confocal microscopy has been performed to validate the induction of cellular apoptosis. Based on these findings, such modified bicyclic benzimidazole nucleosides will make a significant contribution to the development of anticancer drugs.

  3. DNA Binding and Recognition of a CC Mismatch in a DNA Duplex by Water-Soluble Peptidocalix[4]arenes: Synthesis and Applications.

    Science.gov (United States)

    Alavijeh, Nahid S; Zadmard, Reza; Balalaie, Saeed; Alavijeh, Mohammad S; Soltani, Nima

    2016-10-07

    Water-soluble peptidocalix[4]arenes were synthesized by the introduction of arginine-rich narrow groove-binding residues at lower rims through solid-phase synthesis. The study of binding of these water-soluble bidentate ligands to well-matched and mismatched DNA duplexes by fluorescent titrations, ethidium bromide (EB) displacement assays, DNA-melting experiments, and circular dichroism (CD) analysis revealed a sequence-dependent groove-binding mechanism.

  4. A Study on Solubilization of Poorly Soluble Drugs by Cyclodextrins and Micelles: Complexation and Binding Characteristics of Sulfamethoxazole and Trimethoprim

    Directory of Open Access Journals (Sweden)

    Sinem Göktürk

    2012-01-01

    > α-CD. With taking into consideration of solubilization capacity of SDS micelles, it has been found that the solubility enhancement of TMP is much higher than that of SMX in the presence of SDS micelles. The binding constants of SMX and TMP obtained from the Benesi-Hildebrand equation are also confirmed by the estimated surface properties of SDS, employing the surface tension measurements. In order to elucidate the solubilization characteristics the surface tension measurements were also performed for nonionic surfactant Triton X-100. Polarity of the microenvironment and probable location of SMX and TMP were also discussed in the presence of various organic solvents.

  5. Unexpected binding orientation of bulky-B-ring anti-androgens and implications for future drug targets.

    Science.gov (United States)

    Duke, Charles B; Jones, Amanda; Bohl, Casey E; Dalton, James T; Miller, Duane D

    2011-06-01

    Several new androgen receptor antagonists were synthesized and found to have varying activities across typically anti-androgen resistant mutants (Thr877 → Ala and Trp741 → Leu) and markedly improved potency over previously reported pan-antagonists. X-ray crystallography of a new anti-androgen in an androgen receptor mutant (Thr877 → Ala) shows that the receptor can accommodate the added bulk presented by phenyl to naphthyl substitution, casting doubt on previous reports of predicted binding orientation and the causes of antagonism in bulky-B-ring antagonists.

  6. Prevalence of palate-gingival groove in patients of Dhulikhel Hospital

    Directory of Open Access Journals (Sweden)

    D Shreshta

    2015-06-01

    Full Text Available Background: Palato-gingival groove is a rare developmental anomaly leading to pulpal and periodontal diseases. Radicular extensions of these grooves are areas for plaque accumulation which are difficult to clean. Its clinical and radiographic findings mimic endo-perio lesions leading to diagnostic dilemma, ineffective treatment attempts and treatment failures. Objectives: To investigate the prevalence of coronal and radicular palato-gingival groove in dental patients visiting Dhulikhel Hospital and its association with gingival disease. Methods: Patients (N=231 visiting dental out-patient department of Dhulikhel Hospital, were examined for the presence or absence of palato-gingival groove in maxillary anteriors. Loe and Silness Gingival index was also recorded for all the patients using University of North Caroline-15 periodontal probe. Chisquare test was used to test the association of the presence of palato-gingival groove and gingival disease. P value of <0.05 was considered to be significant. Results: A total of 1362 maxillary anterior teeth were included in the study. The prevalence of coronal palatogingival groove among 1362 teeth was 6.6%. Coronal palato-gingival grooves were more common in females (56.6% than in male (43.3% patients. Prevalence of radicular groove was only 0.88% for lateral incisors and 0.2% for canines. There was no significant association between palate-gingival groove and gingival disease (P=0.91. Conclusion: The prevalence of palato-gingival groove is common in dental patients visiting Dhulikhel Hospital. Gingival disease is not significantly associated with palate-gingival groove. DOI: http://dx.doi.org/10.3126/jcmsn.v10i1.12765 Journal of College of Medical Sciences-Nepal, 2014, Vol.10(1; 32-36

  7. Optimally oriented grooves on dental implants improve bone quality around implants under repetitive mechanical loading.

    Science.gov (United States)

    Kuroshima, Shinichiro; Nakano, Takayoshi; Ishimoto, Takuya; Sasaki, Muneteru; Inoue, Maaya; Yasutake, Munenori; Sawase, Takashi

    2017-01-15

    The aim was to investigate the effect of groove designs on bone quality under controlled-repetitive load conditions for optimizing dental implant design. Anodized Ti-6Al-4V alloy implants with -60° and +60° grooves around the neck were placed in the proximal tibial metaphysis of rabbits. The application of a repetitive mechanical load was initiated via the implants (50N, 3Hz, 1800 cycles, 2days/week) at 12weeks after surgery for 8weeks. Bone quality, defined as osteocyte density and degree of biological apatite (BAp) c-axis/collagen fibers, was then evaluated. Groove designs did not affect bone quality without mechanical loading; however, repetitive mechanical loading significantly increased bone-to-implant contact, bone mass, and bone mineral density (BMD). In +60° grooves, the BAp c-axis/collagen fibers preferentially aligned along the groove direction with mechanical loading. Moreover, osteocyte density was significantly higher both inside and in the adjacent region of the +60° grooves, but not -60° grooves. These results suggest that the +60° grooves successfully transmitted the load to the bone tissues surrounding implants through the grooves. An optimally oriented groove structure on the implant surface was shown to be a promising way for achieving bone tissue with appropriate bone quality. This is the first report to propose the optimal design of grooves on the necks of dental implants for improving bone quality parameters as well as BMD. The findings suggest that not only BMD, but also bone quality, could be a useful clinical parameter in implant dentistry.

  8. Applying the Fe(III) binding property of a chemical transferrin mimetic to Ti(IV) anticancer drug design.

    Science.gov (United States)

    Parks, Timothy B; Cruz, Yahaira M; Tinoco, Arthur D

    2014-02-03

    As an endogenous serum protein binder of Ti(IV), transferrin (Tf) serves as an excellent vehicle to stabilize the hydrolysis prone metal ion and successfully transport it into cells. This transporting role is thought to be central to Ti(IV)'s anticancer function, but efforts to synthesize Ti(IV) compounds targeting transferrin have not produced a drug. Nonetheless, the Ti(IV) transferrin complex (Ti2Tf) greatly informs on a new Ti(IV)-based anticancer drug design strategy. Ti2Tf interferes with cellular uptake of Fe(III), which is particularly detrimental to cancer cells because of their higher requirement for iron. Ti(IV) compounds of chemical transferrin mimetic (cTfm) ligands were designed to facilitate Ti(IV) activity by attenuating Fe(III) intracellular levels. In having a higher affinity for Fe(III) than Ti(IV), these ligands feature the appropriate balance between stability and lability to effectively transport Ti(IV) into cancer cells, release Ti(IV) via displacement by Fe(III), and deplete the intracellular Fe(III) levels. The cTfm ligand N,N'-di(o-hydroxybenzyl)ethylenediamine-N,N'-diacetic acid (HBED) was selected to explore the feasibility of the design strategy. Kinetic studies on the Fe(III) displacement process revealed that Ti(IV) can be transported and released into cells by HBED on a physiologically relevant time scale. Cell viability studies using A549 cancerous and MRC5 normal human lung cells and testing the cytotoxicity of HBED and its Ti(IV), Fe(III), and Ga(III) compounds demonstrate the importance of Fe(III) depletion in the proposed drug design strategy and the specificity of the strategy for Ti(IV) activity. The readily derivatized cTfm ligands demonstrate great promise for improved Ti(IV) anticancer drugs.

  9. The effect of combined hypergravity and micro-grooved surface topography on the behaviour of fibroblasts.

    NARCIS (Netherlands)

    Loesberg, W.A.; Walboomers, X.F.; Loon, J.J. van; Jansen, J.A.

    2006-01-01

    This study evaluated in vitro the differences in morphological behaviour between fibroblast cultured on smooth and micro-grooved substrata (groove depth: 1 mum, width: 1, 2, 5, 10 microm), which undergo artificial hypergravity by centrifugation (10, 24 and 50 g; or 1 g control). The aim of the study

  10. Beaming light from a subwavelength slit surrounded by an array of grooves with different depth

    Science.gov (United States)

    Luo, Xiangang; Wang, Changtao; Du, Chunlei; Shi, Haofei; Gao, Hongtao; Ma, Junxian; Fu, Yongqi; Li, Haiying

    2005-08-01

    In this paper, we discussed the beam focusing of light emerged from a subwavlength metallic slit surrounded by a set of grooves with constant space and width but variant depth at the exit side surface. Based on the numerical model presented by L. Martin-Moreno, F. J. Garcia-Vidal etc. (published in PRL 167401), we attempted to optimize grooves depth to obtain general beam manipulation, such as beam focusing. This attempt did not prove successful for many cases with variant focal length in our optimization practice, although some specific results display agreeable beam focusing with elongated focal depth. Further numerical computation shows that the excited electromagnetic field intensity around groove openings has a strong dependence on the groove depth, but the phase only vary with a maximum change value of π by tuning the groove depth. This property restricts greatly the modulation of electromagnetic field by just changing each groove depth. More geometrical parameters, including groove space and width, are recommended for optimization in the design of nano metallic groove and slit structures for specific beam manipulation.

  11. Current Teaching of Proximal Retention Grooves for Class II Amalgam Preparations.

    Science.gov (United States)

    Moore, David L.

    1992-01-01

    A survey gathered information on methods of class II amalgam preparation taught in 59 dental schools. Focus was on the teaching and testing of proximal retention groove use, stated rationale for placing retention grooves, and the relationship of the instruction to board criteria for cavity preparation. (MSE)

  12. Study of the cavitating instability on a grooved Venturi profile

    CERN Document Server

    Danlos, Amélie; Ravelet, Florent; Coutier-Delgosha, Olivier; Bakir, Farid

    2012-01-01

    Cavitation is a limiting phenomenon in many domains of fluid mechanics. Instabilities of a partial cavity developed on an hydrofoil, a converging-diverging step or in an inter-blade channel in turbomachinery, have already been investigated and described in many previous works. The aim of this study is to evaluate a passive control method of the sheet cavity. According to operating conditions, cavitation can be described by two different regimes: an unstable regime with a cloud cavitation shedding and a stable regime with only a pulsating sheet cavity. Avoiding cloud cavitation can limit structure damages since a pulsating sheet cavity is less agressive. The surface condition of a converging-diverging step, like a Venturi-type obstacle, is here studied as a solution for a passive control of the cavitation. This study discusses the effect of an organized roughness, in the shape of longitudinal grooves, on the developed sheet cavity. Analyzes conducted with Laser Doppler Velocimetry, visualisations and pressure ...

  13. Study of surface plasmon chirality induced by Archimedes' spiral grooves.

    Science.gov (United States)

    Ohno, Tomoki; Miyanishi, Shintaro

    2006-06-26

    A chirality of surface plasmons excited on a silver film with Archimedes' spiral grooves during incidence of a circularly polarized light is analytically and numerically studied by using the finite-difference time-domain (FDTD) modeling method. We found that the surface of a plasmon has selective chirality, which is given by the sum of the chiralities of the incident light and the spiral structure. The surface plasmons with the chirality lead to zero-order, first-order, and high-order evanescent Bessel beams with electric charge distributions on the film. This selectivity could be widely applied for chiral detection of the incident light and chiral excitation of several optical modes in nanophotonics.

  14. Design of ANSYS-based Cathode with Complex Groove

    Institute of Scientific and Technical Information of China (English)

    范植坚; 赵刚刚; 张丽娟

    2012-01-01

    The profile of cathode with complex groove needs to be modified time after time during design of electrochemical machining (ECM) cathode.A design scheme using finite element method (FEM) for cathode with complex profile is put forward to shorten the period of cathode design.Based on Laplace equation,the potential distribution on parameter-transformation model was calculated by using ANSYS,which is compared to the potential distribution calculated by substituting conductivity and current efficiency into Laplace equation.According to the difference between the results calculated and simulated by ANSYS,the cathode profile was modified by adjusting the cathode boundary.The experiments show that the dimensions and shape of workpiece machined by numerically simulated cathode conform well with the blueprint.

  15. Dance, Music, Meter and Groove: A Forgotten Partnership

    Science.gov (United States)

    Fitch, W. Tecumseh

    2016-01-01

    I argue that core aspects of musical rhythm, especially “groove” and syncopation, can only be fully understood in the context of their origins in the participatory social experience of dance. Musical meter is first considered in the context of bodily movement. I then offer an interpretation of the pervasive but somewhat puzzling phenomenon of syncopation in terms of acoustic emphasis on certain offbeat components of the accompanying dance style. The reasons for the historical tendency of many musical styles to divorce themselves from their dance-based roots are also briefly considered. To the extent that musical rhythms only make sense in the context of bodily movement, researchers interested in ecologically valid approaches to music cognition should make a more concerted effort to extend their analyses to dance, particularly if we hope to understand the cognitive constraints underlying rhythmic aspects of music like meter and groove. PMID:26973489

  16. Finite Element Analysis of 6300 Deep Groove Ball Bearing

    Institute of Scientific and Technical Information of China (English)

    DENG Chi; YANG Guang-hui

    2013-01-01

    Rolling bearing is widely used in mechanical support, its general components are the inner ring, outer ring, the ball, retainer etc.. Now many companies in developed countries and university in the rolling bearing as the research object, and has made great progress in design theory, the experiment method and production technology etc. We will use the finite element ANSYS to establish the model of deep groove ball bearing. Through the contact analysis, we can get the contact stress between the rings and balls, strain, contact state, penetration, sliding distance and the friction stress distribution. These values are compared to the theoretical values with Hertz theory, and they have better consistency, provide the good theoretical basis for the optimization design of rolling bearings.

  17. New phacoemulsification tip with a grooved, threaded-tip construction.

    Science.gov (United States)

    Watanabe, Akinari

    2011-07-01

    To visually compare ultrasonic tip vibrations between a phaco tip with internal grooves (threaded tip) and a standard phaco tip during continuous-mode ultrasound (US) using ultra-high-speed digital video imaging. Watanabe Eye Clinic, Hyogo, Japan. Experimental study. The threaded tip was constructed by creating grooves inside a standard phaco tip using a screw. An ultra-high-speed digital video camera was used to record the image during continuous-mode US. Samples used in the test chamber during phacoemulsification included a piece of chestnut as a representative human lens sample and actual human lens fragments. Ultra-high-speed digital images showed that the threaded tip created a larger amount of cavitation than the standard phaco tip during US oscillation. Phacoemulsification of the sample using the standard phaco tip produced a chattering motion, making it difficult to maintain a steady tip position. The threaded tip produced little chattering motion, making it relatively easy to maintain a steady tip position. Once a piece of sample was gripped by the threaded tip, it was shaved and aspirated into the threaded tip without chattering motion. The mean effective phacoemulsification time (EPT) of the threaded tip was significantly shorter than that of the normal phaco tip (6.0 seconds ± 1.9 [SD] versus 15.4 ± 1.3 seconds; P=.002). The threaded tip created larger amounts of cavitation and had strong destructive and holding power. This threaded construction is simple to produce and appears to be very effective for phacoemulsification. Copyright © 2011 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  18. High-quality NMR structure of human anti-apoptotic protein domain Mcl-1(171-327 for cancer drug design.

