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Sample records for allosteric enzyme imidazole

  1. Allosteric regulation of epigenetic modifying enzymes.

    Science.gov (United States)

    Zucconi, Beth E; Cole, Philip A

    2017-08-01

    Epigenetic enzymes including histone modifying enzymes are key regulators of gene expression in normal and disease processes. Many drug development strategies to target histone modifying enzymes have focused on ligands that bind to enzyme active sites, but allosteric pockets offer potentially attractive opportunities for therapeutic development. Recent biochemical studies have revealed roles for small molecule and peptide ligands binding outside of the active sites in modulating the catalytic activities of histone modifying enzymes. Here we highlight several examples of allosteric regulation of epigenetic enzymes and discuss the biological significance of these findings. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Enzyme activity and allosteric characteristics of gamma-irradiated solid aspartate transcarbamylase

    International Nuclear Information System (INIS)

    Bigler, W.N.; Tolbert, B.M.

    1977-01-01

    Aspartate transcarbamylase purified from E. coli was lyophilized, irradiated in vacuo with γ radiation from a cesium-137 source, redissolved in buffer under a nitrogen atmosphere, and assayed for enzyme activity. Lyophilized and redissolved enzyme had normal catalytic and allosteric kinetic characteristics. The average D 37 observed with saturating substrate, 25 mM aspartate, was 4.1 Mrad. With less than saturating substrate, 5 mM aspartate, the activity increases from zero to 1.6 Mrad and then decreases with a D 37 of 7.2 Mrad. Inclusion of 1 mM CTP, an allosteric inhibitor, in the 5 mM aspartate assays results in a more pronounced maximum in the activity curve occurring at slightly higher dose, 2.2 Mrad. Inhibitability by CTP has a D 37 of 2.3 Mrad with doses below the activity maximum. Enzyme lyophilized in the presence of 1 mM CTP has a D 37 of 2.9 Mrad. ATCase activity changes caused by irradiation of lyophylized bacteria were qualitatively like the changes observed in the detailed studies with the purified enzyme. Apparent radiation sensitivities of ATCase in lyophilized bacteria were observed to vary with the technique used to disrupt the resuspended bacteria

  3. Caseoperoxidase, mixed β-casein-SDS-hemin-imidazole complex: a nano artificial enzyme.

    Science.gov (United States)

    Moosavi-Movahedi, Zainab; Gharibi, Hussein; Hadi-Alijanvand, Hamid; Akbarzadeh, Mohammad; Esmaili, Mansoore; Atri, Maliheh S; Sefidbakht, Yahya; Bohlooli, Mousa; Nazari, Khodadad; Javadian, Soheila; Hong, Jun; Saboury, Ali A; Sheibani, Nader; Moosavi-Movahedi, Ali A

    2015-01-01

    A novel peroxidase-like artificial enzyme, named "caseoperoxidase", was biomimetically designed using a nano artificial amino acid apo-protein hydrophobic pocket. This four-component nano artificial enzyme containing heme-imidazole-β-casein-SDS exhibited high activity growth and k(cat) performance toward the native horseradish peroxidase demonstrated by the steady state kinetics using UV-vis spectrophotometry. The hydrophobicity and secondary structure of the caseoperoxidase were studied by ANS fluorescence and circular dichroism spectroscopy. Camel β-casein (Cβ-casein) was selected as an appropriate apo-protein for the heme active site because of its innate flexibility and exalted hydrophobicity. This selection was confirmed by homology modeling method. Heme docking into the newly obtained Cβ-casein structure indicated one heme was mainly incorporated with Cβ-casein. The presence of a main electrostatic site for the active site in the Cβ-casein was also confirmed by experimental methods through Wyman binding potential and isothermal titration calorimetry. The existence of Cβ-casein protein in this biocatalyst lowered the suicide inactivation and provided a suitable protective role for the heme active-site. Additional experiments confirmed the retention of caseoperoxidase structure and function as an artificial enzyme.

  4. Cytokinin oxidase from Phaseolus vulgaris callus tissues. Enhanced in vitro activity of the enzyme in the presence of copper-imidazole complexes

    International Nuclear Information System (INIS)

    Chatfield, J.M.; Armstrong, D.J.

    1987-01-01

    The effects of metal ions on cytokinin oxidase activity extracted from callus tissues of Phaseolus vulgaris L. cv Great Northern have been examined using an assay based on the oxidation of N 6 -(Δ 2 -isopentenyl)-adenine-2,8- 3 H (i 6 Ade) to adenine (Ade). The addition of cupric ions to reaction mixtures containing imidazole buffer markedly enhanced cytokinin oxidase activity. In the presence of optimal concentrations of copper and imidazole, cytokinin oxidase activity was stimulated more than 20-fold. The effect was enzyme dependent, specific for copper, and observed only in the presence of imidazole. The substrate specificity of the copper-imidazole enhanced reaction, as judged by substrate competition tests, was the same as that observed in the absence of copper and imidazole. Similarly, in tests involving DEAE-cellulose chromatography, elution profiles of cytokinin oxidase activity determined using a copper-imidazole enhanced assay were identical to those obtained using an assay without copper and imidazole. On the basis of these results, the addition of copper and imidazole to reaction mixtures used to assay for cytokinin oxidase activity is judged to provide a reliable and specific assay of greatly enhanced sensitivity for the enzyme. The mechanism by which copper and imidazole enhance cytokinin oxidase activity is not certain, but the reaction catalyzed by the enzyme was not inhibited by anaerobic conditions when these reagents were present. This observation suggests that copper-imidazole complexes are substituting for oxygen in the reaction mechanism by which cytokinin oxidase effects cleavage of the N 6 -side chain of i 6 Ade

  5. Zinc as Allosteric Ion Channel Modulator: Ionotropic Receptors as Metalloproteins

    Science.gov (United States)

    Peralta, Francisco Andrés; Huidobro-Toro, Juan Pablo

    2016-01-01

    Zinc is an essential metal to life. This transition metal is a structural component of many proteins and is actively involved in the catalytic activity of cell enzymes. In either case, these zinc-containing proteins are metalloproteins. However, the amino acid residues that serve as ligands for metal coordination are not necessarily the same in structural proteins compared to enzymes. While crystals of structural proteins that bind zinc reveal a higher preference for cysteine sulfhydryls rather than histidine imidazole rings, catalytic enzymes reveal the opposite, i.e., a greater preference for the histidines over cysteines for catalysis, plus the influence of carboxylic acids. Based on this paradigm, we reviewed the putative ligands of zinc in ionotropic receptors, where zinc has been described as an allosteric modulator of channel receptors. Although these receptors do not strictly qualify as metalloproteins since they do not normally bind zinc in structural domains, they do transitorily bind zinc at allosteric sites, modifying transiently the receptor channel’s ion permeability. The present contribution summarizes current information showing that zinc allosteric modulation of receptor channels occurs by the preferential metal coordination to imidazole rings as well as to the sulfhydryl groups of cysteine in addition to the carboxyl group of acid residues, as with enzymes and catalysis. It is remarkable that most channels, either voltage-sensitive or transmitter-gated receptor channels, are susceptible to zinc modulation either as positive or negative regulators. PMID:27384555

  6. Sequence analysis and molecular characterization of Clonorchis sinensis hexokinase, an unusual trimeric 50-kDa glucose-6-phosphate-sensitive allosteric enzyme.

    Directory of Open Access Journals (Sweden)

    Tingjin Chen

    Full Text Available Clonorchiasis, which is induced by the infection of Clonorchis sinensis (C. sinensis, is highly associated with cholangiocarcinoma. Because the available examination, treatment and interrupting transmission provide limited opportunities to prevent infection, it is urgent to develop integrated strategies to prevent and control clonorchiasis. Glycolytic enzymes are crucial molecules for trematode survival and have been targeted for drug development. Hexokinase of C. sinensis (CsHK, the first key regulatory enzyme of the glycolytic pathway, was characterized in this study. The calculated molecular mass (Mr of CsHK was 50.0 kDa. The obtained recombinant CsHK (rCsHK was a homotrimer with an Mr of approximately 164 kDa, as determined using native PAGE and gel filtration. The highest activity was obtained with 50 mM glycine-NaOH at pH 10 and 100 mM Tris-HCl at pH 8.5 and 10. The kinetics of rCsHK has a moderate thermal stability. Compared to that of the corresponding negative control, the enzymatic activity was significantly inhibited by praziquantel (PZQ and anti-rCsHK serum. rCsHK was homotropically and allosterically activated by its substrates, including glucose, mannose, fructose, and ATP. ADP exhibited mixed allosteric effect on rCsHK with respect to ATP, while inorganic pyrophosphate (PPi displayed net allosteric activation with various allosteric systems. Fructose behaved as a dose-dependent V activator with the substrate glucose. Glucose-6-phosphate (G6P displayed net allosteric inhibition on rCsHK with respect to ATP or glucose with various allosteric systems in a dose-independent manner. There were differences in both mRNA and protein levels of CsHK among the life stages of adult worm, metacercaria, excysted metacercaria and egg of C. sinensis, suggesting different energy requirements during different development stages. Our study furthers the understanding of the biological functions of CsHK and supports the need to screen for small

  7. Sequence Analysis and Molecular Characterization of Clonorchis sinensis Hexokinase, an Unusual Trimeric 50-kDa Glucose-6-Phosphate-Sensitive Allosteric Enzyme

    Science.gov (United States)

    Chen, Tingjin; Ning, Dan; Sun, Hengchang; Li, Ran; Shang, Mei; Li, Xuerong; Wang, Xiaoyun; Chen, Wenjun; Liang, Chi; Li, Wenfang; Mao, Qiang; Li, Ye; Deng, Chuanhuan; Wang, Lexun; Wu, Zhongdao; Huang, Yan; Xu, Jin; Yu, Xinbing

    2014-01-01

    Clonorchiasis, which is induced by the infection of Clonorchis sinensis (C. sinensis), is highly associated with cholangiocarcinoma. Because the available examination, treatment and interrupting transmission provide limited opportunities to prevent infection, it is urgent to develop integrated strategies to prevent and control clonorchiasis. Glycolytic enzymes are crucial molecules for trematode survival and have been targeted for drug development. Hexokinase of C. sinensis (CsHK), the first key regulatory enzyme of the glycolytic pathway, was characterized in this study. The calculated molecular mass (Mr) of CsHK was 50.0 kDa. The obtained recombinant CsHK (rCsHK) was a homotrimer with an Mr of approximately 164 kDa, as determined using native PAGE and gel filtration. The highest activity was obtained with 50 mM glycine-NaOH at pH 10 and 100 mM Tris-HCl at pH 8.5 and 10. The kinetics of rCsHK has a moderate thermal stability. Compared to that of the corresponding negative control, the enzymatic activity was significantly inhibited by praziquantel (PZQ) and anti-rCsHK serum. rCsHK was homotropically and allosterically activated by its substrates, including glucose, mannose, fructose, and ATP. ADP exhibited mixed allosteric effect on rCsHK with respect to ATP, while inorganic pyrophosphate (PPi) displayed net allosteric activation with various allosteric systems. Fructose behaved as a dose-dependent V activator with the substrate glucose. Glucose-6-phosphate (G6P) displayed net allosteric inhibition on rCsHK with respect to ATP or glucose with various allosteric systems in a dose-independent manner. There were differences in both mRNA and protein levels of CsHK among the life stages of adult worm, metacercaria, excysted metacercaria and egg of C. sinensis, suggesting different energy requirements during different development stages. Our study furthers the understanding of the biological functions of CsHK and supports the need to screen for small molecule inhibitors

  8. Switch I-dependent allosteric signaling in a G-protein chaperone-B12 enzyme complex.

    Science.gov (United States)

    Campanello, Gregory C; Lofgren, Michael; Yokom, Adam L; Southworth, Daniel R; Banerjee, Ruma

    2017-10-27

    G-proteins regulate various processes ranging from DNA replication and protein synthesis to cytoskeletal dynamics and cofactor assimilation and serve as models for uncovering strategies deployed for allosteric signal transduction. MeaB is a multifunctional G-protein chaperone, which gates loading of the active 5'-deoxyadenosylcobalamin cofactor onto methylmalonyl-CoA mutase (MCM) and precludes loading of inactive cofactor forms. MeaB also safeguards MCM, which uses radical chemistry, against inactivation and rescues MCM inactivated during catalytic turnover by using the GTP-binding energy to offload inactive cofactor. The conserved switch I and II signaling motifs used by G-proteins are predicted to mediate allosteric regulation in response to nucleotide binding and hydrolysis in MeaB. Herein, we targeted conserved residues in the MeaB switch I motif to interrogate the function of this loop. Unexpectedly, the switch I mutations had only modest effects on GTP binding and on GTPase activity and did not perturb stability of the MCM-MeaB complex. However, these mutations disrupted multiple MeaB chaperone functions, including cofactor editing, loading, and offloading. Hence, although residues in the switch I motif are not essential for catalysis, they are important for allosteric regulation. Furthermore, single-particle EM analysis revealed, for the first time, the overall architecture of the MCM-MeaB complex, which exhibits a 2:1 stoichiometry. These EM studies also demonstrate that the complex exhibits considerable conformational flexibility. In conclusion, the switch I element does not significantly stabilize the MCM-MeaB complex or influence the affinity of MeaB for GTP but is required for transducing signals between MeaB and MCM. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Structure–activity relationships of imidazole-derived 2-[N-carbamoylmethyl-alkylamino]acetic acids, dual binders of human insulin-degrading enzyme

    Energy Technology Data Exchange (ETDEWEB)

    Charton, Julie; Gauriot, Marion; Totobenazara, Jane; Hennuyer, Nathalie; Dumont, Julie; Bosc, Damien; Marechal, Xavier; Elbakali, Jamal; Herledan, Adrien; Wen, Xiaoan; Ronco, Cyril; Gras-Masse, Helene; Heninot, Antoine; Pottiez, Virginie; Landry, Valerie; Staels, Bart; Liang, Wenguang G.; Leroux, Florence; Tang, Wei-Jen; Deprez, Benoit (INSRM-France); (UC); (IP-France)

    2015-10-30

    Insulin degrading enzyme (IDE) is a zinc metalloprotease that degrades small amyloid peptides such as amyloid-â and insulin. So far the dearth of IDE-specific pharmacological inhibitors impacts the understanding of its role in the physiopathology of Alzheimer's disease, amyloid-â clearance, and its validation as a potential therapeutic target. Hit 1 was previously discovered by high-throughput screening. Here we describe the structure-activity study, that required the synthesis of 48 analogues. We found that while the carboxylic acid, the imidazole and the tertiary amine were critical for activity, the methyl ester was successfully optimized to an amide or a 1,2,4-oxadiazole. Along with improving their activity, compounds were optimized for solubility, lipophilicity and stability in plasma and microsomes. The docking or co-crystallization of some compounds at the exosite or the catalytic site of IDE provided the structural basis for IDE inhibition. The pharmacokinetic properties of best compounds 44 and 46 were measured in vivo. As a result, 44 (BDM43079) and its methyl ester precursor 48 (BDM43124) are useful chemical probes for the exploration of IDE's role.

  10. Iron and Zinc Complexes of Bulky Bis-Imidazole Ligands : Enzyme Mimicry and Ligand-Centered Redox Activity

    NARCIS (Netherlands)

    Folkertsma, E.

    2016-01-01

    The research described in this thesis is directed to the development of cheap and non-toxic iron-based homogeneous catalysts, using enzyme models and redox non-innocent ligands. Inspired by nature, the first approach focuses on the synthesis of structural models of the active site of non-heme iron

  11. Mechanism and activation for allosteric adenosine 5'-monophosphate nucleosidase. Kinetic alpha-deuterium isotope effects for the enzyme-catalyzed hydrolysis of adenosine 5'-monophosphate and nicotinamide mononucleotide

    International Nuclear Information System (INIS)

    Skoog, M.T.

    1986-01-01

    The kinetic alpha-deuterium isotope effect on Vmax/Km for hydrolysis of NMN catalyzed by AMP nucleosidase at saturating concentrations of the allosteric activator MgATP2- is kH/kD = 1.155 +/- 0.012. This value is close to that reported previously for the nonenzymatic hydrolysis of nucleosides of related structure, suggesting that the full intrinsic isotope effect for enzymatic NMN hydrolysis is expressed under these conditions; that is, bond-changing reactions are largely or completely rate-determining and the transition state has marked oxocarbonium ion character. The kinetic alpha-deuterium isotope effect for this reaction is unchanged when deuterium oxide replaces water as solvent, corroborating this conclusion. Furthermore, this isotope effect is independent of pH over the range 6.95-9.25, for which values of Vmax/Km change by a factor of 90, suggesting that the isotope-sensitive and pH-sensitive steps for AMP-nucleosidase-catalyzed NMN hydrolysis are the same. Values of kH/kD for AMP nucleosidase-catalyzed hydrolysis of NMN decrease with decreasing saturation of enzyme with MgATP2- and reach unity when the enzyme is less than half-saturated with this activator. This requires that the rate-determining step changes from cleavage of the covalent C-N bond to one which is isotope-independent. In contrast to the case for NMN hydrolysis, AMP nucleosidase-catalyzed hydrolysis of AMP at saturating concentrations of MgATP2- shows a kinetic alpha-deuterium isotope effect of unity. Thus, covalent bond-changing reactions are largely or completely rate-determining for hydrolysis of a poor substrate, NMN, but make little or no contribution to rate-determining step for hydrolysis of a good substrate, AMP, by maximally activated enzyme. This behavior has several precedents

  12. Uracil phosphoribosyltransferase from the extreme thermoacidophilic archaebacterium Sulfolobus shibatae is an allosteric enzyme, activated by GTP and inhibited by CTP

    DEFF Research Database (Denmark)

    Linde, Lise; Jensen, Kaj Frank

    1996-01-01

    Uracil phosphoribosyltransferase, which catalyses the formation of UMP and pyrophosphate from uracil and 5-phosphoribosyl a-1-pyrophosphate (PRPP), was partly purified from the extreme thermophilic archaebacterium Sulfolobus shibatae. The enzyme required divalent metal ions for activity...... and it showed the highest activity at pH 6.4. The specific activity of the enzyme was 50-times higher at 95°C than at 37°C, but the functional half-life was short at 95°C. The activity of uracil phosphoribosyltransferase was strongly activated by GTP, which increased Vmax of the reaction by approximately 20......-fold without much effect on Km for the substrates. The concentration of GTP required for half-maximal activation was about 80 µM. CTP was a strong inhibitor and acted by raising the concentration of GTP needed for half-maximal activation of the enzyme. We conclude that uracil phosphoribosyltransferase...

  13. p97 Composition Changes Caused by Allosteric Inhibition Are Suppressed by an On-Target Mechanism that Increases the Enzyme's ATPase Activity.

    Science.gov (United States)

    Her, Nam-Gu; Toth, Julia I; Ma, Chen-Ting; Wei, Yang; Motamedchaboki, Khatereh; Sergienko, Eduard; Petroski, Matthew D

    2016-04-21

    The AAA ATPase p97/VCP regulates protein homeostasis using a diverse repertoire of cofactors to fulfill its biological functions. Here we use the allosteric p97 inhibitor NMS-873 to analyze its effects on enzyme composition and the ability of cells to adapt to its cytotoxicity. We found that p97 inhibition changes steady state cofactor-p97 composition, leading to the enrichment of a subset of its cofactors and polyubiquitin bound to p97. We isolated cells specifically insensitive to NMS-873 and identified a new mutation (A530T) in p97. A530T is sufficient to overcome the cytotoxicity of NMS-873 and alleviates p97 composition changes caused by the molecule but not other p97 inhibitors. This mutation does not affect NMS-873 binding but increases p97 catalytic efficiency through altered ATP and ADP binding. Collectively, these findings identify cofactor-p97 interactions sensitive to p97 inhibition and reveal a new on-target mechanism to suppress the cytotoxicity of NMS-873. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Dual role of imidazole as activator/inhibitor of sweet almond (Prunus dulcis β-glucosidase

    Directory of Open Access Journals (Sweden)

    Sara Caramia

    2017-07-01

    Full Text Available The activity of Prunus dulcis (sweet almond β-glucosidase at the expense of p-nitrophenyl-β-d-glucopyranoside at pH 6 was determined, both under steady-state and pre-steady-state conditions. Using crude enzyme preparations, competitive inhibition by 1–5 mM imidazole was observed under both kinetic conditions tested. However, when imidazole was added to reaction mixtures at 0.125–0.250 mM, we detected a significant enzyme activation. To further inspect this effect exerted by imidazole, β-glucosidase was purified to homogeneity. Two enzyme isoforms were isolated, i.e. a full-length monomer, and a dimer containing a full-length and a truncated subunit. Dimeric β-glucosidase was found to perform much better than the monomeric enzyme, independently of the kinetic conditions used to assay enzyme activity. In addition, the sensitivity towards imidazole was found to differ between the two isoforms. While monomeric enzyme was indeed found to be relatively insensitive to imidazole, dimeric β-glucosidase was observed to be significantly activated by 0.125–0.250 mM imidazole under pre-steady-state conditions. Further, steady-state assays revealed that the addition of 0.125 mM imidazole to reaction mixtures increases the Km of dimeric enzyme from 2.3 to 6.7 mM. The activation of β-glucosidase dimer by imidazole is proposed to be exerted via a conformational transition poising the enzyme towards proficient catalysis.

  15. Dual role of imidazole as activator/inhibitor of sweet almond (Prunus dulcis) β-glucosidase.

    Science.gov (United States)

    Caramia, Sara; Gatius, Angela Gala Morena; Dal Piaz, Fabrizio; Gaja, Denis; Hochkoeppler, Alejandro

    2017-07-01

    The activity of Prunus dulcis (sweet almond) β-glucosidase at the expense of p -nitrophenyl-β-d-glucopyranoside at pH 6 was determined, both under steady-state and pre-steady-state conditions. Using crude enzyme preparations, competitive inhibition by 1-5 mM imidazole was observed under both kinetic conditions tested. However, when imidazole was added to reaction mixtures at 0.125-0.250 mM, we detected a significant enzyme activation. To further inspect this effect exerted by imidazole, β-glucosidase was purified to homogeneity. Two enzyme isoforms were isolated, i.e. a full-length monomer, and a dimer containing a full-length and a truncated subunit. Dimeric β-glucosidase was found to perform much better than the monomeric enzyme, independently of the kinetic conditions used to assay enzyme activity. In addition, the sensitivity towards imidazole was found to differ between the two isoforms. While monomeric enzyme was indeed found to be relatively insensitive to imidazole, dimeric β-glucosidase was observed to be significantly activated by 0.125-0.250 mM imidazole under pre-steady-state conditions. Further, steady-state assays revealed that the addition of 0.125 mM imidazole to reaction mixtures increases the K m of dimeric enzyme from 2.3 to 6.7 mM. The activation of β-glucosidase dimer by imidazole is proposed to be exerted via a conformational transition poising the enzyme towards proficient catalysis.

  16. Allosteric Regulation of Proteins

    Indian Academy of Sciences (India)

    ... Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Resonance – Journal of Science Education; Volume 22; Issue 1. Allosteric Regulation of Proteins: A Historical Perspective on the Development of Concepts and Techniques. General Article Volume 22 Issue 1 January 2017 pp 37-50 ...

  17. Imidazole: Having Versatile Biological Activities

    Directory of Open Access Journals (Sweden)

    Amita Verma

    2013-01-01

    Full Text Available Imidazoles have occupied a unique position in heterocyclic chemistry, and its derivatives have attracted considerable interests in recent years for their versatile properties in chemistry and pharmacology. Imidazole is nitrogen-containing heterocyclic ring which possesses biological and pharmaceutical importance. Thus, imidazole compounds have been an interesting source for researchers for more than a century. The imidazole ring is a constituent of several important natural products, including purine, histamine, histidine, and nucleic acid. Being a polar and ionisable aromatic compound, it improves pharmacokinetic characteristics of lead molecules and thus is used as a remedy to optimize solubility and bioavailability parameters of proposed poorly soluble lead molecules. There are several methods used for the synthesis of imidazole-containing compounds, and also their various structure reactions offer enormous scope in the field of medicinal chemistry. The imidazole derivatives possess extensive spectrum of biological activities such as antibacterial, anticancer, antitubercular, antifungal, analgesic, and anti-HIV activities. This paper aims to review the biological activities of imidazole during the past years.

  18. Enzyme

    Science.gov (United States)

    Enzymes are complex proteins that cause a specific chemical change in all parts of the body. For ... use them. Blood clotting is another example of enzymes at work. Enzymes are needed for all body ...

  19. Benzimidazole and imidazole hexachlorocerates

    Energy Technology Data Exchange (ETDEWEB)

    Bayanov, A P; Burylev, B P; Temerdashev, Z A; Gusev, V I [Kubanskij Gosudarstvennyj Univ., Krasnodar (USSR)

    1983-02-01

    The process of hexachlorocerium acid with benzimidazole and imidazole interaction and the reaction products are investigated. The values of thermodynamic characteristics of the hexachlorocerium acid reaction with benzimidazole are equal: ..delta..Gsub(298K)=-16.5+-0.2 kJ/mol, ..delta..Hsub(298K)=-63.6+-0.8 kJ/mol, ..delta..Ssub(298K)=-157+-5 J/mol degrees. By the IR spectroscopy and radiography method the individuality of separated compounds has been found. The thermal stability of compounds is determined. The temperature dependence of splitting off chlorine atom from benzimidazole hexachlorocerate on pressure is investigated. Thermodynamic characteristics and activation energies of the process are calculated.

  20. Benzimidazole and imidazole hexachlorocerates

    International Nuclear Information System (INIS)

    Bayanov, A.P.; Burylev, B.P.; Temerdashev, Z.A.; Gusev, V.I.

    1983-01-01

    The process of hexachlorocerium acid with benzimidazole and imidazole interaction and the reaction products are investigated. The values of thermodynamic characteristics of the hexachlorocerium acid reaction with benzimidazole are equal: ΔGsub(298K)=-16.5+-0.2 kJ/mol, ΔHsub(298K)=-63.6+-0.8 kJ/mol, ΔSsub(298K)=-157+-5 J/mol degrees. By the IR spectroscopy and radiography method the individuality of separated compounds has been found. The thermal stability of compounds is determined. The temperature de-- pendence of splitting off chlorine atom from benzimidazole hexachlorocerate on pressure is investigated. Thermodynamic characteristics and activation energies of the process are calculated

  1. The lattice dynamics of imidazole

    International Nuclear Information System (INIS)

    Link, K.H.

    1983-05-01

    The lattice dynamics of imidazole have been investigated. To this end dispersion curves have been determined at 10 K by inelastic coherent neutron scattering. RAMAN measurements have been done to investigate identical gamma - point modes. The combination of extinction rules for RAMAN - and neutron scattering leads to the symmetry assignment of identical gamma - point modes. The experiment yields a force constant of the streching vibration of the hydrogen bond of 0.33 mdyn/A. A force model has been developed to describe the intermolecular atom - atom Interactions in imidazole. (orig./BHO)

  2. Comprehensive review in current developments of imidazole-based medicinal chemistry.

    Science.gov (United States)

    Zhang, Ling; Peng, Xin-Mei; Damu, Guri L V; Geng, Rong-Xia; Zhou, Cheng-He

    2014-03-01

    Imidazole ring is an important five-membered aromatic heterocycle widely present in natural products and synthetic molecules. The unique structural feature of imidazole ring with desirable electron-rich characteristic is beneficial for imidazole derivatives to readily bind with a variety of enzymes and receptors in biological systems through diverse weak interactions, thereby exhibiting broad bioactivities. The related research and developments of imidazole-based medicinal chemistry have become a rapidly developing and increasingly active topic. Particularly, numerous imidazole-based compounds as clinical drugs have been extensively used in the clinic to treat various types of diseases with high therapeutic potency, which have shown the enormous development value. This work systematically gives a comprehensive review in current developments of imidazole-based compounds in the whole range of medicinal chemistry as anticancer, antifungal, antibacterial, antitubercular, anti-inflammatory, antineuropathic, antihypertensive, antihistaminic, antiparasitic, antiobesity, antiviral, and other medicinal agents, together with their potential applications in diagnostics and pathology. It is hoped that this review will be helpful for new thoughts in the quest for rational designs of more active and less toxic imidazole-based medicinal drugs, as well as more effective diagnostic agents and pathologic probes. © 2013 Wiley Periodicals, Inc.

  3. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.

    Science.gov (United States)

    Keedy, Daniel A; Hill, Zachary B; Biel, Justin T; Kang, Emily; Rettenmaier, T Justin; Brandao-Neto, Jose; Pearce, Nicholas M; von Delft, Frank; Wells, James A; Fraser, James S

    2018-06-07

    Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function. © 2018, Keedy et al.

  4. Evolution of allosteric regulation in chorismate mutases from early plants

    Energy Technology Data Exchange (ETDEWEB)

    Kroll, Kourtney; Holland, Cynthia K.; Starks, Courtney M.; Jez, Joseph M.

    2017-09-28

    Plants, fungi, and bacteria synthesize the aromatic amino acids: l-phenylalanine, l-tyrosine, and l-tryptophan. Chorismate mutase catalyzes the branch point reaction of phenylalanine and tyrosine biosynthesis to generate prephenate. In Arabidopsis thaliana, there are two plastid-localized chorismate mutases that are allosterically regulated (AtCM1 and AtCM3) and one cytosolic isoform (AtCM2) that is unregulated. Previous analysis of plant chorismate mutases suggested that the enzymes from early plants (i.e. bryophytes/moss, lycophytes, and basal angiosperms) formed a clade distinct from the isoforms found in flowering plants; however, no biochemical information on these enzymes is available. To understand the evolution of allosteric regulation in plant chorismate mutases, we analyzed a basal lineage of plant enzymes homologous to AtCM1 based on sequence similarity. The chorismate mutases from the moss/bryophyte Physcomitrella patens (PpCM1 and PpCM2), the lycophyte Selaginella moellendorffii (SmCM), and the basal angiosperm Amborella trichopoda (AmtCM1 and AmtCM2) were characterized biochemically. Tryptophan was a positive effector for each of the five enzymes examined. Histidine was a weak positive effector for PpCM1 and AmtCM1. Neither tyrosine nor phenylalanine altered the activity of SmCM; however, tyrosine was a negative regulator of the other four enzymes. Phenylalanine down-regulates both moss enzymes and AmtCM2. The 2.0 Å X-ray crystal structure of PpCM1 in complex with the tryptophan identified the allosteric effector site and reveals structural differences between the R- (more active) and T-state (less active) forms of plant chorismate mutases. Molecular insight into the basal plant chorismate mutases guides our understanding of the evolution of allosteric regulation in these enzymes.

  5. Evolutionary convergence in the biosyntheses of the imidazole moieties of histidine and purines.

    Directory of Open Access Journals (Sweden)

    Alberto Vázquez-Salazar

    Full Text Available The imidazole group is an ubiquitous chemical motif present in several key types of biomolecules. It is a structural moiety of purines, and plays a central role in biological catalysis as part of the side-chain of histidine, the amino acid most frequently found in the catalytic site of enzymes. Histidine biosynthesis starts with both ATP and the pentose phosphoribosyl pyrophosphate (PRPP, which is also the precursor for the de novo synthesis of purines. These two anabolic pathways are also connected by the imidazole intermediate 5-aminoimidazole-4-carboxamide ribotide (AICAR, which is synthesized in both routes but used only in purine biosynthesis. Rather surprisingly, the imidazole moieties of histidine and purines are synthesized by different, non-homologous enzymes. As discussed here, this phenomenon can be understood as a case of functional molecular convergence.In this work, we analyze these polyphyletic processes and argue that the independent origin of the corresponding enzymes is best explained by the differences in the function of each of the molecules to which the imidazole moiety is attached. Since the imidazole present in histidine is a catalytic moiety, its chemical arrangement allows it to act as an acid or a base. On the contrary, the de novo biosynthesis of purines starts with an activated ribose and all the successive intermediates are ribotides, with the key β-glycosidic bondage joining the ribose and the imidazole moiety. This prevents purine ribonucleotides to exhibit any imidazole-dependent catalytic activity, and may have been the critical trait for the evolution of two separate imidazole-synthesizing-enzymes. We also suggest that, in evolutionary terms, the biosynthesis of purines predated that of histidine.As reviewed here, other biosynthetic routes for imidazole molecules are also found in extant metabolism, including the autocatalytic cyclization that occurs during the formation of creatinine from creatine phosphate

  6. Identification of the Allosteric Regulatory Site of Insulysin

    Energy Technology Data Exchange (ETDEWEB)

    Noinaj, Nicholas; Bhasin, Sonia K.; Song, Eun Suk; Scoggin, Kirsten E.; Juliano, Maria A.; Juliano, Luiz; Hersh, Louis B.; Rodgers, David W. (U. Sao Paulo); (Kentucky)

    2012-05-25

    Insulin degrading enzyme (IDE) is responsible for the metabolism of insulin and plays a role in clearance of the A{beta} peptide associated with Alzheimer's disease. Unlike most proteolytic enzymes, IDE, which consists of four structurally related domains and exists primarily as a dimer, exhibits allosteric kinetics, being activated by both small substrate peptides and polyphosphates such as ATP. The crystal structure of a catalytically compromised mutant of IDE has electron density for peptide ligands bound at the active site in domain 1 and a distal site in domain 2. Mutating residues in the distal site eliminates allosteric kinetics and activation by a small peptide, as well as greatly reducing activation by ATP, demonstrating that this site plays a key role in allostery. Comparison of the peptide bound IDE structure (using a low activity E111F IDE mutant) with unliganded wild type IDE shows a change in the interface between two halves of the clamshell-like molecule, which may enhance enzyme activity by altering the equilibrium between closed and open conformations. In addition, changes in the dimer interface suggest a basis for communication between subunits. Our findings indicate that a region remote from the active site mediates allosteric activation of insulysin by peptides. Activation may involve a small conformational change that weakens the interface between two halves of the enzyme.

  7. Identification of the Allosteric Regulatory Site of Insulysin

    Energy Technology Data Exchange (ETDEWEB)

    Noinaj, Nicholas; Bhasin, Sonia K.; Song, Eun Suk; Scoggin, Kirsten E.; Juliano, Maria A.; Juliano, Luiz; Hersh, Louis B.; Rodgers, David W.; Gerrard, Juliet Ann

    2011-06-24

    Background Insulin degrading enzyme (IDE) is responsible for the metabolism of insulin and plays a role in clearance of the Aβ peptide associated with Alzheimer's disease. Unlike most proteolytic enzymes, IDE, which consists of four structurally related domains and exists primarily as a dimer, exhibits allosteric kinetics, being activated by both small substrate peptides and polyphosphates such as ATP. Principal Findings The crystal structure of a catalytically compromised mutant of IDE has electron density for peptide ligands bound at the active site in domain 1 and a distal site in domain 2. Mutating residues in the distal site eliminates allosteric kinetics and activation by a small peptide, as well as greatly reducing activation by ATP, demonstrating that this site plays a key role in allostery. Comparison of the peptide bound IDE structure (using a low activity E111F IDE mutant) with unliganded wild type IDE shows a change in the interface between two halves of the clamshell-like molecule, which may enhance enzyme activity by altering the equilibrium between closed and open conformations. In addition, changes in the dimer interface suggest a basis for communication between subunits. Conclusions/Significance Our findings indicate that a region remote from the active site mediates allosteric activation of insulysin by peptides. Activation may involve a small conformational change that weakens the interface between two halves of the enzyme.

  8. First steps in the direction of synthetic, allosteric, direct inhibitors of thrombin and factor Xa.

    Science.gov (United States)

    Verghese, Jenson; Liang, Aiye; Sidhu, Preet Pal Singh; Hindle, Michael; Zhou, Qibing; Desai, Umesh R

    2009-08-01

    Designing non-saccharide functional mimics of heparin is a major challenge. In this work, a library of small, aromatic molecules based on the sulfated DHP scaffold was synthesized and screened against thrombin and factor Xa. The results reveal that (i) selected monomeric benzofuran derivatives inhibit the two enzymes, albeit weakly; (ii) the two enzymes recognize different structural features in the benzofurans studied suggesting significant selectivity of recognition; and (iii) the mechanism of inhibition is allosteric. The molecules represent the first allosteric small molecule inhibitors of the two enzymes.

  9. First Steps in the Direction of Synthetic, Allosteric, Direct Inhibitors of Thrombin and Factor Xa

    Science.gov (United States)

    Verghese, Jenson; Liang, Aiye; Sidhu, Preet Pal Singh; Hindle, Michael; Zhou, Qibing; Desai, Umesh R.

    2009-01-01

    Designing non-saccharide functional mimics of heparin is a major challenge. In this work, a library of small, aromatic molecules based on the sulfated DHP scaffold was synthesized and screened against thrombin and factor Xa. The results reveal that i) selected monomeric benzofuran derivatives inhibit the two enzymes, albeit weakly; ii) the two enzymes recognize different structural features in the benzofurans studied suggesting significant selectivity of recognition; and iii) the mechanism of inhibition is allosteric. The molecules represent the first allosteric small molecule inhibitors of the two enzymes. PMID:19540113

  10. Use of allosteric targets in the discovery of safer drugs.

    Science.gov (United States)

    Grover, Ashok Kumar

    2013-01-01

    The need for drugs with fewer side effects cannot be overemphasized. Today, most drugs modify the actions of enzymes, receptors, transporters and other molecules by directly binding to their active (orthosteric) sites. However, orthosteric site configuration is similar in several proteins performing related functions and this leads to a lower specificity of a drug for the desired protein. Consequently, such drugs may have adverse side effects. A new basis of drug discovery is emerging based on the binding of the drug molecules to sites away (allosteric) from the orthosteric sites. It is possible to find allosteric sites which are unique and hence more specific as targets for drug discovery. Of many available examples, two are highlighted here. The first is caloxins - a new class of highly specific inhibitors of plasma membrane Ca²⁺ pumps. The second concerns the modulation of receptors for the neurotransmitter acetylcholine, which binds to 12 types of receptors. Exploitation of allosteric sites has led to the discovery of drugs which can selectively modulate the activation of only 1 (M1 muscarinic) out of the 12 different types of acetylcholine receptors. These drugs are being tested for schizophrenia treatment. It is anticipated that the drug discovery exploiting allosteric sites will lead to more effective therapeutic agents with fewer side effects. Copyright © 2013 S. Karger AG, Basel.

  11. Structural and kinetic studies of the allosteric transition in Sulfolobus solfataricus uracil phosphoribosyltransferase: Permanent activation by engineering of the C-terminus

    DEFF Research Database (Denmark)

    Christoffersen, Stig; Kadziola, Anders; Johansson, Eva

    2009-01-01

    and PPi, in the other sites. Combined with three existing structures of uracil phosphoribosyltransferase in complex with UMP and the allosteric inhibitor cytidine triphosphate (CTP), these structures provide valuable insight into the mechanism of allosteric transition from inhibited to active enzyme...

  12. Allosteric enhancers, allosteric agonists and ago-allosteric modulators: where do they bind and how do they act?

    DEFF Research Database (Denmark)

    Schwartz, Thue W; Holst, Birgitte

    2007-01-01

    Many small-molecule agonists also display allosteric properties. Such ago-allosteric modulators act as co-agonists, providing additive efficacy--instead of partial antagonism--and they can affect--and often improve--the potency of the endogenous agonist. Surprisingly, the apparent binding sites...... different binding modes. In another, dimeric, receptor scenario, the endogenous agonist binds to one protomer while the ago-allosteric modulator binds to the other, 'allosteric' protomer. It is suggested that testing for ago-allosteric properties should be an integral part of the agonist drug discovery...... process because a compound that acts with--rather than against--the endogenous agonist could be an optimal agonist drug....

  13. Allosteric substrate switching in a voltage-sensing lipid phosphatase.

    Science.gov (United States)

    Grimm, Sasha S; Isacoff, Ehud Y

    2016-04-01

    Allostery provides a critical control over enzyme activity, biasing the catalytic site between inactive and active states. We found that the Ciona intestinalis voltage-sensing phosphatase (Ci-VSP), which modifies phosphoinositide signaling lipids (PIPs), has not one but two sequential active states with distinct substrate specificities, whose occupancy is allosterically controlled by sequential conformations of the voltage-sensing domain (VSD). Using fast fluorescence resonance energy transfer (FRET) reporters of PIPs to monitor enzyme activity and voltage-clamp fluorometry to monitor conformational changes in the VSD, we found that Ci-VSP switches from inactive to a PIP3-preferring active state when the VSD undergoes an initial voltage-sensing motion and then into a second PIP2-preferring active state when the VSD activates fully. This two-step allosteric control over a dual-specificity enzyme enables voltage to shape PIP concentrations in time, and provides a mechanism for the complex modulation of PIP-regulated ion channels, transporters, cell motility, endocytosis and exocytosis.

  14. Allosteric substrate switching in a voltage sensing lipid phosphatase

    Science.gov (United States)

    Grimm, Sasha S.; Isacoff, Ehud Y.

    2016-01-01

    Allostery provides a critical control over enzyme activity, biasing the catalytic site between inactive and active states. We find the Ciona intestinalis voltage-sensing phosphatase (Ci-VSP), which modifies phosphoinositide signaling lipids (PIPs), to have not one but two sequential active states with distinct substrate specificities, whose occupancy is allosterically controlled by sequential conformations of the voltage sensing domain (VSD). Using fast FRET reporters of PIPs to monitor enzyme activity and voltage clamp fluorometry to monitor conformational changes in the VSD, we find that Ci-VSP switches from inactive to a PIP3-preferring active state when the VSD undergoes an initial voltage sensing motion and then into a second PIP2-preferring active state when the VSD activates fully. This novel 2-step allosteric control over a dual specificity enzyme enables voltage to shape PIP concentrations in time, and provides a mechanism for the complex modulation of PIP-regulated ion channels, transporters, cell motility and endo/exocytosis. PMID:26878552

  15. Allosteric regulation and communication between subunits in uracil phosphoribosyltransferase from Sulfolobus solfataricus

    DEFF Research Database (Denmark)

    Arent, Susan; Harris, Pernille; Jensen, Kaj Frank

    2005-01-01

    organisms. To understand the allosteric regulation, crystal structures were determined for S. solfataricus UPRTase in complex with UMP and with UMP and the allosteric inhibitor CTP. Also, a structure with UMP bound in half of the active sites was determined. All three complexes form tetramers but reveal...... to rearrangements in the quaternary structure imply that this residue plays a major role in regulation of the enzyme and in communication between subunits. The ribose ring of UMP adopts alternative conformations in the cis and trans subunits of the UPRTase-UMP tetramer with associated differences...

  16. Physicochemical properties of the modeled structure of astacin metalloprotease moulting enzyme NAS-36 and mapping the druggable allosteric space of Heamonchus contortus, Brugia malayi and Ceanorhabditis elegans via molecular dynamics simulation.

    Science.gov (United States)

    Sharma, Om Prakash; Agrawal, Sonali; Kumar, M Suresh

    2013-12-01

    Nematodes represent the second largest phylum in the animal kingdom. It is the most abundant species (500,000) in the planet. It causes chronic, debilitating infections worldwide such as ascariasis, trichuriasis, hookworm, enterobiasis, strongyloidiasis, filariasis and trichinosis, among others. Molecular modeling tools can play an important role in the identification and structural investigation of molecular targets that can act as a vital candidate against filariasis. In this study, sequence analysis of NAS-36 from H. contortus (Heamonchus contortus), B. malayi (Brugia malayi) and C. elegans (Ceanorhabditis elegans) has been performed, in order to identify the conserved residues. Tertiary structure was developed for an insight into the molecular structure of the enzyme. Molecular Dynamics Simulation (MDS) studies have been carried out to analyze the stability and the physical properties of the proposed enzyme models in the H. contortus, B. malayi and C. elegans. Moreover, the drug binding sites have been mapped for inhibiting the function of NAS-36 enzyme. The molecular identity of this protease could eventually demonstrate how ex-sheathment is regulated, as well as provide a potential target of anthelmintics for the prevention of nematode infections.

  17. A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase

    Energy Technology Data Exchange (ETDEWEB)

    Wellington, Samantha; Nag, Partha P.; Michalska, Karolina; Johnston, Stephen E.; Jedrzejczak, Robert P.; Kaushik, Virendar K.; Clatworthy, Anne E.; Siddiqi, Noman; McCarren, Patrick; Bajrami, Besnik; Maltseva, Natalia I.; Combs, Senya; Fisher, Stewart L.; Joachimiak, Andrzej; Schreiber, Stuart L.; Hung, Deborah T.

    2017-07-03

    New antibiotics with novel targets are greatly needed. Bacteria have numerous essential functions, but only a small fraction of such processes—primarily those involved in macromolecular synthesis—are inhibited by current drugs. Targeting metabolic enzymes has been the focus of recent interest, but effective inhibitors have been difficult to identify. We describe a synthetic azetidine derivative, BRD4592, that kills Mycobacterium tuberculosis (Mtb) through allosteric inhibition of tryptophan synthase (TrpAB), a previously untargeted, highly allosterically regulated enzyme. BRD4592 binds at the TrpAB α–β-subunit interface and affects multiple steps in the enzyme's overall reaction, resulting in inhibition not easily overcome by changes in metabolic environment. We show that TrpAB is required for the survival of Mtb and Mycobacterium marinum in vivo and that this requirement may be independent of an adaptive immune response. This work highlights the effectiveness of allosteric inhibition for targeting proteins that are naturally highly dynamic and that are essential in vivo, despite their apparent dispensability under in vitro conditions, and suggests a framework for the discovery of a next generation of allosteric inhibitors.

  18. Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases

    Science.gov (United States)

    Buey, Rubén M.; Ledesma-Amaro, Rodrigo; Velázquez-Campoy, Adrián; Balsera, Mónica; Chagoyen, Mónica; de Pereda, José M.; Revuelta, José L.

    2015-11-01

    Inosine-5'-monophosphate dehydrogenase (IMPDH) plays key roles in purine nucleotide metabolism and cell proliferation. Although IMPDH is a widely studied therapeutic target, there is limited information about its physiological regulation. Using Ashbya gossypii as a model, we describe the molecular mechanism and the structural basis for the allosteric regulation of IMPDH by guanine nucleotides. We report that GTP and GDP bind to the regulatory Bateman domain, inducing octamers with compromised catalytic activity. Our data suggest that eukaryotic and prokaryotic IMPDHs might have developed different regulatory mechanisms, with GTP/GDP inhibiting only eukaryotic IMPDHs. Interestingly, mutations associated with human retinopathies map into the guanine nucleotide-binding sites including a previously undescribed non-canonical site and disrupt allosteric inhibition. Together, our results shed light on the mechanisms of the allosteric regulation of enzymes mediated by Bateman domains and provide a molecular basis for certain retinopathies, opening the door to new therapeutic approaches.

  19. A dynamically coupled allosteric network underlies binding cooperativity in Src kinase.

    Science.gov (United States)

    Foda, Zachariah H; Shan, Yibing; Kim, Eric T; Shaw, David E; Seeliger, Markus A

    2015-01-20

    Protein tyrosine kinases are attractive drug targets because many human diseases are associated with the deregulation of kinase activity. However, how the catalytic kinase domain integrates different signals and switches from an active to an inactive conformation remains incompletely understood. Here we identify an allosteric network of dynamically coupled amino acids in Src kinase that connects regulatory sites to the ATP- and substrate-binding sites. Surprisingly, reactants (ATP and peptide substrates) bind with negative cooperativity to Src kinase while products (ADP and phosphopeptide) bind with positive cooperativity. We confirm the molecular details of the signal relay through the allosteric network by biochemical studies. Experiments on two additional protein tyrosine kinases indicate that the allosteric network may be largely conserved among these enzymes. Our work provides new insights into the regulation of protein tyrosine kinases and establishes a potential conduit by which resistance mutations to ATP-competitive kinase inhibitors can affect their activity.

  20. Epoxy Nanocomposites Containing Zeolitic Imidazolate Framework-8.

    Science.gov (United States)

    Liu, Cong; Mullins, Michael; Hawkins, Spencer; Kotaki, Masaya; Sue, Hung-Jue

    2018-01-10

    Zeolitic imidazole framework-8 (ZIF-8) is utilized as a functional filler and a curing agent in the preparation of epoxy nanocomposites. The imidazole group on the surface of the ZIF-8 initiates epoxy curing, resulting in covalent bonding between the ZIF-8 crystals and epoxy matrix. A substantial reduction in dielectric constant and increase in tensile modulus were observed. The implication of the present study for utilization of metal-organic framework to improve physical and mechanical properties of polymeric matrixes is discussed.

  1. Allosteric transition: a comparison of two models

    DEFF Research Database (Denmark)

    Bindslev, Niels

    2013-01-01

    Introduction Two recent models are in use for analysis of allosteric drug action at receptor sites remote from orthosteric binding sites. One is an allosteric two-state mechanical model derived in 2000 by David Hall. The other is an extended operational model developed in 2007 by Arthur...... of model both for simulation and analysis of allosteric concentration-responses at equilibrium or steady-state. Conclusions As detailed knowledge of receptors systems becomes available, systems with several pathways and states and/ or more than two binding sites should be analysed by extended forms...

  2. Studies on allosteric phenomena in glycogen phosphorylase b.

    Science.gov (United States)

    Madsen, N B; Avramovic-Zikic, O; Lue, P F; Honikel, K O

    1976-03-26

    This article attempts to trace, from a personal point of view, the history of discoveries of allosteric phenomena in phosphorylase b and the later development of systematic attempts to fit the data into comprehensive theoretical models. Work from our own laboratory is emphasized, but we try to integrate this into the results from other investigators and show their contributions to our ideas and experiments. Finally, some recent unpublished data is presented together with some conclusions and predictions from a new hypothesis. The discoveries by Carl and Gerty Cori of the activation of phosphorylase by AMP, the inhibition of glucose and the enzymatic interconversion of two forms fo the enzyme with different control properties helped lay the foundations of our present understanding of allosteric mechanisms. The later discovery of the oligomeric nature of phosphorylase and its relationship to AMP binding served as a basis for many years of research into the structure-function relationships of phosphorylase and other enzymes. Data showing that AMP lowers the entropy of activation is discussed with respect to the role of the nucleotide and its binding close to the active site. The discovery of the control of phosphorylase b by common metabolites and the impetus this gave to the intensive kinetic studies of the last ten years, wherein fitting to theoretical models has been a common feature, is reviewed.

  3. Supramolecular Allosteric Cofacial Porphyrin Complexes

    International Nuclear Information System (INIS)

    Oliveri, Christopher G.; Gianneschi, Nathan C.; Nguyen, Son Binh T.; Mirkin, Chad A.; Stern, Charlotte L.; Wawrzak, Zdzislaw; Pink, Maren

    2008-01-01

    Nature routinely uses cooperative interactions to regulate cellular activity. For years, chemists have designed synthetic systems that aim toward harnessing the reactivity common to natural biological systems. By learning how to control these interactions in situ, one begins to allow for the preparation of man-made biomimetic systems that can efficiently mimic the interactions found in Nature. To this end, we have designed a synthetic protocol for the preparation of flexible metal-directed supramolecular cofacial porphyrin complexes which are readily obtained in greater than 90% yield through the use of new hemilabile porphyrin ligands with bifunctional ether-phosphine or thioether-phosphine substituents at the 5 and 15 positions on the porphyrin ring. The resulting architectures contain two hemilabile ligand-metal domains (Rh I or Cu I sites) and two cofacially aligned porphyrins (Zn II sites), offering orthogonal functionalities and allowing these multimetallic complexes to exist in two states, 'condensed' or 'open'. Combining the ether-phosphine ligand with the appropriate Rh I or Cu I transition-metal precursors results in 'open' macrocyclic products. In contrast, reacting the thioether-phosphine ligand with RhI or CuI precursors yields condensed structures that can be converted into their 'open' macrocyclic forms via introduction of additional ancillary ligands. The change in cavity size that occurs allows these structures to function as allosteric catalysts for the acyl transfer reaction between X-pyridylcarbinol (where X = 2, 3, or 4) and 1-acetylimidazole. For 3- and 4-pyridylcarbinol, the 'open' macrocycle accelerates the acyl transfer reaction more than the condensed analogue and significantly more than the porphyrin monomer. In contrast, an allosteric effect was not observed for 2-pyridylcarbinol, which is expected to be a weaker binder and is unfavorably constrained inside the macrocyclic cavity.

  4. cobaloxime by imidazoles and amino acids

    Indian Academy of Sciences (India)

    Unknown

    to replicate them in experimental model systems with ... Axial ligation kinetics was monitored .... A trans influence study in propyl (aquo)cobaloxime by imidazoles and amino acids. 307 .... unfilled π* anti-bonding orbitals through dπ–pπ back-.

  5. Extreme Flexibility in a Zeolitic Imidazolate Framework

    DEFF Research Database (Denmark)

    Wharmby, M.T.; Henke, S.; Bennett, T.D.

    2015-01-01

    Desolvated zeolitic imidazolate framework ZIF-4(Zn) undergoes a discontinuous porous to dense phase transition on cooling through 140 K, with a 23% contraction in unit cell volume. The structure of the non-porous, low temperature phase was determined from synchrotron X-ray powder diffraction data...

  6. A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase

    Energy Technology Data Exchange (ETDEWEB)

    Wellington, Samantha; Nag, Partha P.; Michalska, Karolina; Johnston, Stephen E.; Jedrzejczak, Robert P.; Kaushik, Virendar K.; Clatworthy, Anne E.; Siddiqi, Noman; McCarren, Patrick; Bajrami, Besnik; Maltseva, Natalia I.; Combs, Senya; Fisher, Stewart L.; Joachimiak, Andrzej; Schreiber, Stuart L.; Hung, Deborah T.

    2017-07-03

    New antibiotics with novel targets are greatly needed. Bacteria have numerous essential functions, but only a small fraction of such processes—primarily those involved in macromolecular synthesis—are inhibited by current drugs. Targeting metabolic enzymes has been the focus of recent interest, but effective inhibitors have been difficult to identify. We describe a synthetic azetidine derivative, BRD4592, that kills Mycobacterium tuberculosis (Mtb) through allosteric inhibition of tryptophan synthase (TrpAB), a previously untargeted, highly allosterically regulated enzyme. BRD4592 binds at the TrpAB a–b-subunit interface and affects multiple steps in the enzyme’s overall reaction, resulting in inhibition not easily overcome by changes in metabolic environment. We show that TrpAB is required for the survival of Mtb and Mycobacterium marinum in vivo and that this requirement may be independent of an adaptive immune response. This work highlights the effectiveness of allosteric inhibition for targeting proteins that are naturally highly dynamic and that are essential in vivo, despite their apparent dispensability under in vitro conditions, and suggests a framework for the discovery of a next generation of allosteric inhibitors.

  7. Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A

    Energy Technology Data Exchange (ETDEWEB)

    Quinlan, Casey L.; Kaiser, Stephen E.; Bolaños, Ben; Nowlin, Dawn; Grantner, Rita; Karlicek-Bryant, Shannon; Feng, Jun Li; Jenkinson, Stephen; Freeman-Cook, Kevin; Dann, Stephen G.; Wang, Xiaoli; Wells, Peter A.; Fantin, Valeria R.; Stewart, Al E.; Grant, Stephan K. (Pfizer)

    2017-05-29

    S-Adenosyl-L-methionine (SAM) is an enzyme cofactor used in methyl transfer reactions and polyamine biosynthesis. The biosynthesis of SAM from ATP and L-methionine is performed by the methionine adenosyltransferase enzyme family (Mat; EC 2.5.1.6). Human methionine adenosyltransferase 2A (Mat2A), the extrahepatic isoform, is often deregulated in cancer. We identified a Mat2A inhibitor, PF-9366, that binds an allosteric site on Mat2A that overlaps with the binding site for the Mat2A regulator, Mat2B. Studies exploiting PF-9366 suggested a general mode of Mat2A allosteric regulation. Allosteric binding of PF-9366 or Mat2B altered the Mat2A active site, resulting in increased substrate affinity and decreased enzyme turnover. These data support a model whereby Mat2B functions as an inhibitor of Mat2A activity when methionine or SAM levels are high, yet functions as an activator of Mat2A when methionine or SAM levels are low. The ramification of Mat2A activity modulation in cancer cells is also described.

  8. The structure of brain glycogen phosphorylase-from allosteric regulation mechanisms to clinical perspectives.

    Science.gov (United States)

    Mathieu, Cécile; Dupret, Jean-Marie; Rodrigues Lima, Fernando

    2017-02-01

    Glycogen phosphorylase (GP) is the key enzyme that regulates glycogen mobilization in cells. GP is a complex allosteric enzyme that comprises a family of three isozymes: muscle GP (mGP), liver GP (lGP), and brain GP (bGP). Although the three isozymes display high similarity and catalyze the same reaction, they differ in their sensitivity to the allosteric activator adenosine monophosphate (AMP). Moreover, inactivating mutations in mGP and lGP have been known to be associated with glycogen storage diseases (McArdle and Hers disease, respectively). The determination, decades ago, of the structure of mGP and lGP have allowed to better understand the allosteric regulation of these two isoforms and the development of specific inhibitors. Despite its important role in brain glycogen metabolism, the structure of the brain GP had remained elusive. Here, we provide an overview of the human brain GP structure and its relationship with the two other members of this key family of the metabolic enzymes. We also summarize how this structure provides valuable information to understand the regulation of bGP and to design specific ligands of potential pharmacological interest. © 2016 Federation of European Biochemical Societies.

  9. Ras activation by SOS: Allosteric regulation by altered fluctuation dynamics

    Science.gov (United States)

    Iversen, Lars; Tu, Hsiung-Lin; Lin, Wan-Chen; Christensen, Sune M.; Abel, Steven M.; Iwig, Jeff; Wu, Hung-Jen; Gureasko, Jodi; Rhodes, Christopher; Petit, Rebecca S.; Hansen, Scott D.; Thill, Peter; Yu, Cheng-Han; Stamou, Dimitrios; Chakraborty, Arup K.; Kuriyan, John; Groves, Jay T.

    2014-01-01

    Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras–guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average. PMID:24994643

  10. Allosteric small-molecule kinase inhibitors

    DEFF Research Database (Denmark)

    Wu, Peng; Clausen, Mads Hartvig; Nielsen, Thomas E.

    2015-01-01

    current barriers of kinase inhibitors, including poor selectivity and emergence of drug resistance. In spite of the small number of identified allosteric inhibitors in comparison with that of inhibitors targeting the ATP pocket, encouraging results, such as the FDA-approval of the first small...

  11. Allosteric Modulation of Muscarinic Acetylcholine Receptors

    Czech Academy of Sciences Publication Activity Database

    Jakubík, Jan; El-Fakahany, E. E.

    2010-01-01

    Roč. 3, č. 9 (2010), s. 2838-2860 ISSN 1424-8247 R&D Projects: GA ČR GA305/09/0681 Institutional research plan: CEZ:AV0Z50110509 Keywords : muscarinic acetylcholine receptors * allosteric modulation * Alzheimer´s disease Subject RIV: CE - Biochemistry

  12. Alkylation of imidazole under ultrasound irradiation over alkaline carbons

    International Nuclear Information System (INIS)

    Costarrosa, L.; Calvino-Casilda, V.; Ferrera-Escudero, S.; Duran-Valle, C.J.; Martin-Aranda, R.M.

    2006-01-01

    N-Alkyl-imidazole has been synthesized by sonochemical irradiation of imidazole and 1-bromobutane using alkaline-promoted carbons (exchanged with the binary combinations of Na, K and Cs). The catalysts were characterized by X-ray photoelectron spectroscopy, thermal analysis and N 2 adsorption isotherms. Under the experimental conditions, N-alkyl-imidazoles can be prepared with a high activity and selectivity. It is observed that imidazole conversion increases in parallel with increasing the basicity of the catalyst. The influence of the alkaline promoter, the reaction temperature, and the amount of catalyst on the catalytic activity has been studied. For comparison, the alkylation of imidazole has also been performed in a batch reactor system under thermal activation

  13. Imidazole incorporated semicarbazone derivatives as a new class of anticonvulsants: design, synthesis and in-vivo screening.

    Science.gov (United States)

    Amir, Mohammad; Ali, Israr; Hassan, Mohd Zaheen

    2013-06-01

    A series of novel imidazole incorporated semicarbazones was synthesized using an appropriate synthetic route and characterized by spectral analysis (IR, 1H NMR, 13C NMR and Mass). The anticonvulsant activity of the synthesized compounds was determined using doses of 30, 100, and 300 mg kg-1 against maximal electroshock seizure (MES), subcutaneous pentylenetetrazole (scPTZ) induced seizure and minimal neurotoxicity test. Six compounds exhibited protection in both models and 2-(1-(4-chlorophenyl)-2-(1H-imidazol-1-yl)ethylidene)-N-p-tolylsemicarbazone emerged as the most active compound of the series without any neurotoxicity and significant CNS depressant effect. Liver enzyme estimations (SGOT, SGPT, Alkaline phosphatase) of the compound also showed no significant change in the enzymes levels. Moreover, it caused 80% elevation of γ-amino butyric acid (GABA) levels in the whole mice brain, thus indicating that it could be a promising candidate in designing of a potent anticonvulsant drug.

  14. Scalable rule-based modelling of allosteric proteins and biochemical networks.

    Directory of Open Access Journals (Sweden)

    Julien F Ollivier

    2010-11-01

    Full Text Available Much of the complexity of biochemical networks comes from the information-processing abilities of allosteric proteins, be they receptors, ion-channels, signalling molecules or transcription factors. An allosteric protein can be uniquely regulated by each combination of input molecules that it binds. This "regulatory complexity" causes a combinatorial increase in the number of parameters required to fit experimental data as the number of protein interactions increases. It therefore challenges the creation, updating, and re-use of biochemical models. Here, we propose a rule-based modelling framework that exploits the intrinsic modularity of protein structure to address regulatory complexity. Rather than treating proteins as "black boxes", we model their hierarchical structure and, as conformational changes, internal dynamics. By modelling the regulation of allosteric proteins through these conformational changes, we often decrease the number of parameters required to fit data, and so reduce over-fitting and improve the predictive power of a model. Our method is thermodynamically grounded, imposes detailed balance, and also includes molecular cross-talk and the background activity of enzymes. We use our Allosteric Network Compiler to examine how allostery can facilitate macromolecular assembly and how competitive ligands can change the observed cooperativity of an allosteric protein. We also develop a parsimonious model of G protein-coupled receptors that explains functional selectivity and can predict the rank order of potency of agonists acting through a receptor. Our methodology should provide a basis for scalable, modular and executable modelling of biochemical networks in systems and synthetic biology.

  15. A tailored biocatalyst achieved by the rational anchoring of imidazole groups on a natural polymer: furnishing a potential artificial nuclease by sustainable materials engineering.

    Science.gov (United States)

    Ferreira, José G L; Grein-Iankovski, Aline; Oliveira, Marco A S; Simas-Tosin, Fernanda F; Riegel-Vidotti, Izabel C; Orth, Elisa S

    2015-04-11

    Foreseeing the development of artificial enzymes by sustainable materials engineering, we rationally anchored reactive imidazole groups on gum arabic, a natural biocompatible polymer. The tailored biocatalyst GAIMZ demonstrated catalytic activity (>10(5)-fold) in dephosphorylation reactions with recyclable features and was effective in cleaving plasmid DNA, comprising a potential artificial nuclease.

  16. Allosteric control of internal electron transfer in cytochrome cd1 nitrite reductase

    DEFF Research Database (Denmark)

    Farver, Ole; Kroneck, Peter M H; Zumft, Walter G

    2003-01-01

    Cytochrome cd1 nitrite reductase is a bifunctional multiheme enzyme catalyzing the one-electron reduction of nitrite to nitric oxide and the four-electron reduction of dioxygen to water. Kinetics and thermodynamics of the internal electron transfer process in the Pseudomonas stutzeri enzyme have...... been studied and found to be dominated by pronounced interactions between the c and the d1 hemes. The interactions are expressed both in dramatic changes in the internal electron-transfer rates between these sites and in marked cooperativity in their electron affinity. The results constitute a prime...... example of intraprotein control of the electron-transfer rates by allosteric interactions....

  17. Tissue factor activates allosteric networks in factor VIIa through structural and dynamic changes

    DEFF Research Database (Denmark)

    Madsen, Jesper Jonasson; Persson, E.; Olsen, O. H.

    2015-01-01

    that are not likely to be inferred from mutagenesis studies. Furthermore, paths from Met306 to Ile153 (N-terminus) and Trp364, both representing hallmark residues of allostery, are 7% and 37% longer, respectively, in free FVIIa. Thus, there is significantly weaker coupling between the TF contact point and key......Background: Tissue factor (TF) promotes colocalization of enzyme (factorVIIa) and substrate (FX or FIX), and stabilizes the active conformation of FVIIa. Details on how TF induces structural and dynamic changes in the catalytic domain of FVIIa to enhance its efficiency remain elusive. Objective......: To elucidate the activation of allosteric networks in the catalytic domain of the FVIIa protease it is when bound to TF.MethodsLong-timescale molecular dynamics simulations of FVIIa, free and in complex with TF, were executed and analyzed by dynamic network analysis. Results: Allosteric paths of correlated...

  18. Diacylglycerol Acyltransferase 1 Is Regulated by Its N-Terminal Domain in Response to Allosteric Effectors.

    Science.gov (United States)

    Caldo, Kristian Mark P; Acedo, Jeella Z; Panigrahi, Rashmi; Vederas, John C; Weselake, Randall J; Lemieux, M Joanne

    2017-10-01

    Diacylglycerol acyltransferase 1 (DGAT1) is an integral membrane enzyme catalyzing the final and committed step in the acyl-coenzyme A (CoA)-dependent biosynthesis of triacylglycerol (TAG). The biochemical regulation of TAG assembly remains one of the least understood areas of primary metabolism to date. Here, we report that the hydrophilic N-terminal domain of Brassica napus DGAT1 (BnaDGAT1 1-113 ) regulates activity based on acyl-CoA/CoA levels. The N-terminal domain is not necessary for acyltransferase activity and is composed of an intrinsically disordered region and a folded segment. We show that the disordered region has an autoinhibitory function and a dimerization interface, which appears to mediate positive cooperativity, whereas the folded segment of the cytosolic region was found to have an allosteric site for acyl-CoA/CoA. Under increasing acyl-CoA levels, the binding of acyl-CoA with this noncatalytic site facilitates homotropic allosteric activation. Enzyme activation, on the other hand, is prevented under limiting acyl-CoA conditions (low acyl-CoA-to-CoA ratio), whereby CoA acts as a noncompetitive feedback inhibitor through interaction with the same folded segment. The three-dimensional NMR solution structure of the allosteric site revealed an α-helix with a loop connecting a coil fragment. The conserved amino acid residues in the loop interacting with CoA were identified, revealing details of this important regulatory element for allosteric regulation. Based on these results, a model is proposed illustrating the role of the N-terminal domain of BnaDGAT1 as a positive and negative modulator of TAG biosynthesis. © 2017 American Society of Plant Biologists. All Rights Reserved.

  19. Characterization of the allosteric binding pocket of human liver fructose-1,6-bisphosphatase by protein crystallography and inhibitor activity studies.

    Science.gov (United States)

    Iversen, L F; Brzozowski, M; Hastrup, S; Hubbard, R; Kastrup, J S; Larsen, I K; Naerum, L; Nørskov-Lauridsen, L; Rasmussen, P B; Thim, L; Wiberg, F C; Lundgren, K

    1997-05-01

    The structures of three complexes of human fructose-1,6-bisphosphatase (FB) with the allosteric inhibitor AMP and two AMP analogues have been determined and all fully refined. The data used for structure determination were collected at cryogenic temperature (110 K), and with the use of synchrotron radiation. The structures reveal a common mode of binding for AMP and formycine monophosphate (FMP). 5-Amino-4-carboxamido-1 beta-D-5-phosphate-ribofuranosyl-1H-imidazole (AICAR-P) shows an unexpected mode of binding to FB, different from that of the other two ligands. The imidazole ring of AICAR-P is rotated 180 degrees compared to the AMP and FMP bases. This rotation results in a slightly different hydrogen bonding pattern and minor changes in the water structure in the binding pocket. Common features of binding are seen for the ribose and phosphate moieties of all three compounds. Although binding in a different mode, AICAR-P is still capable of making all the important interactions with the residues building the allosteric binding pocket. The IC50 values of AMP, FMP, and AICAR-P were determined to be 1.7, 1.4, and 20.9 microM, respectively. Thus, the approximately 10 times lower potency of AICAR-P is difficult to explain solely from the variations observed in the binding pocket. Only one water molecule in the allosteric binding pocket was found to be conserved in all four subunits in all three structures. This water molecule coordinates to a phosphate oxygen atom and the N7 atom of the AMP molecule, and to similarly situated atoms in the FMP and AICAR-P complexes. This implies an important role of the conserved water molecule in binding of the ligand.

  20. Exploiting protein flexibility to predict the location of allosteric sites

    Directory of Open Access Journals (Sweden)

    Panjkovich Alejandro

    2012-10-01

    Full Text Available Abstract Background Allostery is one of the most powerful and common ways of regulation of protein activity. However, for most allosteric proteins identified to date the mechanistic details of allosteric modulation are not yet well understood. Uncovering common mechanistic patterns underlying allostery would allow not only a better academic understanding of the phenomena, but it would also streamline the design of novel therapeutic solutions. This relatively unexplored therapeutic potential and the putative advantages of allosteric drugs over classical active-site inhibitors fuel the attention allosteric-drug research is receiving at present. A first step to harness the regulatory potential and versatility of allosteric sites, in the context of drug-discovery and design, would be to detect or predict their presence and location. In this article, we describe a simple computational approach, based on the effect allosteric ligands exert on protein flexibility upon binding, to predict the existence and position of allosteric sites on a given protein structure. Results By querying the literature and a recently available database of allosteric sites, we gathered 213 allosteric proteins with structural information that we further filtered into a non-redundant set of 91 proteins. We performed normal-mode analysis and observed significant changes in protein flexibility upon allosteric-ligand binding in 70% of the cases. These results agree with the current view that allosteric mechanisms are in many cases governed by changes in protein dynamics caused by ligand binding. Furthermore, we implemented an approach that achieves 65% positive predictive value in identifying allosteric sites within the set of predicted cavities of a protein (stricter parameters set, 0.22 sensitivity, by combining the current analysis on dynamics with previous results on structural conservation of allosteric sites. We also analyzed four biological examples in detail, revealing

  1. The future of type 1 cannabinoid receptor allosteric ligands.

    Science.gov (United States)

    Alaverdashvili, Mariam; Laprairie, Robert B

    2018-02-01

    Allosteric modulation of the type 1 cannabinoid receptor (CB1R) holds great therapeutic potential. This is because allosteric modulators do not possess intrinsic efficacy, but instead augment (positive allosteric modulation) or diminish (negative allosteric modulation) the receptor's response to endogenous ligand. Consequently, CB1R allosteric modulators have an effect ceiling which allows for the tempering of CB1R signaling without the desensitization, tolerance, dependence, and psychoactivity associated with orthosteric compounds. Pain, movement disorders, epilepsy, obesity are all potential therapeutic targets for CB1R allosteric modulation. Several challenges exist for the development of CB1R allosteric modulators, such as receptor subtype specificity, translation to in vivo systems, and mixed allosteric/agonist/inverse agonist activity. Despite these challenges, elucidation of crystal structures of CB1R and compound design based on structure-activity relationships will advance the field. In this review, we will cover recent progress for CB1R allosteric modulators and discuss the future promise of this research.

  2. Complex-forming capacity of some biologically active imidazoles

    Energy Technology Data Exchange (ETDEWEB)

    Lenarcik, B; Wisniewski, M

    1983-01-01

    By using the potentiometric and spectrophotometric methods, formation of Co(2), Cu(2), Zn(2), Ni(2) and Cd(2) complexes of (3S-cis)-3-ethyl-dihydro-4-((1-methyl-1H-imidazol-5-yl)-methyl)-2(3H)-furanone (pilocarpine, PLC), 4,5-dihydro-2-(phenylmethyl)-1H-imidazole (tolazoline, TLZ), 2-methyl-5-nitro-1H-imidazole-1-ethanol (metronidazole, MET) and 1H-imidazole-4-ethanamine (histamine, HIST) was investigated. The stability constants, ..beta../sub n/, of these complexes were determined. It was shown that the electron-donor strength of the ligands was controlled by the heterocyclic nitrogen atom, and that the formation of the Zn(2)-PLC complex was accompanied by the change in the structure of the coordination sphere of the metal. With Cu(2), the PLC and TLZ ligands were shown to enhance the Jahn-Teller deformation.

  3. Multifunctional switches based on bis-imidazole derivative

    Indian Academy of Sciences (India)

    Administrator

    photonic, chemical, electrochemical, or magnetic stimuli and generate ... that upon oxidation with potassium ferricyanide in ethanolic ... cooled to room temperature and filtered to remove ... Recrystaliztion from ethanol afforded the imidazole 3.

  4. Synthesis of Trisubstituted Imidazoles Using Lewis and Bronsted Acid Catalysts

    OpenAIRE

    Hekmatshoar, Rahim; HEKMATSHOAR, Rahim; JAHANBAKHSHI, Hajar; MOUSAVIZADEH, Farnoosh; RAHNAMAFAR, Reyhane

    2010-01-01

    An efficient and one-pot method for the preparation of trisubstituted imidazoles by condensation of benzil, different aldehydes and ammonium acetate in the presence of  a catalytic amount of NiSO4.7H2O or H3BO3 under different conditions is reported.                    Key Words: Trisubstituted imidazoles, Multi-component &a...

  5. Synthesis of the zeolitic imidazolate framework ZIF-4 from the ionic liquid 1-butyl-3-methylimidazolium imidazolate

    Science.gov (United States)

    Hovestadt, Maximilian; Schwegler, Johannes; Schulz, Peter S.; Hartmann, Martin

    2018-05-01

    A new synthesis route for the zeolitic imidazolate framework ZIF-4 using imidazolium imidazolate is reported. Additionally, the ionic liquid-derived material is compared to conventional ZIF-4 with respect to the powder X-ray diffraction pattern pattern, nitrogen uptake, particle size, and separation potential for olefin/paraffin gas mixtures. Higher synthesis yields were obtained, and the different particle size affected the performance in the separation of ethane and ethylene.

  6. Allosteric modulation of G-protein coupled receptors

    DEFF Research Database (Denmark)

    Jensen, Anders A.; Spalding, Tracy A

    2004-01-01

    are believed to activate (agonists) or inhibit (competitive antagonists) receptor signalling by binding the receptor at the same site as the endogenous agonist, the orthosteric site. In contrast, allosteric ligands modulate receptor function by binding to different regions in the receptor, allosteric sites....... In recent years, combinatorial chemistry and high throughput screening have helped identify several allosteric GPCR modulators with novel structures, several of which already have become valuable pharmacological tools and may be candidates for clinical testing in the near future. This mini review outlines...... the current status and perspectives of allosteric modulation of GPCR function with emphasis on the pharmacology of endogenous and synthesised modulators, their receptor interactions and the therapeutic prospects of allosteric ligands compared to orthosteric ligands....

  7. Development of an experimental activity for teaching cooperativity and allosterism

    Directory of Open Access Journals (Sweden)

    B. Manta

    2006-07-01

    Full Text Available Although  enzyme  control  and  regulation  is  an  important  topic  in  most  Biochemistry  and  Enzymology  courses, laboratory  activities  that  allow  an  experimental  approach  to  cooperativity  and  allosterism  are  difficult  to  implement. The objective of this work was to develop a simple and inexpensive experimental activity to teach this topic in basic courses.  We  decided  to  use  the  enzyme  glucosamine-6-phosphate  deaminase  (GNPD,  E.C.  3.5.99.6  from Escherichia coli,  that  is  both  kinetically  and  structurally  well-known.  GNPD  is  an  allosteric  enzyme,  activated  by  N-acetylglucosamine 6-phosphate, that catalyzes the conversion of glucosamine 6-phosphate into fructose 6-phosphate and  ammonia.  The  enzyme  is  a  typical  allosteric  K-system  and  can  be  well  described  by  the  Monod-Wyman-Changeux  (MWC  model.  GNPD  was  partially  purified  through  anionic-exchange  chromatography  from  a  mutant E.coli strain  which  expresses  constitutively  high  levels  of the  enzyme.  In  order  to  measure  activity  we  used  an end point  method  which  consists  in  stopping  the  reaction  at  a  certain  time  point  with  HCl  10  N,  and  quantifying  the fructose-6-phosphate  formed  with  resorcinol  (Selliwanoff  reaction  through  the  formation  of  a  red  color  that  is measured  spectrophotometrically.  We  developed  a  protocol  that  consisted  in  a  4-hour  experiment  in  which  the students  measured  the  activity  of  the  GNPD  with  increasing  concentrations  of  the  substrate,  in  the  presence  or absence  of  allosteric  modulator.  The  students  obtained  a  good  quality  data  set  that  they  analyzed  based  on  the equations  of  Hill,  MWC  and  Acerenza-Mirzaji

  8. A large-scale allosteric transition in cytochrome P450 3A4 revealed by luminescence resonance energy transfer (LRET.

    Directory of Open Access Journals (Sweden)

    Elena V Sineva

    Full Text Available Effector-induced allosteric transitions in cytochrome P450 3A4 (CYP3A4 were investigated by luminescence resonance energy transfer (LRET between two SH-reactive probes attached to various pairs of distantly located cysteine residues, namely the double-cysteine mutants CYP3A4(C64/C468, CYP3A4(C377/C468 and CYP3A4(C64/C121. Successive equimolar labeling of these proteins with the phosphorescent probe erythrosine iodoacetamide (donor and the near-infrared fluorophore DY-731 maleimide (acceptor allowed us to establish donor/acceptor pairs sensitive to conformational motions. The interactions of all three double-labeled mutants with the allosteric activators α-naphthoflavone and testosterone resulted in an increase in the distance between the probes. A similar effect was elicited by cholesterol. These changes in distance vary from 1.3 to 8.5 Å, depending on the position of the donor/acceptor pair and the nature of the effector. In contrast, the changes in the interprobe distance caused by such substrates as bromocriptine or 1-pyrenebutanol were only marginal. Our results provide a decisive support to the paradigm of allosteric modulation of CYP3A4 and indicate that the conformational transition caused by allosteric effectors increases the spatial separation between the beta-domain of the enzyme (bearing residues Cys64 and Cys377 and the alpha-domain, where Cys121 and Cys468 are located.

  9. Imidazole as a parent π-conjugated backbone in charge-transfer chromophores

    Directory of Open Access Journals (Sweden)

    Jiří Kulhánek

    2012-01-01

    Full Text Available Research activities in the field of imidazole-derived push–pull systems featuring intramolecular charge transfer (ICT are reviewed. Design, synthetic pathways, linear and nonlinear optical properties, electrochemistry, structure–property relationships, and the prospective application of such D-π-A organic materials are described. This review focuses on Y-shaped imidazoles, bi- and diimidazoles, benzimidazoles, bis(benzimidazoles, imidazole-4,5-dicarbonitriles, and imidazole-derived chromophores chemically bound to a polymer chain.

  10. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.

    Science.gov (United States)

    Wagner, Jeffrey R; Lee, Christopher T; Durrant, Jacob D; Malmstrom, Robert D; Feher, Victoria A; Amaro, Rommie E

    2016-06-08

    Allosteric drug development holds promise for delivering medicines that are more selective and less toxic than those that target orthosteric sites. To date, the discovery of allosteric binding sites and lead compounds has been mostly serendipitous, achieved through high-throughput screening. Over the past decade, structural data has become more readily available for larger protein systems and more membrane protein classes (e.g., GPCRs and ion channels), which are common allosteric drug targets. In parallel, improved simulation methods now provide better atomistic understanding of the protein dynamics and cooperative motions that are critical to allosteric mechanisms. As a result of these advances, the field of predictive allosteric drug development is now on the cusp of a new era of rational structure-based computational methods. Here, we review algorithms that predict allosteric sites based on sequence data and molecular dynamics simulations, describe tools that assess the druggability of these pockets, and discuss how Markov state models and topology analyses provide insight into the relationship between protein dynamics and allosteric drug binding. In each section, we first provide an overview of the various method classes before describing relevant algorithms and software packages.

  11. A Non-Competitive Inhibitor of VCP/p97 and VPS4 Reveals Conserved Allosteric Circuits in Type I and II AAA ATPases.

    Science.gov (United States)

    Pöhler, Robert; Krahn, Jan H; van den Boom, Johannes; Dobrynin, Grzegorz; Kaschani, Farnusch; Eggenweiler, Hans-Michael; Zenke, Frank T; Kaiser, Markus; Meyer, Hemmo

    2018-02-05

    AAA ATPases have pivotal functions in diverse cellular processes essential for survival and proliferation. Revealing strategies for chemical inhibition of this class of enzymes is therefore of great interest for the development of novel chemotherapies or chemical tools. Here, we characterize the compound MSC1094308 as a reversible, allosteric inhibitor of the type II AAA ATPase human ubiquitin-directed unfoldase (VCP)/p97 and the type I AAA ATPase VPS4B. Subsequent proteomic, genetic and biochemical studies indicate that MSC1094308 binds to a previously characterized drugable hotspot of p97, thereby inhibiting the D2 ATPase activity. Our results furthermore indicate that a similar allosteric site exists in VPS4B, suggesting conserved allosteric circuits and drugable sites in both type I and II AAA ATPases. Our results may thus guide future chemical tool and drug discovery efforts for the biomedically relevant AAA ATPases. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. The allosteric site regulates the voltage sensitivity of muscarinic receptors.

    Science.gov (United States)

    Hoppe, Anika; Marti-Solano, Maria; Drabek, Matthäus; Bünemann, Moritz; Kolb, Peter; Rinne, Andreas

    2018-01-01

    Muscarinic receptors (M-Rs) for acetylcholine (ACh) belong to the class A of G protein-coupled receptors. M-Rs are activated by orthosteric agonists that bind to a specific site buried in the M-R transmembrane helix bundle. In the active conformation, receptor function can be modulated either by allosteric modulators, which bind to the extracellular receptor surface or by the membrane potential via an unknown mechanism. Here, we compared the modulation of M 1 -Rs and M 3 -Rs induced by changes in voltage to their allosteric modulation by chemical compounds. We quantified changes in receptor signaling in single HEK 293 cells with a FRET biosensor for the G q protein cycle. In the presence of ACh, M 1 -R signaling was potentiated by voltage, similarly to positive allosteric modulation by benzyl quinolone carboxylic acid. Conversely, signaling of M 3 -R was attenuated by voltage or the negative allosteric modulator gallamine. Because the orthosteric site is highly conserved among M-Rs, but allosteric sites vary, we constructed "allosteric site" M 3 /M 1 -R chimeras and analyzed their voltage dependencies. Exchanging the entire allosteric sites eliminated the voltage sensitivity of ACh responses for both receptors, but did not affect their modulation by allosteric compounds. Furthermore, a point mutation in M 3 -Rs caused functional uncoupling of the allosteric and orthosteric sites and abolished voltage dependence. Molecular dynamics simulations of the receptor variants indicated a subtype-specific crosstalk between both sites, involving the conserved tyrosine lid structure of the orthosteric site. This molecular crosstalk leads to receptor subtype-specific voltage effects. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Synthesis, characterization and metal coordination of a potential β-lactamase inhibitor: 5-Methyl-2-phenoxymethyl-3-H-imidazole-4-carboxylic acid (PIMA

    Directory of Open Access Journals (Sweden)

    Chiara Romagnoli

    2017-12-01

    Full Text Available Among relevant metal ions in biological systems, zinc and iron play a key role as active partners of the catalytic machinery. In particular, the inhibition of metal enzymes that are involved in physiological and pathological processes has been deeply investigated for the rational design of selective and efficient drugs based on chelators. Since imidazole histidine residue is one of the most versatile sites in proteins, especially in enzymes acting in the presence of metal ions as cofactors, in this work the synthesis and characterization of a new imidazole derivative, namely 5-methyl-2-phenoxymethyl-3-H-imidazole-4-carboxylic acid (PIMA is reported. PIMA was designed as metallo-β-lactamase inhibitor thanks to its similarity with penicillin V, a β-lactam antibiotic inactivated by metallo-β-lactamase, for which there are no commercially available inhibitors. The evaluation of PIMA coordinating ability toward iron, zinc, and gallium, these latter selected as a non-paramagnetic probe for iron, is performed by theoretical DFT calculations and in solution by experimental techniques, i.e. potentiometry, UV–vis and NMR spectroscopy. PIMA exhibits an efficient metal chelating ability; the prevailing species in physiological condition are ML3 for Fe3+ and Ga3+ and ML2 for Zn2+, in which chelation is due to deprotonated carboxylic oxygen and imidazole nitrogen in the N,O donor set. The demonstrated ability of PIMA to chelate zinc ion, combined with its structure similarity with penicillin V, supports further exploration of this imidazole-4-carboxylate as metallo-β-lactamase inhibitor.

  14. The tertiary origin of the allosteric activation of E. coli glucosamine-6-phosphate deaminase studied by sol-gel nanoencapsulation of its T conformer.

    Directory of Open Access Journals (Sweden)

    Sergio Zonszein

    Full Text Available The role of tertiary conformational changes associated to ligand binding was explored using the allosteric enzyme glucosamine-6-phosphate (GlcN6P deaminase from Escherichia coli (EcGNPDA as an experimental model. This is an enzyme of amino sugar catabolism that deaminates GlcN6P, giving fructose 6-phosphate and ammonia, and is allosterically activated by N-acetylglucosamine 6-phosphate (GlcNAc6P. We resorted to the nanoencapsulation of this enzyme in wet silica sol-gels for studying the role of intrasubunit local mobility in its allosteric activation under the suppression of quaternary transition. The gel-trapped enzyme lost its characteristic homotropic cooperativity while keeping its catalytic properties and the allosteric activation by GlcNAc6P. The nanoencapsulation keeps the enzyme in the T quaternary conformation, making possible the study of its allosteric activation under a condition that is not possible to attain in a soluble phase. The involved local transition was slowed down by nanoencapsulation, thus easing the fluorometric analysis of its relaxation kinetics, which revealed an induced-fit mechanism. The absence of cooperativity produced allosterically activated transitory states displaying velocity against substrate concentration curves with apparent negative cooperativity, due to the simultaneous presence of subunits with different substrate affinities. Reaction kinetics experiments performed at different tertiary conformational relaxation times also reveal the sequential nature of the allosteric activation. We assumed as a minimal model the existence of two tertiary states, t and r, of low and high affinity, respectively, for the substrate and the activator. By fitting the velocity-substrate curves as a linear combination of two hyperbolic functions with Kt and Kr as KM values, we obtained comparable values to those reported for the quaternary conformers in solution fitted to MWC model. These results are discussed in the

  15. Coordination compounds of metals with imidazoles and benzimidazoles

    International Nuclear Information System (INIS)

    Novikova, G.A.; Molodkin, A.K.; Kukalenko, S.S.

    1988-01-01

    Methods of preparation, composition and structure of UO 2 2+ , Th 4+ , Mo 3+ , Cd 2+ , Ln 3+ metal ion complexes with imidazoles and benzimidazoles are considered in reviews of native and foreign literature of up to 1985. Complexes are customarily prepared by direct interaction of ligands with inorganic salts in different organic solvents. Complex composition is defined by the nature of complexing metal and inorganic salt anion, ligand volume and basicity, as well as solvent characteristics. Effect of R substituent in imidazole and benzimidazole side chain on composition of coordination compounds is considered

  16. GABAA receptor: Positive and negative allosteric modulators.

    Science.gov (United States)

    Olsen, Richard W

    2018-01-31

    gamma-Aminobutyric acid (GABA)-mediated inhibitory neurotransmission and the gene products involved were discovered during the mid-twentieth century. Historically, myriad existing nervous system drugs act as positive and negative allosteric modulators of these proteins, making GABA a major component of modern neuropharmacology, and suggesting that many potential drugs will be found that share these targets. Although some of these drugs act on proteins involved in synthesis, degradation, and membrane transport of GABA, the GABA receptors Type A (GABA A R) and Type B (GABA B R) are the targets of the great majority of GABAergic drugs. This discovery is due in no small part to Professor Norman Bowery. Whereas the topic of GABA B R is appropriately emphasized in this special issue, Norman Bowery also made many insights into GABA A R pharmacology, the topic of this article. GABA A R are members of the ligand-gated ion channel receptor superfamily, a chloride channel family of a dozen or more heteropentameric subtypes containing 19 possible different subunits. These subtypes show different brain regional and subcellular localization, age-dependent expression, and potential for plastic changes with experience including drug exposure. Not only are GABA A R the targets of agonist depressants and antagonist convulsants, but most GABA A R drugs act at other (allosteric) binding sites on the GABA A R proteins. Some anxiolytic and sedative drugs, like benzodiazepine and related drugs, act on GABA A R subtype-dependent extracellular domain sites. General anesthetics including alcohols and neurosteroids act at GABA A R subunit-interface trans-membrane sites. Ethanol at high anesthetic doses acts on GABA A R subtype-dependent trans-membrane domain sites. Ethanol at low intoxicating doses acts at GABA A R subtype-dependent extracellular domain sites. Thus GABA A R subtypes possess pharmacologically specific receptor binding sites for a large group of different chemical classes of

  17. Defining the Structural Basis for Allosteric Product Release from E. coli Dihydrofolate Reductase Using NMR Relaxation Dispersion.

    Science.gov (United States)

    Oyen, David; Fenwick, R Bryn; Aoto, Phillip C; Stanfield, Robyn L; Wilson, Ian A; Dyson, H Jane; Wright, Peter E

    2017-08-16

    The rate-determining step in the catalytic cycle of E. coli dihydrofolate reductase is tetrahydrofolate (THF) product release, which can occur via an allosteric or an intrinsic pathway. The allosteric pathway, which becomes accessible when the reduced cofactor NADPH is bound, involves transient sampling of a higher energy conformational state, greatly increasing the product dissociation rate as compared to the intrinsic pathway that obtains when NADPH is absent. Although the kinetics of this process are known, the enzyme structure and the THF product conformation in the transiently formed excited state remain elusive. Here, we use side-chain proton NMR relaxation dispersion measurements, X-ray crystallography, and structure-based chemical shift predictions to explore the structural basis of allosteric product release. In the excited state of the E:THF:NADPH product release complex, the reduced nicotinamide ring of the cofactor transiently enters the active site where it displaces the pterin ring of the THF product. The p-aminobenzoyl-l-glutamate tail of THF remains weakly bound in a widened binding cleft. Thus, through transient entry of the nicotinamide ring into the active site, the NADPH cofactor remodels the enzyme structure and the conformation of the THF to form a weakly populated excited state that is poised for rapid product release.

  18. An evolution-based strategy for engineering allosteric regulation

    Science.gov (United States)

    Pincus, David; Resnekov, Orna; Reynolds, Kimberly A.

    2017-04-01

    Allosteric regulation provides a way to control protein activity at the time scale of milliseconds to seconds inside the cell. An ability to engineer synthetic allosteric systems would be of practical utility for the development of novel biosensors, creation of synthetic cell signaling pathways, and design of small molecule pharmaceuticals with regulatory impact. To this end, we outline a general approach—termed rational engineering of allostery at conserved hotspots (REACH)—to introduce novel regulation into a protein of interest by exploiting latent allostery that has been hard-wired by evolution into its structure. REACH entails the use of statistical coupling analysis (SCA) to identify ‘allosteric hotspots’ on protein surfaces, the development and implementation of experimental assays to test hotspots for functionality, and a toolkit of allosteric modulators to impinge on endogenous cellular circuitry. REACH can be broadly applied to rewire cellular processes to respond to novel inputs.

  19. A thermodynamic and theoretical view for enzyme regulation.

    Science.gov (United States)

    Zhao, Qinyi

    2015-01-01

    Precise regulation is fundamental to the proper functioning of enzymes in a cell. Current opinions about this, such as allosteric regulation and dynamic contribution to enzyme regulation, are experimental models and substantially empirical. Here we proposed a theoretical and thermodynamic model of enzyme regulation. The main idea is that enzyme regulation is processed via the regulation of abundance of active conformation in the reaction buffer. The theoretical foundation, experimental evidence, and experimental criteria to test our model are discussed and reviewed. We conclude that basic principles of enzyme regulation are laws of protein thermodynamics and it can be analyzed using the concept of distribution curve of active conformations of enzymes.

  20. Intrasteric control of AMPK via the gamma1 subunit AMP allosteric regulatory site.

    Science.gov (United States)

    Adams, Julian; Chen, Zhi-Ping; Van Denderen, Bryce J W; Morton, Craig J; Parker, Michael W; Witters, Lee A; Stapleton, David; Kemp, Bruce E

    2004-01-01

    AMP-activated protein kinase (AMPK) is a alphabetagamma heterotrimer that is activated in response to both hormones and intracellular metabolic stress signals. AMPK is regulated by phosphorylation on the alpha subunit and by AMP allosteric control previously thought to be mediated by both alpha and gamma subunits. Here we present evidence that adjacent gamma subunit pairs of CBS repeat sequences (after Cystathionine Beta Synthase) form an AMP binding site related to, but distinct from the classical AMP binding site in phosphorylase, that can also bind ATP. The AMP binding site of the gamma(1) CBS1/CBS2 pair, modeled on the structures of the CBS sequences present in the inosine monophosphate dehydrogenase crystal structure, contains three arginine residues 70, 152, and 171 and His151. The yeast gamma homolog, snf4 contains a His151Gly substitution, and when this is introduced into gamma(1), AMP allosteric control is substantially lost and explains why the yeast snf1p/snf4p complex is insensitive to AMP. Arg70 in gamma(1) corresponds to the site of mutation in human gamma(2) and pig gamma(3) genes previously identified to cause an unusual cardiac phenotype and glycogen storage disease, respectively. Mutation of any of AMP binding site Arg residues to Gln substantially abolishes AMP allosteric control in expressed AMPK holoenzyme. The Arg/Gln mutations also suppress the previously described inhibitory properties of ATP and render the enzyme constitutively active. We propose that ATP acts as an intrasteric inhibitor by bridging the alpha and gamma subunits and that AMP functions to derepress AMPK activity.

  1. Model studies of the Cu(B) site of cytochrome c oxidase utilizing a Zn(II) complex containing an imidazole-phenol cross-linked ligand.

    Science.gov (United States)

    Pesavento, Russell P; Pratt, Derek A; Jeffers, Jerry; van der Donk, Wilfred A

    2006-07-21

    Cytochrome c oxidase, the enzyme complex responsible for the four-electron reduction of O2 to H2O, contains an unusual histidine-tyrosine cross-link in its bimetallic heme a3-CuB active site. We have synthesised an unhindered, tripodal chelating ligand, BPAIP, containing the unusual ortho-imidazole-phenol linkage, which mimics the coordination environment of the CuB center. The ligand was used to investigate the physicochemical (pKa, oxidation potential) and coordination properties of the imidazole-phenol linkage when bound to a dication. Zn(II) coordination lowers the pKa of the phenol by 0.6 log units, and increases the potential of the phenolate/phenoxyl radical couple by approximately 50 mV. These results are consistent with inductive withdrawal of electron density from the phenolic ring. Spectroscopic data and theoretical calculations (DFT) were used to establish that the cationic complex [Zn(BPAIP)Br]+ has an axially distorted trigonal bipyramidal structure, with three coordinating nitrogen ligands (two pyridine and one imidazole) occupying the equatorial plane and the bromide and the tertiary amine nitrogen of the tripod in the axial positions. Interestingly, the Zn-Namine bonding interaction is weak or absent in [Zn(BPAIP)Br]+ and the complex gains stability in basic solutions, as indicated by 1H NMR spectroscopy. These observations are supported by theoretical calculations (DFT), which suggest that the electron-donating capacity of the equatorial imidazole ligand can be varied by modulation of the protonation and/or redox state of the cross-linked phenol. Deprotonation of the phenol makes the equatorial imidazole a stronger sigma-donor, resulting in an increased Zn-Nimd interaction and thereby leading to distortion of the axial ligand axis toward a more tetrahedral geometry.

  2. Covalent Allosteric Inactivation of Protein Tyrosine Phosphatase 1B (PTP1B) by an Inhibitor-Electrophile Conjugate.

    Science.gov (United States)

    Punthasee, Puminan; Laciak, Adrian R; Cummings, Andrea H; Ruddraraju, Kasi Viswanatharaju; Lewis, Sarah M; Hillebrand, Roman; Singh, Harkewal; Tanner, John J; Gates, Kent S

    2017-04-11

    Protein tyrosine phosphatase 1B (PTP1B) is a validated drug target, but it has proven difficult to develop medicinally useful, reversible inhibitors of this enzyme. Here we explored covalent strategies for the inactivation of PTP1B using a conjugate composed of an active site-directed 5-aryl-1,2,5-thiadiazolidin-3-one 1,1-dioxide inhibitor connected via a short linker to an electrophilic α-bromoacetamide moiety. Inhibitor-electrophile conjugate 5a caused time-dependent loss of PTP1B activity consistent with a covalent inactivation mechanism. The inactivation occurred with a second-order rate constant of (1.7 ± 0.3) × 10 2 M -1 min -1 . Mass spectrometric analysis of the inactivated enzyme indicated that the primary site of modification was C121, a residue distant from the active site. Previous work provided evidence that covalent modification of the allosteric residue C121 can cause inactivation of PTP1B [Hansen, S. K., Cancilla, M. T., Shiau, T. P., Kung, J., Chen, T., and Erlanson, D. A. (2005) Biochemistry 44, 7704-7712]. Overall, our results are consistent with an unusual enzyme inactivation process in which noncovalent binding of the inhibitor-electrophile conjugate to the active site of PTP1B protects the nucleophilic catalytic C215 residue from covalent modification, thus allowing inactivation of the enzyme via selective modification of allosteric residue C121.

  3. Allosteric regulation of rhomboid intramembrane proteolysis.

    Science.gov (United States)

    Arutyunova, Elena; Panwar, Pankaj; Skiba, Pauline M; Gale, Nicola; Mak, Michelle W; Lemieux, M Joanne

    2014-09-01

    Proteolysis within the lipid bilayer is poorly understood, in particular the regulation of substrate cleavage. Rhomboids are a family of ubiquitous intramembrane serine proteases that harbour a buried active site and are known to cleave transmembrane substrates with broad specificity. In vitro gel and Förster resonance energy transfer (FRET)-based kinetic assays were developed to analyse cleavage of the transmembrane substrate psTatA (TatA from Providencia stuartii). We demonstrate significant differences in catalytic efficiency (kcat/K0.5) values for transmembrane substrate psTatA (TatA from Providencia stuartii) cleavage for three rhomboids: AarA from P. stuartii, ecGlpG from Escherichia coli and hiGlpG from Haemophilus influenzae demonstrating that rhomboids specifically recognize this substrate. Furthermore, binding of psTatA occurs with positive cooperativity. Competitive binding studies reveal an exosite-mediated mode of substrate binding, indicating allostery plays a role in substrate catalysis. We reveal that exosite formation is dependent on the oligomeric state of rhomboids, and when dimers are dissociated, allosteric substrate activation is not observed. We present a novel mechanism for specific substrate cleavage involving several dynamic processes including positive cooperativity and homotropic allostery for this interesting class of intramembrane proteases. © 2014 The Authors.

  4. Notes on stochastic (bio)-logic gates: computing with allosteric cooperativity.

    Science.gov (United States)

    Agliari, Elena; Altavilla, Matteo; Barra, Adriano; Dello Schiavo, Lorenzo; Katz, Evgeny

    2015-05-15

    Recent experimental breakthroughs have finally allowed to implement in-vitro reaction kinetics (the so called enzyme based logic) which code for two-inputs logic gates and mimic the stochastic AND (and NAND) as well as the stochastic OR (and NOR). This accomplishment, together with the already-known single-input gates (performing as YES and NOT), provides a logic base and paves the way to the development of powerful biotechnological devices. However, as biochemical systems are always affected by the presence of noise (e.g. thermal), standard logic is not the correct theoretical reference framework, rather we show that statistical mechanics can work for this scope: here we formulate a complete statistical mechanical description of the Monod-Wyman-Changeaux allosteric model for both single and double ligand systems, with the purpose of exploring their practical capabilities to express noisy logical operators and/or perform stochastic logical operations. Mixing statistical mechanics with logics, and testing quantitatively the resulting findings on the available biochemical data, we successfully revise the concept of cooperativity (and anti-cooperativity) for allosteric systems, with particular emphasis on its computational capabilities, the related ranges and scaling of the involved parameters and its differences with classical cooperativity (and anti-cooperativity).

  5. SigrafW: An Easy-to-Use Program for Fitting Enzyme Kinetic Data

    Science.gov (United States)

    Leone, Francisco Assis; Baranauskas, Jose Augusto; Furriel, Rosa Prazeres Melo; Borin, Ivana Aparecida

    2005-01-01

    SigrafW is Windows-compatible software developed using the Microsoft[R] Visual Basic Studio program that uses the simplified Hill equation for fitting kinetic data from allosteric and Michaelian enzymes. SigrafW uses a modified Fibonacci search to calculate maximal velocity (V), the Hill coefficient (n), and the enzyme-substrate apparent…

  6. Spectroscopic investigation of Bovine Liver Catalase interactions with a novel phen-imidazole derivative of platinum.

    Science.gov (United States)

    Ghobadi, Roohollah; Divsalar, Adeleh; Harifi-Mood, Ali Reza; Saboury, Ali Akbar

    2018-02-01

    Successful clinical experience of using cisplatin and its derivatives in cancer therapy has encouraged scientists to synthesize new metal complexes with the aim of interacting with special targets such as proteins In this regard, biological effects of [Pt(FIP)(Phen)](NO 3 ) 2 compound which contains a novel phen-imidazole ligand, FIP, was investigated on bovine liver catalase (BLC) structure and function. Various spectroscopic methods such as UV-visible, fluorescence, and circular dichroism (CD) were applied at two temperatures 25 and 37°C for kinetics and structural studies. As a consequence, the enzymatic activity decreased slightly with increasing the platinum compound's concentration up to 30 μM and then remained constant at near 80% after this concentration. On the other hand, the fluorescence quenching measurements revealed that despite slight changes in activity, catalase experiences notable alterations in three-dimensional environment around the chromophores of the enzyme structure with increasing platinum complex concentration. Moreover, quenching data showed that BLC has two binding sites for Pt complex and hydrogen bonding interactions play a major role in the binding process. Furthermore, CD spectroscopy data showed that Pt(II) complex induces significant decrease in α-helix content of the secondary structure of BLC, but notable increase in random coil proportion accompanying a slight decrease in β-sheet content. All in all, hydrogen bonding interactions which are mainly involved in the binding process of the novel phen-imidazole compound to BLC significantly alter the protein structure but slightly change its function. This might be a promising outcome for chemotherapists and medicinal chemists to investigate in vivo properties of this novel metal complex with significant binding tendency to a macromolecule in the low concentrations without decreasing its intrinsic function.

  7. Evolution of glycaemia in the blood of mice in the presence or absence of imidazole

    International Nuclear Information System (INIS)

    Polverelli, M.; Teoule, R.

    1969-01-01

    With respect to the radioprotective properties of the heterocyclic compound, imidazole, the authors followed the action of this product on blood sugar levels of mice X irradiated with a lethal dose. The main results of this work are: probably a hypo-glycemic action of the imidazole; an abolishment of the post-irradiation hyperglycemia by imidazole; an appreciably difference between male and female towards irradiation. (author) [fr

  8. Characterization and Solubilization of Pyrrole–Imidazole Polyamide Aggregates

    OpenAIRE

    Hargrove, Amanda E.; Raskatov, Jevgenij A.; Meier, Jordan L.; Montgomery, David C.; Dervan, Peter B.

    2012-01-01

    To optimize the biological activity of pyrrole–imidazole polyamide DNA-binding molecules, we characterized the aggregation propensity of these compounds through dynamic light scattering and fractional solubility analysis. Nearly all studied polyamides were found to form measurable particles 50–500 nm in size under biologically relevant conditions, while HPLC-based analyses revealed solubility trends in both core sequences and peripheral substituents that did not correlate with overall ionic c...

  9. Photoinduced Processes in Hydrogen Bonded System: Photodissociation of Imidazole Clusters

    Czech Academy of Sciences Publication Activity Database

    Poterya, Viktoriya; Profant, V.; Fárník, Michal; Šištík, L.; Slavíček, P.; Buck, U.

    2009-01-01

    Roč. 113, č. 52 (2009), s. 14583-14590 ISSN 1089-5639 R&D Projects: GA AV ČR KAN400400651; GA AV ČR KJB400400902; GA ČR GA203/09/0422 Institutional research plan: CEZ:AV0Z40400503 Keywords : scattering analysis * molecules * imidazole clusters Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.899, year: 2009

  10. Alcohol and water adsorption in zeolitic imidazolate frameworks

    KAUST Repository

    Zhang, Ke; Lively, Ryan P.; Dose, Michelle E.; Brown, Andrew J.; Zhang, Chen; Chung, Jaeyub; Nair, Sankar; Koros, William J.; Chance, Ronald R.

    2013-01-01

    Alcohol (methanol, ethanol, 1-propanol, 2-propanol and 1-butanol) and water vapor adsorption in zeolitic imidazolate frameworks (ZIF-8, ZIF-71 and ZIF-90) with similar crystal sizes was systematically studied. The feasibility of applying these ZIF materials to the recovery of bio-alcohols is evaluated by estimating the vapor-phase alcohol-water sorption selectivity. © 2013 The Royal Society of Chemistry.

  11. Synthesis and Antibacterial Activities of New Metronidazole and Imidazole Derivatives

    Directory of Open Access Journals (Sweden)

    Abdul Jabar Kh. Atia

    2009-07-01

    Full Text Available New imidazole ring derivatives comprising 1,3-oxazoline, Schiff's bases, thiadiazole, oxadiazole and 1,2,4-triazole moieties are reported. 3-Aminobiimidazol-4-one compounds 7a-c were synthesized by the reaction of compounds 6a-c with hydrazine hydrate. Biimidazole esters 9a-c were converted into biimidazole hydrazide esters 10a-c. Compounds 7a-c and 10a-c were converted into a variety of derivatives.

  12. Thermodynamic study of phase transitions of imidazoles and 1-methylimidazoles

    International Nuclear Information System (INIS)

    Almeida, Ana R.R.P.; Monte, Manuel J.S.

    2012-01-01

    Highlights: → Sublimation vapor pressures of imidazole, N-methylimidazole and four derivatives were measured. → Liquid vapor pressures were also measured for four of the compounds studied. → Vapor pressure results enabled determination of sublimation, vaporization, and fusion enthalpy. → From enthalpies of sublimation, enthalpies of intermolecular N-H...N bonds were estimated. - Abstract: The vapor pressures of imidazole, N-methylimidazole and of their dichloro and dicyano substituted compounds were measured at different temperatures, in the crystalline phase for two of them, and in crystalline and liquid phases for the other four. From these measurements, enthalpies and standard entropies of sublimation and vaporization were derived. The results allowed the determination of the triple points (p, T) coordinates of the four compounds studied in both condensed phases as well as the calculation of their enthalpy of fusion. Enthalpies and temperatures of fusion were also determined using d.s.c. The experimental results enabled the estimation of the enthalpy of the intermolecular N-H...N bonds in the imidazoles studied.

  13. Imidazole and Triazole Coordination Chemistry for Antifouling Coatings

    Directory of Open Access Journals (Sweden)

    Markus Andersson Trojer

    2013-01-01

    Full Text Available Fouling of marine organisms on the hulls of ships is a severe problem for the shipping industry. Many antifouling agents are based on five-membered nitrogen heterocyclic compounds, in particular imidazoles and triazoles. Moreover, imidazole and triazoles are strong ligands for Cu2+ and Cu+, which are both potent antifouling agents. In this review, we summarize a decade of work within our groups concerning imidazole and triazole coordination chemistry for antifouling applications with a particular focus on the very potent antifouling agent medetomidine. The entry starts by providing a detailed theoretical description of the azole-metal coordination chemistry. Some attention will be given to ways to functionalize polymers with azole ligands. Then, the effect of metal coordination in azole-containing polymers with respect to material properties will be discussed. Our work concerning the controlled release of antifouling agents, in particular medetomidine, using azole coordination chemistry will be reviewed. Finally, an outlook will be given describing the potential for tailoring the azole ligand chemistry in polymers with respect to Cu2+ adsorption and Cu2+→Cu+ reduction for antifouling coatings without added biocides.

  14. Thermodynamic study of phase transitions of imidazoles and 1-methylimidazoles

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Ana R.R.P., E-mail: ana.figueira@fc.up.pt [Centro de Investigacao em Quimica, Departamento de Quimica e Bioquimica, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto (Portugal); Monte, Manuel J.S., E-mail: mjmonte@fc.up.pt [Centro de Investigacao em Quimica, Departamento de Quimica e Bioquimica, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto (Portugal)

    2012-01-15

    Highlights: > Sublimation vapor pressures of imidazole, N-methylimidazole and four derivatives were measured. > Liquid vapor pressures were also measured for four of the compounds studied. > Vapor pressure results enabled determination of sublimation, vaporization, and fusion enthalpy. > From enthalpies of sublimation, enthalpies of intermolecular N-H...N bonds were estimated. - Abstract: The vapor pressures of imidazole, N-methylimidazole and of their dichloro and dicyano substituted compounds were measured at different temperatures, in the crystalline phase for two of them, and in crystalline and liquid phases for the other four. From these measurements, enthalpies and standard entropies of sublimation and vaporization were derived. The results allowed the determination of the triple points (p, T) coordinates of the four compounds studied in both condensed phases as well as the calculation of their enthalpy of fusion. Enthalpies and temperatures of fusion were also determined using d.s.c. The experimental results enabled the estimation of the enthalpy of the intermolecular N-H...N bonds in the imidazoles studied.

  15. On the mechanism of action of ribonucleases: dinucleotide cleavage catalyzed by imidazole and Zn2+.

    OpenAIRE

    Breslow, R; Huang, D L; Anslyn, E

    1989-01-01

    Cyclization/cleavage of the 2-(p-nitrophenyl) phosphate ester of propylene glycol is catalyzed by imidazole and, much more effectively, by Zn2+ with imidazole. In the latter case, the mechanism involves simultaneous Lewis acid/base catalysis. Similar Zn2+ and imidazole catalysis of cyclization/cleavage is seen with the dinucleotide 3',5'-UpU (uridylyluridine). Again, the zinc system is much more effective than is catalysis by imidazole alone, and in this case simultaneous Lewis acid/base cata...

  16. Imidazole, a New Tunable Reagent for Producing Nanocellulose, Part I: Xylan-Coated CNCs and CNFs

    Directory of Open Access Journals (Sweden)

    Jia Mao

    2017-09-01

    Full Text Available Imidazole is reported to be an effective reactant for the production of nanocellulose from hardwood pulp. The morphologies and surface properties of the nanocellulose can be simply tailored according to the water content in the imidazole system: with pure imidazole, cellulose nanofibrils (CNFs in a yield of 10 wt % can be produced. With 25 wt % of water in imidazole, cellulose nanocrystals (CNCs are obtained in 20 wt % yield. Both nanocelluloses exhibit crystallinity indices in the order of 70%. Interestingly, they retain the original xylan from the pulp with ca. 9–10 wt % of residual xylan content.

  17. Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase SpeG

    OpenAIRE

    Filippova, Ekaterina V.; Weigand, Steven; Osipiuk, Jerzy; Kiryukhina, Olga; Joachimiak, Andrzej; Anderson, Wayne F.

    2015-01-01

    The spermidine N-acetyltransferase SpeG is a dodecameric enzyme that catalyzes the transfer of an acetyl group from acetyl-coenzyme A to polyamines such as spermidine and spermine. SpeG has an allosteric polyamine-binding site and acetylating polyamines regulates their intracellular concentrations. The structures of SpeG from Vibrio cholerae in complexes with polyamines and cofactor have been characterized earlier. Here, we present the dodecameric structure of SpeG from V. cholerae in a ligan...

  18. DFT study on the standard electrode potentials of imidazole, tetrathiafulvalene, and tetrathiafulvalene-imidazole.

    Science.gov (United States)

    Tugsuz, Tugba

    2010-12-30

    Extensive DFT calculations on the standard electrode potentials of imidazole (Im), tetrathiafulvalene (TTF), and 2-, 4-, and 5-TTF-Im were carried out. Geometries and Gibbs free energies of H-bonded dimer, anion, protonated cation, and neutral structures of Im, mono- and dication, and neutral structures of TTF in gas and acetonitrile solvent were computed by using 10 hybrid density functionals (B3LYP, TPSSH, PBEH1PBE, M06, M062X, X3LYP, BMK, B1B95, M05, M052X) combined with the TZVP basis set. CPCM and SMD solvation models were applied to predict the Gibbs free energies of molecules in acetonitrile solvent. Frequency calculations were carried out for all structures, and none of them has been found to exhibit any imaginary frequency. Finally, the BMK hybrid functional was selected for computation of the standard electrode potential of TTF-Im, because it gives the most accurate values in both Im and TTF, differing by 0.05 V from the experimental ones. Moreover, frequencies from the BMK functional are reasonably close to the experimental ones. The standard electrode potentials of 2-, 4-, and 5-TTF-Im predicted for two-electron oxidation are 0.946, 0.870, and 0.839 V in CPCM and 0.927, 0.866, and 0.824 V in SMD. For one-electron oxidation these are 0.491, 0.421, and 0.400 V in CPCM and 0.476, 0.377, and 0.360 V in SMD, respectively.

  19. Molecular kinetics. Ras activation by SOS: allosteric regulation by altered fluctuation dynamics.

    Science.gov (United States)

    Iversen, Lars; Tu, Hsiung-Lin; Lin, Wan-Chen; Christensen, Sune M; Abel, Steven M; Iwig, Jeff; Wu, Hung-Jen; Gureasko, Jodi; Rhodes, Christopher; Petit, Rebecca S; Hansen, Scott D; Thill, Peter; Yu, Cheng-Han; Stamou, Dimitrios; Chakraborty, Arup K; Kuriyan, John; Groves, Jay T

    2014-07-04

    Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras-guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average. Copyright © 2014, American Association for the Advancement of Science.

  20. A novel polyamine allosteric site of SpeG from Vibrio cholerae is revealed by its dodecameric structure.

    Science.gov (United States)

    Filippova, Ekaterina V; Kuhn, Misty L; Osipiuk, Jerzy; Kiryukhina, Olga; Joachimiak, Andrzej; Ballicora, Miguel A; Anderson, Wayne F

    2015-03-27

    Spermidine N-acetyltransferase, encoded by the gene speG, catalyzes the initial step in the degradation of polyamines and is a critical enzyme for determining the polyamine concentrations in bacteria. In Escherichia coli, studies have shown that SpeG is the enzyme responsible for acetylating spermidine under stress conditions and for preventing spermidine toxicity. Not all bacteria contain speG, and many bacterial pathogens have developed strategies to either acquire or silence it for pathogenesis. Here, we present thorough kinetic analyses combined with structural characterization of the VCA0947 SpeG enzyme from the important human pathogen Vibrio cholerae. Our studies revealed the unexpected presence of a previously unknown allosteric site and an unusual dodecameric structure for a member of the Gcn5-related N-acetyltransferase superfamily. We show that SpeG forms dodecamers in solution and in crystals and describe its three-dimensional structure in several ligand-free and liganded structures. Importantly, these structural data define the first view of a polyamine bound in an allosteric site of an N-acetyltransferase. Kinetic characterization of SpeG from V. cholerae showed that it acetylates spermidine and spermine. The behavior of this enzyme is complex and exhibits sigmoidal curves and substrate inhibition. We performed a detailed non-linear regression kinetic analysis to simultaneously fit families of substrate saturation curves to uncover a simple kinetic mechanism that explains the apparent complexity of this enzyme. Our results provide a fundamental understanding of the bacterial SpeG enzyme, which will be key toward understanding the regulation of polyamine levels in bacteria during pathogenesis. Copyright © 2015. Published by Elsevier Ltd.

  1. Development of allosteric modulators of GPCRs for treatment of CNS disorders.

    Science.gov (United States)

    Nickols, Hilary Highfield; Conn, P Jeffrey

    2014-01-01

    The discovery of allosteric modulators of G protein-coupled receptors (GPCRs) provides a promising new strategy with potential for developing novel treatments for a variety of central nervous system (CNS) disorders. Traditional drug discovery efforts targeting GPCRs have focused on developing ligands for orthosteric sites which bind endogenous ligands. Allosteric modulators target a site separate from the orthosteric site to modulate receptor function. These allosteric agents can either potentiate (positive allosteric modulator, PAM) or inhibit (negative allosteric modulator, NAM) the receptor response and often provide much greater subtype selectivity than orthosteric ligands for the same receptors. Experimental evidence has revealed more nuanced pharmacological modes of action of allosteric modulators, with some PAMs showing allosteric agonism in combination with positive allosteric modulation in response to endogenous ligand (ago-potentiators) as well as "bitopic" ligands that interact with both the allosteric and orthosteric sites. Drugs targeting the allosteric site allow for increased drug selectivity and potentially decreased adverse side effects. Promising evidence has demonstrated potential utility of a number of allosteric modulators of GPCRs in multiple CNS disorders, including neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, as well as psychiatric or neurobehavioral diseases such as anxiety, schizophrenia, and addiction. © 2013.

  2. The allosteric communication pathways in KIX domain of CBP

    Science.gov (United States)

    Palazzesi, Ferruccio; Barducci, Alessandro; Tollinger, Martin; Parrinello, Michele

    2013-01-01

    Allosteric regulation plays an important role in a myriad of biomacromolecular processes. Specifically, in a protein, the process of allostery refers to the transmission of a local perturbation, such as ligand binding, to a distant site. Decades after the discovery of this phenomenon, models built on static images of proteins are being reconsidered with the knowledge that protein dynamics plays an important role in its function. Molecular dynamics simulations are a valuable tool for studying complex biomolecular systems, providing an atomistic description of their structure and dynamics. Unfortunately, their predictive power has been limited by the complexity of the biomolecule free-energy surface and by the length of the allosteric timescale (in the order of milliseconds). In this work, we are able to probe the origins of the allosteric changes that transcription factor mixed lineage leukemia (MLL) causes to the interactions of KIX domain of CREB-binding protein (CBP) with phosphorylated kinase inducible domain (pKID), by combing all-atom molecular dynamics with enhanced sampling methods recently developed in our group. We discuss our results in relation to previous NMR studies. We also develop a general simulations protocol to study allosteric phenomena and many other biological processes that occur in the micro/milliseconds timescale. PMID:23940332

  3. Formation and structure of inhibitive molecular film of imidazole on iron surface

    International Nuclear Information System (INIS)

    Kokalj, Anton

    2013-01-01

    Highlights: ► Atomic scale details of interaction between imidazole and Fe(1 0 0) elucidated by DFT calculations. ► Imidazole dehydrogenates upon adsorption with the C2-H bond cleaved. ► Stablest identified structure consists of high coverage C2 dehydrogenated imidazoles. ► Passivation of Fe(1 0 0) due to strong adsorbate-surface bond and high adsorbate coverage. ► Previously suggested polymerization of imidazole molecules at high coverage is found improbable. - Abstract: Adsorption of imidazole on clean Fe(1 0 0) was addressed by DFT calculations. It is shown that even though the imidazole in protonated form binds stronger to the surface than the neutral form, it is prone to deprotonation (dehydrogenation) resulting in neutral form, which further dehydrogenates due to the breaking of the C2–H bond. Thermodynamically the stablest identified structures thus consist of strongly bound and densely packed C2 dehydrogenated imidazole molecules, which may act as a thin protective film. On the other hand, the polymerization of imidazole molecules upon adsorption has been found improbable.

  4. Phosphoric acid doped polysulfone membranes with aminopyridine pendant groups and imidazole cross-links

    DEFF Research Database (Denmark)

    Hink, Steffen; Elsøe, Katrine; Cleemann, Lars Nilausen

    2015-01-01

    Udel polysulfone based membranes with 4-aminopyridine pendant groups and cross-linking imidazole units are synthesized in a simple two step reaction. The ratio of 4-aminopyridine and imidazole is varied and the materials are extensively characterized. The average phosphoric acid uptake (in 85 wt%...

  5. Novel synthesis of 4(5)-monosubstituted imidazoles via cycloaddition of tosylmethyl isocyanide to aldimines

    NARCIS (Netherlands)

    ten Have, Ronald; Huisman, M; Meetsma, A; van Leusen, A.M.

    1997-01-01

    4(5)-Monosubstituted imidazoles (9) have been prepared via base-induced cycloaddition of tosylmethyl isocyanide (TosMIC) to N-(dimethylsulfamoyl)aldimines (2) or N-tosylaldimines (3). In the first case, N-(dimethylsulfamoyl)imidazoles 8 are the initial reaction products, from which the

  6. Some thiocyanato complexes of cadmium(II) with substituted pyridines and imidazoles

    Energy Technology Data Exchange (ETDEWEB)

    Mishra, B P; Ramana Rao, D V [Regional Engineering Coll., Rourkela (India). Dept. of Chemistry

    1979-05-01

    The complexes formed by cadmium(II) thiocyanate with 3-acetyl-, 3-bromo-, 3-methyl-, 4-acetyl-, 4-cyano-, 4-benzoyl pyridines, isoquinoline, 3,5-lutidine and imidazole, 2-methyl imidazole, 2-methyl benzimidazoles have been characterised through elemental analysis and molar conductance data. On the basis of infra-red spectroscopic studies, probable structures are discussed.

  7. Extracellular loop 2 of the free Fatty Acid receptor 2 mediates allosterism of a phenylacetamide ago-allosteric modulator

    DEFF Research Database (Denmark)

    Smith, Nicola J; Ward, Richard J; Stoddart, Leigh A

    2011-01-01

    Allosteric agonists are powerful tools for exploring the pharmacology of closely related G protein-coupled receptors that have nonselective endogenous ligands, such as the short chain fatty acids at free fatty acid receptors 2 and 3 (FFA2/GPR43 and FFA3/GPR41, respectively). We explored the molec...

  8. Biochemistry and structural studies of kynurenine 3-monooxygenase reveal allosteric inhibition by Ro 61-8048.

    Science.gov (United States)

    Gao, Jingjing; Yao, Licheng; Xia, Tingting; Liao, Xuebin; Zhu, Deyu; Xiang, Ye

    2018-04-01

    The human kynurenine 3-monooxygenase (hKMO) is a potential therapeutic target for neurodegenerative and neurologic disorders. Inhibition of KMO by Ro 61-8048, a potent, selective, and the most widely used inhibitor of KMO, was shown effective in various models of neurodegenerative or neurologic disorders. However, the molecular basis of hKMO inhibition by Ro 61-8048 is not clearly understood. Here, we report biochemistry studies on hKMO and crystal structures of an hKMO homolog, pfKMO from Pseudomonas fluorescens, in complex with the substrate l-kynurenine and Ro 61-8048. We found that the C-terminal ∼110 aa are essential for the enzymatic activity of hKMO and the homologous C-terminal region of pfKMO folds into a distinct, all-α-helical domain, which associates with the N-terminal catalytic domain to form a unique tunnel in proximity to the substrate-binding pocket. The tunnel binds the Ro 61-8048 molecule, which fills most of the tunnel, and Ro 61-8048 is hydrogen bonded with several completely conserved residues, including an essential catalytic residue. Modification of Ro 61-8048 and biochemical studies of the modified Ro 61-8048 derivatives suggested that Ro 61-8048 inhibits the enzyme in an allosteric manner by affecting the conformation of the essential catalytic residue and by blocking entry of the substrate or product release. The unique binding sites distinguish Ro 61-8048 as a noncompetitive and highly selective inhibitor from other competitive inhibitors, which should facilitate further optimization of Ro 61-8048 and the development of new inhibitory drugs to hKMO.-Gao, J., Yao, L., Xia, T., Liao, X., Zhu, D., Xiang, Y. Biochemistry and structural studies of kynurenine 3-monooxygenase reveal allosteric inhibition by Ro 61-8048.

  9. The relative importance of kinetic mechanisms and variable enzyme abundances for the regulation of hepatic glucose metabolism--insights from mathematical modeling.

    Science.gov (United States)

    Bulik, Sascha; Holzhütter, Hermann-Georg; Berndt, Nikolaus

    2016-03-02

    Adaptation of the cellular metabolism to varying external conditions is brought about by regulated changes in the activity of enzymes and transporters. Hormone-dependent reversible enzyme phosphorylation and concentration changes of reactants and allosteric effectors are the major types of rapid kinetic enzyme regulation, whereas on longer time scales changes in protein abundance may also become operative. Here, we used a comprehensive mathematical model of the hepatic glucose metabolism of rat hepatocytes to decipher the relative importance of different regulatory modes and their mutual interdependencies in the hepatic control of plasma glucose homeostasis. Model simulations reveal significant differences in the capability of liver metabolism to counteract variations of plasma glucose in different physiological settings (starvation, ad libitum nutrient supply, diabetes). Changes in enzyme abundances adjust the metabolic output to the anticipated physiological demand but may turn into a regulatory disadvantage if sudden unexpected changes of the external conditions occur. Allosteric and hormonal control of enzyme activities allow the liver to assume a broad range of metabolic states and may even fully reverse flux changes resulting from changes of enzyme abundances alone. Metabolic control analysis reveals that control of the hepatic glucose metabolism is mainly exerted by enzymes alone, which are differently controlled by alterations in enzyme abundance, reversible phosphorylation, and allosteric effects. In hepatic glucose metabolism, regulation of enzyme activities by changes of reactants, allosteric effects, and reversible phosphorylation is equally important as changes in protein abundance of key regulatory enzymes.

  10. Defying c-Abl signaling circuits through small allosteric compounds

    Directory of Open Access Journals (Sweden)

    Stefania eGonfloni

    2014-11-01

    Full Text Available Many extracellular and intracellular signals promote the c-Abl tyrosine kinase activity. c-Abl in turn triggers a multitude of changes either in protein phosphorylation or in gene expression in the cell. Yet, c-Abl takes part in diverse signaling routes because of several domains linked to its catalytic core. Complex conformational changes turn on and off its kinase activity. These changes affect surface features of the c-Abl kinase and likely its capability to bind actin and/or DNA. Two specific inhibitors (ATP-competitive or allosteric compounds regulate the c-Abl kinase through different mechanisms. NMR studies show that a c-Abl fragment (SH3-SH2-linker-SH1 adopts different conformational states upon binding to each inhibitor. This supports an unconventional use for allosteric compounds to unraveling physiological c-Abl signaling circuits.

  11. Photoinduced electron-transfer from imidazole derivative to nano-semiconductors.

    Science.gov (United States)

    Karunakaran, C; Jayabharathi, J; Jayamoorthy, K; Devi, K Brindha

    2012-04-01

    Bioactive imidazole derivative absorbs in the UV region at 305 nm. The interaction of imidazole derivative with nanoparticulate WO3, Fe2O3, Fe3O4, CuO, ZrO2 and Al2O3 has been studied by UV-visible absorption, FT-IR and fluorescence spectroscopies. The imidazole derivative adsorbs strongly on the surfaces of nanosemiconductor, the apparent binding constants for the association between nanomaterials and imidazole derivative have been determined from the fluorescence quenching. In the case of nanocrystalline insulator, fluorescence quenching through electron transfer from the excited state of the imidazole derivative to alumina is not possible. However, a possible mechanism for the quenching of fluorescence by the insulator is energy transfer, that is, energy transferred from the organic molecule to the alumina lattice. Based on Forster's non-radiation energy transfer theory, the distance between the imidazole derivative and nanoparticles (r0∼2.00 nm) as well as the critical energy transfer distance (R0∼1.70 nm) has been calculated. The interaction between the imidazole derivative and nanosurfaces occurs through static quenching mechanism. The free energy change (ΔGet) for electron transfer process has been calculated by applying Rehm-Weller equation. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Pancreatic Enzymes

    Science.gov (United States)

    ... Contact Us DONATE NOW GENERAL DONATION PURPLESTRIDE Pancreatic enzymes Home Facing Pancreatic Cancer Living with Pancreatic Cancer ... and see a registered dietitian. What are pancreatic enzymes? Pancreatic enzymes help break down fats, proteins and ...

  13. Inhibiting effects of imidazole on copper corrosion in 1 M HNO3 solution

    International Nuclear Information System (INIS)

    Lee, Woo-Jin

    2003-01-01

    The present work deals with the inhibiting effects of imidazole on the pure copper (Cu) corrosion in 1 M HNO 3 solution analysing potentiodynamic polarisation curves, potentiostatic anodic current transient, AC impedance spectra and X-ray photoelectron spectra (XPS). By adding imidazole to HNO 3 solution, the polarisation curves showed decrease in the corrosion current and the cathodic current, suggesting that imidazole acts as an effective cathodic inhibitor to Cu corrosion. From the measured anodic current transients, it is inferred that the protective Cu-imidazole complex film is simultaneously formed with the Cu oxide in the presence of imidazole during the early stage of the anodic polarisation. Analysis of the AC impedance spectra revealed that the values of the charge transfer resistance R ct obtained in imidazole-containing HNO 3 solution were greater than that value in imidazole-free one and at the same time steadily increased with immersion time to the constant value. Contrarily, the capacitance value was abruptly lowered from the double layer capacitance C dl to the complex film capacitance C cf in the progress of immersion time. Furthermore, the Warburg coefficient σ value for the ion diffusion through the complex film was observed to increase with immersion time. This means that the Cu(N-OH) complex film becomes thicker during immersion in the HNO 3 solution with imidazole through the inward growth of the N-rich outer layer to the O-rich inner layer, as well validated by XPS. Based upon the experimental results, it is suggested that the Cu corrosion in 1 M HNO 3 solution is efficiently inhibited with the addition of imidazole by retarding both the charge transfer on cathodic sites of the Cu surface in the early stage of immersion time and the subsequent ion diffusion through the steadily growing complex film

  14. Prediction of allosteric sites on protein surfaces with an elastic-network-model-based thermodynamic method.

    Science.gov (United States)

    Su, Ji Guo; Qi, Li Sheng; Li, Chun Hua; Zhu, Yan Ying; Du, Hui Jing; Hou, Yan Xue; Hao, Rui; Wang, Ji Hua

    2014-08-01

    Allostery is a rapid and efficient way in many biological processes to regulate protein functions, where binding of an effector at the allosteric site alters the activity and function at a distant active site. Allosteric regulation of protein biological functions provides a promising strategy for novel drug design. However, how to effectively identify the allosteric sites remains one of the major challenges for allosteric drug design. In the present work, a thermodynamic method based on the elastic network model was proposed to predict the allosteric sites on the protein surface. In our method, the thermodynamic coupling between the allosteric and active sites was considered, and then the allosteric sites were identified as those where the binding of an effector molecule induces a large change in the binding free energy of the protein with its ligand. Using the proposed method, two proteins, i.e., the 70 kD heat shock protein (Hsp70) and GluA2 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor, were studied and the allosteric sites on the protein surface were successfully identified. The predicted results are consistent with the available experimental data, which indicates that our method is a simple yet effective approach for the identification of allosteric sites on proteins.

  15. The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing

    International Nuclear Information System (INIS)

    Lesne, Annick; Victor, Jean–Marc; Bécavin, Christophe

    2012-01-01

    Allostery is a key concept of molecular biology which refers to the control of an enzyme activity by an effector molecule binding the enzyme at another site rather than the active site (allos = other in Greek). We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for spacetime coordination of gene expression at all scales from DNA to the whole chromosome. We further suggest that this functional architecture is provided by the chromatin fiber itself. The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or nonspecific) effectors to specific (or nonspecific) active sites. Mechanical constraints can travel along the fiber all the better since the fiber is more compact and regular, which speaks in favor of the actual existence of the (so-called 30 nm) chromatin fiber. Chromatin fiber allostery reconciles both the physical and biochemical approaches of chromatin. We illustrate this view with two supporting specific examples. Moreover, from a methodological point of view, we suggest that the notion of chromatin fiber allostery is particularly relevant for systemic approaches. Finally we discuss the evolutionary power of allostery in the context of chromatin and its relation to modularity. (perspective)

  16. The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing

    Science.gov (United States)

    Lesne, Annick; Bécavin, Christophe; Victor, Jean–Marc

    2012-02-01

    Allostery is a key concept of molecular biology which refers to the control of an enzyme activity by an effector molecule binding the enzyme at another site rather than the active site (allos = other in Greek). We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for spacetime coordination of gene expression at all scales from DNA to the whole chromosome. We further suggest that this functional architecture is provided by the chromatin fiber itself. The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or nonspecific) effectors to specific (or nonspecific) active sites. Mechanical constraints can travel along the fiber all the better since the fiber is more compact and regular, which speaks in favor of the actual existence of the (so-called 30 nm) chromatin fiber. Chromatin fiber allostery reconciles both the physical and biochemical approaches of chromatin. We illustrate this view with two supporting specific examples. Moreover, from a methodological point of view, we suggest that the notion of chromatin fiber allostery is particularly relevant for systemic approaches. Finally we discuss the evolutionary power of allostery in the context of chromatin and its relation to modularity.

  17. Characterization for coating processes of imidazole powders using an ultrasonic atomizer

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jun Sik; Kim, Jun Ki [Korea Institute of Industrial Technology, Incheon (Korea, Republic of); Kim, Mok Soon [Inha University, Incheon (Korea, Republic of); Lee, Jong Hyun [Seoul National University, Seoul (Korea, Republic of)

    2010-01-15

    Imidazole-curing accelerator powders were coated with stearic acid to increase the pot life of anisotropic conductive adhesive (ACA) formulations. To accomplish an efficient coating process, the coating was tested using an ultrasonic atomizer after mixing imidazole powders with a molten coating agent. Design of experiments analysis was organized to elucidate the effect of process parameters and to determine the most crucial parameter. The final formulation incorporating well-processed imidazole loaded powders indicated longer pot life, higher shear strength, and excellent highly accelerated stress test (HAST) reliability. Results show that the coating process using an ultrasonic atomizer is effective in increasing the pot life of ACA formulations

  18. Allosteric analysis of glucocorticoid receptor-DNA interface induced by cyclic Py-Im polyamide: a molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Yaru Wang

    Full Text Available BACKGROUND: It has been extensively developed in recent years that cell-permeable small molecules, such as polyamide, can be programmed to disrupt transcription factor-DNA interfaces and can silence aberrant gene expression. For example, cyclic pyrrole-imidazole polyamide that competes with glucocorticoid receptor (GR for binding to glucocorticoid response elements could be expected to affect the DNA dependent binding by interfering with the protein-DNA interface. However, how such small molecules affect the transcription factor-DNA interfaces and gene regulatory pathways through DNA structure distortion is not fully understood so far. METHODOLOGY/PRINCIPAL FINDINGS: In the present work, we have constructed some models, especially the ternary model of polyamides+DNA+GR DNA-binding domain (GRDBD dimer, and carried out molecular dynamics simulations and free energy calculations for them to address how polyamide molecules disrupt the GRDBD and DNA interface when polyamide and protein bind at the same sites on opposite grooves of DNA. CONCLUSIONS/SIGNIFICANCE: We found that the cyclic polyamide binding in minor groove of DNA can induce a large structural perturbation of DNA, i.e. a >4 Å widening of the DNA minor groove and a compression of the major groove by more than 4 Å as compared with the DNA molecule in the GRDBD dimer+DNA complex. Further investigations for the ternary system of polyamides+DNA+GRDBD dimer and the binary system of allosteric DNA+GRDBD dimer revealed that the compression of DNA major groove surface causes GRDBD to move away from the DNA major groove with the initial average distance of ∼4 Å to the final average distance of ∼10 Å during 40 ns simulation course. Therefore, this study straightforward explores how small molecule targeting specific sites in the DNA minor groove disrupts the transcription factor-DNA interface in DNA major groove, and consequently modulates gene expression.

  19. A Submarine Journey: The Pyrrole-Imidazole Alkaloids

    Directory of Open Access Journals (Sweden)

    Alessandra Scolaro

    2009-11-01

    Full Text Available In his most celebrated tale “The Picture of Dorian Gray”, Oscar Wilde stated that “those who go beneath the surface do so at their peril”. This sentence could be a prophetical warning for the practitioner who voluntarily challenges himself with trying to synthesize marine sponge-deriving pyrrole-imidazole alkaloids. This now nearly triple-digit membered community has been growing exponentially in the last 20 years, both in terms of new representatives and topological complexity − from simple, achiral oroidin to the breathtaking 12-ring stylissadines A and B, each possessing 16 stereocenters. While the biosynthesis and the role in the sponge economy of most of these alkaloids still lies in the realm of speculations, significant biological activities for some of them have clearly emerged. This review will account for the progress in achieving the total synthesis of the more biologically enticing members of this class of natural products.

  20. Thermal and mechanical stability of zeolitic imidazolate frameworks polymorphs

    Directory of Open Access Journals (Sweden)

    Lila Bouëssel du Bourg

    2014-12-01

    Full Text Available Theoretical studies on the experimental feasibility of hypothetical Zeolitic Imidazolate Frameworks (ZIFs have focused so far on relative energy of various polymorphs by energy minimization at the quantum chemical level. We present here a systematic study of stability of 18 ZIFs as a function of temperature and pressure by molecular dynamics simulations. This approach allows us to better understand the limited stability of some experimental structures upon solvent or guest removal. We also find that many of the hypothetical ZIFs proposed in the literature are not stable at room temperature. Mechanical and thermal stability criteria thus need to be considered for the prediction of new MOF structures. Finally, we predict a variety of thermal expansion behavior for ZIFs as a function of framework topology, with some materials showing large negative volume thermal expansion.

  1. Pore closure in zeolitic imidazolate frameworks under mechanical pressure.

    Science.gov (United States)

    Henke, Sebastian; Wharmby, Michael T; Kieslich, Gregor; Hante, Inke; Schneemann, Andreas; Wu, Yue; Daisenberger, Dominik; Cheetham, Anthony K

    2018-02-14

    We investigate the pressure-dependent mechanical behaviour of the zeolitic imidazolate framework ZIF-4 (M(im) 2 ; M 2+ = Co 2+ or Zn 2+ , im - = imidazolate) with high pressure, synchrotron powder X-ray diffraction and mercury intrusion measurements. A displacive phase transition from a highly compressible open pore ( op ) phase with continuous porosity (space group Pbca , bulk modulus ∼1.4 GPa) to a closed pore ( cp ) phase with inaccessible porosity (space group P 2 1 / c , bulk modulus ∼3.3-4.9 GPa) is triggered by the application of mechanical pressure. Over the course of the transitions, both ZIF-4 materials contract by about 20% in volume. However, the threshold pressure, the reversibility and the immediate repeatability of the phase transition depend on the metal cation. ZIF-4(Zn) undergoes the op-cp phase transition at a hydrostatic mechanical pressure of only 28 MPa, while ZIF-4(Co) requires about 50 MPa to initiate the transition. Interestingly, ZIF-4(Co) fully returns to the op phase after decompression, whereas ZIF-4(Zn) remains in the cp phase after pressure release and requires subsequent heating to switch back to the op phase. These variations in high pressure behaviour can be rationalised on the basis of the different electron configurations of the respective M 2+ ions (3d 10 for Zn 2+ and 3d 7 for Co 2+ ). Our results present the first examples of op-cp phase transitions ( i.e. breathing transitions) of ZIFs driven by mechanical pressure and suggest potential applications of these functional materials as shock absorbers, nanodampers, or in mechanocalorics.

  2. Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase SpeG.

    Science.gov (United States)

    Filippova, Ekaterina V; Weigand, Steven; Osipiuk, Jerzy; Kiryukhina, Olga; Joachimiak, Andrzej; Anderson, Wayne F

    2015-11-06

    The spermidine N-acetyltransferase SpeG is a dodecameric enzyme that catalyzes the transfer of an acetyl group from acetyl coenzyme A to polyamines such as spermidine and spermine. SpeG has an allosteric polyamine-binding site and acetylating polyamines regulate their intracellular concentrations. The structures of SpeG from Vibrio cholerae in complexes with polyamines and cofactor have been characterized earlier. Here, we present the dodecameric structure of SpeG from V. cholerae in a ligand-free form in three different conformational states: open, intermediate and closed. All structures were crystallized in C2 space group symmetry and contain six monomers in the asymmetric unit cell. Two hexamers related by crystallographic 2-fold symmetry form the SpeG dodecamer. The open and intermediate states have a unique open dodecameric ring. This SpeG dodecamer is asymmetric except for the one 2-fold axis and is unlike any known dodecameric structure. Using a fluorescence thermal shift assay, size-exclusion chromatography with multi-angle light scattering, small-angle X-ray scattering analysis, negative-stain electron microscopy and structural analysis, we demonstrate that this unique open dodecameric state exists in solution. Our combined results indicate that polyamines trigger conformational changes and induce the symmetric closed dodecameric state of the protein when they bind to their allosteric sites. Copyright © 2015. Published by Elsevier Ltd.

  3. Hybrid Zeolitic Imidazolate Frameworks: Controlling Framework Porosity and Functionality by Mixed-Linker Synthesis

    KAUST Repository

    Thompson, Joshua A.; Blad, Catherine R.; Brunelli, Nicholas A.; Lydon, Megan E.; Lively, Ryan P.; Jones, Christopher W.; Nair, Sankar

    2012-01-01

    Zeolitic imidazolate frameworks (ZIFs) are a subclass of nanoporous metal-organic frameworks (MOFs) that exhibit zeolite-like structural topologies and have interesting molecular recognition properties, such as molecular sieving and gate

  4. Titanium-based zeolitic imidazolate framework for chemical fixation of carbon dioxide

    Data.gov (United States)

    U.S. Environmental Protection Agency — A titanium-based zeolitic imidazolate framework (Ti-ZIF) with high surface area and porous morphology has been synthesized and its application as a recyclable...

  5. An Imidazole based probe for relay recognition of Cu and OH ions ...

    Indian Academy of Sciences (India)

    biological activities.1 Biological activity of imidazole derivatives is the main motive for ... These systems use physical or chemical inputs to gen- erate outputs based on a set ... exhibit α-glucosidase inhibition to treat diabetes.21. 2. Experimental.

  6. {Tris[2-(imidazol-2-ylmethyliminoethyl]methylammonium}iron(II tris(perchlorate dihydrate

    Directory of Open Access Journals (Sweden)

    Greg A. Brewer

    2008-01-01

    Full Text Available The title complex, [Fe(C19H27N10](ClO43·2H2O, is a new polymorph of an iron(II Schiff base complex of tris(2-aminoethylmethylammonium with imidazole-2-carboxaldehyde. The octahedral FeII atom is bound to three facial imidazole N atoms with average Fe—Nimidazole and Fe—Nimine bond distances of 1.963 (5 and 1.951 (5 Å, respectively. The central N atom of the tripodal ligand is outside the bonding distance at 3.92 Å. The crystal packing is stabilized by the hydrogen-bonding interactions between the two water molecules (acceptor and two of the three imidazole NH groups (donor. The third imidazole NH group (donor forms a hydrogen bond to one of the three perchlorate counter-ions (acceptor.

  7. Investigation of the Linker Swing Motion in the Zeolitic Imidazolate Framework ZIF-90

    KAUST Repository

    Zheng, Bin; Fu, Fang; Wang, Lian Li; Yang, Limin; Zhu, Yihan; Du, Huiling

    2018-01-01

    The linker swing motion in the zeolitic imidazolate framework ZIF-90 is investigated by density functional theory (DFT) calculation, molecular dynamics (MD) and grand-canonical Monte Carlo (GCMC) simulations. The relation between the terminal

  8. Titanium-based zeolitic imidazolate framework for chemical fixation of carbon dioxide

    Science.gov (United States)

    A titanium-based zeolitic imidazolate framework (Ti-ZIF) with high surface area and porous morphology was synthesized and itsefficacy was demonstrated in the synthesis of cyclic carbonates from epoxides and carbon dioxide.

  9. Imidazole as a pH Probe: An NMR Experiment for the General Chemistry Laboratory

    Science.gov (United States)

    Hagan, William J., Jr.; Edie, Dennis L.; Cooley, Linda B.

    2007-01-01

    The analysis describes an NMR experiment for the general chemistry laboratory, which employs an unknown imidazole solution to measure the pH values. The described mechanism can also be used for measuring the acidity within the isolated cells.

  10. Electronic structure tautomerism, and mechanism of H-D exchange in imidazole aqueous solutions

    International Nuclear Information System (INIS)

    Borisov, Yu.A.; Vorob'eva, N.P.; Abronin, I.A.; Kolomiets, A.F.

    1988-01-01

    The imidazole electronic structure in a gaseous phase is studied taking into account the influence of solvation effects in aqueous solutions. Possible mechanisms of tautomeric transformations and H-D exchange reactions with water molecules are discussed. Using the quantum chemistry methods, it is shown that the intramolecular mechanism of imidazole isomerization in the gaseous phase and the aqueous solution is unprofitable, and the intermolecular mechanism can proceed through the stage of protonated and carbene form formation

  11. High-Resolution Infrared Spectroscopy of Imidazole Clusters in Helium Droplets Using Quantum Cascade Lasers

    Science.gov (United States)

    Mani, Devendra; Can, Cihad; Pal, Nitish; Schwaab, Gerhard; Havenith, Martina

    2017-06-01

    Imidazole ring is a part of many biologically important molecules and drugs. Imidazole monomer, dimer and its complexes with water have earlier been studied using infrared spectroscopy in helium droplets^{1,2} and molecular beams^{3}. These studies were focussed on the N-H and O-H stretch regions, covering the spectral region of 3200-3800 \\wn. We have extended the studies on imidazole clusters into the ring vibration region. The imidazole clusters were isolated in helium droplets and were probed using a combination of infrared spectroscopy and mass spectrometry. The spectra in the region of 1000-1100 \\wn and 1300-1460 \\wn were recorded using quantum cascade lasers. Some of the observed bands could be assigned to imidazole monomer and higher order imidazole clusters, using pickup curve analysis and ab initio calculations. Work is still in progress. The results will be discussed in detail in the talk. References: 1) M.Y. Choi and R.E. Miller, J. Phys. Chem. A, 110, 9344 (2006). 2) M.Y. Choi and R.E. Miller, Chem. Phys. Lett., 477, 276 (2009). 3) J. Zischang, J. J. Lee and M. Suhm, J. Chem. Phys., 135, 061102 (2011). Note: This work was supported by the Cluster of Excellence RESOLV (Ruhr-Universitat EXC1069) funded by the Deutsche Forschungsgemeinschaft.

  12. Non equivalence of the chains in the allosteric interaction of the hemoglobin

    International Nuclear Information System (INIS)

    Jacchieri, S.G.

    1983-01-01

    The importance, for the temperature dependence of the cooperative behaviour of hemoglobin, of the functional non equivalence of the polypeptide chains from which the hemoglobin molecule is built is studied. With such purpose thermodynamic allosteric parameters are introduced called 'mean allosteric parameters' which relate the last two oxygen bindings to the firsttwo ones. It is shown that the mean allosteric free energy is strongly correlated to the Hill parameter which is a classic measure of cooperativity; hence, the mean allosteric free energy measures the hemoglobin cooperativity. Recent experimental data show that the mean allosteric free energy decreasses with temperature; this is due to the mean allosteric enthalphy and entropy being positive quantities. To analise such behaviour in terms of thermodynamic's arguments equations are derived for the thermodynamic parameters of oxygen binding to hemoglobin in terms of those of its chains. Since the obtained equations have a great number of terms the same treatment is applied to a hypothetic dimer from which simpler relations are derived. From both cases it is concluded that the positive character of the mean allosteric enthalpy and entropy is due to the presence of cooperative and anticooperative terms. Since the last terms are absent in the equations of allosteric homoproteins, the characteristic temperature-dependence of hemoglobin's cooperativity depends on the presence of non-equivalent chains. (Author) [pt

  13. The second extracellular loop of the adenosine A1 receptor mediates activity of allosteric enhancers.

    Science.gov (United States)

    Kennedy, Dylan P; McRobb, Fiona M; Leonhardt, Susan A; Purdy, Michael; Figler, Heidi; Marshall, Melissa A; Chordia, Mahendra; Figler, Robert; Linden, Joel; Abagyan, Ruben; Yeager, Mark

    2014-02-01

    Allosteric enhancers of the adenosine A1 receptor amplify signaling by orthosteric agonists. Allosteric enhancers are appealing drug candidates because their activity requires that the orthosteric site be occupied by an agonist, thereby conferring specificity to stressed or injured tissues that produce adenosine. To explore the mechanism of allosteric enhancer activity, we examined their action on several A1 receptor constructs, including (1) species variants, (2) species chimeras, (3) alanine scanning mutants, and (4) site-specific mutants. These findings were combined with homology modeling of the A1 receptor and in silico screening of an allosteric enhancer library. The binding modes of known docked allosteric enhancers correlated with the known structure-activity relationship, suggesting that these allosteric enhancers bind to a pocket formed by the second extracellular loop, flanked by residues S150 and M162. We propose a model in which this vestibule controls the entry and efflux of agonists from the orthosteric site and agonist binding elicits a conformational change that enables allosteric enhancer binding. This model provides a mechanism for the observations that allosteric enhancers slow the dissociation of orthosteric agonists but not antagonists.