    Directory of Open Access Journals (Sweden)

    Gaohua Liu

    Full Text Available A high-quality NMR solution structure is presented for protein hMcl-1(171-327 which comprises residues 171-327 of the human anti-apoptotic protein Mcl-1 (hMcl-1. Since this construct contains the three Bcl-2 homology (BH sequence motifs which participate in forming a binding site for inhibitors of hMcl-1, it is deemed to be crucial for structure-based design of novel anti-cancer drugs blocking the Mcl1 related anti-apoptotic pathway. While the coordinates of an NMR solution structure for a corresponding construct of the mouse homologue (mMcl-1 are publicly available, our structure is the first atomic resolution structure reported for the 'apo form' of the human protein. Comparison of the two structures reveals that hMcl-1(171-327 exhibits a somewhat wider ligand/inhibitor binding groove as well as a different charge distribution within the BH3 binding groove. These findings strongly suggest that the availability of the human structure is of critical importance to support future design of cancer drugs.

  19. Novel experimental design for steady-state processes: a systematic Bayesian approach for enzymes, drug transport, receptor binding, continuous culture and cell transport kinetics.

    Science.gov (United States)

    Crabbe, M James C; Murphy, Emma F; Gilmour, Steven G

    2005-01-01

    We demonstrate that a Bayesian approach (the use of prior knowledge) to the design of steady-state experiments can produce major gains quantifiable in terms of information, productivity and accuracy of each experiment. Developing the use of Bayesian utility functions, we have used a systematic method to identify the optimum experimental designs for a number of kinetic model data sets. This has enabled the identification of trends between kinetic model types, sets of design rules and the key conclusion that such designs should be based on some prior knowledge of the kinetic model. We suggest an optimal and iterative method for selecting features of the design such as the substrate range, number of measurements and choice of intermediate points. The final design collects data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. It is equally applicable to enzymes, drug transport, receptor binding, microbial culture and cell transport kinetics.

  20. Dielectric effect on the rf characteristics of a helical groove travelling wave tube

    Institute of Scientific and Technical Information of China (English)

    Wei Yan-Yu(魏彦玉); Wang Wen-Xiang(王文祥); Sun Jia-Hong(孙嘉鸿); Liu Sheng-Gang(刘盛纲); Baofu Jia; Gun-Sik Park

    2002-01-01

    A new type of partial-dielectric-loaded helical groove slow-wave structure (SWS) for millimetre wave travellingwave tube (TWT) is presented in this paper. The radio-frequency characteristics including the dispersion properties,the longitudinal electric field distribution and the beam-wave coupling impedance of this structure are analysed. Theresults show that the dispersion of the helical groove circuit is weakened, the phase velocity is reduced and the positionof the maximum Ez is moved from the mouth to the inside of the groove after partially filling the dielectric materialsin the helical groove SWS. Therefore, the dielectric-loaded helical groove SWS is suitable for a multi-beam TWT withbroad band and high gain.

  1. Source-model technique analysis of electromagnetic scattering by surface grooves and slits.

    Science.gov (United States)

    Trotskovsky, Konstantin; Leviatan, Yehuda

    2011-04-01

    A computational tool, based on the source-model technique (SMT), for analysis of electromagnetic wave scattering by surface grooves and slits is presented. The idea is to use a superposition of the solution of the unperturbed problem and local corrections in the groove/slit region (the grooves and slits are treated as perturbations). In this manner, the solution is obtained in a much faster way than solving the original problem. The proposed solution is applied to problems of grooves and slits in otherwise planar or periodic surfaces. Grooves and slits of various shapes, both smooth ones as well as ones with edges, empty or filled with dielectric material, are considered. The obtained results are verified against previously published data.

  2. Some effects of grooved runway configurations on aircraft tire braking traction under flooded runway conditions

    Science.gov (United States)

    Byrdsong, T. A.

    1973-01-01

    An experimental investigation was conducted to study the effect of grooved runway configurations on aircraft tire braking traction on flooded runway surfaces. The investigation was performed, utilizing size 49 x 17, type VII, aircraft tires with an inflation pressure of 170 lb per square inch at ground speeds up to approximately 120 knots. The results of this investigation indicate that when the runway is flooded, grooved surfaces provide better braking traction than an ungrooved surface and, in general, the level of braking traction was found to improve as the tire bearing pressure was increased because of an increase in the groove area of either the surface or the tire tread. Rounding the groove edges tended to degrade the tire braking capability from that developed on the same groove configuration with sharp edges. Results also indicate that braking friction coefficients for the test tires and runway surfaces decreased as ground speed was increased because of the hydroplaning effects.

  3. Dispersion characteristics of planar grating with arbitrary grooves for terahertz Smith-Purcell radiation

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Miaomiao, E-mail: mona486@yeah.net; Li, Ke, E-mail: like3714@163.com [Key Laboratory of High Power Microwave Sources and Technologies, Institute of Electronics, Chinese Academy of Sciences, Beijing 100190 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Liu, Wenxin, E-mail: lwenxin@mail.ie.ac.cn; Wang, Yong, E-mail: wangyong3845@sina.com [Key Laboratory of High Power Microwave Sources and Technologies, Institute of Electronics, Chinese Academy of Sciences, Beijing 100190 (China)

    2015-03-15

    In this paper, a novel method of getting the dispersion relations in planar grating with arbitrary grooves for terahertz Smith-Purcell radiation is investigated analytically. The continuous profile of the groove is approximately replaced by a series of rectangular steps. By making use of field matches method and the continuity of transverse admittance, the universal dispersion equation for grating with arbitrarily shaped grooves is derived. By solving the dispersion equation in presence of electron beam, the growth rate is obtained directly and the dependence on beam parameters is analyzed. Comparisons of the dispersion characteristics among some special groove shapes have been made by numerical calculation. The results show that the rectangular-step approximation method provides a novel approach to obtain the universal dispersion relation for grating with arbitrary grooves for Smith-Purcell radiation.

  4. Dielectric effect on the rf characteristics of a helical groove travelling wave tube

    Science.gov (United States)

    Wei, Yan-Yu; Wang, Wen-Xiang; Sun, Jia-Hong; Liu, Sheng-Gang; Baofu, Jia; Gun-Sik, Park

    2002-03-01

    A new type of partial-dielectric-loaded helical groove slow-wave structure (SWS) for millimetre wave travelling wave tube (TWT) is presented in this paper. The radio-frequency characteristics including the dispersion properties, the longitudinal electric field distribution and the beam-wave coupling impedance of this structure are analysed. The results show that the dispersion of the helical groove circuit is weakened, the phase velocity is reduced and the position of the maximum Ez is moved from the mouth to the inside of the groove after partially filling the dielectric materials in the helical groove SWS. Therefore, the dielectric-loaded helical groove SWS is suitable for a multi-beam TWT with broad band and high gain.

  5. Experimental Study of Turbulent Boundary Layers on Groove/Smooth Flat Surfaces

    Institute of Scientific and Technical Information of China (English)

    Hongwei MA; Qiao TIAN; Hui WU

    2005-01-01

    This paper presents an experimental investigation of the turbulent boundary layers on both groove and smooth flat surfaces. The flow structures were shown in a water tunnel using the hydrogen-bubble flow visualization technique. The measurement results indicate that: (1) the grooves can effectively reduce accumulation of low-speed fluids, decrease the number of the low-speed streaks and depress oscillation of the streaks in the sublayer; (2) the grooves can restrain forming of the horseshoe vortices in the buffer region; (3) the grooves bate oscillation and kinking of the quasi-streamwise vortices and restrain production of the hairpin vortices and the ring vortices, reducing both frequency and intensity of the turbulence bursting; (4) the grooves directly affect the flow structures in the sublayer of the boundary layer and then modulate the flow field up to the buffer region and the logarithmic region by restraining development and interaction of the vortices.

  6. Treatment of a Developmental Groove and Supernumerary Root Using Guided Tissue Regeneration Technique

    Directory of Open Access Journals (Sweden)

    Zahra Alizadeh Tabari

    2016-01-01

    Full Text Available Introduction. The radicular groove is a developmental groove which is usually found on the palatal or lateral aspects of the maxillary incisor teeth. The present case is a maxillary lateral incisor with a small second root and a deep radicular groove. The developmental groove caused a combined periodontal-endodontic lesion. Methods. Case was managed using a combined treatment procedure involving nonsurgical root canal therapy and surgical periodontal treatment. After completion of root canal treatment, guided tissue regeneration (GTR was carried out using decalcified freeze dried bone allograft (DFDBA and a bioabsorbable collagenous membrane. Tooth also was splinted for two months. Results. After 12 months the tooth was asymptomatic. The periapical radiolucency disappeared and probing depth did not exceed 3 mm. Conclusion. Combined treatment procedure involving nonsurgical root canal therapy and surgical periodontal regenerative treatment can be a predictable technique in treating combined endodontic-periodontal lesions caused by radicular groove.

  7. A simple method for fabrication of high-aspect-ratio all-silicon grooves

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Yuncan; Pan, An; Si, Jinhai, E-mail: jinhaisi@mail.xjtu.edu.cn; Chen, Tao; Chen, Feng; Hou, Xun

    2013-11-01

    A simple method using 800-nm femtosecond laser irradiation and chemical selective etching has been proposed for fabrication of high-aspect-ratio all-silicon grooves. Grooves with the maximum aspect ratio of 44 were produced. A scanning electronic microscopy equipped with an energy dispersive X-ray spectroscopy was employed to characterize the morphology and chemical composition of the grooves respectively. The formation mechanism of the grooves was attributed to the chemical reaction of the laser induced refractive index change microstructures and hydrofluoric acid solution. The dependences of the aspect ratio of the grooves on the laser irradiation parameters, such as: the numerical aperture of the microscope objective lens, the laser average power and the laser scanning velocity, are discussed.

  8. Treatment of a Developmental Groove and Supernumerary Root Using Guided Tissue Regeneration Technique.

    Science.gov (United States)

    Alizadeh Tabari, Zahra; Homayouni, Hamed; Pourseyediyan, Tahere; Arvin, Armita; Eiland, Derrick; Moradi Majd, Nima

    2016-01-01

    Introduction. The radicular groove is a developmental groove which is usually found on the palatal or lateral aspects of the maxillary incisor teeth. The present case is a maxillary lateral incisor with a small second root and a deep radicular groove. The developmental groove caused a combined periodontal-endodontic lesion. Methods. Case was managed using a combined treatment procedure involving nonsurgical root canal therapy and surgical periodontal treatment. After completion of root canal treatment, guided tissue regeneration (GTR) was carried out using decalcified freeze dried bone allograft (DFDBA) and a bioabsorbable collagenous membrane. Tooth also was splinted for two months. Results. After 12 months the tooth was asymptomatic. The periapical radiolucency disappeared and probing depth did not exceed 3 mm. Conclusion. Combined treatment procedure involving nonsurgical root canal therapy and surgical periodontal regenerative treatment can be a predictable technique in treating combined endodontic-periodontal lesions caused by radicular groove.

  9. Thermal performance of heat pipe with different micro-groove structures

    Institute of Scientific and Technical Information of China (English)

    白鹏飞; 汤勇; 唐彪; 陆龙生

    2008-01-01

    Four kinds of micro heat pipe of trapezoidal groove wick structure with different numbers of grooves or aspect ratios were studied and compared about thermal transfer performances in order to optimize the manufacture of micro heat pipe with groove wick structure. The results show that these micro heat pipes have excellent performance in heat transfer; the equivalent thermal conductivity coefficient is two orders of magnitude compared with that of copper; the number and aspect ratio of grooves have a prominent effect on the performance of such thermal transfer. The optimum number of grooves is lower than 60 and the best aspect ratio is near to 1.5. The temperature and thermal transport rate are almost directly proportional relationship, but this relationship will be broken up suddenly when the critical heat flux is reached.

  10. An Optimum Method for a Grooved 2D Planar Ion Trap Design

    Institute of Scientific and Technical Information of China (English)

    JI Wei-Bang; WAN Jin-Yin; CHENG Hua-Dong; LIU Liang

    2011-01-01

    We investigate an effective grooved 2D ion chip design and optimize the ratio between the size of the rf electrodes and the groove.We calculate the optimal size of the groove using the analyticai model,which was introduced by House,and the optimum result is obtained. We aiso obtain the simulated scattering points with the finite element analysis method.The analytical curve and simulated scattering points are coincident with each other.It is shown that this analytical model also fits for the grooved planar ion chip.Thus the optimum grooved 2D planar ion chip design could be obtained.It is effective for scalable quantum information processing.

  11. Treatment of a Developmental Groove and Supernumerary Root Using Guided Tissue Regeneration Technique

    Science.gov (United States)

    Alizadeh Tabari, Zahra; Pourseyediyan, Tahere; Eiland, Derrick

    2016-01-01

    Introduction. The radicular groove is a developmental groove which is usually found on the palatal or lateral aspects of the maxillary incisor teeth. The present case is a maxillary lateral incisor with a small second root and a deep radicular groove. The developmental groove caused a combined periodontal-endodontic lesion. Methods. Case was managed using a combined treatment procedure involving nonsurgical root canal therapy and surgical periodontal treatment. After completion of root canal treatment, guided tissue regeneration (GTR) was carried out using decalcified freeze dried bone allograft (DFDBA) and a bioabsorbable collagenous membrane. Tooth also was splinted for two months. Results. After 12 months the tooth was asymptomatic. The periapical radiolucency disappeared and probing depth did not exceed 3 mm. Conclusion. Combined treatment procedure involving nonsurgical root canal therapy and surgical periodontal regenerative treatment can be a predictable technique in treating combined endodontic-periodontal lesions caused by radicular groove. PMID:27965900

  12. LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria.

    Science.gov (United States)

    González-Díaz, Humberto; Munteanu, Cristian R; Postelnicu, Lucian; Prado-Prado, Francisco; Gestal, Marcos; Pazos, Alejandro

    2012-03-01

    Lipid-Binding Proteins (LIBPs) or Fatty Acid-Binding Proteins (FABPs) play an important role in many diseases such as different types of cancer, kidney injury, atherosclerosis, diabetes, intestinal ischemia and parasitic infections. Thus, the computational methods that can predict LIBPs based on 3D structure parameters became a goal of major importance for drug-target discovery, vaccine design and biomarker selection. In addition, the Protein Data Bank (PDB) contains 3000+ protein 3D structures with unknown function. This list, as well as new experimental outcomes in proteomics research, is a very interesting source to discover relevant proteins, including LIBPs. However, to the best of our knowledge, there are no general models to predict new LIBPs based on 3D structures. We developed new Quantitative Structure-Activity Relationship (QSAR) models based on 3D electrostatic parameters of 1801 different proteins, including 801 LIBPs. We calculated these electrostatic parameters with the MARCH-INSIDE software and they correspond to the entire protein or to specific protein regions named core, inner, middle, and surface. We used these parameters as inputs to develop a simple Linear Discriminant Analysis (LDA) classifier to discriminate 3D structure of LIBPs from other proteins. We implemented this predictor in the web server named LIBP-Pred, freely available at , along with other important web servers of the Bio-AIMS portal. The users can carry out an automatic retrieval of protein structures from PDB or upload their custom protein structural models from their disk created with LOMETS server. We demonstrated the PDB mining option performing a predictive study of 2000+ proteins with unknown function. Interesting results regarding the discovery of new Cancer Biomarkers in humans or drug targets in parasites have been discussed here in this sense.