  14. Selective Negative Allosteric Modulation Of Metabotropic Glutamate Receptors - A Structural Perspective of Ligands and Mutants

    DEFF Research Database (Denmark)

    Harpsøe, Kasper; Isberg, Vignir; Tehan, Benjamin G

    2015-01-01

    modulators. In this analysis, we make the first comprehensive structural comparison of all metabotropic glutamate receptors, placing selective negative allosteric modulators and critical mutants into the detailed context of the receptor binding sites. A better understanding of how the different m......Glu allosteric modulator binding modes relates to selective pharmacological actions will be very valuable for rational design of safer drugs....

  15. Transition-metal-free synthesis of N-(1-alkenyl)imidazoles by potassium phosphate-promoted addition reaction of alkynes to imidazoles.

    Science.gov (United States)

    Lu, Linhua; Yan, Hong; Liu, Defu; Rong, Guangwei; Mao, Jincheng

    2014-01-01

    The addition reaction of alkynes to N-heterocycles by simply heating in DMSO with potassium phosphate is reported. Good yields with high stereoselectivity could be achieved for a range of substrates. The scope is quite general for both amines and phenylacetylenes. In addition, internal alkynes and α-bromostyrene were also examined in this reaction. This process is efficient and useful for the synthesis of (Z)-N-(1-alkenyl)imidazoles and related Z products. Thus, the reaction is useful because of the importance of the imidazole scaffold. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Orthosteric and Allosteric Regulation in Trypsin-Like Peptidases

    DEFF Research Database (Denmark)

    Kromann-Tofting, Tobias

    Trypsin-like serine peptidases play an important role in many physiological and pathophysiological processes, the latter including cardiovascular diseases and cancer. Binding of natural ligands to functional sites on the peptidase surface balances the level of activity and substrate specificity......-ray crystallography to determine crystal structures of active and inactive conformations of muPA, combined with biochemical analysis, elucidated an allosteric regulatory mechanism, which is now believed to be highly conserved in the trypsin-like serine peptidases. Targeting zymogen activation represents an attractive...

  17. The allosteric switching mechanism in bacteriophage MS2

    Energy Technology Data Exchange (ETDEWEB)

    Perkett, Matthew R.; Mirijanian, Dina T.; Hagan, Michael F., E-mail: hagan@brandeis.edu [Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474 (United States)

    2016-07-21

    We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.

  18. Allosteric behavior in the activation of transducin mediated by rhodopsin

    International Nuclear Information System (INIS)

    Wessling-Resnick, M.; Johnson, G.I.

    1986-01-01

    Transducin is a member of the family of regulatory GTP-binding proteins which provide a signal transduction mechanism for many cell surface receptors. These receptors act in a catalytic manner to displace GDP bound to the G protein in exchange for GTP during a process referred to as activation. The authors have studied the steady-state kinetics of the activation of transducin mediated by rhodopsin by employing the non-hydrolyzable GTP analog, [ 35 S]-GTPγS. The substrate-velocity curves display remarkable allosteric behavior with a Hill coefficient, n/sub H/ = 2. Lineweaver-Burke plots with respect to reciprocal [transducin] show curvilinearity indicative of positive cooperativity. However, a series of parallel lines are generated by plotting the linear transformation as [transducin] -2 . The double reciprocal plots with respect to [GTPγS] are a series of parallel lines. The initial rate analysis supports a double displacement catalytic mechanism for the molecular interactions between the photon receptor, G protein, and guanine nucleotides. It remains to be determined whether the positive cooperative behavior the authors observe can be assigned to the interaction of multiple transducins with rhodopsin, the presence of an allosteric effector, or hysteresis in the receptor's activity. These unique observations also provide insight into the molecular interactions of members of the family of G protein-coupled receptors

  19. Allosteric inhibitors of Coxsackie virus A24 RNA polymerase.

    Science.gov (United States)

    Schein, Catherine H; Rowold, Diane; Choi, Kyung H

    2016-02-15

    Coxsackie virus A24 (CVA24), a causative agent of acute hemorrhagic conjunctivitis, is a prototype of enterovirus (EV) species C. The RNA polymerase (3D(pol)) of CVA24 can uridylylate the viral peptide linked to the genome (VPg) from distantly related EV and is thus, a good model for studying this reaction. Once UMP is bound, VPgpU primes RNA elongation. Structural and mutation data have identified a conserved binding surface for VPg on the RNA polymerase (3D(pol)), located about 20Å from the active site. Here, computational docking of over 60,000 small compounds was used to select those with the lowest (best) specific binding energies (BE) for this allosteric site. Compounds with varying structures and low BE were assayed for their effect on formation of VPgU by CVA24-3D(pol). Two compounds with the lowest specific BE for the site inhibited both uridylylation and formation of VPgpolyU at 10-20μM. These small molecules can be used to probe the role of this allosteric site in polymerase function, and may be the basis for novel antiviral compounds. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Allosteric Inhibition of Macrophage Migration Inhibitory Factor Revealed by Ibudilast

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Y.; Crichlow, G; Vermeire, J; Leng, L; Du, X; Hodsdon, M; Bucala, R; Cappello, M; Gross, M; et al.

    2010-01-01

    AV411 (ibudilast; 3-isobutyryl-2-isopropylpyrazolo-[1,5-a]pyridine) is an antiinflammatory drug that was initially developed for the treatment of bronchial asthma but which also has been used for cerebrovascular and ocular indications. It is a nonselective inhibitor of various phosphodiesterases (PDEs) and has varied antiinflammatory activity. More recently, AV411 has been studied as a possible therapeutic for the treatment of neuropathic pain and opioid withdrawal through its actions on glial cells. As described herein, the PDE inhibitor AV411 and its PDE-inhibition-compromised analog AV1013 inhibit the catalytic and chemotactic functions of the proinflammatory protein, macrophage migration inhibitory factor (MIF). Enzymatic analysis indicates that these compounds are noncompetitive inhibitors of the p-hydroxyphenylpyruvate (HPP) tautomerase activity of MIF and an allosteric binding site of AV411 and AV1013 is detected by NMR. The allosteric inhibition mechanism is further elucidated by X-ray crystallography based on the MIF/AV1013 binary and MIF/AV1013/HPP ternary complexes. In addition, our antibody experiments directed against MIF receptors indicate that CXCR2 is the major receptor for MIF-mediated chemotaxis of peripheral blood mononuclear cells.

  1. Study of the improvement of the radioprotective power of imidazole; Etude de l'amelioration du pouvoir radioprotecteur de l'imidazole

    Energy Technology Data Exchange (ETDEWEB)

    Mourret, A; Rinaldi, R [Commissariat a l' Energie Atomique, 38 - Grenoble (France). Centre d' Etudes Nucleaires

    1968-07-01

    In studies made on the Imidazole radioprotective power, the authors have attempted to neutralize its convulsive properties by the Depamide so as to decrease drug toxicity. Then, having studied in what manner the two products simultaneous action could carry one increase of radioprotective activity, they have established that if the Depamide permits to decrease very much the Imidazole toxicity, the variation of radioprotection power which is subject to animal sex, generally increases for females and decreases for males. (authors) [French] Dans le cadre de l'etude du pouvoir radioprotecteur de l'Imidazole, les auteurs ont essaye de neutraliser les proprietes convulsivantes de cette substance par le Depamide afin d'en dimunuer la toxicite. Ayant ensuite etudie dans quelle mesure l'action simultanee de ces deux produits pouvait apporter une amelioration de l'activite radioprotectrice, ils ont constate que si le Depamide permet de diminuer tres sensiblement la toxicite de l'Imidazole, la variation du pouvoir radioprotecteur, qui depend du sexe de l'animal, augmente en general pour les femelles et diminue pour les males. (auteurs)

  2. Unexpected Molecular Sieving Properties of Zeolitic Imidazolate Framework-8

    KAUST Repository

    Zhang, Chen

    2012-08-16

    We studied molecular sieving properties of zeolitic imidazolate framework-8 (ZIF-8) by estimating the thermodynamically corrected diffusivities of probe molecules at 35 °C. From helium (2.6 Å) to iso-C 4H 10 (5.0 Å), the corrected diffusivity drops 14 orders of magnitude. Our results further suggest that the effective aperture size of ZIF-8 for molecular sieving is in the range of 4.0 to 4.2 Å, which is significantly larger than the XRD-derived value (3.4 Å) and between the well-known aperture size of zeolite 4A (3.8 Å) and 5A (4.3 Å). Interestingly, because of aperture flexibility, the studied C 4 hydrocarbon molecules that are larger than this effective aperture size still adsorb in the micropores of ZIF-8 with kinetic selectivities for iso-C 4H 8/iso-C 4H 10 of 180 and n-C 4H 10/iso-C 4H 10 of 2.5 × 10 6. These unexpected molecular sieving properties open up new opportunities for ZIF materials for separations that cannot be economically achieved by traditional microporous adsorbents such as synthetic zeolites. © 2012 American Chemical Society.

  3. Unexpected Molecular Sieving Properties of Zeolitic Imidazolate Framework-8

    KAUST Repository

    Zhang, Chen; Lively, Ryan P.; Zhang, Ke; Johnson, Justin R.; Karvan, Oguz; Koros, William J.

    2012-01-01

    We studied molecular sieving properties of zeolitic imidazolate framework-8 (ZIF-8) by estimating the thermodynamically corrected diffusivities of probe molecules at 35 °C. From helium (2.6 Å) to iso-C 4H 10 (5.0 Å), the corrected diffusivity drops 14 orders of magnitude. Our results further suggest that the effective aperture size of ZIF-8 for molecular sieving is in the range of 4.0 to 4.2 Å, which is significantly larger than the XRD-derived value (3.4 Å) and between the well-known aperture size of zeolite 4A (3.8 Å) and 5A (4.3 Å). Interestingly, because of aperture flexibility, the studied C 4 hydrocarbon molecules that are larger than this effective aperture size still adsorb in the micropores of ZIF-8 with kinetic selectivities for iso-C 4H 8/iso-C 4H 10 of 180 and n-C 4H 10/iso-C 4H 10 of 2.5 × 10 6. These unexpected molecular sieving properties open up new opportunities for ZIF materials for separations that cannot be economically achieved by traditional microporous adsorbents such as synthetic zeolites. © 2012 American Chemical Society.

  4. Biological applications of zinc imidazole framework through protein encapsulation

    Directory of Open Access Journals (Sweden)

    Pawan Kumar

    2015-12-01

    Full Text Available Abstract The robustness of biomolecules is always a significant challenge in the application of biostorage in biotechnology or pharmaceutical research. To learn more about biostorage in porous materials, we investigated the feasibility of using zeolite imidazolate framework (ZIF-8 with respect to protein encapsulation. Here, bovine serum albumin (BSA was selected as a model protein for encapsulation with the synthesis of ZIF-8 using water as a media. ZIF-8 exhibited excellent protein adsorption capacity through successive adsorption of free BSA with the formation of hollow crystals. The loading of protein in ZIF-8 crystals is affected by the molecular weight due to diffusion-limited permeation inside the crystals and also by the affinity of the protein to the pendent group on the ZIF-8 surface. The polar nature of BSA not only supported adsorption on the solid surface, but also enhanced the affinity of crystal spheres through weak coordination interactions with the ZIF-8 framework. The novel approach tested in this study was therefore successful in achieving protein encapsulation with porous, biocompatible, and decomposable microcrystalline ZIF-8. The presence of both BSA and FITC–BSA in ZIF-8 was confirmed consistently by spectroscopy as well as optical and electron microscopy.

  5. Behind the curtain: cellular mechanisms for allosteric modulation of calcium-sensing receptors

    Science.gov (United States)

    Cavanaugh, Alice; Huang, Ying; Breitwieser, Gerda E

    2012-01-01

    Calcium-sensing receptors (CaSR) are integral to regulation of systemic Ca2+ homeostasis. Altered expression levels or mutations in CaSR cause Ca2+ handling diseases. CaSR is regulated by both endogenous allosteric modulators and allosteric drugs, including the first Food and Drug Administration-approved allosteric agonist, Cinacalcet HCl (Sensipar®). Recent studies suggest that allosteric modulators not only alter function of plasma membrane-localized CaSR, but regulate CaSR stability at the endoplasmic reticulum. This brief review summarizes our current understanding of the role of membrane-permeant allosteric agonists in cotranslational stabilization of CaSR, and highlights additional, indirect, signalling-dependent role(s) for membrane-impermeant allosteric drugs. Overall, these studies suggest that allosteric drugs act at multiple cellular organelles to control receptor abundance and hence function, and that drug hydrophobicity can bias the relative contributions of plasma membrane and intracellular organelles to CaSR abundance and signalling. LINKED ARTICLES This article is part of a themed section on the Molecular Pharmacology of G Protein-Coupled Receptors (GPCRs). To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2012.165.issue-6. To view the 2010 themed section on the same topic visit http://onlinelibrary.wiley.com/doi/10.1111/bph.2010.159.issue-5/issuetoc PMID:21470201

  6. In Vivo Investigation of Escitalopram’s Allosteric Site on the Serotonin Transporter

    Science.gov (United States)

    Murray, Karen E.; Ressler, Kerry J.; Owens, Michael J.

    2015-01-01

    Escitalopram is a commonly prescribed antidepressant of the selective serotonin reuptake inhibitor class. Clinical evidence and mapping of the serotonin transporter (SERT) identified that escitalopram, in addition to its binding to a primary uptake-blocking site, is capable of binding to the SERT via an allosteric site that is hypothesized to alter escitalopram’s kinetics at the SERT. The studies reported here examined the in vivo role of the SERT allosteric site in escitalopram action. A knockin mouse model that possesses an allosteric-null SERT was developed. Autoradiographic studies indicated that the knockin protein was expressed at a lower density than endogenous mouse SERT (approximately 10–30% of endogenous mouse SERT), but the knockin mice are a viable tool to study the allosteric site. Microdialysis studies in the ventral hippocampus found no measurable decrease in extracellular serotonin response after local escitalopram challenge in mice without the allosteric site compared to mice with the site (p = 0.297). In marble burying assays there was a modest effect of the absence of the allosteric site, with a larger systemic dose of escitalopram (10-fold) necessary for the same effect as in mice with intact SERT (p = 0.023). However, there was no effect of the allosteric site in the tail suspension test. Together these data suggest that there may be a regional specificity in the role of the allosteric site. The lack of a robust effect overall suggests that the role of the allosteric site for escitalopram on the SERT may not produce meaningful in vivo effects. PMID:26621784

  7. Enzyme Informatics

    Science.gov (United States)

    Alderson, Rosanna G.; Ferrari, Luna De; Mavridis, Lazaros; McDonagh, James L.; Mitchell, John B. O.; Nath, Neetika

    2012-01-01

    Over the last 50 years, sequencing, structural biology and bioinformatics have completely revolutionised biomolecular science, with millions of sequences and tens of thousands of three dimensional structures becoming available. The bioinformatics of enzymes is well served by, mostly free, online databases. BRENDA describes the chemistry, substrate specificity, kinetics, preparation and biological sources of enzymes, while KEGG is valuable for understanding enzymes and metabolic pathways. EzCatDB, SFLD and MACiE are key repositories for data on the chemical mechanisms by which enzymes operate. At the current rate of genome sequencing and manual annotation, human curation will never finish the functional annotation of the ever-expanding list of known enzymes. Hence there is an increasing need for automated annotation, though it is not yet widespread for enzyme data. In contrast, functional ontologies such as the Gene Ontology already profit from automation. Despite our growing understanding of enzyme structure and dynamics, we are only beginning to be able to design novel enzymes. One can now begin to trace the functional evolution of enzymes using phylogenetics. The ability of enzymes to perform secondary functions, albeit relatively inefficiently, gives clues as to how enzyme function evolves. Substrate promiscuity in enzymes is one example of imperfect specificity in protein-ligand interactions. Similarly, most drugs bind to more than one protein target. This may sometimes result in helpful polypharmacology as a drug modulates plural targets, but also often leads to adverse side-effects. Many cheminformatics approaches can be used to model the interactions between druglike molecules and proteins in silico. We can even use quantum chemical techniques like DFT and QM/MM to compute the structural and energetic course of enzyme catalysed chemical reaction mechanisms, including a full description of bond making and breaking. PMID:23116471

  8. Allosteric and orthosteric sites in CC chemokine receptor (CCR5), a chimeric receptor approach

    DEFF Research Database (Denmark)

    Thiele, Stefanie; Steen, Anne; Jensen, Pia C

    2011-01-01

    -allosteric molecules. A chimera was successfully constructed between CCR5 and the closely related CCR2 by transferring all extracellular regions of CCR2 to CCR5, i.e. a Trojan horse that resembles CCR2 extracellularly but signals through a CCR5 transmembrane unit. The chimera bound CCR2 (CCL2 and CCL7), but not CCR5...... preserved, the allosteric enhancement of chemokine binding was disrupted. In summary, the Trojan horse chimera revealed that orthosteric and allosteric sites could be structurally separated and still act together with transmission of agonism and antagonism across the different receptor units....

  9. Orthosteric and allosteric potentiation of heteromeric neuronal nicotinic acetylcholine receptors.

    Science.gov (United States)

    Wang, Jingyi; Lindstrom, Jon

    2018-06-01

    Heteromeric nicotinic ACh receptors (nAChRs) were thought to have two orthodox agonist-binding sites at two α/β subunit interfaces. Highly selective ligands are hard to develop by targeting orthodox agonist sites because of high sequence similarity of this binding pocket among different subunits. Recently, unorthodox ACh-binding sites have been discovered at some α/α and β/α subunit interfaces, such as α4/α4, α5/α4 and β3/α4. Targeting unorthodox sites may yield subtype-selective ligands, such as those for (α4β2) 2 α5, (α4β2) 2 β3 and (α6β2) 2 β3 nAChRs. The unorthodox sites have unique pharmacology. Agonist binding at one unorthodox site is not sufficient to activate nAChRs, but it increases activation from the orthodox sites. NS9283, a selective agonist for the unorthodox α4/α4 site, was initially thought to be a positive allosteric modulator (PAM). NS9283 activates nAChRs with three engineered α4/α4 sites. PAMs, on the other hand, act at allosteric sites where ACh cannot bind. Known PAM sites include the ACh-homologous non-canonical site (e.g. morantel at β/α), the C-terminus (e.g. Br-PBTC and 17β-estradiol), a transmembrane domain (e.g. LY2087101) or extracellular and transmembrane domain interfaces (e.g. NS206). Some of these PAMs, such as Br-PBTC and 17β-estradiol, require only one subunit to potentiate activation of nAChRs. In this review, we will discuss differences between activation from orthosteric and allosteric sites, their selective ligands and clinical implications. These studies have advanced understanding of the structure, assembly and pharmacology of heteromeric neuronal nAChRs. This article is part of a themed section on Nicotinic Acetylcholine Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.11/issuetoc. © 2017 The British Pharmacological Society.

  10. Evolution of glycaemia in the blood of mice in the presence or absence of imidazole; Evolution de la glycemie sanguine chez la souris protegee ou non par l'imidazole

    Energy Technology Data Exchange (ETDEWEB)

    Polverelli, M; Teoule, R [Commissariat a l' Energie Atomique, Grenoble (France). Centre d' Etudes Nucleaires

    1969-07-01

    With respect to the radioprotective properties of the heterocyclic compound, imidazole, the authors followed the action of this product on blood sugar levels of mice X irradiated with a lethal dose. The main results of this work are: probably a hypo-glycemic action of the imidazole; an abolishment of the post-irradiation hyperglycemia by imidazole; an appreciably difference between male and female towards irradiation. (author) [French] Dans le cadre de l'etude des proprietes radioprotectrices de l'imidazole, nous nous sommes attaches a suivre l'action de ce produit sur le taux de glucose sanguin de souris irradiees a dose letale. Les principaux resultats de ce travail sont les suivants: l'action probablement hypoglycemiante de l'imidazole; en tant que radioprotecteur, cet heterocycle azote supprime l'hyperglycemie consecutive a l'irradiation; une difference assez sensible entre males et femelles vis-a-vis de l'irradiation. (auteur)

  11. First catalytic hetero-Diels-Alder reaction of imidazole-2-thiones and in silico biological evaluation of the cycloadducts

    NARCIS (Netherlands)

    Eleftheriadis, Nikolaos; Samatidou, Evanthia; Neochoritis, Constantinos G.

    The Lewis acid-catalyzed Diels-Alder reactions of suitably substituted imidazole-2-thiones with dienes were studied. It was found that the electron density of the imidazole core influenced the reaction, since electron withdrawing groups led to the novel spiro-derivatives 2 whereas electron donating

  12. Exploring Covalent Allosteric Inhibition of Antigen 85C from Mycobacterium tuberculosis by Ebselen Derivatives.

    Science.gov (United States)

    Goins, Christopher M; Dajnowicz, Steven; Thanna, Sandeep; Sucheck, Steven J; Parks, Jerry M; Ronning, Donald R

    2017-05-12

    rearrangement due to covalent allosteric modification creates a sizable solvent network that encompasses the active site and extends to the modified Cys209 residue. In all, this study outlines factors that influence enzyme inhibition by ebselen and its derivatives while further highlighting the effects of the covalent modification of Cys209 by said inhibitors on the structure and stability of Ag85C. Furthermore, the results suggest a strategy for developing new classes of Ag85 inhibitors with increased specificity and potency.

  13. Enhancing NMDA Receptor Function: Recent Progress on Allosteric Modulators

    Directory of Open Access Journals (Sweden)

    Lulu Yao

    2017-01-01

    Full Text Available The N-methyl-D-aspartate receptors (NMDARs are subtype glutamate receptors that play important roles in excitatory neurotransmission and synaptic plasticity. Their hypo- or hyperactivation are proposed to contribute to the genesis or progression of various brain diseases, including stroke, schizophrenia, depression, and Alzheimer’s disease. Past efforts in targeting NMDARs for therapeutic intervention have largely been on inhibitors of NMDARs. In light of the discovery of NMDAR hypofunction in psychiatric disorders and perhaps Alzheimer’s disease, efforts in boosting NMDAR activity/functions have surged in recent years. In this review, we will focus on enhancing NMDAR functions, especially on the recent progress in the generation of subunit-selective, allosteric positive modulators (PAMs of NMDARs. We shall also discuss the usefulness of these newly developed NMDAR-PAMs.

  14. Building blocks for ionic liquids: Vapor pressures and vaporization enthalpies of 1-(n-alkyl)-imidazoles

    International Nuclear Information System (INIS)

    Emel'yanenko, Vladimir N.; Portnova, Svetlana V.; Verevkin, Sergey P.; Skrzypczak, Andrzej; Schubert, Thomas

    2011-01-01

    Highlights: → We measured vapor pressures of the 1-(n-alkyl)-imidazoles by transpiration method. → Variations on the alkyl chain length n were C 3 , C 5 -C 7 , and C 9 -C 10 . → Enthalpies of vaporization were derived from (p, T) dependencies. → Enthalpies of vaporization at 298.15 K were linear dependent on the chain length. - Abstract: Vapor pressures of the linear 1-(n-alkyl)-imidazoles with the alkyl chain C 3 , C 5 -C 7 , and C 9 -C 10 have been measured by the transpiration method. The molar enthalpies of vaporization Δ l g H m of these compounds were derived from the temperature dependencies of vapor pressures. A linear correlation of enthalpies of vaporization Δ l g H m (298.15 K) of the 1-(n-alkyl)-imidazoles with the chain length has been found.

  15. Comparative study between phenol and imidazole derivatives in radiolabeling of some steroid hormones

    International Nuclear Information System (INIS)

    Sallam, Kh.M.

    2010-01-01

    A phenol or imidazole ring is rarely present in steroid hormones, So, the molecule of steroid hormone requires chemical modification by addition of an iodinable residue like phenol or imedazole. So that the comparative study between phenol derivatives, include tyrosine methyl ester (TME) and tyramine, and imidazole derivatives, like histamine and histedine methyl ester (HME), for radiolabeling of some steroid hormones include estradiol and testosterone is the aim of the present study. The conjugation step was carried using mixed anhydride method and followed by radioiodination using iodogen as an oxidizing agent. Purification step was carried out using high performance liquid chromatography (HPLC). Optimization and validation of the tracer were carried out. Immunoreactivity of the all obtained tracers was check by using specific polyclonal antibodies. The results indicated that imidazols derivatives are more suitable from immunoreactivity view and storage period.

  16. 15N Hyperpolarization of Imidazole-15N2 for Magnetic Resonance pH Sensing via SABRE-SHEATH.

    Science.gov (United States)

    Shchepin, Roman V; Barskiy, Danila A; Coffey, Aaron M; Theis, Thomas; Shi, Fan; Warren, Warren S; Goodson, Boyd M; Chekmenev, Eduard Y

    2016-06-24

    15 N nuclear spins of imidazole- 15 N 2 were hyperpolarized using NMR signal amplification by reversible exchange in shield enables alignment transfer to heteronuclei (SABRE-SHEATH). A 15 N NMR signal enhancement of ∼2000-fold at 9.4 T is reported using parahydrogen gas (∼50% para-) and ∼0.1 M imidazole- 15 N 2 in methanol:aqueous buffer (∼1:1). Proton binding to a 15 N site of imidazole occurs at physiological pH (p K a ∼ 7.0), and the binding event changes the 15 N isotropic chemical shift by ∼30 ppm. These properties are ideal for in vivo pH sensing. Additionally, imidazoles have low toxicity and are readily incorporated into a wide range of biomolecules. 15 N-Imidazole SABRE-SHEATH hyperpolarization potentially enables pH sensing on scales ranging from peptide and protein molecules to living organisms.

  17. A Novel Tetrasubstituted Imidazole as a Prototype for the Development of Anti-inflammatory Drugs.

    Science.gov (United States)

    Nascimento, Marcus Vinicius P S; Munhoz, Antonio C M; Theindl, Lais C; Mohr, Eduarda Talita B; Saleh, Najla; Parisotto, Eduardo B; Rossa, Thaís A; Zamoner, Ariane; Creczynski-Pasa, Tania B; Filippin-Monteiro, Fabíola B; Sá, Marcus M; Dalmarco, Eduardo Monguilhott

    2018-04-14

    Although inflammation is a biological phenomenon that exists to protect the host against infections and/or related problems, its unceasing activation results in the aggravation of several medical conditions. Imidazoles, whether natural or synthetic, are molecules related to a broad spectrum of biological effects, including anti-inflammatory properties. In this study, we screened eight novel small molecules of the imidazole class synthesized by our research group for their in vitro anti-inflammatory activity. The effect of the selected molecules was confirmed in an in vivo inflammatory model. We also analyzed whether the effects were caused by inhibition of nuclear factor kappa B (NF-κB) transcription factor transmigration. Of the eight imidazoles tested, methyl 1-allyl-2-(4-fluorophenyl)-5-phenyl-1H-imidazole-4-acetate (8) inhibited nitric oxide metabolites and pro-inflammatory cytokine (TNF-α, IL-6, and IL-1β) secretion in J774 macrophages stimulated with LPS. It also attenuated leukocyte migration and exudate formation in the pleural cavity of mice challenged with carrageenan. Furthermore, imidazole 8 reverted the oxidative stress pattern triggered by carrageenan in the pleural cavity by diminishing myeloperoxidase, superoxide dismutase, catalase, and glutathione S-transferase activities and reducing the production of nitric oxide metabolites and thiobarbituric acid-reactive substances. Finally, these effects can be attributed, at least in part, to the ability of this compound to prevent NF-κB transmigration. In this context, our results demonstrate that imidazole 8 has promising potential as a prototype for the development of a new anti-inflammatory drug to treat inflammatory conditions in which NF-κB and oxidative stress play a prominent role. Graphical Abstract ᅟ.

  18. Structural insight into activity enhancement and inhibition of H64A carbonic anhydrase II by imidazoles

    Directory of Open Access Journals (Sweden)

    Mayank Aggarwal

    2014-03-01

    Full Text Available Human carbonic anhydrases (CAs are zinc metalloenzymes that catalyze the hydration and dehydration of CO2 and HCO3−, respectively. The reaction follows a ping-pong mechanism, in which the rate-limiting step is the transfer of a proton from the zinc-bound solvent (OH−/H2O in/out of the active site via His64, which is widely believed to be the proton-shuttling residue. The decreased catalytic activity (∼20-fold lower with respect to the wild type of a variant of CA II in which His64 is replaced with Ala (H64A CA II can be enhanced by exogenous proton donors/acceptors, usually derivatives of imidazoles and pyridines, to almost the wild-type level. X-ray crystal structures of H64A CA II in complex with four imidazole derivatives (imidazole, 1-methylimidazole, 2-methylimidazole and 4-methylimidazole have been determined and reveal multiple binding sites. Two of these imidazole binding sites have been identified that mimic the positions of the `in' and `out' rotamers of His64 in wild-type CA II, while another directly inhibits catalysis by displacing the zinc-bound solvent. The data presented here not only corroborate the importance of the imidazole side chain of His64 in proton transfer during CA catalysis, but also provide a complete structural understanding of the mechanism by which imidazoles enhance (and inhibit when used at higher concentrations the activity of H64A CA II.

  19. Coordination compounds of metals with imidazoles and benzimidazoles. [Metals: V, Th, Mo, Cd, rare earths, etc

    Energy Technology Data Exchange (ETDEWEB)

    Novikova, G A; Molodkin, A K; Kukalenko, S S

    1988-12-01

    Methods of preparation, composition and structure of UO/sub 2//sup 2+/, Th/sup 4+/, Mo/sup 3+/, Cd/sup 2+/, Ln/sup 3+/ metal ion complexes with imidazoles and benzimidazoles are considered in reviews of native and foreign literature of up to 1985. Complexes are customarily prepared by direct interaction of ligands with inorganic salts in different organic solvents. Complex composition is defined by the nature of complexing metal and inorganic salt anion, ligand volume and basicity, as well as solvent characteristics. Effect of R substituent in imidazole and benzimidazole side chain on composition of coordination compounds is considered.

  20. Ab initio study of the EFG at the N sites in imidazole

    Energy Technology Data Exchange (ETDEWEB)

    Brown Goncalves, Marcos, E-mail: browngon@if.usp.br [Universidade de Sao Paulo, Instituto de Fisica (Brazil); Di Felice, R. [National Center on Nanostructures and Biosystems at Surfaces (S3) of INFM-CNR (Italy); Poleshchuk, O. Kh. [Tomsk State Pedagogical University (Russian Federation); Petrilli, H. M. [Universidade de Sao Paulo, Instituto de Fisica (Brazil)

    2008-01-15

    We study the nuclear quadrupole interaction at the nitrogen sites in the molecular and crystalline phases of the imidazole compound. We use PAW which is a state-of-the-art method to calculate the electronic structure and electric field gradient at the nucleus in the framework of the density functional theory. The quadrupole frequencies at both imino and amino N sites are in excellent agreement with measurements. This is the first time that the electric field gradient at crystalline imidazole is correctly treated by an ab initio theoretical approach.

  1. Inversion of allosteric effect of arginine on N-acetylglutamate synthase, a molecular marker for evolution of tetrapods

    Directory of Open Access Journals (Sweden)

    Cabrera-Luque Juan

    2008-09-01

    Full Text Available Abstract Background The efficient conversion of ammonia, a potent neurotoxin, into non-toxic metabolites was an essential adaptation that allowed animals to move from the aquatic to terrestrial biosphere. The urea cycle converts ammonia into urea in mammals, amphibians, turtles, snails, worms and many aquatic animals and requires N-acetylglutamate (NAG, an essential allosteric activator of carbamylphosphate synthetase I (CPSI in mammals and amphibians, and carbamylphosphate synthetase III (CPSIII in fish and invertebrates. NAG-dependent CPSI and CPSIII catalyze the formation of carbamylphosphate in the first and rate limiting step of ureagenesis. NAG is produced enzymatically by N-acetylglutamate synthase (NAGS, which is also found in bacteria and plants as the first enzyme of arginine biosynthesis. Arginine is an allosteric inhibitor of microbial and plant NAGS, and allosteric activator of mammalian NAGS. Results Information from mutagenesis studies of E. coli and P. aeruginosa NAGS was combined with structural information from the related bacterial N-acetylglutamate kinases to identify four residues in mammalian NAGS that interact with arginine. Substitutions of these four residues were engineered in mouse NAGS and into the vertebrate-like N-acetylglutamate synthase-kinase (NAGS-K of Xanthomonas campestris, which is inhibited by arginine. All mutations resulted in arginine losing the ability to activate mouse NAGS, and inhibit X. campestris NAGS-K. To examine at what point in evolution inversion of arginine effect on NAGS occur, we cloned NAGS from fish and frogs and examined the arginine response of their corresponding proteins. Fish NAGS were partially inhibited by arginine and frog NAGS were activated by arginine. Conclusion Difference in arginine effect on bacterial and mammalian NAGS most likely stems from the difference in the type of conformational change triggered by arginine binding to these proteins. The change from arginine

  2. Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning

    Science.gov (United States)

    Gerek, Z. Nevin; Ozkan, S. Banu

    2011-01-01

    The allosteric mechanism plays a key role in cellular functions of several PDZ domain proteins (PDZs) and is directly linked to pharmaceutical applications; however, it is a challenge to elaborate the nature and extent of these allosteric interactions. One solution to this problem is to explore the dynamics of PDZs, which may provide insights about how intramolecular communication occurs within a single domain. Here, we develop an advancement of perturbation response scanning (PRS) that couples elastic network models with linear response theory (LRT) to predict key residues in allosteric transitions of the two most studied PDZs (PSD-95 PDZ3 domain and hPTP1E PDZ2 domain). With PRS, we first identify the residues that give the highest mean square fluctuation response upon perturbing the binding sites. Strikingly, we observe that the residues with the highest mean square fluctuation response agree with experimentally determined residues involved in allosteric transitions. Second, we construct the allosteric pathways by linking the residues giving the same directional response upon perturbation of the binding sites. The predicted intramolecular communication pathways reveal that PSD-95 and hPTP1E have different pathways through the dynamic coupling of different residue pairs. Moreover, our analysis provides a molecular understanding of experimentally observed hidden allostery of PSD-95. We show that removing the distal third alpha helix from the binding site alters the allosteric pathway and decreases the binding affinity. Overall, these results indicate that (i) dynamics plays a key role in allosteric regulations of PDZs, (ii) the local changes in the residue interactions can lead to significant changes in the dynamics of allosteric regulations, and (iii) this might be the mechanism that each PDZ uses to tailor their binding specificities regulation. PMID:21998559

  3. Spectroscopic study of 2-, 4- and 5-substituents on p Ka values of imidazole heterocycles prone to intramolecular proton-electrons transfer

    Science.gov (United States)

    Eseola, Abiodun O.; Obi-Egbedi, Nelson O.

    2010-02-01

    New 2-(1H-imidazol-2-yl)phenols ( L1Et- L8tBuPt) bearing a phenolic proton in the vicinity of the imidazole base were prepared and characterized. Experimental studies of the dependence of their protonation/deprotonation equilibrium on substituent identities and intramolecular hydrogen bonding tendencies were carried out using electronic absorption spectroscopy at varying pH values. In order to make comparison, 2-(anthracen-10-yl)-4,5-diphenyl-1H-imidazole ( L9Anthr) bearing no phenolic proton and 4,5-diphenyl-2-(4,5-diphenyl-1H-imidazol-2-yl)-1H-imidazole ( L10BisIm) bearing two symmetrical imidazole base fragments were also prepared and experimentally investigated. DFT calculations were carried out to study frontier orbitals of the investigated molecules. While electron-releasing substituents produced increase in protonation-deprotonation p Kas for the hydroxyl group, values for the imidazole base were mainly affected by polarization of the imidazole ring aromaticity across the 2-imidazole carbon and the 4,5-imidazole carbons axis of the imidazole ring. It was concluded that electron-releasing substituents on the phenol ring and/or electron-withdrawing substituents on 4,5-imidazole carbons negatively affects donor strengths/coordination chemistries of 2-(1H-imidazol-2-yl)phenols, and vice versa. Change of substituents on the phenol ring significantly altered the donor strength of the imidazole base. The understanding of p Ka variation on account of electronic effects of substituents in this work should aid the understanding of biochemical properties and substituent environments of imidazole-containing biomacromolecules.

  4. An allosteric conduit facilitates dynamic multisite substrate recognition by the SCFCdc4 ubiquitin ligase

    Science.gov (United States)

    Csizmok, Veronika; Orlicky, Stephen; Cheng, Jing; Song, Jianhui; Bah, Alaji; Delgoshaie, Neda; Lin, Hong; Mittag, Tanja; Sicheri, Frank; Chan, Hue Sun; Tyers, Mike; Forman-Kay, Julie D.

    2017-01-01

    The ubiquitin ligase SCFCdc4 mediates phosphorylation-dependent elimination of numerous substrates by binding one or more Cdc4 phosphodegrons (CPDs). Methyl-based NMR analysis of the Cdc4 WD40 domain demonstrates that Cyclin E, Sic1 and Ash1 degrons have variable effects on the primary Cdc4WD40 binding pocket. Unexpectedly, a Sic1-derived multi-CPD substrate (pSic1) perturbs methyls around a previously documented allosteric binding site for the chemical inhibitor SCF-I2. NMR cross-saturation experiments confirm direct contact between pSic1 and the allosteric pocket. Phosphopeptide affinity measurements reveal negative allosteric communication between the primary CPD and allosteric pockets. Mathematical modelling indicates that the allosteric pocket may enhance ultrasensitivity by tethering pSic1 to Cdc4. These results suggest negative allosteric interaction between two distinct binding pockets on the Cdc4WD40 domain may facilitate dynamic exchange of multiple CPD sites to confer ultrasensitive dependence on substrate phosphorylation.

  5. An antibody that prevents serpin polymerisation acts by inducing a novel allosteric behaviour.

    Science.gov (United States)

    Motamedi-Shad, Neda; Jagger, Alistair M; Liedtke, Maximilian; Faull, Sarah V; Nanda, Arjun Scott; Salvadori, Enrico; Wort, Joshua L; Kay, Christopher W M; Heyer-Chauhan, Narinder; Miranda, Elena; Perez, Juan; Ordóñez, Adriana; Haq, Imran; Irving, James A; Lomas, David A

    2016-10-01

    Serpins are important regulators of proteolytic pathways with an antiprotease activity that involves a conformational transition from a metastable to a hyperstable state. Certain mutations permit the transition to occur in the absence of a protease; when associated with an intermolecular interaction, this yields linear polymers of hyperstable serpin molecules, which accumulate at the site of synthesis. This is the basis of many pathologies termed the serpinopathies. We have previously identified a monoclonal antibody (mAb4B12) that, in single-chain form, blocks α1-antitrypsin (α1-AT) polymerisation in cells. Here, we describe the structural basis for this activity. The mAb4B12 epitope was found to encompass residues Glu32, Glu39 and His43 on helix A and Leu306 on helix I. This is not a region typically associated with the serpin mechanism of conformational change, and correspondingly the epitope was present in all tested structural forms of the protein. Antibody binding rendered β-sheet A - on the opposite face of the molecule - more liable to adopt an 'open' state, mediated by changes distal to the breach region and proximal to helix F. The allosteric propagation of induced changes through the molecule was evidenced by an increased rate of peptide incorporation and destabilisation of a preformed serpin-enzyme complex following mAb4B12 binding. These data suggest that prematurely shifting the β-sheet A equilibrium towards the 'open' state out of sequence with other changes suppresses polymer formation. This work identifies a region potentially exploitable for a rational design of ligands that is able to dynamically influence α1-AT polymerisation. © 2016 The Author(s).

  6. Evidence for allosterism in ribulose-1,5-bisphosphate carboxylase/oxygenase from comfrey

    International Nuclear Information System (INIS)

    Mueller, D.D.; Bolden, T.D.

    1986-01-01

    Evidence has been obtained suggesting that ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is an allosteric enzyme in the sense that it shows cooperative active site binding, cooperative interactions between the activation and active sites and significant binding of some metabolites at a second site. Investigation of the binding of a potent competitive inhibitor. 2-carboxymannitol-1,6-bisphosphate (CMBP) by 31 P-NMR indicated essentially 1:1 binding with the active sites of comfrey RuBisCo. Among the interactions of competitive inhibitors, as measured by difference UV spectroscopy, the binding curves for ortho-phosphate and ribose-5-phosphate were better fitted by a Monod-Wyman-Changeux model than by an independent site model, whereas the binding of CMBP and 2-phosphoglycolate were not. Difference UV methods also were used to study activation by CO 2 which at pH 7.9 in 10 mM MgCl 2 showed positive cooperativity with k = 100 +/- 3 μM (based on pK/sub a/ = 6.4 for the CO 2 -HCO 3 - equilibrium) and L = 3.5 +/- 0.7. Addition of saturating amounts of CMBP and lowering the MgCl 2 to 2 mM still gave a sigmoidal curve but it was shifted to higher CO 2 concentrations (k = 124 +/- 2 μM and L = 31 +/- 3). In the absence of CMBP the same conditions gave k = 26 +/- 2 μM for L = 3.5. Conversely, k was 0.96 +/- 0.08 μM for CMBP in 0.5 mM MgCl 2 without added NaHCO 3 but was 21 +/- 0.06 μM in 10 MgCl 2 and 2 mM NaHCO 3 , pH 7.3

  7. Efficient library synthesis of imidazoles using a multicomponent reaction and microwave irradiation

    NARCIS (Netherlands)

    Gelens, E.; De Kanter, F.J.J.; Schmitz, R.F.; Sliedregt, L.A.; Van Steen, B.J.; Kruse, C.G.; Leurs, R.; Groen, M.B.; Orru, R.V.A.

    2006-01-01

    Optimization of Radziszewski's four-component reaction employing a microwave-assisted protocol, led to a small library of 48 imidazoles with a success rate of 65% (conversion >45%). All three diversity points of the four-component reaction were varied. Aromatic and aliphatic inputs were successfully

  8. Increased urinary imidazolepropionic acid, n-acetylhistamine and other imidazole compounds in patients with intestinal disorders

    NARCIS (Netherlands)

    Heiden, C. van der; Wadman, S.K.; Bree, P.K. de; Wauters, E.A.K.

    In 26 out of a large group of patients with gastrointestinal disorders abnormal urinary imidazole excretion patterns were found. Most frequently excessive or increased amounts of imidazolepropionic acid (ImPA) occurred, and as next N-acetylhistamine was excreted in excess. In a number of cases the

  9. Tannic acid Catalyzed an Efficient Synthesis of 2,4,5-Triaryl-1H-Imidazole

    Directory of Open Access Journals (Sweden)

    Shitole Nana Vikram

    2013-05-01

    Full Text Available Tannic acid (C76H52O46 has been found to be an efficient catalyst for one-pot synthesis of 2,4,5-triaryl substituted imidazoles by the reaction of an arylaldehyde, benzyl/benzoin and an ammonium acetate. The short reaction time and excellent yields making this protocol practical and economically attractive.

  10. Structural, photophysical, and theoretical studies of imidazole-based excited-state intramolecular proton transfer molecules

    Science.gov (United States)

    Somasundaram, Sivaraman; Kamaraj, Eswaran; Hwang, Su Jin; Park, Sanghyuk

    2018-02-01

    Imidazole-based excited state intramolecular proton transfer (ESIPT) blue fluorescent molecules, 2-(1-(4-chlorophenyl)-4,5-diphenyl-1H-imidazol-2-yl)phenol (BHPI-Cl) and 2-(1-(4-bromophenyl)-4,5-diphenyl-1H-imidazol-2-yl)phenol (BHPI-Br) were designed and synthesized by Debus-Radziszewski method through a one-pot multicomponent reaction in high yield. The synthesized compounds were fully characterized by 1H NMR, 13C NMR, FT-IR, FT-Raman, GC-Mass, and elemental analysis. The molecular structures in single crystal lattice were studied by X-ray crystallographic analysis. Because of the intramolecular hydrogen bonding, hydroxyphenyl group is planar to the central imidazole ring, while the other phenyl rings gave distorted conformations to the central heterocyclic ring. BHPI-Cl and BHPI-Br molecules showed intense ESIPT fluorescence at 480 nm, because the two twisted phenyl rings on 4- and 5-positions have reduced intermolecular interaction between adjacent molecules in each crystal through a head-to-tail packing manner. Quantum chemical calculations of energies were carried out by (TD-)DFT using B3LYP/6-31G(d, p) basis set to predict the electronic absorption spectra of the compounds, and they showed good agreement between the computational and the experimental values. The thermal analyses of the synthesized molecules were also carried out by TGA/DSC method.

  11. Synthesis and properties of imidazole-grafted hybrid inorganic-organic polymer membranes

    International Nuclear Information System (INIS)

    Li Siwen; Zhou Zhen; Liu Meilin; Li Wen; Ukai, Junzo; Hase, Kohei; Nakanishi, Masatsugu

    2006-01-01

    Imidazole rings were grafted on alkoxysilane with a simple nucleophilic substitute reaction to form hybrid inorganic-organic polymers with imidazole rings. Proton exchange membranes (PEM) based on these hybrid inorganic-organic polymers and H 3 PO 4 exhibit high proton conductivity and high thermal stability in an atmosphere of low relative humidity. The grafted imidazole rings improved the proton conductivity of the membranes in the high temperature range. It is found that the proton conductivities increase with H 3 PO 4 content and temperature, reaching 3.2 x 10 -3 S/cm at 110 deg. C in a dry atmosphere for a membrane with 1 mole of imidazole ring and 7 moles of H 3 PO 4 . The proton conductivity increases with relative humidity (RH) as well, reaching 4.3 x 10 -2 S/cm at 110 deg. C when the RH is increased to about 20%. Thermogravimetric analysis (TGA) indicates that these membranes are thermally stable up to 250 deg. C in dry air, implying that they have a good potential to be used as the membranes for high-temperature PEM fuel cells

  12. Changes in the hydration structure of imidazole upon protonation: Neutron scattering and molecular simulations

    Czech Academy of Sciences Publication Activity Database

    Duboué-Dijon, Elise; Mason, Philip E.; Fischer, H. E.; Jungwirth, Pavel

    2017-01-01

    Roč. 146, č. 18 (2017), č. článku 185102. ISSN 0021-9606 R&D Projects: GA ČR(CZ) GBP208/12/G016 Institutional support: RVO:61388963 Keywords : imidazole protonation * molecular dynamics * neutron scattering Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 2.965, year: 2016

  13. Controlled synthesis of phase-pure zeolitic imidazolate framework Co-ZIF-9

    NARCIS (Netherlands)

    Öztürk, Z.; Hofmann, J.P.; Lutz, M.; Mazaj, M.; Zabukovec Logar, N.; Weckhuysen, B.M.

    2015-01-01

    The synthesis of phase-pure Co-ZIF-9, an important cobalt-based zeolitic imidazolate framework, could be achieved by modification of the reported synthesis procedure through pH adjustment of the starting synthesis mixture. The phase-pure Co-ZIF-9 material obtained has been characterized by a

  14. Metal-containing Complexes of Lactams, Imidazoles, and Benzimidazoles and Their Biological Activity

    Science.gov (United States)

    Kukalenko, S. S.; Bovykin, B. A.; Shestakova, S. I.; Omel'chenko, A. M.

    1985-07-01

    The results of the latest investigations of the problem of the synthesis of metal-containing complexes of lactams, imidazoles, and benzimidazoles, their structure, and their stability in solutions are surveyed. Some data on their biological activity (pesticide and pharmacological) and the mechanism of their physiological action are presented. The bibliography includes 190 references.

  15. Carbon dioxide selective adsorption within a highly stable mixed-ligand Zeolitic Imidazolate Framework

    KAUST Repository

    Huang, Lin; Xue, Ming; Song, Qingshan; Chen, Siru; Pan, Ying; Qiu, Shilun

    2014-01-01

    A new mixed-ligand Zeolitic Imidazolate Framework Zn4(2-mbIm) 3(bIm)5·4H2O (named JUC-160, 2-mbIm = 2-methylbenzimidazole, bIm = benzimidazole and JUC = Jilin University China) was synthesized with a solvothermal reaction of Zn(NO3) 2·6H2O, b

  16. Synthesis and potential cytotoxic activity of some new benzoxazoles, imidazoles, benzimidazoles and tetrazoles.

    Science.gov (United States)

    Arulmurugan, Subramaniyan; Kavitha, Helen P

    2013-06-01

    2 The present work deals with the synthesis of some novel heterocyclic compounds such as benzoxazoles , 7, 13 and 19, imidazoles 3, 8, 14 and 20, benzimidazoles 4, 9, 15 and 21, and tetrazoles 10, 16, and 22. The synthesized compounds were characterized by IR, 1H NMR, mass spectrometry and elemental analysis. The compounds were evaluated for cytotoxicity against human cancer cell lines such as MCF-7 (breast cancer) and HT-29 (colon cancer) by the MTT assay method. Among the tested compounds, 4,4'-sulfonylbis(N-(2-(1H-benzo[d]imidazol- -2-yl)ethyl)aniline (9), N-bis(2-(benzo[d]oxazol-2-yl)-ethyl)- 6-phenyl-1,3,5-triazine-2,4-diamine (13), N-bis(2-(1H-benzo[ d]imidazol-2-yl)ethyl)-6-phenyl-1,3,5-triazine-2,4-diamine (15) and N-tris(2-1H-benzo[d]imidazol-2-yl)ethyl)- 1,3,5-triazine-2,4,6-triamine (21) showed potent cytotoxicity.

  17. Pharmacology of basimglurant (RO4917523, RG7090), a unique metabotropic glutamate receptor 5 negative allosteric modulator in clinical development for depression.

    Science.gov (United States)

    Lindemann, Lothar; Porter, Richard H; Scharf, Sebastian H; Kuennecke, Basil; Bruns, Andreas; von Kienlin, Markus; Harrison, Anthony C; Paehler, Axel; Funk, Christoph; Gloge, Andreas; Schneider, Manfred; Parrott, Neil J; Polonchuk, Liudmila; Niederhauser, Urs; Morairty, Stephen R; Kilduff, Thomas S; Vieira, Eric; Kolczewski, Sabine; Wichmann, Juergen; Hartung, Thomas; Honer, Michael; Borroni, Edilio; Moreau, Jean-Luc; Prinssen, Eric; Spooren, Will; Wettstein, Joseph G; Jaeschke, Georg

    2015-04-01

    Major depressive disorder (MDD) is a serious public health burden and a leading cause of disability. Its pharmacotherapy is currently limited to modulators of monoamine neurotransmitters and second-generation antipsychotics. Recently, glutamatergic approaches for the treatment of MDD have increasingly received attention, and preclinical research suggests that metabotropic glutamate receptor 5 (mGlu5) inhibitors have antidepressant-like properties. Basimglurant (2-chloro-4-[1-(4-fluoro-phenyl)-2,5-dimethyl-1H-imidazol-4-ylethynyl]-pyridine) is a novel mGlu5 negative allosteric modulator currently in phase 2 clinical development for MDD and fragile X syndrome. Here, the comprehensive preclinical pharmacological profile of basimglurant is presented with a focus on its therapeutic potential for MDD and drug-like properties. Basimglurant is a potent, selective, and safe mGlu5 inhibitor with good oral bioavailability and long half-life supportive of once-daily administration, good brain penetration, and high in vivo potency. It has antidepressant properties that are corroborated by its functional magnetic imaging profile as well as anxiolytic-like and antinociceptive features. In electroencephalography recordings, basimglurant shows wake-promoting effects followed by increased delta power during subsequent non-rapid eye movement sleep. In microdialysis studies, basimglurant had no effect on monoamine transmitter levels in the frontal cortex or nucleus accumbens except for a moderate increase of accumbal dopamine, which is in line with its lack of pharmacological activity on monoamine reuptake transporters. These data taken together, basimglurant has favorable drug-like properties, a differentiated molecular mechanism of action, and antidepressant-like features that suggest the possibility of also addressing important comorbidities of MDD including anxiety and pain as well as daytime sleepiness and apathy or lethargy. Copyright © 2015 by The American Society for

  18. Stochastic thermodynamics of a chemical nanomachine: The channeling enzyme tryptophan synthase.

    Science.gov (United States)

    Loutchko, Dimitri; Eisbach, Maximilian; Mikhailov, Alexander S

    2017-01-14

    The enzyme tryptophan synthase is characterized by a complex pattern of allosteric interactions that regulate the catalytic activity of its two subunits and opening or closing of their ligand gates. As a single macromolecule, it implements 13 different reaction steps, with an intermediate product directly channeled from one subunit to another. Based on experimental data, a stochastic model for the operation of tryptophan synthase has been earlier constructed [D. Loutchko, D. Gonze, and A. S. Mikhailov, J. Phys. Chem. B 120, 2179 (2016)]. Here, this model is used to consider stochastic thermodynamics of such a chemical nanomachine. The Gibbs energy landscape of the internal molecular states is determined, the production of entropy and its flow within the enzyme are analyzed, and the information exchange between the subunits resulting from allosteric cross-regulations and channeling is discussed.

  19. Allosteric mechanism controls traffic in the chaperone/usher pathway.

    Science.gov (United States)

    Di Yu, Xiao; Dubnovitsky, Anatoly; Pudney, Alex F; Macintyre, Sheila; Knight, Stefan D; Zavialov, Anton V

    2012-11-07

    Many virulence organelles of Gram-negative bacterial pathogens are assembled via the chaperone/usher pathway. The chaperone transports organelle subunits across the periplasm to the outer membrane usher, where they are released and incorporated into growing fibers. Here, we elucidate the mechanism of the usher-targeting step in assembly of the Yersinia pestis F1 capsule at the atomic level. The usher interacts almost exclusively with the chaperone in the chaperone:subunit complex. In free chaperone, a pair of conserved proline residues at the beginning of the subunit-binding loop form a "proline lock" that occludes the usher-binding surface and blocks usher binding. Binding of the subunit to the chaperone rotates the proline lock away from the usher-binding surface, allowing the chaperone-subunit complex to bind to the usher. We show that the proline lock exists in other chaperone/usher systems and represents a general allosteric mechanism for selective targeting of chaperone:subunit complexes to the usher and for release and recycling of the free chaperone. Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. Are AMPA Receptor Positive Allosteric Modulators Potential Pharmacotherapeutics for Addiction?

    Directory of Open Access Journals (Sweden)

    Lucas R. Watterson

    2013-12-01

    Full Text Available Positive allosteric modulators (PAMs of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA receptors are a diverse class of compounds that increase fast excitatory transmission in the brain. AMPA PAMs have been shown to facilitate long-term potentiation, strengthen communication between various cortical and subcortical regions, and some of these compounds increase the production and release of brain-derived neurotrophic factor (BDNF in an activity-dependent manner. Through these mechanisms, AMPA PAMs have shown promise as broad spectrum pharmacotherapeutics in preclinical and clinical studies for various neurodegenerative and psychiatric disorders. In recent years, a small collection of preclinical animal studies has also shown that AMPA PAMs may have potential as pharmacotherapeutic adjuncts to extinction-based or cue-exposure therapies for the treatment of drug addiction. The present paper will review this preclinical literature, discuss novel data collected in our laboratory, and recommend future research directions for the possible development of AMPA PAMs as anti-addiction medications.

  1. Allosteric conformational barcodes direct signaling in the cell.

    Science.gov (United States)

    Nussinov, Ruth; Ma, Buyong; Tsai, Chung-Jung; Csermely, Peter

    2013-09-03

    The cellular network is highly interconnected. Pathways merge and diverge. They proceed through shared proteins and may change directions. How are cellular pathways controlled and their directions decided, coded, and read? These questions become particularly acute when we consider that a small number of pathways, such as signaling pathways that regulate cell fates, cell proliferation, and cell death in development, are extensively exploited. This review focuses on these signaling questions from the structural standpoint and discusses the literature in this light. All co-occurring allosteric events (including posttranslational modifications, pathogen binding, and gain-of-function mutations) collectively tag the protein functional site with a unique barcode. The barcode shape is read by an interacting molecule, which transmits the signal. A conformational barcode provides an intracellular address label, which selectively favors binding to one partner and quenches binding to others, and, in this way, determines the pathway direction, and, eventually, the cell's response and fate. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Coarse-grained molecular simulations of allosteric cooperativity

    Energy Technology Data Exchange (ETDEWEB)

    Nandigrami, Prithviraj; Portman, John J. [Department of Physics, Kent State University, Kent, Ohio 44242 (United States)

    2016-03-14

    Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein’s functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two Ca{sup 2+} ions to each domain of Calmodulin (CaM) through simulations of a simple coarse-grained model. In this model, the protein’s conformational transitions between open and closed conformational ensembles are simulated explicitly and ligand binding and unbinding are treated implicitly within the grand canonical ensemble. Ligand binding is cooperative because the binding sites are coupled through a shift in the dominant conformational ensemble upon binding. The classic Monod-Wyman-Changeux model of allostery with appropriate binding free energies to the open and closed ensembles accurately describes the simulated binding thermodynamics. The simulations predict that the two domains of CaM have distinct binding affinity and cooperativity. In particular, the C-terminal domain binds Ca{sup 2+} with higher affinity and greater cooperativity than the N-terminal domain. From a structural point of view, the affinity of an individual binding loop depends sensitively on the loop’s structural compatibility with the ligand in the bound ensemble, as well as the conformational flexibility of the binding site in the unbound ensemble.

  3. Role of allosteric switch residue histidine 195 in maintaining active-site asymmetry in presynaptic filaments of bacteriophage T4 UvsX recombinase.

    Science.gov (United States)

    Farb, Joshua N; Morrical, Scott W

    2009-01-16

    Recombinases of the highly conserved RecA/Rad51 family play central roles in homologous recombination and DNA double-stranded break repair. RecA/Rad51 enzymes form presynaptic filaments on single-stranded DNA (ssDNA) that are allosterically activated to catalyze ATPase and DNA strand-exchange reactions. Information is conveyed between DNA- and ATP-binding sites, in part, by a highly conserved glutamine residue (Gln194 in Escherichia coli RecA) that acts as an allosteric switch. The T4 UvsX protein is a divergent RecA ortholog and contains histidine (His195) in place of glutamine at the allosteric switch position. UvsX and RecA catalyze similar strand-exchange reactions, but differ in other properties. UvsX produces both ADP and AMP as products of its ssDNA-dependent ATPase activity--a property that is unique among characterized recombinases. Details of the kinetics of ssDNA-dependent ATP hydrolysis reactions indicate that UvsX-ssDNA presynaptic filaments are asymmetric and contain two classes of ATPase active sites: one that generates ADP, and another that generates AMP. Active-site asymmetry is reduced by mutations at the His195 position, since UvsX-H195Q and UvsX-H195A mutants both exhibit stronger ssDNA-dependent ATPase activity, with lower cooperativity and markedly higher ADP/AMP product ratios, than wild-type UvsX. Reduced active-site asymmetry correlates strongly with reduced ssDNA-binding affinity and DNA strand-exchange activity in both H195Q and H195A mutants. These and other results support a model in which allosteric switch residue His195 controls the formation of an asymmetric conformation of UvsX-ssDNA filaments that is active in DNA strand exchange. The implications of our findings for UvsX recombination functions, and for RecA functions in general, are discussed.

  4. Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions.

    Science.gov (United States)

    Hacisuleyman, Aysima; Erman, Burak

    2017-06-01

    A fast and approximate method of generating allosteric communication landscapes in proteins is presented by using Schreiber's entropy transfer concept in combination with the Gaussian Network Model of proteins. Predictions of the model and the allosteric communication landscapes generated show that information transfer in proteins does not necessarily take place along a single path, but an ensemble of pathways is possible. The model emphasizes that knowledge of entropy only is not sufficient for determining allosteric communication and additional information based on time delayed correlations should be introduced, which leads to the presence of causality in proteins. The model provides a simple tool for mapping entropy sink-source relations into pairs of residues. By this approach, residues that should be manipulated to control protein activity may be determined. This should be of great importance for allosteric drug design and for understanding the effects of mutations on function. The model is applied to determine allosteric communication in three proteins, Ubiquitin, Pyruvate Kinase, and the PDZ domain. Predictions are in agreement with molecular dynamics simulations and experimental evidence. Proteins 2017; 85:1056-1064. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  5. Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure.

    Science.gov (United States)

    Takayanagi, Masayoshi; Kurisaki, Ikuo; Nagaoka, Masataka

    2014-04-08

    Protein allostery is essential for vital activities. Allosteric regulation of human hemoglobin (HbA) with two quaternary states T and R has been a paradigm of allosteric structural regulation of proteins. It is widely accepted that oxygen molecules (O2) act as a "site-specific" homotropic effector, or the successive O2 binding to the heme brings about the quaternary regulation. However, here we show that the site-specific allosteric effect is not necessarily only a unique mechanism of O2 allostery. Our simulation results revealed that the solution environment of high O2 partial pressure enhances the quaternary change from T to R without binding to the heme, suggesting an additional "non-site-specific" allosteric effect of O2. The latter effect should play a complementary role in the quaternary change by affecting the intersubunit contacts. This analysis must become a milestone in comprehensive understanding of the allosteric regulation of HbA from the molecular point of view.

  6. Synthesis of 1-(2,3-dihydroxypropyl)-2-nitro-1H-imidazole-2-14C and N-(2-hydroxyethyl)-2-(2-nitro-1H-imidazol-1-YL-2-14C)acetamide

    International Nuclear Information System (INIS)

    Fong, M.T.; Leaffer, M.A.

    1986-01-01

    We have prepared the 14 C-labeled analogs of NSC 261036, 1-(2,3-dihydroxypropyl)-2-nitro-1H-imidazole-2- 14 C, and NSC 301467, N-(2-hydroxyethyl)-2-(2-nitro-1H-imidazol-1-yl-2- 14 C) acetamide, for pharmacological, drug distribution, and mechanisms of action studies. The latter is an analog designed for lower toxicity and improved properties. The former is a metabolite of, and appears to be less toxic than, misonidazole. (author)

  7. Mixed-linker zeolitic imidazolate framework mixed-matrix membranes for aggressive CO2 separation from natural gas

    KAUST Repository

    Thompson, Joshua A.; Vaughn, Justin T.; Brunelli, Nicholas A.; Koros, William J.; Jones, Christopher W.; Nair, Sankar

    2014-01-01

    Zeolitic imidazolate framework (ZIF) materials are a promising subclass of metal-organic frameworks (MOF) for gas separations. However, due to the deleterious effects of gate-opening phenomena associated with organic linker rotation near

  8. Synthesis and characterization of new chiral ketopinic acid-derived catalysts immobilized on polystyrene-bound imidazole

    Directory of Open Access Journals (Sweden)

    Hassan Yusuf

    2017-02-01

    Full Text Available Four new chiral ketopinic acid-derived catalysts were anchored on a polystyrene-bound imidazole via non-covalent bond. The resulting heterogeneous catalysts were successfully characterized using IR, SEM, and TGA analyses.

  9. High-performance polyamide thin-film-nanocomposite reverse osmosis membranes containing hydrophobic zeolitic imidazolate framework-8

    KAUST Repository

    Duan, Jintang; Pan, Yichang; Pacheco Oreamuno, Federico; Litwiller, Eric; Lai, Zhiping; Pinnau, Ingo

    2015-01-01

    A hydrophobic, hydrothermally stable metal-organic framework (MOF) - zeolitic imidazolate framework-8 (ZIF-8) was successfully incorporated into the selective polyamide (PA) layer of thin-film nanocomposite (TFN) membranes for water desalination

  10. Purification, kinetic behavior, and regulation of NAD(P)+ malic enzyme of tumor mitochondria.

    Science.gov (United States)

    Moreadith, R W; Lehninger, A L

    1984-05-25

    The purification and kinetic characterization of an NAD(P)+-malic enzyme from 22aH mouse hepatoma mitochondria are described. The enzyme was purified 328-fold with a final yield of 51% and specific activity of 38.1 units/mg of protein by employing DEAE-cellulose chromatography and an ATP affinity column. Sephadex G-200 chromatography yielded a native Mr = 240,000. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a major subunit with Mr = 61,000, suggesting a tetrameric structure, and also showed that the preparation contained less than 10% polypeptide impurities. Use of the ATP affinity column required the presence of MnCl2 and fumarate (an allosteric activator) in the elution buffers. In the absence of fumarate, the Michaelis constants for malate, NAD+, and NADP+ were 3.6 mM, 55 microM, and 72 microM, respectively; in the presence of fumarate (2 mM), the constants were 0.34 mM, 9 microM, and 13 microM, respectively. ATP was shown to be an allosteric inhibitor, competitive with malate. However, the inhibition by ATP displayed hyperbolic competitive kinetics with a KI (ATP) of 80 microM (minus fumarate) and 0.5 mM (plus 2 mM fumarate). The allosteric properties of the enzyme are integrated into a rationale for its specific role in the pathways of malate and glutamate oxidation in tumor mitochondria.

  11. Steric hindrance mutagenesis in the conserved extracellular vestibule impedes allosteric binding of antidepressants to the serotonin transporter

    DEFF Research Database (Denmark)

    Plenge, Per; Shi, Lei; Beuming, Thijs

    2012-01-01

    be involved in the allosteric binding in the extracellular vestibule located above the central substrate binding (S1) site. Indeed, mutagenesis of selected residues in the vestibule reduces the allosteric potency of (S)-citalopram and clomipramine. The identified site is further supported by the inhibitory...

  12. Phase transition behavior of novel pH-sensitive polyaspartamide derivatives grafted with 1-(3-aminopropyl)imidazole.

    Science.gov (United States)

    Seo, Kwangwon; Kim, Dukjoon

    2006-09-15

    New pH-sensitive polyaspartamide derivatives were synthesized by grafting 1-(3-aminopropyl)imidazole and/or O-(2-aminoethyl)-O'-methylpoly(ethylene glycol) 5000 on polysuccinimide for application in intracellular drug delivery systems. The DS of 1-(3-aminopropyl)imidazole was adjusted by the feed molar ratio, and the structure of the prepared polymer was confirmed using FT-IR and 1H NMR spectroscopy. Their pH-sensitive properties were characterized by light transmittance measurements, and the particle size and its distribution were investigated by dynamic light scattering measurements at varying pH values. The pH-sensitive phase transition was clearly observed in polymer solutions with a high substitution of 1-(3-aminopropyl)imidazole. The prepared polymers showed a high buffering capacity between pH 5 and 7, and this increased with the DS of 1-(3-aminopropyl)imidazole. The pH dependence of the aggregation and de-aggregation behavior was examined using a fluorescence spectrometer. For MPEG/imidazole-g-polyaspartamides with a DS of 1-(3-aminopropyl)imidazole over 82%, self aggregates associated with the hydrophobic interactions of the unprotonated imidazole groups were observed at pH values above 7, and their mean size was over 200 nm, while the aggregates of polymers were dissociated at pH values below 7 by the protonation of imidazole groups. These pH-sensitive polyaspartamide derivatives are potential basic candidates for intracellular drug delivery carriers triggered by small pH changes.

  13. Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins.

    Science.gov (United States)

    Yao, Xin-Qiu; Malik, Rabia U; Griggs, Nicholas W; Skjærven, Lars; Traynor, John R; Sivaramakrishnan, Sivaraj; Grant, Barry J

    2016-02-26

    G protein α subunits cycle between active and inactive conformations to regulate a multitude of intracellular signaling cascades. Important structural transitions occurring during this cycle have been characterized from extensive crystallographic studies. However, the link between observed conformations and the allosteric regulation of binding events at distal sites critical for signaling through G proteins remain unclear. Here we describe molecular dynamics simulations, bioinformatics analysis, and experimental mutagenesis that identifies residues involved in mediating the allosteric coupling of receptor, nucleotide, and helical domain interfaces of Gαi. Most notably, we predict and characterize novel allosteric decoupling mutants, which display enhanced helical domain opening, increased rates of nucleotide exchange, and constitutive activity in the absence of receptor activation. Collectively, our results provide a framework for explaining how binding events and mutations can alter internal dynamic couplings critical for G protein function. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Allosteric cross-talk in chromatin can mediate drug-drug synergy

    Science.gov (United States)

    Adhireksan, Zenita; Palermo, Giulia; Riedel, Tina; Ma, Zhujun; Muhammad, Reyhan; Rothlisberger, Ursula; Dyson, Paul J.; Davey, Curt A.

    2017-03-01

    Exploitation of drug-drug synergism and allostery could yield superior therapies by capitalizing on the immensely diverse, but highly specific, potential associated with the biological macromolecular landscape. Here we describe a drug-drug synergy mediated by allosteric cross-talk in chromatin, whereby the binding of one drug alters the activity of the second. We found two unrelated drugs, RAPTA-T and auranofin, that yield a synergistic activity in killing cancer cells, which coincides with a substantially greater number of chromatin adducts formed by one of the compounds when adducts from the other agent are also present. We show that this occurs through an allosteric mechanism within the nucleosome, whereby defined histone adducts of one drug promote reaction of the other drug at a distant, specific histone site. This opens up possibilities for epigenetic targeting and suggests that allosteric modulation in nucleosomes may have biological relevance and potential for therapeutic interventions.

  15. Investigation of cobalt porphyrin doped polymer membrane films for the optical sensing of imidazole and its derivatives

    Directory of Open Access Journals (Sweden)

    Yueyang Tan

    2015-03-01

    Full Text Available A cobalt(II porphyrin was successfully incorporated into polymer membranes for the optical sensing of imidazole and its derivatives. This research has led to a better understanding of the behavior of Co(II porphyrin in solution and in polymeric membranes. In aprotic dichloromethane (DCM, the Co(II tetraphenylporphyrin (CoTPP and Co(II octaethylporphyrin (CoOEP show a sensitive response to imidazole due to the strong ligation of the N-3 on the imidazole ring to the Co(II center, which induces an absorbance change to the Soret band. However, when doped in polymeric films, only the CoTPP exhibits moderate sensitivity towards aqueous imidazole, histamine and histidine. This weakened coordination ability of CoTPP towards imidazole in the polymer films may be due to the coordination of the plasticizer, the impurities from the THF and polymer matrix at the Co(II center. The selectivity of the polymer films towards imidazole over common anions is high. Lifetime of the cobalt(II porphyrin incorporated polymer film was relatively short.

  16. Synthesis, chemical and biological properties of the new mono- and bis-derivatives of imidazoles

    Directory of Open Access Journals (Sweden)

    E. V. Welchinska

    2014-12-01

    Full Text Available The aim of research. The problem of finding effective antitumour medical preparation with low toxicity is an important issue of medical and pharmaceutical chemistry. Knowledge of cancer cell features and its metabolism enables to predict the direction of chemical and biological research, to conduct a targeted synthesis of potential drugs, and to assess their applicability in oncological practice as antitumor agents. The purpose of work is to explain preformed heterocycles as purines, its synthesis and investigation of chemical and biological properties. After construction of the potential active structures we proposed the new method of original derivatives synthesis which are received on the base of imidazole, from one side, and fluorocontaining common anesthetic halothane (2-bromo-1,1,1-trifluoro-2-chloroethane from other side. Molecular complex of more perspective biologically active bis-imidazole with antitumour bacterial lectine has been received. With the purpose to synthesize potential antitumour compounds on the base of halothane and imidazole, new convenient methods for the preparation of original heterocyclic derivatives of imidazole have been described. The structure and composition of synthesized compound has been confirmed by the methods of elemental analysis, IR- and NMRІН-spectra. Materials and methods. The majority of the absolute organic solvents (benzene, dimethylformamide, ethyl ester employed in the present studies were distilled before their use. Organic solvents were dried over anhydrous magnesium sulfate or metallic sodium. Gas-liquid chromatography was carried out by Perkin Elmer chromatograph with UV-detector ("Perkin", Germany. IR spectra were recorded in a UR-20 spectrometer ("Charles Ceise Hena", Germany. The 1HNMR spectra were recorded in DMSO-d6 on a 200 MHz BrakerWP-200 ("Braker", Switzerland or Varian T-60 spectrometer ("Varian", USA. Investigation of critical toxicity of new compounds was carried out at

  17. Biased signaling of lipids and allosteric actions of synthetic molecules for GPR119

    DEFF Research Database (Denmark)

    Hassing, Helle A; Fares, Suzan; Larsen, Olav

    2016-01-01

    for 2h with the 2-MAG-lipase inhibitor JZL84 doubled the constitutive activity, indicating that endogenous lipids contribute to the apparent constitutive activity. Finally, besides being an agonist, AR231453 acted as a positive allosteric modulator of OEA and increased its potency by 54-fold at 100nM AR......231453. Our studies uncovering broad and biased signaling, masked constitutive activity by endogenous MAGs, and ago-allosteric properties of synthetic ligands may explain why many GPR119 drug-discovery programs have failed so far....

  18. Mitochondria Targeted Nanoscale Zeolitic Imidazole Framework-90 for ATP Imaging in Live Cells.

    Science.gov (United States)

    Deng, Jingjing; Wang, Kai; Wang, Ming; Yu, Ping; Mao, Lanqun

    2017-04-26

    Zeolitic imidazole frameworks (ZIFs) are an emerging class of functional porous materials with promising biomedical applications such as molecular sensing and intracellular drug delivery. We report herein the first example of using nanoscale ZIFs (i.e., ZIF-90), self-assembled from Zn 2+ and imidazole-2-carboxyaldehyde, to target subcellular mitochondria and image dynamics of mitochondrial ATP in live cells. Encapsulation of fluorescent Rhodamine B (RhB) into ZIF-90 suppresses the emission of RhB, while the competitive coordination between ATP and the metal node of ZIF-90 dissembles ZIFs, resulting in the release of RhB for ATP sensing. With this method, we are able to image mitochondrial ATP in live cells and study the ATP level fluctuation in cellular glycolysis and apoptosis processes. The strategy reported here could be further extended to tune nanoscale ZIFs inside live cells for targeted delivery of therapeutics to subcellular organelles for advanced biomedical applications.