  13. Individual differences in beat perception affect gait responses to low- and high-groove music.

    Directory of Open Access Journals (Sweden)

    Li-Ann eLeow

    2014-10-01

    Full Text Available Slowed gait in Parkinson’s disease (PD patients can be improved when patients synchronize footsteps to isochronous metronome cues, but limited retention of such improvements suggest that permanent cueing regimes are needed for long-term improvements. If so, music might make permanent cueing regimes more pleasant, improving adherence; however, music cueing requires patients to synchronize movements to the beat, which might be difficult for PD patients who tend to show weak beat perception. One solution may be to use high groove music, which has high beat salience that may facilitate synchronization, and affective properties which may improve motivation to move. As a first step in understanding how beat perception affects gait in complex neurological disorders, we examined how beat perception ability affected gait in neurotypical adults. Synchronization performance and gait parameters were assessed as healthy young adults with strong or weak beat perception synchronized to low groove music, high groove music, and metronome cues. High groove music was predicted to elicit better synchronization than low groove music, due to its higher beat salience. Two musical tempi, or rates, were used: (1 preferred tempo: beat rate matched to preferred step rate and (2 faster tempo: beat rate adjusted to 22.5% faster than preferred step rate. For both strong and weak beat-perceivers, synchronization performance was best with metronome cues, followed by high groove music, and worst with low groove music. In addition, high groove music elicited longer and faster steps than low groove music, both at preferred tempo and at faster tempo. Low groove music was particularly detrimental to gait in weak beat-perceivers, who showed slower and shorter steps compared to uncued walking. The findings show that individual differences in beat perception affect gait when synchronizing footsteps to music, and have implications for using music in gait rehabilitation.

  14. Individual differences in beat perception affect gait responses to low- and high-groove music.

    Science.gov (United States)

    Leow, Li-Ann; Parrott, Taylor; Grahn, Jessica A

    2014-01-01

    Slowed gait in patients with Parkinson's disease (PD) can be improved when patients synchronize footsteps to isochronous metronome cues, but limited retention of such improvements suggest that permanent cueing regimes are needed for long-term improvements. If so, music might make permanent cueing regimes more pleasant, improving adherence; however, music cueing requires patients to synchronize movements to the "beat," which might be difficult for patients with PD who tend to show weak beat perception. One solution may be to use high-groove music, which has high beat salience that may facilitate synchronization, and affective properties, which may improve motivation to move. As a first step to understanding how beat perception affects gait in complex neurological disorders, we examined how beat perception ability affected gait in neurotypical adults. Synchronization performance and gait parameters were assessed as healthy young adults with strong or weak beat perception synchronized to low-groove music, high-groove music, and metronome cues. High-groove music was predicted to elicit better synchronization than low-groove music, due to its higher beat salience. Two musical tempi, or rates, were used: (1) preferred tempo: beat rate matched to preferred step rate and (2) faster tempo: beat rate adjusted to 22.5% faster than preferred step rate. For both strong and weak beat-perceivers, synchronization performance was best with metronome cues, followed by high-groove music, and worst with low-groove music. In addition, high-groove music elicited longer and faster steps than low-groove music, both at preferred tempo and at faster tempo. Low-groove music was particularly detrimental to gait in weak beat-perceivers, who showed slower and shorter steps compared to uncued walking. The findings show that individual differences in beat perception affect gait when synchronizing footsteps to music, and have implications for using music in gait rehabilitation.

  15. Determination of covalent binding to intact DNA, RNA, and oligonucleotides by intercalating anticancer drugs using high-performance liquid chromatography. Studies with doxorubicin and NADPH cytochrome P-450 reductase

    Energy Technology Data Exchange (ETDEWEB)

    Cummings, J.; Bartoszek, A.; Smyth, J.F. (Imperial Cancer Research Fund Medical Oncology Unit, Western General Hospital, Edinburgh, Scotland (Ireland))

    1991-04-01

    An HPLC method is described which can determine covalent binding to intact nucleic acid by intercalating anticancer drugs and at the same time remove noncovalently bound intercalated drug. The method uses a column containing a nonporous 2-microns DEAE anion-exchange resin capable of chromatographing nucleic acids greater than 50,000 bases in size in under 1 h. After priming with 1 mg of DNA, the column behaves as an intercalator affinity column, strongly retaining the drug while allowing the nucleic acid to pass through normally. Retained drug is released with an injection of 0.1 M potassium hydroxide. Incubations were performed with the intercalator doxorubicin, which is also believed to bind covalently to DNA. When (14C)doxorubicin was mixed with DNA, at a concentration where all the drug would bind by intercalation, the column retained 82% of the total radioactivity, only 18% migrated with the nucleic acid. If the DNA was mildly denatured by treatment with 2 M sodium chloride at 50 degrees C for 45 min before chromatography, then 99.8% of total radioactivity was retained, only background counts migrated with the nucleic acid, as was the case with single-stranded DNA and RNA without any treatment. Purified NADPH cytochrome P-450 reductase was used to activate doxorubicin. DNA inhibited the metabolism of the drug by the enzyme, no covalent binding occurred with RNA, low levels occurred with single-stranded DNA, and the highest levels were recorded with oligonucleotides. The assay was sufficiently sensitive to measure covalent binding to DNA extracted from MCF-7 human breast cancer cells treated with 50 microM (14C)doxorubicin. Thus, covalent binding to DNA, RNA, and oligonucleotides by intercalators can be measured quickly (20 min) without the need to either digest the nucleic acid or subject it to long sample preparation techniques.

  16. Experimental studies on heat transfer and friction factor characteristics of a turbulent flow for internally grooved tubes

    Directory of Open Access Journals (Sweden)

    Ponnusamy Selvaraj

    2016-01-01

    Full Text Available This paper reports experimental studies on friction factor, Nusselt number, and thermal hydraulic performance of a tube equipped with the classic three modified internally grooved tubes. Heat transfer and friction factor characteristics and pres- sure drop results have been obtained experimentally for a fully developed water flow in a grooved tube is also reported. Tests were performed for Reynolds number ranges from 5000-13500 for different geometric grooved tubes (circular, square, and rapezium. The ratio of length-to-diameter is 38.69 D. Among the grooved tubes, heat transfer enhancement obtained up to 47% for circular grooved tube, 31% for square grooved tube, and 52% for trapezoidal grooved tube in comparison with the smooth tube. It has been observed that the friction factor high in the case of square grooved tube than those of other tubes.

  17. Characteristics of Arbitrarily-Shaped Helical Groove Slow-Wave Structure Loaded with a Concentric Dielectric-Rod

    Science.gov (United States)

    Gong, Yu-Bin; Wei, Yan-Yu; Liu, Hong-Tao

    2010-12-01

    The dielectric-rod is loaded on the central axis of the arbitrarily-shaped helical groove slow-wave structure. Meanwhile, the profile of the groove is replaced by a series of continuous rectangular steps. The unified dispersion equation of the arbitrarily-shaped helical groove waveguide loaded with a concentric dielectric-rod is obtained by means of a combination of filed-matching method and admittance-matching technique. Then, the effect of the change of groove shape and the dielectric-rod parameters on the dispersion and coupling impedance is approached by theory calculation. The results show that: loaded with dielectric-rod, the bandwidth of the helical groove traveling wave tube (TWT) is effectively broadened, but the coupling impedance is reduced. Among the five different groove shapes, the triangle-type groove has the widest bandwidth but the smallest coupling impedance, and the swallow-tailed-type groove has the narrowest bandwidth but the largest coupling impedance.

  18. Determination of Tongue and Groove parameters for multileaf collimators; Determinaco de parametros de Tongue and Groove de colimadores de multilaminas

    Energy Technology Data Exchange (ETDEWEB)

    Castro, Aluisio; Almeida, Carlos E. de, E-mail: alu_neto@hotmail.com [Universidade Estadual do Rio de Janeiro (UERJ), RJ (Brazil). Laboratorio de Ciencias Radiologicas; Nguyen, Bihn [Prowess Inc., Concord, CA (United States)

    2012-08-15

    The Tongue and Groove effect (TandG) is characterized by an additional attenuation between adjacent and opposing leaves on multileaf collimators (MLCs) in adjacent or complementary fields. This is a typical situation in of intensity-modulated radiotherapy treatments. The aim of this study was to measure the width and transmission of TandG effect for two commercial MLCs: Varian Millennium 120 (6 MV and 16 MV beams) and BrainLab m3 (only for 6 MV). The methodology used was based on the creation of MLC shapes that emphasizes TandG effect, the irradiation of these fields on radiochromic film and the sensitometric evaluation of the films in order to determine the TandG width and transmission. The results for TandG width for studied MLCs were 2.5, 1.8 and 2 mm, respectively, whit transmission TandG values of 87, 90 and 85%. (author)

  19. Binding of small molecules at interface of protein-protein complex - A newer approach to rational drug design.

    Science.gov (United States)

    Gurung, A B; Bhattacharjee, A; Ajmal Ali, M; Al-Hemaid, F; Lee, Joongku

    2017-02-01

    Protein-protein interaction is a vital process which drives many important physiological processes in the cell and has also been implicated in several diseases. Though the protein-protein interaction network is quite complex but understanding its interacting partners using both in silico as well as molecular biology techniques can provide better insights for targeting such interactions. Targeting protein-protein interaction with small molecules is a challenging task because of druggability issues. Nevertheless, several studies on the kinetics as well as thermodynamic properties of protein-protein interactions have immensely contributed toward better understanding of the affinity of these complexes. But, more recent studies on hot spots and interface residues have opened up new avenues in the drug discovery process. This approach has been used in the design of hot spot based modulators targeting protein-protein interaction with the objective of normalizing such interactions.

  20. Global alteration of the drug-binding pocket of human P-glycoprotein (ABCB1) by substitution of fifteen conserved residues reveals a negative correlation between substrate size and transport efficiency.

    Science.gov (United States)

    Vahedi, Shahrooz; Chufan, Eduardo E; Ambudkar, Suresh V

    2017-11-01

    P-glycoprotein (P-gp), an ATP-dependent efflux pump, is linked to the development of multidrug resistance in cancer cells. However, the drug-binding sites and translocation pathways of this transporter are not yet well-characterized. We recently demonstrated the important role of tyrosine residues in regulating P-gp ATP hydrolysis via hydrogen bond formations with high affinity modulators. Since tyrosine is both a hydrogen bond donor and acceptor, and non-covalent interactions are key in drug transport, in this study we investigated the global effect of enrichment of tyrosine residues in the drug-binding pocket on the drug binding and transport function of P-gp. By employing computational analysis, 15 conserved residues in the drug-binding pocket of human P-gp that interact with substrates were identified and then substituted with tyrosine, including 11 phenylalanine (F72, F303, F314, F336, F732, F759, F770, F938, F942, F983, F994), two leucine (L339, L975), one isoleucine (I306), and one methionine (M949). Characterization of the tyrosine-rich P-gp mutant in HeLa cells demonstrated that this major alteration in the drug-binding pocket by introducing fifteen additional tyrosine residues is well tolerated and has no measurable effect on total or cell surface expression of this mutant. Although the tyrosine-enriched mutant P-gp could transport small to moderate size (1000 Daltons) substrates such as NBD-cyclosporine A, Bodipy-paclitaxel and Bodipy-vinblastine was significantly decreased. This was further supported by the physico-chemical characterization of seventeen tested substrates, which revealed a negative correlation between drug transport and molecular size for the tyrosine-enriched P-gp mutant. Published by Elsevier Inc.

  1. Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites

    Directory of Open Access Journals (Sweden)

    Sirota Fernanda L

    2009-05-01

    Full Text Available Abstract In this work, we study the consequences of sequence variations of the "2009 H1N1" (swine or Mexican flu influenza A virus strain neuraminidase for drug treatment and vaccination. We find that it is phylogenetically more closely related to European H1N1 swine flu and H5N1 avian flu rather than to the H1N1 counterparts in the Americas. Homology-based 3D structure modeling reveals that the novel mutations are preferentially located at the protein surface and do not interfere with the active site. The latter is the binding cavity for 3 currently used neuraminidase inhibitors: oseltamivir (Tamiflu®, zanamivir (Relenza® and peramivir; thus, the drugs should remain effective for treatment. However, the antigenic regions of the neuraminidase relevant for vaccine development, serological typing and passive antibody treatment can differ from those of previous strains and already vary among patients. Reviewers This article was reviewed by Sandor Pongor and L. Aravind.

  2. Effect of groove on socket welds under the condition of vibration fatigue

    Science.gov (United States)

    Xiu, Junjie; Jing, Hongyang; Han, Yongdian; Zhao, Lei; Xu, Lianyong

    2013-02-01

    Root failures of socket welds in small bore piping caused by vibration mainly occur at nuclear power plants (NPPs). It was observed that at higher stress level failures tended to originate at the toe while for the case of lower stress failures tended to occur at the root. The groove can increase the penetration depth (PD) of root, which is beneficial to the fatigue life. The effect of groove was also investigated by finite element method (FEM). The simulation results show that groove can decline the stress distribution, stress triaxiality and maximum principal plastic strain in the weld root, and the 5 mm groove suffering σmax (the highest stress of root failure) is almost same as no groove subjecting to σf (fatigue limit). The test results show that the socket weld with groove can increase the natural frequency and damping of specimen, which make the system more difficult to vibrate. Moreover, the groove can also improve the fatigue property of specimen which do not exist the root failure even under high cycle fatigue (HCF).

  3. Phase-Field Modeling of Grain-Boundary Grooving Under Electromigration

    Science.gov (United States)

    Mukherjee, Arnab; Ankit, Kumar; Mukherjee, Rajdip; Nestler, Britta

    2016-12-01

    In the present work, we study the phenomenon of grain-boundary grooving under electromigration using a phase-field method. The specific focus of the work is to explore the role of grain boundaries as potential electromigration pathways. We consider the evolution of grooves under the combined influence of capillary and electromigration-mediated surface diffusion and electromigration-induced grain-boundary diffusion. Mechanisms of grooving are elucidated using flux density maps that indicate various regimes depending upon the direction of net material transport. When grain-boundary atomic mobility is lower than the surface mobility, the groove depth is found to be lower than that evolving solely under surface diffusion (no electromigration). At comparable or larger values of grain-boundary atomic mobility, grooving is initially expedited but shows groove replenishment at later stages. A detailed investigation using the phase-field method reveals the influence of an incumbent healing mechanism on grain-boundary grooving which is electrically induced. The drift characteristics such as edge and root displacement and velocity are examined in light of this assuaging effect.