  19. Synthesis, characterization and toxicity of azanonaborane-containing imidazoles for boron neutron capture therapy

    International Nuclear Information System (INIS)

    El-Zaria, Mohamed E.; Genady, Afaf R.; Gabel, Detlef

    2006-01-01

    The exo-NH 2 R group of the azanonaborane of the type [(RH 2 N)B 8 H 11 NHR] can be exchanged by one hetero-nitrogen atom of the imidazole ring. In the case of histamine, the exchange takes place on the aliphatic amino group, the hetero-nitrogen atom of the imidazole ring or both of them. In vitro experiments using B16 melanoma cells showed that incorporation of B 8 N cluster unit into primary amino group of the histamine increases the compound's toxicity. In contrast, this specificity for cytotoxicity effect was not observed in the case of histamine containing two B 8 N clusters which was relatively nontoxic and did not inhibit colony formation up to 2 mM. (author)

  20. Crystal structure of 2-diazo-imidazole-4,5-dicarbo-nitrile.

    Science.gov (United States)

    Parrish, Damon A; Kramer, Stephanie; Windler, G Kenneth; Chavez, David E; Leonard, Philip W

    2015-07-01

    In the title compound, C5N6, all the atoms are approximately coplanar. In the crystal, mol-ecules are packed with short contact distances of 2.885 (2) (between the diazo N atom connected to the ring and a cyano N atom on a neighboring mol-ecule) and 3.012 (2) Å (between the terminal diazo N atom and an N atom of a neighboring imidazole ring).

  1. Chemical structure, network topology, and porosity effects on the mechanical properties of Zeolitic Imidazolate Frameworks

    OpenAIRE

    Tan, J. C.; Bennett, T. D.; Cheetham, A. K.

    2010-01-01

    The mechanical properties of seven zeolitic imidazolate frameworks (ZIFs) based on five unique network topologies have been systematically characterized by single-crystal nanoindentation studies. We demonstrate that the elastic properties of ZIF crystal structures are strongly correlated to the framework density and the underlying porosity. For the systems considered here, the elastic modulus was found to range from 3 to 10 GPa, whereas the hardness property lies between 300 MPa and 1.1 GPa. ...

  2. Bromidotetra?kis?(2-isopropyl-1H-imidazole-?N 3)copper(II) bromide

    OpenAIRE

    Godlewska, Sylwia; Socha, Joanna; Baranowska, Katarzyna; Do??ga, Anna

    2011-01-01

    The CuII atom in the title salt, [CuBr(C6H10N2)4]Br, is coordinated in a square-pyramidal geometry by four imidazole N atoms and one bromide anion that is located at the apex of the pyramid. The cations and the anions form a two-dimensional network parallel to (001) through N—H...Br hydrogen bonds.

  3. CNTs grown on nanoporous carbon from zeolitic imidazolate frameworks for supercapacitors.

    Science.gov (United States)

    Kim, Jeonghun; Young, Christine; Lee, Jaewoo; Park, Min-Sik; Shahabuddin, Mohammed; Yamauchi, Yusuke; Kim, Jung Ho

    2016-10-27

    Carbon nanotubes (CNT) grown on nanoporous carbon (NPC), which yields coexisting amorphous and graphitic nanoarchitectures, have been prepared on a large scale from zeolitic imidazolate framework (ZIF) by introducing bimetallic ions (Co 2+ and Zn 2+ ). Interestingly, the hybrid Co/Zn-ZIF-derived NPC showed rich graphitic CNTs on the surface. This NPC was utilized for a coin-type supercapacitor cell with an aqueous electrolyte, which showed enhanced retention at high current density and good stability over 10 000 cycles.

  4. Antibacterial activity of synthesized 2,4,5-trisubstituted imidazole derivatives

    Digital Repository Service at National Institute of Oceanography (India)

    Khan, M.S.; Siddiqui, S.A.; Siddiqui, M.S.R.A.; Goswami, U.; Srinivasan, K.V.; Khan, M.I.

    release or inhibiting the p38 MAP kinase (1), anti-allergic activity (2) and analgesic activity (3). They are also sensitizers of multidrug-resistant cancer cells (4), pesticides (5), antibiotics (6) or sodium-channel mod- ulators (7). Some imidazole... (ATCC 25922), Klebsiella pneumoniae (ATCC 13883), Pseudomonas aeruginosa (ATCC 27853) and Serratia morganii (ATCC 31665), obtained from Goa Medical college, Goa, India, grown to mid-logarithmic phase were harvested by centrifu- gation, washed with 10 m...

  5. Toward Anhydrous Proton Conductivity Based on Imidazole Functionalized Mesoporous Silica/Nafion Composite Membranes

    International Nuclear Information System (INIS)

    Amiinu, Ibrahim Saana; Li, Wei; Wang, Guangjin; Tu, Zhengkai; Tang, Haolin; Pan, Mu; Zhang, Haining

    2015-01-01

    Highlights: • Imidazole-functionalized mesoporous silica/Nafion composite is formed. • Electrostatic interaction between ionic clusters leads to enhanced molecular rigidity and T g . • Charge transfer resistance decreases with increase in temperature up to 130 °C. • The composite membrane exhibited considerable stability over 70 h at 130 °C. - Abstract: Although Nafion is regarded as the most preferred electrolyte membrane and often used as a benchmark for comparative evaluation of other electrolyte membranes, its wide spread for commercial PEM fuel cells is limited by the poor electrochemical properties at elevated temperatures and low relative humidity conditions. Herein, sol–gel synthesized mesoporous silica functionalized with a protogenic molecule (imidazole) is introduced into the Nafion matrix via a colloid mediated process. The formation of a stable colloid enables homogeneous dispersion of the silica-imidazole nanoparticles without aggregation. Under non-humidified conditions, the amphoteric and self-dissociative character of the tethered imidazole within the matrix functions as a transporting medium to facilitate proton conductivity. The structural and chemical phases are characterized, and qualitatively evaluated by XRD, TEM, FT-IR, TGA, and DMA. The results show that the average proton conductivity of the composite membrane with the optimal amount of functionalized nanoparticles increases progressively to 1.06 × 10 −2 S cm −1 at 130 °C, corresponding to an activation energy of 6.95 kJ mol −1 under non-humidified conditions. The mechanism governing the dynamics of proton conductivity and structural limitations as a function of temperature is discussed

  6. Tuning the crystal morphology and size of zeolitic imidazolate framework-8 in aqueous solution by surfactants

    KAUST Repository

    Pan, Yichang

    2011-01-01

    Herein we report a facile synthesis method using surfactant cetyltrimethylammonium bromide (CTAB) as a capping agent for controlling the crystal size and morphology of zeolitic imidazolate framework-8 (ZIF-8) crystals in aqueous systems. The particle sizes can be precisely adjusted from ca. 100 nm to 4 μm, and the morphology can be changed from truncated cubic to rhombic dodecahedron. This journal is © The Royal Society of Chemistry.

  7. Non-specific vaginitis: diagnostic features and response to imidazole therapy (metronidazole, ornidazole).

    Science.gov (United States)

    Meech, R J; Loutit, J

    1985-05-22

    Detailed quantitative aerobic, anaerobic, fungal and mycoplasma flora was obtained for 43 women presenting with complaints of vaginal discharge and malodour. Clinical response was associated with eradication of the abnormal anaerobic flora, despite persistence of G vaginalis in nine (26%). Topical imidazole therapy appeared to have some advantage over oral therapy. Gram stains of vaginal swabs were found to be the most useful laboratory investigation.

  8. γ-Alumina Nanoparticle Catalyzed Efficient Synthesis of Highly Substituted Imidazoles

    Directory of Open Access Journals (Sweden)

    Bandapalli Palakshi Reddy

    2015-10-01

    Full Text Available γ-Alumina nano particle catalyzed multi component reaction of benzil, arylaldehyde and aryl amines afforded the highly substituted 1,2,4,5-tetraaryl imidazoles with good to excellent yield in less reaction time under the sonication as well as the conventional methods. Convenient operational simplicity, mild conditions and the reusability of catalyst were the other advantages of this developed protocol.

  9. cis-Tetra­chloridobis(1H-imidazole-κN 3)platinum(IV)

    Science.gov (United States)

    Bokach, Nadezhda A.; Kukushkin, Vadim Yu.; Izotova, Yulia A.; Usenko, Natalia I.; Haukka, Matti

    2012-01-01

    In the title complex, cis-[PtCl4(C3H4N2)2], the PtIV ion lies on a twofold rotation axis and is coordinated in a slightly distorted octa­hedral geometry. The dihedral angle between the imidazole rings is 69.9 (2)°. In the crystal, mol­ecules are linked by N—H⋯Cl hydrogen bonds, forming a three-dimensional network. PMID:22590070

  10. cis-Tetrachloridobis(1H-imidazole-κN3platinum(IV

    Directory of Open Access Journals (Sweden)

    Vadim Yu. Kukushkin

    2012-05-01

    Full Text Available In the title complex, cis-[PtCl4(C3H4N22], the PtIV ion lies on a twofold rotation axis and is coordinated in a slightly distorted octahedral geometry. The dihedral angle between the imidazole rings is 69.9 (2°. In the crystal, molecules are linked by N—H...Cl hydrogen bonds, forming a three-dimensional network.

  11. Tioconazole, a new imidazole-antifungal agent for the treatment of dermatomycoses. Antifungal and pharmacologic properties.

    Science.gov (United States)

    Marriott, M S; Baird, J R; Brammer, K W; Faulkner, J K; Halliwell, G; Jevons, S; Tarbit, M H

    1983-01-01

    Tioconazole is a new imidazole antifungal agent with broad-spectrum activity. Its in vitro activity against common dermal pathogens is generally better than miconazole by a factor of 2-8. This activity is paralleled by good topical efficacy in a guinea pig dermatomycosis model. Pharmacokinetic studies in animals have demonstrated minimal systemic exposure following dermal application. Acute general pharmacology studies have shown that the compound is well tolerated in animals and unlikely to produce side-effects in man.

  12. Spectral, biological screening of metal chelates of chalcone based Schiff bases of N-(3-aminopropyl) imidazole.

    Science.gov (United States)

    Kalanithi, M; Rajarajan, M; Tharmaraj, P; Sheela, C D

    2012-02-15

    Tridentate chelate complexes of Co(II), Ni(II), Cu(II) and Zn(II) have been synthesized from the chalcone based ligands 2-[1-(3-(1H-imidazol-1-yl)propylimino)-3-(phenylallyl)]phenol(HL(1)), 2-[1-(3-(1H-imidazol-1-yl)propylimino)-3-p-tolylallyl]phenol(HL(2)), 2-[1-(3-(1H-imidazol-1-yl)propylimino)-3-4-nitrophenylallyl]phenol(HL(3)). Microanalytical data, UV-vis spectrophotometric method, magnetic susceptibility measurements, IR, 1H NMR, Mass, and EPR techniques were used to characterize the structure of chelates. The electronic absorption spectra and magnetic susceptibility measurements suggest a distorted square planar geometry for the copper(II) ion. The other metal complexes show distorted tetrahedral geometry. The coordination of the ligands with metal(II) ions was further confirmed by solution fluorescence spectrum. The antimicrobial activity of the ligands and metal(II) complexes against the species Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Bacillus subtilis, Candida albigans and Aspergillus niger has been carried out and compared. The electrochemical behavior of copper(II) complex is studied by cyclic voltammetry. Copyright © 2011 Elsevier B.V. All rights reserved.

  13. Study of Antibacterial Effect of Novel Thiazole, Imidazole and Tetrahydropyridine Derivatives against Escherichia coli

    Directory of Open Access Journals (Sweden)

    Behzad Ghasemi

    2016-01-01

    Full Text Available > Introduction: Escherichia coli is one of the important pathogens in human with globalimportance. Because of the necessity for identification and the use of novel antibacterialcompounds against E. coli, in this present study we focused on the antibacterial effects ofsynthesized thiazole, imidazole and tetrahydropyridine derivatives on E. coli.Methods: For evaluation of antibacterial effect, the disk diffusion method was applied to measurethe growth inhibition zone diameter and broth micro-dilution was performed to determine theminimum inhibitory concentration (MIC.Results: Assessing the antibacterial effect showed that only 6d derivative of thiazole hadinhibitory effect on E. coli and the other thiazole, imidazole and tetrahydropyridine derivativeslacked any inhibitory result on this organism. The inhibitory effect of 6d derivative of thiazolewas MIC=125 and growth inhibition zone diameter of 16±0.1.Discussion: The antibacterial effect of thiazole, imidazole and tetrahydropyridine derivativesdiffers from each other and chemical linkages such as oxygen to thiazole ring in 6d derivative,could have reinforced this effect. The next step is determination of the toxicity and therapeuticeffects in the laboratory animals.

  14. Trapped in imidazole: how to accumulate multiple photoelectrons on a black-absorbing ruthenium complex.

    Science.gov (United States)

    Zedler, Linda; Kupfer, Stephan; de Moraes, Inês Rabelo; Wächtler, Maria; Beckert, Rainer; Schmitt, Michael; Popp, Jürgen; Rau, Sven; Dietzek, Benjamin

    2014-03-24

    Ruthenium dyes incorporating a 4H-imidazole chromophore as a ligand exhibit a spectrally broad absorption in the UV/Vis region. Furthermore, they show the ability to store two electrons within the 4H-imidazole ligand. These features render them promising molecular systems, for example, as inter- or intramolecular electron relays. To optimize the structures with respect to their electron-storage capability, it is crucial to understand the impact of structural changes accompanying photoinduced charge transfer in the electronic intermediates of multistep electron-transfer processes. The photophysical properties of these (reactive) intermediates might impact the function of the molecular systems quite substantially. However, the spectroscopic study of short-lived intermediates in stepwise multielectron-transfer processes is experimentally challenging. To this end, this contribution reports on the electrochemical generation of anions identical to intermediate structures and their spectroscopic characterization by in situ resonance Raman and UV/Vis spectroelectrochemistry and computational methods. Thereby, an efficient two-electron pathway to the 4H-imidazole electron-accepting ligand is identified. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Theoretical prediction of the mechanical properties of zeolitic imidazolate frameworks (ZIFs)

    KAUST Repository

    Zheng, Bin

    2017-08-25

    A good resistance against mechanical stress is essential for the utilization of metal-organic frameworks (MOFs) in practical applications such as gas sorption, separation, catalysis or energy conversion. Here, we report on the successful modification of the mechanical properties of zeolitic imidazolate frameworks (ZIFs) achieved through a substitution of the terminal group. The mechanical modulus of SALEM-2 was found to significantly improve when the -H groups at position 2 of the imidazole linkers were replaced with electron withdrawing groups (-CHO, -Cl, or -Br). The charge distribution and electron density were analyzed to reveal the mechanism behind the observed variation of the elastic stiffness. Furthermore, ZIF-I with a -I group at position 2 of the imidazole linkers was predicted to exhibit an excellent mechanical strength in our study and then prepared experimentally. The results indicate that an inconspicuous change of the structure of ZIFs, i.e., additional groups strengthening the ZnN4 tetrahedron, will lead to a stiffer framework.

  16. Theoretical prediction of the mechanical properties of zeolitic imidazolate frameworks (ZIFs)

    KAUST Repository

    Zheng, Bin; Zhu, Yihan; Fu, Fang; Wang, Lian Li; Wang, Jinlei; Du, Huiling

    2017-01-01

    A good resistance against mechanical stress is essential for the utilization of metal-organic frameworks (MOFs) in practical applications such as gas sorption, separation, catalysis or energy conversion. Here, we report on the successful modification of the mechanical properties of zeolitic imidazolate frameworks (ZIFs) achieved through a substitution of the terminal group. The mechanical modulus of SALEM-2 was found to significantly improve when the -H groups at position 2 of the imidazole linkers were replaced with electron withdrawing groups (-CHO, -Cl, or -Br). The charge distribution and electron density were analyzed to reveal the mechanism behind the observed variation of the elastic stiffness. Furthermore, ZIF-I with a -I group at position 2 of the imidazole linkers was predicted to exhibit an excellent mechanical strength in our study and then prepared experimentally. The results indicate that an inconspicuous change of the structure of ZIFs, i.e., additional groups strengthening the ZnN4 tetrahedron, will lead to a stiffer framework.

  17. Hydrogen-deuterium exchange in imidazole as a tool for studying histidine phosphorylation.

    Science.gov (United States)

    Cebo, Małgorzata; Kielmas, Martyna; Adamczyk, Justyna; Cebrat, Marek; Szewczuk, Zbigniew; Stefanowicz, Piotr

    2014-12-01

    Isotope exchange at the histidine C2 atom of imidazole in D2O solution is well known to occur at a significantly slower rate than the exchange of amide protons. Analysis of the kinetics of this isotope-exchange reaction is proposed herein as a method of detecting histidine phosphorylation. This modification of His-containing peptides is challenging to pinpoint because of its instability under acidic conditions as well as during CID-MS analysis. In this work, we investigated the effect of phosphorylation of the histidine side chain in peptides on deuterium-hydrogen exchange (DHX) in the imidazole. The results demonstrate that phosphorylation dramatically slows the rate of the DHX reaction. This phenomenon can be applied to detect phosphorylation of peptides at the histidine residue (e.g., in enzymatic digests). We also found that the influence of the peptide sequence on the exchange kinetics is relatively small. A CID fragmentation experiment revealed that there was no detectable hydrogen scrambling in peptides deuterated at C2 of the imidazole ring. Therefore, MS/MS can be used to directly identify the locations of deuterium ions incorporated into peptides containing multiple histidine moieties.

  18. Understanding reactivity of two newly synthetized imidazole derivatives by spectroscopic characterization and computational study

    Science.gov (United States)

    Hossain, Mossaraf; Thomas, Renjith; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Vijayakumar, G.; Van Alsenoy, C.

    2018-04-01

    Two newly synthetized imidazole derivatives (1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole-2-yl acetate (MPDIA) and 1-(4-bromophenyl)-4,5-dimethyl-1H-imidazole-2-yl acetate (BPDIA)) have been prepared by solvent-free synthesis pathway and their specific spectroscopic and reactive properties have been discussed based on combined experimental and computational approaches. Aside of synthesis, experimental part of this work included measurements of IR, FT-Raman and NMR spectra. All of the aforementioned spectra were also obtained computationally, within the framework of density functional theory (DFT) approach. Additionally, DFT calculations have been used in order to investigate local reactivity properties based on molecular orbital theory, molecular electrostatic potential (MEP), average local ionization energy (ALIE), Fukui functions and bond dissociation energy (BDE). Molecular dynamics (MD) simulations have been used in order to obtain radial distribution functions (RDF), which were used for identification of the atoms with pronounced interactions with water molecules. MEP showed negative regions are mainly localized over N28, O29, O35 atoms, it is represent with red colour in rainbow color scheme for MPDIA and BPDIA (which are most reactive sites for electrophilic attack). The first order hyperpolarizabilities of MPDIA and BPDIA are 20.15 and 6.10 times that of the standard NLO material urea. Potential interaction with antihypertensive protein hydrolase.

  19. Imidazoles and benzimidazoles as tubulin-modulators for anti-cancer therapy.

    Science.gov (United States)

    Torres, Fernando C; García-Rubiño, M Eugenia; Lozano-López, César; Kawano, Daniel F; Eifler-Lima, Vera L; von Poser, Gilsane L; Campos, Joaquín M

    2015-01-01

    Imidazoles and benzimidazoles are privileged heterocyclic bioactive compounds used with success in the clinical practice of innumerous diseases. Although there are many advancements in cancer therapy, microtubules remain as one of the few macromolecular targets validated for planning active anti-cancer compounds, and the design of drugs that modulate microtubule dynamics in unknown sites of tubulin is one of the goals of the medicinal chemistry. The discussion of the role of new and commercially available imidazole and benzimidazole derivatives as tubulin modulators is scattered throughout scientific literature, and indicates that these compounds have a tubulin modulation mechanism different from that of tubulin modulators clinically available, such as paclitaxel, docetaxel, vincristine and vinblastine. In fact, recent literature indicates that these derivatives inhibit microtubule formation binding to the colchicine site, present good pharmacokinetic properties and are capable of overcoming multidrug resistance in many cell lines. The understanding of the mechanisms involved in the imidazoles/benzimidazoles modulation of microtubule dynamics is very important to develop new strategies to overcome the resistance to anti-cancer drugs and to discover new biomarkers and targets for cancer chemotherapy.

  20. Imidazole derivatives as angiotensin II AT1 receptor blockers: Benchmarks, drug-like calculations and quantitative structure-activity relationships modeling

    Science.gov (United States)

    Alloui, Mebarka; Belaidi, Salah; Othmani, Hasna; Jaidane, Nejm-Eddine; Hochlaf, Majdi

    2018-03-01

    We performed benchmark studies on the molecular geometry, electron properties and vibrational analysis of imidazole using semi-empirical, density functional theory and post Hartree-Fock methods. These studies validated the use of AM1 for the treatment of larger systems. Then, we treated the structural, physical and chemical relationships for a series of imidazole derivatives acting as angiotensin II AT1 receptor blockers using AM1. QSAR studies were done for these imidazole derivatives using a combination of various physicochemical descriptors. A multiple linear regression procedure was used to design the relationships between molecular descriptor and the activity of imidazole derivatives. Results validate the derived QSAR model.

  1. Studies on the π-π stacking features of imidazole units present in a series of 5-amino-1-alkylimidazole-4-carboxamides

    Science.gov (United States)

    Ray, Sibdas; Das, Aniruddha

    2015-06-01

    Reaction of 2-ethoxymethyleneamino-2-cyanoacetamide with primary alkyl amines in acetonitrile solvent affords 1-substituted-5-aminoimidazole-4-carboxamides. Single crystal X-ray diffraction studies of these imidazole compounds show that there are both anti-parallel and syn-parallel π-π stackings between two imidazole units in parallel-displaced (PD) conformations and the distance between two π-π stacked imidazole units depends mainly on the anti/ syn-parallel nature and to some extent on the alkyl group attached to N-1 of imidazole; molecules with anti-parallel PD-stacking arrangements of the imidazole units have got vertical π-π stacking distance short enough to impart stabilization whereas the imidazole unit having syn-parallel stacking arrangement have got much larger π-π stacking distances. DFT studies on a pair of anti-parallel imidazole units of such an AICA lead to curves for 'π-π stacking stabilization energy vs. π-π stacking distance' which have got similarity with the 'Morse potential energy diagram for a diatomic molecule' and this affords to find out a minimum π-π stacking distance corresponding to the maximum stacking stabilization energy between the pair of imidazole units. On the other hand, a DFT calculation based curve for 'π-π stacking stabilization energy vs. π-π stacking distance' of a pair of syn-parallel imidazole units is shown to have an exponential nature.

  2. Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications.

    Directory of Open Access Journals (Sweden)

    Kristin Blacklock

    2014-06-01

    Full Text Available A fundamental role of the Hsp90 chaperone in regulating functional activity of diverse protein clients is essential for the integrity of signaling networks. In this work we have combined biophysical simulations of the Hsp90 crystal structures with the protein structure network analysis to characterize the statistical ensemble of allosteric interaction networks and communication pathways in the Hsp90 chaperones. We have found that principal structurally stable communities could be preserved during dynamic changes in the conformational ensemble. The dominant contribution of the inter-domain rigidity to the interaction networks has emerged as a common factor responsible for the thermodynamic stability of the active chaperone form during the ATPase cycle. Structural stability analysis using force constant profiling of the inter-residue fluctuation distances has identified a network of conserved structurally rigid residues that could serve as global mediating sites of allosteric communication. Mapping of the conformational landscape with the network centrality parameters has demonstrated that stable communities and mediating residues may act concertedly with the shifts in the conformational equilibrium and could describe the majority of functionally significant chaperone residues. The network analysis has revealed a relationship between structural stability, global centrality and functional significance of hotspot residues involved in chaperone regulation. We have found that allosteric interactions in the Hsp90 chaperone may be mediated by modules of structurally stable residues that display high betweenness in the global interaction network. The results of this study have suggested that allosteric interactions in the Hsp90 chaperone may operate via a mechanism that combines rapid and efficient communication by a single optimal pathway of structurally rigid residues and more robust signal transmission using an ensemble of suboptimal multiple

  3. Two-state dynamics of the SH3-SH2 tandem of Abl kinase and the allosteric role of the N-cap.

    Science.gov (United States)

    Corbi-Verge, Carles; Marinelli, Fabrizio; Zafra-Ruano, Ana; Ruiz-Sanz, Javier; Luque, Irene; Faraldo-Gómez, José D

    2013-09-03

    The regulation and localization of signaling enzymes is often mediated by accessory modular domains, which frequently function in tandems. The ability of these tandems to adopt multiple conformations is as important for proper regulation as the individual domain specificity. A paradigmatic example is Abl, a ubiquitous tyrosine kinase of significant pharmacological interest. SH3 and SH2 domains inhibit Abl by assembling onto the catalytic domain, allosterically clamping it in an inactive state. We investigate the dynamics of this SH3-SH2 tandem, using microsecond all-atom simulations and differential scanning calorimetry. Our results indicate that the Abl tandem is a two-state switch, alternating between the conformation observed in the structure of the autoinhibited enzyme and another configuration that is consistent with existing scattering data for an activated form. Intriguingly, we find that the latter is the most probable when the tandem is disengaged from the catalytic domain. Nevertheless, an amino acid stretch preceding the SH3 domain, the so-called N-cap, reshapes the free-energy landscape of the tandem and favors the interaction of this domain with the SH2-kinase linker, an intermediate step necessary for assembly of the autoinhibited complex. This allosteric effect arises from interactions between N-cap and the SH2 domain and SH3-SH2 connector, which involve a phosphorylation site. We also show that the SH3-SH2 connector plays a determinant role in the assembly equilibrium of Abl, because mutations thereof hinder the engagement of the SH2-kinase linker. These results provide a thermodynamic rationale for the involvement of N-cap and SH3-SH2 connector in Abl regulation and expand our understanding of the principles of modular domain organization.

  4. Two-state dynamics of the SH3–SH2 tandem of Abl kinase and the allosteric role of the N-cap

    Science.gov (United States)

    Corbi-Verge, Carles; Marinelli, Fabrizio; Zafra-Ruano, Ana; Ruiz-Sanz, Javier; Luque, Irene; Faraldo-Gómez, José D.

    2013-01-01

    The regulation and localization of signaling enzymes is often mediated by accessory modular domains, which frequently function in tandems. The ability of these tandems to adopt multiple conformations is as important for proper regulation as the individual domain specificity. A paradigmatic example is Abl, a ubiquitous tyrosine kinase of significant pharmacological interest. SH3 and SH2 domains inhibit Abl by assembling onto the catalytic domain, allosterically clamping it in an inactive state. We investigate the dynamics of this SH3–SH2 tandem, using microsecond all-atom simulations and differential scanning calorimetry. Our results indicate that the Abl tandem is a two-state switch, alternating between the conformation observed in the structure of the autoinhibited enzyme and another configuration that is consistent with existing scattering data for an activated form. Intriguingly, we find that the latter is the most probable when the tandem is disengaged from the catalytic domain. Nevertheless, an amino acid stretch preceding the SH3 domain, the so-called N-cap, reshapes the free-energy landscape of the tandem and favors the interaction of this domain with the SH2-kinase linker, an intermediate step necessary for assembly of the autoinhibited complex. This allosteric effect arises from interactions between N-cap and the SH2 domain and SH3–SH2 connector, which involve a phosphorylation site. We also show that the SH3–SH2 connector plays a determinant role in the assembly equilibrium of Abl, because mutations thereof hinder the engagement of the SH2-kinase linker. These results provide a thermodynamic rationale for the involvement of N-cap and SH3–SH2 connector in Abl regulation and expand our understanding of the principles of modular domain organization. PMID:23959873

  5. Evidence for allosterism in ribulose-1,5-bisphosphate carboxylase/oxygenase from comfrey

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, D.D.; Bolden, T.D.

    1986-05-01

    Evidence has been obtained suggesting that ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is an allosteric enzyme in the sense that it shows cooperative active site binding, cooperative interactions between the activation and active sites and significant binding of some metabolites at a second site. Investigation of the binding of a potent competitive inhibitor. 2-carboxymannitol-1,6-bisphosphate (CMBP) by /sup 31/P-NMR indicated essentially 1:1 binding with the active sites of comfrey RuBisCo. Among the interactions of competitive inhibitors, as measured by difference UV spectroscopy, the binding curves for ortho-phosphate and ribose-5-phosphate were better fitted by a Monod-Wyman-Changeux model than by an independent site model, whereas the binding of CMBP and 2-phosphoglycolate were not. Difference UV methods also were used to study activation by CO/sub 2/ which at pH 7.9 in 10 mM MgCl/sub 2/ showed positive cooperativity with k = 100 +/- 3 ..mu..M (based on pK/sub a/ = 6.4 for the CO/sub 2/-HCO/sub 3//sup -/ equilibrium) and L = 3.5 +/- 0.7. Addition of saturating amounts of CMBP and lowering the MgCl/sub 2/ to 2 mM still gave a sigmoidal curve but it was shifted to higher CO/sub 2/ concentrations (k = 124 +/- 2 ..mu..M and L = 31 +/- 3). In the absence of CMBP the same conditions gave k = 26 +/- 2 ..mu..M for L = 3.5. Conversely, k was 0.96 +/- 0.08 ..mu..M for CMBP in 0.5 mM MgCl/sub 2/ without added NaHCO/sub 3/ but was 21 +/- 0.06 ..mu..M in 10 MgCl/sub 2/ and 2 mM NaHCO/sub 3/, pH 7.3.

  6. Structural changes at the myrtenol backbone reverse its positive allosteric potential into inhibitory GABAA receptor modulation

    DEFF Research Database (Denmark)

    Milanos, Sinem; Kuenzel, Katharina; Gilbert, Daniel F

    2017-01-01

    monoterpenes, e.g. myrtenol as positive allosteric modulator at α1β2 GABAA receptors. Here, along with pharmacophore-based virtual screening studies, we demonstrate that scaffold modifications of myrtenol resulted in loss of modulatory activity. Two independent approaches, fluorescence-based compound analysis...

  7. The different ways through which specificity works in orthosteric and allosteric drugs.

    Science.gov (United States)

    Nussinov, Ruth; Tsai, Chung-Jung

    2012-01-01

    Currently, there are two types of drugs on the market: orthosteric, which bind at the active site; and allosteric, which bind elsewhere on the protein surface, and allosterically change the conformation of the protein binding site. In this perspective we argue that the different mechanisms through which the two drug types affect protein activity and their potential pitfalls call for different considerations in drug design. The key problem facing orthosteric drugs is side effects which can occur by drug binding to homologous proteins sharing a similar binding site. Hence, orthosteric drugs should have very high affinity to the target; this would allow a low dosage to selectively achieve the goal of target-only binding. By contrast, allosteric drugs work by shifting the free energy landscape. Their binding to the protein surface perturbs the protein surface atoms, and the perturbation propagates like waves, finally reaching the binding site. Effective drugs should have atoms in good contact with the 'right' protein atoms; that is, the contacts should elicit propagation waves optimally reaching the protein binding site target. While affinity is important, the design should consider the protein conformational ensemble and the preferred propagation states. We provide examples from functional in vivo scenarios for both types of cases, and suggest how high potency can be achieved in allosteric drug development.

  8. Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.

    Directory of Open Access Journals (Sweden)

    Aysima Hacisuleyman

    2017-01-01

    Full Text Available It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.

  9. Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.

    Science.gov (United States)

    Hacisuleyman, Aysima; Erman, Burak

    2017-01-01

    It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.

  10. Nootropic α7 nicotinic receptor allosteric modulator derived from GABAA receptor modulators

    Science.gov (United States)

    Ng, Herman J.; Whittemore, Edward R.; Tran, Minhtam B.; Hogenkamp, Derk J.; Broide, Ron S.; Johnstone, Timothy B.; Zheng, Lijun; Stevens, Karen E.; Gee, Kelvin W.

    2007-01-01

    Activation of brain α7 nicotinic acetylcholine receptors (α7 nAChRs) has broad therapeutic potential in CNS diseases related to cognitive dysfunction, including Alzheimer's disease and schizophrenia. In contrast to direct agonist activation, positive allosteric modulation of α7 nAChRs would deliver the clinically validated benefits of allosterism to these indications. We have generated a selective α7 nAChR-positive allosteric modulator (PAM) from a library of GABAA receptor PAMs. Compound 6 (N-(4-chlorophenyl)-α-[[(4-chloro-phenyl)amino]methylene]-3-methyl-5-isoxazoleacet-amide) evokes robust positive modulation of agonist-induced currents at α7 nAChRs, while preserving the rapid native characteristics of desensitization, and has little to no efficacy at other ligand-gated ion channels. In rodent models, it corrects sensory-gating deficits and improves working memory, effects consistent with cognitive enhancement. Compound 6 represents a chemotype for allosteric activation of α7 nAChRs, with therapeutic potential in CNS diseases with cognitive dysfunction. PMID:17470817

  11. 2013 Philip S. Portoghese Medicinal Chemistry Lectureship: Drug Discovery Targeting Allosteric Sites†

    Science.gov (United States)

    2015-01-01

    The identification of sites on receptors topographically distinct from the orthosteric sites, so-called allosteric sites, has heralded novel approaches and modes of pharmacology for target modulation. Over the past 20 years, our understanding of allosteric modulation has grown significantly, and numerous advantages, as well as caveats (e.g., flat structure–activity relationships, species differences, “molecular switches”), have been identified. For multiple receptors and proteins, numerous examples have been described where unprecedented levels of selectivity are achieved along with improved physiochemical properties. While not a panacea, these novel approaches represent exciting opportunities for tool compound development to probe the pharmacology and therapeutic potential of discrete molecular targets, as well as new medicines. In this Perspective, in commemoration of the 2013 Philip S. Portoghese Medicinal Chemistry Lectureship (LindsleyC. W.Adventures in allosteric drug discovery. Presented at the 246th National Meeting of the American Chemical Society, Indianapolis, IN, September 10, 2013; The 2013 Portoghese Lectureship), several vignettes of drug discovery campaigns targeting novel allosteric mechanisms will be recounted, along with lessons learned and guidelines that have emerged for successful lead optimization. PMID:25180768

  12. Divergence of allosteric effects of rapacuronium on binding and function of muscarinic receptors

    Czech Academy of Sciences Publication Activity Database

    Jakubík, Jan; Randáková, Alena; El-Fakahany, E. E.; Doležal, Vladimír

    2009-01-01

    Roč. 9, č. 15 (2009), s. 1-20 ISSN 1471-2210 R&D Projects: GA ČR GA305/09/0681; GA MŠk(CZ) LC554; GA AV ČR(CZ) IAA500110703 Institutional research plan: CEZ:AV0Z50110509 Keywords : muscarinic receptors * allosteric modulation * rapacuronium Subject RIV: ED - Physiology

  13. Identification of an allosteric binding site for RORγt inhibition

    NARCIS (Netherlands)

    Scheepstra, M.; Leysen, S.; van Almen, G.; Miller, J.R.; Piesvaux, J.; Kutilek, V.; van Eenennaam, H.; Zhang, H.; Barr, K.; Nagpal, S.; Soisson, S.M.; Kornienko, M.; Wiley, K.; Elsen, N.; Sharma, S.; Correll, C.C.; Trotter, B.W.; Stelt, van der M.; Oubrie, A.; Ottmann, C.; Parthasarathy, G.; Brunsveld, L.

    2015-01-01

    RORγt is critical for the differentiation and proliferation of Th17 cells associated with several chronic autoimmune diseases. We report the discovery of a novel allosteric binding site on the nuclear receptor RORγt. Co-crystallization of the ligand binding domain (LBD) of RORγt with a series of

  14. Molecular Basis for Allosteric Inhibition of Acid-Sensing Ion Channel 1a by Ibuprofen

    DEFF Research Database (Denmark)

    Lynagh, Timothy; Romero-Rojo, José Luis; Lund, Camilla

    2017-01-01

    -clamp fluorometry. Our results show that ibuprofen is an allosteric inhibitor of ASIC1a, which binds to a crucial site in the agonist transduction pathway and causes conformational changes that oppose channel activation. Ibuprofen inhibits several ASIC subtypes, but certain ibuprofen derivatives show some...

  15. A generalized allosteric mechanism for cis-regulated cyclic nucleotide binding domains.

    Directory of Open Access Journals (Sweden)

    Alexandr P Kornev

    2008-04-01

    Full Text Available Cyclic nucleotides (cAMP and cGMP regulate multiple intracellular processes and are thus of a great general interest for molecular and structural biologists. To study the allosteric mechanism of different cyclic nucleotide binding (CNB domains, we compared cAMP-bound and cAMP-free structures (PKA, Epac, and two ionic channels using a new bioinformatics method: local spatial pattern alignment. Our analysis highlights four major conserved structural motifs: 1 the phosphate binding cassette (PBC, which binds the cAMP ribose-phosphate, 2 the "hinge," a flexible helix, which contacts the PBC, 3 the beta(2,3 loop, which provides precise positioning of an invariant arginine from the PBC, and 4 a conserved structural element consisting of an N-terminal helix, an eight residue loop and the A-helix (N3A-motif. The PBC and the hinge were included in the previously reported allosteric model, whereas the definition of the beta(2,3 loop and the N3A-motif as conserved elements is novel. The N3A-motif is found in all cis-regulated CNB domains, and we present a model for an allosteric mechanism in these domains. Catabolite gene activator protein (CAP represents a trans-regulated CNB domain family: it does not contain the N3A-motif, and its long range allosteric interactions are substantially different from the cis-regulated CNB domains.

  16. Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Federica Chiappori

    Full Text Available Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD modulate substrate recognition at the Substrate Binding Domain (SBD. Herein, a comparative analysis of an allosteric (Hsp70-DnaK and a non-allosteric structural homolog (Hsp110-Sse1 of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.

  17. Imidazole-containing phthalazine derivatives inhibit Fe-SOD performance in Leishmania species and are active in vitro against visceral and mucosal leishmaniasis.

    Science.gov (United States)

    Sánchez-Moreno, M; Gómez-Contreras, F; Navarro, P; Marín, C; Ramírez-Macías, I; Rosales, M J; Campayo, L; Cano, C; Sanz, A M; Yunta, M J R

    2015-07-01

    The in vitro leishmanicidal activity of a series of imidazole-containing phthalazine derivatives 1-4 was tested on Leishmania infantum, Leishmania braziliensis and Leishmania donovani parasites, and their cytotoxicity on J774·2 macrophage cells was also measured. All compounds tested showed selectivity indexes higher than that of the reference drug glucantime for the three Leishmania species, and the less bulky monoalkylamino substituted derivatives 2 and 4 were clearly more effective than their bisalkylamino substituted counterparts 1 and 3. Both infection rate measures and ultrastructural alterations studies confirmed that 2 and 4 were highly leishmanicidal and induced extensive parasite cell damage. Modifications to the excretion products of parasites treated with 2 and 4 were also consistent with substantial cytoplasmic alterations. On the other hand, the most active compounds 2 and 4 were potent inhibitors of iron superoxide dismutase enzyme (Fe-SOD) in the three species considered, whereas their impact on human CuZn-SOD was low. Molecular modelling suggests that 2 and 4 could deactivate Fe-SOD due to a sterically favoured enhanced ability to interact with the H-bonding net that supports the antioxidant features of the enzyme.

  18. Evolution of glycaemia in the blood of mice in the presence or absence of imidazole; Evolution de la glycemie sanguine chez la souris protegee ou non par l'imidazole

    Energy Technology Data Exchange (ETDEWEB)

    Polverelli, M.; Teoule, R. [Commissariat a l' Energie Atomique, Grenoble (France). Centre d' Etudes Nucleaires

    1969-07-01

    With respect to the radioprotective properties of the heterocyclic compound, imidazole, the authors followed the action of this product on blood sugar levels of mice X irradiated with a lethal dose. The main results of this work are: probably a hypo-glycemic action of the imidazole; an abolishment of the post-irradiation hyperglycemia by imidazole; an appreciably difference between male and female towards irradiation. (author) [French] Dans le cadre de l'etude des proprietes radioprotectrices de l'imidazole, nous nous sommes attaches a suivre l'action de ce produit sur le taux de glucose sanguin de souris irradiees a dose letale. Les principaux resultats de ce travail sont les suivants: l'action probablement hypoglycemiante de l'imidazole; en tant que radioprotecteur, cet heterocycle azote supprime l'hyperglycemie consecutive a l'irradiation; une difference assez sensible entre males et femelles vis-a-vis de l'irradiation. (auteur)

  19. Heat Capacity Changes and Disorder-to-Order Transitions in Allosteric Activation.

    Science.gov (United States)

    Cressman, William J; Beckett, Dorothy

    2016-01-19

    Allosteric coupling in proteins is ubiquitous but incompletely understood, particularly in systems characterized by coupling over large distances. Binding of the allosteric effector, bio-5'-AMP, to the Escherichia coli biotin protein ligase, BirA, enhances the protein's dimerization free energy by -4 kcal/mol. Previous studies revealed that disorder-to-order transitions at the effector binding and dimerization sites, which are separated by 33 Å, are integral to functional coupling. Perturbations to the transition at the ligand binding site alter both ligand binding and coupled dimerization. Alanine substitutions in four loops on the dimerization surface yield a range of energetic effects on dimerization. A glycine to alanine substitution at position 142 in one of these loops results in a complete loss of allosteric coupling, disruption of the disorder-to-order transitions at both functional sites, and a decreased affinity for the effector. In this work, allosteric communication between the effector binding and dimerization surfaces in BirA was further investigated by performing isothermal titration calorimetry measurements on nine proteins with alanine substitutions in three dimerization surface loops. In contrast to BirAG142A, at 20 °C all variants bind to bio-5'-AMP with free energies indistinguishable from that measured for wild-type BirA. However, the majority of the variants exhibit altered heat capacity changes for effector binding. Moreover, the ΔCp values correlate with the dimerization free energies of the effector-bound proteins. These thermodynamic results, combined with structural information, indicate that allosteric activation of the BirA monomer involves formation of a network of intramolecular interactions on the dimerization surface in response to bio-5'-AMP binding at the distant effector binding site.

  20. Allosteric modulation of endogenous metabolites as an avenue for drug discovery.

    Science.gov (United States)

    Wootten, Denise; Savage, Emilia E; Valant, Celine; May, Lauren T; Sloop, Kyle W; Ficorilli, James; Showalter, Aaron D; Willard, Francis S; Christopoulos, Arthur; Sexton, Patrick M

    2012-08-01

    G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors and a key drug target class. Recently, allosteric drugs that can co-bind with and modulate the activity of the endogenous ligand(s) for the receptor have become a major focus of the pharmaceutical and biotechnology industry for the development of novel GPCR therapeutic agents. This class of drugs has distinct properties compared with drugs targeting the endogenous (orthosteric) ligand-binding site that include the ability to sculpt cellular signaling and to respond differently in the presence of discrete orthosteric ligands, a behavior termed "probe dependence." Here, using cell signaling assays combined with ex vivo and in vivo studies of insulin secretion, we demonstrate that allosteric ligands can cause marked potentiation of previously "inert" metabolic products of neurotransmitters and peptide hormones, a novel consequence of the phenomenon of probe dependence. Indeed, at the muscarinic M(2) receptor and glucagon-like peptide 1 (GLP-1) receptor, allosteric potentiation of the metabolites, choline and GLP-1(9-36)NH(2), respectively, was ~100-fold and up to 200-fold greater than that seen with the physiological signaling molecules acetylcholine and GLP-1(7-36)NH(2). Modulation of GLP-1(9-36)NH(2) was also demonstrated in ex vivo and in vivo assays of insulin secretion. This work opens up new avenues for allosteric drug discovery by directly targeting modulation of metabolites, but it also identifies a behavior that could contribute to unexpected clinical outcomes if interaction of allosteric drugs with metabolites is not part of their preclinical assessment.

  1. SH2-catalytic domain linker heterogeneity influences allosteric coupling across the SFK family.

    Science.gov (United States)

    Register, A C; Leonard, Stephen E; Maly, Dustin J

    2014-11-11

    Src-family kinases (SFKs) make up a family of nine homologous multidomain tyrosine kinases whose misregulation is responsible for human disease (cancer, diabetes, inflammation, etc.). Despite overall sequence homology and identical domain architecture, differences in SH3 and SH2 regulatory domain accessibility and ability to allosterically autoinhibit the ATP-binding site have been observed for the prototypical SFKs Src and Hck. Biochemical and structural studies indicate that the SH2-catalytic domain (SH2-CD) linker, the intramolecular binding epitope for SFK SH3 domains, is responsible for allosterically coupling SH3 domain engagement to autoinhibition of the ATP-binding site through the conformation of the αC helix. As a relatively unconserved region between SFK family members, SH2-CD linker sequence variability across the SFK family is likely a source of nonredundant cellular functions between individual SFKs via its effect on the availability of SH3 and SH2 domains for intermolecular interactions and post-translational modification. Using a combination of SFKs engineered with enhanced or weakened regulatory domain intramolecular interactions and conformation-selective inhibitors that report αC helix conformation, this study explores how SH2-CD sequence heterogeneity affects allosteric coupling across the SFK family by examining Lyn, Fyn1, and Fyn2. Analyses of Fyn1 and Fyn2, isoforms that are identical but for a 50-residue sequence spanning the SH2-CD linker, demonstrate that SH2-CD linker sequence differences can have profound effects on allosteric coupling between otherwise identical kinases. Most notably, a dampened allosteric connection between the SH3 domain and αC helix leads to greater autoinhibitory phosphorylation by Csk, illustrating the complex effects of SH2-CD linker sequence on cellular function.

  2. Screening for Methylated Poly(⌊-histidine with Various Dimethylimidazolium/Methylimidazole/Imidazole Contents as DNA Carrier

    Directory of Open Access Journals (Sweden)

    Shoichiro Asayama

    2015-08-01

    Full Text Available Methylated poly(l-histidine (PLH-Me, our original polypeptide, has controlled the contents of dimethylimidazolium, τ/π-methylimidazole and imidazole groups for efficient gene delivery. The screening for the PLH-Me as DNA carrier has been carried out by use of the PLH with 25 mol% (τ-methyl, 16 mol%; π-methyl, 17 mol%; deprotonated imidazole, 41 mol%, 68 mol% (τ-methyl, 16 mol%; π-methyl, 8 mol%; deprotonated imidazole, 8 mol% and 87 mol% (τ-methyl, 7 mol%; π-methyl, 4 mol%; deprotonated imidazole, 2 mol% dimethylimidazolium groups, that is, PLH-Me(25, PLH-Me(68 and PLH-Me(87, respectively. The screening of the chemical structure of PLH-Me has been carried out for DNA carrier properties, which are the stability of its DNA polyion complexes and gene expression. The DNA complexes with the 25 mol% and 68 mol% dimethylated PLH-Me possessed almost same ability to retain DNA, as compared with the 87 mol% dimethylated PLH-Me, which was examined by competitive exchange with dextran sulfate. From the gene transfection experiment against HepG2 cells, human hepatoma cell line, the PLH-Me(25/DNA complex was revealed to mediate highest gene expression. These results suggest that the dimethyl-imidazolium/methylimidazole/imidazole balance of the PLH-Me is important for DNA carrier design.

  3. Regio- and Enantioselective N-Allylations of Imidazole, Benzimidazole, and Purine Heterocycles Catalyzed by Single-Component Metallacyclic Iridium Complexes

    Science.gov (United States)

    Stanley, Levi M.

    2010-01-01

    Highly regio- and enantioselective iridium-catalyzed N-allylations of benzimidazoles, imidazoles, and purines have been developed. N-Allylated benzimidazoles and imidazoles were isolated in high yields (up to 97%) with high branched-to-linear selectivity (up to 99:1) and enantioselectivity (up to 98% ee) from the reactions of benzimidazole and imidazole nucleophiles with unsymmetrical allylic carbonates in the presence of single component, ethylene-bound, metallacyclic iridium catalysts. N-Allylated purines were also obtained in high yields (up to 91%) with high N9:N7 selectivity (up to 96:4), high branched-to-linear selectivity (98:2), and high enantioselectivity (up to 98% ee) under similar conditions. The reactions encompass a range of benzimidazole, imidazole, and purine nucleophiles, as well as a variety of unsymmetrical aryl, heteroaryl, and aliphatic allylic carbonates. Competition experiments between common amine nucleophiles and the heterocyclic nitrogen nucleophiles studied in this work illustrate the effect of nucleophile pKa on the rate of iridium-catalyzed N-allylation reactions. Kinetic studies on the allylation of benzimidazole catalyzed by metallacyclic iridium-phosphoramidite complexes, in combination with studies on the deactivation of these catalysts in the presence of heterocyclic nucleophiles, provide insight into the effects of the structure of the phosphoramidite ligands on the stability of the metallacyclic catalysts. The data obtained from these studies has led to the development of N-allylations of benzimidazoles and imidazoles in the absence of an exogenous base. PMID:19480431

  4. 1-[(3-Aryloxy-3-aryl)propyl]-1H-imidazoles, new imidazoles with potent activity against Candida albicans and dermatophytes. Synthesis, structure-activity relationship, and molecular modeling studies.

    Science.gov (United States)

    La Regina, Giuseppe; D'Auria, Felicia Diodata; Tafi, Andrea; Piscitelli, Francesco; Olla, Stefania; Caporuscio, Fabiana; Nencioni, Lucia; Cirilli, Roberto; La Torre, Francesco; De Melo, Nadja Rodrigues; Kelly, Steven L; Lamb, David C; Artico, Marino; Botta, Maurizio; Palamara, Anna Teresa; Silvestri, Romano

    2008-07-10

    New 1-[(3-aryloxy-3-aryl)propyl]-1 H-imidazoles were synthesized and evaluated against Candida albicans and dermatophytes in order to develop structure-activity relationships (SARs). Against C. albicans the new imidazoles showed minimal inhibitory concentrations (MICs) comparable to those of ketoconazole, miconazole, and econazole, and were more potent than fluconazole. Several derivatives ( 10, 12, 14, 18- 20, 24, 28, 29, 30, and 34) turned out to be potent inhibitors of C. albicans strains resistant to fluconazole, with MIC values less than 10 microg/mL. Against dermatophytes strains, compounds 20, 25, and 33 (MIC imidazoles 10- 44 were rationalized with reasonable accuracy by a previously developed quantitative pharmacophore for antifungal agents.

  5. Thermodynamics of organic mixtures containing amines. X. Phase equilibria for binary systems formed by imidazoles and hydrocarbons: Experimental data and modelling using DISQUAC

    Energy Technology Data Exchange (ETDEWEB)

    Domanska, Urszula; Zawadzki, Maciej [Physical Chemistry Division, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw (Poland); Gonzalez, Juan Antonio, E-mail: jagl@termo.uva.e [G.E.T.E.F., Grupo Especializado en Termodinamica de Equilibrio entre Fases, Departamento de Fisica Aplicada, Facultad de Ciencias, Universidad de Valladolid, E-47071, Valladolid (Spain)

    2010-04-15

    (Solid + liquid) equilibrium (SLE) temperatures have been determined using a dynamic method for the systems (1H-imidazole, + benzene, + toluene, + hexane, or + cyclohexane; 1-methylimidazole + benzene, or + toluene, 2-methyl-1H-imidazole + benzene, + toluene, or + cyclohexane, and benzimidazole + benzene). In addition (liquid + liquid) equilibrium (LLE) temperatures have been obtained using a cloud point method for (1H-imidazole, + hexane, or + cyclohexane; 1-methylimidazole + toluene, and 2-methyl-1H-imidazole + cyclohexane). The measured systems show positive deviations from the Raoult's law, due to strong dipolar interactions between amine molecules related to the high dipole moment of imidazoles. On the other hand, DISQUAC interaction parameters for the contacts present in these solutions and for the amine/hydroxyl contacts in (1H-imidazole + 1-alkanol) mixtures have been determined. The model correctly represents the available data for the examined systems. Deviations between experimental and calculated SLE temperatures are similar to those obtained using the Wilson or NRTL equations, or the UNIQUAC association solution model. The quasichemical interaction parameters are the same for mixtures containing 1H-imidazole, 1-methylimidazole, or 2-methyl-1H-imidazole and hydrocarbons. This may be interpreted assuming that they are members of a homologous series. Benzimidazole behaves differently.

  6. Thermodynamics of organic mixtures containing amines. X. Phase equilibria for binary systems formed by imidazoles and hydrocarbons: Experimental data and modelling using DISQUAC

    International Nuclear Information System (INIS)

    Domanska, Urszula; Zawadzki, Maciej; Gonzalez, Juan Antonio

    2010-01-01

    (Solid + liquid) equilibrium (SLE) temperatures have been determined using a dynamic method for the systems (1H-imidazole, + benzene, + toluene, + hexane, or + cyclohexane; 1-methylimidazole + benzene, or + toluene, 2-methyl-1H-imidazole + benzene, + toluene, or + cyclohexane, and benzimidazole + benzene). In addition (liquid + liquid) equilibrium (LLE) temperatures have been obtained using a cloud point method for (1H-imidazole, + hexane, or + cyclohexane; 1-methylimidazole + toluene, and 2-methyl-1H-imidazole + cyclohexane). The measured systems show positive deviations from the Raoult's law, due to strong dipolar interactions between amine molecules related to the high dipole moment of imidazoles. On the other hand, DISQUAC interaction parameters for the contacts present in these solutions and for the amine/hydroxyl contacts in (1H-imidazole + 1-alkanol) mixtures have been determined. The model correctly represents the available data for the examined systems. Deviations between experimental and calculated SLE temperatures are similar to those obtained using the Wilson or NRTL equations, or the UNIQUAC association solution model. The quasichemical interaction parameters are the same for mixtures containing 1H-imidazole, 1-methylimidazole, or 2-methyl-1H-imidazole and hydrocarbons. This may be interpreted assuming that they are members of a homologous series. Benzimidazole behaves differently.

  7. Synthesis and characterization of novel polyamide-ethers based on bis-imidazole containing bulky aryl pendant groups

    Directory of Open Access Journals (Sweden)

    Seyed Mahdi Saadati

    2013-01-01

    Full Text Available A series of novel polyamide-ethers (PAEs based on bis-imidazole containing bulky aryl pendant groups was prepared by direct polycondensation of a diamine, 4-(1-(4-(4-(2-(4-aminophenyl-4,5-diphenyl-1H-imidazol-1-ylphenoxyphenyl-4,5-diphenyl-1H-imidazol-2-ylbenzenamine (DABI, and various dicarboxylic acids. All the resulting polyamide-ethers were amorphous with inherent viscosities ranged from 0.52 to 0.61 dL/g and were readily soluble in many organic solvents which could be solution-cast into transparent and tough films. The glass transition temperatures (Tg of these polymers were affected considerably by their chemical structure and ranged from 230 to 310 ºC. They had useful levels of thermal stability associated with relatively high temperatures of 10% weight loss (T10 in the range of 329-399 ºC in air atmosphere.

  8. Parallel Synthesis of a Library of Symmetrically- and Dissymmetrically-disubstituted Imidazole-4,5-dicarboxamides Bearing Amino Acid Esters

    Directory of Open Access Journals (Sweden)

    Rosanna Solinas

    2009-01-01

    Full Text Available The imidazole-4,5-dicarboxylic acid scaffold is readily derivatized with amino acid esters to afford symmetrically- and dissymmetrically-disubstituted imidazole-4,5-dicarboxamides with intramolecularly hydrogen bonded conformations that predispose the presentation of amino acid pharmacophores. In this work, a total of 45 imidazole-4,5-dicarboxamides bearing amino acid esters were prepared by parallel synthesis. The library members were purified by column chromatography on silica gel and the purified compounds characterized by LC-MS with LC detection at 214 nm. A selection of the final compounds was also analyzed by 1H-NMR spectroscopy. The analytically pure final products have been submitted to the Molecular Library Small Molecule Repository (MLSMR for screening in the Molecular Library Screening Center Network (MLSCN as part of the NIH Roadmap.

  9. Silylation of leached-vermiculites following reaction with imidazole and copper sorption behavior

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Saloana S.G.; Pereira, Mariana B.B. [Chemistry Department of Paraíba Federal University, João Pessoa, Paraíba (Brazil); Almeida, Ramon K.S. [Instituto de Química, Universidade Estadual de Campinas, Caixa Postal 6154, 13083-970 Campinas, São Paulo (Brazil); Souza, Antônio G. [Chemistry Department of Paraíba Federal University, João Pessoa, Paraíba (Brazil); Fonseca, Maria G., E-mail: mgardennia@quimica.ufpb.br [Chemistry Department of Paraíba Federal University, João Pessoa, Paraíba (Brazil); Jaber, M. [Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8220, Laboratoire d' archéologie moléculaire et structurale (LAMS), Boîte courrier 225, 4 place Jussieu, 75005 Paris (France)

    2016-04-05

    Highlights: • Silylated vermiculites reacted covalently with imidazole. • Modified vermiculites adsorbed copper from aqueous solution. • Copper retention in all solids occurred at rapid time of 80 min. • Higher organic content on the solid improved the copper adsorption. - Abstract: Organically modified vermiculites were synthesized by previous silylation of three leached vermiculites, V0.3Cl, V0.5Cl and V0.8Cl, under anhydrous conditions following reaction with imidazole (Im), which acted as chelating agent for copper retention. Elemental analysis, X-ray diffraction, infrared spectroscopy, scanning electronic microscopy, transmission electron microscopy, {sup 29}Si and {sup 13}C NMR and nitrogen adsorption/desorption measurements were used to characterize pristine, leached and organofunctionalized solids. X-ray photoelectron spectroscopy (XPS) was used to evaluate the surface after copper sorption. Parameters such as contact time, pH and initial cation concentration for the adsorption of Cu(II) ions were investigated. The adsorption equilibrium data were fitted using the Langmuir isotherm model and the monolayer adsorption capacities were 2.38, 2.52 and 2.69 mmol g{sup −1} for V0.5Cl-Im, V0.3Cl-Im and V0.8Cl-Im, respectively, at pH 6.0 and 298 K for a time reaction of 80 min. The sorption rates were described by pseudo-second-order kinetics. The chloropropyl imidazole vermiculites are promising adsorbents for the rapid removal of Cu(II) ions from aqueous solution.

  10. Synthesis of backbone P-functionalized imidazol-2-ylidene complexes: en route to novel functional ionic liquids.

    Science.gov (United States)

    Majhi, Paresh Kumar; Sauerbrey, Susanne; Schnakenburg, Gregor; Arduengo, Anthony J; Streubel, Rainer

    2012-10-01

    1-Alkyl-3-methyl-4-diphenylphosphoryl-imidazolium hydrogensulfate (4a,b) (a: R(1) = R(2) = Me; b: R(1) = (i)Pr, R(2) = Me) and 1-alkyl-3-methyl-4,5-bis(diphenylphosphoryl)imidazolium hydrogensulfate (6a,c) (c: R(1) = (n)Bu, R(2) = Me) were obtained selectively and in good yields by oxidative desulfurization of 1-alkyl-3-methyl-4-diphenylphosphino-imidazole-2-thiones (2a,b) and 1-n-butyl-3-methyl-4,5-bis(diphenylphosphoryl)imidazole-2-thione (3c) or 1,3-dimethyl-4-diphenylthiophosphoryl-5-diphenylphosphino-imidazole-2-thione (5a), respectively, with hydrogen peroxide. Synthesis of phosphoryl functionalized imidazol-2-ylidene complexes of group VI metal pentacarbonyls (7a-9a) and (10b-12b) and bis(phosphoryl) functionalized imidazol-2-ylidene complexes of group VI metal pentacarbonyls (13c-15c) and (16a) with low steric demand (methyl, isopropyl, n-butyl) at both N-centers was achieved through deprotonation of imidazolium salts (4a,b) and (6a,c), respectively,-having HSO(4)(-) as a counterion-with potassium tert-butoxide followed by rapid addition of metal pentacarbonyl acetonitrile complexes [M(CO)(5)(CH(3)CN)] (M = Cr, Mo, W). The products were unambiguously characterized by elemental analyses, spectroscopic and spectrometric methods, and in addition, by single-crystal X-ray structure studies in the cases of 4b, 8a, 15c, and 16a; the latter two reveal imidazole ring bond distance alternation in contrast to 8a.

  11. Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling

    Science.gov (United States)

    Bharatham, Kavitha; Bharatham, Nagakumar; Kwon, Yong Jung; Lee, Keun Woo

    2008-12-01

    Allosteric inhibition of protein tyrosine phosphatase 1B (PTP1B), has paved a new path to design specific inhibitors for PTP1B, which is an important drug target for the treatment of type II diabetes and obesity. The PTP1B1-282-allosteric inhibitor complex crystal structure lacks α7 (287-298) and moreover there is no available 3D structure of PTP1B1-298 in open form. As the interaction between α7 and α6-α3 helices plays a crucial role in allosteric inhibition, α7 was modeled to the PTP1B1-282 in open form complexed with an allosteric inhibitor (compound-2) and a 5 ns MD simulation was performed to investigate the relative orientation of the α7-α6-α3 helices. The simulation conformational space was statistically sampled by clustering analyses. This approach was helpful to reveal certain clues on PTP1B allosteric inhibition. The simulation was also utilized in the generation of receptor based pharmacophore models to include the conformational flexibility of the protein-inhibitor complex. Three cluster representative structures of the highly populated clusters were selected for pharmacophore model generation. The three pharmacophore models were subsequently utilized for screening databases to retrieve molecules containing the features that complement the allosteric site. The retrieved hits were filtered based on certain drug-like properties and molecular docking simulations were performed in two different conformations of protein. Thus, performing MD simulation with α7 to investigate the changes at the allosteric site, then developing receptor based pharmacophore models and finally docking the retrieved hits into two distinct conformations will be a reliable methodology in identifying PTP1B allosteric inhibitors.

  12. Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide

    OpenAIRE

    Hargrove, Amanda E.; Martinez, Thomas F.; Hare, Alissa A.; Kurmis, Alexis A.; Phillips, John W.; Sud, Sudha; Pienta, Kenneth J; Dervan, Peter B.

    2015-01-01

    Pyrrole-imidazole (Py-Im) polyamides are high affinity DNA-binding small molecules that can inhibit protein-DNA interactions. In VCaP cells, a human prostate cancer cell line overexpressing both AR and the TMPRSS2-ERG gene fusion, an androgen response element (ARE)-targeted Py-Im polyamide significantly downregulates AR driven gene expression. Polyamide exposure to VCaP cells reduced proliferation without causing DNA damage. Py-Im polyamide treatment also reduced tumor growth in a VCaP mouse ...

  13. Microwave-Assisted Solvent-Free Synthesis of Zeolitic Imidazolate Framework-67

    Directory of Open Access Journals (Sweden)

    Heng Zhang

    2016-01-01

    Full Text Available A microporous metal-organic framework (MOF, cobalt-based zeolitic imidazolate framework-67 (ZIF-67, was synthesized by the combination of solvent-free hand-mill and microwave irradiation, without any organic solvent and within 30 minutes. The hand-milling process can mix the reactants well by the virtue of high moisture/water absorption capacity of reactants. In addition, the outstanding electromagnetic wave absorption capability of cobalt leads to efficient conversion to MOF structures before carbonization. The obtained ZIF-67 possesses high surface area and micropore volume.

  14. Crystal structure of 2-methyl-1H-imidazol-3-ium hydrogen oxalate dihydrate

    Directory of Open Access Journals (Sweden)

    Mouhamadou Birame Diop

    2016-08-01

    Full Text Available Single crystals of the title molecular salt, C4H7N2+·HC2O4−·2H2O, were isolated from the reaction of 2-methyl-1H-imidazole and oxalic acid in a 1:1 molar ratio in water. In the crystal, the cations and anions are positioned alternately along an infinite [010] ribbon and linked together through bifurcated N—H...(O,O hydrogen bonds. The water molecules of crystallization link the chains into (10-1 bilayers, with the methyl groups of the cations organized in an isotactic manner.

  15. 1-[(1-Methyl-1H-imidazol-5-ylmethyl]-1H-indole-5-carbonitrile

    Directory of Open Access Journals (Sweden)

    Josephus Jacobus de Jager

    2012-12-01

    Full Text Available In the title compound, C14H12N4, the dihedral angle between the indole ring system (r.m.s. deviation = 0.010 Å and the imidazole ring is 77.70 (6°. In the crystal, molecules are linked by C—H...N hydrogen bonds. One set of hydrogen bonds forms an undulating chain running parallel to the b-axis direction, while the other undulating chain is parallel to the c-axis direction. In combination, (100 sheets result.

  16. Ultrasound-promoted synthesis of (4 or 5-aryl-2-aryloyl-(1H-imidazoles in water

    Directory of Open Access Journals (Sweden)

    Behzad Khalili

    2014-01-01

    Full Text Available A green and efficient method for the synthesis of (4 or 5-aryl-2-aryloyl-(1H-imidazoles via self-condensation reaction of arylglyoxal hydrates in the presence of ammonium acetate using water as solvent under ultrasonic irradiation was reported. The reactions proceeded in high yields and very short reaction time. Introduced procedure is completely ecofriendly and don’t need any toxic organic solvent in all performing steps. In addition we use computational chemistry for acquiring some information about the thermochemistry and geometrical structure of these imidazole derivatives.

  17. Dichloridobis[1-(2,4,6-trimethylphenyl-1H-imidazole-κN3]copper(II

    Directory of Open Access Journals (Sweden)

    Yantao Zhang

    2013-11-01

    Full Text Available In the title complex, [CuCl2(C12H14N22], the Cu2+ cation is situated on an inversion centre and is coordinated by two N atoms from symmetry-related 1-mesityl-1H-imidazole ligands and by two chloride anions in a slightly distorted square-planar geometry. In the organic ligand, the dihedral angle between the benzene ring of the mesityl moiety and the imidazole ring is 76.99 (18°. Weak intramolecular C—H...Cl hydrogen-bonding interactions consolidate the molecular conformation.

  18. Sniffer patch laser uncaging response (SPLURgE): an assay of regional differences in allosteric receptor modulation and neurotransmitter clearance.

    Science.gov (United States)

    Christian, Catherine A; Huguenard, John R

    2013-10-01

    Allosteric modulators exert actions on neurotransmitter receptors by positively or negatively altering the effective response of these receptors to their respective neurotransmitter. γ-Aminobutyric acid (GABA) type A ionotropic receptors (GABAARs) are major targets for allosteric modulators such as benzodiazepines, neurosteroids, and barbiturates. Analysis of substances that produce similar effects has been hampered by the lack of techniques to assess the localization and function of such agents in brain slices. Here we describe measurement of the sniffer patch laser uncaging response (SPLURgE), which combines the sniffer patch recording configuration with laser photolysis of caged GABA. This methodology enables the detection of allosteric GABAAR modulators endogenously present in discrete areas of the brain slice and allows for the application of exogenous GABA with spatiotemporal control without altering the release and localization of endogenous modulators within the slice. Here we demonstrate the development and use of this technique for the measurement of allosteric modulation in different areas of the thalamus. Application of this technique will be useful in determining whether a lack of modulatory effect on a particular category of neurons or receptors is due to insensitivity to allosteric modulation or a lack of local release of endogenous ligand. We also demonstrate that this technique can be used to investigate GABA diffusion and uptake. This method thus provides a biosensor assay for rapid detection of endogenous GABAAR modulators and has the potential to aid studies of allosteric modulators that exert effects on other classes of neurotransmitter receptors, such as glutamate, acetylcholine, or glycine receptors.

  19. mGluR5 Positive Allosteric Modulation Enhances Extinction Learning Following Cocaine Self-Administration

    OpenAIRE

    Cleva, Richard M.; Hicks, Megan P.; Gass, Justin T.; Wischerath, Kelly C.; Plasters, Elizabeth T.; Widholm, John J.; Olive, M. Foster

    2011-01-01

    Extinction of classically and instrumentally conditioned behaviors, such as conditioned fear and drug-seeking behavior, is a process of active learning, and recent studies indicate that potentiation of glutamatergic transmission facilitates extinction learning. In this study we investigated the effects of the type 5 metabotropic glutamate receptors (mGluR5) positive allosteric modulator 3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide (CDPPB) on the extinction of cocaine-seeking behavior in ...

  20. The therapeutic potential of allosteric ligands for free fatty acid sensitive GPCRs

    DEFF Research Database (Denmark)

    Hudson, Brian D; Ulven, Trond; Milligan, Graeme

    2013-01-01

    G protein coupled receptors (GPCRs) are the most historically successful therapeutic targets. Despite this success there are many important aspects of GPCR pharmacology and function that have yet to be exploited to their full therapeutic potential. One in particular that has been gaining attention...... safety, more physiologically appropriate responses, better target selectivity, and reduced likelihood of desensitisation and tachyphylaxis. Despite these advantages, the development of allosteric ligands is often difficult from a medicinal chemistry standpoint due to the more complex challenge...

  1. Allosteric regulation by oleamide of the binding properties of 5-hydroxytryptamine7 receptors.

    Science.gov (United States)

    Hedlund, P B; Carson, M J; Sutcliffe, J G; Thomas, E A

    1999-12-01

    Oleamide belongs to a family of amidated lipids with diverse biological activities, including sleep induction and signaling modulation of several 5-hydroxytryptamine (5-HT) receptor subtypes, including 5-HT1A, 5-HT2A/2C, and 5-HT7. The 5-HT7 receptor, predominantly localized in the hypothalamus, hippocampus, and frontal cortex, stimulates cyclic AMP formation and is thought to be involved in the regulation of sleep-wake cycles. Recently, it was proposed that oleamide acts at an allosteric site on the 5-HT7 receptor to regulate cyclic AMP formation. We have further investigated the interaction between oleamide and 5-HT7 receptors by performing radioligand binding assays with HeLa cells transfected with the 5-HT7 receptor. Methiothepin, clozapine, and 5-HT all displaced specific [3H]5-HT (100 nM) binding, with pK(D) values of 7.55, 7.85, and 8.39, respectively. Oleamide also displaced [3H]5-HT binding, but the maximum inhibition was only 40% of the binding. Taking allosteric (see below) cooperativity into account, a K(D) of 2.69 nM was calculated for oleamide. In saturation binding experiments, oleamide caused a 3-fold decrease in the affinity of [3H]5-HT for the 5-HT7 receptor, without affecting the number of binding sites. A Schild analysis showed that the induced shift in affinity of [3H]5-HT reached a plateau, unlike that of a competitive inhibitor, illustrating the allosteric nature of the interaction between oleamide and the 5-HT7 receptor. Oleic acid, the product of oleamide hydrolysis, had a similar effect on [3H]5-HT binding, whereas structural analogs of oleamide, trans-9,10-octadecenamide, cis-8,9-octadecenamide, and erucamide, did not alter [3H]5-HT binding significantly. The findings support the hypothesis that oleamide acts via an allosteric site on the 5-HT7 receptor regulating receptor affinity.

  2. Allosteric ligands and their binding sites define γ-aminobutyric acid (GABA) type A receptor subtypes.

    Science.gov (United States)

    Olsen, Richard W

    2015-01-01

    GABAA receptors (GABA(A)Rs) mediate rapid inhibitory transmission in the brain. GABA(A)Rs are ligand-gated chloride ion channel proteins and exist in about a dozen or more heteropentameric subtypes exhibiting variable age and brain regional localization and thus participation in differing brain functions and diseases. GABA(A)Rs are also subject to modulation by several chemotypes of allosteric ligands that help define structure and function, including subtype definition. The channel blocker picrotoxin identified a noncompetitive channel blocker site in GABA(A)Rs. This ligand site is located in the transmembrane channel pore, whereas the GABA agonist site is in the extracellular domain at subunit interfaces, a site useful for low energy coupled conformational changes of the functional channel domain. Two classes of pharmacologically important allosteric modulatory ligand binding sites reside in the extracellular domain at modified agonist sites at other subunit interfaces: the benzodiazepine site and the high-affinity, relevant to intoxication, ethanol site. The benzodiazepine site is specific for certain GABA(A)R subtypes, mainly synaptic, while the ethanol site is found at a modified benzodiazepine site on different, extrasynaptic, subtypes. In the transmembrane domain are allosteric modulatory ligand sites for diverse chemotypes of general anesthetics: the volatile and intravenous agents, barbiturates, etomidate, propofol, long-chain alcohols, and neurosteroids. The last are endogenous positive allosteric modulators. X-ray crystal structures of prokaryotic and invertebrate pentameric ligand-gated ion channels, and the mammalian GABA(A)R protein, allow homology modeling of GABA(A)R subtypes with the various ligand sites located to suggest the structure and function of these proteins and their pharmacological modulation. © 2015 Elsevier Inc. All rights reserved.

  3. Modulation in selectivity and allosteric properties of small-molecule ligands for CC-chemokine receptors

    DEFF Research Database (Denmark)

    Thiele, Stefanie; Malmgaard-Clausen, Mikkel; Engel-Andreasen, Jens

    2012-01-01

    Among 18 human chemokine receptors, CCR1, CCR4, CCR5, and CCR8 were activated by metal ion Zn(II) or Cu(II) in complex with 2,2'-bipyridine or 1,10-phenanthroline with similar potencies (EC(50) from 3.9 to 172 μM). Besides being agonists, they acted as selective allosteric enhancers of CCL3. Thes...

  4. Structure and allosteric effects of low-molecular-weight activators on the protein kinase PDK1

    DEFF Research Database (Denmark)

    Hindie, Valerie; Stroba, Adriana; Zhang, Hua

    2009-01-01

    -dependent activation of AGC kinases. The AGC kinase PDK1 is activated by the docking of a phosphorylated motif from substrates. Here we present the crystallography of PDK1 bound to a rationally developed low-molecular-weight activator and describe the conformational changes induced by small compounds in the crystal...... molecular details of the allosteric changes induced by small compounds that trigger the activation of PDK1 through mimicry of phosphorylation-dependent conformational changes....

  5. Molecular sites for the positive allosteric modulation of glycine receptors by endocannabinoids.

    Directory of Open Access Journals (Sweden)

    Gonzalo E Yévenes

    Full Text Available Glycine receptors (GlyRs are transmitter-gated anion channels of the Cys-loop superfamily which mediate synaptic inhibition at spinal and selected supraspinal sites. Although they serve pivotal functions in motor control and sensory processing, they have yet to be exploited as drug targets partly because of hitherto limited possibilities for allosteric control. Endocannabinoids (ECs have recently been characterized as direct allosteric GlyR modulators, but the underlying molecular sites have remained unknown. Here, we show that chemically neutral ECs (e.g. anandamide, AEA are positive modulators of α(1, α(2 and α(3 GlyRs, whereas acidic ECs (e.g. N-arachidonoyl-glycine; NA-Gly potentiate α(1 GlyRs but inhibit α(2 and α(3. This subunit-specificity allowed us to identify the underlying molecular sites through analysis of chimeric and mutant receptors. We found that alanine 52 in extracellular loop 2, glycine 254 in transmembrane (TM region 2 and intracellular lysine 385 determine the positive modulation of α(1 GlyRs by NA-Gly. Successive substitution of non-conserved extracellular and TM residues in α(2 converted NA-Gly-mediated inhibition into potentiation. Conversely, mutation of the conserved lysine within the intracellular loop between TM3 and TM4 attenuated NA-Gly-mediated potentiation of α(1 GlyRs, without affecting inhibition of α(2 and α(3. Notably, this mutation reduced modulation by AEA of all three GlyRs. These results define molecular sites for allosteric control of GlyRs by ECs and reveal an unrecognized function for the TM3-4 intracellular loop in the allosteric modulation of Cys-loop ion channels. The identification of these sites may help to understand the physiological role of this modulation and facilitate the development of novel therapeutic approaches to diseases such as spasticity, startle disease and possibly chronic pain.

  6. Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteins.

    Science.gov (United States)

    Soltan Ghoraie, Laleh; Burkowski, Forbes; Zhu, Mu

    2015-03-01

    Recent studies have highlighted the role of coupled side-chain fluctuations alone in the allosteric behavior of proteins. Moreover, examination of X-ray crystallography data has recently revealed new information about the prevalence of alternate side-chain conformations (conformational polymorphism), and attempts have been made to uncover the hidden alternate conformations from X-ray data. Hence, new computational approaches are required that consider the polymorphic nature of the side chains, and incorporate the effects of this phenomenon in the study of information transmission and functional interactions of residues in a molecule. These studies can provide a more accurate understanding of the allosteric behavior. In this article, we first present a novel approach to generate an ensemble of conformations and an efficient computational method to extract direct couplings of side chains in allosteric proteins, and provide sparse network representations of the couplings. We take the side-chain conformational polymorphism into account, and show that by studying the intrinsic dynamics of an inactive structure, we are able to construct a network of functionally crucial residues. Second, we show that the proposed method is capable of providing a magnified view of the coupled and conformationally polymorphic residues. This model reveals couplings between the alternate conformations of a coupled residue pair. To the best of our knowledge, this is the first computational method for extracting networks of side chains' alternate conformations. Such networks help in providing a detailed image of side-chain dynamics in functionally important and conformationally polymorphic sites, such as binding and/or allosteric sites. © 2014 Wiley Periodicals, Inc.

  7. Allosteric mechanisms within the adenosine A2A-dopamine D2 receptor heterotetramer

    Science.gov (United States)

    Ferré, Sergi; Bonaventura, Jordi; Tomasi, Dardo; Navarro, Gemma; Moreno, Estefanía; Cortés, Antonio; Lluís, Carme; Casadó, Vicent; Volkow, Nora D.

    2017-01-01

    The structure constituted by a G protein coupled receptor (GPCR) homodimer and a G protein provides a main functional unit and oligomeric entities can be viewed as multiples of dimers. For GPCR heteromers, experimental evidence supports a tetrameric structure, comprised of two different homodimers, each able to signal with its preferred G protein. GPCR homomers and heteromers can act as the conduit of allosteric interactions between orthosteric ligands. The well-known agonist/agonist allosteric interaction in the adenosine A2A receptor (A2AR)-dopamine D2 receptor (D2R) heteromer, by which A2AR agonists decrease the affinity of D2R agonists, gave the first rationale for the use of A2AR antagonists in Parkinson’s disease. We review new pharmacological findings that can be explained in the frame of a tetrameric structure of the A2AR-D2R heteromer: first, ligand-independent allosteric modulations by the D2R that result in changes of the binding properties of A2AR ligands; second, differential modulation of the intrinsic efficacy of D2R ligands for G protein-dependent and independent signaling; third, the canonical antagonistic Gs-Gi interaction within the frame of the heteromer; and fourth, the ability of A2AR antagonists, including caffeine, to also exert the same allosteric modulations of D2R ligands than A2AR agonists, while A2AR agonists and antagonists counteract each other’s effects. These findings can have important clinical implications when evaluating the use of A2AR antagonists. They also call for the need of monitoring caffeine intake when evaluating the effect of D2R ligands, when used as therapeutic agents in neuropsychiatric disorders or as probes in imaging studies. PMID:26051403

  8. Enzyme detection by microfluidics

    DEFF Research Database (Denmark)

    2013-01-01

    Microfluidic-implemented methods of detecting an enzyme, in particular a DNA-modifying enzyme, are provided, as well as methods for detecting a cell, or a microorganism expressing said enzyme. The enzyme is detected by providing a nucleic acid substrate, which is specifically targeted...... by that enzyme...

  9. Green synthesis of novel quinoline based imidazole derivatives and evaluation of their antimicrobial activity

    Directory of Open Access Journals (Sweden)

    N.C. Desai

    2014-12-01

    Full Text Available We have described the conventional and microwave method for the synthesis of N-(4-((2-chloroquinolin-3-ylmethylene-5-oxo-2-phenyl-4,5-dihydro-1H-imidazol-1-yl(arylamides 3a–l. It is observed that the solvent-free microwave thermolysis is a convenient, rapid, high-yielding, and environmental friendly protocol for the synthesis of quinoline based imidazole derivatives when compared with conventional reaction in a solution phase. Antimicrobial activity of the newly synthesized compounds is screened in vitro on the following microbial cultures: Escherichia coli (MTCC 443, Pseudomonas aeruginosa (MTCC 1688, Staphylococcus aureus (MTCC 96, Streptococcus pyogenes (MTCC 442, Candida albicans (MTCC 227, Aspergillus niger (MTCC 282, Aspergillus clavatus (MTCC 1323. All the synthesized bio-active molecules are tested for their in vitro antimicrobial activity by bioassay namely serial broth dilution. Among these compounds 3c, 3d, 3f, 3h and 3j show significant potency against different microbial strains. All the compounds have been characterized by IR, 1H NMR, 13C NMR and mass spectral data. On the basis of statistical analysis, it is observed that these compounds give significant co-relation.

  10. Nonenzymatic electrochemical sensor based on imidazole-functionalized graphene oxide for progesterone detection.

    Science.gov (United States)

    Gevaerd, Ava; Blaskievicz, Sirlon F; Zarbin, Aldo J G; Orth, Elisa S; Bergamini, Márcio F; Marcolino-Junior, Luiz H

    2018-07-30

    The modification of electrode surfaces has been the target of study for many researchers in order to improve the analytical performance of electrochemical sensors. Herein, the use of an imidazole-functionalized graphene oxide (GO-IMZ) as an artificial enzymatic active site for voltammetric determination of progesterone (P4) is described for the first time. The morphology and electrochemical performance of electrode modified with GO-IMZ were characterized by scanning electron microscopy and cyclic voltammetry, respectively. Under optimized conditions, the proposed sensor showed a synergistic effect of the GO sheets and the imidazole groups anchored on its backbone, which promoted a significant enhancement on electrochemical reduction of P4. Figures of merits such as linear dynamic response for P4 concentration ranging from 0.22 to 14.0 μmol L -1 , limit of detection of 68 nmol L -1 and limit of quantification and 210 nmol L -1 were found. In addition, presented a higher sensitivity, 426 nA L µmol -1 , when compared to the unmodified electrode. Overall, the proposed device showed to be a promising platform for a simple, rapid, and direct analysis of progesterone. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. Effect of phenols and carboxylic acids on photochromism of 1-alkyl-2-(arylazo)imidazoles

    Energy Technology Data Exchange (ETDEWEB)

    Gayen, Pallab [Inorganic Chemistry Section, Department of Chemistry, Jadavpur University, Kolkata 700032 (India); Sinha, Chittaranjan, E-mail: c_r_sinha@yahoo.com [Inorganic Chemistry Section, Department of Chemistry, Jadavpur University, Kolkata 700032 (India)

    2012-09-15

    Light irradiated trans-to-cis isomerization of 1-alkyl-2-(arylazo)imidazole in the presence of phenol, catechol, benzoic acid and salicylic acid (called co-factors) has been studied in this work. The rate of trans{yields}cis photoisomerization is decreased in the presence of co-factor in the medium and is dependent on the concentration of active quotient about photochrome. The decrease in rate follows catechol>benzoic acid>phenol>salicylic acid. This trend is due to the effects of dissociation ability of -O-H/-COOH, intermolecular association of the molecules etc. The reverse change, cis-to-trans, is very slow in light irradiation and has been carried out by a thermal process in the dark. The quantum yield of isomerization follows the same sequence of effects of co-factors. - Highlights: Black-Right-Pointing-Pointer Photoisomerisation of 1-alkyl-2-(arylazo)imidazoles, trans-to-cis, is described in this work. Black-Right-Pointing-Pointer The process is sensitive to the environment of the photochrome and the solution. Black-Right-Pointing-Pointer The rate of photoisomerization decreases as catechol>benzoic acid>phenol>salicylic acid. Black-Right-Pointing-Pointer The reverse isomerization, cis-to-trans is very slow with light and has been carried out with heat. Black-Right-Pointing-Pointer The activation energy is less than these values when carried out in fresh solution only.

  12. Effect of phenols and carboxylic acids on photochromism of 1-alkyl-2-(arylazo)imidazoles

    International Nuclear Information System (INIS)

    Gayen, Pallab; Sinha, Chittaranjan

    2012-01-01

    Light irradiated trans-to-cis isomerization of 1-alkyl-2-(arylazo)imidazole in the presence of phenol, catechol, benzoic acid and salicylic acid (called co-factors) has been studied in this work. The rate of trans→cis photoisomerization is decreased in the presence of co-factor in the medium and is dependent on the concentration of active quotient about photochrome. The decrease in rate follows catechol>benzoic acid>phenol>salicylic acid. This trend is due to the effects of dissociation ability of –O–H/–COOH, intermolecular association of the molecules etc. The reverse change, cis-to-trans, is very slow in light irradiation and has been carried out by a thermal process in the dark. The quantum yield of isomerization follows the same sequence of effects of co-factors. - Highlights: ► Photoisomerisation of 1-alkyl-2-(arylazo)imidazoles, trans-to-cis, is described in this work. ► The process is sensitive to the environment of the photochrome and the solution. ► The rate of photoisomerization decreases as catechol>benzoic acid>phenol>salicylic acid. ► The reverse isomerization, cis-to-trans is very slow with light and has been carried out with heat. ► The activation energy is less than these values when carried out in fresh solution only.

  13. Structure of eight molecular salts assembled from noncovalent bonding between carboxylic acids, imidazole, and benzimidazole

    Science.gov (United States)

    Jin, Shouwen; Zhang, Huan; Liu, Hui; Wen, Xianhong; Li, Minghui; Wang, Daqi

    2015-09-01

    Eight organic salts of imidazole/benzimidazole have been prepared with carboxylic acids as 2-methyl-2-phenoxypropanoic acid, α-ketoglutaric acid, 5-nitrosalicylic acid, isophthalic acid, 4-nitro-phthalic acid, and 3,5-dinitrosalicylic acid. The eight crystalline forms reported are proton-transfer compounds of which the crystals and compounds were characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. These structures adopted hetero supramolecular synthons, with the most common R22(7) motif observed at salts 2, 3, 5, 6 and 8. Analysis of the crystal packing of 1-8 suggests that there are extensive strong Nsbnd H⋯O, and Osbnd H⋯O hydrogen bonds (charge assisted or neutral) between acid and imidazolyl components in all of the salts. Except the classical hydrogen bonding interactions, the secondary propagating interactions also play important roles in structure extension. This variety, coupled with the varying geometries and number of acidic groups of the acids utilized, has led to the creation of eight supramolecular arrays with 1D-3D structure. The role of weak and strong noncovalent interactions in the crystal packing is analyzed. The results presented herein indicate that the strength and directionality of the Nsbnd H⋯O, and Osbnd H⋯O hydrogen bonds between acids and imidazole/benzimidazole are sufficient to bring about the formation of organic salts.

  14. Imidazole and beta-carotene photoprotection against photodynamic therapy evaluated by synchrotron infrared microscopy

    Science.gov (United States)

    Bosio, Gabriela N.; Parisi, Julieta; García Einschlag, Fernando S.; Mártire, Daniel O.

    2018-04-01

    In order to better understand the role of β-carotene and imidazole on the Photodynamic Therapy (PDT) mechanism, synchrotron infrared microscopy was used to detect the associated intracellular biochemical modifications following the visible light irradiation of HeLa cells incubated with these compounds as typical hydrophobic and hydrophilic singlet oxygen quenchers, respectively. For this purpose, PDT was performed employing the hydrophilic sensitizer 5,10,15,20-Tetrakis (1-methyl-4-pyridinio) porphyrin tetra (p-toluenesulfonate), TMPyP, and the hydrophobic sensitizer 5-(4-Methoxycarboxyphenyl)-10,15,20-triphenyl-21H,23H-porphyrin. The single cell IR spectra of PDT-treated, PDT plus quencher-treated and control HeLa cells were recorded at the SOLEIL Synchrotron Infrared SMIS beamline targeting specifically the cell nucleus. Principal Component Analysis (PCA) was used to assess the IR spectral changes. PCA revealed that there is a frequency shift of the protein Amide I vibrational band for the assays with the TMPyP sensitizer, indicating changes in the protein secondary structures of the PDT-treated cancer cells compared to the controls. In addition, the scores in those cells treated with both quenchers appear to be similar to the controls indicating a photoprotective effect. Comparative experiments carried out with SKMEL-28 and HaCat cells showed non- significant photoprotective effects of β-carotene and imidazole.

  15. Identification of an allosteric binding site for RORγt inhibition

    Energy Technology Data Exchange (ETDEWEB)

    Scheepstra, Marcel; Leysen, Seppe; vanAlmen, Geert C.; Miller, J. Richard; Piesvaux, Jennifer; Kutilek, Victoria; van Eenennaam, Hans; Zhang, Hongjun; Barr, Kenneth; Nagpal, Sunil; Soisson, Stephen M.; Kornienko, Maria; Wiley, Kristen; Elsen, Nathaniel; Sharma, Sujata; Correll, Craig C.; Trotter, B. Wesley; van der Stelt, Mario; Oubrie, Arthur; Ottmann, Christian; Parthasarathy, Gopal; Brunsveld, Luc (Merck); (Eindhoven)

    2015-12-07

    RORγt is critical for the differentiation and proliferation of Th17 cells associated with several chronic autoimmune diseases. We report the discovery of a novel allosteric binding site on the nuclear receptor RORγt. Co-crystallization of the ligand binding domain (LBD) of RORγt with a series of small-molecule antagonists demonstrates occupancy of a previously unreported allosteric binding pocket. Binding at this non-canonical site induces an unprecedented conformational reorientation of helix 12 in the RORγt LBD, which blocks cofactor binding. The functional consequence of this allosteric ligand-mediated conformation is inhibition of function as evidenced by both biochemical and cellular studies. RORγt function is thus antagonized in a manner molecularly distinct from that of previously described orthosteric RORγt ligands. This brings forward an approach to target RORγt for the treatment of Th17-mediated autoimmune diseases. The elucidation of an unprecedented modality of pharmacological antagonism establishes a mechanism for modulation of nuclear receptors.

  16. Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction.

    Science.gov (United States)

    Razo-Mejia, Manuel; Barnes, Stephanie L; Belliveau, Nathan M; Chure, Griffin; Einav, Tal; Lewis, Mitchell; Phillips, Rob

    2018-04-25

    Allosteric regulation is found across all domains of life, yet we still lack simple, predictive theories that directly link the experimentally tunable parameters of a system to its input-output response. To that end, we present a general theory of allosteric transcriptional regulation using the Monod-Wyman-Changeux model. We rigorously test this model using the ubiquitous simple repression motif in bacteria by first predicting the behavior of strains that span a large range of repressor copy numbers and DNA binding strengths and then constructing and measuring their response. Our model not only accurately captures the induction profiles of these strains, but also enables us to derive analytic expressions for key properties such as the dynamic range and [EC 50 ]. Finally, we derive an expression for the free energy of allosteric repressors that enables us to collapse our experimental data onto a single master curve that captures the diverse phenomenology of the induction profiles. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  17. Activation of Hsp90 Enzymatic Activity and Conformational Dynamics through Rationally Designed Allosteric Ligands.

    Science.gov (United States)

    Sattin, Sara; Tao, Jiahui; Vettoretti, Gerolamo; Moroni, Elisabetta; Pennati, Marzia; Lopergolo, Alessia; Morelli, Laura; Bugatti, Antonella; Zuehlke, Abbey; Moses, Mike; Prince, Thomas; Kijima, Toshiki; Beebe, Kristin; Rusnati, Marco; Neckers, Len; Zaffaroni, Nadia; Agard, David A; Bernardi, Anna; Colombo, Giorgio

    2015-09-21

    Hsp90 is a molecular chaperone of pivotal importance for multiple cell pathways. ATP-regulated internal dynamics are critical for its function and current pharmacological approaches block the chaperone with ATP-competitive inhibitors. Herein, a general approach to perturb Hsp90 through design of new allosteric ligands aimed at modulating its functional dynamics is proposed. Based on the characterization of a first set of 2-phenylbenzofurans showing stimulatory effects on Hsp90 ATPase and conformational dynamics, new ligands were developed that activate Hsp90 by targeting an allosteric site, located 65 Å from the active site. Specifically, analysis of protein responses to first-generation activators was exploited to guide the design of novel derivatives with improved ability to stimulate ATP hydrolysis. The molecules' effects on Hsp90 enzymatic, conformational, co-chaperone and client-binding properties were characterized through biochemical, biophysical and cellular approaches. These designed probes act as allosteric activators of the chaperone and affect the viability of cancer cell lines for which proper functioning of Hsp90 is necessary. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Allosteric Mutant IDH1 Inhibitors Reveal Mechanisms for IDH1 Mutant and Isoform Selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Xiaoling; Baird, Daniel; Bowen, Kimberly; Capka, Vladimir; Chen, Jinyun; Chenail, Gregg; Cho, YoungShin; Dooley, Julia; Farsidjani, Ali; Fortin, Pascal; Kohls, Darcy; Kulathila, Raviraj; Lin, Fallon; McKay, Daniel; Rodrigues, Lindsey; Sage, David; Touré, B. Barry; van der Plas, Simon; Wright, Kirk; Xu, Ming; Yin, Hong; Levell, Julian; Pagliarini, Raymond A. (Novartis)

    2017-03-01

    Oncogenic IDH1 and IDH2 mutations contribute to cancer via production of R-2-hydroxyglutarate (2-HG). Here, we characterize two structurally distinct mutant- and isoform-selective IDH1 inhibitors that inhibit 2-HG production. Both bind to an allosteric pocket on IDH1, yet shape it differently, highlighting the plasticity of this site. Oncogenic IDH1R132H mutation destabilizes an IDH1 “regulatory segment,” which otherwise restricts compound access to the allosteric pocket. Regulatory segment destabilization in wild-type IDH1 promotes inhibitor binding, suggesting that destabilization is critical for mutant selectivity. We also report crystal structures of oncogenic IDH2 mutant isoforms, highlighting the fact that the analogous segment of IDH2 is not similarly destabilized. This intrinsic stability of IDH2 may contribute to observed inhibitor IDH1 isoform selectivity. Moreover, discrete residues in the IDH1 allosteric pocket that differ from IDH2 may also guide IDH1 isoform selectivity. These data provide a deeper understanding of how IDH1 inhibitors achieve mutant and isoform selectivity.

  19. A Study of the Radioprotective Activity of the Imidazole Nucleus and Some of Its Derivatives; Etude de l'activite radioprotectrice du noyau imidazole et de quelquesuns de ses derives

    Energy Technology Data Exchange (ETDEWEB)

    Rinaldi, R; Bernard, Y [Commissariat a l' Energie Atomique. Centre d' Etudes Nucleaires, 38 - Grenoble (France)

    1962-07-01

    A study was made of the radioprotective properties of 8 compounds derived from imidazole. The effectiveness of the compounds was tested in mice exposed to a lethal dose of x radiation. Results showed that imidazole afforded protection to about 85% of the animals. Little protection was afforded by imidazoline and thione-imidazoline compounds in spite of the existence of a free sulfhydryl group in these compounds. (authors) [French] Cette etude a ete consacree a la determination des proprietes radioprotectrices eventuelles de huit composes derives de l'imidazole. Ces substances ont ete, soit synthetisees, soit obtenues dans le commerce. Leur efficacite a ete mise en evidence par le pourcentage de survie obtenu chez des souris soumises a une dose mortelle de rayons X. Les resultats ont fait apparaitre: - l'activite remarquable de l'imidazole qui protege environ 85 pour cent des animaux; - la protection faible ou nulle obtenue avec les imidazolinones et les thione-imidazolines, malgre la presence dans la molecule de ces dernieres d'un groupement sulfhydrile libre. (auteurs)

  20. Elevated Liver Enzymes

    Science.gov (United States)

    Symptoms Elevated liver enzymes By Mayo Clinic Staff Elevated liver enzymes may indicate inflammation or damage to cells in the liver. Inflamed or ... than normal amounts of certain chemicals, including liver enzymes, into the bloodstream, which can result in elevated ...

  1. Synthesis of pyrido[1,2-a]benzimidazoles and other fused imidazole derivatives with a bridgehead nitrogen atom

    Science.gov (United States)

    Begunov, Roman S.; Ryzvanovich, Galina A.

    2013-01-01

    Main methods for the synthesis of fused imidazole derivatives with a bridgehead nitrogen atom are systematically considered and summarized. The reaction mechanisms that underlie the methods for the synthesis of pyrido[1,2-a]benzimidazoles and related compounds are described. Biological properties and mechanisms of the biological activity of fused azaheterocycles are discussed. The bibliography includes 152 references.

  2. Exploring allosteric coupling in the α-subunit of Heterotrimeric G proteins using evolutionary and ensemble-based approaches

    Directory of Open Access Journals (Sweden)

    Hilser Vincent J

    2008-05-01

    Full Text Available Abstract Background Allosteric coupling, which can be defined as propagation of a perturbation at one region of the protein molecule (such as ligand binding to distant sites in the same molecule, constitutes the most general mechanism of regulation of protein function. However, unlike molecular details of ligand binding, structural elements involved in allosteric effects are difficult to diagnose. Here, we identified allosteric linkages in the α-subunits of heterotrimeric G proteins, which were evolved to transmit membrane receptor signals by allosteric mechanisms, by using two different approaches that utilize fundamentally different and independent information. Results We analyzed: 1 correlated mutations in the family of G protein α-subunits, and 2 cooperativity of the native state ensemble of the Gαi1 or transducin. The combination of these approaches not only recovered already-known details such as the switch regions that change conformation upon nucleotide exchange, and those regions that are involved in receptor, effector or Gβγ interactions (indicating that the predictions of the analyses can be viewed with a measure of confidence, but also predicted new sites that are potentially involved in allosteric communication in the Gα protein. A summary of the new sites found in the present analysis, which were not apparent in crystallographic data, is given along with known functional and structural information. Implications of the results are discussed. Conclusion A set of residues and/or structural elements that are potentially involved in allosteric communication in Gα is presented. This information can be used as a guide to structural, spectroscopic, mutational, and theoretical studies on the allosteric network in Gα proteins, which will provide a better understanding of G protein-mediated signal transduction.

  3. Synthesis and characterization of some complexes with imidazole and pyrazole from saccharinate transition ions in oxidation state (II)

    International Nuclear Information System (INIS)

    Pineda Cedeno, Leslie William

    2001-01-01

    The synthesis and characterization of metal ions saccharinate of the first serie of transition with the imidazole and pyrazole molecules in water and absolute ethanol were studied. In general, it found that in this series of saccharinate of coordinated water molecules are replaced by imidazole and pyrazole molecules with different substitution patterns, generating neutral complex of molecular formula [M(Sac) 2 (L) n (H 2 O) n-4 ] and cationic complex of molecular formula [M(L) n (H 2 O) 2 ]x2Sac, [M(L) n (H 2 O) 3 ]x2Sac, [M(L) n ]x2Sac, where M = V(II), Cr(II), Mc(II), Fe(II), Co(II), Ni(II) y Zn(II); Sac = saccharinate ion; L = imidazole (imd) and pyrazole (pir) and n = 6,4,3 and 2. These compounds are soluble in DMF and insoluble in all other common solvents. In turn, synthesized compounds in water were characterized by X ray crystallography, where preliminary data of refinement cycles, generate formulas of isostructural type [M(imd) 4 (H 2 O) 2 ]x2Sac and [M(Sac) 2 (pir) 2 (H 2 O) 2 ] where M = Co(II), Ni(II). The imidazole complex crystallize in the triclinic crystal system and space group P-1, while the pyrazole complexes crystallize in the monoclinic crystal system and space group P2 (1)/n. Gradual diminution was observed in the bond distances of M-N (saccharinate ion), M-N (imidazole) and M-N (pyrazole). The complex was characterized by spectroscopic methods, magnetic and electrochemical. (author) [es

  4. Synthetic polyspermine imidazole-4, 5-amide as an efficient and cytotoxicity-free gene delivery system

    Directory of Open Access Journals (Sweden)

    Duan S

    2012-07-01

    Full Text Available Shi-Yue Duan, Xue-Mei Ge, Nan Lu, Fei Wu, Weien Yuan, Tuo JinSchool of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of ChinaAbstract: A chemically dynamic spermine-based polymer: polyspermine imidazole-4, 5-amide (PSIA, Mw > 7 kDa was designed, synthesized, and evaluated in terms of its ability to deliver nucleic acids. This polymer was made from an endogenous monomer professionally condensing genes in sperms, spermine, and a known safety drug metabolite, imidazole-4, 5-dicarboxylic acid, through a bis-amide bond conjugated with the imidazole ring. This polymer can condense pDNA at a W/W ratio above 10 to form polyplexes (100–200 nm in diameter, which is consistent with the observation by transmission electron microscopy (TEM, and the zeta potential was in the range of 10–20 mV. The pDNA packaged polymer was stable in phosphate buffer solution (PBS at pH 7.4 (simulated body fluid while the polyplexes were releasing pDNA into the solution at pH 5.8 (simulated endo-lysosomes due to the degradation of the bis-amide linkages in response to changes in pH values. PSIA-polyplexes were able to achieve efficient cellular uptake and luciferase gene silencing by co-transfection of pDNA and siRNA in COS-7 cells and HepG2 cells with negligible cytotoxicity. Biodistribution of Rhodamine B-labeled PSIA-polyplexes after being systemically injected in BALB/c nude-mice showed that the polyplexes circulated throughout the body, accumulated mainly in the kidney at 4 hours of sample administration, and moved to the liver and spleen after 24 hours. All the results suggested that PSIA offered a promising example to balance the transfection efficiency and toxicity of a synthetic carrier system for the delivery of therapeutic nucleic acids.Keywords: gene delivery, polyspermine, cytotoxicity, transfection efficiency, biodistribution

  5. A monomeric variant of insulin degrading enzyme (IDE loses its regulatory properties.

    Directory of Open Access Journals (Sweden)

    Eun Suk Song

    2010-03-01

    Full Text Available Insulin degrading enzyme (IDE is a key enzyme in the metabolism of both insulin and amyloid beta peptides. IDE is unique in that it is subject to allosteric activation which is hypothesized to occur through an oligomeric structure.IDE is known to exist as an equilibrium mixture of monomers, dimers, and higher oligomers, with the dimer being the predominant form. Based on the crystal structure of IDE we deleted the putative dimer interface in the C-terminal region, which resulted in a monomeric variant. Monomeric IDE retained enzymatic activity, however instead of the allosteric behavior seen with wild type enzyme it displayed Michaelis-Menten kinetic behavior. With the substrate Abz-GGFLRKHGQ-EDDnp, monomeric IDE retained approximately 25% of the wild type activity. In contrast with the larger peptide substrates beta-endorphin and amyloid beta peptide 1-40, monomeric IDE retained only 1 to 0.25% of wild type activity. Unlike wild type IDE neither bradykinin nor dynorphin B-9 activated the monomeric variant of the enzyme. Similarly, monomeric IDE was not activated by polyphosphates under conditions in which the activity of wild type enzyme was increased more than 50 fold.These findings serve to establish the dimer interface in IDE and demonstrate the requirement for an oligomeric form of the enzyme for its regulatory properties. The data support a mechanism where the binding of activators to oligomeric IDE induces a conformational change that cannot occur in the monomeric variant. Since a conformational change from a closed to a more open structure is likely the rate-determining step in the IDE reaction, the subunit induced conformational change likely shifts the structure of the oligomeric enzyme to a more open conformation.

  6. Allosteric regulation of 6-phosphofructo-1-kinase activity of fat body and flight muscle from the bloodsucking bug Rhodnius prolixus

    Directory of Open Access Journals (Sweden)

    Gutemberg G. Alves

    2007-03-01

    Full Text Available 6-phosphofructo-1-kinase (phosphofructokinase; PFK activity from Rhodnius prolixus, a haematophagous insect which is usually a poor flyer, was measured and compared in two metabolically active tissues - flight muscle and fat body. The activity of this important regulatory glycolytic enzyme was much more pronounced in muscle (15.1 ± 1.4 U/mg than in fat body extracts (3.6±0.4 U/mg, although the latter presented higher levels of enzyme per protein content, as measured by western-blotting. Muscle extracts are more responsible than fat body to ATP and fructose 6-phosphate, both substrates of PFK. Allosteric regulation exerted by different effectors such as ADP, AMP and fructose 2,6-phosphate presented a singular pattern for each tissue. Optimal pH (8.0-8.5 and sensitivity to pH variation was very similar, and citrate was unable to inhibit PFK activity in both extracts. Our results suggest the existence of a particular PFK activity for each tissue, with regulatory patterns that are consistent with their physiological roles.A atividade da fosfofrutocinase (PFK de Rodnius prolixus, um inseto hematófago, o qual vôa somente pequenas distâncias, foi medida e comparada em dois tecidos metabolicamente ativos - músculo de asa e corpo gorduroso. A atividade desta importante enzima glicolítica regulatória foi muito mais pronunciada em músculo de asa (15,1 ±1,4 U/mg do que em extrato de corpo gorduroso (3,6 ±0,4 U/mg embora este último tenha apresentado níveis mais altos da enzima por quantidade de proteína, como medido por western-blotting. Extratos de músculo foram mais responsivos do que corpo gorduroso para ATP e frutose-6-fosfato, ambos substratos da PFK. A regulação alostérica exercida por diferentes efetores tais como ADP, AMP, frutose-2,6-bisfosfato apresentou um padrão singular para cada tecido. O pH ótimo (8,0-8,5 e a sensibilidade a variações de pH, foram muito similares e o citrato foi incapaz de inibir a atividade da PFK em

  7. AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems.

    Science.gov (United States)

    LeVine, Michael V; Weinstein, Harel

    2015-05-01

    In performing their biological functions, molecular machines must process and transmit information with high fidelity. Information transmission requires dynamic coupling between the conformations of discrete structural components within the protein positioned far from one another on the molecular scale. This type of biomolecular "action at a distance" is termed allostery . Although allostery is ubiquitous in biological regulation and signal transduction, its treatment in theoretical models has mostly eschewed quantitative descriptions involving the system's underlying structural components and their interactions. Here, we show how Ising models can be used to formulate an approach to allostery in a structural context of interactions between the constitutive components by building simple allosteric constructs we termed Allosteric Ising Models (AIMs). We introduce the use of AIMs in analytical and numerical calculations that relate thermodynamic descriptions of allostery to the structural context, and then show that many fundamental properties of allostery, such as the multiplicative property of parallel allosteric channels, are revealed from the analysis of such models. The power of exploring mechanistic structural models of allosteric function in more complex systems by using AIMs is demonstrated by building a model of allosteric signaling for an experimentally well-characterized asymmetric homodimer of the dopamine D2 receptor.

  8. Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide.

    Directory of Open Access Journals (Sweden)

    Amanda E Hargrove

    Full Text Available Pyrrole-imidazole (Py-Im polyamides are high affinity DNA-binding small molecules that can inhibit protein-DNA interactions. In VCaP cells, a human prostate cancer cell line overexpressing both AR and the TMPRSS2-ERG gene fusion, an androgen response element (ARE-targeted Py-Im polyamide significantly downregulates AR driven gene expression. Polyamide exposure to VCaP cells reduced proliferation without causing DNA damage. Py-Im polyamide treatment also reduced tumor growth in a VCaP mouse xenograft model. In addition to the effects on AR regulated transcription, RNA-seq analysis revealed inhibition of topoisomerase-DNA binding as a potential mechanism that contributes to the antitumor effects of polyamides in cell culture and in xenografts. These studies support the therapeutic potential of Py-Im polyamides to target multiple aspects of transcriptional regulation in prostate cancers without genotoxic stress.

  9. High-Flux Zeolitic Imidazolate Framework Membranes for Propylene/Propane Separation by Postsynthetic Linker Exchange.

    Science.gov (United States)

    Lee, Moon Joo; Kwon, Hyuk Taek; Jeong, Hae-Kwon

    2018-01-02

    While zeolitic imidazolate framework, ZIF-8, membranes show impressive propylene/propane separation, their throughput needs to be greatly improved for practical applications. A method is described that drastically reduces the effective thickness of ZIF-8 membranes, thereby substantially improving their propylene permeance (that is, flux). The new strategy is based on a controlled single-crystal to single-crystal linker exchange of 2-methylimidazole in ZIF-8 membrane grains with 2-imidazolecarboxaldehyde (ZIF-90 linker), thereby enlarging the effective aperture size of ZIF-8. The linker-exchanged ZIF-8 membranes showed a drastic increase in propylene permeance by about four times, with a negligible loss in propylene/propane separation factor when compared to as-prepared membranes. The linker-exchange effect depends on the membrane synthesis method. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Novel fluorescent pH sensor based on coumarin with piperazine and imidazole substituents.

    Science.gov (United States)

    Saleh, Na'il; Al-Soud, Yaseen A; Nau, Werner M

    2008-12-01

    A new coumarin derivative containing piperazine and imidazole moieties is reported as a fluorophore for hydrogen ions sensing. The fluorescence enhancement of the studied sensor with an increase in hydrogen ions concentration is based on the hindering of photoinduced electron transfer from the piperazinyl amine and the imidazolyl amine to the coumarin fluorophore by protonation. The presented sensor has a novel design of fluorophore-spacer-receptor(1)-receptor(2) format, which is proposed to sense two ranges of pH (from 2.5 to 5.5) and (from 10 to 12) instead of sensing one pH range. A model compound, in which the piperazinyl ring is absent, was synthesized as well to confirm the novel pH sensing of the proposed sensor.

  11. Characterization and application of zeolitic imidazolate framework-8@polyvinyl alcohol nanofibers mats prepared by electrospinning

    Science.gov (United States)

    Fan, Xiaoxiao; Yu, Linling; Li, Lianghao; Yang, Cao; Wen, Junjie; Ye, Xiaokun; Cheng, Jianhua; Hu, Yongyou

    2017-02-01

    In this study, Zeolitic imidazolate framework-8@polyvinyl alcohol (ZIF-8@PVA) nanofibers were creatively fabricated by electrospinning technique, and the nanofibers membranes were characterized by SEM, TEM, XRD, FTIR, TG, DSC, DTA, BET. Its thermal stability, mechanical property, water stability and adsorption nature were also performed. The optimized fabrication parameter of the ZIF-8@PVA was 10 wt% and the uniform diameters of the nanofibers has been obtained. In addition, the ZIF-8@PVA nanofibers displayed unique properties such as a water stable and flexible structure. The adsorption test for Congo red treatment revealed that the nanofibers had a great adsorption performance. The results indicated that the nonwoven fiber mats had a great potential as a new type of membrane adsorbents in wastewater purification. The possible mechanism of CR adsorption onto ZIF-8@PVA was researched.

  12. Use of imidazole 4,5-dicarboxylic acid in vanadium speciation

    International Nuclear Information System (INIS)

    Banerjee, D.; Mondal, B.C.; Das, D.; Das, A.K.

    2003-01-01

    A new resin has been synthesized by fictionalization of polystyrene-divinylbenzene (8 %) with imidazole 4,5-dicarboxylic acid through -N=N- bonding. The resulting resin has been characterized by elemental analysis, thermogravimetric analysis, infrared spectroscopy, hydrogen ion capacity and metal ion capacity. The speciation study of vanadium has been studied by using this resin and the maximum exchange capacity was found to be 0.45 mmol g -1 for V 4+ and that for V 5+ was 1.57 mmol g -1 at pH 3 for both. The eluents malonic acid and sodium hydroxide have been used for the selective separation of vanadium(IV) and vanadium(V) species respectively. The effects of diverse ions on the sorption and recovery of each species have been studied. Finally, the developed method has been applied for the speciation and determination of these two species in natural water samples. (author)

  13. Electric properties and fabrication of IMI-O LB films containing the imidazole group

    CERN Document Server

    Yoo, S Y; Kwon, Y S; Park, J C

    1999-01-01

    We fabricated an IMI-O polymer containing an imidazole group that could form a complex structure between the monolayer and the metal ions at the air-water interface. Also, the monolayer behavior at the air-water interface and the electrical properties of metal-complexed Langmuir-Blodgett (LB) films were investigated by using Brewster angle microscopy (BAM) and current-voltage(I-V) measurements. The difference in the BAM images between the pure water and the aqueous metal ions is attributed to the interactions of the copolymers with the metal ions at the interface and the consequent change of the monolayer organization. In the I-V characteristics, the current for LB films with different metal ion depended on the quantity of the metal-ion complexed with the LB film due to the interaction between the metal ion and the IMI-O polymer.

  14. Investigation of the Linker Swing Motion in the Zeolitic Imidazolate Framework ZIF-90

    KAUST Repository

    Zheng, Bin

    2018-03-13

    The linker swing motion in the zeolitic imidazolate framework ZIF-90 is investigated by density functional theory (DFT) calculation, molecular dynamics (MD) and grand-canonical Monte Carlo (GCMC) simulations. The relation between the terminal aldehyde group rotation and the linker swing motion is revealed. The extremely high activation energy of the linker swing motion in ZIF-90 can be attributed to the asymmetric geometry and electron distribution of aldehyde groups. The change in the gate structure resulting from the linker rotation is used to understand the guest adsorption in ZIF-90. This study shows that it is possible to tune the linker swing motion and then the properties of ZIF-90 by manipulating the terminal group rotation. The results highlight the importance of considering the internal freedom effects to correctly describe the linker swing motion and the flexibility of metal-organic frameworks (MOFs).

  15. Zeolitic Imidazolate Framework-8 (ZIF-8) Membranes for Kr/Xe Separation

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Ting; Feng, Xuhui; Elsaidi, Sameh K.; Thallapally, Praveen K.; Carreon, Moises A.

    2017-01-30

    Herein, we demonstrate that a prototypical type of metal organic framework, zeolitic imidazolate framework-8 (ZIF-8), in membrane form, can effectively separate Kr/Xe gas mixtures at industrially relevant compositions. The best membranes separated Kr/Xe mixtures with average Kr permeances as high as 1.5 × 10-8 ± 0.2 mol/m2 s Pa and average separation selectivities of 14.2 ± 1.9 for molar feed compositions corresponding to Kr/Xe ratio encountered typically in air. Molecular sieving, competitive adsorption, and differences in diffusivities were identified as the prevailing separation mechanisms. These membranes potentially represent a less-energy-intensive alternative to cryogenic distillation, which is the benchmark technology used to separate this challenging gas mixture. To our best knowledge, this is the first example of any metal organic membrane composition displaying separation ability for Kr/Xe gas mixtures.

  16. Carbon dioxide selective adsorption within a highly stable mixed-ligand Zeolitic Imidazolate Framework

    KAUST Repository

    Huang, Lin

    2014-08-01

    A new mixed-ligand Zeolitic Imidazolate Framework Zn4(2-mbIm) 3(bIm)5·4H2O (named JUC-160, 2-mbIm = 2-methylbenzimidazole, bIm = benzimidazole and JUC = Jilin University China) was synthesized with a solvothermal reaction of Zn(NO3) 2·6H2O, bIm and 2-mbIm in DMF solution at 180 °C. Topological analysis indicated that JUC-160 has a zeolite GIS (gismondine) topology. Study of the gas adsorption and thermal and chemical stability of JUC-160 demonstrated its selective adsorption property for carbon dioxide, high thermal stability, and remarkable chemical resistance to boiling alkaline water and organic solvent for up to one week. © 2014 Elsevier B.V.

  17. Gas-Phase Thermal Tautomerization of Imidazole-Acetic Acid: Theoretical and Computational Investigations

    Directory of Open Access Journals (Sweden)

    Saadullah G. Aziz

    2015-11-01

    Full Text Available The gas-phase thermal tautomerization reaction between imidazole-4-acetic (I and imidazole-5-acetic (II acids was monitored using the traditional hybrid functional (B3LYP and the long-range corrected functionals (CAM-B3LYP and ωB97XD with 6-311++G** and aug-cc-pvdz basis sets. The roles of the long-range and dispersion corrections on their geometrical parameters, thermodynamic functions, kinetics, dipole moments, Highest Occupied Molecular Orbital–Lowest Unoccupied Molecular Orbital (HOMO–LUMO energy gaps and total hyperpolarizability were investigated. All tested levels of theory predicted the preference of I over II by 0.750–0.877 kcal/mol. The origin of predilection of I is assigned to the H-bonding interaction (nN8→σ*O14–H15. This interaction stabilized I by 15.07 kcal/mol. The gas-phase interconversion between the two tautomers assumed a 1,2-proton shift mechanism, with two transition states (TS, TS1 and TS2, having energy barriers of 47.67–49.92 and 49.55–52.69 kcal/mol, respectively, and an sp3-type intermediate. A water-assisted 1,3-proton shift route brought the barrier height down to less than 20 kcal/mol in gas-phase and less than 12 kcal/mol in solution. The relatively high values of total hyperpolarizability of I compared to II were interpreted and discussed.

  18. Synthesis and DNA-binding study of imidazole linked thiazolidinone derivatives.

    Science.gov (United States)

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

    2017-02-01

    A novel series of imidazole-linked thiazolidinone hybrid molecules were designed and synthesized through a feasible synthetic protocol. The molecules were characterized with Fourier transform infrared (FT-IR), 1 H nuclear magnetic resonance (NMR), 13 C NMR and high-resolution mass spectrometry (HRMS) techniques. In vitro susceptibility tests against Gram-positive (S. aureus and B. subtilis) and Gram-negative bacteria (E. coli and P. aeruginosa) gave highly promising results. The most active molecule (3e) gave a minimal inhibitory concentration (MIC) value of 3.125 μg/mL which is on par with the reference drug streptomycin. Structure-activity relationships revealed activity enhancement by nitro and chloro groups when they occupied meta position of the arylidene ring in 2-((3-(imidazol-1-yl)propyl)amino)-5-benzylidenethiazolidin-4-ones. DNA-binding study of the most potent molecule 3e with salmon milt DNA (sm-DNA) under simulated physiological pH was probed with UV-visible absorption, fluorescence quenching, gel electrophoresis and molecular docking techniques. These studies established that compound 3e has a strong affinity towards DNA and binds at DNA minor groove with a binding constant (K b ) 0.18 × 10 2  L mol -1 . Molecular docking simulations predicted strong affinity of 3e towards DNA with a binding affinity (ΔG) -8.5 kcal/mol. Van der Waals forces, hydrogen bonding and hydrophobic interactions were predicted as the main forces of interaction. The molecule 3e exhibited specific affinity towards adenine-thiamine base pairs. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  19. Zeolitic imidazolate framework membranes and methods of making and using same for separation of c2- and c3+ hydrocarbons and separation of propylene and propane mixtures

    KAUST Repository

    Lai, Zhiping

    2012-12-06

    Certain embodiments are directed to processes for fabrication of zeolitic imidazolate framework (ZIF) membranes. These ZIF membranes can be used in separating C2-hydrocarbons from C3+ hydrocarbons and propylene/propane mixtures.

  20. Zeolitic imidazolate framework membranes and methods of making and using same for separation of c2- and c3+ hydrocarbons and separation of propylene and propane mixtures

    KAUST Repository

    Lai, Zhiping; Pan, Yichang

    2012-01-01

    Certain embodiments are directed to processes for fabrication of zeolitic imidazolate framework (ZIF) membranes. These ZIF membranes can be used in separating C2-hydrocarbons from C3+ hydrocarbons and propylene/propane mixtures.

  1. Mutations that silence constitutive signaling activity in the allosteric ligand-binding site of the thyrotropin receptor.

    Science.gov (United States)

    Haas, Ann-Karin; Kleinau, Gunnar; Hoyer, Inna; Neumann, Susanne; Furkert, Jens; Rutz, Claudia; Schülein, Ralf; Gershengorn, Marvin C; Krause, Gerd

    2011-01-01

    The thyrotropin receptor (TSHR) exhibits elevated cAMP signaling in the basal state and becomes fully activated by thyrotropin. Previously we presented evidence that small-molecule ligands act allosterically within the transmembrane region in contrast to the orthosteric extracellular hormone-binding sites. Our goal in this study was to identify positions that surround the allosteric pocket and that are sensitive for inactivation of TSHR. Homology modeling combined with site-directed mutagenesis and functional characterization revealed seven mutants located in the allosteric binding site that led to a decrease of basal cAMP signaling activity. The majority of these silencing mutations, which constrain the TSHR in an inactive conformation, are found in two clusters when mapped onto the 3D structural model. We suggest that the amino acid positions identified herein are indicating locations where small-molecule antagonists, both neutral antagonists and inverse agonists, might interfere with active TSHR conformations.

  2. SB265610 is an allosteric, inverse agonist at the human CXCR2 receptor

    Science.gov (United States)

    Bradley, ME; Bond, ME; Manini, J; Brown, Z; Charlton, SJ

    2009-01-01

    Background and purpose: In several previous studies, the C-X-C chemokine receptor (CXCR)2 antagonist 1-(2-bromo-phenyl)-3-(7-cyano-3H-benzotriazol-4-yl)-urea (SB265610) has been described as binding competitively with the endogenous agonist. This is in contrast to many other chemokine receptor antagonists, where the mechanism of antagonism has been described as allosteric. Experimental approach: To determine whether it displays a unique mechanism among the chemokine receptor antagonists, the mode of action of SB265610 was investigated at the CXCR2 receptor using radioligand and [35S]-GTPγS binding approaches in addition to chemotaxis of human neutrophils. Key results: In equilibrium saturation binding studies, SB265610 depressed the maximal binding of [125I]-interleukin-8 ([125I]-IL-8) without affecting the Kd. In contrast, IL-8 was unable to prevent binding of [3H]-SB265610. Kinetic binding experiments demonstrated that this was not an artefact of irreversible or slowly reversible binding. In functional experiments, SB265610 caused a rightward shift of the concentration-response curves to IL-8 and growth-related oncogene α, but also a reduction in maximal response elicited by each agonist. Fitting these data to an operational allosteric ternary complex model suggested that, once bound, SB265610 completely blocks receptor activation. SB265610 also inhibited basal [35S]-GTPγS binding in this preparation. Conclusions and implications: Taken together, these data suggest that SB265610 behaves as an allosteric inverse agonist at the CXCR2 receptor, binding at a region distinct from the agonist binding site to prevent receptor activation, possibly by interfering with G protein coupling. PMID:19422399

  3. Convergent transmission of RNAi guide-target mismatch information across Argonaute internal allosteric network.

    Science.gov (United States)

    Joseph, Thomas T; Osman, Roman

    2012-01-01

    In RNA interference, a guide strand derived from a short dsRNA such as a microRNA (miRNA) is loaded into Argonaute, the central protein in the RNA Induced Silencing Complex (RISC) that silences messenger RNAs on a sequence-specific basis. The positions of any mismatched base pairs in an miRNA determine which Argonaute subtype is used. Subsequently, the Argonaute-guide complex binds and silences complementary target mRNAs; certain Argonautes cleave the target. Mismatches between guide strand and the target mRNA decrease cleavage efficiency. Thus, loading and silencing both require that signals about the presence of a mismatched base pair are communicated from the mismatch site to effector sites. These effector sites include the active site, to prevent target cleavage; the binding groove, to modify nucleic acid binding affinity; and surface allosteric sites, to control recruitment of additional proteins to form the RISC. To examine how such signals may be propagated, we analyzed the network of internal allosteric pathways in Argonaute exhibited through correlations of residue-residue interactions. The emerging network can be described as a set of pathways emanating from the core of the protein near the active site, distributed into the bulk of the protein, and converging upon a distributed cluster of surface residues. Nucleotides in the guide strand "seed region" have a stronger relationship with the protein than other nucleotides, concordant with their importance in sequence selectivity. Finally, any of several seed region guide-target mismatches cause certain Argonaute residues to have modified correlations with the rest of the protein. This arises from the aggregation of relatively small interaction correlation changes distributed across a large subset of residues. These residues are in effector sites: the active site, binding groove, and surface, implying that direct functional consequences of guide-target mismatches are mediated through the cumulative effects of

  4. Convergent transmission of RNAi guide-target mismatch information across Argonaute internal allosteric network.

    Directory of Open Access Journals (Sweden)

    Thomas T Joseph

    Full Text Available In RNA interference, a guide strand derived from a short dsRNA such as a microRNA (miRNA is loaded into Argonaute, the central protein in the RNA Induced Silencing Complex (RISC that silences messenger RNAs on a sequence-specific basis. The positions of any mismatched base pairs in an miRNA determine which Argonaute subtype is used. Subsequently, the Argonaute-guide complex binds and silences complementary target mRNAs; certain Argonautes cleave the target. Mismatches between guide strand and the target mRNA decrease cleavage efficiency. Thus, loading and silencing both require that signals about the presence of a mismatched base pair are communicated from the mismatch site to effector sites. These effector sites include the active site, to prevent target cleavage; the binding groove, to modify nucleic acid binding affinity; and surface allosteric sites, to control recruitment of additional proteins to form the RISC. To examine how such signals may be propagated, we analyzed the network of internal allosteric pathways in Argonaute exhibited through correlations of residue-residue interactions. The emerging network can be described as a set of pathways emanating from the core of the protein near the active site, distributed into the bulk of the protein, and converging upon a distributed cluster of surface residues. Nucleotides in the guide strand "seed region" have a stronger relationship with the protein than other nucleotides, concordant with their importance in sequence selectivity. Finally, any of several seed region guide-target mismatches cause certain Argonaute residues to have modified correlations with the rest of the protein. This arises from the aggregation of relatively small interaction correlation changes distributed across a large subset of residues. These residues are in effector sites: the active site, binding groove, and surface, implying that direct functional consequences of guide-target mismatches are mediated through the

  5. Zinc (II) [tetra(4-methylphenyl)] Porphyrin: a Novel and Reusable Catalyst for Efficient Synthesis of 2,4,5-trisubstituted Imidazoles Under Ultrasound Irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Safari, Javad; Khalili, Shiva Dehghan; Banitaba, Sayed Hossein; Dehghani, Hossein [Univ. of Kashan, Kashan (Iran, Islamic Republic of)

    2011-10-15

    An efficient three-component one-step synthesis of 2,4,5-trisubstituted imidazoles by condensation reaction of 1,2-diketones or α-hydroxyketones with aromatic aldehydes and ammonium acetate using Zinc (II) [tetra (4-methylphenyl)] porphyrin as a novel and reusable catalyst under ultrasound irradiation at ambient temperature is described. In this method, α-hydroxyketones as well as 1,2-diketones were converted to their corresponding 2,4,5-trisubstituted imidazoles in excellent yields.

  6. Enzyme organization in the proline biosynthetic pathway of Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Gamper, H; Moses, V

    1974-01-01

    The conversion of glutamic acid to proline by an Escherichia coli extract was studied. The activity was dependent upon the presence of ATP and NADPH and was largely unaffected by the presence of NH/sub 3/ or imidazole. The first two pathway enzymes appear to exist as a complex which stabilizes a labile intermediate postulated as ..gamma..-glutamyl phosphate. Attempted synthesis of this compound was unsuccessful due to its spontaneous cyclization to 2-pyrrolidone 5-carboxylate. Dissociation of the enzyme complex upon dilution of the extract is presumed responsible for an experimentally observed dilution effect. E. coli pro/sub A//sup -/ and pro/sub B//sup -/ auxotroph extracts failed to complement one another in the biosynthesis of proline. This is attributed to the lack of a dynamic equilibrium between the complex and its constituent enzymes. In vivo studies with E. coli showed no evidence for metabolic channeling in the final reaction of proline synthesis, the reduction of ..delta../sup 1/-pyrroline 5-carboxylate.

  7. Chemogenomic discovery of allosteric antagonists at the GPRC6A receptor

    DEFF Research Database (Denmark)

    Gloriam, David E.; Wellendorph, Petrine; Johansen, Lars Dan

    2011-01-01

    and pharmacological character: (1) chemogenomic lead identification through the first, to our knowledge, ligand inference between two different GPCR families, Families A and C; and (2) the discovery of the most selective GPRC6A allosteric antagonists discovered to date. The unprecedented inference of...... pharmacological activity across GPCR families provides proof-of-concept for in silico approaches against Family C targets based on Family A templates, greatly expanding the prospects of successful drug design and discovery. The antagonists were tested against a panel of seven Family A and C G protein-coupled receptors...

  8. Structural insight to mutation effects uncover a common allosteric site in class C GPCRs

    DEFF Research Database (Denmark)

    Harpsøe, Kasper; Boesgaard, Michael W; Munk, Christian

    2017-01-01

    MOTIVATION: Class C G protein-coupled receptors (GPCRs) regulate important physiological functions and allosteric modulators binding to the transmembrane domain constitute an attractive and, due to a lack of structural insight, a virtually unexplored potential for therapeutics and the food industry....... Combining pharmacological site-directed mutagenesis data with the recent class C GPCR experimental structures will provide a foundation for rational design of new therapeutics. RESULTS: We uncover one common site for both positive and negative modulators with different amino acid layouts that can...

  9. Substituted 3-Benzylcoumarins as Allosteric MEK1 Inhibitors: Design, Synthesis and Biological Evaluation as Antiviral Agents

    Directory of Open Access Journals (Sweden)

    Ping Xu

    2013-05-01

    Full Text Available In order to find novel antiviral agents, a series of allosteric MEK1 inhibitors were designed and synthesized. Based on docking results, multiple optimizations were made on the coumarin scaffold. Some of the derivatives showed excellent MEK1 binding affinity in the appropriate enzymatic assays and displayed obvious inhibitory effects on the ERK pathway in a cellular assay. These compounds also significantly inhibited virus (EV71 replication in HEK293 and RD cells. Several compounds showed potential as agents for the treatment of viral infective diseases, with the most potent compound 18 showing an IC50 value of 54.57 nM in the MEK1 binding assay.

  10. Discovery of a novel allosteric modulator of 5-HT3 receptor

    DEFF Research Database (Denmark)

    Trattnig, Sarah M; Harpsøe, Kasper; Thygesen, Sarah B

    2012-01-01

    The ligand-gated ion channels in the Cysloop receptor superfamily mediate the effects of neurotransmitters acetylcholine, serotonin, GABA and glycine. Cysloop receptor signaling is susceptible to modulation by ligands acting through numerous allosteric sites. Here we report the discovery of a novel...... receptor guided by a homology model, PU02 is demonstrated to act through a transmembrane intersubunit site situated in the upper three helical turns of TM2 and TM3 in the (+)subunit and TM1 and TM2 in the (minus)subunit. The Ser248, Leu288, Ile290, Thr294 and Gly306 residues are identified as important...

  11. In vitro pharmacological characterization of RXFP3 allosterism: an example of probe dependency.

    Directory of Open Access Journals (Sweden)

    Lily Alvarez-Jaimes

    Full Text Available Recent findings suggest that the relaxin-3 neural network may represent a new ascending arousal pathway able to modulate a range of neural circuits including those affecting circadian rhythm and sleep/wake states, spatial and emotional memory, motivation and reward, the response to stress, and feeding and metabolism. Therefore, the relaxin-3 receptor (RXFP3 is a potential therapeutic target for the treatment of various CNS diseases. Here we describe a novel selective RXFP3 receptor positive allosteric modulator (PAM, 3-[3,5-Bis(trifluoromethylphenyl]-1-(3,4-dichlorobenzyl-1-[2-(5-methoxy-1H-indol-3-ylethyl]urea (135PAM1. Calcium mobilization and cAMP accumulation assays in cell lines expressing the cloned human RXFP3 receptor show the compound does not directly activate RXFP3 receptor but increases functional responses to amidated relaxin-3 or R3/I5, a chimera of the INSL5 A chain and the Relaxin-3 B chain. 135PAM1 increases calcium mobilization in the presence of relaxin-3(NH2 and R3/I5(NH2 with pEC50 values of 6.54 (6.46 to 6.64 and 6.07 (5.94 to 6.20, respectively. In the cAMP accumulation assay, 135PAM1 inhibits the CRE response to forskolin with a pIC50 of 6.12 (5.98 to 6.27 in the presence of a probe (10 nM concentration of relaxin-3(NH2. 135PAM1 does not compete for binding with the orthosteric radioligand, [(125I] R3I5 (amide, in membranes prepared from cells expressing the cloned human RXFP3 receptor. 135PAM1 is selective for RXFP3 over RXFP4, which also responds to relaxin-3. However, when using the free acid (native form of relaxin-3 or R3/I5, 135PAM1 doesn't activate RXFP3 indicating that the compound's effect is probe dependent. Thus one can exchange the entire A-chain of the probe peptide while retaining PAM activity, but the state of the probe's c-terminus is crucial to allosteric activity of the PAM. These data demonstrate the existence of an allosteric site for modulation of this GPCR as well as the subtlety of changes in probe

  12. Complex pharmacology of novel allosteric free fatty acid 3 receptor ligands

    DEFF Research Database (Denmark)

    Hudson, Brian D; Christiansen, Elisabeth; Murdoch, Hannah

    2014-01-01

    this series resulted in compounds completely lacking activity, acting as FFA3 PAMs, or appearing to act as FFA3-negative allosteric modulators. However, the pharmacology of this series was further complicated in that certain analogs displaying overall antagonism of FFA3 function actually appeared to generate......, considerable care must be taken to define the pharmacological characteristics of specific compounds before useful predictions of their activity and their use in defining specific roles of FFA3 in either in vitro and in vivo settings can be made....

  13. Allosteric Binding in the Serotonin Transporter - Pharmacology, Structure, Function and Potential Use as a Novel Drug Target

    DEFF Research Database (Denmark)

    Loland, Claus J.; Sanchez, Connie; Plenge, Per

    2017-01-01

    The serotonin transporter (SERT) is an important drug target and the majority of currently used antidepressants are potent inhibitors of SERT, binding primarily to the substrate binding site. However, even though the existence of an allosteric modulator site was realized more than 30 years ago......, the research into this mechanism is still in its early days. The current knowledge about the allosteric site with respect to pharmacology, structure and function, and pharmacological tool compounds, is reviewed and a perspective is given on its potential as a drug target....

  14. Cu(II) coordination polymers constructed by tetrafluoroterephthalic acid and varied imidazole-containing ligands: Syntheses, structures and properties

    Science.gov (United States)

    Liu, Kang; Sun, Yayong; Deng, Liming; Cao, Fan; Han, Jishu; Wang, Lei

    2018-02-01

    Six new copper(II) coordination polymers combining 2,3,5,6-tetrafluoroterephthalatic acid (H2tfBDC) and diverse imidazole-containing ligands, {[Cu(tfBDC)(1,2-bix)2]·2(H2O)}n (1), {Cu(tfBDC)(Im)2}n (2), {[Cu(1,4-bmimb)2(H2O)]·(tfBDC)·2(H2O)}n (3), {Cu(1,4-bimb)2(H2O)2·(tfBDC)}n (4), {[Cu(1,3-bix)2(H2O)2]·(tfBDC)·6(H2O)}n (5) and {[Cu(1,4-bix)2(H2O)2]·(tfBDC)·(1,4-bix)·4(H2O)}n (6) (1,2-bix = 1,2-bis(imidazole-1-ylmethyl)-benzene, Im = imidazole, 1,4-bmimb = 1,4-bis((2-methyl-1H-imidazol-1-yl)methyl)benzene, 1,4-bimb = 1,4-bis(imidazol-1-yl)-butane, 1,3-bix = 1,3-bis(imidazole-1-ylmethyl)-benzene, 1,4-bix = 1,4-bis(imidazole-1-ylmethyl)-benzene), have been obtained and structurally verified by single-crystal X-ray diffraction analyses and further characterized by powder X-ray diffraction (PXRD), elemental analyses and infrared spectroscopy (IR). Single crystal X-ray diffraction analysis revealed that 1 is 2D 4-connected sql topology (point symbol: {44·62}) based on a single metal ion node. Compound 2 is characterized as an infinite 1D chain structure, which is further extended into a 2D layer through N-H···O hydrogen bonds and then a 3D supramolecular architecture via π···π stacking interactions. Note that 2 was prepared through an in situ ligand reaction in which N,N'-carbonyldiimidazole (cdi) broke up into imidazole ligand. Compound 3 possesses a 3D 4-fold interpenetrated architecture with 4-connected dia topology (Schläfli symbol: {66}) in which tfBDC2- is stabilized in the channel by hydrogen bonds. Compounds 4-6 are all linear 1D coordination polymers. In 4, the free tfBDC2- ligand acts as a μ4-bridge to link four coordinated water molecules from the chain to construct a 2D structure via hydrogen bonds. While in 5 and 6, the uncoordinated tfBDC2- ligands and multimeric water clusters is responsible for the conversion of these 1D coordination polymers into 3D supramolecular assemblies through O-H⋯O hydrogen bonding interactions. Moreover

  15. Endosomal Escape and Delivery of CRISPR/Cas9 Genome Editing Machinery Enabled by Nanoscale Zeolitic Imidazolate Framework

    KAUST Repository

    Alsaiari, Shahad K.

    2017-12-22

    CRISPR/Cas9 is a combined protein (Cas9) and an engineered single guide RNA (sgRNA) genome editing platform that offers revolutionary solutions to genetic diseases. It has, however, a double delivery problem owning to the large protein size and the highly charged RNA component. In this work, we report the first example of CRISPR/Cas9 encapsulated by nanoscale zeolitic imidazole frameworks (ZIFs) with a loading efficiency of 17% and enhanced endosomal escape promoted by the protonated imidazole moieties. The gene editing potential of CRISPR/Cas9 encapsulated by ZIF-8 (CC-ZIFs) is further verified by knocking down the gene expression of green fluorescent protein by 37% over 4 days employing CRISPR/Cas9 machinery. The nanoscale CC-ZIFs are biocompatible and easily scaled-up offering excellent loading capacity and controlled co-delivery of intact Cas9 protein and sgRNA.

  16. Endosomal Escape and Delivery of CRISPR/Cas9 Genome Editing Machinery Enabled by Nanoscale Zeolitic Imidazolate Framework

    KAUST Repository

    Alsaiari, Shahad K.; Patil, Sachin; Alyami, Mram Z.; Alamoudi, Kholod; Aleisa, Fajr A; Merzaban, Jasmeen; Li, Mo; Khashab, Niveen M.

    2017-01-01

    CRISPR/Cas9 is a combined protein (Cas9) and an engineered single guide RNA (sgRNA) genome editing platform that offers revolutionary solutions to genetic diseases. It has, however, a double delivery problem owning to the large protein size and the highly charged RNA component. In this work, we report the first example of CRISPR/Cas9 encapsulated by nanoscale zeolitic imidazole frameworks (ZIFs) with a loading efficiency of 17% and enhanced endosomal escape promoted by the protonated imidazole moieties. The gene editing potential of CRISPR/Cas9 encapsulated by ZIF-8 (CC-ZIFs) is further verified by knocking down the gene expression of green fluorescent protein by 37% over 4 days employing CRISPR/Cas9 machinery. The nanoscale CC-ZIFs are biocompatible and easily scaled-up offering excellent loading capacity and controlled co-delivery of intact Cas9 protein and sgRNA.

  17. Synthesis, Crystal Structure and Luminescent Property of A Novel Cd(II) Coordination Polymer with Bis-imidazole Ligand

    International Nuclear Information System (INIS)

    Zhou, Yong Hong

    2013-01-01

    The key to the successful design of metal-organic coordination polymers is the judicious selection of organic ligand. Recently, polydentate aromatic nitrogen heterocyclic ligands with five-membered rings have been well-studied in the construction of supramolecular structure for their N-coordinated sites apt to coordinating to transition metals. Similar to six-membered N-heterocyclic ligands, the azole-based five-membered N-heterocyclic ligands, such as imidazoles, triazoles and tetrazoles have been extensively employed in the construction of various coordination polymers with diverse topologies and interesting properties. The bis(azole) ligands in which N-donor azole rings (imidazole, triazole, or tetrazole) are separated by alkyl, (CH 2 ) n , spacers are good choices for flexible bridging ligands. The conformational flexibility of the spacers makes the ligands adaptable to various coordination networks with one-, two-, and three dimensional structures

  18. Synthesis and Characterization of New Silver (I N-Heterocyclic Ccarbene Ccomplex Dderived from Imidazol-2-ylidene salt

    Directory of Open Access Journals (Sweden)

    Mohammedl Mujbe Hasson

    2018-04-01

    Full Text Available A new N, N'-imidazolium salt 1-(2,6-diisopropylphenyl-3- (4,6-dimorpholino -1,3,5-traizine-2-yl-1H-imidazol-3-ium chloride as a precursor of N - heterocyclic carbene ligand was prepared via the reaction of 1 - (2, 6 - diisopropyl phenyl - 1H - imidazole with 1, 3, 5 - triazine derivative bearing morpholine substituent (2, 6 -dimorpholine - 6- chloro-1, 3, 5-triaziazine. Linear coordi-nated Ag (І NHC complex was synthesised via deprotonation of the imidazolium salt and reac-tion with Ag2O in darkness at room temperature by in situ method. The complex was synthesised for using as transfer agent to prepare another transition metals complexes by transmetallation method in the future. The imidazolium salt and their silver complex have been characterized by 1 H and 13C NMR spectroscopy as well as mass spectrometry.

  19. Solidification of liquid electrolyte with imidazole polymers for quasi-solid-state dye-sensitized solar cells

    International Nuclear Information System (INIS)

    Wang Miao; Lin Yuan; Zhou Xiaowen; Xiao Xurui; Yang Lei; Feng Shujing; Li Xueping

    2008-01-01

    Quasi-solid-state electrolytes were prepared by employing the imidazole polymers to solidify the liquid electrolyte containing lithium iodide, iodine and ethylene carbonate (EC)/propylene carbonate (PC) mixed solvent. The ionic conductivity and diffusion behavior of triiodide in the quasi-solid-state electrolytes were examined in terms of the polymer content. Application of the quasi-solid-state electrolytes to the dye-sensitized solar cells, the maximum energy conversion efficiency of 7.6% (AM 1.5, 100 mW cm -2 ) was achieved. The dependence of the photovoltaic performance on the polymer content and on the different anions of the imidazole polymers was studied by electrochemical impedance spectroscopy and cyclic voltammetry. The results indicate the charge transfer behaviors occurred at nanocrystalline TiO 2 /electrolyte and Pt/electrolyte interface play an important role in influencing the photovoltaic performance of quasi-solid-state dye-sensitized solar cells

  20. Bis(1H-imidazole-κN3bis(1-naphthaleneacetato-κ2O,O′cadmium(II

    Directory of Open Access Journals (Sweden)

    Hong-Mian Wu

    2008-05-01

    Full Text Available In the mononuclear title compound, [Cd(C12H9O22(C3H4N22], the CdII centre has a distorted octahedral coordination geometry defined by four O atoms from two naphthaleneacetate ligands and two N atoms from two imidazole ligands. The molecules are linked by N—H...O hydrogen bonds, forming a layer network.

  1. Aryloxyalkanoic Acids as Non-Covalent Modifiers of the Allosteric Properties of Hemoglobin

    Directory of Open Access Journals (Sweden)

    Abdelsattar M. Omar

    2016-08-01

    Full Text Available Hemoglobin (Hb modifiers that stereospecifically inhibit sickle hemoglobin polymer formation and/or allosterically increase Hb affinity for oxygen have been shown to prevent the primary pathophysiology of sickle cell disease (SCD, specifically, Hb polymerization and red blood cell sickling. Several such compounds are currently being clinically studied for the treatment of SCD. Based on the previously reported non-covalent Hb binding characteristics of substituted aryloxyalkanoic acids that exhibited antisickling properties, we designed, synthesized and evaluated 18 new compounds (KAUS II series for enhanced antisickling activities. Surprisingly, select test compounds showed no antisickling effects or promoted erythrocyte sickling. Additionally, the compounds showed no significant effect on Hb oxygen affinity (or in some cases, even decreased the affinity for oxygen. The X-ray structure of deoxygenated Hb in complex with a prototype compound, KAUS-23, revealed that the effector bound in the central water cavity of the protein, providing atomic level explanations for the observed functional and biological activities. Although the structural modification did not lead to the anticipated biological effects, the findings provide important direction for designing candidate antisickling agents, as well as a framework for novel Hb allosteric effectors that conversely, decrease the protein affinity for oxygen for potential therapeutic use for hypoxic- and/or ischemic-related diseases.

  2. Allosteric Inhibition of SHP2: Identification of a Potent, Selective, and Orally Efficacious Phosphatase Inhibitor

    Energy Technology Data Exchange (ETDEWEB)

    Fortanet, Jorge Garcia; Chen, Christine Hiu-Tung; Chen, Ying-Nan P.; Chen, Zhouliang; Deng, Zhan; Firestone, Brant; Fekkes, Peter; Fodor, Michelle; Fortin, Pascal D.; Fridrich, Cary; Grunenfelder, Denise; Ho, Samuel; Kang, Zhao B.; Karki, Rajesh; Kato, Mitsunori; Keen, Nick; LaBonte, Laura R.; Larrow, Jay; Lenoir, Francois; Liu, Gang; Liu, Shumei; Lombardo, Franco; Majumdar, Dyuti; Meyer, Matthew J.; Palermo, Mark; Perez, Lawrence; Pu, Minying; Ramsey, Timothy; Sellers, William R.; Shultz, Michael D.; Stams, Travis; Towler, Christopher; Wang, Ping; Williams, Sarah L.; Zhang, Ji-Hu; LaMarche, Matthew J. (Novartis)

    2016-09-08

    SHP2 is a nonreceptor protein tyrosine phosphatase (PTP) encoded by the PTPN11 gene involved in cell growth and differentiation via the MAPK signaling pathway. SHP2 also purportedly plays an important role in the programmed cell death pathway (PD-1/PD-L1). Because it is an oncoprotein associated with multiple cancer-related diseases, as well as a potential immunomodulator, controlling SHP2 activity is of significant therapeutic interest. Recently in our laboratories, a small molecule inhibitor of SHP2 was identified as an allosteric modulator that stabilizes the autoinhibited conformation of SHP2. A high throughput screen was performed to identify progressable chemical matter, and X-ray crystallography revealed the location of binding in a previously undisclosed allosteric binding pocket. Structure-based drug design was employed to optimize for SHP2 inhibition, and several new protein–ligand interactions were characterized. These studies culminated in the discovery of 6-(4-amino-4-methylpiperidin-1-yl)-3-(2,3-dichlorophenyl)pyrazin-2-amine (SHP099, 1), a potent, selective, orally bioavailable, and efficacious SHP2 inhibitor.

  3. Allosteric mechanism of action of the therapeutic anti-IgE antibody omalizumab.

    Science.gov (United States)

    Davies, Anna M; Allan, Elizabeth G; Keeble, Anthony H; Delgado, Jean; Cossins, Benjamin P; Mitropoulou, Alkistis N; Pang, Marie O Y; Ceska, Tom; Beavil, Andrew J; Craggs, Graham; Westwood, Marta; Henry, Alistair J; McDonnell, James M; Sutton, Brian J

    2017-06-16

    Immunoglobulin E and its interactions with receptors FcϵRI and CD23 play a central role in allergic disease. Omalizumab, a clinically approved therapeutic antibody, inhibits the interaction between IgE and FcϵRI, preventing mast cell and basophil activation, and blocks IgE binding to CD23 on B cells and antigen-presenting cells. We solved the crystal structure of the complex between an omalizumab-derived Fab and IgE-Fc, with one Fab bound to each Cϵ3 domain. Free IgE-Fc adopts an acutely bent structure, but in the complex it is only partially bent, with large-scale conformational changes in the Cϵ3 domains that inhibit the interaction with FcϵRI. CD23 binding is inhibited sterically due to overlapping binding sites on each Cϵ3 domain. Studies of omalizumab Fab binding in solution demonstrate the allosteric basis for FcϵRI inhibition and, together with the structure, reveal how omalizumab may accelerate dissociation of receptor-bound IgE from FcϵRI, exploiting the intrinsic flexibility and allosteric potential of IgE. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Engineering integrated digital circuits with allosteric ribozymes for scaling up molecular computation and diagnostics.

    Science.gov (United States)

    Penchovsky, Robert

    2012-10-19

    Here we describe molecular implementations of integrated digital circuits, including a three-input AND logic gate, a two-input multiplexer, and 1-to-2 decoder using allosteric ribozymes. Furthermore, we demonstrate a multiplexer-decoder circuit. The ribozymes are designed to seek-and-destroy specific RNAs with a certain length by a fully computerized procedure. The algorithm can accurately predict one base substitution that alters the ribozyme's logic function. The ability to sense the length of RNA molecules enables single ribozymes to be used as platforms for multiple interactions. These ribozymes can work as integrated circuits with the functionality of up to five logic gates. The ribozyme design is universal since the allosteric and substrate domains can be altered to sense different RNAs. In addition, the ribozymes can specifically cleave RNA molecules with triplet-repeat expansions observed in genetic disorders such as oculopharyngeal muscular dystrophy. Therefore, the designer ribozymes can be employed for scaling up computing and diagnostic networks in the fields of molecular computing and diagnostics and RNA synthetic biology.

  5. Structural Insights into the Allosteric Operation of the Lon AAA+ Protease.

    Science.gov (United States)

    Lin, Chien-Chu; Su, Shih-Chieh; Su, Ming-Yuan; Liang, Pi-Hui; Feng, Chia-Cheng; Wu, Shih-Hsiung; Chang, Chung-I

    2016-05-03

    The Lon AAA+ protease (LonA) is an evolutionarily conserved protease that couples the ATPase cycle into motion to drive substrate translocation and degradation. A hallmark feature shared by AAA+ proteases is the stimulation of ATPase activity by substrates. Here we report the structure of LonA bound to three ADPs, revealing the first AAA+ protease assembly where the six protomers are arranged alternately in nucleotide-free and bound states. Nucleotide binding induces large coordinated movements of conserved pore loops from two pairs of three non-adjacent protomers and shuttling of the proteolytic groove between the ATPase site and a previously unknown Arg paddle. Structural and biochemical evidence supports the roles of the substrate-bound proteolytic groove in allosteric stimulation of ATPase activity and the conserved Arg paddle in driving substrate degradation. Altogether, this work provides a molecular framework for understanding how ATP-dependent chemomechanical movements drive allosteric processes for substrate degradation in a major protein-destruction machine. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Interdomain allosteric regulation of Polo kinase by Aurora B and Map205 is required for cytokinesis

    Science.gov (United States)

    Kachaner, David; Pinson, Xavier; El Kadhi, Khaled Ben; Normandin, Karine; Talje, Lama; Lavoie, Hugo; Lépine, Guillaume; Carréno, Sébastien; Kwok, Benjamin H.; Hickson, Gilles R.