  4. Effective slip for flow through a channel bounded by lubricant-impregnated grooved surfaces

    Science.gov (United States)

    Sun, Rui; Ng, Chiu-On

    2017-04-01

    This study aims to investigate effective slip arising from pressure-driven flow through a slit channel bounded by lubricant-impregnated grooved surfaces. The problem for flow over longitudinal grooves is solved analytically using the methods of domain decomposition and eigenfunction expansion, while that for flow over transverse grooves is solved numerically using the front tracking method. It is found that the effective slip length and the lubricant flow rate can depend strongly on the geometry of the microstructure, the direction of flow, and the lubricant viscosity. In particular, the effective slip can be effectively enhanced by increasing the thickness of a lubricating film atop the ribs. Under the same conditions, a flow that is parallel to the lubricant-impregnated grooves will have a larger effective slip, but also a larger lubricant flow rate, when compared with the case of flow normal to the grooves. It is also shown that, in the case of transverse grooves, because of the downward displacement of the interface between the working/lubricating fluids, the effective slip length and lubricant flow rate may vary non-monotonically with the groove depth.

  5. The Effect of Expert Performance Microtiming on Listeners' Experience of Groove in Swing or Funk Music

    Science.gov (United States)

    Senn, Olivier; Kilchenmann, Lorenz; von Georgi, Richard; Bullerjahn, Claudia

    2016-01-01

    This study tested the influence of expert performance microtiming on listeners' experience of groove. Two professional rhythm section performances (bass/drums) in swing and funk style were recorded, and the performances' original microtemporal deviations from a regular metronomic grid were scaled to several levels of magnitude. Music expert (n = 79) and non-expert (n = 81) listeners rated the groove qualities of stimuli using a newly developed questionnaire that measures three dimensions of the groove experience (Entrainment, Enjoyment, and the absence of Irritation). Findings show that music expert listeners were more sensitive to microtiming manipulations than non-experts. Across both expertise groups and for both styles, groove ratings were high for microtiming magnitudes equal or smaller than those originally performed and decreased for exaggerated microtiming magnitudes. In particular, both the fully quantized music and the music with the originally performed microtiming pattern were rated equally high on groove. This means that neither the claims of PD theory (that microtiming deviations are necessary for groove) nor the opposing exactitude hypothesis (that microtiming deviations are detrimental to groove) were supported by the data. PMID:27761117

  6. The Effect of Expert Performance Microtiming on Listeners' Experience of Groove in Swing or Funk Music.

    Science.gov (United States)

    Senn, Olivier; Kilchenmann, Lorenz; von Georgi, Richard; Bullerjahn, Claudia

    2016-01-01

    This study tested the influence of expert performance microtiming on listeners' experience of groove. Two professional rhythm section performances (bass/drums) in swing and funk style were recorded, and the performances' original microtemporal deviations from a regular metronomic grid were scaled to several levels of magnitude. Music expert (n = 79) and non-expert (n = 81) listeners rated the groove qualities of stimuli using a newly developed questionnaire that measures three dimensions of the groove experience (Entrainment, Enjoyment, and the absence of Irritation). Findings show that music expert listeners were more sensitive to microtiming manipulations than non-experts. Across both expertise groups and for both styles, groove ratings were high for microtiming magnitudes equal or smaller than those originally performed and decreased for exaggerated microtiming magnitudes. In particular, both the fully quantized music and the music with the originally performed microtiming pattern were rated equally high on groove. This means that neither the claims of PD theory (that microtiming deviations are necessary for groove) nor the opposing exactitude hypothesis (that microtiming deviations are detrimental to groove) were supported by the data.

  7. The effect of expert performance microtiming on listeners’ experience of groove in swing or funk music

    Directory of Open Access Journals (Sweden)

    Olivier Senn

    2016-10-01

    Full Text Available This study tested the influence of expert performance microtiming on listeners' groove experience. Two professional rhythm section (bass/drums performances in swing and funk style were recorded, and the performances' original microtemporal deviations from a regular metronomic grid were scaled to several magnitude levels. Music expert (n=79 and non-expert (n=81 listeners rated the groove qualities of stimuli using a newly developed questionnaire that measures three dimensions of the groove experience (Entrainment, Enjoyment, and the absence of Irritation. Findings show that music expert listeners were more sensitive to microtiming manipulations than non-experts. Across both expertise groups and for both styles, groove ratings were high for microtiming magnitudes equal or smaller than those originally performed and decreased for exaggerated microtiming magnitudes. In particular, both the fully quantized music and the music with the originally performed microtiming pattern were rated equally high on groove. This means that neither the claims of PD theory (that microtiming deviations are necessary for groove nor the opposing exactitude hypothesis (that microtiming deviations are detrimental to groove were supported by the data.

  8. Electrowetting actuated microfluidic transport in surface grooves with triangular cross section.

    Science.gov (United States)

    Barman, Jitesh; Swain, Digendranath; Law, Bruce M; Seemann, Ralf; Herminghaus, Stephan; Khare, Krishnacharya

    2015-01-27

    Liquids show different static wetting morphologies in open triangular grooves depending upon the wedge angle (ψ) of the groove and the liquid contact angle (θ) with the substrate. Switching between different morphologies can be achieved either by varying the contact angle of the liquid or by changing the wedge angle of the groove. In the present work we manipulate the apparent contact angle of a liquid by electrowetting to switch between liquid morphologies, from droplet to filament, to achieve microfluidic transport of the liquid into open triangular grooves. The static length of liquid filaments in grooves is analyzed as a function of applied voltage for different applied ac frequencies. The dynamic advancement of the filament lengths in grooves is analyzed as a function of time for different applied voltages for two different liquids: first with contact angle greater than the wedge angle and second with contact angle smaller than the wedge angle. Later an exact electrical model is derived to explain the liquid transport in triangular grooves actuated by electrowetting which includes the precise geometry of the liquid morphology.

  9. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2007-01-01

    the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance...

  10. Impact, Spreading and Bouncing of Water Drops on Steel Surfaces with U and V Grooves

    Science.gov (United States)

    R, Kannan; S, Chandra

    2012-11-01

    The impact, spreading and bouncing of water drops (2 mm dia) was photographed as for velocities ranging from (0.26-1.1m/s) on two textured stainless steel plates, one with U-shaped and the other with V-shaped grooves running the length of the surface. Grooves were made using wire EDM, and groove volume per unit width (0.043mm3) was kept approximately the same for both surfaces and the groove depths were 236 μm and 194 μm for the U (TS1) and V grooved (TS2) surfaces, respectively. Surface wetting by gently deposited drops was different on TS1 and TS2; drops on TS1 rested on the tips of the protrusions (C-B state) while on TS2 liquid penetrated the spaces between the grooves (Wenzel state). At low We (We drops impacting on TS1 spread at the same rate in both directions, perpendicular and parallel to the channel direction. Conversely, the spreading on TS2 was anisotropic, with liquid travelling faster along compared to across the grooves. This anisotropy grew more pronounced as We increased and was observed on both TS1 and TS2 for We >10. The changes in the spreading behavior with increasing impact velocity (and therefore greater We) corresponded to a greater volume of liquid penetrating into the grooves. Photographs showed that when droplets were at their maximum spread the amount of liquid penetrating into the grooves increased sharply for We >10 on TS1. This increased S/L contact area and enhanced spreading along channels. Recoiling drops completely bounced off the surface during impact on TS1, but not on TS2. Bouncing was observed for We <35.

  11. Expression, characterization, and evaluation of a RANK-binding single chain fraction variable: an osteoclast targeting drug delivery strategy.

    Science.gov (United States)

    Newa, Madhuri; Lam, Michael; Bhandari, Krishna Hari; Xu, Biwen; Doschak, Michael R

    2014-01-06

    A single chain Fraction variable (scFv) employs antibody-like target recognition specificity. Osteoclasts, responsible for bone resorption, express Receptor Activator of Nuclear factor Kappa B (RANK) receptors. This study aimed to express, characterize, and evaluate scFv against RANK receptors that may serve as a platform to target osteoclasts. Using phage display technology, scFv against RANK receptor was expressed and characterized by DNA sequencing, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), matrix-assisted laser desorption-ionization time-of-flight (MALDI TOF), enzyme-linked immunosorbent assay (ELISA), Western blot, and immunocytochemistry. The potential for cytotoxicity was evaluated using an MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide) assay, and its cross reactivity was evaluated using ELISA. Osteoclast-like cells were generated from RAW 264.7 cells, and the osteoclast targeting ability of scFv was evaluated using immunocytochemistry. ScFv's antiresorptive efficacy was studied using a tartrate-resistant acid phosphatase (TRAP) assay and resorption assay. Anti-RANK scFv was successfully expressed and characterized. No cross reactivity with other tumor necrosis factor receptor (TNFR) members and no cytotoxic effect on a non-RANK bearing cell line were observed. It showed specificity toward a RANK receptor and an inhibitory effect on osteoclast activity. With the increase in development trends for biologics as therapeutics and growing knowledge on the importance of osteoclast targeted therapy, this study may provide a drug delivery strategy to target osteoclasts, thereby leading to a promising therapy for resorptive bone diseases.

  12. Diverse modes of binding in structures of Leishmania majorN-myristoyltransferase with selective inhibitors

    Directory of Open Access Journals (Sweden)

    James A. Brannigan

    2014-07-01

    Full Text Available The leishmaniases are a spectrum of global diseases of poverty associated with immune dysfunction and are the cause of high morbidity. Despite the long history of these diseases, no effective vaccine is available and the currently used drugs are variously compromised by moderate efficacy, complex side effects and the emergence of resistance. It is therefore widely accepted that new therapies are needed. N-Myristoyltransferase (NMT has been validated pre-clinically as a target for the treatment of fungal and parasitic infections. In a previously reported high-throughput screening program, a number of hit compounds with activity against NMT from Leishmania donovani have been identified. Here, high-resolution crystal structures of representative compounds from four hit series in ternary complexes with myristoyl-CoA and NMT from the closely related L. major are reported. The structures reveal that the inhibitors associate with the peptide-binding groove at a site adjacent to the bound myristoyl-CoA and the catalytic α-carboxylate of Leu421. Each inhibitor makes extensive apolar contacts as well as a small number of polar contacts with the protein. Remarkably, the compounds exploit different features of the peptide-binding groove and collectively occupy a substantial volume of this pocket, suggesting that there is potential for the design of chimaeric inhibitors with significantly enhanced binding. Despite the high conservation of the active sites of the parasite and human NMTs, the inhibitors act selectively over the host enzyme. The role of conformational flexibility in the side chain of Tyr217 in conferring selectivity is discussed.

  13. An Improvement on the Method for Calculating the Capillary Limit of Axial—Grooved Heat Piper

    Institute of Scientific and Technical Information of China (English)

    ChenHanzhuo; MaTongze

    1993-01-01

    A new model has been developed to predict the capillary limit of axial-grooved heat pipe.In the model the concepts of liquid saturation or liquid fraction of the cross-sectional area of groove,the modified relative permeability,absolute permeability of groove and Leverrt's function are used.The Leverrt's function is well represented by the functionf(s)=1(1/√5)(1/2-)0.175.In the model the effects of gravitational force,capillary force and viscous force are considered.The calcuated results are in good agreement with existing experimental data reported in the literature.

  14. Mathematical modeling of photovoltaic thermal PV/T system with v-groove collector

    Science.gov (United States)

    Zohri, M.; Fudholi, A.; Ruslan, M. H.; Sopian, K.

    2017-07-01

    The use of v-groove in solar collector has a higher thermal efficiency in references. Dropping the working heat of photovoltaic panel was able to raise the electrical efficiency performance. Electrical and thermal efficiency were produced by photovoltaic thermal (PV/T) system concurrently. Mathematical modeling based on steady-state thermal analysis of PV/T system with v-groove was conducted. With matrix inversion method, the energy balance equations are explained by means of the investigative method. The comparison results show that in the PV/T system with the V-groove collector is higher temperature, thermal and electrical efficiency than other collectors.

  15. Torsional sensing of small-molecule binding using magnetic tweezers

    NARCIS (Netherlands)

    Lipfert, J.; Klijnhout, S.; Dekker, N.H.

    2010-01-01

    DNA-binding small molecules are widespread in the cell and heavily used in biological applications. Here, we use magnetic tweezers, which control the force and torque applied to single DNAs, to study three small molecules: ethidium bromide (EtBr), a well-known intercalator; netropsin, a minor-groove

  16. Characterisation of a grooved heat pipe with an anodised surface

    Science.gov (United States)

    Solomon, A. Brusly; Ram Kumar, A. M.; Ramachandran, K.; Pillai, B. C.; Senthil Kumar, C.; Sharifpur, Mohsen; Meyer, Josua P.

    2017-03-01

    A grooved heat pipe (GHP) is an important device for managing heat in space applications such as satellites and space stations, as it works efficiently in the absence of gravity. Apart from the above application, axial GHPs are used in many applications, such as electronic cooling units for temperature control and permafrost cooling. Improving the performance of GHPs is essential for better cooling and thermal management. In the present study, the effect of anodization on the heat transfer characteristics of a GHP is studied with R600a as a working fluid. In addition, the effects of fill ratio, inclination angle and heat inputs on the heat transfer performance of a GHP are studied. Furthermore, the effect of heat flux on dimensional numbers, such as the Webber, Bond, Kutateladze and condensation numbers, are studied. The inclination angle, heat input and fill ratio of GHPs are varied in the range of 0°-90°, 25-250 W and 10-70 % respectively. It is found that the above parameters have a significant effect on the performance of a GHP. Due to the anodisation, the maximum enhancement in heat transfer coefficient at the evaporator is 39 % for a 90° inclination at a heat flux of 11 kW/m2. The reported performance enhancement of a GHP may be due to the large numbers of nucleation sites created by the anodisation process and enhancement in the capillary force due to the coating.

  17. Characterisation of a grooved heat pipe with an anodised surface

    Science.gov (United States)

    Solomon, A. Brusly; Ram Kumar, A. M.; Ramachandran, K.; Pillai, B. C.; Senthil Kumar, C.; Sharifpur, Mohsen; Meyer, Josua P.

    2016-06-01

    A grooved heat pipe (GHP) is an important device for managing heat in space applications such as satellites and space stations, as it works efficiently in the absence of gravity. Apart from the above application, axial GHPs are used in many applications, such as electronic cooling units for temperature control and permafrost cooling. Improving the performance of GHPs is essential for better cooling and thermal management. In the present study, the effect of anodization on the heat transfer characteristics of a GHP is studied with R600a as a working fluid. In addition, the effects of fill ratio, inclination angle and heat inputs on the heat transfer performance of a GHP are studied. Furthermore, the effect of heat flux on dimensional numbers, such as the Webber, Bond, Kutateladze and condensation numbers, are studied. The inclination angle, heat input and fill ratio of GHPs are varied in the range of 0°-90°, 25-250 W and 10-70 % respectively. It is found that the above parameters have a significant effect on the performance of a GHP. Due to the anodisation, the maximum enhancement in heat transfer coefficient at the evaporator is 39 % for a 90° inclination at a heat flux of 11 kW/m2. The reported performance enhancement of a GHP may be due to the large numbers of nucleation sites created by the anodisation process and enhancement in the capillary force due to the coating.

  18. Homology modeling of human γ-butyric acid transporters and the binding of pro-drugs 5-aminolevulinic acid and methyl aminolevulinic acid used in photodynamic therapy.

    Directory of Open Access Journals (Sweden)

    Yan Baglo

    Full Text Available Photodynamic therapy (PDT is a safe and effective method currently used in the treatment of skin cancer. In ALA-based PDT, 5-aminolevulinic acid (ALA, or ALA esters, are used as pro-drugs to induce the formation of the potent photosensitizer protoporphyrin IX (PpIX. Activation of PpIX by light causes the formation of reactive oxygen species (ROS and toxic responses. Studies have indicated that ALA and its methyl ester (MAL are taken up into the cells via γ-butyric acid (GABA transporters (GATs. Uptake via GATs into peripheral sensory nerve endings may also account for one of the few adverse side effects of ALA-based PDT, namely pain. In the present study, homology models of the four human GAT subtypes were constructed using three x-ray crystal structures of the homologous leucine transporter (LeuT as templates. Binding of the native substrate GABA and the possible substrates ALA and MAL was investigated by molecular docking of the ligands into the central putative substrate binding sites in the outward-occluded GAT models. Electrostatic potentials (ESPs of the putative substrate translocation pathway of each subtype were calculated using the outward-open and inward-open homology models. Our results suggested that ALA is a substrate of all four GATs and that MAL is a substrate of GAT-2, GAT-3 and BGT-1. The ESP calculations indicated that differences likely exist in the entry pathway of the transporters (i.e. in outward-open conformations. Such differences may be exploited for development of inhibitors that selectively target specific GAT subtypes and the homology models may hence provide tools for design of therapeutic inhibitors that can be used to reduce ALA-induced pain.

  19. Analyzing radioligand binding data.

    Science.gov (United States)

    Motulsky, Harvey; Neubig, Richard

    2002-08-01

    Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  20. Research on adverse drug events. I. Muscarinic M3 receptor binding affinity could predict the risk of antipsychotics to induce type 2 diabetes.

    Science.gov (United States)

    Silvestre, J S; Prous, J

    2005-06-01

    Antipsychotics are associated with a wide range of adverse effects, several of which may represent a serious health risk to patients. There is an increased concern about metabolic disturbances associated with antipsychotics, including weight gain, dyslipidemia, hyperglycemia, and type 2 diabetes. However, little is known about the mechanisms underlying antipsychotic-induced metabolic disturbances and, in particular, those related to the induction of abnormal glucose metabolism and diabetes. The present article aimed to identify those receptor(s) that are most likely to be involved with or mediate antipsychotics-induced diabetes. Two independent measures taken from literature to indicate the risk of type 2 diabetes associated with 25 typical and atypical antipsychotic drugs were considered, along with their binding affinities to 21 specific receptors (obtained from the resources of Prous Science Integrity). A range of both exploratory and predictive statistical analyses were applied, including principal component factorial analysis, multivariable linear regression analysis, and discriminant analysis. Binding affinities (pKi) to human neurotransmitter receptors and monoaminergic transporters were used as independent variables (predictors). Measures to determine the risk to induce new-onset type 2 diabetes associated with each antipsychotic, logistic regression odds-ratio (dOR) and a discrete scale-based risk (three levels: 'low,' 'moderate,' 'high'), were used as the dependent variables (criteria). Similarly, parallel analyses were also conducted for other measures (average effective therapeutic dose) or adverse effects (weight gain, extrapyramidal side effects, hyperprolactinemia, anticholinergic, hypotension, and sedation) associated with antipsychotics, where underlying mechanisms have been previously established and, therefore, serve as positive-control references. Affinity for the cholinergic muscarinic M3 receptor subtype was presented as the best predictor for

  1. Analysis of flurbiprofen, ketoprofen and etodolac enantiomers by pre-column derivatization RP-HPLC and application to drug-protein binding in human plasma.

    Science.gov (United States)

    Jin, Yin-Xiu; Tang, Yi-Hong; Zeng, Su

    2008-04-14

    A stereoselective reversed-phase high-performance liquid chromatography (HPLC) assay to determine the enantiomers of flurbiprofen, ketoprofen and etodolac in human plasma was developed. Chiral drug enantiomers were extracted from human plasma with liquid-liquid extraction. Then flurbiprofen and ketoprofen enantiomers reacted with the acylation reagent thionyl chloride and pre-column chiral derivatization reagent (S)-(-)-alpha-(1-naphthyl)ethylamine (S-NEA), and etodolac enantiomers reacted with S-NEA using 1-(3-dimethylaminopropyl)-3-ethyl-carbodiimide (EDC) and 1-hydroxybenzotriazole (HOBT) as coupling agents. The derivatized products were separated on an Agilent Zorbax C18 (4.6 mm x 250 mm, 5 microm) column with a mixture of acetonitrile-0.01 mol.L(-1) phosphate buffer (pH 4.5) (70:30, v/v) for flurbiprofen enantiomers, acetonitrile-0.01 mol.L(-1) phosphate buffer (pH 4.5) (60:40, v/v) for ketoprofen enantiomers and methonal-0.01 mol.L(-1) potassium dihydrogen phosphate buffer (pH 4.5) (88:12, v/v) for etodolac enantiomers as mobile phase. The flow of mobile phase was set at 0.8 mL.min(-1) and the detection wavelength of UV detector was set at 250 nm for flurbiprofen and ketoprofen enantiomers and 278 nm for etodolac enantiomers. The assay was linear from 0.5 to 50 microg.mL(-1) for each enantiomer. The inter- and intra-day precision (R.S.D.) was less than 10% and the average extraction recovery was more than 87% for each enantiomer. The limit of quantification for the method was 0.5 microg.mL(-1) (R.S.D.<10%, n=5). The method developed was used to study the drug-protein binding of flurbiprofen, ketoprofen and etodolac enantiomers in human plasma. The results showed that the stereoselective binding of etodolac enantiomer was observed and flurbiprofen and ketoprofen enantiomers were not.

  2. Solution structure of DAPI selectively bound in the minor groove of a DNA T.T mismatch-containing site: NMR and molecular dynamics studies.

    Science.gov (United States)

    Trotta, E; Paci, M

    1998-01-01

    The solution structure of the complex between 4', 6-diamidino-2-phenylindole (DAPI) and DNA oligomer [d(GCGATTCGC)]2, containing a central T.T mismatch, has been characterized by combined use of proton one- and two-dimensional NMR spectroscopy, molecular mechanics and molecular dynamics computations including relaxation matrix refinement. The results show that the DAPI molecule binds in the minor groove of the central region 5'-ATT-3' of the DNA oligomer, which predominantly adopts a duplex structure with a global right-handed B-like conformation. In the final models of the complex, the DAPI molecule is located nearly isohelical with its NH indole proton oriented towards the DNA helix axis and forming a bifurcated hydrogen bond with the carbonyl O2 groups of a mismatched T5 and the T6 residue of the opposite strand. Mismatched thymines adopt a wobble base pair conformation and are found stacked between the flanking base pairs, inducing only minor local conformational changes in global duplex structure. In addition, no other binding mechanisms were observed, showing that minor groove binding of DAPI to the mismatch-containing site is favoured in comparison with any other previously reported interaction with G.C sequences. PMID:9753740

  3. Investigation of four classical groove patterns with three typical tool types for use in the rigid tool smoothing process

    Science.gov (United States)

    Wu, Hsing-Yu; Meng, Kai

    2016-07-01

    When a surface experiencing robotic processing to improve its optical performance (such as removing mid-spatial frequencies, localized grinding errors, and regional surface scratches), spindle speed, tool travel speed, pressure, slurry density as well as groove patterns are main factors to influence surface finishes. Based on the desired material removal rate, the Preston equation can provide optimized pressures and velocities between the tool and processed surface. Various groove patterns, however, can hardly predict by the equation because different patterns can cause unique tool deformation and pressure distribution, leading to determine unique smoothing result. In this paper, four typical groove patterns are studied: non-groove, grid grove, annular groove and radial groove with three typical tool types are evaluated by Finite Element Method (FEM) and statistics. Characteristics of these tools and groove patterns are presented in the end of this paper.

  4. The resistance of high frequency inductive welded pipe to grooving corrosion in salt water

    Energy Technology Data Exchange (ETDEWEB)

    Duran, C.; Triess, E.; Herbsleb, G.

    1986-09-01

    When exposed to neutral, salt-containing waters, electric resistant welded pipe in carbon and low alloy steels with increased sulfur contents may suffer preferential corrosion attack in the weld area. Because of its appearance, this type of corrosion is called grooving corrosion. The susceptibility to grooving corrosion may be determined and quantitatively described by means of an accelerated potentiostatic exposure test. The importance of type, concentration, and temperature of the electrolytic solution; potential; test duration; and the sulfur content of the steel in the accelerated corrosion test and the susceptibility of steels to grooving corrosion are described. Line pipe in high frequency inductive (HFI) welded carbon and low alloy steels are resistant to grooving corrosion particularly because of their low sulfur content.

  5. Groove Pancreatitis with Several Cystic Lesions around the Pancreatic Head Treated Conservatively: Report of a Case

    Directory of Open Access Journals (Sweden)

    Ryusuke Ito

    2008-11-01

    Full Text Available A 61-year-old man was admitted to our hospital with epigastric pain and vomiting. Enhanced abdominal computed tomography revealed inflammatory change of the pancreatic groove and focal wall thickening of the second portion of the duodenum with several cystic lesions around the head of the pancreas. We diagnosed atypical type of groove pancreatitis. The patient made a satisfactory recovery by conservative medication treatment for acute on chronic pancreatitis and cystic lesions disappeared in parallel with pancreatitis. Groove pancreatitis is a rare form of chronic pancreatitis, and to the best of our knowledge, our patient is the first case in the English literature of groove pancreatitis with cystic lesions around the head of the pancreas, which disappeared after conservative treatment for pancreatitis.

  6. Investigation of mechanism: spoof SPPs on periodically textured metal surface with pyramidal grooves

    Science.gov (United States)

    Tian, Lili; Liu, Jianlong; Zhou, Keya; Gao, Yang; Liu, Shutian

    2016-08-01

    In microwave and terahertz frequency band, a textured metal surface can support spoof surface plasmon polaritons (SSPPs). In this paper, we explore a SSPPs waveguide composed of a metal block with pyramidal grooves. Under the deep subwavelength condition, theoretical formulas for calculation of dispersion relations are derived based on the modal expansion method (MEM). Using the obtained formulas, a general analysis is given about the properties of the SSPPs in the waveguides with upright and downward pyramidal grooves. It is demonstrated that the SSPPs waveguides with upright pyramidal grooves give better field-confinement. Numerical simulations are used to check the theoretical analysis and show good agreement with the analytical results. In addition, the group velocity of the SSPPs propagating along the waveguide is explored and two structures are designed to show how to trap the SSPPs on the metal surface. The calculation methodology provided in this paper can also be used to deal with the SSPPs waveguides with irregular grooves.

  7. Theory of groove-envelope phase effects in self-diffraction

    CERN Document Server

    Reislöhner, Jan; Pfeiffer, Adrian N

    2016-01-01

    If two laser beams cross in a medium under shallow angle, the laser-induced grating consists of only a few grooves. In this situation, the phase between the grooves of the grating and its envelope is a decisive parameter for nonlinear effects. Here, models are established for reproducing the groove-envelope phase effects that have been observed in the interference pattern of self-diffraction. Four-wave mixing leads to interferences that are dominant in the spatial region between the orders of diffraction and with tilted interference fringes in the diagram of transverse coordinate vs. pulse delay. The vertical interference fringes that are dominant directly on the diffraction orders, experimentally observed at high intensity close to the damage threshold, require a model beyond four-wave mixing. A model is suggested that is based on optical transmission changes with confinement to regions in the medium that are smaller than the groove spacing.

  8. The potential impact of groove modes on Type II planetary migration

    CERN Document Server

    Meschiari, Stefano

    2008-01-01

    In this letter, we briefly describe the evolution of a variety of self-gravitating protoplanetary disk models that contain annular grooves (e.g. gaps) in their surface density. These grooves are inspired by the density gaps that are presumed to open in response to the formation of a giant planet. Our work provides an extension of the previously studied groove modes that are known in the context of stellar disks. The emergence of spiral gravitational instabilities (GI) is predicted via a generalized eigenvalue code that performs a linear analysis, and confirmed with hydrodynamical simulations. We find the presence of a groove drives a fast-growing two-armed mode in moderately massive disks, and extends the importance of self-gravitating instabilities down to lower disk masses than for which they would otherwise occur. We discuss the potential importance of this instability in the context of planet formation, e.g. the modification of the torques driving Type II migration.

  9. Palatal radicular groove: Clinical implications of early diagnosis and surgical sealing

    Directory of Open Access Journals (Sweden)

    P Corrêa-Faria

    2011-01-01

    Full Text Available Palatal radicular groove is a discreet alteration in tooth morphology, characterized by an invagination that begins near the cingulum of the tooth and moves in an apical direction. Clinically, palatal radicular groove may be associated with periodontal and/or endodontic problems. This paper describes a clinical case of a young patient with palatal radicular groove with no signs of periodontal disease or endodontic impairment. An early diagnosis was made and treatment consisted of surgical sealing of the defect. After a 2-year period, reexaminations demonstrated adequate hygiene, maintenance of tooth vitality and periodontal health. The early diagnosis and sealing of the groove observed surgically made the root surface smooth, avoiding subgingival bacterial plaque buildup, and preventing possible periodontal and/or pulp impairment stemming from the defect.

  10. Buckling Analysis of Supporting Legs and Steel Groove in Uranium Liquor Critical Facility

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    <正>The main structure of the uranium liquor critical facility is sit on the long steel tubal supporting legs, and the main vessel is connected with the supporting legs by steel groove, it is possible for the supporting

  11. Large eddy simulation of the subcritical flow over a V grooved circular cylinder

    Energy Technology Data Exchange (ETDEWEB)

    Alonzo-García, A. [Instituto Politécnico Nacional, SEPI-ESIME Zacatenco, U.P. Adolfo López Mateos Edif. 5, 3er. Piso, LABINTHAP, Av. Instituto Politénicno Nacional s/n, Col. Lindavista, C.P. 07738, México D.F., México (Mexico); Gutiérrez-Torres, C. del C., E-mail: cgutierrezt@ipn.mx [Instituto Politécnico Nacional, SEPI-ESIME Zacatenco, U.P. Adolfo López Mateos Edif. 5, 3er. Piso, LABINTHAP, Av. Instituto Politénicno Nacional s/n, Col. Lindavista, C.P. 07738, México D.F., México (Mexico); Jiménez-Bernal, J.A. [Instituto Politécnico Nacional, SEPI-ESIME Zacatenco, U.P. Adolfo López Mateos Edif. 5, 3er. Piso, LABINTHAP, Av. Instituto Politénicno Nacional s/n, Col. Lindavista, C.P. 07738, México D.F., México (Mexico); and others

    2015-09-15

    Highlights: • We compared numerically the turbulent flow over a smooth circular cylinder and a V grooved cylinder in the subcritical regime. • Turbulence intensities in both streamwise and normal direction suffered attenuations. • The swirls structures on grooves peaks seemed to have a cyclic behavior. • The evolution of the flow inside grooves showed that swirls structures located in peaks suffered elongations in the normal direction. • The secondary vortex structures formed in the grooved cylinder near wake were smaller in comparison of the smooth cylinder flow. - Abstract: In this paper, a comparative numerical study of the subcritical flow over a smooth cylinder and a cylinder with V grooves (Re = 140,000) is presented. The implemented technique was the Large Eddy Simulation (LES), which according to Kolmogorov's theory, resolves directly the most energetic largest eddies and models the smallest and considered universal high frequency ones. The Navier-Stokes (N-S) equations were solved using the commercial software ANSYS FLUENT V.12.1, which applied the finite volume method (FVM) to discretize these equations in their unsteady and incompressible forms. The grid densities were 2.6 million cells and 13.5 million cells for the smooth and V grooved cylinder, respectively. Both meshes were composed of structured hexahedral cells and close to the wall of the cylinders, additional refinements were employed in order to obtain y{sup +<5} values. All cases were simulated during at least 15 vortex shedding cycles with the aim of obtaining significant statistical data. Results: showed that for both cases (smooth and V grooved cylinder flow), the numerical code was capable of reproducing the most important physical quantities of the subcritical regime. Velocity distribution and turbulence intensity in the flow direction suffered a slight attenuation along the wake, as a consequence of grooves perturbation, which also caused an increase in the pressure

  12. [(3) H]-L685,458 binding sites are abundant in multiple peripheral organs in rats: implications for safety assessment of putative γ-secretase targeting drugs.