    2014-01-01

    Drosophila melanogaster Polo and its human orthologue Polo-like kinase 1 fulfill essential roles during cell division. Members of the Polo-like kinase (Plk) family contain an N-terminal kinase domain (KD) and a C-terminal Polo-Box domain (PBD), which mediates protein interactions. How Plks are regulated in cytokinesis is poorly understood. Here we show that phosphorylation of Polo by Aurora B is required for cytokinesis. This phosphorylation in the activation loop of the KD promotes the dissociation of Polo from the PBD-bound microtubule-associated protein Map205, which acts as an allosteric inhibitor of Polo kinase activity. This mechanism allows the release of active Polo from microtubules of the central spindle and its recruitment to the site of cytokinesis. Failure in Polo phosphorylation results in both early and late cytokinesis defects. Importantly, the antagonistic regulation of Polo by Aurora B and Map205 in cytokinesis reveals that interdomain allosteric mechanisms can play important roles in controlling the cellular functions of Plks. PMID:25332165

  7. The Allosterically Unregulated Isoform of ADP-Glucose Pyrophosphorylase from Barley Endosperm Is the Most Likely Source of ADP-Glucose Incorporated into Endosperm Starch1

    Science.gov (United States)

    Doan, Danny N.P.; Rudi, Heidi; Olsen, Odd-Arne

    1999-01-01

    We present the results of studies of an unmodified version of the recombinant major barley (Hordeum vulgare) endosperm ADP-glucose pyrophoshorylase (AGPase) expressed in insect cells, which corroborate previous data that this isoform of the enzyme acts independently of the allosteric regulators 3-phosphoglycerate and inorganic phosphate. We also present a characterization of the individual subunits expressed separately in insect cells, showing that the SS AGPase is active in the presence of 3-phosphoglycerate and is inhibited by inorganic phosphate. As a step toward the elucidation of the role of the two AGPase isoforms in barley, the temporal and spatial expression profile of the four barley AGPase transcripts encoding these isoforms were studied. The results show that the steady-state level of beps and bepl, the transcripts encoding the major endosperm isoform, correlated positively with the rate of endosperm starch accumulation. In contrast, blps and blpl, the transcripts encoding the major leaf isoform, were constitutively expressed at a very low steady-state level throughout the barley plant. The implications of these findings for the evolution of plant AGPases are discussed. PMID:10557246

  8. The Allosterically Unregulated Isoform of ADP-Glucose Pyrophosphorylase from Barley Endosperm Is the Most Likely Source of ADP-Glucose Incorporated into Endosperm Starch.

    Science.gov (United States)

    Doan; Rudi; Olsen

    1999-11-01

    We present the results of studies of an unmodified version of the recombinant major barley (Hordeum vulgare) endosperm ADP-glucose pyrophoshorylase (AGPase) expressed in insect cells, which corroborate previous data that this isoform of the enzyme acts independently of the allosteric regulators 3-phosphoglycerate and inorganic phosphate. We also present a characterization of the individual subunits expressed separately in insect cells, showing that the SS AGPase is active in the presence of 3-phosphoglycerate and is inhibited by inorganic phosphate. As a step toward the elucidation of the role of the two AGPase isoforms in barley, the temporal and spatial expression profile of the four barley AGPase transcripts encoding these isoforms were studied. The results show that the steady-state level of beps and bepl, the transcripts encoding the major endosperm isoform, correlated positively with the rate of endosperm starch accumulation. In contrast, blps and blpl, the transcripts encoding the major leaf isoform, were constitutively expressed at a very low steady-state level throughout the barley plant. The implications of these findings for the evolution of plant AGPases are discussed.

  9. Interplay between Structure and Charge as a Key to Allosteric Modulation of Human 20S Proteasome by the Basic Fragment of HIV-1 Tat Protein.

    Directory of Open Access Journals (Sweden)

    Przemysław Karpowicz

    Full Text Available The proteasome is a giant protease responsible for degradation of the majority of cytosolic proteins. Competitive inhibitors of the proteasome are used against aggressive blood cancers. However, broadening the use of proteasome-targeting drugs requires new mechanistic approaches to the enzyme's inhibition. In our previous studies we described Tat1 peptide, an allosteric inhibitor of the proteasome derived from a fragment of the basic domain of HIV-Tat1 protein. Here, we attempted to dissect the structural determinants of the proteasome inhibition by Tat1. Single- and multiple- alanine walking scans were performed. Tat1 analogs with stabilized beta-turn conformation at positions 4-5 and 8-9, pointed out by the molecular dynamics modeling and the alanine scan, were synthesized. Structure of Tat1 analogs were analyzed by circular dichroism, Fourier transform infrared and nuclear magnetic resonance spectroscopy studies, supplemented by molecular dynamics simulations. Biological activity tests and structural studies revealed that high flexibility and exposed positive charge are hallmarks of Tat1 peptide. Interestingly, stabilization of a beta-turn at the 8-9 position was necessary to significantly improve the inhibitory potency.

  10. A convenient method for 14C-labeling of 2-methylthio-1-[4-N-α-ethoxycarbonylbenzyl)-amino-benzyl] -5-hydroxymethyl-2-[14C]-1H-imidazole and 1-[4-N-α-ethoxy-carbonylbenzyl)-aminobenzyl]-5-hydroxymethyl-2-[14C] -1H-imidazole as potential antihypertensives

    International Nuclear Information System (INIS)

    Nader Saemian; Gholamhossein Shirvani; Mohsen Javaheri; Sayed Sajad Oliyaee

    2012-01-01

    The key synthetic intermediate, (2-mercapto-1-(4-nitrobenzyl)-1H-imidazol-5-yl)methanol-[2- 14 C], has been synthesized by using one pot procedure from potassium[ 14 C]-thiocyanate. It was converted to two nonpeptide angiotensin II receptor antagonists, 2-methylthio-1-[4-N-α-ethoxycarbonyl benzyl)-aminobenzyl]-5-hydroxymethyl-1H-imidazole-[2- 14 C] and 1-[4-N-α-ethoxy-carbonylbenzyl)-aminobenzyl] -5-hydroxymethyl-1H-imidazole-[2- 14 C] via a 3-step sequence synthetic pathway. (author)

  11. Spectroscopic analysis and molecular docking of imidazole derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Thomas, Renjith; Hossain, Mossaraf; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Ranjan, Vivek Kumar; Vijayakumar, G.; Van Alsenoy, C.

    2018-04-01

    Solvent-free synthesis pathway for obtaining two imidazole derivatives (2-chloro-1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole (CLMPDI) and 1-(4-bromophenyl)-2-chloro-4,5-dimethyl-1H-imidazole (BPCLDI) has been reported in this work, followed by detailed experimental and computational spectroscopic characterization and reactivity study. Spectroscopic methods encompassed IR, FT-Raman and NMR techniques, with the mutual comparison of experimentally and computationally obtained results at DFT/B3LYP level of theory. Reactivity study based on DFT calculations encompassed molecular orbitals analysis, followed by calculations of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) values, Fukui functions and bond dissociation energies (BDE). Additionally, the stability of title molecules in water has been investigated via molecular dynamics (MD) simulations, while interactivity with aspulvinonedimethylallyl transferase protein has been evaluated by molecular docking procedure. CLMPDI compound showed antimicrobial activity against all four bacterial strain in both gram positive and gram negative bacteria while, BPCLDI showed only in gram positive bacteria, Staphylococcus Aureus (MTCC1144). The first order hyperpolarizability of CLMPDI and BPCLDI are 20.15 and 6.10 times that of the standard NLO material urea.

  12. Construction, Structural Diversity and Properties of Five Coordination Polymers Based on 5-Nitroisophthalate and Bis(imidazole) Linkers

    Science.gov (United States)

    Arıcı, Mürsel

    2018-06-01

    Five coordination polymers, namely, [Cd(μ3-5-nip)(μ-obix)]n (1), [Co(μ3-5-nip)(μ-obix)]n (2), [Zn(μ-5-nip)(μ-obix)]n (3 and 4) and [Cd(μ-5-nip)(μ-bisobix)]n (5) (5-nip: 5-nitroisophthalate, obix: 1,2-bis(imidazol-1ylmethyl)benzene, bisobix: 1,2-bis(2-isopropylimidazol-1ylmethyl)benzene) were hydrothermally synthesized and characterized by IR spectroscopy, elemental analysis, single crystal and powder X-ray diffraction and thermal analysis (TG/DTA). X-ray results showed that the complexes displayed structural diversity depending on metal ions and conformations of bis(imidazole) linkers. Complexes 1 and 2 were 1D structures and obix ligand displayed cis-conformation. Complexes 3 and 4 exhibited 2D and 3D structures with same components depending on obix conformation. In complex 5, 3D+3D→3D interpenetrated structure was obtained with dia topology when bisobix having sterically hindered groups on imidazole rings was used. Moreover, thermal, photoluminescence and optical properties of the complexes were also investigated.

  13. Synthesis, spectroscopic, computational (DFT/B3LYP), AChE inhibition and antioxidant studies of imidazole derivative

    Science.gov (United States)

    Ahmad, Faheem; Alam, Mohammad Jane; Alam, Mahboob; Azaz, Shaista; Parveen, Mehtab; Park, Soonheum; Ahmad, Shabbir

    2018-01-01

    The present study reports the synthesis and evaluation of biological properties of 3a,8a-dihydroxy-8-oxo-1,3,3a,8a-tetrahydroindeno[1,2-d]imidazol-2(1H)-iminium chloride (3). The structure was confirmed by the FTIR, NMR, MS, CHN microanalysis and X-ray crystallographic analysis. Quantum chemical calculations have been performed at B3LYP-D3/6-311++G(d,p) level of theory to study the molecular geometry, IR, (1H and 13C) NMR, UV/Vis spectra and other molecular parameters of the asymmetric unit of crystal of imidazole compound (3). An empirical dispersion correction to hybrid functional (B3LYP-D3) has been incorporated in the present calculations due to presence of non-covalent interaction, Cl⋯H-O, in the present compound. The remarkable agreement has been observed between theoretical data and those measured experimentally. Moreover, the Hirshfeld analysis was carried out to ascertain the secondary interactions and associated 2D fingerprint plots. The synthesized imidazole derivative showed promising antioxidant property and inhibitory activity against acetylcholinesterase (AChE). Molecular docking was also performed in order to explain in silico antioxidant studies and to ascertain the probable binding mode of compound with the amino acid residues of protein.

  14. Enzyme inhibition by iminosugars

    DEFF Research Database (Denmark)

    López, Óscar; Qing, Feng-Ling; Pedersen, Christian Marcus

    2013-01-01

    Imino- and azasugar glycosidase inhibitors display pH dependant inhibition reflecting that both the inhibitor and the enzyme active site have groups that change protonation state with pH. With the enzyme having two acidic groups and the inhibitor one basic group, enzyme-inhibitor complexes...

  15. Mycobacterium tuberculosis phosphoribosylpyrophosphate synthetase: biochemical features of a crucial enzyme for mycobacterial cell wall biosynthesis.

    Directory of Open Access Journals (Sweden)

    Anna P Lucarelli

    Full Text Available The selection and soaring spread of Mycobacterium tuberculosis multidrug-resistant (MDR-TB and extensively drug-resistant strains (XDR-TB is a severe public health problem. Currently, there is an urgent need for new drugs for tuberculosis treatment, with novel mechanisms of action and, moreover, the necessity to identify new drug targets. Mycobacterial phosphoribosylpyrophosphate synthetase (MtbPRPPase is a crucial enzyme involved in the biosynthesis of decaprenylphosphoryl-arabinose, an essential precursor for the mycobacterial cell wall biosynthesis. Moreover, phosphoribosylpyrophosphate, which is the product of the PRPPase catalyzed reaction, is the precursor for the biosynthesis of nucleotides and of some amino acids such as histidine and tryptophan. In this context, the elucidation of the molecular and functional features of MtbPRPPase is mandatory. MtbPRPPase was obtained as a recombinant form, purified to homogeneity and characterized. According to its hexameric form, substrate specificity and requirement of phosphate for activity, the enzyme proved to belong to the class I of PRPPases. Although the sulfate mimicked the phosphate, it was less effective and required higher concentrations for the enzyme activation. MtbPRPPase showed hyperbolic response to ribose 5-phosphate, but sigmoidal behaviour towards Mg-ATP. The enzyme resulted to be allosterically activated by Mg(2+ or Mn(2+ and inhibited by Ca(2+ and Cu(2+ but, differently from other characterized PRPPases, it showed a better affinity for the Mn(2+ and Cu(2+ ions, indicating a different cation binding site geometry. Moreover, the enzyme from M. tuberculosis was allosterically inhibited by ADP, but less sensitive to inhibition by GDP. The characterization of M. tuberculosis PRPPase provides the starting point for the development of inhibitors for antitubercular drug design.

  16. The Low-Affinity Binding of Second Generation Radiotracers Targeting TSPO is Associated with a Unique Allosteric Binding Site

    Czech Academy of Sciences Publication Activity Database

    Rojas, C.; Stathis, M.; Coughlin, J. M.; Pomper, M.; Slusher, Barbara S.

    2018-01-01

    Roč. 13, č. 1 (2018), s. 1-5 ISSN 1557-1890 Institutional support: RVO:61388963 Keywords : translocator protein 18KDa (TSPO) * allosteric modulation * residence time Subject RIV: CC - Organic Chemistry OBOR OECD: Organic chemistry Impact factor: 3.339, year: 2016

  17. Positive allosteric modulation of the human metabotropic glutamate receptor 4 (hmGluR4) by SIB-1893 and MPEP

    DEFF Research Database (Denmark)

    Mathiesen, Jesper Mosolff; Svendsen, Nannette; Bräuner-Osborne, Hans

    2003-01-01

    We have identified 2-methyl-6-(2-phenylethenyl)pyridine (SIB-1893) and 2-methyl-6-phenylethynyl pyridine hydrochloride (MPEP) as positive allosteric modulators for the hmGluR4. SIB-1893 and MPEP enhanced the potency and efficacy of L-2-amino-4-phophonobutyrate (L-AP4) in guanosine 5'-O-(3-[(35)S...

  18. A3 Adenosine Receptor Allosteric Modulator Induces an Anti-Inflammatory Effect: In Vivo Studies and Molecular Mechanism of Action

    Directory of Open Access Journals (Sweden)

    Shira Cohen

    2014-01-01

    Full Text Available The A3 adenosine receptor (A3AR is overexpressed in inflammatory cells and in the peripheral blood mononuclear cells of individuals with inflammatory conditions. Agonists to the A3AR are known to induce specific anti-inflammatory effects upon chronic treatment. LUF6000 is an allosteric compound known to modulate the A3AR and render the endogenous ligand adenosine to bind to the receptor with higher affinity. The advantage of allosteric modulators is their capability to target specifically areas where adenosine levels are increased such as inflammatory and tumor sites, whereas normal body cells and tissues are refractory to the allosteric modulators due to low adenosine levels. LUF6000 administration induced anti-inflammatory effect in 3 experimental animal models of rat adjuvant induced arthritis, monoiodoacetate induced osteoarthritis, and concanavalin A induced liver inflammation in mice. The molecular mechanism of action points to deregulation of signaling proteins including PI3K, IKK, IκB, Jak-2, and STAT-1, resulting in decreased levels of NF-κB, known to mediate inflammatory effects. Moreover, LUF6000 induced a slight stimulatory effect on the number of normal white blood cells and neutrophils. The anti-inflammatory effect of LUF6000, mechanism of action, and the differential effects on inflammatory and normal cells position this allosteric modulator as an attractive and unique drug candidate.

  19. Thermodynamics and structural analysis of positive allosteric modulation of the ionotropic glutamate receptor GluA2

    DEFF Research Database (Denmark)

    Krintel, Christian; Frydenvang, Karla; Olsen, Lars

    2012-01-01

    Positive allosteric modulators of the ionotropic glutamate receptor-2 (GluA2) are promising compounds for the treatment of cognitive disorders, e.g. Alzheimer's disease. These modulators bind within the dimer interface of the ligand-binding domain and stabilize the agonist-bound conformation slow...

  20. Allosteric modulation of Ras and the PI3K/AKT/mTOR pathway: emerging therapeutic opportunities

    Science.gov (United States)

    Hubbard, Paul A.; Moody, Colleen L.; Murali, Ramachandran

    2014-01-01

    GTPases and kinases are two predominant signaling modules that regulate cell fate. Dysregulation of Ras, a GTPase, and the three eponymous kinases that form key nodes of the associated phosphatidylinositol 4,5-bisphosphate 3-kinase (PI3K)/AKT/mTOR pathway have been implicated in many cancers, including pancreatic cancer, a disease noted for its current lack of effective therapeutics. The K-Ras isoform of Ras is mutated in over 90% of pancreatic ductal adenocarcinomas (PDAC) and there is growing evidence linking aberrant PI3K/AKT/mTOR pathway activity to PDAC. Although these observations suggest that targeting one of these nodes might lead to more effective treatment options for patients with pancreatic and other cancers, the complex regulatory mechanisms and the number of sequence-conserved isoforms of these proteins have been viewed as significant barriers in drug development. Emerging insights into the allosteric regulatory mechanisms of these proteins suggest novel opportunities for development of selective allosteric inhibitors with fragment-based drug discovery (FBDD) helping make significant inroads. The fact that allosteric inhibitors of Ras and AKT are currently in pre-clinical development lends support to this approach. In this article, we will focus on the recent advances and merits of developing allosteric drugs targeting these two inter-related signaling pathways. PMID:25566081

  1. Surface dynamics in allosteric regulation of protein-protein interactions: modulation of calmodulin functions by Ca2+.

    Directory of Open Access Journals (Sweden)

    Yosef Y Kuttner

    2013-04-01

    Full Text Available Knowledge of the structural basis of protein-protein interactions (PPI is of fundamental importance for understanding the organization and functioning of biological networks and advancing the design of therapeutics which target PPI. Allosteric modulators play an important role in regulating such interactions by binding at site(s orthogonal to the complex interface and altering the protein's propensity for complex formation. In this work, we apply an approach recently developed by us for analyzing protein surfaces based on steered molecular dynamics simulation (SMD to the study of the dynamic properties of functionally distinct conformations of a model protein, calmodulin (CaM, whose ability to interact with target proteins is regulated by the presence of the allosteric modulator Ca(2+. Calmodulin is a regulatory protein that acts as an intracellular Ca(2+ sensor to control a wide variety of cellular processes. We demonstrate that SMD analysis is capable of pinpointing CaM surfaces implicated in the recognition of both the allosteric modulator Ca(2+ and target proteins. Our analysis of changes in the dynamic properties of the CaM backbone elicited by Ca(2+ binding yielded new insights into the molecular mechanism of allosteric regulation of CaM-target interactions.

  2. Positive allosteric modulation of GABA-A receptors reduces capsaicin-induced primary and secondary hypersensitivity in rats

    DEFF Research Database (Denmark)

    Hansen, Rikke Rie; Erichsen, Helle K; Brown, David T

    2012-01-01

    GABA-A receptor positive allosteric modulators (PAMs) mediate robust analgesia in animal models of pathological pain, in part via enhancing injury-induced loss of GABA-A-α2 and -α3 receptor function within the spinal cord. As yet, a lack of clinically suitable tool compounds has prevented this co...

  3. Allosteric inactivation of a trypsin-like serine protease by an antibody binding to the 37- and 70-loops

    DEFF Research Database (Denmark)

    Kromann-Hansen, Tobias; Lund, Ida K; Liu, Zhuo

    2013-01-01

    for elucidating fundamental allosteric mechanisms. The monoclonal antibody mU1 has previously been shown to be able to inhibit the function of murine urokinase-type plasminogen activator in vivo. We have now mapped the epitope of mU1 to the catalytic domain's 37- and 70-loops, situated about 20 Å from the S1...

  4. The allosteric HIV-1 integrase inhibitor BI-D affects virion maturation but does not influence packaging of a functional RNA genome.

    Directory of Open Access Journals (Sweden)

    Nikki van Bel

    Full Text Available The viral integrase (IN is an essential protein for HIV-1 replication. IN inserts the viral dsDNA into the host chromosome, thereby aided by the cellular co-factor LEDGF/p75. Recently a new class of integrase inhibitors was described: allosteric IN inhibitors (ALLINIs. Although designed to interfere with the IN-LEDGF/p75 interaction to block HIV DNA integration during the early phase of HIV-1 replication, the major impact was surprisingly found on the process of virus maturation during the late phase, causing a reverse transcription defect upon infection of target cells. Virus particles produced in the presence of an ALLINI are misformed with the ribonucleoprotein located outside the virus core. Virus assembly and maturation are highly orchestrated and regulated processes in which several viral proteins and RNA molecules closely interact. It is therefore of interest to study whether ALLINIs have unpredicted pleiotropic effects on these RNA-related processes. We confirm that the ALLINI BI-D inhibits virus replication and that the produced virus is non-infectious. Furthermore, we show that the wild-type level of HIV-1 genomic RNA is packaged in virions and these genomes are in a dimeric state. The tRNAlys3 primer for reverse transcription was properly placed on this genomic RNA and could be extended ex vivo. In addition, the packaged reverse transcriptase enzyme was fully active when extracted from virions. As the RNA and enzyme components for reverse transcription are properly present in virions produced in the presence of BI-D, the inhibition of reverse transcription is likely to reflect the mislocalization of the components in the aberrant virus particle.

  5. The allosteric HIV-1 integrase inhibitor BI-D affects virion maturation but does not influence packaging of a functional RNA genome.

    Science.gov (United States)

    van Bel, Nikki; van der Velden, Yme; Bonnard, Damien; Le Rouzic, Erwann; Das, Atze T; Benarous, Richard; Berkhout, Ben

    2014-01-01

    The viral integrase (IN) is an essential protein for HIV-1 replication. IN inserts the viral dsDNA into the host chromosome, thereby aided by the cellular co-factor LEDGF/p75. Recently a new class of integrase inhibitors was described: allosteric IN inhibitors (ALLINIs). Although designed to interfere with the IN-LEDGF/p75 interaction to block HIV DNA integration during the early phase of HIV-1 replication, the major impact was surprisingly found on the process of virus maturation during the late phase, causing a reverse transcription defect upon infection of target cells. Virus particles produced in the presence of an ALLINI are misformed with the ribonucleoprotein located outside the virus core. Virus assembly and maturation are highly orchestrated and regulated processes in which several viral proteins and RNA molecules closely interact. It is therefore of interest to study whether ALLINIs have unpredicted pleiotropic effects on these RNA-related processes. We confirm that the ALLINI BI-D inhibits virus replication and that the produced virus is non-infectious. Furthermore, we show that the wild-type level of HIV-1 genomic RNA is packaged in virions and these genomes are in a dimeric state. The tRNAlys3 primer for reverse transcription was properly placed on this genomic RNA and could be extended ex vivo. In addition, the packaged reverse transcriptase enzyme was fully active when extracted from virions. As the RNA and enzyme components for reverse transcription are properly present in virions produced in the presence of BI-D, the inhibition of reverse transcription is likely to reflect the mislocalization of the components in the aberrant virus particle.

  6. Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors.

    Science.gov (United States)

    Rodgers, Thomas L; Townsend, Philip D; Burnell, David; Jones, Matthew L; Richards, Shane A; McLeish, Tom C B; Pohl, Ehmke; Wilson, Mark R; Cann, Martin J

    2013-09-01

    Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distinct site. There is growing evidence that allosteric cooperativity can be communicated by modulation of protein dynamics without conformational change. The mechanisms, however, for communicating dynamic fluctuations between sites are debated. We provide a foundational theory for how allostery can occur as a function of low-frequency dynamics without a change in structure. We have generated coarse-grained models that describe the protein backbone motions of the CRP/FNR family transcription factors, CAP of Escherichia coli and GlxR of Corynebacterium glutamicum. The latter we demonstrate as a new exemplar for allostery without conformation change. We observe that binding the first molecule of cAMP ligand is correlated with modulation of the global normal modes and negative cooperativity for binding the second cAMP ligand without a change in mean structure. The theory makes key experimental predictions that are tested through an analysis of variant proteins by structural biology and isothermal calorimetry. Quantifying allostery as a free energy landscape revealed a protein "design space" that identified the inter- and intramolecular regulatory parameters that frame CRP/FNR family allostery. Furthermore, through analyzing CAP variants from diverse species, we demonstrate an evolutionary selection pressure to conserve residues crucial for allosteric control. This finding provides a link between the position of CRP/FNR transcription factors within the allosteric free energy landscapes and evolutionary selection pressures. Our study therefore reveals significant features of the mechanistic basis for allostery. Changes in low-frequency dynamics correlate with allosteric effects on ligand binding without the requirement for a defined spatial pathway. In addition to evolving suitable three-dimensional structures, CRP/FNR family transcription factors have been selected to

  7. Allosteric Inhibition of Factor XIIIa. Non-Saccharide Glycosaminoglycan Mimetics, but Not Glycosaminoglycans, Exhibit Promising Inhibition Profile.

    Directory of Open Access Journals (Sweden)

    Rami A Al-Horani

    Full Text Available Factor XIIIa (FXIIIa is a transglutaminase that catalyzes the last step in the coagulation process. Orthostery is the only approach that has been exploited to design FXIIIa inhibitors. Yet, allosteric inhibition of FXIIIa is a paradigm that may offer a key advantage of controlled inhibition over orthosteric inhibition. Such an approach is likely to lead to novel FXIIIa inhibitors that do not carry bleeding risks. We reasoned that targeting a collection of basic amino acid residues distant from FXIIIa's active site by using sulfated glycosaminoglycans (GAGs or non-saccharide GAG mimetics (NSGMs would lead to the discovery of the first allosteric FXIIIa inhibitors. We tested a library of 22 variably sulfated GAGs and NSGMs against human FXIIIa to discover promising hits. Interestingly, although some GAGs bound to FXIIIa better than NSGMs, no GAG displayed any inhibition. An undecasulfated quercetin analog was found to inhibit FXIIIa with reasonable potency (efficacy of 98%. Michaelis-Menten kinetic studies revealed an allosteric mechanism of inhibition. Fluorescence studies confirmed close correspondence between binding affinity and inhibition potency, as expected for an allosteric process. The inhibitor was reversible and at least 9-fold- and 26-fold selective over two GAG-binding proteins factor Xa (efficacy of 71% and thrombin, respectively, and at least 27-fold selective over a cysteine protease papain. The inhibitor also inhibited the FXIIIa-mediated polymerization of fibrin in vitro. Overall, our work presents the proof-of-principle that FXIIIa can be allosterically modulated by sulfated non-saccharide agents much smaller than GAGs, which should enable the design of selective and safe anticoagulants.

  8. Conopeptide ρ-TIA defines a new allosteric site on the extracellular surface of the α1B-adrenoceptor.

    Science.gov (United States)

    Ragnarsson, Lotten; Wang, Ching-I Anderson; Andersson, Åsa; Fajarningsih, Dewi; Monks, Thea; Brust, Andreas; Rosengren, K Johan; Lewis, Richard J

    2013-01-18

    The G protein-coupled receptor (GPCR) superfamily is an important drug target that includes over 1000 membrane receptors that functionally couple extracellular stimuli to intracellular effectors. Despite the potential of extracellular surface (ECS) residues in GPCRs to interact with subtype-specific allosteric modulators, few ECS pharmacophores for class A receptors have been identified. Using the turkey β(1)-adrenergic receptor crystal structure, we modeled the α(1B)-adrenoceptor (α(1B)-AR) to help identify the allosteric site for ρ-conopeptide TIA, an inverse agonist at this receptor. Combining mutational radioligand binding and inositol 1-phosphate signaling studies, together with molecular docking simulations using a refined NMR structure of ρ-TIA, we identified 14 residues on the ECS of the α(1B)-AR that influenced ρ-TIA binding. Double mutant cycle analysis and docking confirmed that ρ-TIA binding was dominated by a salt bridge and cation-π between Arg-4-ρ-TIA and Asp-327 and Phe-330, respectively, and a T-stacking-π interaction between Trp-3-ρ-TIA and Phe-330. Water-bridging hydrogen bonds between Asn-2-ρ-TIA and Val-197, Trp-3-ρ-TIA and Ser-318, and the positively charged N terminus and Glu-186, were also identified. These interactions reveal that peptide binding to the ECS on transmembrane helix 6 (TMH6) and TMH7 at the base of extracellular loop 3 (ECL3) is sufficient to allosterically inhibit agonist signaling at a GPCR. The ligand-accessible ECS residues identified provide the first view of an allosteric inhibitor pharmacophore for α(1)-adrenoceptors and mechanistic insight and a new set of structural constraints for the design of allosteric antagonists at related GPCRs.

  9. Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors.

    Directory of Open Access Journals (Sweden)

    Thomas L Rodgers

    2013-09-01

    Full Text Available Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distinct site. There is growing evidence that allosteric cooperativity can be communicated by modulation of protein dynamics without conformational change. The mechanisms, however, for communicating dynamic fluctuations between sites are debated. We provide a foundational theory for how allostery can occur as a function of low-frequency dynamics without a change in structure. We have generated coarse-grained models that describe the protein backbone motions of the CRP/FNR family transcription factors, CAP of Escherichia coli and GlxR of Corynebacterium glutamicum. The latter we demonstrate as a new exemplar for allostery without conformation change. We observe that binding the first molecule of cAMP ligand is correlated with modulation of the global normal modes and negative cooperativity for binding the second cAMP ligand without a change in mean structure. The theory makes key experimental predictions that are tested through an analysis of variant proteins by structural biology and isothermal calorimetry. Quantifying allostery as a free energy landscape revealed a protein "design space" that identified the inter- and intramolecular regulatory parameters that frame CRP/FNR family allostery. Furthermore, through analyzing CAP variants from diverse species, we demonstrate an evolutionary selection pressure to conserve residues crucial for allosteric control. This finding provides a link between the position of CRP/FNR transcription factors within the allosteric free energy landscapes and evolutionary selection pressures. Our study therefore reveals significant features of the mechanistic basis for allostery. Changes in low-frequency dynamics correlate with allosteric effects on ligand binding without the requirement for a defined spatial pathway. In addition to evolving suitable three-dimensional structures, CRP/FNR family transcription factors have

  10. Zeolitic imidazolate frameworks with optimized pore structure for olefin/paraffin-separation

    Energy Technology Data Exchange (ETDEWEB)

    Paula, C.; Boehme, U.; Hartmann, M. [Erlangen-Nuernberg Univ. (Germany). Erlangen Catalysis Resource Center

    2013-11-01

    In the chemical industry, the largest part of energy is spent on separation processes such as the separation of olefin/paraffin mixtures from steam cracker effluents by low-temperature rectification. A suitable alternative to this energy and cost intensive process is separation by selective adsorption with suitable microporous adsorbent. In this work, different ZIFs (Zeolitic Imidazolate Frameworks) have been explored with respect to their separation of olefins and paraffins. The studied materials (e.g. ZIF-8 (SOD-Topology), ZIF-71 (RHO-Topology)) were selected because of their low diameter of the largest pore entrance (0.29 to 4.2 nm) which is close to the kinetic diameter of the C{sub 2} to C{sub 4} olefins and paraffins under study. In contrast to other MOF- or zeolite-based adsorbents, in ZIF-8 and ZIF-71, the paraffin is preferentially adsorbed, which is evident from the single-component adsorption isotherms at different temperature. In the corresponding mixture breakthrough curves, the olefin breaks through first and the alkane even displaces the olefin from the pores. Thus, ZIF-8 and ZIF-71 are interesting candidates for the envisaged paraffin/olefin separation. Whether the observed separation behavior is due to the structural properties of the studied ZIFs or a consequence of peculiar chemical properties is subject to further studies. (orig.) (Published in summary form only)

  11. Polyacrylonitrile nanofibers with added zeolitic imidazolate frameworks (ZIF-7) to enhance mechanical and thermal stability

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Min Wook [Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, 842 W. Taylor St., Chicago, Illinois 60607-7022 (United States); An, Seongpil; Song, Kyo Yong; Joshi, Bhavana N.; Jo, Hong Seok; Yoon, Sam S., E-mail: skyoon@korea.ac.kr, E-mail: ayarin@uic.edu [School of Mechanical Engineering, Korea University, Seoul 136-713 (Korea, Republic of); Al-Deyab, Salem S. [Department of Chemistry, King Saud University, Riyadh 11451 (Saudi Arabia); Yarin, Alexander L., E-mail: skyoon@korea.ac.kr, E-mail: ayarin@uic.edu [Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, 842 W. Taylor St., Chicago, Illinois 60607-7022 (United States); School of Mechanical Engineering, Korea University, Seoul 136-713 (Korea, Republic of)

    2015-12-28

    Zeolitic imidazolate framework 7/polyacrylonitrile (ZIF-7/PAN) nanofiber mat of high porosity and surface area can be used as a flexible fibrous filtration membrane that is subjected to various modes of mechanical loading resulting in stresses and strains. Therefore, the stress-strain relation of ZIF-7/PAN nanofiber mats in the elastic and plastic regimes of deformation is of significant importance for numerous practical applications, including hydrogen storage, carbon dioxide capture, and molecular sensing. Here, we demonstrated the fabrication of ZIF-7/PAN nanofiber mats via electrospinning and report their mechanical properties measured in tensile tests covering the elastic and plastic domains. The effect of the mat fabrication temperature on the mechanical properties is elucidated. We showed the superior mechanical strength and thermal stability of the compound ZIF-7/PAN nanofiber mats in comparison with that of pure PAN nanofiber mats. Material characterization including scanning electron microscope, energy-dispersive X-ray spectroscopy, tensile tests, differential scanning calorimetry, and Fourier transform infrared spectroscopy revealed the enhanced chemical bonds of the ZIF-7/PAN complex.

  12. Hybrid Zeolitic Imidazolate Frameworks: Controlling Framework Porosity and Functionality by Mixed-Linker Synthesis

    KAUST Repository

    Thompson, Joshua A.

    2012-05-22

    Zeolitic imidazolate frameworks (ZIFs) are a subclass of nanoporous metal-organic frameworks (MOFs) that exhibit zeolite-like structural topologies and have interesting molecular recognition properties, such as molecular sieving and gate-opening effects associated with their pore apertures. The synthesis and characterization of hybrid ZIFs with mixed linkers in the framework are described in this work, producing materials with properties distinctly different from the parent frameworks (ZIF-8, ZIF-90, and ZIF-7). NMR spectroscopy is used to assess the relative amounts of the different linkers included in the frameworks, whereas nitrogen physisorption shows the evolution of the effective pore size distribution in materials resulting from the framework hybridization. X-ray diffraction shows these hybrid materials to be crystalline. In the case of ZIF-8-90 hybrids, the cubic space group of the parent frameworks is continuously maintained, whereas in the case of the ZIF-7-8 hybrids there is a transition from a cubic to a rhombohedral space group. Nitrogen physisorption data reveal that the hybrid materials exhibit substantial changes in gate-opening phenomena, either occurring at continuously tunable partial pressures of nitrogen (ZIF-8-90 hybrids) or loss of gate-opening effects to yield more rigid frameworks (ZIF-7-8 hybrids). With this synthetic approach, significant alterations in MOF properties may be realized to suit a desired separation or catalytic process. © 2012 American Chemical Society.

  13. Hydrothermal Synthesis of Zeolitic Imidazolate Frameworks-8 (ZIF-8) Crystals with Controllable Size and Morphology

    KAUST Repository

    Lestari, Gabriella

    2012-05-01

    Zeolitic imidazolate frameworks (ZIFs) is a new class of metal-organic frameworks (MOFs) with zeolite-like properties such as permanent porosity, uniform pore size, and exceptional thermal and chemical stability. Until recently, ZIF materials have been mostly synthesized by solvothermal method. In this thesis, further analysis to tune the size and morphology of ZIF-8 is done upon our group’s recent success in preparing ZIF-8 crystals in pure aqueous solutions. Compositional parameters (molar ratio of 2-methylimidazole/Zn2+, type of zinc salt reagents, reagent concentrations, addition of surfactants) as well as process parameters (temperature and time) were systematically investigated. Upon characterizations of as-synthesized samples by X-ray powder diffraction, thermal gravimetric analysis, N2 adsorption, and field-emission scanning electron microscope, the results show that the particle size and morphology of ZIF-8 crystals are extremely sensitive to the compotional parameters of reagent concentration and addition of surfactants. The particle size and morphology of hydrothermally synthesized ZIF-8 crystals can be finely tuned; with the size ranging from 90 nm to 4 μm and the shape from truncated cubic to rhombic dodecahedron.

  14. Adsorptive removal of 1-naphthol from water with Zeolitic imidazolate framework-67

    Science.gov (United States)

    Yan, Xinlong; Hu, Xiaoyan; Chen, Tao; Zhang, Shiyu; Zhou, Min

    2017-08-01

    1-Naphthol is widely used as an intermediate in the plastics, dyes, fibers and rubbers production areas, leading to the increasing detection of 1-naphthol in the soil and water environment, which is of particular concern due to its acute toxicity and negative environmental impacts. Considering the high surface area and good stability of ZIFs (zeolitic imidazole frameworks) material, ZIF-67 (a representative cobalt-based ZIFs material) was synthesized and applied as an adsorbent for removal of 1-naphthol from aqueous solution. The obtained ZIF-67 was characterized by XRD, TEM, XPS, N2 physisorption and TG, and the adsorption isotherm, kinetics, and regeneration of the adsorbent were studied in detail. The adsorption of 1-naphthol on ZIF-67 followed a pseudo-second-order equation kinetics and fitted Langmuir adsorption model with a maximum adsorption capacity of 339 mg/g at 313 K, which is much higher than that of the common adsorbents reported such as activated carbon and carbon nanotubes et al. The solution pH was found to be an important factor influencing the adsorption process, which could be explained by the predominant mechanism controlling the process, i.e. electrostatic attraction. In addition, the ZIF-67 showed desirable reusability toward 1-naphthol removal from alkaline aqueous solution.

  15. Comparing gas separation performance between all known zeolites and their zeolitic imidazolate framework counterparts.

    Science.gov (United States)

    Gómez-Álvarez, Paula; Hamad, Said; Haranczyk, Maciej; Ruiz-Salvador, A Rabdel; Calero, Sofia

    2016-01-07

    To find optimal porous materials for adsorption-based separations is a challenging task due to the extremely large number of possible pore topologies and compositions. New porous material classes such as Metal Organic Frameworks (MOFs) are emerging, and hope to replace traditionally used materials such as zeolites. Computational screening offers relatively fast searching for candidate structures as well as side-by-side comparisons between material families. This work is pioneering at examining the families comprised by the experimentally known zeolites and their respective Zeolitic Imidazolate Framework (ZIF) counterparts in the context of a number of environmental and industrial separations involving carbon dioxide, nitrogen, methane, oxygen, and argon. Additionally, unlike related published work, here all the targeted structures have been previously relaxed through energy minimization. On the first level of characterization, we considered a detailed pore characterization, identifying 24 zeolites as promising candidates for gas separation based on adsorbate sizes. The second level involved interatomic potential-based calculations to assess the adsorption performance of the materials. We found no correlation in the values of heat of adsorption between zeolites and ZIFs sharing the same topology. A number of structures were identified as potential experimental targets for CO2/N2, and CO2/CH4 affinity-based separations.

  16. Imidazole Alkaloids from the South China Sea Sponge Pericharax heteroraphis and Their Cytotoxic and Antiviral Activities

    Directory of Open Access Journals (Sweden)

    Kai-Kai Gong

    2016-01-01

    Full Text Available Marine sponges continue to serve as a rich source of alkaloids possessing interesting biological activities and often exhibiting unique structural frameworks. In the current study, chemical investigation on the marine sponge Pericharax heteroraphis collected from the South China Sea yielded one new imidazole alkaloid named naamidine J (1 along with four known ones (2–5. Their structures were established by extensive spectroscopic methods and comparison of their data with those of the related known compounds. All the isolates possessed a central 2-aminoimidazole ring, substituted by one or two functionalized benzyl groups in some combination of the C4 and C5 positions. The cytotoxicities against selected HL-60, HeLa, A549 and K562 tumor cell lines and anti-H1N1 (Influenza a virus (IAV activity for the isolates were evaluated. Compounds 1 and 2 exhibited cytotoxicities against the K562 cell line with IC50 values of 11.3 and 9.4 μM, respectively. Compound 5 exhibited weak anti-H1N1 (influenza a virus, IAV activity with an inhibition ratio of 33%.

  17. Effect of imidazole and indomethacin on hemodynamics of the obstructed canine kidney

    International Nuclear Information System (INIS)

    Balint, P.; Laszlo, K.

    1985-01-01

    In the anesthetized dog renal blood flow (RBF) and its intrarenal distribution were investigated by the radioactive microsphere technique 24 hr after bilateral (BUL) and unilateral (UUL) ureteral ligation. In the control series indomethacin (IM) led to a decrease in RBF with outward shifting of zonal perfusions; imidazole (IA) did not cause significant changes in renal hemodynamics. In the BUL series there was a sharp drop in RBF with a proportional decrease in outer (OC) and inner (IC) cortical perfusion; IM treatment resulted in a further decrease in overall and zonal perfusions. IA, a selective inhibitor of thromboxane synthetase, relieved IC vasoconstriction. In the ligated kidney of the UUL preparations decrease in RBF was due to OC vasoconstriction, while IC perfusion equalled controls. IM led to an overall vasoconstriction in all cortical layers; IA did not influence either total RBF or its distribution. It was concluded that BUL ''unmasked'' TXA2 production in the IC layers, while IM treatment, by inhibiting the production of PGE2, PGI2, and TXA2, resulted in an overall vasoconstriction both in controls and the BUL and UUL preparations

  18. Novel catalytic micromotor of porous zeolitic imidazolate framework-67 for precise drug delivery.

    Science.gov (United States)

    Wang, Linlin; Zhu, Hongli; Shi, Ying; Ge, You; Feng, Xiaomiao; Liu, Ruiqing; Li, Yi; Ma, Yanwen; Wang, Lianhui

    2018-06-07

    Micromotors hold promise as drug carriers for targeted drug delivery owing to the characteristics of self-propulsion and directional navigation. However, several defects still exist, including high cost, short movement life, low drug loading and slow release rate. Herein, a novel catalytic micromotor based on porous zeolitic imidazolate framework-67 (ZIF-67) synthesized by a greatly simplified wet chemical method assisted with ultrasonication is described as an efficient anticancer drug carrier. These porous micromotors display effective autonomous motion in hydrogen peroxide and long durable movement life of up to 90 min. Moreover, the multifunctional micromotor ZIF-67/Fe3O4/DOX exhibits excellent performance in precise drug delivery under external magnetic field with high drug loading capacity of fluorescent anticancer drug DOX up to 682 μg mg-1 owing to its porous nature, high surface area and rapid drug release based on dual stimulus of catalytic reaction and solvent effects. Therefore, these porous ZIF-67-based catalytic micromotors combine the domains of metal-organic frameworks (MOFs) and micomotors, thus developing potential resources for micromotors and holding great potential as label-free and precisely controlled high-quality candidates of drug delivery systems for biomedical applications.

  19. Efficient adsorptive removal of Congo red from aqueous solution by synthesized zeolitic imidazolate framework-8

    Directory of Open Access Journals (Sweden)

    Canlan Jiang

    2016-10-01

    Full Text Available Dyes exposure in aquatic environment creates risks to human health and biota due to their intrinsic toxic mutagenic and carcinogenic characteristics. In this work, a metal-organic frameworks materials, zeolitic imidazolate framework-8 (ZIF-8, was synthesized through hydrothermal reaction for the adsorptive removal of harmful Congo red (CR from aqueous solution. Results showed that the maximum adsorption capacity of CR onto ZIF-8 was ultrahigh as 1250 mg g−1. Adsorption behaviors can be successfully fitted by the pseudo-second order kinetic model and the Langmuir isotherm equation. Solution conditions (pH condition and the co-exist anions may influent the adsorption behaviors. The adsorption performance at various temperatures indicated the process was a spontaneous and endothermic adsorption reaction. The enhanced adsorption capacity was determined due to large surface area of ZIF-8 and the strong interactions between surface groups of ZIF-8 and CR molecules including the electrostatic interaction between external active sites Zn−OH on ZIF-8 -and −SO3 or –N=N– sites in CR molecule, and the π–π interaction.

  20. Synthesis of triazole-based and imidazole-based zinc catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Valdez, Carlos A.; Satcher, Jr., Joe H.; Aines, Roger D.; Baker, Sarah E.

    2013-03-12

    Various methods and structures of complexes and molecules are described herein related to a zinc-centered catalyst for removing carbon dioxide from atmospheric or aqueous environments. According to one embodiment, a method for creating a tris(triazolyl)pentaerythritol molecule includes contacting a pentaerythritol molecule with a propargyl halide molecule to create a trialkyne molecule, and contacting the trialkyne molecule with an azide molecule to create the tris(triazolyl)pentaerythritol molecule. In another embodiment, a method for creating a tris(imidazolyl)pentaerythritol molecule includes alkylating an imidazole 2-carbaldehyde molecule to create a monoalkylated aldehyde molecule, reducing the monoalkylated aldehyde molecule to create an alcohol molecule, converting the alcohol molecule to create an alkyl halide molecule using thionyl halide, and reacting the alkyl halide molecule with a pentaerythritol molecule to create a tris(imidazolyl)pentaerythritol molecule. In another embodiment, zinc is bound to the tris(triazolyl)pentaerythritol molecule to create a zinc-centered tris(triazolyl)pentaerythritol catalyst for removing carbon dioxide from atmospheric or aqueous environments.

  1. Imidazole-containing farnesyltransferase inhibitors: 3D quantitative structure-activity relationships and molecular docking

    Science.gov (United States)

    Xie, Aihua; Odde, Srinivas; Prasanna, Sivaprakasam; Doerksen, Robert J.

    2009-07-01

    One of the most promising anticancer and recent antimalarial targets is the heterodimeric zinc-containing protein farnesyltransferase (FT). In this work, we studied a highly diverse series of 192 Abbott-initiated imidazole-containing compounds and their FT inhibitory activities using 3D-QSAR and docking, in order to gain understanding of the interaction of these inhibitors with FT to aid development of a rational strategy for further lead optimization. We report several highly significant and predictive CoMFA and CoMSIA models. The best model, composed of CoMFA steric and electrostatic fields combined with CoMSIA hydrophobic and H-bond acceptor fields, had r 2 = 0.878, q 2 = 0.630, and r pred 2 = 0.614. Docking studies on the statistical outliers revealed that some of them had a different binding mode in the FT active site based on steric bulk and available active site space, explaining why the predicted activities differed from the experimental activities.

  2. Recognition properties of receptors consisting of imidazole and indole recognition units towards carbohydrates

    Directory of Open Access Journals (Sweden)

    Monika Mazik

    2010-02-01

    Full Text Available Compounds 4 and 5, including both 4(5-substituted imidazole or 3-substituted indole units as the entities used in nature, and 2-aminopyridine group as a heterocyclic analogue of the asparagine/glutamine primary amide side chain, were prepared and their binding properties towards carbohydrates were studied. The design of these receptors was inspired by the binding motifs observed in the crystal structures of protein–carbohydrate complexes. 1H NMR spectroscopic titrations in competitive and non-competitive media as well as binding studies in two-phase systems, such as dissolution of solid carbohydrates in apolar media, revealed both highly effective recognition of neutral carbohydrates and interesting binding preferences of these acyclic compounds. Compared to the previously described acyclic receptors, compounds 4 and 5 showed significantly increased binding affinity towards β-galactoside. Both receptors display high β- vs. α-anomer binding preferences in the recognition of glycosides. It has been shown that both hydrogen bonding and interactions of the carbohydrate CH units with the aromatic rings of the receptors contribute to the stabilization of the receptor–carbohydrate complexes. The molecular modeling calculations, synthesis and binding properties of 4 and 5 towards selected carbohydrates are described and compared with those of the previously described receptors.

  3. Tunable CO 2 Adsorbents by Mixed-Linker Synthesis and Postsynthetic Modification of Zeolitic Imidazolate Frameworks

    KAUST Repository

    Thompson, Joshua A.

    2013-04-25

    The incorporation of accessible amine functionality in zeolitic imidazolate frameworks (ZIFs) is used to improve the adsorption selectivity for CO 2/CH4 gas separation applications. Two synthetic approaches are described in this work to introduce functionality into the ZIF: (i) mixed-linker ZIF synthesis with 2-aminobenzimidazole as a substitution linker and (ii) postsynthetic modification of a mixed-linker ZIF with ethylenediamine. Using 2-aminobenzimidazole, a linker with a primary amine functional group, substitution of the ZIF-8 linker during synthesis allows for control over the adsorption properties while maintaining the ZIF-8 structure with up to nearly 50% substitution in the mixed-linker ZIF framework, producing a material with tunable pore size and amine functionality. Alternatively, postsynthetic modification of a mixed-linker ZIF containing an aldehyde functional group produces a ZIF material with a primary amine without detrimental loss of micropore volume by controlling the amount of functional group sites for modification. Both approaches using mixed-linker ZIFs yield new materials that show improvement in adsorption selectivity for the CO 2/CH4 gas pair over ZIF-8 and commercially available adsorbents as well as an increase in the heat of adsorption for CO2 without significant changes to the crystal structure. These results indicate that tuning the surface properties of ZIFs by either mixed-linker synthesis and/or postsynthetic modification may generate new materials with improved gas separation properties, thereby providing a new method for tailoring metal-organic frameworks. © 2013 American Chemical Society.

  4. Tunable CO 2 Adsorbents by Mixed-Linker Synthesis and Postsynthetic Modification of Zeolitic Imidazolate Frameworks

    KAUST Repository

    Thompson, Joshua A.; Brunelli, Nicholas A.; Lively, Ryan P.; Johnson, J. R.; Jones, Christopher W.; Nair, Sankar

    2013-01-01

    The incorporation of accessible amine functionality in zeolitic imidazolate frameworks (ZIFs) is used to improve the adsorption selectivity for CO 2/CH4 gas separation applications. Two synthetic approaches are described in this work to introduce functionality into the ZIF: (i) mixed-linker ZIF synthesis with 2-aminobenzimidazole as a substitution linker and (ii) postsynthetic modification of a mixed-linker ZIF with ethylenediamine. Using 2-aminobenzimidazole, a linker with a primary amine functional group, substitution of the ZIF-8 linker during synthesis allows for control over the adsorption properties while maintaining the ZIF-8 structure with up to nearly 50% substitution in the mixed-linker ZIF framework, producing a material with tunable pore size and amine functionality. Alternatively, postsynthetic modification of a mixed-linker ZIF containing an aldehyde functional group produces a ZIF material with a primary amine without detrimental loss of micropore volume by controlling the amount of functional group sites for modification. Both approaches using mixed-linker ZIFs yield new materials that show improvement in adsorption selectivity for the CO 2/CH4 gas pair over ZIF-8 and commercially available adsorbents as well as an increase in the heat of adsorption for CO2 without significant changes to the crystal structure. These results indicate that tuning the surface properties of ZIFs by either mixed-linker synthesis and/or postsynthetic modification may generate new materials with improved gas separation properties, thereby providing a new method for tailoring metal-organic frameworks. © 2013 American Chemical Society.

  5. A NEW COPPER (II)-IMIDAZOLE DERIVATIVE EFFECTIVELY INHIBITS REPLICATION OF DENV-2 IN VERO CELL

    Science.gov (United States)

    Sucipto, Teguh Hari; Churrotin, Siti; Setyawati, Harsasi; Martak, Fahimah; Mulyatno, Kris Cahyo; Amarullah, Ilham Harlan; Kotaki, Tomohiro; Kameoka, Masanori; Yotopranoto, Subagyo; Soegijanto, and Soegeng

    2018-01-01

    Background: Dengue is a kind of infectious disease that was distributed in the tropical and sub-tropical areas. To date, there is no clinically approved dengue vaccine or antiviral for humans, even though there have been great efforts towards this end. Therefore, finding the effective compound against dengue virus (DENV) replication is very important. Among the complex compounds, copper(II)-imidazole derivatives are of interest because of their biological and medicinal benefits. Materials and Methods: In the present study, antiviral activity of [Cu(2,4,5-triphenylimidazole)2]n, was evaluated against different stages of dengue virus type 2 (DENV-2) replication in Vero cell using focus forming unit reduction assay and quantitative ELISA. Results: [Cu(2,4,5-triphenylimidazole)2]n inhibited DENV-2 replication in Vero cells with IC50 = 2.3 μg/ml and SI= 19.42 when cells were treated 2 days after virus infection, whereas its CC50 for cytotoxicity to Vero cells was 44.174 μg/ml. Conclusion: The compound has high anti-DENV2 activity, less toxicity, and a high possibility to be considered a drug candidate. PMID:29619441

  6. Novel Zeolitic Imidazolate Framework/Polymer Membranes for Hydrogen Separations in Coal Processing

    Energy Technology Data Exchange (ETDEWEB)

    Musselman, Inga H.

    2013-01-31

    Nanoparticles of zeolitic imidazolate frameworks and other related hybrid materials were prepared by modifying published synthesis procedures by introducing bases, changing stoichiometric ratios, or adjusting reaction conditions. These materials were stable at temperatures >300 °C and were compatible with the polymer matrices used to prepare mixed-matrix membranes (MMMs). MMMs tested at 300 °C exhibited a >30 fold increase in permeability, compared to those measured at 35 °C, while maintaining H{sub 2}/CO{sub 2} selectivity. Measurements at high pressure (up to 30 atm) and high temperature (up to 300 °C) resulted in an increase in gas flux across the membrane with retention of selectivity. No variations in permeability were observed at high pressures at either 35 or 300 °C. CO{sub 2}-induced plasticization was not observed for Matrimid®, VTEC, and PBI polymers or their MMMs at 30 atm and 300 °C. Membrane surface modification by cross-linking with ethylenediamine resulted in an increase in H{sub 2}/CO{sub 2} selectivity at 35 °C. Spectrometric analysis showed that the cross-linking was effective to temperatures <150 °C. At higher temperatures, the cross-linked membranes exhibit a H2/CO2 selectivity similar to the uncrosslinked polymer.

  7. Antifungal activity of tioconazole (UK-20,349), a new imidazole derivative.

    Science.gov (United States)

    Jevons, S; Gymer, G E; Brammer, K W; Cox, D A; Leeming, M R

    1979-04-01

    Tioconazole (UK-20,349), a new antifungal imidazole derivative, was compared with miconazole for activity in vitro against Candida spp., Torulopsis glabrata, Cryptococcus neoformans, Aspergillus spp., and dermatophyte fungi (Trichophyton spp. and Microsporum spp.). Tioconazole was more active than miconazole against all the fungal species examined except Aspergillus, against which both agents showed similar activity. Both tioconazole and miconazole inhibited the growth of all fungi examined at concentrations well below their quoted minimum inhibitory concentrations. Their activity against fungi in vivo was investigated in mice infected systemically with Candida albicans. Both agents significantly reduced the numbers of viable Candida cells recoverable from the kidneys of infected animals, with tioconazole producing a generally more marked reduction. After administration of a single oral dose (25 mg/kg) to beagle dogs or white mice, higher and more sustained circulating levels of bioactive drug were detectable of tioconazole than of miconazole. These observations suggest that tioconazole may have potential in the treatment of both superficial and systemic mycoses in humans.

  8. Fine-scale tribological performance of zeolitic imidazolate framework (ZIF-8 based polymer nanocomposite membranes

    Directory of Open Access Journals (Sweden)

    Nay Win Khun

    2014-12-01

    Full Text Available We combined zeolitic imidazolate framework nanoparticles (ZIF-8: ˜150 nm diameter with Matrimid® 5218 polymer to form permeable mixed matrix membranes, featuring different weight fractions of nanoparticles (up to 30 wt. % loading. We used ball-on-disc micro-tribological method to measure the frictional coefficient of the nanocomposite membranes, as a function of nanoparticle loading and annealing heat treatment. The tribological results reveal that the friction and wear of the unannealed samples rise steadily with greater nanoparticle loading because ZIF-8 is relatively harder than the matrix, thus promoting abrasive wear mechanism. After annealing, however, we discover that the nanocomposites display an appreciably lower friction and wear damage compared with the unannealed counterparts. Evidence shows that the major improvement in tribological performance is associated with the greater amounts of wear debris derived from the annealed nanocomposite membranes. We propose that detached Matrimid-encapsulated ZIF-8 nanoparticles could function as “spacers,” which are capable of not only reducing direct contact between two rubbing surfaces but also enhancing free-rolling under the action of lateral forces.

  9. High-Pressure Chemistry of a Zeolitic Imidazolate Framework Compound in the Presence of Different Fluids.

    Science.gov (United States)

    Im, Junhyuck; Yim, Narae; Kim, Jaheon; Vogt, Thomas; Lee, Yongjae

    2016-09-14

    Pressure-dependent structural and chemical changes of the zeolitic imidazolate framework compound ZIF-8 have been investigated using different pressure transmitting media (PTM) up to 4 GPa. The unit cell of ZIF-8 expands and contracts under hydrostatic pressure depending on the solvent molecules used as PTM. When pressurized in water up to 2.2(1) GPa, the unit cell of ZIF-8 reveals a gradual contraction. In contrast, when alcohols are used as PTM, the ZIF-8 unit cell volume initially expands by 1.2% up to 0.3(1) GPa in methanol, and by 1.7% up to 0.6(1) GPa in ethanol. Further pressure increase then leads to a discontinuous second volume expansion by 1.9% at 1.4(1) GPa in methanol and by 0.3% at 2.3(1) GPa in ethanol. The continuous uptake of molecules under pressure, modeled by the residual electron density derived from Rietveld refinements of X-ray powder diffraction, reveals a saturation pressure near 2 GPa. In non-penetrating PTM (silicone oil), ZIF-8 becomes amorphous at 0.9(1) GPa. The structural changes observed in the ZIF-8-PTM system under pressure point to distinct molecular interactions within the pores.

  10. Kinetic and photochemical studies and alteration of ultraviolet sensitivity of Escherichia coli thymidine kinase of halogenated allosteric regulators and substrate analogues

    International Nuclear Information System (INIS)

    Chen, M.S.; Prusoff, W.H.

    1977-01-01

    The effect of various halogenated and nonhalogenated allosteric effectors on the sensitivity of Escherichia coli thymidine kinase to ultraviolet radiations (uv,253.7 nm) was investigated. All naturally occurring dNTPs convert the monomeric form of the enzyme into the dimeric form which is less sensitive to uv inactivation. Whereas 5-iodo-2'-deoxycytidine triphosphate (IdCTP) and 5-iodo-2' deoxyuridine triphosphate (IdUTP) enhance the uv inactivation of the enzyme, 5-bromo-2'-deoxyuridine triphosphate and 5-bromo-2'-deoxycytidine triphosphate exert a protective effect similar to that produced by the corresponding naturally occurring effectors, dTTP and dCTP. The enhanced uv inactivation by IdUTP is prevented totally by dTTP, but only partially by dCTP or dThd, whereas the enhanced sensitization by IdCTP is prevented almost totally by dCTP, partially by dTTP, and not at all by dThd. The uv sensitization of thymidine kinase by IdCTP appears to be at the regulatory site since a maximum saturation effect is observed, and the concentration required to exert a 50% maximal uv sensitization is similar to its K/sub m/ for enhancement of catalytic activity. When the enzyme was irradiated in the presence of either [2- 14 C]IdUTP or [2- 14 C]IdUrd, zone sedimentation analysis in sucrose density gradients showed the sedimentation coefficient of the radioactive labeled proteins to be the same, 3.8 S. Hence uv irradiation of the effector-induced dimer resulted in not only dissociation to the monomer, but also complete loss of catalytic activity. The substitution of an azido group for the 5'-OH group of 5-iodo-, 5-bromo-, 5-chloro-, or 5-fluorodeoxyuridine greatly decreased their affinity for thymidine kinase, and in addition the kinetics of inhibition changed from a competitive to a noncompetitive pattern. The presence of the azido moiety in the 5' position of the halogenated nucleosides did not enhance the rate of uv inactivation of the enzyme

  11. Enzymes for improved biomass conversion

    Science.gov (United States)

    Brunecky, Roman; Himmel, Michael E.

    2016-02-02

    Disclosed herein are enzymes and combinations of the enzymes useful for the hydrolysis of cellulose and the conversion of biomass. Methods of degrading cellulose and biomass using enzymes and cocktails of enzymes are also disclosed.

  12. Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol

    DEFF Research Database (Denmark)

    Manna, Moutusi; Niemelä, Miia; Tynkkynen, Joona

    2016-01-01

    ) - a prototypical G protein-coupled receptor - is modulated by cholesterol in an allosteric fashion. Extensive atomistic simulations show that cholesterol regulates b2AR by limiting its conformational variability. The mechanism of action is based on the binding of cholesterol at specific high-affinity sites located...... near the transmembrane helices 5-7 of the receptor. The alternative mechanism, where the β2AR conformation would be modulated by membrane-mediated interactions, plays only a minor role. Cholesterol analogues also bind to cholesterol binding sites and impede the structural flexibility of β2AR, however...... cholesterol generates the strongest effect. The results highlight the capacity of lipids to regulate the conformation of membrane receptors through specific interactions....

  13. Evidence for a Common Mechanism of SIRT1 Regulation by Allosteric Activators

    Science.gov (United States)

    Hubbard, Basil P.; Gomes, Ana P.; Dai, Han; Li, Jun; Case, April W.; Considine, Thomas; Riera, Thomas V.; Lee, Jessica E.; Sook Yen, E; Lamming, Dudley W.; Pentelute, Bradley L.; Schuman, Eli R.; Stevens, Linda A.; Ling, Alvin J. Y.; Armour, Sean M.; Michan, Shaday; Zhao, Huizhen; Jiang, Yong; Sweitzer, Sharon M.; Blum, Charles A.; Disch, Jeremy S.; Ng, Pui Yee; Howitz, Konrad T.; Rolo, Anabela P.; Hamuro, Yoshitomo; Moss, Joel; Perni, Robert B.; Ellis, James L.; Vlasuk, George P.; Sinclair, David A.

    2013-01-01

    A molecule that treats multiple age-related diseases would have a major impact on global health and economics. The SIRT1 deacetylase has drawn attention in this regard as a target for drug design. Yet controversy exists around the mechanism of sirtuin-activating compounds (STACs). We found that specific hydrophobic motifs found in SIRT1 substrates such as PGC-1α and FOXO3a facilitate SIRT1 activation by STACs. A single amino acid in SIRT1, Glu230, located in a structured N-terminal domain, was critical for activation by all previously reported STAC scaffolds and a new class of chemically distinct activators. In primary cells reconstituted with activation-defective SIRT1, the metabolic effects of STACs were blocked. Thus, SIRT1 can be directly activated through an allosteric mechanism common to chemically diverse STACs. PMID:23471411

  14. Gs protein peptidomimetics as allosteric modulators of the β2-adrenergic receptor

    DEFF Research Database (Denmark)

    Boyhus, Lotte Emilie; Danielsen, Mia; Bengtson, Nina Smidt

    2018-01-01

    A series of Gs protein peptidomimetics were designed and synthesised based on the published X-ray crystal structure of the active state β2-Adrenergic receptor (β2AR) in complex with the Gs protein (PDB 3SN6). We hypothesised that such peptidomimetics may function as allosteric modulators...... that target the intracellular Gs protein binding site of the β2AR. Peptidomimetics were designed to mimic the 15 residue C-Terminal α-helix of the Gs protein and were pre-organised in a helical conformation by (i, i + 4)-stapling using copper catalysed azide alkyne cycloaddition. Linear and stapled...... be able to compete with the native Gs protein for the intracellular binding site to block ISO-induced cAMP formation, but are unable to stabilise an active-like receptor conformation....

  15. A2A adenosine receptor ligand binding and signalling is allosterically modulated by adenosine deaminase.

    Science.gov (United States)

    Gracia, Eduard; Pérez-Capote, Kamil; Moreno, Estefanía; Barkešová, Jana; Mallol, Josefa; Lluís, Carme; Franco, Rafael; Cortés, Antoni; Casadó, Vicent; Canela, Enric I

    2011-05-01

    A2ARs (adenosine A2A receptors) are highly enriched in the striatum, which is the main motor control CNS (central nervous system) area. BRET (bioluminescence resonance energy transfer) assays showed that A2AR homomers may act as cell-surface ADA (adenosine deaminase; EC 3.5.4.4)-binding proteins. ADA binding affected the quaternary structure of A2ARs present on the cell surface. ADA binding to adenosine A2ARs increased both agonist and antagonist affinity on ligand binding to striatal membranes where these proteins are co-expressed. ADA also increased receptor-mediated ERK1/2 (extracellular-signal-regulated kinase 1/2) phosphorylation. Collectively, the results of the present study show that ADA, apart from regulating the concentration of extracellular adenosine, may behave as an allosteric modulator that markedly enhances ligand affinity and receptor function. This powerful regulation may have implications for the physiology and pharmacology of neuronal A2ARs.

  16. Design and optimization of selective azaindole amide M1 positive allosteric modulators.

    Science.gov (United States)

    Davoren, Jennifer E; O'Neil, Steven V; Anderson, Dennis P; Brodney, Michael A; Chenard, Lois; Dlugolenski, Keith; Edgerton, Jeremy R; Green, Michael; Garnsey, Michelle; Grimwood, Sarah; Harris, Anthony R; Kauffman, Gregory W; LaChapelle, Erik; Lazzaro, John T; Lee, Che-Wah; Lotarski, Susan M; Nason, Deane M; Obach, R Scott; Reinhart, Veronica; Salomon-Ferrer, Romelia; Steyn, Stefanus J; Webb, Damien; Yan, Jiangli; Zhang, Lei

    2016-01-15

    Selective activation of the M1 receptor via a positive allosteric modulator (PAM) is a new approach for the treatment of the cognitive impairments associated with schizophrenia and Alzheimer's disease. A novel series of azaindole amides and their key pharmacophore elements are described. The nitrogen of the azaindole core is a key design element as it forms an intramolecular hydrogen bond with the amide N-H thus reinforcing the bioactive conformation predicted by published SAR and our homology model. Representative compound 25 is a potent and selective M1 PAM that has well aligned physicochemical properties, adequate brain penetration and pharmacokinetic (PK) properties, and is active in vivo. These favorable properties indicate that this series possesses suitable qualities for further development and studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Optimization of Allosteric With-No-Lysine (WNK) Kinase Inhibitors and Efficacy in Rodent Hypertension Models

    Energy Technology Data Exchange (ETDEWEB)

    Yamada, Ken; Levell, Julian; Yoon, Taeyong; Kohls, Darcy; Yowe, David; Rigel, Dean F.; Imase, Hidetomo; Yuan, Jun; Yasoshima, Kayo; DiPetrillo, Keith; Monovich, Lauren; Xu, Lingfei; Zhu, Meicheng; Kato, Mitsunori; Jain, Monish; Idamakanti, Neeraja; Taslimi, Paul; Kawanami, Toshio; Argikar, Upendra A.; Kunjathoor, Vidya; Xie, Xiaoling; Yagi, Yukiko I.; Iwaki, Yuki; Robinson, Zachary; Park, Hyi-Man (Novartis)

    2017-08-03

    The observed structure–activity relationship of three distinct ATP noncompetitive With-No-Lysine (WNK) kinase inhibitor series, together with a crystal structure of a previously disclosed allosteric inhibitor bound to WNK1, led to an overlay hypothesis defining core and side-chain relationships across the different series. This in turn enabled an efficient optimization through scaffold morphing, resulting in compounds with a good balance of selectivity, cellular potency, and pharmacokinetic profile, which were suitable for in vivo proof-of-concept studies. When dosed orally, the optimized compound reduced blood pressure in mice overexpressing human WNK1, and induced diuresis, natriuresis and kaliuresis in spontaneously hypertensive rats (SHR), confirming that this mechanism of inhibition of WNK kinase activity is effective at regulating cardiovascular homeostasis.

  18. Evidence for a common mechanism of SIRT1 regulation by allosteric activators.

    Science.gov (United States)

    Hubbard, Basil P; Gomes, Ana P; Dai, Han; Li, Jun; Case, April W; Considine, Thomas; Riera, Thomas V; Lee, Jessica E; E, Sook Yen; Lamming, Dudley W; Pentelute, Bradley L; Schuman, Eli R; Stevens, Linda A; Ling, Alvin J Y; Armour, Sean M; Michan, Shaday; Zhao, Huizhen; Jiang, Yong; Sweitzer, Sharon M; Blum, Charles A; Disch, Jeremy S; Ng, Pui Yee; Howitz, Konrad T; Rolo, Anabela P; Hamuro, Yoshitomo; Moss, Joel; Perni, Robert B; Ellis, James L; Vlasuk, George P; Sinclair, David A

    2013-03-08

    A molecule that treats multiple age-related diseases would have a major impact on global health and economics. The SIRT1 deacetylase has drawn attention in this regard as a target for drug design. Yet controversy exists around the mechanism of sirtuin-activating compounds (STACs). We found that specific hydrophobic motifs found in SIRT1 substrates such as PGC-1α and FOXO3a facilitate SIRT1 activation by STACs. A single amino acid in SIRT1, Glu(230), located in a structured N-terminal domain, was critical for activation by all previously reported STAC scaffolds and a new class of chemically distinct activators. In primary cells reconstituted with activation-defective SIRT1, the metabolic effects of STACs were blocked. Thus, SIRT1 can be directly activated through an allosteric mechanism common to chemically diverse STACs.

  19. Immobilized enzymes and cells

    Energy Technology Data Exchange (ETDEWEB)

    Bucke, C; Wiseman, A

    1981-04-04

    This article reviews the current state of the art of enzyme and cell immobilization and suggests advances which might be made during the 1980's. Current uses of immobilized enzymes include the use of glucoamylase in the production of glucose syrups from starch and glucose isomerase in the production of high fructose corn syrup. Possibilities for future uses of immobilized enzymes and cells include the utilization of whey and the production of ethanol.

  20. Profiling the orphan enzymes

    Science.gov (United States)

    2014-01-01

    The emergence of Next Generation Sequencing generates an incredible amount of sequence and great potential for new enzyme discovery. Despite this huge amount of data and the profusion of bioinformatic methods for function prediction, a large part of known enzyme activities is still lacking an associated protein sequence. These particular activities are called “orphan enzymes”. The present review proposes an update of previous surveys on orphan enzymes by mining the current content of public databases. While the percentage of orphan enzyme activities has decreased from 38% to 22% in ten years, there are still more than 1,000 orphans among the 5,000 entries of the Enzyme Commission (EC) classification. Taking into account all the reactions present in metabolic databases, this proportion dramatically increases to reach nearly 50% of orphans and many of them are not associated to a known pathway. We extended our survey to “local orphan enzymes” that are activities which have no representative sequence in a given clade, but have at least one in organisms belonging to other clades. We observe an important bias in Archaea and find that in general more than 30% of the EC activities have incomplete sequence information in at least one superkingdom. To estimate if candidate proteins for local orphans could be retrieved by homology search, we applied a simple strategy based on the PRIAM software and noticed that candidates may be proposed for an important fraction of local orphan enzymes. Finally, by studying relation between protein domains and catalyzed activities, it appears that newly discovered enzymes are mostly associated with already known enzyme domains. Thus, the exploration of the promiscuity and the multifunctional aspect of known enzyme families may solve part of the orphan enzyme issue. We conclude this review with a presentation of recent initiatives in finding proteins for orphan enzymes and in extending the enzyme world by the discovery of new

  1. Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL Kinase Function.

    Science.gov (United States)

    Grover, Prerna; Shi, Haibin; Baumgartner, Matthew; Camacho, Carlos J; Smithgall, Thomas E

    2015-01-01

    The ABL protein-tyrosine kinase regulates intracellular signaling pathways controlling diverse cellular processes and contributes to several forms of cancer. The kinase activity of ABL is repressed by intramolecular interactions involving its regulatory Ncap, SH3 and SH2 domains. Small molecules that allosterically regulate ABL kinase activity through its non-catalytic domains may represent selective probes of ABL function. Here we report a screening assay for chemical modulators of ABL kinase activity that target the regulatory interaction of the SH3 domain with the SH2-kinase linker. This fluorescence polarization (FP) assay is based on a purified recombinant ABL protein consisting of the N-cap, SH3 and SH2 domains plus the SH2-kinase linker (N32L protein) and a short fluorescein-labeled probe peptide that binds to the SH3 domain. In assay development experiments, we found that the probe peptide binds to the recombinant ABL N32L protein in vitro, producing a robust FP signal that can be competed with an excess of unlabeled peptide. The FP signal is not observed with control N32L proteins bearing either an inactivating mutation in the SH3 domain or enhanced SH3:linker interaction. A pilot screen of 1200 FDA-approved drugs identified four compounds that specifically reduced the FP signal by at least three standard deviations from the untreated controls. Secondary assays showed that one of these hit compounds, the antithrombotic drug dipyridamole, enhances ABL kinase activity in vitro to a greater extent than the previously described ABL agonist, DPH. Docking studies predicted that this compound binds to a pocket formed at the interface of the SH3 domain and the linker, suggesting that it activates ABL by disrupting this regulatory interaction. These results show that screening assays based on the non-catalytic domains of ABL can identify allosteric small molecule regulators of kinase function, providing a new approach to selective drug discovery for this important

  2. Theoretical Analysis of Allosteric and Operator Binding for Cyclic-AMP Receptor Protein Mutants

    Science.gov (United States)

    Einav, Tal; Duque, Julia; Phillips, Rob

    2018-02-01

    Allosteric transcription factors undergo binding events both at their inducer binding sites as well as at distinct DNA binding domains, and it is often difficult to disentangle the structural and functional consequences of these two classes of interactions. In this work, we compare the ability of two statistical mechanical models - the Monod-Wyman-Changeux (MWC) and the Koshland-N\\'emethy-Filmer (KNF) models of protein conformational change - to characterize the multi-step activation mechanism of the broadly acting cyclic-AMP receptor protein (CRP). We first consider the allosteric transition resulting from cyclic-AMP binding to CRP, then analyze how CRP binds to its operator, and finally investigate the ability of CRP to activate gene expression. In light of these models, we examine data from a beautiful recent experiment that created a single-chain version of the CRP homodimer, thereby enabling each subunit to be mutated separately. Using this construct, six mutants were created using all possible combinations of the wild type subunit, a D53H mutant subunit, and an S62F mutant subunit. We demonstrate that both the MWC and KNF models can explain the behavior of all six mutants using a small, self-consistent set of parameters. In comparing the results, we find that the MWC model slightly outperforms the KNF model in the quality of its fits, but more importantly the parameters inferred by the MWC model are more in line with structural knowledge of CRP. In addition, we discuss how the conceptual framework developed here for CRP enables us to not merely analyze data retrospectively, but has the predictive power to determine how combinations of mutations will interact, how double mutants will behave, and how each construct would regulate gene expression.