    Science.gov (United States)

    Yang, Zhi-Ying; Li, Jian-Ming; Xiao, Ling; Mou, Lin; Cai, Yan; Huang, He; Luo, Xue-Gang; Yan, Xiao-Xin

    2014-12-01

    γ-Secretase is a multimeric enzyme complex that carries out proteolytic processing to a variety of cellular proteins. It is currently explored as a therapeutic target for Alzheimer's disease (AD) and cancer. Mechanism-based toxicity needs to be thoroughly evaluated for γ-secretase inhibitory and/or modulatory drugs. This study comparatively assessed putative γ-secretase catalytic sites in rat peripheral tissues relative to brain and explored an effort of its pharmacological inhibition on hair regeneration. Using [(3) H]-labelled L685,458, a potent γ-secretase inhibitor, as probe, we found more abundant presence of γ-secretase binding sites in the liver, gastrointestinal tract, hair follicle, pituitary gland, ovary and testis, as compared to the brain. Local application of L658,458 delayed vibrissal regrowth following whisker removal. These results suggest that γ-secretase may execute important biological functions in many peripheral systems, as in the brain. The development of γ-secretase inhibitors/modulators for AD and cancer therapy should include close monitoring of toxicological panels for hepatic, gastrointestinal, endocrinal and reproductive functions.

  13. Glycosylated Platinum(IV) Complexes as Substrates for Glucose Transporters (GLUTs) and Organic Cation Transporters (OCTs) Exhibited Cancer Targeting and Human Serum Albumin Binding Properties for Drug Delivery.

    Science.gov (United States)

    Ma, Jing; Wang, Qingpeng; Huang, Zhonglv; Yang, Xiande; Nie, Quandeng; Hao, Wenpei; Wang, Peng George; Wang, Xin

    2017-07-13

    Glycosylated platinum(IV) complexes were synthesized as substrates for GLUTs and OCTs for the first time, and the cytotoxicity and detailed mechanism were determined in vitro and in vivo. Galactoside Pt(IV), glucoside Pt(IV), and mannoside Pt(IV) were highly cytotoxic and showed specific cancer-targeting properties in vitro and in vivo. Glycosylated platinum(IV) complexes 5, 6, 7, and 8 (IC50 0.24-3.97 μM) had better antitumor activity of nearly 166-fold higher than the positive controls cisplatin (1a), oxaliplatin (3a), and satraplatin (5a). The presence of a hexadecanoic chain allowed binding with human serum albumin (HSA) for drug delivery, which not only enhanced the stability of the inert platinum(IV) prodrugs but also decreased their reduction by reductants present in human whole blood. Their preferential accumulation in cancer cells compared to noncancerous cells (293T and 3T3 cells) suggested that they were potentially safe for clinical therapeutic use.

  14. Conformational response of influenza A M2 transmembrane domain to amantadine drug binding at low pH (pH 5.5

    Directory of Open Access Journals (Sweden)

    Elka R. Georgieva

    2016-07-01

    Full Text Available The M2 protein from influenza A plays important roles in its viral cycle. It contains a single transmembrane helix, which oligomerizes into a homotetrameric proton channel that conducts in the low-pH environment of the host-cell endosome and Golgi apparatus, leading to virion uncoating at an early stage of infection. We studied conformational rearrangements that occur in the M2 core transmembrane domain residing on the lipid bilayer, flanked by juxtamembrane residues (M2TMD21-49 fragment, upon its interaction with amantadine drug at pH 5.5 when M2 is conductive. We also tested the role of specific mutation and lipid chain length. Electron spin resonance (ESR spectroscopy and electron microscopy were applied to M2TMD21-49, labeled at the residue L46C with either nitroxide spin-label or Nanogold® reagent, respectively. Electron microscopy confirmed that M2TMD21-49 reconstituted into DOPC/POPS at 1:10,000 peptide-to-lipid molar ratio (P/L either with or without amantadine, is an admixture of monomers, dimers, and tetramers, confirming our model based on a dimer intermediate in the assembly of M2TMD21-49. As reported by double electron-electron resonance (DEER, in DOPC/POPS membranes amantadine shifts oligomer equilibrium to favor tetramers, as evidenced by an increase in DEER modulation depth for P/L’s ranging from 1:18,000 to 1:160. Furthermore, amantadine binding shortens the inter-spin distances (for nitroxide labels by 5-8 Å, indicating drug induced channel closure on the C-terminal side. No such effect was observed for the thinner membrane of DLPC/DLPS, emphasizing the role of bilayer thickness. The analysis of continuous wave (cw ESR spectra of spin-labeled L46C residue provides additional support to a more compact helix bundle in amantadine-bound M2TMD21-49 through increased motional ordering. In contrast to wild-type M2TMD21-49, the amantadine-bound form does not exhibit noticeable conformational changes in the case of G34A mutation

  15. Direct numerical simulation of Taylor-Couette flow with grooved walls: torque scaling and flow structure

    CERN Document Server

    Zhu, Xiaojue; Verzicco, Roberto; Lohse, Detlef

    2015-01-01

    We present direct numerical simulations of Taylor-Couette flow with grooved walls at a fixed radius ratio $\\eta=r_i/r_o=0.714$ with inner cylinder Reynolds number up to $Re_i=3.76\\times10^4$, corresponding to Taylor number up to $Ta=2.15\\times10^9$. The grooves are axisymmetric V-shaped obstacles attached to the wall with a tip angle of $90^\\circ$. Results are compared with the smooth wall case in order to investigate the effects of grooves on Taylor-Couette flow. We focus on the effective scaling laws for the torque, flow structures, and boundary layers. It is found that, when the groove height is smaller than the boundary layer thickness, the torque is the same as that of the smooth wall cases. With increasing $Ta$, the boundary layer thickness becomes smaller than the groove height. Plumes are ejected from tips of the grooves and a secondary circulation between the latter is formed. This is associated to a sharp increase of the torque and thus the effective scaling law for the torque vs. $Ta$ becomes much ...

  16. Grooved surface topography alters matrix-metalloproteinase production by human fibroblasts

    Energy Technology Data Exchange (ETDEWEB)

    Brydone, Alistair S; Dominic Meek, R M [Department of Orthopaedics, Southern General Hospital, 1345 Govan Road, Glasgow G51 4TF (United Kingdom); Dalby, Matthew J; Berry, Catherine C; McNamara, Laura E, E-mail: alibrydone@gmail.com [Centre for Cell Engineering, Joseph Black Building, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ (United Kingdom)

    2011-06-15

    Extracellular matrix (ECM) remodelling is an essential physiological process in which matrix-metalloproteinases (MMPs) have a key role. Manipulating the manner in which cells produce MMPs and ECMs may enable the creation of a desired tissue type, i.e. effect repair, or the prevention of tissue invasion (e.g. metastasis). The aim of this project was to determine if culturing fibroblasts on grooved topography altered collagen deposition or MMP production. Human fibroblasts were seeded on planar or grooved polycaprolactone substrates (grooves were 12.5 {mu}m wide with varying depths of 240 nm, 540 nm or 2300 nm). Cell behaviour and collagen production were studied using fluorescence microscopy and the spent culture medium was assessed using gel zymography to detect MMPs. Total collagen deposition was high on the 240 nm deep grooves, but decreased as the groove depth increased, i.e. as cell contact guidance decreased. There was an increase in gelatinase on the 2300 nm deep grooved topography and there was a difference in the temporal expression of MMP-3 observed on the planar surface compared to the 540 nm and 2300 nm topographies. These results show that topography can alter collagen and MMP production. A fuller understanding of these processes may permit the design of surfaces tailored to tissue regeneration e.g. tendon repair.

  17. Large Eddy Simulation of the Subcritical Flow over a U-Grooved Circular Cylinder

    Directory of Open Access Journals (Sweden)

    A. Alonzo-García

    2014-07-01

    Full Text Available With the aim of numerically replicating a drag reduction phenomenon induced by grooves presence, this paper presents a comparative large eddy simulation study of the flow over a smooth circular cylinder, and the flow over a U-grooved cylinder, at Re = 140,000, which is near transition between the subcritical and critical flow regimes. The grid densities were 2.6 million cells and 20.7 million cells for the smooth and the U-grooved cylinder, respectively. Both meshes were composed of hexahedral cells disposed in a structured form with additional refinements in near-wall regions, in order to obtain y+< 5 values. The cases were simulated during 25 vortex shedding cycles with the purpose of obtaining significant statistic data through the commercial software FLUENT V.12.1, which solved the Navier-Stokes equations in their unsteady and incompressible forms. Regarding the U-grooved cylinder flow, parameters such as the drag coefficient, lengths of recirculation, the transition from subcritical to critical flow, and the formation of a wake formed by secondary vortices of smaller sizes were predicted satisfactorily by the LES technique. From the manner in which the flow separates at different angles for both valleys and peaks of the U-grooves, a distinctive transitional mechanism induced by grooves presence is conjectured.

  18. Numerical Simulation of the Flow Field in Circumferential Grooved Liquid Seals

    Directory of Open Access Journals (Sweden)

    Meng Zhang

    2013-01-01

    Full Text Available Circumferential grooved liquid seals are utilized inside turbomachinery to provide noncontacting control of internal incompressible fluid leakage. Accurate prediction of the flow field is fundamental in producing robust and efficient designs. To validate the capabilities of the computational fluid dynamics FLUENT for incompressible fluid seal flow, comparisons of velocity parameters are made to the published experimental results and other CFD code for a circumferential grooved liquid seal. This work employs a pressure-based CFD code FLUENT to calculate the flow field in the seal, using four different turbulence models respectively. The velocity contours are compared with experimental values. It shows good overall agreement of the axial, radial, and azimuthal velocities in the through-flow jet, shear layer, and recirculation zone. Quantitative comparisons of velocity profiles at the center of the groove are made to experiment. This study verifies the prediction accuracy of three turbulence models. Various structures were considered to obtain a better understanding of the circumferential grooved liquid flow characteristics. The best groove structure to control leakage was also found within the limited designed seal. This study will provide a useful reference for designing the circumferential grooved liquid seal.

  19. Temperature Approach Optimization in the Double Pipe Heat Exchanger with Groove

    Directory of Open Access Journals (Sweden)

    Sunu Putu Wijaya

    2016-01-01

    Full Text Available Heat transfer in double pipe heat exchanger with circumference-rectangular grooves has been investigated experimentally. The volume flowrate of cold and hot water were varied to determine its influence on the approach temperature of the outlet terminals. In this experimental design, the grooves were incised in annular room that is placed on the outside surface of the inner pipe. The shell diameter is 38.1 mm and tube diameter 19.4 mm with 1 m length, which is made of aluminum. The flow pattern of the two fluids in the heat exchanger is a parallel flow. The working fluid is water with volume flow rate of 27.1, 23.8 and 19.8 l/minute. The temperature of water on the inlet terminals are 50±1°C for hot stream and 30±1°C for cold stream. Temperature measurements conducted on each terminal of the inlet and outlet heat exchanger. The results showed that the grooves induced the approach temperature. The change of the approach temperature from the grooves compared to that of without grooves decreased by 37.9%. This phenomenon indicates an increase in heat transfer process and performance of the heat exchanger. Groove improves the heat surface area of the inner pipe, increasing the momentum transfer and in the other hand, reducing the weight of heat exchangers itself.

  20. Relationship Between Measured Friction Coefficients and Two Tread Groove Design Parameters for Footwear Pads

    Institute of Scientific and Technical Information of China (English)

    LI Kai Way; CHEN Chin Jung; LIN Ching-Hua; HSU Yao Wen

    2006-01-01

    The shoe sole geometrical design parameters are believed to be important factors affecting the coefficient of friction (COF) between the shoe/floor interface. This study is concerned with the relationship between the measured COF and the tread groove orientation and width on the footwear pad. Friction measurements using the Brungraber Mark Ⅱ slipmeter were conducted. Six tread groove width/orientations designs on the footwear pads under 27 footwear material/floor/contamination conditions were tested. The results show that tread orientation and width affect the measured COF significantly. Wider grooved footwear pads result in higher COF values and footwear pads with tread grooves perpendicular to the friction measurement direction have higher COF values. A regression model using measured COF as the dependent variable and tread groove width, groove orientation, footwear material, floor, and contamination conditions as independent variables was established. The models are significant at p<0.0001 with R2 of 0.97, which may be used in predicting the COF at the shoe-floor interface.

  1. Numerical modeling and verification of gas flow through a network of crossed narrow v-grooves

    Science.gov (United States)

    Bejhed, Johan; Nguyen, Hugo; Åstrand, Peter; Eriksson, Anders; Köhler, Johan

    2006-10-01

    The gas flow through a network of crossing thin micro-machined channels has been successfully modeled and simulated. The crossings are formed by two sets of v-grooves that intersect as two silicon wafers are bonded together. The gas is distributed from inlets via a manifold of channels to the narrow v-grooves. The narrow v-grooves could work as a particle filter. The fluidic model is derived from the Navier-Stokes equation and assumes laminar isothermal flow and incorporates small Knudsen number corrections and Poiseuille number calculations. The simulations use the finite element method. Several elements of the full crossing network model are treated separately before lumping them together: the straight v-grooves, a single crossing in an infinite set and a set of exactly four crossings along the flow path. The introduction of a crossing effectively corresponds to a virtual reduction of the length of the flow path, thereby defining a new effective length. The first and last crossings of each flow path together contribute to a pressure drop equal to that from three ordinary crossings. The derived full network model has been compared to previous experimental results on several differently shaped crossed v-groove networks. Within the experimental errors, the model corresponds to the mass flow and pressure drop measurements. The main error source is the uncertainty in v-groove width which has a profound impact on the fluidic behavior.

  2. Clinical, radiological, surgical, and pathological determinants of olfactory groove schwannoma

    Directory of Open Access Journals (Sweden)

    Andi Sadayandi Ramesh

    2014-01-01

    Full Text Available Background: Olfactory groove schwannomas (OGS are rare anterior cranial fossa base tumors with only 41 cases reported in literature. Olfactory ensheathing cell schwannoma (OECS has similar clinico-radiological features as OGS, but a different cell of origin. In recent years, there is growing interest in OECS as more cases are being reported. Aims: The objective was to study the clinico-radiological features of OGS and define the histological differentiation from OECS. Materials and Methods: We retrospectively analyzed clinical, radiological, surgical and histopathological picture of all cases of OGS managed in our institute. Immuno histochemical studies were performed in these tumors for differentiating from OECS. A comprehensive review of articles published until date describing the operative treatment was done. Results: All three cases had presented with seizures, two had anosmia and papilledema. Gross-total resection was achieved in all our patients. One patient expired in the postoperative period due to septicemia. Positive expression to newer immuno histochemical biomarker CD57 (Leu7, with negative staining to smooth muscle α-actin (SMA was helpful in confirming the diagnosis of OGS and differentiating it from OECS in all our cases. Conclusions: OECS, though rare has to be differentiated from OGS using immuno histochemistry. Gross-total resection of OGS with preservation of olfactory function is often possible and curative. Although these tumors are commonly treated with microsurgical skull base approaches, an endoscopic endonasal approach can be considered in some cases, with repair using mucoperiosteal pedicled flap to prevent cerebrospinal fluid leak.