  3. Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions.

    Directory of Open Access Journals (Sweden)

    Massimo Lai

    2015-01-01

    Full Text Available Calmodulin is a calcium-binding protein ubiquitous in eukaryotic cells, involved in numerous calcium-regulated biological phenomena, such as synaptic plasticity, muscle contraction, cell cycle, and circadian rhythms. It exibits a characteristic dumbell shape, with two globular domains (N- and C-terminal lobe joined by a linker region. Each lobe can take alternative conformations, affected by the binding of calcium and target proteins. Calmodulin displays considerable functional flexibility due to its capability to bind different targets, often in a tissue-specific fashion. In various specific physiological environments (e.g. skeletal muscle, neuron dendritic spines several targets compete for the same calmodulin pool, regulating its availability and affinity for calcium. In this work, we sought to understand the general principles underlying calmodulin modulation by different target proteins, and to account for simultaneous effects of multiple competing targets, thus enabling a more realistic simulation of calmodulin-dependent pathways. We built a mechanistic allosteric model of calmodulin, based on an hemiconcerted framework: each calmodulin lobe can exist in two conformations in thermodynamic equilibrium, with different affinities for calcium and different affinities for each target. Each lobe was allowed to switch conformation on its own. The model was parameterised and validated against experimental data from the literature. In spite of its simplicity, a two-state allosteric model was able to satisfactorily represent several sets of experiments, in particular the binding of calcium on intact and truncated calmodulin and the effect of different skMLCK peptides on calmodulin's saturation curve. The model can also be readily extended to include multiple targets. We show that some targets stabilise the low calcium affinity T state while others stabilise the high affinity R state. Most of the effects produced by calmodulin targets can be

  4. Computational redesign reveals allosteric mutation hotspots of organophosphate hydrolase that enhance organophosphate hydrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Jacob, Reed B. [Univ. of North Carolina, Chapel Hill, NC (United States); Ding, Feng [Clemson Univ., SC (United States); Ye, Dongmei [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ackerman, Eric [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Dokholyan, Nikolay V. [Univ. of North Carolina, Chapel Hill, NC (United States)

    2015-04-01

    Organophosphates are widely used for peaceful (agriculture) and military purposes (chemical warfare agents). The extraordinary toxicity of organophosphates and the risk of deployment, make it critical to develop means for their rapid and efficient deactivation. Organophosphate hydrolase (OPH) already plays an important role in organophosphate remediation, but is insufficient for therapeutic or prophylactic purposes primarily due to low substrate affinity. Current efforts focus on directly modifying the active site to differentiate substrate specificity and increase catalytic activity. Here, we present a novel strategy for enhancing the general catalytic efficiency of OPH through computational redesign of the residues that are allosterically coupled to the active site and validated our design by mutagenesis. Specifically, we identify five such hot-spot residues for allosteric regulation and assay these mutants for hydrolysis activity against paraoxon, a chemical-weapons simulant. A high percentage of the predicted mutants exhibit enhanced activity over wild-type (kcat =16.63 s-1), such as T199I/T54I (899.5 s-1) and C227V/T199I/T54I (848 s-1), while the Km remains relatively unchanged in our high-throughput cell-free expression system. Further computational studies of protein dynamics reveal four distinct distal regions coupled to the active site that display significant changes in conformation dynamics upon these identified mutations. These results validate a computational design method that is both efficient and easily adapted as a general procedure for enzymatic enhancement.

  5. Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Yi; Qin, Ling; Ortiz Zacarías, Natalia V.; de Vries, Henk; Han, Gye Won; Gustavsson, Martin; Dabros, Marta; Zhao, Chunxia; Cherney, Robert J.; Carter, Percy; Stamos, Dean; Abagyan, Ruben; Cherezov, Vadim; Stevens, Raymond C.; IJzerman, Adriaan P.; Heitman, Laura H.; Tebben, Andrew; Kufareva, Irina; Handel , Tracy M. (Vertex Pharm); (Leiden-MC); (USC); (BMS); (UCSD)

    2016-12-07

    CC chemokine receptor 2 (CCR2) is one of 19 members of the chemokine receptor subfamily of human class A G-protein-coupled receptors. CCR2 is expressed on monocytes, immature dendritic cells, and T-cell subpopulations, and mediates their migration towards endogenous CC chemokine ligands such as CCL2 (ref. 1). CCR2 and its ligands are implicated in numerous inflammatory and neurodegenerative diseases2 including atherosclerosis, multiple sclerosis, asthma, neuropathic pain, and diabetic nephropathy, as well as cancer3. These disease associations have motivated numerous preclinical studies and clinical trials4 (see http://www.clinicaltrials.gov) in search of therapies that target the CCR2–chemokine axis. To aid drug discovery efforts5, here we solve a structure of CCR2 in a ternary complex with an orthosteric (BMS-681 (ref. 6)) and allosteric (CCR2-RA-[R]7) antagonist. BMS-681 inhibits chemokine binding by occupying the orthosteric pocket of the receptor in a previously unseen binding mode. CCR2-RA-[R] binds in a novel, highly druggable pocket that is the most intracellular allosteric site observed in class A G-protein-coupled receptors so far; this site spatially overlaps the G-protein-binding site in homologous receptors. CCR2-RA-[R] inhibits CCR2 non-competitively by blocking activation-associated conformational changes and formation of the G-protein-binding interface. The conformational signature of the conserved microswitch residues observed in double-antagonist-bound CCR2 resembles the most inactive G-protein-coupled receptor structures solved so far. Like other protein–protein interactions, receptor–chemokine complexes are considered challenging therapeutic targets for small molecules, and the present structure suggests diverse pocket epitopes that can be exploited to overcome obstacles in drug design.

  6. Signaling-sensitive amino acids surround the allosteric ligand binding site of the thyrotropin receptor.

    Science.gov (United States)

    Kleinau, Gunnar; Haas, Ann-Karin; Neumann, Susanne; Worth, Catherine L; Hoyer, Inna; Furkert, Jens; Rutz, Claudia; Gershengorn, Marvin C; Schülein, Ralf; Krause, Gerd

    2010-07-01

    The thyrotropin receptor [thyroid-stimulating hormone receptor (TSHR)], a G-protein-coupled receptor (GPCR), is endogenously activated by thyrotropin, which binds to the extracellular region of the receptor. We previously identified a low-molecular-weight (LMW) agonist of the TSHR and predicted its allosteric binding pocket within the receptor's transmembrane domain. Because binding of the LMW agonist probably disrupts interactions or leads to formation of new interactions among amino acid residues surrounding the pocket, we tested whether mutation of residues at these positions would lead to constitutive signaling activity. Guided by molecular modeling, we performed site-directed mutagenesis of 24 amino acids in this spatial region, followed by functional characterization of the mutant receptors in terms of expression and signaling, measured as cAMP accumulation. We found that mutations V421I, Y466A, T501A, L587V, M637C, M637W, S641A, Y643F, L645V, and Y667A located in several helices exhibit constitutive activity. Of note is mutation M637W at position 6.48 in transmembrane helix 6, which has a significant effect on the interaction of the receptor with the LMW agonist. In summary, we found that a high proportion of residues in several helices surrounding the allosteric binding site of LMW ligands in the TSHR when mutated lead to constitutively active receptors. Our findings of signaling-sensitive residues in this region of the transmembrane bundle may be of general importance as this domain appears to be evolutionarily retained among GPCRs.

  7. Characterisation of the first enzymes committed to lysine biosynthesis in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Michael D W Griffin

    Full Text Available In plants, the lysine biosynthetic pathway is an attractive target for both the development of herbicides and increasing the nutritional value of crops given that lysine is a limiting amino acid in cereals. Dihydrodipicolinate synthase (DHDPS and dihydrodipicolinate reductase (DHDPR catalyse the first two committed steps of lysine biosynthesis. Here, we carry out for the first time a comprehensive characterisation of the structure and activity of both DHDPS and DHDPR from Arabidopsis thaliana. The A. thaliana DHDPS enzyme (At-DHDPS2 has similar activity to the bacterial form of the enzyme, but is more strongly allosterically inhibited by (S-lysine. Structural studies of At-DHDPS2 show (S-lysine bound at a cleft between two monomers, highlighting the allosteric site; however, unlike previous studies, binding is not accompanied by conformational changes, suggesting that binding may cause changes in protein dynamics rather than large conformation changes. DHDPR from A. thaliana (At-DHDPR2 has similar specificity for both NADH and NADPH during catalysis, and has tighter binding of substrate than has previously been reported. While all known bacterial DHDPR enzymes have a tetrameric structure, analytical ultracentrifugation, and scattering data unequivocally show that At-DHDPR2 exists as a dimer in solution. The exact arrangement of the dimeric protein is as yet unknown, but ab initio modelling of x-ray scattering data is consistent with an elongated structure in solution, which does not correspond to any of the possible dimeric pairings observed in the X-ray crystal structure of DHDPR from other organisms. This increased knowledge of the structure and function of plant lysine biosynthetic enzymes will aid future work aimed at improving primary production.

  8. Synthesis and characterization of new N-heterocyclic carbene ligands: 1,3-Bis(acetamide)imidazol-3-ium bromide and 3-(acetamide)-1-(3-aminopropyl)-1H-imidazol-3-ium bromide

    Science.gov (United States)

    Turkyilmaz, Murat; Uluçam, Gühergül; Aktaş, Şaban; Okan, S. Erol

    2017-05-01

    Two new pincer type N-heterocyclic carbene ligands were synthesized. The compounds were characterized by FTIR, NMR (1H, 13C) GC-MS and elemental analyses. They were also both modelled by DFT calculations as the crystal structure of 1,3-bis(acetamide)imidazol-3-ium bromide was determined by XRD which is an orthorhombic system with space group P21212. The structural analyses in gas phase were realized by comparing the experimental NMR and IR spectra with those of the theoretical calculations. In vitro biological activities of the molecules were determined and found that one of them exhibits significant cytotoxic activity.

  9. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge.

    Science.gov (United States)

    Perryman, Alexander L; Santiago, Daniel N; Forli, Stefano; Martins, Diogo Santos; Olson, Arthur J

    2014-04-01

    To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new "Rank Difference Ratio" metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAM replica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4's very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational

  10. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge

    Science.gov (United States)

    Perryman, Alexander L.; Santiago, Daniel N.; Forli, Stefano; Santos-Martins, Diogo; Olson, Arthur J.

    2014-04-01

    To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new "Rank Difference Ratio" metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAM replica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4's very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational

  11. Crystal structures of eight 3D molecular adducts derived from bis-imidazole, bis(benzimidazole), and organic acids

    Science.gov (United States)

    Ding, Aihua; Jin, Shouwen; Jin, Shide; Hu, KaiKai; Lin, Zhihao; Liu, Hui; Wang, Daqi

    2018-01-01

    Cocrystallization of the bis(imidazole)/bis(benzimidazole) with a series of organic acids gave a total of eight molecular adducts with the compositions: (3,6-bis(imidazole-1-yl)pyridazine): (trichloroacetic acid)2(1) [(H2L1)2+ · (tca-)2, L1 = 3,6-bis(imidazole-1-yl)pyridazine, tca- = trichloroacetate], (bis(N-imidazolyl)methane): (suberic acid) (2) [(L2) · (H2suba), L2 = bis(N-imidazolyl)methane, H2suba = suberic acid], bis(N-imidazolyl)methane: (3-nitrophthalic acid): 3H2O (3) [(H2L2)2+ · (3-Hnpa-)2 · 3H2O, 3-Hnpa- = 3-nitro hydrogenphthalate], (bis(N-imidazolyl)butane)0.5: (4-nitrophthalic acid): H2O (4) [(H2L3)0.5+ · (4-Hnpa-)- · H2O, L3 = bis(N-imidazolyl)butane, 4-Hnpa- = 4-nitro hydrogenphthalate], (1-(3-(1H-benzimidazol-1-yl)propyl)-1H-benzimidazole): (3,5-dinitrosalicylic acid) (5) [(HL4) · (3,5-dns-), L4 = 1-(3-(1H-benzimidazol-1-yl)propyl)-1H-benzimidazole, 3,5-dns- = 3,5-dinitrosalicylate], (1-(3-(1H-benzimidazol-1-yl)propyl)-1H-benzimidazole): (3-nitrophthalic acid) (6) [(H2L4) · (3-npa2-), L4 = 1-(3-(1H-benzimidazol-1-yl)propyl)-1H-benzimidazole, 3-npa2-=3-nitrogenphthalate], (bis(N-imidazolyl)butane): (pamoic acid) (7) [(H2L3) · (pam), pam = pamoate], and (3,6-bis(imidazole-1-yl)pyridazine): (1,5-naphthalenedisulfonic acid) [(H2L1)2+ · (npda)2- = 1,5-naphthalenedisulfonate] (8). The eight adducts have been characterized by X-ray diffraction technique, infrared spectrum, and elemental analysis, and the melting points of all adducts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the eight investigated crystals both the end ring N in the bis(imidazole) moieties are protonated when the organic acids are deprotonated except 2, and 5, and the crystal packing is interpreted in terms of the strong ionic Nsbnd H⋯O H-bond between the imidazolium and the deprotonated acidic groups. Except the Nsbnd H⋯O H-bond, the Osbnd H⋯O H-bonds were also found at the salts 3, 4

  12. Synthesis and spectroscopic characterization of Y-shaped fluorophores with an imidazole core containing crown ether moieties

    International Nuclear Information System (INIS)

    Doğru, Ümit; Öztürk Ürüt, Gülsiye; Bayramin, Dilek

    2015-01-01

    In this study three new Y-shaped fluorophores, 4,5-(2,2'-diphenyl)vinyl-{2-[(1,4,7,10-tetraoxa-13-azacyclopentadecyl) phenyl]}-1H-imidazole (1a), 4,5-{[2,2'-bis(4-methoxyphenyl)vinyl]-[2-(1,4,7,10-tetraoxa-13- azacyclopentadecyl)-phenyl]}-1H-imidazole (1b) and 4,5-(2,2'-diphenyl)vinyl-{2-(1,4,7,10,13-benzopentaoxacyclopentadecyl)} -1H-imidazole (1c) were synthesized. 1,6-Diphenylhexa-1,5-diene-3,4-dione (2a) and 1,6-bis(4-methoxyphenyl)hexa-1,5-diene-3,4-dione (2b) were synthesized as preliminary fluorophores and then reacted with 4-formylbenzo-aza-15-crown-5 (3a) and 4-formylbenzo-15-crown-5 (3b) to obtain the three Y-shaped fluorophores 1a, 1b and 1c. 4-formylbenzo-aza-15-crown-5 and 4-formylbenzo-15-crown-5 intermediates were synthesized with Vilsmeier–Haack reaction. The photophysical properties such as maximum absorption wavelengths, maximum emission wavelengths, Stokes' shifts, singlet energies, fluorescence quantum yields and photostabilities of the compounds were investigated by measuring absorption and emission spectra in a series of solvents of varying polarities of toluene (TOL), dichloromethane (DCM), tetrahydrofuran (THF), ethyl acetate (EA), acetonitrile (ACN), and N,N-dimethylformamide (DMF). The three compounds 1a, 1b and 1c exhibited emission maxima in the 412–677 nm range. All the derivatives synthesized exhibited excellent photostability in all the solvents tested. - Highlights: • Three new Y-shaped fluorophores were synthesized for the first time. • Their absorption and emission properties were investigated. • All the derivatives synthesized exhibited excellent photostability

  13. Synthesis and spectroscopic characterization of Y-shaped fluorophores with an imidazole core containing crown ether moieties

    Energy Technology Data Exchange (ETDEWEB)

    Doğru, Ümit; Öztürk Ürüt, Gülsiye, E-mail: gulsiye.ozturk@deu.edu.tr; Bayramin, Dilek

    2015-07-15

    In this study three new Y-shaped fluorophores, 4,5-(2,2'-diphenyl)vinyl-{2-[(1,4,7,10-tetraoxa-13-azacyclopentadecyl) phenyl]}-1H-imidazole (1a), 4,5-{[2,2'-bis(4-methoxyphenyl)vinyl]-[2-(1,4,7,10-tetraoxa-13- azacyclopentadecyl)-phenyl]}-1H-imidazole (1b) and 4,5-(2,2'-diphenyl)vinyl-{2-(1,4,7,10,13-benzopentaoxacyclopentadecyl)} -1H-imidazole (1c) were synthesized. 1,6-Diphenylhexa-1,5-diene-3,4-dione (2a) and 1,6-bis(4-methoxyphenyl)hexa-1,5-diene-3,4-dione (2b) were synthesized as preliminary fluorophores and then reacted with 4-formylbenzo-aza-15-crown-5 (3a) and 4-formylbenzo-15-crown-5 (3b) to obtain the three Y-shaped fluorophores 1a, 1b and 1c. 4-formylbenzo-aza-15-crown-5 and 4-formylbenzo-15-crown-5 intermediates were synthesized with Vilsmeier–Haack reaction. The photophysical properties such as maximum absorption wavelengths, maximum emission wavelengths, Stokes' shifts, singlet energies, fluorescence quantum yields and photostabilities of the compounds were investigated by measuring absorption and emission spectra in a series of solvents of varying polarities of toluene (TOL), dichloromethane (DCM), tetrahydrofuran (THF), ethyl acetate (EA), acetonitrile (ACN), and N,N-dimethylformamide (DMF). The three compounds 1a, 1b and 1c exhibited emission maxima in the 412–677 nm range. All the derivatives synthesized exhibited excellent photostability in all the solvents tested. - Highlights: • Three new Y-shaped fluorophores were synthesized for the first time. • Their absorption and emission properties were investigated. • All the derivatives synthesized exhibited excellent photostability.

  14. Racemic cobalt phosphonates incorporating flexible bis(imidazole) co-ligands.

    Science.gov (United States)

    Feng, Jian-Shen; Cai, Zhong-Sheng; Ren, Min; Bao, Song-Song; Zheng, Li-Min

    2015-11-07

    By incorporating flexible bis(imidazol-1-ylmethyl)benzene (bix) co-ligands, four new racemic cobalt phosphonates with formulae Co3(3-ppap)2(1,4-bix)2(H2O)4·4H2O (1), Co3(3-ppap)2(1,3-bix)2(H2O)4·5H2O (2), Co3(3-ppap)2(1,2-bix)2(H2O)4·4H2O (3) and Co3(ppa)2(1,2-bix)2·4H2O (4) are isolated, where 3-ppapH3 represents 3-phenyl-3-((phosphonomethyl)amino)propanoic acid and ppaH3 is 2-phenyl-2-(phosphonomethylamino)acetic acid. Compounds 1-3 crystallize in the monoclinic space group P21/c and show two-dimensional structures in which the Co3(3-ppap)2 chains are bridged by 1,4-bix, 1,3-bix and 1,2-bix ligands in trans-modes, respectively. Within the chain, a racemic dimer of Co2(3-ppap)2(2-) is found, where the Co atoms are doubly bridged by O-P-O units from the (S)- and (R)-3-ppap(3-) ligands. The dimers are connected by another crystallographically independent Co atom through O-P-O linkages to form an infinite racemic chain. The packing modes of the layers in 1-3 are quite different, however, which are ABAB in the cases of 1 and 3 while ABCDABCD in the case of 2, attributed to the positional isomerism of the bix co-ligands. Compound 4 displays a chain structure in which the 1,2-bix bridges the Co atoms in cis-mode within the chain. Magnetic properties are investigated for all compounds.

  15. Structural Contraction of Zeolitic Imidazolate Frameworks: Membrane Application on Porous Metallic Hollow Fibers for Gas Separation.

    Science.gov (United States)

    Cacho-Bailo, Fernando; Etxeberría-Benavides, Miren; David, Oana; Téllez, Carlos; Coronas, Joaquín

    2017-06-21

    Positive thermal expansion coefficients (TECs) of 52 × 10 -6 and 35 × 10 -6 K -1 were experimentally calculated in the -116 to 250 °C range for the III-phases of zeolitic imidazolate frameworks (ZIF) ZIF-9(Co) and ZIF-7(Zn), respectively, by means of the unit cell dimensions and volume of the materials in the monoclinic crystal system calculated from the XRD patterns. The unit cell dimensions and volume showed a significant expansion phenomenon as the temperature increased, by as much as 5.5% for ZIF-9-III in the studied range. To exploit the advantages of such thermal behavior, a new approach to the fabrication of ZIF-9-III membranes on thin, flexible, and highly porous nickel hollow fiber (Ni HF) supports by a versatile and easy-controllable microfluidic setup is herein reported. These Ni HF supports result from the sintering of 25-μm Ni particles and display very positive mechanical properties and bending resistance. As compared to the traditional polymer-based HF membranes, the ZIF metal-supported membrane exhibited good durability and robustness throughout its operation in a wide temperature range and after heating and cooling cycles. These benefits derive from (1) the pore-plugging membrane configuration resulting from the high porosity of the support and (2) the similarity between the TECs of the ZIF and the metallic support, both positive, which enhances their mutual compatibility. An increase in the H 2 /CO 2 separation selectivity at low temperatures (as high as 22.2 at -10 °C, along with 102 GPU permeance of H 2 ) was achieved, in agreement with the structural variations observed in the ZIF material.

  16. Antitumor activity of sequence-specific alkylating agents: pyrolle-imidazole CBI conjugates with indole linker.

    Science.gov (United States)

    Shinohara, Ken-ichi; Bando, Toshikazu; Sasaki, Shunta; Sakakibara, Yogo; Minoshima, Masafumi; Sugiyama, Hiroshi

    2006-03-01

    DNA-targeting agents, including cisplatin, bleomycin and mitomycin C, are used routinely in cancer treatments. However, these drugs are extremely toxic, attacking normal cells and causing severe side effects. One important question to consider in designing anticancer agents is whether the introduction of sequence selectivity to DNA-targeting agents can improve their efficacy as anticancer agents. In the present study, the growth inhibition activities of an indole-seco 1,2,9,9a-tetrahydrocyclopropa[1,2-c]benz[1,2-e]indol-4-one (CBI) (1) and five conjugates with hairpin pyrrole-imidazole polyamides (2-6), which have different sequence specificities for DNA alkylation, were compared using 10 different cell lines. The average values of -log GI50 (50% growth inhibition concentration) for compounds 1-6 against the 10 cell lines were 8.33, 8.56, 8.29, 8.04, 8.23 and 8.83, showing that all of these compounds strongly inhibit cell growth. Interestingly, each alkylating agent caused significantly different growth inhibition patterns with each cell line. In particular, the correlation coefficients between the -log GI50 of compound 1 and its conjugates 2-6 showed extremely low values (Ralkylation lead to marked differences in biological activity. Comparison of the correlation coefficients between compounds 6 and 7, with the same sequence specificity as 6, and MS-247, with sequence specificity different from 6, when used against a panel of 37 human cancer cell lines further confirmed the above hypothesis.

  17. Artificial Enzymes, "Chemzymes"

    DEFF Research Database (Denmark)

    Bjerre, Jeannette; Rousseau, Cyril Andre Raphaël; Pedersen, Lavinia Georgeta M

    2008-01-01

    Enzymes have fascinated scientists since their discovery and, over some decades, one aim in organic chemistry has been the creation of molecules that mimic the active sites of enzymes and promote catalysis. Nevertheless, even today, there are relatively few examples of enzyme models that successf......Enzymes have fascinated scientists since their discovery and, over some decades, one aim in organic chemistry has been the creation of molecules that mimic the active sites of enzymes and promote catalysis. Nevertheless, even today, there are relatively few examples of enzyme models...... that successfully perform Michaelis-Menten catalysis under enzymatic conditions (i.e., aqueous medium, neutral pH, ambient temperature) and for those that do, very high rate accelerations are seldomly seen. This review will provide a brief summary of the recent developments in artificial enzymes, so called...... "Chemzymes", based on cyclodextrins and other molecules. Only the chemzymes that have shown enzyme-like activity that has been quantified by different methods will be mentioned. This review will summarize the work done in the field of artificial glycosidases, oxidases, epoxidases, and esterases, as well...

  18. Magnetically responsive enzyme powders

    Energy Technology Data Exchange (ETDEWEB)

    Pospiskova, Kristyna, E-mail: kristyna.pospiskova@upol.cz [Regional Centre of Advanced Technologies and Materials, Palacky University, Slechtitelu 11, 783 71 Olomouc (Czech Republic); Safarik, Ivo, E-mail: ivosaf@yahoo.com [Regional Centre of Advanced Technologies and Materials, Palacky University, Slechtitelu 11, 783 71 Olomouc (Czech Republic); Department of Nanobiotechnology, Institute of Nanobiology and Structural Biology of GCRC, Na Sadkach 7, 370 05 Ceske Budejovice (Czech Republic)

    2015-04-15

    Powdered enzymes were transformed into their insoluble magnetic derivatives retaining their catalytic activity. Enzyme powders (e.g., trypsin and lipase) were suspended in various liquid media not allowing their solubilization (e.g., saturated ammonium sulfate and highly concentrated polyethylene glycol solutions, ethanol, methanol, 2-propanol) and subsequently cross-linked with glutaraldehyde. Magnetic modification was successfully performed at low temperature in a freezer (−20 °C) using magnetic iron oxides nano- and microparticles prepared by microwave-assisted synthesis from ferrous sulfate. Magnetized cross-linked enzyme powders were stable at least for two months in water suspension without leakage of fixed magnetic particles. Operational stability of magnetically responsive enzymes during eight repeated reaction cycles was generally without loss of enzyme activity. Separation of magnetically modified cross-linked powdered enzymes from reaction mixtures was significantly simplified due to their magnetic properties. - Highlights: • Cross-linked enzyme powders were prepared in various liquid media. • Insoluble enzymes were magnetized using iron oxides particles. • Magnetic iron oxides particles were prepared by microwave-assisted synthesis. • Magnetic modification was performed under low (freezing) temperature. • Cross-linked powdered trypsin and lipase can be used repeatedly for reaction.

  19. Targeted enzyme prodrug therapies.

    Science.gov (United States)

    Schellmann, N; Deckert, P M; Bachran, D; Fuchs, H; Bachran, C

    2010-09-01

    The cure of cancer is still a formidable challenge in medical science. Long-known modalities including surgery, chemotherapy and radiotherapy are successful in a number of cases; however, invasive, metastasized and inaccessible tumors still pose an unresolved and ongoing problem. Targeted therapies designed to locate, detect and specifically kill tumor cells have been developed in the past three decades as an alternative to treat troublesome cancers. Most of these therapies are either based on antibody-dependent cellular cytotoxicity, targeted delivery of cytotoxic drugs or tumor site-specific activation of prodrugs. The latter is a two-step procedure. In the first step, a selected enzyme is accumulated in the tumor by guiding the enzyme or its gene to the neoplastic cells. In the second step, a harmless prodrug is applied and specifically converted by this enzyme into a cytotoxic drug only at the tumor site. A number of targeting systems, enzymes and prodrugs were investigated and improved since the concept was first envisioned in 1974. This review presents a concise overview on the history and latest developments in targeted therapies for cancer treatment. We cover the relevant technologies such as antibody-directed enzyme prodrug therapy (ADEPT), gene-directed enzyme prodrug therapy (GDEPT) as well as related therapies such as clostridial- (CDEPT) and polymer-directed enzyme prodrug therapy (PDEPT) with emphasis on prodrug-converting enzymes, prodrugs and drugs.

  20. Enzymes in Fermented Fish.

    Science.gov (United States)

    Giyatmi; Irianto, H E

    Fermented fish products are very popular particularly in Southeast Asian countries. These products have unique characteristics, especially in terms of aroma, flavor, and texture developing during fermentation process. Proteolytic enzymes have a main role in hydrolyzing protein into simpler compounds. Fermentation process of fish relies both on naturally occurring enzymes (in the muscle or the intestinal tract) as well as bacteria. Fermented fish products processed using the whole fish show a different characteristic compared to those prepared from headed and gutted fish. Endogenous enzymes like trypsin, chymotrypsin, elastase, and aminopeptidase are the most involved in the fermentation process. Muscle tissue enzymes like cathepsins, peptidases, transaminases, amidases, amino acid decarboxylases, glutamic dehydrogenases, and related enzymes may also play a role in fish fermentation. Due to the decreased bacterial number during fermentation, contribution of microbial enzymes to proteolysis may be expected prior to salting of fish. Commercial enzymes are supplemented during processing for specific purposes, such as quality improvement and process acceleration. In the case of fish sauce, efforts to accelerate fermentation process and to improve product quality have been studied by addition of enzymes such as papain, bromelain, trypsin, pepsin, and chymotrypsin. © 2017 Elsevier Inc. All rights reserved.

  1. Mutagenicity of 1-Ethyl-2,4,5-triphenyl-1H-imidazole and Six Derivatives in Salmonella typhimurium

    OpenAIRE

    KORKMAZ, Ferhan; Korkmaz, Ferhan; MERCANGOZ, Ayse

    2010-01-01

     Newly synthesized 1-Ethyl-2,4,5-triphenyl-1H-imidazole and its six derivatives were tested by Ames assay. In order to reveal the mutagenic activities of the compounds, two different mutant strains of Salmonella typhimurium (TA98 and TA100) were used in an Ames assay with/without S9 microsomal fraction from rat liver. It was found that the compounds have no mutagenic activities.          &nb...

  2. Bromidotetra?kis?(1H-2-ethyl-5-methyl?imidazole-?N 3)copper(II) bromide

    OpenAIRE

    Godlewska, Sylwia; Baranowska, Katarzyna; Socha, Joanna; Do??ga, Anna

    2011-01-01

    The CuII ion in the title compound, [CuBr(C6H10N2)4]Br, is coordinated in a square-based-pyramidal geometry by the N atoms of four imidazole ligands and a bromide anion in the apical site. Both the CuII and Br− atoms lie on a crystallographic fourfold axis. In the crystal, the [CuBr(C6H10N2)4]+ complex cations are linked to the uncoordinated Br− anions (site symmetry overline{4}) by N—H...Br hydrogen bonds, generating a three-dimensional network. The ethyl group ...

  3. Preparation of poly(vinyl alcohol) membranes grafted with N-vinyl imidazole/acrylic acid binary monomers

    International Nuclear Information System (INIS)

    Ajji, Zaki; Ali, Ali

    2006-01-01

    Poly(vinyl alcohol) films were grafted with two monomers using gamma radiation, acrylic acid and N-vinyl imidazole. The influence of different parameters on the grafting yield was investigated as: type of solvent and solvent composition, comonomer concentration and composition, addition of mineral acids, and irradiation dose. Water uptake in respect to the grafting yield was also evaluated. The ability of the grafted films to adsorb copper ions was elaborated and discussed for different grafting yields and ph values of the solution. (authors)

  4. Stacking Faults and Mechanical Behavior beyond the Elastic Limit of an Imidazole-Based Metal Organic Framework: ZIF-8.

    Science.gov (United States)

    Hegde, Vinay I; Tan, Jin-Chong; Waghmare, Umesh V; Cheetham, Anthony K

    2013-10-17

    We determine the nonlinear mechanical behavior of a prototypical zeolitic imidazolate framework (ZIF-8) along two modes of mechanical failure in response to tensile and shear forces using first-principles simulations. Our generalized stacking fault energy surface reveals an intrinsic stacking fault of surprisingly low energy comparable to that in copper, though the energy barrier associated with its formation is much higher. The lack of vibrational spectroscopic evidence for such faults in experiments can be explained with the structural instability of the barrier state to form a denser and disordered state of ZIF-8 seen in our analysis, that is, large shear leads to its amorphization rather than formation of faults.

  5. Sequential one-pot synthesis of imidazoles and 2H-imidazolones from β-ketoamines, acylating agents and ammonium acetate

    Energy Technology Data Exchange (ETDEWEB)

    Jalani, Hitesh B.; Venkateswararao, Edda; Manickam, Manoj; Jung, Sang Hun [College of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon (Korea, Republic of)

    2016-12-15

    An efficient, practical, straight forward, and transition metal-free three-component synthesis of diversely substituted imidazoles and 2H-imidazolones from β-ketoamines, acylating agents, and ammonium acetate has been described herein. This approach involves [3+1+1] cyclization through consecutive formation of three C–N bonds as a sequence of initial amidation of β-ketoamines with acylating agent, β-iminoketoamide formation with ammonia, and acid catalyzed concomitant cyclodehydration to afford the imidazoles and 2H-imidazolones. This methodology has advantages such as single flask operation, readily available starting materials, mild conditions, broad functional groups tolerance, and simple work-up procedure.

  6. Model Studies of the Histidine-Tyrosine Cross-Link in Cytochrome c Oxidase Reveal the Flexible Substituent Effect of the Imidazole Moiety

    Science.gov (United States)

    Pratt, Derek A.; Pesavento, Russell P.; van der Donk, Wilfred A.

    2010-01-01

    Experimental and theoretical studies were carried out to interrogate the effect of an imidazole substituent in each of the ortho, meta, and para positions on the pKa, E°, and O–H BDE of phenol. The results reveal that imidazole substitution lowers the pKa of phenol and increases the E° of phenoxide due to its σ-electron withdrawing ability (σp− = +0.21, σm− = +0.45) but decreases the O–H BDE and E° of phenol due to its σ-electron-donating ability (σp+ = −0.45). PMID:15957934

  7. Identification of halosalicylamide derivatives as a novel class of allosteric inhibitors of HCV NS5B polymerase.

    Science.gov (United States)

    Liu, Yaya; Donner, Pamela L; Pratt, John K; Jiang, Wen W; Ng, Teresa; Gracias, Vijaya; Baumeister, Steve; Wiedeman, Paul E; Traphagen, Linda; Warrior, Usha; Maring, Clarence; Kati, Warren M; Djuric, Stevan W; Molla, Akhteruzzaman

    2008-06-01

    Halosalicylamide derivatives were identified from high-throughput screening as potent inhibitors of HCV NS5B polymerase. The subsequent structure and activity relationship revealed the absolute requirement of the salicylamide moiety for optimum activity. Methylation of either the hydroxyl group or the amide group of the salicylamide moiety abolished the activity while the substitutions on both phenyl rings are acceptable. The halosalicylamide derivatives were shown to be non-competitive with respect to elongation nucleotide and demonstrated broad genotype activity against genotype 1-3 HCV NS5B polymerases. Inhibitor competition studies indicated an additive binding mode to the initiation pocket that is occupied by the thiadiazine class of compounds and an additive binding mode to the elongation pocket that is occupied by diketoacids, but a mutually exclusive binding mode with respect to the allosteric thumb pocket that is occupied by the benzimidazole class of inhibitors. Therefore, halosalicylamides represent a novel class of allosteric inhibitors of HCV NS5B polymerase.

  8. Overlapping binding site for the endogenous agonist, small-molecule agonists, and ago-allosteric modulators on the ghrelin receptor

    DEFF Research Database (Denmark)

    Holst, Birgitte; Frimurer, Thomas M; Mokrosinski, Jacek

    2008-01-01

    A library of robust ghrelin receptor mutants with single substitutions at 22 positions in the main ligand-binding pocket was employed to map binding sites for six different agonists: two peptides (the 28-amino-acid octanoylated endogenous ligand ghrelin and the hexapeptide growth hormone......, and PheVI:23 on the opposing face of transmembrane domain (TM) VI. Each of the agonists was also affected selectively by specific mutations. The mutational map of the ability of L-692,429 and GHRP-6 to act as allosteric modulators by increasing ghrelin's maximal efficacy overlapped with the common....... It is concluded that although each of the ligands in addition exploits other parts of the receptor, a large, common binding site for both small-molecule agonists--including ago-allosteric modulators--and the endogenous agonist is found on the opposing faces of TM-III and -VI of the ghrelin receptor....

  9. A novel strategy for selection of allosteric ribozymes yields RiboReporter™ sensors for caffeine and aspartame

    Science.gov (United States)

    Ferguson, Alicia; Boomer, Ryan M.; Kurz, Markus; Keene, Sara C.; Diener, John L.; Keefe, Anthony D.; Wilson, Charles; Cload, Sharon T.

    2004-01-01

    We have utilized in vitro selection technology to develop allosteric ribozyme sensors that are specific for the small molecule analytes caffeine or aspartame. Caffeine- or aspartame-responsive ribozymes were converted into fluorescence-based RiboReporter™ sensor systems that were able to detect caffeine or aspartame in solution over a concentration range from 0.5 to 5 mM. With read-times as short as 5 min, these caffeine- or aspartame-dependent ribozymes function as highly specific and facile molecular sensors. Interestingly, successful isolation of allosteric ribozymes for the analytes described here was enabled by a novel selection strategy that incorporated elements of both modular design and activity-based selection methods typically used for generation of catalytic nucleic acids. PMID:15026535

  10. A New Negative Allosteric Modulator AP14145 for the Study of Small Conductance Calcium-Activated Potassium Channels

    DEFF Research Database (Denmark)

    Simo Vicens, Rafel; Kirchhoff, Jeppe Egedal; Dolce, Bernardo

    2017-01-01

    ) prolongation in anaesthetised rats and a beam walk test was performed in mice to determine acute CNS related effects of the drug. Key results: AP14145 was found to be an equipotent negative allosteric modulator of KCa2.2 and KCa2.3 channels (IC50 = 1.1 ± 0.3 μM L-1). The presence of AP14145 (10 μM L-1...

  11. Screening and identification of potential PTP1B allosteric inhibitors using in silico and in vitro approaches.

    Science.gov (United States)

    Shinde, Ranajit Nivrutti; Kumar, G Siva; Eqbal, Shahbaz; Sobhia, M Elizabeth

    2018-01-01

    Protein tyrosine phosphatase 1B (PTP1B) is a validated therapeutic target for Type 2 diabetes due to its specific role as a negative regulator of insulin signaling pathways. Discovery of active site directed PTP1B inhibitors is very challenging due to highly conserved nature of the active site and multiple charge requirements of the ligands, which makes them non-selective and non-permeable. Identification of the PTP1B allosteric site has opened up new avenues for discovering potent and selective ligands for therapeutic intervention. Interactions made by potent allosteric inhibitor in the presence of PTP1B were studied using Molecular Dynamics (MD). Computationally optimized models were used to build separate pharmacophore models of PTP1B and TCPTP, respectively. Based on the nature of interactions the target residues offered, a receptor based pharmacophore was developed. The pharmacophore considering conformational flexibility of the residues was used for the development of pharmacophore hypothesis to identify potentially active inhibitors by screening large compound databases. Two pharmacophore were successively used in the virtual screening protocol to identify potential selective and permeable inhibitors of PTP1B. Allosteric inhibition mechanism of these molecules was established using molecular docking and MD methods. The geometrical criteria values confirmed their ability to stabilize PTP1B in an open conformation. 23 molecules that were identified as potential inhibitors were screened for PTP1B inhibitory activity. After screening, 10 molecules which have good permeability values were identified as potential inhibitors of PTP1B. This study confirms that selective and permeable inhibitors can be identified by targeting allosteric site of PTP1B.

  12. Determinants of positive cooperativity between strychnine-like allosteric modulators and N-methylscopolamine at muscarinic receptors

    Czech Academy of Sciences Publication Activity Database

    Jakubík, Jan; Doležal, Vladimír

    2006-01-01

    Roč. 30, č. 1-2 (2006), s. 111-112 ISSN 0895-8696 R&D Projects: GA ČR(CZ) GA305/05/0452; GA MŠk(CZ) LC554 Institutional research plan: CEZ:AV0Z50110509 Keywords : muscarinic receptors * strychnine -like allosteric modulators * cooperativity Subject RIV: ED - Physiology Impact factor: 2.965, year: 2006

  13. [Pharmacological characteristics of drugs targeted on calcium-sensing receptor.-properties of cinacalcet hydrochloride as allosteric modulator].

    Science.gov (United States)

    Nagano, Nobuo; Tsutsui, Takaaki

    2016-06-01

    Calcimimetics act as positive allosteric modulators of the calcium-sensing receptor (CaSR), thereby decreasing parathyroid hormone (PTH) secretion from the parathyroid glands. On the other hand, negative allosteric modulators of the CaSR with stimulatory effect on PTH secretion are termed calcilytics. The calcimimetic cinacalcet hydrochloride (cinacalcet) is the world's first allosteric modulator of G protein-coupled receptor to enter the clinical market. Cinacalcet just tunes the physiological effects of Ca(2+), an endogenous ligand, therefore, shows high selectivity and low side effects. Calcimimetics also increase cell surface CaSR expression by acting as pharmacological chaperones (pharmacoperones). It is considered that the cinacalcet-induced upper gastrointestinal problems are resulted from enhanced physiological responses to Ca(2+) and amino acids via increased sensitivity of digestive tract CaSR by cinacalcet. While clinical developments of calcilytics for osteoporosis were unfortunately halted or terminated due to paucity of efficacy, it is expected that calcilytics may be useful for the treatment of patients with activating CaSR mutations, asthma, and idiopathic pulmonary artery hypertension.

  14. Allosteric interactions between agonists and antagonists within the adenosine A2A receptor-dopamine D2 receptor heterotetramer.

    Science.gov (United States)

    Bonaventura, Jordi; Navarro, Gemma; Casadó-Anguera, Verònica; Azdad, Karima; Rea, William; Moreno, Estefanía; Brugarolas, Marc; Mallol, Josefa; Canela, Enric I; Lluís, Carme; Cortés, Antoni; Volkow, Nora D; Schiffmann, Serge N; Ferré, Sergi; Casadó, Vicent

    2015-07-07

    Adenosine A2A receptor (A2AR)-dopamine D2 receptor (D2R) heteromers are key modulators of striatal neuronal function. It has been suggested that the psychostimulant effects of caffeine depend on its ability to block an allosteric modulation within the A2AR-D2R heteromer, by which adenosine decreases the affinity and intrinsic efficacy of dopamine at the D2R. We describe novel unsuspected allosteric mechanisms within the heteromer by which not only A2AR agonists, but also A2AR antagonists, decrease the affinity and intrinsic efficacy of D2R agonists and the affinity of D2R antagonists. Strikingly, these allosteric modulations disappear on agonist and antagonist coadministration. This can be explained by a model that considers A2AR-D2R heteromers as heterotetramers, constituted by A2AR and D2R homodimers, as demonstrated by experiments with bioluminescence resonance energy transfer and bimolecular fluorescence and bioluminescence complementation. As predicted by the model, high concentrations of A2AR antagonists behaved as A2AR agonists and decreased D2R function in the brain.

  15. Reversible uptake of molecular oxygen by heteroligand Co(II)-L-α-amino acid-imidazole systems: equilibrium models at full mass balance.

    Science.gov (United States)

    Pająk, Marek; Woźniczka, Magdalena; Vogt, Andrzej; Kufelnicki, Aleksander

    2017-09-19

    The paper examines Co(II)-amino acid-imidazole systems (where amino acid = L-α-amino acid: alanine, asparagine, histidine) which, when in aqueous solutions, activate and reversibly take up dioxygen, while maintaining the structural scheme of the heme group (imidazole as axial ligand and O 2 uptake at the sixth, trans position) thus imitating natural respiratory pigments such as myoglobin and hemoglobin. The oxygenated reaction shows higher reversibility than for Co(II)-amac systems with analogous amino acids without imidazole. Unlike previous investigations of the heteroligand Co(II)-amino acid-imidazole systems, the present study accurately calculates all equilibrium forms present in solution and determines the [Formula: see text]equilibrium constants without using any simplified approximations. The equilibrium concentrations of Co(II), amino acid, imidazole and the formed complex species were calculated using constant data obtained for analogous systems under oxygen-free conditions. Pehametric and volumetric (oxygenation) studies allowed the stoichiometry of O 2 uptake reaction and coordination mode of the central ion in the forming oxygen adduct to be determined. The values of dioxygen uptake equilibrium constants [Formula: see text] were evaluated by applying the full mass balance equations. Investigations of oxygenation of the Co(II)-amino acid-imidazole systems indicated that dioxygen uptake proceeds along with a rise in pH to 9-10. The percentage of reversibility noted after acidification of the solution to the initial pH ranged within ca 30-60% for alanine, 40-70% for asparagine and 50-90% for histidine, with a rising tendency along with the increasing share of amino acid in the Co(II): amino acid: imidazole ratio. Calculations of the share of the free Co(II) ion as well as of the particular complex species existing in solution beside the oxygen adduct (regarding dioxygen bound both reversibly and irreversibly) indicated quite significant values for the

  16. Binding of the sphingolipid S1P to hTERT stabilizes telomerase at the nuclear periphery by allosterically mimicking protein phosphorylation†

    Science.gov (United States)

    Selvam, Shanmugam P.; De Palma, Ryan M.; Oaks, Joshua J.; Oleinik, Natalia; Peterson, Yuri K.; Stahelin, Robert V.; Skordalakes, Emmanuel; Ponnusamy, Suriyan; Garrett-Mayer, Elizabeth; Smith, Charles D.; Ogretmen, Besim

    2015-01-01

    During DNA replication, the enzyme telomerase maintains the ends of chromosomes, called telomeres. Shortened telomeres trigger cell senescence, and cancer cells often have increased telomerase activity to promote their ability to proliferate indefinitely. The catalytic subunit, human telomerase reverse transcriptase (hTERT), is stabilized by phosphorylation. Here, we found that the lysophospholipid sphingosine 1-phosphate (S1P), generated by sphingosine kinase 2 (SK2), bound hTERT at the nuclear periphery in human and mouse fibroblasts. Docking predictions and mutational analyses revealed that binding occurred between a hydroxyl group (C′3-OH) in S1P and Asp684 in hTERT. Inhibiting or depleting SK2 or mutating the S1P binding site decreased the stability of hTERT in cultured cells and promoted senescence and loss of telomere integrity. S1P binding inhibited the interaction of hTERT with MKRN1, an E3 ubiquitin ligase that tags hTERT for degradation. Murine Lewis lung carcinoma (LLC) cells formed smaller tumors in mice lacking SK2 than in wild-type mice, and knocking down SK2 in LLC cells before implantation into mice suppressed their growth. Pharmacologically inhibiting SK2 decreased the growth of subcutaneous A549 lung cancer cell-derived xenografts in mice, and expression of wild-type hTERT, but not an S1P-binding mutant, restored tumor growth. Thus, our data suggest that S1P binding to hTERT allosterically mimicks phosphorylation, promoting telomerase stability and hence telomere maintenance, cell proliferation, and tumor growth PMID:26082434

  17. Dimerization-Induced Allosteric Changes of the Oxyanion-Hole Loop Activate the Pseudorabies Virus Assemblin pUL26N, a Herpesvirus Serine Protease.

    Directory of Open Access Journals (Sweden)

    Martin Zühlsdorf

    2015-07-01

    Full Text Available Herpesviruses encode a characteristic serine protease with a unique fold and an active site that comprises the unusual triad Ser-His-His. The protease is essential for viral replication and as such constitutes a promising drug target. In solution, a dynamic equilibrium exists between an inactive monomeric and an active dimeric form of the enzyme, which is believed to play a key regulatory role in the orchestration of proteolysis and capsid assembly. Currently available crystal structures of herpesvirus proteases correspond either to the dimeric state or to complexes with peptide mimetics that alter the dimerization interface. In contrast, the structure of the native monomeric state has remained elusive. Here, we present the three-dimensional structures of native monomeric, active dimeric, and diisopropyl fluorophosphate-inhibited dimeric protease derived from pseudorabies virus, an alphaherpesvirus of swine. These structures, solved by X-ray crystallography to respective resolutions of 2.05, 2.10 and 2.03 Å, allow a direct comparison of the main conformational states of the protease. In the dimeric form, a functional oxyanion hole is formed by a loop of 10 amino-acid residues encompassing two consecutive arginine residues (Arg136 and Arg137; both are strictly conserved throughout the herpesviruses. In the monomeric form, the top of the loop is shifted by approximately 11 Å, resulting in a complete disruption of the oxyanion hole and loss of activity. The dimerization-induced allosteric changes described here form the physical basis for the concentration-dependent activation of the protease, which is essential for proper virus replication. Small-angle X-ray scattering experiments confirmed a concentration-dependent equilibrium of monomeric and dimeric protease in solution.

  18. Synthesis of Iron Doped Zeolite Imidazolate Framework-8 and Its Remazol Deep Black RGB Dye Adsorption Ability

    Directory of Open Access Journals (Sweden)

    Mai Thi Thanh

    2017-01-01

    Full Text Available Zeolite imidazole framework-8 (ZIF-8 and the iron doped ZIF-8 (Fe-ZIF-8 were synthesized by the hydrothermal process. The obtained materials were characteristic of X-ray diffraction (XRD, X-ray photoelectron spectroscopy (XPS, scanning electron microscope (SEM, nitrogen adsorption/desorption isotherms, and atomic absorption spectroscopy (AAS. The results showed that the obtained Fe-ZIF-8 possessed the ZIF-8 structure with a large specific area. ZIF-8 and Fe-ZIF-8 were used for the removal of Remazol Deep Black (RDB RGB dye from aqueous solutions. The various factors affecting adsorption such as pH, initial concentration, contact time, and temperature were investigated. The results showed that the introduction of iron into ZIF-8 provided a much larger adsorption capacity and faster adsorption kinetics than ZIF-8 without iron. The electrostatic interaction and π-π interaction between the aromatic rings of the RDB dye and the aromatic imidazolate rings of the adsorbent were responsible for the RDB adsorption. Moreover, the coordination of the nitrogen atoms and oxygen in carboxyl group in RDB molecules with the Fe2+ ions in the ZIF-8 framework played a vital role for the effective removal of RDB from aqueous solution.

  19. A study of the vaporization enthalpies of some 1-substituted imidazoles and pyrazoles by correlation-gas chromatography.

    Science.gov (United States)

    Lipkind, Dmitry; Plienrasri, Chatchawat; Chickos, James S

    2010-12-23

    The vaporization enthalpies of 1-methyl-, 1-ethyl-, 1-phenyl-, and 1-benzylimidazole, 1-methyl- and 1-phenylpyrazole, and trans-azobenzene are evaluated by correlation-gas chromatography (C-GC) using a variety of azines and diazines as standards. The vaporization enthalpies obtained by C-GC when compared to literature values are approximately 14 kJ·mol(-1) smaller for the imidazoles and 6 kJ·mol(-1) smaller for the pyrazoles. The literature vaporization enthalpies of 1-methylpyrrole and 1-methylindole, two closely related compounds with one less nitrogen, are reproduced by C-GC. These results suggest that the magnitude of the intermolecular interactions present in 1-substituted imidazoles and pyrazoles are significantly larger than the those present in the reference compounds and greater than or equal in magnitude to the enhanced intermolecular interactions observed previously in aromatic 1,2-diazines. The vaporization enthalpy and vapor pressure of a trans-1,2-diazine, trans-azobenzene, measured by C-GC using similar standards reproduced the literature values within experimental error.

  20. Luminescent pH sensor of a novel imidazole-containing hexanuclear Ru(II) polypyridyl complex

    Science.gov (United States)

    Cheng, Feixiang; Tang, Ning; Chen, Jishu; Chen, Guang

    2013-10-01

    Hexapodal ligand H6L containing imidazole rings has been prepared by the reaction of 1,10-phenanthroline-5,6-dione with 1,2,3,4,5,6-hexakis[(3-formylphenoxy)methyl]benzene. The Ru(II) polypyridyl complex [{Ru(bpy)2}6(μ6-H6L)](PF6)12 (bpy = 2,2'-bipyridine) has been synthesized by the reaction of Ru(bpy)2Cl2·2H2O with ligand H6L. The pH effects on the UV-vis absorption and emission spectra of the complex have been studied. The ground- and excited-state ionization constants of the acid-base equilibria have been calculated according to the absorbance and emission data. The complex acts as an off-on-off luminescent pH sensor through two successive deprotonation processes of imidazole rings, with a maximum on-off ratio of 5 in buffer solution.

  1. Faradaic impedance titration and control of electron transfer of 1-(12-mercaptododecyl)imidazole monolayer on a gold electrode

    International Nuclear Information System (INIS)

    Hwang, Seongpil; Lee, Bang Sook; Chi, Young Shik; Kwak, Juhyoun; Choi, Insung S.; Lee, Sang-gi

    2008-01-01

    In this work, we studied interfacial proton transfer of the self-assembled monolayer (SAM) of 1-(12-mercaptododecyl)imidazole on a gold electrode by faradaic impedance titration method with Fe(CN) 6 3- as an anionic redox probe molecule. The surface pK 1/2 was found to be 7.3, which was nearly the same as that of 1-alkylimidazole in solution. We also investigated the electrochemical properties of the SAM-modified electrode by cyclic voltammetry. Cyclic voltammetry was performed (1) in the solution containing Fe(CN) 6 3- with repeated alternation of pH values to investigate the electrostatic interaction of the protonated or deprotonated imidazole with Fe(CN) 6 3- and (2) in the acidic or basic electrolyte containing Ru(NH 3 ) 6 3+ as a cationic redox probe to verify the effect of the polarity of a redox probe. We observed the reversible adsorption/desorption of Fe(CN) 6 3- and concluded that the adsorbed Fe(CN) 6 3- catalyzed the electron transfer of both Fe(CN) 6 3- itself and cationic Ru(NH 3 ) 6 3+

  2. Positive allosteric modulation of TRPV1 as a novel analgesic mechanism

    Directory of Open Access Journals (Sweden)

    Lebovitz Evan E

    2012-09-01

    Full Text Available Abstract Background The prevalence of long-term opiate use in treating chronic non-cancer pain is increasing, and prescription opioid abuse and dependence are a major public health concern. To explore alternatives to opioid-based analgesia, the present study investigates a novel allosteric pharmacological approach operating through the cation channel TRPV1. This channel is highly expressed in subpopulations of primary afferent unmyelinated C- and lightly-myelinated Aδ-fibers that detect low and high rates of noxious heating, respectively, and it is also activated by vanilloid agonists and low pH. Sufficient doses of exogenous vanilloid agonists, such as capsaicin or resiniferatoxin, can inactivate/deactivate primary afferent endings due to calcium overload, and we hypothesized that positive allosteric modulation of agonist-activated TRPV1 could produce a selective, temporary inactivation of nociceptive nerve terminals in vivo. We previously identified MRS1477, a 1,4-dihydropyridine that potentiates vanilloid and pH activation of TRPV1 in vitro, but displays no detectable intrinsic agonist activity of its own. To study the in vivo effects of MRS1477, we injected the hind paws of rats with a non-deactivating dose of capsaicin, MRS1477, or the combination. An infrared diode laser was used to stimulate TRPV1-expressing nerve terminals and the latency and intensity of paw withdrawal responses were recorded. qRT-PCR and immunohistochemistry were performed on dorsal root ganglia to examine changes in gene expression and the cellular specificity of such changes following treatment. Results Withdrawal responses of the capsaicin-only or MRS1477-only treated paws were not significantly different from the untreated, contralateral paws. However, rats treated with the combination of capsaicin and MRS1477 exhibited increased withdrawal latency and decreased response intensity consistent with agonist potentiation and inactivation or lesion of TRPV1-containing

  3. Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL Kinase Function.

    Directory of Open Access Journals (Sweden)

    Prerna Grover

    Full Text Available The ABL protein-tyrosine kinase regulates intracellular signaling pathways controlling diverse cellular processes and contributes to several forms of cancer. The kinase activity of ABL is repressed by intramolecular interactions involving its regulatory Ncap, SH3 and SH2 domains. Small molecules that allosterically regulate ABL kinase activity through its non-catalytic domains may represent selective probes of ABL function. Here we report a screening assay for chemical modulators of ABL kinase activity that target the regulatory interaction of the SH3 domain with the SH2-kinase linker. This fluorescence polarization (FP assay is based on a purified recombinant ABL protein consisting of the N-cap, SH3 and SH2 domains plus the SH2-kinase linker (N32L protein and a short fluorescein-labeled probe peptide that binds to the SH3 domain. In assay development experiments, we found that the probe peptide binds to the recombinant ABL N32L protein in vitro, producing a robust FP signal that can be competed with an excess of unlabeled peptide. The FP signal is not observed with control N32L proteins bearing either an inactivating mutation in the SH3 domain or enhanced SH3:linker interaction. A pilot screen of 1200 FDA-approved drugs identified four compounds that specifically reduced the FP signal by at least three standard deviations from the untreated controls. Secondary assays showed that one of these hit compounds, the antithrombotic drug dipyridamole, enhances ABL kinase activity in vitro to a greater extent than the previously described ABL agonist, DPH. Docking studies predicted that this compound binds to a pocket formed at the interface of the SH3 domain and the linker, suggesting that it activates ABL by disrupting this regulatory interaction. These results show that screening assays based on the non-catalytic domains of ABL can identify allosteric small molecule regulators of kinase function, providing a new approach to selective drug discovery

  4. Enzymic lactose hydrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Miller, J J; Brand, J C

    1980-01-01

    Acid or enzymic hydrolysis can be used to hydrolyze lactose. Advantages of both are compared and details of enzymic hydrolysis using yeast or fungal enzymes given. The new scheme outlined involves recycling lactase. Because lactose and lactase react to ultrafiltration (UF) membranes differently separation is possible. Milk or milk products are ultrafiltered to separate a concentrate from a lactose-rich permeate which is treated with lactase in a reactor until hydrolysis reaches a required level. The lactase can be removed by UF as it does not permeate the membrane, and it is recycled back to the reactor. Permeate from the second UF stage may or may not be recombined with the concentrate from the first stage to produce a low lactose product (analysis of a typical low-lactose dried whole milk is given). Batch or continuous processes are explained and a batch process without enzyme recovery is discussed. (Refs. 4).

  5. Indicators: Sediment Enzymes

    Science.gov (United States)

    Sediment enzymes are proteins that are produced by microorganisms living in the sediment or soil. They are indicators of key ecosystem processes and can help determine which nutrients are affecting the biological community of a waterbody.

  6. Enzyme Vs. Extremozyme -32 ...

    Indian Academy of Sciences (India)

    Enzymes are biocatalytic protein molecules that enhance the rates of ... to physical forces (hydrogen bonds, hydrophobic 1, electrostatic and Van der ... conformation. In 1995 ... surface against 14.7% in Klenow poll (some of the hydrophobic.

  7. Overproduction of ligninolytic enzymes

    Science.gov (United States)

    Elisashvili, Vladimir; Kachlishvili, Eva; Torok, Tamas

    2014-06-17

    Methods, compositions, and systems for overproducing ligninolytic enzymes from the basidiomycetous fungus are described herein. As described, the method can include incubating a fungal strain of Cerrena unicolor IBB 303 in a fermentation system having growth medium which includes lignocellulosic material and then cultivating the fungal strain in the fermentation system under conditions wherein the fungus expresses the ligninolytic enzymes. In some cases, the lignocellulosic material is mandarin peel, ethanol production residue, walnut pericarp, wheat bran, wheat straw, or banana peel.

  8. Zeolitic imidazolate framework-coated acoustic sensors for room temperature detection of carbon dioxide and methane.

    Science.gov (United States)

    Devkota, Jagannath; Kim, Ki-Joong; Ohodnicki, Paul R; Culp, Jeffrey T; Greve, David W; Lekse, Jonathan W

    2018-05-03

    The integration of nanoporous materials such as metal organic frameworks (MOFs) with sensitive transducers can result in robust sensing platforms for monitoring gases and chemical vapors for a range of applications. Here, we report on an integration of the zeolitic imidazolate framework - 8 (ZIF-8) MOF with surface acoustic wave (SAW) and thickness shear mode quartz crystal microbalance (QCM) devices to monitor carbon dioxide (CO2) and methane (CH4) under ambient conditions. The MOF was directly coated on the Y-Z LiNbO3 SAW delay lines (operating frequency, f0 = 436 MHz) and AT-cut quartz TSM resonators (resonant frequency, f0 = 9 MHz) and the devices were tested for various gases in N2 under ambient conditions. The devices were able to detect the changes in CO2 or CH4 concentrations with relatively higher sensitivity to CO2, which was due to its higher adsorption potential and heavier molecular weight. The sensors showed full reversibility and repeatability which were attributed to the physisorption of the gases into the MOF and high stability of the devices. Both types of sensors showed linear responses relative to changes in the binary gas compositions thereby allowing to construct calibration curves which correlated well with the expected mass changes in the sorbent layer based on mixed-gas gravimetric adsorption isotherms measured on bulk samples. For 200 nm thick films, the SAW sensitivities to CO2 and CH4 were 1.44 × 10-6/vol% and 8 × 10-8/vol%, respectively, against the QCM sensitivities 0.24 × 10-6/vol% and 1 × 10-8/vol%, respectively, which were evaluated as the fractional change in the signal. The SAW sensors were also evaluated for 100 nm-300 nm thick films, the sensitivities of which were found to increase with the thickness due to the increased number of pores for the adsorption of a larger amount of gases. In addition, the MOF-coated SAW delay lines had a good response in wireless mode, demonstrating their potential to operate remotely for the

  9. Poly(hydroxyethyl methacrylate) nanobeads containing imidazole groups for removal of Cu(II) ions

    Energy Technology Data Exchange (ETDEWEB)

    Tuerkmen, Deniz; Yilmaz, Erkut [Department of Chemistry, Hacettepe University, Ankara (Turkey); Oztuerk, Nevra; Akgoel, Sinan [Department of Chemistry, Adnan Menderes University, Aydin (Turkey); Denizli, Adil, E-mail: denizli@hacettepe.edu.tr [Department of Chemistry, Hacettepe University, Ankara (Turkey)

    2009-08-01

    Poly(hydroxyethyl methacrylate) (PHEMA) nanobeads with an average size of 300 nm in diameter and with a polydispersity index of 1.156 were produced by a surfactant free emulsion polymerization. Specific surface area of the PHEMA nanobeads was found to be 996 m{sup 2}/g. Imidazole containing 3-(2-imidazoline-1-yl)propyl(triethoxysilane) (IMEO) was used as a metal-chelating ligand. IMEO was covalently attached to the nanobeads. PHEMA-IMEO nanobeads were used for the removal of copper(II) ions from aqueous solutions. To evaluate the degree of IMEO loading, the PHEMA nanobeads were subjected to Si analysis by using flame atomizer atomic absorption spectrometer and it was estimated as 973 {mu}mol IMEO/g of polymer. The PHEMA nanobeads were characterized by transmission electron microscopy and fourier transform infrared spectroscopy. Adsorption equilibrium was achieved in about 8 min. The adsorption of Cu{sup 2+} ions onto the PHEMA nanobeads was negligible (0.2 mg/g). The IMEO attachment into the PHEMA nanobeads significantly increased the Cu{sup 2+} adsorption capacity (58 mg/g). Adsorption capacity of the PHEMA-IMEO nanobeads increased significantly with increasing concentration. The adsorption of Cu{sup 2+} ions increased with increasing pH and reached a plateau value at around pH 5.0. Competitive heavy metal adsorption from aqueous solutions containing Cu{sup +}, Cd{sup 2+}, Pb{sup 2+} and Hg{sup 2+} was also investigated. The adsorption capacities are 61.4 mg/g (966.9 {mu}mol/g) for Cu{sup 2+}; 180.5 mg/g (899.8 {mu}mol/g) for Hg{sup 2+}; 34.9 mg/g (310.5 {mu}mol/g) for Cd{sup 2+} and 14.3 mg/g (69 {mu}mol/g) for Pb{sup 2+}. The affinity order in molar basis is observed as Cu{sup 2+} > Hg{sup 2+} > Cd{sup 2+} > Pb{sup 2+}. These results may be considered as an indication of higher specificity of the PHEMA-IMEO nanobeads for the Cu{sup 2+} comparing to other ions. Consecutive adsorption and elution operations showed the feasibility of repeated use for PHEMA

  10. Rapid, convenient method for screening imidazole-containing compounds for heme oxygenase inhibition.

    Science.gov (United States)

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

    2011-01-01

    Sensitive assays for measuring heme oxygenase activity have been based on the gas-chromatographic detection of carbon monoxide using elaborate, expensive equipment. The present study describes a rapid and convenient method for screening imidazole-containing candidates for inhibitory activity against heme oxygenase using a plate reader, based on the spectroscopic evaluation of heme degradation. A PowerWave XS plate reader was used to monitor the absorbance (as a function of time) of heme bound to purified truncated human heme oxygenase-1 (hHO-1) in the individual wells of a standard 96-well plate (with or without the addition of a test compound). The degradation of heme by heme oxygenase-1 was initiated using l-ascorbic acid, and the collected relevant absorbance data were analyzed by three different methods to calculate the percent control activity occurring in wells containing test compounds relative to that occurring in control wells with no test compound present. In the cases of wells containing inhibitory compounds, significant shifts in λ(max) from 404 to near 412 nm were observed as well as a decrease in the rate of heme degradation relative to that of the control. Each of the three methods of data processing (overall percent drop in absorbance over 1.5h, initial rate of reaction determined over the first 5 min, and estimated pseudo first-order reaction rate constant determined over 1.5h) gave similar and reproducible results for percent control activity. The fastest and easiest method of data analysis was determined to be that using initial rates, involving data acquisition for only 5 min once reactions have been initiated using l-ascorbic acid. The results of the study demonstrate that this simple assay based on the spectroscopic detection of heme represents a rapid, convenient method to determine the relative inhibitory activity of candidate compounds, and is useful in quickly screening a series or library of compounds for heme oxygenase inhibition

  11. Heterogeneous photochemistry of imidazole-2-carboxaldehyde: HO2 radical formation and aerosol growth

    Directory of Open Access Journals (Sweden)

    L. González Palacios

    2016-09-01

    Full Text Available The multiphase chemistry of glyoxal is a source of secondary organic aerosol (SOA, including its light-absorbing product imidazole-2-carboxaldehyde (IC. IC is a photosensitizer that can contribute to additional aerosol ageing and growth when its excited triplet state oxidizes hydrocarbons (reactive uptake via H-transfer chemistry. We have conducted a series of photochemical coated-wall flow tube (CWFT experiments using films of IC and citric acid (CA, an organic proxy and H donor in the condensed phase. The formation rate of gas-phase HO2 radicals (PHO2 was measured indirectly by converting gas-phase NO into NO2. We report on experiments that relied on measurements of NO2 formation, NO loss and HONO formation. PHO2 was found to be a linear function of (1 the [IC]  ×  [CA] concentration product and (2 the photon actinic flux. Additionally, (3 a more complex function of relative humidity (25 %  <  RH  <  63 % and of (4 the O2 ∕ N2 ratio (15 %  <  O2 ∕ N2  <  56 % was observed, most likely indicating competing effects of dilution, HO2 mobility and losses in the film. The maximum PHO2 was observed at 25–55 % RH and at ambient O2 ∕ N2. The HO2 radicals form in the condensed phase when excited IC triplet states are reduced by H transfer from a donor, CA in our system, and subsequently react with O2 to regenerate IC, leading to a catalytic cycle. OH does not appear to be formed as a primary product but is produced from the reaction of NO with HO2 in the gas phase. Further, seed aerosols containing IC and ammonium sulfate were exposed to gas-phase limonene and NOx in aerosol flow tube experiments, confirming significant PHO2 from aerosol surfaces. Our results indicate a potentially relevant contribution of triplet state photochemistry for gas-phase HO2 production, aerosol growth and ageing in the atmosphere.

  12. Measurement of enzyme activity.

    Science.gov (United States)

    Harris, T K; Keshwani, M M

    2009-01-01

    To study and understand the nature of living cells, scientists have continually employed traditional biochemical techniques aimed to fractionate and characterize a designated network of macromolecular components required to carry out a particular cellular function. At the most rudimentary level, cellular functions ultimately entail rapid chemical transformations that otherwise would not occur in the physiological environment of the cell. The term enzyme is used to singularly designate a macromolecular gene product that specifically and greatly enhances the rate of a chemical transformation. Purification and characterization of individual and collective groups of enzymes has been and will remain essential toward advancement of the molecular biological sciences; and developing and utilizing enzyme reaction assays is central to this mission. First, basic kinetic principles are described for understanding chemical reaction rates and the catalytic effects of enzymes on such rates. Then, a number of methods are described for measuring enzyme-catalyzed reaction rates, which mainly differ with regard to techniques used to detect and quantify concentration changes of given reactants or products. Finally, short commentary is given toward formulation of reaction mixtures used to measure enzyme activity. Whereas a comprehensive treatment of enzymatic reaction assays is not within the scope of this chapter, the very core principles that are presented should enable new researchers to better understand the logic and utility of any given enzymatic assay that becomes of interest.

  13. Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery

    Directory of Open Access Journals (Sweden)

    Daura Xavier

    2010-03-01

    Full Text Available Abstract Background With the classical, active-site oriented drug-development approach reaching its limits, protein ligand-binding sites in general and allosteric sites in particular are increasingly attracting the interest of medicinal chemists in the search for new types of targets and strategies to drug development. Given that allostery represents one of the most common and powerful means to regulate protein function, the traditional drug discovery approach of targeting active sites can be extended by targeting allosteric or regulatory protein pockets that may allow the discovery of not only novel drug-like inhibitors, but activators as well. The wealth of available protein structural data can be exploited to further increase our understanding of allosterism, which in turn may have therapeutic applications. A first step in this direction is to identify and characterize putative effector sites that may be present in already available structural data. Results We performed a large-scale study of protein cavities as potential allosteric and functional sites, by integrating publicly available information on protein sequences, structures and active sites for more than a thousand protein families. By identifying common pockets across different structures of the same protein family we developed a method to measure the pocket's structural conservation. The method was first parameterized using known active sites. We characterized the predicted pockets in terms of sequence and structural conservation, backbone flexibility and electrostatic potential. Although these different measures do not tend to correlate, their combination is useful in selecting functional and regulatory sites, as a detailed analysis of a handful of protein families shows. We finally estimated the numbers of potential allosteric or regulatory pockets that may be present in the data set, finding that pockets with putative functional and effector characteristics are widespread across

  14. Biology-oriented drug synthesis (BIODS) of 2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl aryl ether derivatives, in vitro α-amylase inhibitory activity and in silico studies.

    Science.gov (United States)

    Taha, Muhammad; Imran, Syahrul; Ismail, Nor Hadiani; Selvaraj, Manikandan; Rahim, Fazal; Chigurupati, Sridevi; Ullah, Hayat; Khan, Fahad; Salar, Uzma; Javid, Muhammad Tariq; Vijayabalan, Shantini; Zaman, Khalid; Khan, Khalid Mohammed

    2017-10-01

    A new library of 2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl aryl ether derivatives (1-23) were synthesized and characterized by EI-MS and 1 H NMR, and screened for their α-amylase inhibitory activity. Out of twenty-three derivatives, two molecules 19 (IC 50 =0.38±0.82µM) and 23 (IC 50 =1.66±0.14µM), showed excellent activity whereas the remaining compounds, except 10 and 17, showed good to moderate inhibition in the range of IC 50 =1.77-2.98µM when compared with the standard acarbose (IC 50 =1.66±0.1µM). A plausible structure-activity relationship has also been presented. In addition, in silico studies was carried out in order to rationalize the binding interaction of compounds with the active site of enzyme. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Yeast allosteric chorismate mutase is locked in the activated state by a single amino acid substitution

    International Nuclear Information System (INIS)

    Schmidheini, T.; Moesch, H.U.; Braus, G.; Evans, J.N.S.

    1990-01-01

    Chorismate mutase, a branch-point enzyme in the aromatic amino acid pathway of Saccharomyces cerevisiae, and also a mutant chorismate mutase with a single amino acid substitution in the C-terminal part of the protein have been purified approximately 20-fold and 64-fold from overproducing strains, respectively. The wild-type enzyme is activated by tryptophan and subject to feedback inhibition by tyrosine, whereas the mutant enzyme does not respond to activation by tryptophan nor inhibition by tyrosine. Both enzymes are dimers consisting of two identical subunits of M r 30,000, each one capable of binding one substrate and one activator molecule. Each subunit of the wild-type enzyme also binds one inhibitor molecule, whereas the mutant enzyme lost this ability. The enzyme reaction was observed by 1 H NMR and shows a direct and irreversible conversion of chorismate to prephenate without the accumulation of any enzyme-free intermediates. The kinetic data of the wild-type chorismate mutase show positive cooperativity toward the substrate with a Hill coefficient of 1.71 and a [S] 0.5 value of 4.0 mM. In the presence of the activator tryptophan, the cooperativity is lost. The enzyme has an [S] 0.5 value of 1.2 mM in the presence of 10 μM tryptophan and an increased [S] 0.5 value of 8.6 mM in the presence of 300 μM tyrosine. In the mutant enzyme, a loss of the cooperativity was observed, and [S] 0.5 was reduced to 1.0 mM. This enzyme is therefore locked in the activated state by a single amino acid substitution

  16. Preparation of an aminopropyl imidazole-modified silica gel as a sorbent for solid-phase extraction of carboxylic acid compounds and polycyclic aromatic hydrocarbons.

    Science.gov (United States)

    Wang, Na; Guo, Yong; Wang, Licheng; Liang, Xiaojing; Liu, Shujuan; Jiang, Shengxiang

    2014-05-21

    In this paper, a kind of aminopropyl imidazole-modified silica sorbent was synthesized and used as a solid-phase extraction (SPE) sorbent for the determination of carboxylic acid compounds and polycyclic aromatic hydrocarbons (PAHs). The resultant aminopropyl imidazole-modified silica sorbent was characterized by Fourier transform infrared spectroscopy (FT-IR) and elemental analysis (EA) to ensure the successful binding of aminopropyl imidazole on the surface of silica gel. Then the aminopropyl imidazole-modified silica sorbent served as a SPE sorbent for the enrichment of carboxylic acid compounds and PAHs. The new sorbent exhibited high extraction efficiency towards the tested compounds and the results show that such a sorbent can offer multiple intermolecular interactions: electrostatic, π-π, and hydrophobic interactions. Several parameters affecting the extraction recovery, such as the pH of sample solution, the pH of eluent, the solubility of eluent, the volume of eluent, and sample loading, were also investigated. Under the optimized conditions, the proposed method was applied to the analysis of four carboxylic acid compounds and four PAHs in environmental water samples. Good linearities were obtained for all the tested compounds with R(2) larger than 0.9903. The limits of detection were found to be in the range of 0.0065-0.5 μg L(-1). The recovery values of spiked river water samples were from 63.2% to 112.3% with relative standard deviations (RSDs) less than 10.1% (n = 4).