  3. Experimental study of partially flattened axial grooved heat pipes

    Institute of Scientific and Technical Information of China (English)

    TAO HanZhong; ZHANG Hong; ZHUANG Jun; Jerry W. BOWMANS

    2008-01-01

    This article made experimental study on mini-axial grooved heat pipes (AGHP) with 11 flattening forms. It analyzed how the flattening form, flattening thickness and working temperature affect axial tem-perature distribution, thermal resistance, heat transfer limit and the phase-change heat transfer coeffi-cients in evaporator and condenser sections. The result indicates that all forms of AGHPs can maintain good isothermal performance under normal operating condition. The geometric shape of AGHP has obvious impact on heat transfer limit. With respect to an AGHP with 2 mm-thick evaporator section, when the thickness of its condenser section increases from 2 to 3 mm, its heat transfer limit increases by 81%; with respect to an AGHP with 3 mm-thick evaporator section, when the thickness of its con-denser section increases from 2 to 3 mm, its heat transfer limit increases by 134%; with respect to an AGHP with 4 mm-thick condenser section, when the thickness of its evaporator section increases from 2 to 3 mm, its heat transfer limit increases by 26%. When the thickness of the evaporator section in-creases by 1 mm, the heat transfer limit will increase by 9%-26%, while when the thickness of the condenser section increases by 1 mm, the heat transfer limit will increase by 20%-86%. The thickness of the condenser section has greater impact on heat transfer performance of an AGHP than the thick-ness of the evaporator section does. The study content of this article will help understand the heat transfer performance of AGHP, and electronic thermal design process.

  4. Proton NMR studies of (N-MeCys sup 3 ,N-MeCys sup 7 )TANDEM binding to DNA oligonucleotides: Sequence-specific binding at the TpA site

    Energy Technology Data Exchange (ETDEWEB)

    Addess, K.J.; Gilbert, D.E.; Feigon, J. (Univ. of California, Los Angeles (United States)); Olsen, R.K. (Utah State Univ., Logan (United States))

    1992-01-21

    (N-MeCys{sup 3},N-MeCys{sup 7})TANDEM, an undermethylated analogue of Triostin A, contains two N-methyl groups on the cysteine residues only. Footprinting results showed that (N-MeCys{sup 3},N-Me-Cys{sup 7})TANDEM binds strongly to DNA rich in A{center dot}T residues. However, it was not known whether specific binding of (N-MeCys{sup 3},N-MeCys{sup 7})TANDEM requires a TpA step or an ApT step. In 1:1 saturated complexes with the octamers (d(GGATATCC)){sub 2} and (d(GGTTAACC)){sub 2}, (N-MeCys{sup 3},N-MeCys{sup 7})TANDEM binds to each octamer as a bis-intercalator bracketing the TpA step. The octadepsipeptide ring binds in the minor groove of the DNA. Analysis of sugar coupling constants from the phase-sensitive COSY data indicates that the sugar of the thymine in the TpA binding site adopts predominantly an N-type sugar conformation, while the remaining sugars on the DNA adopt an S-type conformation, as has been observed in other Triostin A and echinomycin complexes. The drug does not bind to the octamer (d(GGAATTCC)){sub 2} as a bis-intercalator. Only weak nonintercalative binding is observed to this DNA octamer. These results show unambiguously that (N-MeCys{sup 3},N-MeCys{sup 7})TANDEM binds sequence specifically at TpA sites in DNA. The factors underlying the sequence specificity of (N-MeCys{sup 3},N-MeCys{sup 7})TANDEM binding to DNA are discussed.

  5. Conjugation of benzylvanillin and benzimidazole structure improves DNA binding with enhanced antileukemic properties.

    Science.gov (United States)

    Al-Mudaris, Zena A; Majid, Aman S A; Ji, Dan; Al-Mudarris, Ban A; Chen, Shih-Hsun; Liang, Po-Huang; Osman, Hasnah; Jamal Din, Shah Kamal Khan; Abdul Majid, Amin M S

    2013-01-01

    Benzyl-o-vanillin and benzimidazole nucleus serve as important pharmacophore in drug discovery. The benzyl vanillin (2-(benzyloxy)-3-methoxybenzaldehyde) compound shows anti-proliferative activity in HL60 leukemia cancer cells and can effect cell cycle progression at G2/M phase. Its apoptosis activity was due to disruption of mitochondrial functioning. In this study, we have studied a series of compounds consisting of benzyl vanillin and benzimidazole structures. We hypothesize that by fusing these two structures we can produce compounds that have better anticancer activity with improved specificity particularly towards the leukemia cell line. Here we explored the anticancer activity of three compounds namely 2-(2-benzyloxy-3-methoxyphenyl)-1H-benzimidazole, 2MP, N-1-(2-benzyloxy-3-methoxybenzyl)-2-(2-benzyloxy-3-methoxyphenyl)-1H-benzimidazole, 2XP, and (R) and (S)-1-(2-benzyloxy-3-methoxyphenyl)-2, 2, 2-trichloroethyl benzenesulfonate, 3BS and compared their activity to 2-benzyloxy-3-methoxybenzaldehyde, (Bn1), the parent compound. 2XP and 3BS induces cell death of U937 leukemic cell line through DNA fragmentation that lead to the intrinsic caspase 9 activation. DNA binding study primarily by the equilibrium binding titration assay followed by the Viscosity study reveal the DNA binding through groove region with intrinsic binding constant 7.39 µM/bp and 6.86 µM/bp for 3BS and 2XP respectively. 2XP and 3BS showed strong DNA binding activity by the UV titration method with the computational drug modeling showed that both 2XP and 3BS failed to form any electrostatic linkages except via hydrophobic interaction through the minor groove region of the nucleic acid. The benzylvanillin alone (Bn1) has weak anticancer activity even after it was combined with the benzimidazole (2MP), but after addition of another benzylvanillin structure (2XP), stronger activity was observed. Also, the combination of benzylvanillin with benzenesulfonate (3BS) significantly improved the

  6. Conjugation of benzylvanillin and benzimidazole structure improves DNA binding with enhanced antileukemic properties.

    Directory of Open Access Journals (Sweden)

    Zena A Al-Mudaris

    Full Text Available Benzyl-o-vanillin and benzimidazole nucleus serve as important pharmacophore in drug discovery. The benzyl vanillin (2-(benzyloxy-3-methoxybenzaldehyde compound shows anti-proliferative activity in HL60 leukemia cancer cells and can effect cell cycle progression at G2/M phase. Its apoptosis activity was due to disruption of mitochondrial functioning. In this study, we have studied a series of compounds consisting of benzyl vanillin and benzimidazole structures. We hypothesize that by fusing these two structures we can produce compounds that have better anticancer activity with improved specificity particularly towards the leukemia cell line. Here we explored the anticancer activity of three compounds namely 2-(2-benzyloxy-3-methoxyphenyl-1H-benzimidazole, 2MP, N-1-(2-benzyloxy-3-methoxybenzyl-2-(2-benzyloxy-3-methoxyphenyl-1H-benzimidazole, 2XP, and (R and (S-1-(2-benzyloxy-3-methoxyphenyl-2, 2, 2-trichloroethyl benzenesulfonate, 3BS and compared their activity to 2-benzyloxy-3-methoxybenzaldehyde, (Bn1, the parent compound. 2XP and 3BS induces cell death of U937 leukemic cell line through DNA fragmentation that lead to the intrinsic caspase 9 activation. DNA binding study primarily by the equilibrium binding titration assay followed by the Viscosity study reveal the DNA binding through groove region with intrinsic binding constant 7.39 µM/bp and 6.86 µM/bp for 3BS and 2XP respectively. 2XP and 3BS showed strong DNA binding activity by the UV titration method with the computational drug modeling showed that both 2XP and 3BS failed to form any electrostatic linkages except via hydrophobic interaction through the minor groove region of the nucleic acid. The benzylvanillin alone (Bn1 has weak anticancer activity even after it was combined with the benzimidazole (2MP, but after addition of another benzylvanillin structure (2XP, stronger activity was observed. Also, the combination of benzylvanillin with benzenesulfonate (3BS significantly improved

  7. Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing.

    Directory of Open Access Journals (Sweden)

    Rohan Patil

    Full Text Available BACKGROUND: Weak intermolecular interactions such as hydrogen bonding and hydrophobic interactions are key players in stabilizing energetically-favored ligands, in an open conformational environment of protein structures. However, it is still poorly understood how the binding parameters associated with these interactions facilitate a drug-lead to recognize a specific target and improve drugs efficacy. To understand this, comprehensive analysis of hydrophobic interactions, hydrogen bonding and binding affinity have been analyzed at the interface of c-Src and c-Abl kinases and 4-amino substituted 1H-pyrazolo [3, 4-d] pyrimidine compounds. METHODOLOGY: In-silico docking studies were performed, using Discovery Studio software modules LigandFit, CDOCKER and ZDOCK, to investigate the role of ligand binding affinity at the hydrophobic pocket of c-Src and c-Abl kinase. Hydrophobic and hydrogen bonding interactions of docked molecules were compared using LigPlot program. Furthermore, 3D-QSAR and MFA calculations were scrutinized to quantify the role of weak interactions in binding affinity and drug efficacy. CONCLUSIONS: The in-silico method has enabled us to reveal that a multi-targeted small molecule binds with low affinity to its respective targets. But its binding affinity can be altered by integrating the conformationally favored functional groups at the active site of the ligand-target interface. Docking studies of 4-amino-substituted molecules at the bioactive cascade of the c-Src and c-Abl have concluded that 3D structural folding at the protein-ligand groove is also a hallmark for molecular recognition of multi-targeted compounds and for predicting their biological activity. The results presented here demonstrate that hydrogen bonding and optimized hydrophobic interactions both stabilize the ligands at the target site, and help alter binding affinity and drug efficacy.

  8. Molecular docking of intercalators and groove-binders to nucleic acids using Autodock and Surflex.

    Science.gov (United States)

    Holt, Patrick A; Chaires, Jonathan B; Trent, John O

    2008-08-01

    The molecular docking tools Autodock and Surflex accurately reproduce the crystallographic structures of a collection of small molecule ligands that have been shown to bind nucleic acids. Docking studies were performed with the intercalators daunorubicin and ellipticine and the minor groove binders distamycin and pentamidine. Autodock and Surflex dock daunorubicin and distamycin to their nucleic acid targets within a resolution of approximately 2 A, which is similar to the limit of the crystal structure resolution. However, for the top ranked poses, Autodock and Surflex both dock ellipticine into the correct site but in a different orientation compared to the crystal structure. This appears not only to be partly related to the symmetry of the target nucleic acid, as ellipticine is able to dock from either side of the intercalation site, but also due to the shape of the ligand and docking accuracy. Surflex docks pentamidine in a symmetrically equivalent orientation relative to the crystal structure, while Autodock was able to dock this molecule in the original orientation. In the case of the Surflex docking of pentamidine, the initial rmsd is misleading, given the symmetrical structure of pentamidine. Importantly, the ranking functions of both of these programs are able to return a top pose within approximately 2 A rmsd for daunorubicin, distamycin, and pentamidine and approximately 3 A rmsd for ellipticine compared to their respective crystal structures. Some docking challenges and potential pitfalls are explored, such as the importance of hydrogen treatment on ligands as well as the scoring functions of Autodock and Surflex. Overall for this set of complexes, Surflex is preferred over Autodock for virtual screening, as although the results are comparable, Surflex has significantly faster performance and ease of use under the optimal software conditions tested. These experiments show that molecular docking techniques can be successfully extended to include nucleic

  9. Effects of Collector Temperature on the Performance of Grooved Electrode Thermionic Converters

    Science.gov (United States)

    Momozaki, Yoichi; El-Genk, Mohamed S.

    2003-01-01

    Experiments are conducted to compare the performance of the smooth electrodes, grooved emitter, and grooved collector converters at the same emitter and collector temperatures. The focus of the experiments is to investigate the effects of collector temperature on the performance of grooved electrode converters. The converters with various electrode configurations and a 0.5 mm gap are tested at emitter temperatures, TE = 1473 - 1673 K, collector temperatures, TC = 773 - 1023 K, and cesium pressures, PCs = 10 - 500 Pa. All electrodes are planar and fabricated with polycrystalline Molybdenum. The grooved electrodes have concentric macro-grooves 0.5 mm wide, 0.5 mm deep, and 1.0 mm apart. The output electrical power density and the conversion efficiency are calculated from the measured I-V curves and the maximum power density and conversion efficiency are determined from the calculated PD-V and ɛ-V envelopes. At TE = 1473 K, the electrical power density for the smooth electrodes converter at the optimum collector temperature (873 K) is 2.25 W/cm2 at ɛ = 13.8 %, decreasing to 1.46 W/cm2 at ɛ = 12.4 % as TC increases by only 75 K to 948 K. However, the corresponding decrease in the electrical power density for the grooved collector converter is only 0.04 W/cm2 (from 1.24 W/cm2 at ɛ = 11.4 % and TC = 873 K to 1.20 W/cm2 at ɛ =10.7 % and TC = 948 K) and that for the grooved emitter converter is 0.12 W/cm2 (from 0.82 W/cm2 at ɛ = 8.1 % and TC = 873 K to 0.70 W/cm2 at ɛ = 6.8 % and TC = 948 K). At the higher emitter temperatures of 1573 K and 1673 K, similar results are obtained. In all experimental conditions, however, the grooved emitter converter shows the lowest power density and conversion efficiency, followed by the grooved collector converter, and the smooth electrodes converter, except for TF = 1673 K and TC = 1023 K at which the converter with a grooved collector operates at the highest power density (2.38 W/cm2) and conversion efficiency (14.0 %).

  10. Instantaneous slip length in superhydrophobic microchannels having grooves with curved or dissimilar walls

    Science.gov (United States)

    Hemeda, A. A.; Vahedi Tafreshi, H.

    2015-10-01

    Superhydrophobic (SHP) surfaces can be used to reduce the skin-friction drag in a microchannel. This is due to the peculiar ability of these surfaces to entrap air in their pores and thereby reduce the contact area between water and the solid surface. The favorable drag-reduction effect, however, can quickly deteriorate if the surface geometry is not designed properly. The deterioration can be sudden, caused by exposure to excessive pressures, or gradual, due to the dissolution of the entrapped air into the ambient water. The formulations presented here provide a means for studying the time-dependent drag-reduction in a microchannel enhanced with transverse or longitudinal SHP grooves of varying wall profiles or wettabilities. Moreover, different mathematical approaches are developed to distinguish the performance of a sharp-edged groove from that of a groove with round entrance. The work starts by deriving an equation for the balance of forces on the air-water interface (AWI) inside a groove and solving this differential equation, along with Henry's law, for the rate of dissolution of the entrapped air into water over time. It was shown that the performance of a SHP groove depends mostly on the interplay between the effects of the apparent contact angle of the AWI and the initial volume of the groove. The instantaneous slip length is then calculated by solving the Navier-Stokes equations for flow in microchannels with SHP grooves. Our results are compared with the studies in the literature whenever available, and good agreement has been observed.

  11. Exploring the strength, mode, dynamics, and kinetics of binding interaction of a cationic biological photosensitizer with DNA: implication on dissociation of the drug-DNA complex via detergent sequestration.

    Science.gov (United States)

    Paul, Bijan Kumar; Guchhait, Nikhil

    2011-10-20

    The present study aims at exploring a detailed characterization of the binding interaction of a promising cancer cell photosensitizer, harmane (HM), with DNA extracted from herring sperm. The polarity-sensitive prototropic transformation of HM, a naturally occurring, fluorescent, drug-binding alkaloid, β-carboline, is remarkably modified upon interaction with DNA and is manifested through significant modulations on the absorption and emission profiles of HM. From the series of studies undertaken in the present program, for example, absorption; steady-state emission; the effect of chaotrope (urea); iodide ion-induced steady-state fluorescence quenching; circular dichroism (CD); and helix melting from absorption spectroscopy; the mode of binding of HM into the DNA helix has been substantiated to be principally intercalative. Concomitantly, a discernible dependence of the photophysics of the DNA-bound drug on the medium ionic strength indicates that electrostatic attraction should not be ignored in the interaction. Efforts have also been delivered to delineate the dynamical aspects of the interaction, such as modulation in time-resolved fluorescence decay and rotational relaxation dynamics of the drug within the DNA environment. In view of the prospective biological applications of HM, the issue of facile dissociation of intercalated HM from the DNA helix also comprises a crucial prerequisite for the functioning as an effective therapeutic agent. In this context, our results imply that the concept of detergent-sequestered dissociation of the drug from the drug-DNA complex can be a prospective strategy through an appropriate choice of the detergent molecule. The utility of the present work resides in exploring the potential applicability of the fluorescence property of HM for studying its interactions with a relevant biological target, for example, DNA. In addition, the methods and techniques used in the present work can also be exploited to study the interaction of

  12. DNA binding studies of tartrazine food additive.

    Science.gov (United States)

    Kashanian, Soheila; Zeidali, Sahar Heidary

    2011-07-01

    The interaction of native calf thymus DNA with tartrazine in 10 mM Tris-HCl aqueous solution at neutral pH 7.4 was investigated. Tartrazine is a nitrous derivative and may cause allergic reactions, with a potential of toxicological risk. Also, tartrazine induces oxidative stress and DNA damage. Its DNA binding properties were studied by UV-vis and circular dichroism spectra, competitive binding with Hoechst 33258, and viscosity measurements. Tartrazine molecules bind to DNA via groove mode as illustrated by hyperchromism in the UV absorption band of tartrazine, decrease in Hoechst-DNA solution fluorescence, unchanged viscosity of DNA, and conformational changes such as conversion from B-like to C-like in the circular dichroism spectra of DNA. The binding constants (K(b)) of DNA with tartrazine were calculated at different temperatures. Enthalpy and entropy changes were calculated to be +37 and +213 kJ mol(-1), respectively, according to the Van't Hoff equation, which indicated that the reaction is predominantly entropically driven. Also, tartrazine does not cleave plasmid DNA. Tartrazine interacts with calf thymus DNA via a groove interaction mode with an intrinsic binding constant of 3.75 × 10(4) M(-1).

  13. Structure elucidation and DNA binding specificity of natural compounds from Cassia siamea leaves: A biophysical approach.

    Science.gov (United States)

    Parveen, Mehtab; Ahmad, Faheem; Malla, Ali Mohammed; Khan, Mohd Sohrab; Rehman, Sayeed Ur; Tabish, Mohammad; Silva, Manuela Ramos; Silva, P S Pereira

    2016-06-01

    A novel isoflavone, 5,6,7-trimethoxy-3-(3',4',5'-trimethoxyphenyl)-4H-chromen-4-one (1) along with a known pyranocoumarin, Seselin (2) have been isolated from the ethanolic extract of the leaves of Cassia siamea (Family: Fabaceae). Compound 1 has been reported for the first time from any natural source and has not been synthesized so far. Their structures were elucidated on the basis of chemical and physical evidences viz. elemental analysis, UV, FT-IR, (1)H-NMR, (13)C-NMR and mass spectral analysis. Structure of compound (1) was further authenticated by single-crystal X-ray analysis and density functional theory (DFT) calculations. A multi-technique approach employing UV-Visible spectroscopy, fluorescence, KI quenching studies, competitive displacement assay, circular dichroism and viscosity studies have been utilized to probe the extent of interaction and possible binding modes of isolated compounds (1-2) with calf thymus DNA (CT-DNA). Both the compounds were found to interact with DNA via non-intercalative binding mode with moderate proficiencies. Groove binding was the major interaction mode in the case of compound 2 while compound 1 probably interacts with DNA through electrostatic interactions. These studies provide deeper insight in understanding of DNA-drug (natural products) interaction which could be helpful to improve their bioavailability for therapeutic purposes. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Harvesting candidate genes responsible for serious adverse drug reactions from a chemical-protein interactome.

    Directory of Open Access Journals (Sweden)

    Lun Yang

    2009-07-01

    Full Text Available Identifying genetic factors responsible for serious adverse drug reaction (SADR is of critical importance to personalized medicine. However, genome-wide association studies are hampered due to the lack of case-control samples, and the selection of candidate genes is limited by the lack of understanding of the underlying mechanisms of SADRs. We hypothesize that drugs causing the same type of SADR might share a common mechanism by targeting unexpectedly the same SADR-mediating protein. Hence we propose an approach of identifying the common SADR-targets through constructing and mining an in silico chemical-protein interactome (CPI, a matrix of binding strengths among 162 drug molecules known to cause at least one type of SADR and 845 proteins. Drugs sharing the same SADR outcome were also found to possess similarities in their CPI profiles towards this 845 protein set. This methodology identified the candidate gene of sulfonamide-induced toxic epidermal necrolysis (TEN: all nine sulfonamides that cause TEN were found to bind strongly to MHC I (Cw*4, whereas none of the 17 control drugs that do not cause TEN were found to bind to it. Through an insight into the CPI, we found the Y116S substitution of MHC I (B*5703 enhances the unexpected binding of abacavir to its antigen presentation groove, which explains why B*5701, not B*5703, is the risk allele of abacavir-induced hypersensitivity. In conclusion, SADR targets and the patient-specific off-targets could be identified through a systematic investigation of the CPI, generating important hypotheses for prospective experimental validation of the candidate genes.

  15. Grooved Terrain on Ganymede: First Results from Galileo High-Resolution Imaging

    Science.gov (United States)

    Pappalardo, R.T.; Head, J.W.; Collins, G.C.; Kirk, R.L.; Neukum, G.; Oberst, J.; Giese, B.; Greeley, R.; Chapman, C.R.; Helfenstein, P.; Moore, Johnnie N.; McEwen, A.; Tufts, B.R.; Senske, D.A.; Herbert, Breneman H.; Klaasen, K.

    1998-01-01

    High-resolution Galileo imaging has provided important insight into the origin and evolution of grooved terrain on Ganymede. The Uruk Sulcus target site was the first imaged at high resolution, and considerations of resolution, viewing geometry, low image compression, and complementary stereo imaging make this region extremely informative. Contrast variations in these low-incidence angle images are extreme and give the visual impression of topographic shading. However, photometric analysis shows that the scene must owe its character to albedo variations. A close correlation of albedo variations to topography is demonstrated by limited stereo coverage, allowing extrapolation of the observed brightness and topographic relationships to the rest of the imaged area. Distinct geological units are apparent across the region, and ridges and grooves are ubiquitous within these units. The stratigraphically lowest and most heavily cratered units ("lineated grooved terrain") generally show morphologies indicative of horst-and-graben-style normal faulting. The stratigraphically highest groove lanes ("parallel ridged terrain") exhibit ridges of roughly triangular cross section, suggesting that tilt-block-style normal faulting has shaped them. These extensional-tectonic models are supported by crosscutting relationships at the margins of groove lanes. Thus, a change in tectonic style with time is suggested in the Uruk Sulcus region, varying from horst and graben faulting for the oldest grooved terrain units to tilt block normal faulting for the latest units. The morphologies and geometries of some stratigraphically high units indicate that a strike-slip component of deformation has played an important role in shaping this region of grooved terrain. The most recent tectonic episode is interpreted as right-lateral transtension, with its tectonic pattern of two contemporaneous structural orientations superimposed on older units of grooved terrain. There is little direct evidence for

  16. The colonic groove or furrow: a comparative morphological study of six species of African mole-rats (Rodentia, Bathyergidae).

    Science.gov (United States)

    Kotzé, S H; van der Merwe, E L; Ndou, R; O'Riain, M J; Bennett, N C

    2009-08-01

    Herbivorous mammals such as nutrias, guinea pigs, chinchillas, and mole-rats have a longitudinal mucosal colonic groove (furrow) in their ascending colon, which is thought to play a role in the colonic separation mechanism (CSM). It is not known whether this groove is structurally modified to adapt to this function in mole-rat species. The morphology of this groove was studied in 32 mol-rats, four species, one of which consisted of three subspecies, endemic to southern Africa and two species found in eastern Africa. The macroscopic morphology of the groove was documented, and samples for histological examination were taken. The groove was wide at its origin at the cecocolic junction and was lined on either side by a row of papillae with the opposing papillae slightly offset in arrangement. The papillated groove gradually decreased in size toward the distal part of the ascending colon where it disappeared. This pattern was similar in all species except in Heterocephalus glaber, where the papillae were absent and the groove was lined by two longitudinal ridges. A histological examination of cross sections revealed that the mucosa covering the inner and outer walls of the groove was rich in mucous-secreting goblet cells. The walls of the groove contained smooth muscle extending from the inner circular smooth muscle layer at the base to the tips of the papillae in all species examined as well as arteries, lymphatic vessels, and prominent sinusoid-like veins. The groove could be demonstrated both macroscopically and histologically in three Bathyergus suillus fetuses of varying sizes. The sinusoid-like veins present in all grooves, regardless of macroscopic shape, suggest that they have a role in the functioning of the groove. (c) 2009 Wiley-Liss, Inc.

  17. What musicians do to induce the sensation of groove in simple and complex melodies, and how listeners perceive it

    Directory of Open Access Journals (Sweden)

    Guy eMadison

    2014-08-01

    Full Text Available Groove is the experience of wanting to move when hearing music, such as snapping fingers or tapping feet. This is a central aspect of much music, in particular of music intended for dancing. While previous research has found considerable consistency in ratings of groove across individuals, it remains unclear how groove is induced, that is, what are the physical properties of the acoustic signal that differ between more and less groove-inducing versions. Here, we examined this issue with a performance experiment, in which 4 musicians performed 6 simple and 6 complex melodies in two conditions with the intention of minimizing and maximizing groove. Analyses of rhythmical and temporal properties from the performances demonstrated some general effects. For example, more groove was associated with more notes on faster metrical levels and syncopation, and less groove was associated with deadpan timing and destruction of the regular pulse. We did not observe that deviations from the metrical grid (i.e. micro-timing were a predictor of groove. A listener experiment confirmed that the musicians’ manipulations had the intended effects on the experience of groove. A Brunswikian lens model was applied, which estimates the performer-perceiver communication across the two experiments. It showed that the communication achievement for simple melodies was 0.62, and that the matching of performers’ and listeners’ use of 9 rhythmical cues was 0.83. For complex melodies with an already high level of groove, the corresponding values were 0.39 and 0.34, showing that it was much more difficult to take out groove from musical structures designed to induce groove.

  18. STUDY ON RECTANGULAR WAVEGUIDE GRATING SLOW-WAVE STRUCTURE WITH COSINE-SHAPED GROOVES

    Institute of Scientific and Technical Information of China (English)

    Lu Zhigang; Wei Yanyu; Gong Yubin; Wu Zhoumiao; Wang Wenxiang

    2007-01-01

    This paper focuses on a new rectangular waveguide grating Slow-Wave Structure(SWS)with cosine-shaped grooves and studies the propagation characteristics of the wave in the SWS.By using the approximate field-matching conditions,the dispersion equation and the coupling impedance of this circuit are obtained.The dispersion curves and coupling impedances of the fundamental wave are calculated and the influences of the various geometrical dimensions are discussed.The results show that the bandwidth of the cosine-shaped groove SWS is much wider than that of rectangular-shaped groove one.And reducing the groove width can broaden the frequency-band and decrease the phase-velocity,while increment of the groove-depth can also decrease phase-velocity.For above cases,the coupling impedance is more than 16Ω.The present analysis will be helpful on further study and design of the RF systems used in millimeter wave Traveling Wave Tube(TWT).

  19. Measuring phacoemulsification groove depth using probe tip dimensions and biometry lens thickness readings

    Directory of Open Access Journals (Sweden)

    Dunne K

    2016-08-01

    Full Text Available Kevin Dunne, Alex J Buller Department of Ophthalmology, Hawkes Bay District Health Board, Hastings, New Zealand Aim: To describe a useful technique utilizing lens thickness from biometric data as well as phacoemulsification (phaco probe tip dimensions, in order to more accurately determine safe groove depth during divide and conquer techniques for cataract surgery. Methods: Single center, selection of patients for cataract surgery deemed low risk and suitable for surgical teaching cases. Individual lens thickness measurements from biometry were calculated with known phaco tip dimensions to give an individualized safe number of phaco tip depths for grooving during divide and conquer. This technique was then applied during cataract surgery. Results: Utilization of this technique allows calculation and determination of an appropriate number of phaco tip depths of grooving for each individual patient. This technique was applied as a teaching tool for surgical trainees, with subsequent successful safe cataract surgeries completed. No posterior capsule ruptures were noted for these cases. Conclusion: By combining the biometric measurements of an individual patient’s lens thickness together with known phaco tip dimensions, individualized safe groove depths can be theoretically determined and applied during divide and conquer cataract surgery. Keywords: cataract, divide and conquer, groove depth, lens thickness, probe tip

  20. Wide polytef (Gore-Tex) implants in lip augmentation and nasolabial groove correction.

    Science.gov (United States)

    Conrad, K; MacDonald, M R

    1996-06-01

    To describe a new technique of polytef (Gore-Tex) implantation into the upper and lower lips and nasolabial grooves by using large implants as a method that achieves effective cosmetic improvement. A private cosmetic surgery center. Thirty-three (female) patients who desired fuller lips and 62 patients (52 female and 10 male) who requested less prominent cheek lip grooves. Significant patient satisfaction after 12 to 54 months. Conspicuous aesthetic effect that related to both lip and nasolabial groove correction was documented. All patients but 4 (2 in each group) were pleased with the final outcome of the treatment. In the opinion of the authors, the threading technique of polytef implantation creates inconspicuous improvement-both in lip augmentation and nasolabial groove correction. Large polytef implants that were inserted through a tunneling technique produced consistently good results. Implants (lip augmentation: width, < or = 10 mm, and thickness, 4 mm; nasolabial groove correction: width, 8 mm, and thickness, < or = 8 mm) were found to be safe, simple, and effective.