  17. alpha,beta-unsaturated 2-acyl imidazoles as a practical class of dienophiles for the DNA-Based catalytic asymmetric diels-alder reaction in water

    NARCIS (Netherlands)

    Boersma, A.J.; Feringa, B.L.; Roelfes, G.

    2007-01-01

    alpha,beta-Unsaturated 2-acyl imidazoles are a novel and practical class of dienophiles for the DNA-based catalytic asymmetric Diels-Alder reaction in water. The Diels-Alder products are obtained with very high diastereoselectivities and enantioselectivities in the range of 83-98%. The catalytic

  18. Magnetic graphene oxide modified by imidazole-based ionic liquids for the magnetic-based solid-phase extraction of polysaccharides from brown alga.

    Science.gov (United States)

    Wang, Xiaoqin; Li, Guizhen; Row, Kyung Ho

    2017-08-01

    Magnetic graphene oxide was modified by four imidazole-based ionic liquids to synthesize materials for the extraction of polysaccharides by magnetic solid-phase extraction. Fucoidan and laminarin were chosen as the representative polysaccharides owing to their excellent pharmaceutical value and availability. Fourier transform infrared spectroscopy, field-emission scanning electron microscopy, and thermogravimetric analysis were applied to characterize the synthesized materials. Single-factor experiments showed that the extraction efficiency of polysaccharides was affected by the amount of ionic liquids for modification, solid-liquid ratio of brown alga and ethanol, the stirring time of brown alga and ionic liquid-modified magnetic graphene oxide materials, and amount of 1-(3-aminopropyl)imidazole chloride modified magnetic graphene oxide materials added to the brown alga sample solution. The results indicated that 1-(3-aminopropyl)imidazole chloride modified magnetic graphene oxide possessed better extraction ability than graphene oxide, magnetic graphene oxide, and other three ionic-liquid-modified magnetic graphene oxide materials. The highest extraction recoveries of fucoidan and laminarin extracted by 1-(3-aminopropyl)imidazole chloride modified magnetic graphene oxide were 93.3 and 87.2%, respectively. In addition, solid materials could be separated and reused easily owing to their magnetic properties. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Reactivity of Hydroxy and Amino Derivatives of 2-Phenyl-1H-imidazoline and 2-Phenyl-1H-imidazole toward Isocyanates: Synthesis of Appropriate Carbamates and Ureas

    Czech Academy of Sciences Publication Activity Database

    Pařík, P.; Jansa, J.; Holešová, S.; Marek, Aleš; Klimešová, V.

    2013-01-01

    Roč. 50, č. 4 (2013), s. 903-910 ISSN 0022-152X Grant - others:GA ČR(CZ) GA205/08/0869 Institutional support: RVO:61388963 Keywords : elevated-temperature * hydrolysis * imidazoles * alkylation Subject RIV: CC - Organic Chemistry Impact factor: 0.873, year: 2013

  20. Water swelling, brine soluble imidazole based zwitterionic polymers-synthesis and study of reversible UCST behaviour and gel-sol transitions

    NARCIS (Netherlands)

    Vasantha, Vivek Arjunan; Jana, Satyasankar; Parthiban, Anbanandam; Vancso, Julius G.

    2014-01-01

    New vinylbenzene substituted imidazole based zwitterionic polymers with unique characteristics like swelling in water and solubility in concentrated brine solution in which they exhibited a reversible upper critical solution temperature (UCST) and gel-sol transitions are reported herein. © 2014 The

  1. Directly oxidized chemiluminescence of 2-substituted-4,5-di(2-furyl)-1H -imidazole by acidic potassium permanganate and its analytical application for determination of albumin.

    Science.gov (United States)

    Kang, Jing; Zhang, Yumin; Huang, Zhongxiu; Han, Lu; Tang, Jieli; Wang, Shuaijun; Zhang, Yihua

    2011-07-01

    In the paper, 2,4,5-tri(2-furyl)-1H-imidazole (TFI) and 2-phenyl-4,5-di(2-furyl)-1H-imidazole (PDFI), were chosen to investigate chemiluminescence (CL) properties of 2-substituted-4,5-di(2-furyl)-1H-imidazoles. The directly oxidized CL of analytes by potassium permanganate (KMnO(4)) was in detail studied. The KMnO(4) could directly oxidize TFI/PDFI to produce strong CL emission in acidic solution. The effects of experimental conditions were investigated. Under the optimal conditions, the effect of albumin on the TFI/PDFI-KMnO(4) system was investigated. It was found that the addition of albumin into the system could induce enhancement of CL signal, and the enhanced CL intensity is linearly related to the logarithm of concentration of albumin. Based on this study, a novel CL method has been developed for the determination of albumin with high sensitivity and good selectivity. The method was applied to the determination of albumin in human serum samples, and the results were in agreement with those obtained by the bromcresol green (BCG) method. The relative errors for the analytical results were from -5.8% to 4.2%. These new phenomena would further enable people to exploit more CL analytical application of the heterocyclic imidazole derivatives. © Springer Science+Business Media, LLC 2011

  2. Pure white OLED based on an organic small molecule: 2,6-Di(1H-benzo[d]imidazol-2-yl)pyridine

    Science.gov (United States)

    Liu, Jian

    2015-10-01

    2,6-Di(1H-benzo[d]imidazol-2-yl)pyridine (DBIP) was synthesized. The single-crystal structure of DBIP was resolved. DBIP-based OLED was fabricated. The electroluminescence for the device corresponds to a pure white emission. In addition, thermal stability, UV-vis, photoluminescence and electrochemical behaviors of DBIP were investigated as well.

  3. Deoxyribonucleotide pool analysis: functional association of thymidylate synthase with the other enzymes of DNA biosynthesis in mammalian cells

    International Nuclear Information System (INIS)

    Reddy, G.P.V.; Christiansen, E.

    1986-01-01

    Allosteric interaction between thymidylate synthase (TS) and the other enzymes of DNA biosynthesis was suggested from the authors observation that inhibitors of ribonucleotide reductase, topoisomerase of DNA polymerase-α inhibit TS in intact S phase CHEF/18 cells, but not in their soluble extracts. In addition the authors observed that 4'-(9-acridinylamino)-methanesulfon-m-anisidide (m-AMSA), a poison of topoisomerase II, had similar effects on TS activity in mammalian cells. They have examined if the inhibitory effects of these antimetabolites on TS is due to the accumulation of thymidine nucleotide(s) in intact cells, rather than to an allosteric interaction in the replitase complex. A novel method of nucleotide pool analysis revealed that in the presence of these antimetabolites the incorporation of radioactivity from 3 H-deoxyuridine (dUrd) into thymidine nucleotide pools inside the cell did not increase as compared to the control. Furthermore, TS activity as measured in-vitro was not inhibited by supraphysiological concentrations (50μM) of thymidine mono- or tri-phosphates. None of these antimetabolites dramatically influenced the uptake of dUrd and its subsequent phosphorylation to deoxyuridine monophosphate. Therefore, they suggest that the inhibitory effect of these antimetabolites is due to the functional association of their target enzymes with TS

  4. Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors

    Energy Technology Data Exchange (ETDEWEB)

    Malaby, Andrew W.; Das, Sanchaita; Chakravarthy, Srinivas; Irving, Thomas C.; Bilsel, Osman; Lambright, David G.

    2018-01-01

    Membrane dynamic processes including vesicle biogenesis depend on Arf guanosine triphosphatase (GTPase) activation by guanine nucleotide exchange factors (GEFs) containing a catalytic Sec7 domain and a membrane-targeting module such as a pleckstrin homology (PH) domain. The catalytic output of cytohesin family Arf GEFs is controlled by autoinhibitory interactions that impede accessibility of the exchange site in the Sec7 domain. These restraints can be relieved through activator Arf-GTP binding to an allosteric site comprising the PH domain and proximal autoinhibitory elements (Sec7-PH linker and C-terminal helix). Small-angle X-ray scattering and negative-stain electron microscopy were used to investigate the structural organization and conformational dynamics of cytohesin-3 (Grp1) in autoinhibited and active states. The results support a model in which hinge dynamics in the autoinhibited state expose the activator site for Arf-GTP binding, while subsequent C-terminal helix unlatching and repositioning unleash conformational entropy in the Sec7-PH linker to drive exposure of the exchange site.

  5. Models, theory structure and mechanisms in biochemistry: The case of allosterism.

    Science.gov (United States)

    Alleva, Karina; Díez, José; Federico, Lucia

    2017-06-01

    From the perspective of the new mechanistic philosophy, it has been argued that explanatory causal mechanisms in some special sciences such as biochemistry and neurobiology cannot be captured by any useful notion of theory, or at least by any standard notion. The goal of this paper is to show that a model-theoretic notion of theory, and in particular the structuralist notion of a theory-net already applied to other unified explanatory theories, adequately suits the MWC allosteric mechanism explanatory set-up. We also argue, contra some mechanistic claims questioning the use of laws in biological explanations, that the theory reconstructed in this way essentially contains non-accidental regularities that qualify as laws, and that taking into account these lawful components, it is possible to explicate the unified character of the theory. Finally, we argue that, contrary to what some mechanists also claim, functional explanations that do not fully specify the mechanistic structure are not defective or incomplete in any relevant sense, and that functional components are perfectly explanatory. The conclusion is that, as some authors have emphasized in other fields (Walmsley 2008), particular elements of traditional approaches do not contradict but rather complement the new mechanist philosophy, and taken together they may offer a more complete understanding of special sciences and the variety of explanations they provide. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Self-phosphorylation of epidermal growth factor receptor: evidence for a model of intermolecular allosteric activation

    International Nuclear Information System (INIS)

    Yarden, Y.; Schlessinger, J.

    1987-01-01

    The membrane receptor for epidermal growth factor (EGF) is a 170,000 dalton glycoprotein composed of an extracellular EGF-binding domain and a cytoplasmic kinase domain connected by a stretch of 23 amino acids traversing the plasma membrane. The binding of EGF to the extracellular domain activates the cytoplasmic kinase function even in highly purified preparations of EGF receptor, suggesting that the activation occurs exclusively within the EGF receptor moiety. Conceivably, kinase activation may require the transfer of a conformational change through the single transmembrane region from the ligand binding domain to the cytoplasmic kinase region. Alternatively, ligand-induced receptor-receptor interactions may activate the kinase and thus bypass this requirement. Both mechanisms were contrasted by employing independent experimental approaches. On the basis of these results, an allosteric aggregation model is formulated for the activation of the cytoplasmic kinase function of the receptor by EGF. This model may be relevant to the mechanism by which the mitogenic signal of EGF is transferred across the membrane

  7. RET Functions as a Dual-Specificity Kinase that Requires Allosteric Inputs from Juxtamembrane Elements

    Directory of Open Access Journals (Sweden)

    Iván Plaza-Menacho

    2016-12-01

    Full Text Available Receptor tyrosine kinases exhibit a variety of activation mechanisms despite highly homologous catalytic domains. Such diversity arises through coupling of extracellular ligand-binding portions with highly variable intracellular sequences flanking the tyrosine kinase domain and specific patterns of autophosphorylation sites. Here, we show that the juxtamembrane (JM segment enhances RET catalytic domain activity through Y687. This phospho-site is also required by the JM region to rescue an otherwise catalytically deficient RET activation-loop mutant lacking tyrosines. Structure-function analyses identified interactions between the JM hinge, αC helix, and an unconventional activation-loop serine phosphorylation site that engages the HRD motif and promotes phospho-tyrosine conformational accessibility and regulatory spine assembly. We demonstrate that this phospho-S909 arises from an intrinsic RET dual-specificity kinase activity and show that an equivalent serine is required for RET signaling in Drosophila. Our findings reveal dual-specificity and allosteric components for the mechanism of RET activation and signaling with direct implications for drug discovery.

  8. Comparison of crystal and solution hemoglobin binding of selected antigelling agents and allosteric modifiers

    International Nuclear Information System (INIS)

    Mehanna, A.S.; Abraham, D.J.

    1990-01-01

    This paper details comprehensive binding studies (solution and X-ray) of human hemoglobin A with a group of halogenated carboxylic acids that were investigated as potential antisickling agents. It is, to our knowledge, the first study to compare solution and crystal binding for a series of compounds under similar high-salt conditions used for cocrystallization. The compounds include [(3,4-dichlorobenzyl)oxy]acetic acid, [(p-bromobenzyl)oxy]acetic acid, clofibric acid, and bezafibrate. The location and stereochemistry of binding sites have been established by X-ray crystallography, while the number of binding sites and affinity constants were measured by using equilibrium dialysis. The observed crystal structures are consistent with the binding observed in solution and that the number of binding sites is independent of salt concentration, while the binding constant increases with increasing salt concentration. The studies also reveal that relatively small changes in the chemical structure of a drug molecule can result in entirely different binding sites on the protein. Moreover, the X-ray studies provide a possible explanation for the multiplicity in function exhibited by these compounds as allosteric modulators and/or antisickling agents. Finally, the studies indicate that these compounds bind differently to the R and T states of hemoglobin, and observation of special significance to the original design of these agents

  9. Nonequilibrium dissipation-free transport in F₁-ATPase and the thermodynamic role of asymmetric allosterism.

    Science.gov (United States)

    Kawaguchi, Kyogo; Sasa, Shin-Ichi; Sagawa, Takahiro

    2014-06-03

    F1-ATPase (or F1), the highly efficient and reversible biochemical engine, has motivated physicists as well as biologists to imagine the design principles governing machines in the fluctuating world. Recent experiments have clarified yet another interesting property of F1; the dissipative heat inside the motor is very small, irrespective of the velocity of rotation and energy transport. Conceptual interest is devoted to the fact that the amount of internal dissipation is not simply determined by the sequence of equilibrium pictures, but also relies on the rotational-angular dependence of nucleotide affinity, which is a truly nonequilibrium aspect. We propose that the totally asymmetric allosteric model (TASAM), where adenosine triphosphate (ATP) binding to F1 is assumed to have low dependence on the angle of the rotating shaft, produces results that are most consistent with the experiments. Theoretical analysis proves the crucial role of two time scales in the model, which explains the universal mechanism to produce the internal dissipation-free feature. The model reproduces the characteristic torque dependence of the rotational velocity of F1 and predicts that the internal dissipation upon the ATP synthesis direction rotation becomes large at the low nucleotide condition. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  10. Conformational changes and allosteric communications in human serum albumin due to ligand binding.

    Science.gov (United States)

    Ahalawat, Navjeet; Murarka, Rajesh K

    2015-01-01

    It is well recognized that knowledge of structure alone is not sufficient to understand the fundamental mechanism of biomolecular recognition. Information of dynamics is necessary to describe motions involving relevant conformational states of functional importance. We carried out principal component analysis (PCA) of structural ensemble, derived from 84 crystal structures of human serum albumin (HSA) with different ligands and/or different conditions, to identify the functionally important collective motions, and compared with the motions along the low-frequency modes obtained from normal mode analysis of the elastic network model (ENM) of unliganded HSA. Significant overlap is observed in the collective motions derived from PCA and ENM. PCA and ENM analysis revealed that ligand selects the most favored conformation from accessible equilibrium structures of unliganded HSA. Further, we analyzed dynamic network obtained from molecular dynamics simulations of unliganded HSA and fatty acids- bound HSA. Our results show that fatty acids-bound HSA has more robust community network with several routes to communicate among different parts of the protein. Critical nodes (residues) identified from dynamic network analysis are in good agreement with allosteric residues obtained from sequence-based statistical coupling analysis method. This work underscores the importance of intrinsic structural dynamics of proteins in ligand recognition and can be utilized for the development of novel drugs with optimum activity.

  11. Intracellular calcium levels determine differential modulation of allosteric interactions within G protein-coupled receptor heteromers.

    Science.gov (United States)

    Navarro, Gemma; Aguinaga, David; Moreno, Estefania; Hradsky, Johannes; Reddy, Pasham P; Cortés, Antoni; Mallol, Josefa; Casadó, Vicent; Mikhaylova, Marina; Kreutz, Michael R; Lluís, Carme; Canela, Enric I; McCormick, Peter J; Ferré, Sergi

    2014-11-20

    The pharmacological significance of the adenosine A2A receptor (A2AR)-dopamine D2 receptor (D2R) heteromer is well established and it is being considered as an important target for the treatment of Parkinson’s disease and other neuropsychiatric disorders. However, the physiological factors that control its distinctive biochemical properties are still unknown. We demonstrate that different intracellular Ca2+ levels exert a differential modulation of A2AR-D2R heteromer-mediated adenylyl-cyclase and MAPK signaling in striatal cells. This depends on the ability of low and high Ca2+ levels to promote a selective interaction of the heteromer with the neuronal Ca2+-binding proteins NCS-1 and calneuron-1, respectively. These Ca2+-binding proteins differentially modulate allosteric interactions within the A2AR-D2R heteromer, which constitutes a unique cellular device that integrates extracellular (adenosine and dopamine) and intracellular (Ca+2) signals to produce a specific functional response.

  12. Energy transfer by way of an exciplex intermediate in flexible boron dipyrromethene-based allosteric architectures.

    Science.gov (United States)

    Mula, Soumyaditya; Elliott, Kristopher; Harriman, Anthony; Ziessel, Raymond

    2010-10-07

    We have designed and synthesized a series of modular, dual-color dyes comprising a conventional boron dipyrromethene (Bodipy) dye, as a yellow emitter, and a Bodipy dye possessing extended conjugation that functions as a red emitter. A flexible tether of variable length, built from ethylene glycol residues, connects the terminal dyes. A critical design element of this type of dyad relates to a secondary amine linkage interposed between the conventional Bodipy and the tether. Cyclic voltammetry shows both Bodipy dyes to be electroactive and indicates that the secondary amine is quite easily oxidized. The ensuing fluorescence quenching is best explained in terms of the rapid formation of an intermediate charge-transfer state. In fact, exciplex-type emission is observed in weakly polar solvents and over a critical temperature range. In the dual-color dyes, direct excitation of the yellow emitter results in the appearance of red fluorescence, indicating that the exciplex is likely involved in the energy-transfer event, and provides for a virtual Stokes shift of 5000 cm(-1). Replacing the red emitter with a higher energy absorber (namely, pyrene) facilitates the collection of near-UV light and extends the virtual Stokes shift to 8000 cm(-1). Modulation of the efficacy of intramolecular energy transfer is achieved by preorganization of the connector in the presence of certain cations. This latter behavior, which is fully reversible, corresponds to an artificial allosteric effect.

  13. Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Jun; Byrne, Noel; Wang, John; Bricogne, Gerard; Brown, Frank K.; Chobanian, Harry R.; Colletti, Steven L.; Di Salvo, Jerry; Thomas-Fowlkes, Brande; Guo, Yan; Hall, Dawn L.; Hadix, Jennifer; Hastings, Nicholas B.; Hermes, Jeffrey D.; Ho, Thu; Howard, Andrew D.; Josien, Hubert; Kornienko, Maria; Lumb, Kevin J.; Miller, Michael W.; Patel, Sangita B.; Pio, Barbara; Plummer, Christopher W.; Sherborne, Bradley S.; Sheth, Payal; Souza, Sarah; Tummala, Srivanya; Vonrhein, Clemens; Webb, Maria; Allen, Samantha J.; Johnston, Jennifer M.; Weinglass, Adam B.; Sharma, Sujata; Soisson, Stephen M. (Merck); (Globel Phasing)

    2017-06-05

    Clinical studies indicate that partial agonists of the G-protein-coupled, free fatty acid receptor 1 GPR40 enhance glucose-dependent insulin secretion and represent a potential mechanism for the treatment of type 2 diabetes mellitus. Full allosteric agonists (AgoPAMs) of GPR40 bind to a site distinct from partial agonists and can provide additional efficacy. We report the 3.2-Å crystal structure of human GPR40 (hGPR40) in complex with both the partial agonist MK-8666 and an AgoPAM, which exposes a novel lipid-facing AgoPAM-binding pocket outside the transmembrane helical bundle. Comparison with an additional 2.2-Å structure of the hGPR40–MK-8666 binary complex reveals an induced-fit conformational coupling between the partial agonist and AgoPAM binding sites, involving rearrangements of the transmembrane helices 4 and 5 (TM4 and TM5) and transition of the intracellular loop 2 (ICL2) into a short helix. These conformational changes likely prime GPR40 to a more active-like state and explain the binding cooperativity between these ligands.

  14. Characterization of an allosteric citalopram-binding site at the serotonin transporter

    DEFF Research Database (Denmark)

    Chen, Fenghua; Breum Larsen, Mads; Neubauer, Henrik Amtoft

    2005-01-01

    The serotonin transporter (SERT), which belongs to a family of       sodium/chloride-dependent transporters, is the major pharmacological       target in the treatment of several clinical disorders, including       depression and anxiety. In the present study we show that the dissociation......       rate, of [3H]S-citalopram from human SERT, is retarded by the presence of       serotonin, as well as by several antidepressants, when present in the       dissociation buffer. Dissociation of [3H]S-citalopram from SERT is most       potently inhibited by S-citalopram followed by R......-citalopram, sertraline,       serotonin and paroxetine. EC50 values for S- and R-citalopram are 3.6 +/-       0.4 microm and 19.4 +/- 2.3 microm, respectively. Fluoxetine, venlafaxine       and duloxetine have no significant effect on the dissociation of       [3H]S-citalopram. Allosteric modulation of dissociation...

  15. D-glucose-6-phosphate dehydrogenase (Entner-Doudoroff enzyme) from Pseudomonas fluorescens

    International Nuclear Information System (INIS)

    Lessmann, D.; Schimz, K.L.; Kurz, G.

    1975-01-01

    The existence of two different D-glucose-6-phosphate dehydrogenases in Pseudomonas fluorescens has been demonstrated. Based on their different specificity and their different metabolic regulation one enzyme is appointed to the Entner-Doudoroff pathway and the other to the hexose monophosphate pathway. A procedure is described for the isolation of that D-glucose-6-phosphate dehydrogenase which forms part of the Entner-Doudoroff pathway (Entner-Doudoroff enzyme). A 950-fold purification was achieved with an overall yield of 44%. The final preparation, having a specific activity of about 300μmol NADH formed per min per mg protein, was shown to be homogeneous. The molecular weight of the Entner-Doudoroff enzyme has been determined to be 220,000 by gel permeation chromatography, and that of the other enzyme (Zwischenferment) has been shown to be 265,000. The pI of the Entner-Doudoroff enzyme has been shown to be 5.24 and that of the Zwischenferment 4.27. The Entner-Doudoroff enzyme is stable in the range of pH 6 to 10.5 and shows its maximal acivity at pH 8.9. The Entner-Doudoroff enzyme showed specificity for NAD + as well as for NADP + and exhibited homotropic effects for D-glucose 6-phosphate. It is inhibited by ATP which acts as a negative allosteric effector. Other nucleoside triphosphates as well as ADP are also inhibitory. The enzyme catalyzes the transfer of the axial hydrogen at carbon-1 of β-D-glucopyranose 6-phosphate to the si face of carbon-4 of the nicotinamide ring and must be classified as B-side stereospecific dehydrogenase. (orig.) [de

  16. Enhancement of photoassimilate utilization by manipulation of starch regulatory enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Okita, Thomas W. [Washington State Univ., Pullman, WA (United States)

    2016-05-11

    ADPglucose pyrophosphorylase (AGPase) and the plastidial starch phosphorylase1 (Pho1) are two regulatory enzymes whose catalytic activities are essential for starch granule synthesis. Conversion of the pre-starch granule to the mature form is dependent on AGPase, which produces ADPglucose, the substrate used by starch synthases. The catalytic activity of AGPase is controlled by small effector molecules and a prime goal of this project was to decipher the role of the two subunit types that comprise the heterotetrameric enzyme structure. Extensive genetic and biochemical studies showed that catalysis was contributed mainly by the small subunit although the large subunit was required for maximum activity. Both subunits were needed for allosteric regulatory properties. We had also demonstrated that the AGPase catalyzed reaction limits the amount of starch accumulation in developing rice seeds and that carbon flux into rice seed starch can be increased by expression of a cytoplasmic-localized, up-regulated bacterial AGPase enzyme form. Results of subsequent physiological and metabolite studies showed that the AGPase reaction is no longer limiting in the AGPase transgenic rice lines and that one or more downstream processes prevent further increases in starch biosynthesis. Further studies showed that over-production of ADPglucose dramatically alters the gene program during rice seed development. Although the expression of nearly all of the genes are down-regulated, levels of a starch binding domain containing protein (SBDCP) are elevated. This SBDCP was found to bind to and inhibit the catalytic activity of starch synthase III and, thereby preventing maximum starch synthesis from occurring. Surprisingly, repression of SBDCP elevated expression of starch synthase III resulting in increasing rice grain weight. A second phase of this project examined the structure-function of Pho1, the enzyme required during the initial phase of pre-starch granule formation and its

  17. Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.

    Directory of Open Access Journals (Sweden)

    Gabrielle Stetz

    2017-01-01

    Full Text Available Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of

  18. Random-walk enzymes

    Science.gov (United States)

    Mak, Chi H.; Pham, Phuong; Afif, Samir A.; Goodman, Myron F.

    2015-09-01

    Enzymes that rely on random walk to search for substrate targets in a heterogeneously dispersed medium can leave behind complex spatial profiles of their catalyzed conversions. The catalytic signatures of these random-walk enzymes are the result of two coupled stochastic processes: scanning and catalysis. Here we develop analytical models to understand the conversion profiles produced by these enzymes, comparing an intrusive model, in which scanning and catalysis are tightly coupled, against a loosely coupled passive model. Diagrammatic theory and path-integral solutions of these models revealed clearly distinct predictions. Comparison to experimental data from catalyzed deaminations deposited on single-stranded DNA by the enzyme activation-induced deoxycytidine deaminase (AID) demonstrates that catalysis and diffusion are strongly intertwined, where the chemical conversions give rise to new stochastic trajectories that were absent if the substrate DNA was homogeneous. The C →U deamination profiles in both analytical predictions and experiments exhibit a strong contextual dependence, where the conversion rate of each target site is strongly contingent on the identities of other surrounding targets, with the intrusive model showing an excellent fit to the data. These methods can be applied to deduce sequence-dependent catalytic signatures of other DNA modification enzymes, with potential applications to cancer, gene regulation, and epigenetics.

  19. Syntheses and structure characterization of ten acid-base hybrid crystals based on imidazole derivatives and mineral acids

    Science.gov (United States)

    Hu, Kaikai; Deng, Bowen; Jin, Shouwen; Ding, Aihua; Jin, Shide; Zhu, Jin; Zhang, Huan; Wang, Daqi

    2018-04-01

    Cocrystallization of the imidazole derivatives with a series of mineral acids gave a total of ten hybrid salts with the compositions: [(H2bzm)(Cl)2·3H2O] (1), [(H2bzm)(ClO4)2] (2), [(H2bze)(Cl)2·2H2O] (3), [(H2bze)(Br)2·2H2O] (4), [(H2bzp)(Cl)2·4H2O] (5), [(H2bzp)(Br)2·4H2O] (6), (2-(imidazol-1-yl)-1-phenylethanone): (phosphoric acid) [(Himpeta)+(H2PO4)-] (7), [(H2impd)(Br)2] (8), [(H2impd)(ClO4)2] (9), and [(Hbzml)(Cl)] (10). The ten salts have been characterised by X-ray diffraction analysis, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the ten investigated crystals the ring N atoms of the imidazole are protonated when the acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted classical H-bonds between the NH+ and deprotonated acidic groups. Further analysis of the crystal packing of the salts indicated that a different set of additional CHsbnd O, CH2sbnd O, CHsbnd Cl, CH2sbnd Cl, CHsbnd N, CHsbnd Br, CH2sbnd Br, Osbnd O, O-π, Br-π, CH-π, and π-π associations contribute to the stabilization and expansion of the total high-dimensional frameworks. For the coexistence of the various weak nonbonding interactions these structures adopted homo or hetero supramolecular synthons or both. Some classical supramolecular synthons, such as R21(7), R22(7), R22(8), and R42(8), usually observed in the organic solids, were again shown to be involved in constructing some of these H-bonding networks.

  20. Cytoprotection of human endothelial cells against oxidative stress by 1-[2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole (CDDO-Im): application of systems biology to understand the mechanism of action.

    Science.gov (United States)

    Wang, Xinyu; Bynum, James A; Stavchansky, Solomon; Bowman, Phillip D

    2014-07-05

    Cellular damage from oxidative stress, in particular following ischemic injury, occurs during heart attack, stroke, or traumatic injury, and is potentially reducible with appropriate drug treatment. We previously reported that caffeic acid phenethyl ester (CAPE), a plant-derived polyphenolic compound, protected human umbilical vein endothelial cells (HUVEC) from menadione-induced oxidative stress and that this cytoprotective effect was correlated with the capacity to induce heme oxygenase-1 (HMOX1) and its protein product, a phase II cytoprotective enzyme. To further improve this cytoprotective effect, we studied a synthetic triterpenoid, 1-[2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole (CDDO-Im), which is known as a potent phase II enzyme inducer with antitumor and anti-inflammatory activities, and compared it to CAPE. CDDO-Im at 200nM provided more protection to HUVEC against oxidative stress than 20μM CAPE. We explored the mechanism of CDDO-Im cytoprotection with gene expression profiling and pathway analysis and compared to that of CAPE. In addition to potent up-regulation of HMOX1, heat shock proteins (HSP) were also found to be highly induced by CDDO-Im in HUVEC. Pathway analysis results showed that transcription factor Nrf2-mediated oxidative stress response was among the top canonical pathways commonly activated by both CDDO-Im and CAPE. Compared to CAPE, CDDO-Im up-regulated more HSP and some of them to a much higher extent. In addition, CDDO-Im treatment affected Nrf2 pathway more significantly. These findings may provide an explanation why CDDO-Im is a more potent cytoprotectant than CAPE against oxidative stress in HUVEC. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Matrix Metalloproteinase Enzyme Family

    Directory of Open Access Journals (Sweden)

    Ozlem Goruroglu Ozturk

    2013-04-01

    Full Text Available Matrix metalloproteinases play an important role in many biological processes such as embriogenesis, tissue remodeling, wound healing, and angiogenesis, and in some pathological conditions such as atherosclerosis, arthritis and cancer. Currently, 24 genes have been identified in humans that encode different groups of matrix metalloproteinase enzymes. This review discuss the members of the matrix metalloproteinase family and their substrate specificity, structure, function and the regulation of their enzyme activity by tissue inhibitors. [Archives Medical Review Journal 2013; 22(2.000: 209-220

  2. Relief of autoinhibition by conformational switch explains enzyme activation by a catalytically dead paralog

    Energy Technology Data Exchange (ETDEWEB)

    Volkov, Oleg A.; Kinch, Lisa; Ariagno, Carson; Deng, Xiaoyi; Zhong, Shihua; Grishin, Nick; Tomchick, Diana R.; Chen, Zhe; Phillips, Margaret A.

    2016-12-15

    Catalytically inactive enzyme paralogs occur in many genomes. Some regulate their active counterparts but the structural principles of this regulation remain largely unknown. We report X-ray structures ofTrypanosoma brucei S-adenosylmethionine decarboxylase alone and in functional complex with its catalytically dead paralogous partner, prozyme. We show monomericTbAdoMetDC is inactive because of autoinhibition by its N-terminal sequence. Heterodimerization with prozyme displaces this sequence from the active site through a complex mechanism involving acis-to-transproline isomerization, reorganization of a β-sheet, and insertion of the N-terminal α-helix into the heterodimer interface, leading to enzyme activation. We propose that the evolution of this intricate regulatory mechanism was facilitated by the acquisition of the dimerization domain, a single step that can in principle account for the divergence of regulatory schemes in the AdoMetDC enzyme family. These studies elucidate an allosteric mechanism in an enzyme and a plausible scheme by which such complex cooperativity evolved.

  3. The surface science of enzymes

    DEFF Research Database (Denmark)

    Rod, Thomas Holm; Nørskov, Jens Kehlet

    2002-01-01

    One of the largest challenges to science in the coming years is to find the relation between enzyme structure and function. Can we predict which reactions an enzyme catalyzes from knowledge of its structure-or from its amino acid sequence? Can we use that knowledge to modify enzyme function......? To solve these problems we must understand in some detail how enzymes interact with reactants from its surroundings. These interactions take place at the surface of the enzyme and the question of enzyme function can be viewed as the surface science of enzymes. In this article we discuss how to describe...... catalysis by enzymes, and in particular the analogies between enzyme catalyzed reactions and surface catalyzed reactions. We do this by discussing two concrete examples of reactions catalyzed both in nature (by enzymes) and in industrial reactors (by inorganic materials), and show that although analogies...

  4. INHIBITORY ACTIVITY OF AN IMIDAZOLE COMPOUND ON ECDYSIOSYNTHETIC ORGANS IN MEALWORMS UNDER IN VIVO AND IN VITRO CONDITIONS

    Directory of Open Access Journals (Sweden)

    N SOLTANI-MAZOUNI

    2000-12-01

    Full Text Available KK-42, an imidazole derivative was tested on adult females of Tenebrio molitor L. (Insecta: Coleoptera. The compound was applied topically (1, 5, 10 mg/insect on 0- or 2-day old adult females or added to the culture medium (1 and 10 mM of abdominal sternites explanted from newly ecdysed pupae or ovaries removed from 2- and 4-day old adult females. Ecdysteroid measurements using an enzymo-immunoassay demonstrated that this compound applied on newly emerged adult females reduced the hormonal amounts in ovaries. However, when applied later, i.e. on 2-day old females corresponding to the beginning of the vitellogenesis, it had no significant effect on the amount of ovarian ecdysteroids with the lowest dose. Finally, the compound was also tested on the in vitro production of ecdysteroids. The amount of ecdysteroid released into the culture medium by ovaries or integumental explants were significantly reduced by KK-42.

  5. SYNTHESIS AND STUDY OF ANTIOXIDANT ACTIVITY OF [(1-ARYL-5-FORMYL-1H-IMIDAZOLE-4-ILTHIO]PROPIONIC ACIDS

    Directory of Open Access Journals (Sweden)

    A. O. Palamar

    2014-12-01

    Full Text Available Introduction. Derivatives of imidazole belong to the promising group of compounds for antioxidant activity study, due to the series of recent publications. This is defined by special features of their structure, specific reactivity and significant potential of pharmacological action. Earlier during process of looking for new antioxidants we studied significant amount of imidazole derivatives, among which the [(1-aryl-5-formylimidazole-4-ilthio]acetic acids structurally modified by the formyl group and thioacetic acid fragment, are especially worth noting. The purpose of the study. Synthesis of [(1-aryl-5-formylimidazole-4-ilthio]propionic acids and comparison of their antioxidant effect with [(1-aryl-5-formylimidazole-4-ilthio]acetic acids with to identify prospects of in-depth study of the most active compounds as antioxidants. Materials and methods. The method based on interaction of available 4-chloro-5-formylimidazoles with thiopropionic acid was proposed for the synthesis of [(1-aryl-5-formylimidazole-4-ilthio]propionic acids. The reaction takes place in ethanol in presence of potassium hydroxide and leads to the target compounds with yields of 81-86%. The study of antioxidant activity of synthesized compounds was conducted in vitro by speed inhibition value of rats’ liver endogenous lipids ascorbate-dependent peroxide oxidation. It was determined by concentration of one of the final products of free radical oxidation of lipids (FROL – maleic aldehyde (MA in the investigated sample. Concentrations of synthesized compounds were chosen within concentrations which were studied for thiotriazolin (manufactured by corporation “Arterium”, Ukraine, solution for injection, 25 mg/ml. The results of the study and their discussion. Preparative method for the synthesis of [(1-aryl-5-formylimidazole-4-ilthio]propionic acids has been designed. Imidazolylthiopropionic acids have been synthesized; they are crystalline compounds, of light

  6. Inhibition of RecBCD enzyme by antineoplastic DNA alkylating agents.

    Science.gov (United States)

    Dziegielewska, Barbara; Beerman, Terry A; Bianco, Piero R

    2006-09-01

    To understand how bulky adducts might perturb DNA helicase function, three distinct DNA-binding agents were used to determine the effects of DNA alkylation on a DNA helicase. Adozelesin, ecteinascidin 743 (Et743) and hedamycin each possess unique structures and sequence selectivity. They bind to double-stranded DNA and alkylate one strand of the duplex in cis, adding adducts that alter the structure of DNA significantly. The results show that Et743 was the most potent inhibitor of DNA unwinding, followed by adozelesin and hedamycin. Et743 significantly inhibited unwinding, enhanced degradation of DNA, and completely eliminated the ability of the translocating RecBCD enzyme to recognize and respond to the recombination hotspot chi. Unwinding of adozelesin-modified DNA was accompanied by the appearance of unwinding intermediates, consistent with enzyme entrapment or stalling. Further, adozelesin also induced "apparent" chi fragment formation. The combination of enzyme sequestering and pseudo-chi modification of RecBCD, results in biphasic time-courses of DNA unwinding. Hedamycin also reduced RecBCD activity, albeit at increased concentrations of drug relative to either adozelesin or Et743. Remarkably, the hedamycin modification resulted in constitutive activation of the bottom-strand nuclease activity of the enzyme, while leaving the ability of the translocating enzyme to recognize and respond to chi largely intact. Finally, the results show that DNA alkylation does not significantly perturb the allosteric interaction that activates the enzyme for ATP hydrolysis, as the efficiency of ATP utilization for DNA unwinding is affected only marginally. These results taken together present a unique response of RecBCD enzyme to bulky DNA adducts. We correlate these effects with the recently determined crystal structure of the RecBCD holoenzyme bound to DNA.

  7. Magnetically responsive enzyme powders

    Czech Academy of Sciences Publication Activity Database

    Pospišková, K.; Šafařík, Ivo

    2015-01-01

    Roč. 380, APR 2015 (2015), s. 197-200 ISSN 0304-8853 R&D Projects: GA MŠk(CZ) LD13021 Institutional support: RVO:67179843 Keywords : enzyme powders * cross-linking * magnetic modification * magnetic separation * magnetic iron oxides particles * microwave-assisted synthesis Subject RIV: CE - Biochemistry Impact factor: 2.357, year: 2015

  8. Enzyme with rhamnogalacturonase activity.

    NARCIS (Netherlands)

    Kofod, L.V.; Andersen, L.N.; Dalboge, H.; Kauppinen, M.S.; Christgau, S.; Heldt-Hansen, H.P.; Christophersen, C.; Nielsen, P.M.; Voragen, A.G.J.; Schols, H.A.

    1998-01-01

    An enzyme exhibiting rhamnogalacturonase activity, capable of cleaving a rhamnogalacturonan backbone in such a manner that galacturonic acids are left as the non-reducing ends, and which exhibits activity on hairy regions from a soy bean material and/or on saponified hairy regions from a sugar beet

  9. Implantable enzyme amperometric biosensors.

    Science.gov (United States)

    Kotanen, Christian N; Moussy, Francis Gabriel; Carrara, Sandro; Guiseppi-Elie, Anthony

    2012-05-15

    The implantable enzyme amperometric biosensor continues as the dominant in vivo format for the detection, monitoring and reporting of biochemical analytes related to a wide range of pathologies. Widely used in animal studies, there is increasing emphasis on their use in diabetes care and management, the management of trauma-associated hemorrhage and in critical care monitoring by intensivists in the ICU. These frontier opportunities demand continuous indwelling performance for up to several years, well in excess of the currently approved seven days. This review outlines the many challenges to successful deployment of chronically implantable amperometric enzyme biosensors and emphasizes the emerging technological approaches in their continued development. The foreign body response plays a prominent role in implantable biotransducer failure. Topics considering the approaches to mitigate the inflammatory response, use of biomimetic chemistries, nanostructured topographies, drug eluting constructs, and tissue-to-device interface modulus matching are reviewed. Similarly, factors that influence biotransducer performance such as enzyme stability, substrate interference, mediator selection and calibration are reviewed. For the biosensor system, the opportunities and challenges of integration, guided by footprint requirements, the limitations of mixed signal electronics, and power requirements, has produced three systems approaches. The potential is great. However, integration along the multiple length scales needed to address fundamental issues and integration across the diverse disciplines needed to achieve success of these highly integrated systems, continues to be a challenge in the development and deployment of implantable amperometric enzyme biosensor systems. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. Advances in enzyme bioelectrochemistry

    Directory of Open Access Journals (Sweden)

    ANDRESSA R. PEREIRA

    Full Text Available ABSTRACT Bioelectrochemistry can be defined as a branch of Chemical Science concerned with electron-proton transfer and transport involving biomolecules, as well as electrode reactions of redox enzymes. The bioelectrochemical reactions and system have direct impact in biotechnological development, in medical devices designing, in the behavior of DNA-protein complexes, in green-energy and bioenergy concepts, and make it possible an understanding of metabolism of all living organisms (e.g. humans where biomolecules are integral to health and proper functioning. In the last years, many researchers have dedicated itself to study different redox enzymes by using electrochemistry, aiming to understand their mechanisms and to develop promising bioanodes and biocathodes for biofuel cells as well as to develop biosensors and implantable bioelectronics devices. Inside this scope, this review try to introduce and contemplate some relevant topics for enzyme bioelectrochemistry, such as the immobilization of the enzymes at electrode surfaces, the electron transfer, the bioelectrocatalysis, and new techniques conjugated with electrochemistry vising understand the kinetics and thermodynamics of redox proteins. Furthermore, examples of recent approaches in designing biosensors and biofuel developed are presented.

  11. Cold-Adapted Enzymes

    Science.gov (United States)

    Georlette, D.; Bentahir, M.; Claverie, P.; Collins, T.; D'amico, S.; Delille, D.; Feller, G.; Gratia, E.; Hoyoux, A.; Lonhienne, T.; Meuwis, M.-a.; Zecchinon, L.; Gerday, Ch.

    In the last few years, increased attention has been focused on enzymes produced by cold-adapted micro-organisms. It has emerged that psychrophilic enzymes represent an extremely powerful tool in both protein folding investigations and for biotechnological purposes. Such enzymes are characterised by an increased thermosensitivity and, most of them, by a higher catalytic efficiency at low and moderate temperatures, when compared to their mesophilic counterparts. The high thermosensitivity probably originates from an increased flexibility of either a selected area of the molecular edifice or the overall protein structure, providing enhanced abilities to undergo conformational changes during catalysis at low temperatures. Structure modelling and recent crystallographic data have allowed to elucidate the structural parameters that could be involved in this higher resilience. It was demonstrated that each psychrophilic enzyme adopts its own adaptive strategy. It appears, moreover, that there is a continuum in the strategy of protein adaptation to temperature, as the previously mentioned structural parameters are implicated in the stability of thermophilic proteins. Additional 3D crystal structures, site-directed and random mutagenesis experiments should now be undertaken to further investigate the stability-flexibility-activity relationship.

  12. Embedded enzymes catalyse capture

    Science.gov (United States)

    Kentish, Sandra

    2018-05-01

    Membrane technologies for carbon capture can offer economic and environmental advantages over conventional amine-based absorption, but can suffer from limited gas flux and selectivity to CO2. Now, a membrane based on enzymes embedded in hydrophilic pores is shown to exhibit combined flux and selectivity that challenges the state of the art.

  13. Photoperiodism and Enzyme Activity

    Science.gov (United States)

    Queiroz, Orlando; Morel, Claudine

    1974-01-01

    Metabolic readjustments after a change from long days to short days appear, in Kalanchoe blossfeldiana, to be achieved through the operation of two main mechanisms: variation in enzyme capacity, and circadian rhythmicity. After a lag time, capacity in phosphoenolpyruvate carboxylase and capacity in aspartate aminotransferase increase exponentially and appear to be allometrically linked during 50 to 60 short days; then a sudden fall takes place in the activity of the former. Malic enzyme and alanine aminotransferase behave differently. Thus, the operation of the two sections of the pathway (before and after the malate step) give rise to a continuously changing functional compartmentation in the pathway. Circadian rhythmicity, on the other hand, produces time compartmentation through phase shifts and variation in amplitude, independently for each enzyme. These characteristics suggest that the operation of a so-called biological clock would be involved. We propose the hypothesis that feedback regulation would be more accurate and efficient when applied to an already oscillating, clock-controlled enzyme system. PMID:16658749

  14. ISFET based enzyme sensors

    NARCIS (Netherlands)

    van der Schoot, Bart H.; Bergveld, Piet

    1987-01-01

    This paper reviews the results that have been reported on ISFET based enzyme sensors. The most important improvement that results from the application of ISFETs instead of glass membrane electrodes is in the method of fabrication. Problems with regard to the pH dependence of the response and the

  15. A novel poly(propylene-co-imidazole) based biofuel cell: System optimization and operation for energy generation

    Energy Technology Data Exchange (ETDEWEB)

    Kilic, Muhammet Samet [Department of Chemistry, Bulent Ecevit University, 67100 Zonguldak (Turkey); Korkut, Seyda, E-mail: s.korkut@beun.edu.tr [Department of Environmental Engineering, Bulent Ecevit University, 67100 Zonguldak (Turkey); Hazer, Baki [Department of Chemistry, Bulent Ecevit University, 67100 Zonguldak (Turkey)

    2015-02-01

    This study describes the construction of an enzymatic fuel cell comprised of novel gold nanoparticles embedded poly(propylene-co-imidazole) coated anode and cathode. Working electrode fabrication steps and operational conditions for the fuel cell have been optimized to get enhanced power output. Electrical generation capacity of the optimized cell was tested by using the municipal wastewater sample. The enzymatic fuel cell system reached to maximum power density with 1 μg and 8 μg of polymer quantity and bilirubin oxidase on electrode surface, respectively. The maximum power output was calculated to be 5 μW cm{sup −2} at + 0.56 V (vs. Ag/AgCl) in phosphate buffer (pH 7.4, 100 mM, 20 °C) by the addition of 15 mM of glucose as a fuel source. The optimized enzymatic fuel cell generated a power density of 0.46 μW cm{sup −2} for the municipal wastewater sample. Poly(propylene-co-imidazole) was easily used for a fuel cell system owing to its metallic nanoparticle content. The developed fuel cell will play a significant role for energy conversion by using glucose readily found in wastewater and in vivo mediums. - Highlights: • Gold nanoparticles provided faster electron transfer in the circuit. • The maximum power density of 5 μW cm{sup −2} was generated at + 0.56 V cell potential. • The cell can be easily operated for in vivo mediums.

  16. 2-(2-Hydroxyphenyl)imidazole-based four-coordinate organoboron compounds with efficient deep blue photoluminescence and electroluminescence.

    Science.gov (United States)

    Zhang, Zhenyu; Zhang, Zuolun; Zhang, Hongyu; Wang, Yue

    2017-12-19

    Two new four-coordinate organoboron compounds with 2-(2-hydroxyphenyl)imidazole derivatives as the chelating ligands have been synthesized. They possess high thermal stability and are able to form an amorphous glass state. Crystallographic analyses indicate that the differences in ligand structure cause the change of ππ stacking character. The CH 2 Cl 2 solutions and thin films of these compounds display bright blue emission, and these compounds have appropriate HOMO and LUMO energy levels for carrier injection in OLEDs. By utilizing the good thermal and luminescent properties, as well as the proper frontier orbital energy levels, bright non-doped OLEDs with a simple structure have been realized. Notably, these simple devices show deep blue electroluminescence with the Commission Internationale de l'Éclairage (CIE) coordinate of ca. (0.16, 0.08), which is close to the CIE coordinate of (0.14, 0.08) for standard blue defined by the National Television System Committee. In addition, one of the devices exhibits good performance, showing brightness, current efficiency, power efficiency and external quantum efficiency up to 2692 cd m -2 , 2.50 cd A -1 , 1.81 lm W -1 and 3.63%, respectively. This study not only provides good deep-blue emitting OLED materials that are rarely achieved by using four-coordinate organoboron compounds, but also allows a deeper understanding of the structure-property relationship of 2-(2-hydroxyphenyl)imidazole-based boron complexes, which benefits the further structural design of this type of material.

  17. Probing the hydrogen equilibrium and kinetics in zeolite imidazolate frameworks via molecular dynamics and quasi-elastic neutron scattering experiments.

    Science.gov (United States)

    Pantatosaki, Evangelia; Jobic, Hervé; Kolokolov, Daniil I; Karmakar, Shilpi; Biniwale, Rajesh; Papadopoulos, George K

    2013-01-21

    The problem of simulating processes involving equilibria and dynamics of guest sorbates within zeolitic imidazolate frameworks (ZIF) by means of molecular dynamics (MD) computer experiments is of growing importance because of the promising role of ZIFs as molecular "traps" for clean energy applications. A key issue for validating such an atomistic modeling attempt is the possibility of comparing the MD results, with real experiments being able to capture analogous space and time scales to the ones pertained to the computer experiments. In the present study, this prerequisite is fulfilled through the quasi-elastic neutron scattering technique (QENS) for measuring self-diffusivity, by elaborating the incoherent scattering signal of hydrogen nuclei. QENS and MD experiments were performed in parallel to probe the hydrogen motion, for the first time in ZIF members. The predicted and measured dynamics behaviors show considerable concentration variation of the hydrogen self-diffusion coefficient in the two topologically different ZIF pore networks of this study, the ZIF-3 and ZIF-8. Modeling options such as the flexibility of the entire matrix versus a rigid framework version, the mobility of the imidazolate ligand, and the inclusion of quantum mechanical effects in the potential functions were examined in detail for the sorption thermodynamics and kinetics of hydrogen and also of deuterium, by employing MD combined with Widom averaging towards studying phase equilibria. The latter methodology ensures a rigorous and efficient way for post-processing the dynamics trajectory, thereby avoiding stochastic moves via Monte Carlo simulation, over the large number of configurational degrees of freedom a nonrigid framework encompasses.

  18. Designing inhibitors of cytochrome c/cardiolipin peroxidase complexes: mitochondria-targeted imidazole-substituted fatty acids.

    Science.gov (United States)

    Jiang, Jianfei; Bakan, Ahmet; Kapralov, Alexandr A; Silva, K Ishara; Huang, Zhentai; Amoscato, Andrew A; Peterson, James; Garapati, Venkata Krishna; Saxena, Sunil; Bayir, Hülya; Atkinson, Jeffrey; Bahar, Ivet; Kagan, Valerian E

    2014-06-01

    Mitochondria have emerged as the major regulatory platform responsible for the coordination of numerous metabolic reactions as well as cell death processes, whereby the execution of intrinsic apoptosis includes the production of reactive oxygen species fueling oxidation of cardiolipin (CL) catalyzed by cytochrome (Cyt) c. As this oxidation occurs within the peroxidase complex of Cyt c with CL, the latter represents a promising target for the discovery and design of drugs with antiapoptotic mechanisms of action. In this work, we designed and synthesized a new group of mitochondria-targeted imidazole-substituted analogs of stearic acid TPP-n-ISAs with various positions of the attached imidazole group on the fatty acid (n = 6, 8, 10, 13, and 14). By using a combination of absorption spectroscopy and EPR protocols (continuous wave electron paramagnetic resonance and electron spin echo envelope modulation) we demonstrated that TPP-n-ISAs indeed were able to potently suppress CL-induced structural rearrangements in Cyt c, paving the way to its peroxidase competence. TPP-n-ISA analogs preserved the low-spin hexa-coordinated heme-iron state in Cyt c/CL complexes whereby TPP-6-ISA displayed a significantly more effective preservation pattern than TPP-14-ISA. Elucidation of these intermolecular stabilization mechanisms of Cyt c identified TPP-6-ISA as an effective inhibitor of the peroxidase function of Cyt c/CL complexes with a significant antiapoptotic potential realized in mouse embryonic cells exposed to ionizing irradiation. These experimental findings were detailed and supported by all-atom molecular dynamics simulations. Based on the experimental data and computation predictions, we identified TPP-6-ISA as a candidate drug with optimized antiapoptotic potency. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. Cd(II)-coordination polymers based on tetracarboxylic acid and diverse bis(imidazole) ligands: Synthesis, structural diversity and photoluminescence properties

    Energy Technology Data Exchange (ETDEWEB)

    Arıcı, Mürsel, E-mail: marici@ogu.edu.tr [Department of Chemistry, Faculty of Arts and Sciences, Eskişehir Osmangazi University, 26480 Eskişehir (Turkey); Yeşilel, Okan Zafer [Department of Chemistry, Faculty of Arts and Sciences, Eskişehir Osmangazi University, 26480 Eskişehir (Turkey); Taş, Murat [Department of Science Education, Education Faculty, Ondokuz Mayıs University, 55139 Samsun (Turkey)

    2017-01-15

    Three new Cd(II)-coordination polymers, namely, ([Cd{sub 2}(μ{sub 6}-ao{sub 2}btc)(μ-1,5-bipe){sub 2}]·2H{sub 2}O){sub n} (1), ([Cd{sub 2}(μ{sub 6}-ao{sub 2}btc)(μ-1,4-bix){sub 2}]{sub n}·2DMF) (2) and ([Cd{sub 2}(μ{sub 8}-abtc)(μ-1,4-betix)]·DMF·H{sub 2}O){sub n} (3) (ao{sub 2}btc=di-oxygenated form of 3,3′,5,5′-azobenzenetetracarboxylate, 1,5-bipe: 1,5-bis(imidazol-1yl)pentane, 1,4-bix=1,4-bis(imidazol-1ylmethyl)benzene, 1,4-betix=1,4-bis(2-ethylimidazol-1ylmethyl)benzene) were synthesized with 3,3′,5,5′-azobenzenetetracarboxylic acid and flexible, semi-flexible and semi-flexible substituted bis(imidazole) linkers. They were characterized by IR spectroscopy, elemental analysis, single-crystal X-ray diffraction, powder X-ray diffractions (PXRD) and thermal analyses (TG/DTA). Complexes 1–3 exhibited structural diversities depending on flexible, semi-flexible and semi-flexible substituted bis(imidazole) ligands. Complex 1 was 2D structure with 3,6L18 topology. Complex 2 had a 3D pillar-layered framework with the rare sqc27 topology. When semi-flexible substituted bis(imidazole) linker was used, 3D framework of complex 3 was obtained with the paddlewheel Cd{sub 2}(CO{sub 2}){sub 4}-type binuclear SBU. Moreover, thermal and photoluminescence properties of the complexes were determined in detailed. - Graphical abstract: In this study, three novel Cd(II)-coordination polymers were synthesized with 3,3′,5,5′-azobenzenetetracarboxylic acid and flexible, semi-flexible and semi-flexible substituted bis(imidazole) linkers. They were characterized by IR spectroscopy, elemental analysis, single-crystal X-ray diffraction, powder X-ray diffractions (PXRD) and thermal analyses (TG/DTA). Complexes 1–3 exhibited structural diversities depending on flexible, semi-flexible and semi-flexible substituted bis(imidazole) ligands. Complex 1 was 2D structure with 3,6L18 topology. Complex 2 had a 3D pillar-layered framework with the rare sqc27 topology. When semi

  20. Allosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Ying-Nan P.; LaMarche, Matthew J.; Chan, Ho Man; Fekkes, Peter; Garcia-Fortanet, Jorge; Acker, Michael G.; Antonakos, Brandon; Chen, Christine Hiu-Tung; Chen, Zhouliang; Cooke, Vesselina G.; Dobson, Jason R.; Deng, Zhan; Fei, Feng; Firestone, Brant; Fodor, Michelle; Fridrich, Cary; Gao, Hui; Grunenfelder, Denise; Hao, Huai-Xiang; Jacob, Jaison; Ho, Samuel; Hsiao, Kathy; Kang, Zhao B.; Karki, Rajesh; Kato, Mitsunori; Larrow, Jay; La Bonte, Laura R.; Lenoir, Francois; Liu, Gang; Liu, Shumei; Majumdar, Dyuti; Meyer, Matthew J.; Palermo, Mark; Perez, Lawrence; Pu, Minying; Price, Edmund; Quinn, Christopher; Shakya, Subarna; Shultz, Michael D.; Slisz, Joanna; Venkatesan, Kavitha; Wang, Ping; Warmuth, Markus; Williams, Sarah; Yang, Guizhi; Yuan, Jing; Zhang, Ji-Hu; Zhu, Ping; Ramsey, Timothy; Keen, Nicholas J.; Sellers, William R.; Stams, Travis; Fortin , Pascal D. (Novartis)

    2016-06-29

    The non-receptor protein tyrosine phosphatase SHP2, encoded by PTPN11, has an important role in signal transduction downstream of growth factor receptor signalling and was the first reported oncogenic tyrosine phosphatase1. Activating mutations of SHP2 have been associated with developmental pathologies such as Noonan syndrome and are found in multiple cancer types, including leukaemia, lung and breast cancer and neuroblastoma1, 2, 3, 4, 5. SHP2 is ubiquitously expressed and regulates cell survival and proliferation primarily through activation of the RAS–ERK signalling pathway2, 3. It is also a key mediator of the programmed cell death 1 (PD-1) and B- and T-lymphocyte attenuator (BTLA) immune checkpoint pathways6, 7. Reduction of SHP2 activity suppresses tumour cell growth and is a potential target of cancer therapy8, 9. Here we report the discovery of a highly potent (IC50 = 0.071 μM), selective and orally bioavailable small-molecule SHP2 inhibitor, SHP099, that stabilizes SHP2 in an auto-inhibited conformation. SHP099 concurrently binds to the interface of the N-terminal SH2, C-terminal SH2, and protein tyrosine phosphatase domains, thus inhibiting SHP2 activity through an allosteric mechanism. SHP099 suppresses RAS–ERK signalling to inhibit the proliferation of receptor-tyrosine-kinase-driven human cancer cells in vitro and is efficacious in mouse tumour xenograft models. Together, these data demonstrate that pharmacological inhibition of SHP2 is a valid therapeutic approach for the treatment of cancers.

  1. The allosteric behavior of Fur mediates oxidative stress signal transduction in Helicobacter pylori

    Directory of Open Access Journals (Sweden)

    Simone ePelliciari

    2015-08-01

    Full Text Available The microaerophilic gastric pathogen Helicobacter pylori is exposed to oxidative stress originating from the aerobic environment, the oxidative burst of phagocytes and the formation of reactive oxygen species, catalyzed by iron excess. Accordingly, the expression of genes involved in oxidative stress defense have been repeatedly linked to the ferric uptake regulator Fur. Moreover, mutations in the Fur protein affect the resistance to metronidazole, likely due to loss-of-function in the regulation of genes involved in redox control. Although many advances in the molecular understanding of HpFur function were made, little is known about the mechanisms that enable Fur to mediate the responses to oxidative stress.Here we show that iron-inducible, apo-Fur repressed genes, such as pfr and hydA, are induced shortly after oxidative stress, while their oxidative induction is lost in a fur knockout strain. On the contrary, holo-Fur repressed genes, such as frpB1 and fecA1, vary modestly in response to oxidative stress. This indicates that the oxidative stress signal specifically targets apo-Fur repressed genes, rather than impairing indiscriminately the regulatory function of Fur. Footprinting analyses showed that the oxidative signal strongly impairs the binding affinity of Fur towards apo-operators, while the binding towards holo-operators is less affected. Further evidence is presented that a reduced state of Fur is needed to maintain apo-repression, while oxidative conditions shift the preferred binding architecture of Fur towards the holo-operator binding conformation, even in the absence of iron. Together the results demonstrate that the allosteric regulation of Fur enables transduction of oxidative stress signals in H. pylori, supporting the concept that apo-Fur repressed genes can be considered oxidation inducible Fur regulatory targets. These findings may have important implications in the study of H. pylori treatment and resistance to

  2. Binding and Signaling Studies Disclose a Potential Allosteric Site for Cannabidiol in Cannabinoid CB2 Receptors

    Directory of Open Access Journals (Sweden)

    Eva Martínez-Pinilla

    2017-10-01

    Full Text Available The mechanism of action of cannabidiol (CBD, the main non-psychotropic component of Cannabis sativa L., is not completely understood. First assumed that the compound was acting via cannabinoid CB2 receptors (CB2Rs it is now suggested that it interacts with non-cannabinoid G-protein-coupled receptors (GPCRs; however, CBD does not bind with high affinity to the orthosteric site of any GPCR. To search for alternative explanations, we tested CBD as a potential allosteric ligand of CB2R. Radioligand and non-radioactive homogeneous binding, intracellular cAMP determination and ERK1/2 phosphorylation assays were undertaken in heterologous systems expressing the human version of CB2R. Using membrane preparations from CB2R-expressing HEK-293T (human embryonic kidney 293T cells, we confirmed that CBD does not bind with high affinity to the orthosteric site of the human CB2R where the synthetic cannabinoid, [3H]-WIN 55,212-2, binds. CBD was, however, able to produce minor but consistent reduction in the homogeneous binding assays in living cells using the fluorophore-conjugated CB2R-selective compound, CM-157. The effect on binding to CB2R-expressing living cells was different to that exerted by the orthosteric antagonist, SR144528, which decreased the maximum binding without changing the KD. CBD at nanomolar concentrations was also able to significantly reduce the effect of the selective CB2R agonist, JWH133, on forskolin-induced intracellular cAMP levels and on activation of the MAP kinase pathway. These results may help to understand CBD mode of action and may serve to revisit its therapeutic possibilities.

  3. Allosteric communication in myosin V: from small conformational changes to large directed movements.

    Directory of Open Access Journals (Sweden)

    M Cecchini

    Full Text Available The rigor to post-rigor transition in myosin, a consequence of ATP binding, plays an essential role in the Lymn-Taylor functional cycle because it results in the dissociation of the actomyosin complex after the powerstroke. On the basis of the X-ray structures of myosin V, we have developed a new normal mode superposition model for the transition path between the two states. Rigid-body motions of the various subdomains and specific residues at the subdomain interfaces are key elements in the transition. The allosteric communication between the nucleotide binding site and the U50/L50 cleft is shown to result from local changes due to ATP binding, which induce large amplitude motions that are encoded in the structure of the protein. The triggering event is the change in the interaction of switch I and the P-loop, which is stabilized by ATP binding. The motion of switch I, which is a relatively rigid element of the U50 subdomain, leads directly to a partial opening of the U50/L50 cleft; the latter is expected to weaken the binding of myosin to actin. The calculated transition path demonstrates the nature of the subdomain coupling and offers an explanation for the mutual exclusion of ATP and actin binding. The mechanism of the uncoupling of the converter from the motor head, an essential part of the transition, is elucidated. The origin of the partial untwisting of the central beta-sheet in the rigor to post-rigor transition is described.

  4. Allosteric activation of the follicle-stimulating hormone (FSH) receptor by selective, nonpeptide agonists.

    Science.gov (United States)

    Yanofsky, Stephen D; Shen, Emily S; Holden, Frank; Whitehorn, Erik; Aguilar, Barbara; Tate, Emily; Holmes, Christopher P; Scheuerman, Randall; MacLean, Derek; Wu, May M; Frail, Donald E; López, Francisco J; Winneker, Richard; Arey, Brian J; Barrett, Ronald W

    2006-05-12

    The pituitary glycoprotein hormones, luteinizing hormone and follicle-stimulating hormone (FSH), act through their cognate receptors to initiate a series of coordinated physiological events that results in germ cell maturation. Given the importance of FSH in regulating folliculogenesis and fertility, the development of FSH mimetics has been sought to treat infertility. Currently, purified and recombinant human FSH are the only FSH receptor (FSH-R) agonists available for infertility treatment. By screening unbiased combinatorial chemistry libraries, using a cAMP-responsive luciferase reporter assay, we discovered thiazolidinone agonists (EC50's = 20 microm) of the human FSH-R. Subsequent analog library screening and parallel synthesis optimization resulted in the identification of a potent agonist (EC50 = 2 nm) with full efficacy compared with FSH that was FSH-R-selective and -dependent. The compound mediated progesterone production in Y1 cells transfected with the human FSH-R (EC50 = 980 nm) and estradiol production from primary rat ovarian granulosa cells (EC50 = 10.5 nm). This and related compounds did not compete with FSH for binding to the FSH-R. Use of human FSH/thyroid-stimulating hormone (TSH) receptor chimeras suggested a novel mechanism for receptor activation through a binding site independent of the natural hormone binding site. This study is the first report of a high affinity small molecule agonist that activates a glycoprotein hormone receptor through an allosteric mechanism. The small molecule FSH receptor agonists described here could lead to an oral alternative to the current parenteral FSH treatments used clinically to induce ovarian stimulation for both in vivo and in vitro fertilization therapy.

  5. A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein.

    Directory of Open Access Journals (Sweden)

    Anurag Sethi

    Full Text Available The HIV-1 envelope (Env spike, which consists of a compact, heterodimeric trimer of the glycoproteins gp120 and gp41, is the target of neutralizing antibodies. However, the high mutation rate of HIV-1 and plasticity of Env facilitates viral evasion from neutralizing antibodies through various mechanisms. Mutations that are distant from the antibody binding site can lead to escape, probably by changing the conformation or dynamics of Env; however, these changes are difficult to identify and define mechanistically. Here we describe a network analysis-based approach to identify potential allosteric immune evasion mechanisms using three known HIV-1 Env gp120 protein structures from two different clades, B and C. First, correlation and principal component analyses of molecular dynamics (MD simulations identified a high degree of long-distance coupled motions that exist between functionally distant regions within the intrinsic dynamics of the gp120 core, supporting the presence of long-distance communication in the protein. Then, by integrating MD simulations with network theory, we identified the optimal and suboptimal communication pathways and modules within the gp120 core. The results unveil both strain-dependent and -independent characteristics of the communication pathways in gp120. We show that within the context of three structurally homologous gp120 cores, the optimal pathway for communication is sequence sensitive, i.e. a suboptimal pathway in one strain becomes the optimal pathway in another strain. Yet the identification of conserved elements within these communication pathways, termed inter-modular hotspots, could present a new opportunity for immunogen design, as this could be an additional mechanism that HIV-1 uses to shield vulnerable antibody targets in Env that induce neutralizing antibody breadth.

  6. Allosteric Regulation in the Ligand Binding Domain of Retinoic Acid Receptorγ.

    Directory of Open Access Journals (Sweden)

    Yassmine Chebaro

    Full Text Available Retinoic acid (RA plays key roles in cell differentiation and growth arrest through nuclear retinoic acid receptors (RARs, which are ligand-dependent transcription factors. While the main trigger of RAR activation is the binding of RA, phosphorylation of the receptors has also emerged as an important regulatory signal. Phosphorylation of the RARγ N-terminal domain (NTD is known to play a functional role in neuronal differentiation. In this work, we investigated the phosphorylation of RARγ ligand binding domain (LBD, and present evidence that the phosphorylation status of the LBD affects the phosphorylation of the NTD region. We solved the X-ray structure of a phospho-mimetic mutant of the LBD (RARγ S371E, which we used in molecular dynamics simulations to characterize the consequences of the S371E mutation on the RARγ structural dynamics. Combined with simulations of the wild-type LBD, we show that the conformational equilibria of LBD salt bridges (notably R387-D340 are affected by the S371E mutation, which likely affects the recruitment of the kinase complex that phosphorylates the NTD. The molecular dynamics simulations also showed that a conservative mutation in this salt bridge (R387K affects the dynamics of the LBD without inducing large conformational changes. Finally, cellular assays showed that the phosphorylation of the NTD of RARγ is differentially regulated by retinoic acid in RARγWT and in the S371N, S371E and R387K mutants. This multidisciplinary work highlights an allosteric coupling between phosphorylations of the LBD and the NTD of RARγ and supports the importance of structural dynamics involving electrostatic interactions in the regulation of RARs activity.

  7. Adaptive response and genomic instability: allosteric response of genome to negative impact

    International Nuclear Information System (INIS)

    Sasaki, Masao S.

    2010-01-01

    Currently, there is an upsurge concern on the unique response of living cells to low dose ionizing radiation for its inconformity to the existing paradigm of the biological action of radiation and its impact on the current understanding of risk evaluation of health effect of radiation in our workplace and environment. For the allosteric response to have significance, the cells must have an excellent sensing mechanism to discriminate tolerable and intolerable signals. In a series of experiments with mammalian, including human, cells, we demonstrated a novel sensing and signaling mechanism in the low-dose irradiated cells that was mediated by a PKCα-p3BMAPK-PLCδ1 feedback regulatory loop. Upon irradiation, PKCα is immediately activated, which in turn activate p38MAPK. The activation of p38MAPK is feedbacked to the activation of PKCα via PLCδ1, which catalyzes the hydrolysis of PtdInsP2 to generate PKCα-directed second messengers DAG and lnsP3. At low doses, the PKCα and p38MAPK continue to be activated for long time through this feedback loop, but when the cells encounter the high dose (>10 cGy or equivalent), the feedback loop is immediately comes to shutdown by deprivation of PKCα protein, known as down-regulation of PKC signaling. Thus, PKCα plays a key role in the long lasting nature of adaptive response to low doses and a binary switch to the genomic instability by too much signals. Tumor suppressor protein, p53, is a downstream effecter

  8. Rational Design and Tuning of Functional RNA Switch to Control an Allosteric Intermolecular Interaction.

    Science.gov (United States)

    Endoh, Tamaki; Sugimoto, Naoki

    2015-08-04

    Conformational transitions of biomolecules in response to specific stimuli control many biological processes. In natural functional RNA switches, often called riboswitches, a particular RNA structure that has a suppressive or facilitative effect on gene expression transitions to an alternative structure with the opposite effect upon binding of a specific metabolite to the aptamer region. Stability of RNA secondary structure (-ΔG°) can be predicted based on thermodynamic parameters and is easily tuned by changes in nucleobases. We envisioned that tuning of a functional RNA switch that causes an allosteric interaction between an RNA and a peptide would be possible based on a predicted switching energy (ΔΔG°) that corresponds to the energy difference between the RNA secondary structure before (-ΔG°before) and after (-ΔG°after) the RNA conformational transition. We first selected functional RNA switches responsive to neomycin with predicted ΔΔG° values ranging from 5.6 to 12.2 kcal mol(-1). We then demonstrated a simple strategy to rationally convert the functional RNA switch to switches responsive to natural metabolites thiamine pyrophosphate, S-adenosyl methionine, and adenine based on the predicted ΔΔG° values. The ΔΔG° values of the designed RNA switches proportionally correlated with interaction energy (ΔG°interaction) between the RNA and peptide, and we were able to tune the sensitivity of the RNA switches for the trigger molecule. The strategy demonstrated here will be generally applicable for construction of functional RNA switches and biosensors in which mechanisms are based on conformational transition of nucleic acids.

  9. Binding and Signaling Studies Disclose a Potential Allosteric Site for Cannabidiol in Cannabinoid CB2 Receptors.

    Science.gov (United States)

    Martínez-Pinilla, Eva; Varani, Katia; Reyes-Resina, Irene; Angelats, Edgar; Vincenzi, Fabrizio; Ferreiro-Vera, Carlos; Oyarzabal, Julen; Canela, Enric I; Lanciego, José L; Nadal, Xavier; Navarro, Gemma; Borea, Pier Andrea; Franco, Rafael

    2017-01-01

    The mechanism of action of cannabidiol (CBD), the main non-psychotropic component of Cannabis sativa L., is not completely understood. First assumed that the compound was acting via cannabinoid CB 2 receptors (CB 2 Rs) it is now suggested that it interacts with non-cannabinoid G-protein-coupled receptors (GPCRs); however, CBD does not bind with high affinity to the orthosteric site of any GPCR. To search for alternative explanations, we tested CBD as a potential allosteric ligand of CB 2 R. Radioligand and non-radioactive homogeneous binding, intracellular cAMP determination and ERK1/2 phosphorylation assays were undertaken in heterologous systems expressing the human version of CB 2 R. Using membrane preparations from CB 2 R-expressing HEK-293T (human embryonic kidney 293T) cells, we confirmed that CBD does not bind with high affinity to the orthosteric site of the human CB 2 R where the synthetic cannabinoid, [ 3 H]-WIN 55,212-2, binds. CBD was, however, able to produce minor but consistent reduction in the homogeneous binding assays in living cells using the fluorophore-conjugated CB 2 R-selective compound, CM-157. The effect on binding to CB 2 R-expressing living cells was different to that exerted by the orthosteric antagonist, SR144528, which decreased the maximum binding without changing the K D . CBD at nanomolar concentrations was also able to significantly reduce the effect of the selective CB 2 R agonist, JWH133, on forskolin-induced intracellular cAMP levels and on activation of the MAP kinase pathway. These results may help to understand CBD mode of action and may serve to revisit its therapeutic possibilities.

  10. Cyclophilin40 isomerase activity is regulated by a temperature-dependent allosteric interaction with Hsp90.

    Science.gov (United States)

    Blackburn, Elizabeth A; Wear, Martin A; Landré, Vivian; Narayan, Vikram; Ning, Jia; Erman, Burak; Ball, Kathryn L; Walkinshaw, Malcolm D

    2015-09-01

    Cyclophilin 40 (Cyp40) comprises an N-terminal cyclophilin domain with peptidyl-prolyl isomerase (PPIase) activity and a C-terminal tetratricopeptide repeat (TPR) domain that binds to the C-terminal-EEVD sequence common to both heat shock protein 70 (Hsp70) and Hsp90. We show in the present study that binding of peptides containing the MEEVD motif reduces the PPIase activity by ∼30%. CD and fluorescence assays show that the TPR domain is less stable than the cyclophilin domain and is stabilized by peptide binding. Isothermal titration calorimetry (ITC) shows that the affinity for the-MEEVD peptide is temperature sensitive in the physiological temperature range. Results from these biophysical studies fit with the MD simulations of the apo and holo (peptide-bound) structures which show a significant reduction in root mean square (RMS) fluctuation in both TPR and cyclophilin domains when-MEEVD is bound. The MD simulations of the apo-protein also highlight strong anti-correlated motions between residues around the PPIase-active site and a band of residues running across four of the seven helices in the TPR domain. Peptide binding leads to a distortion in the shape of the active site and a significant reduction in these strongly anti-correlated motions, providing an explanation for the allosteric effect of ligand binding and loss of PPIase activity. Together the experimental and MD results suggest that on heat shock, dissociation of Cyp40 from complexes mediated by the TPR domain leads to an increased pool of free Cyp40 capable of acting as an isomerase/chaperone in conditions of cellular stress. © 2015 Authors.

  11. Hemoglobin function and allosteric regulation in semi-fossorial rodents (family Sciuridae) with different altitudinal ranges

    Science.gov (United States)

    Revsbech, Inge G.; Tufts, Danielle M.; Projecto-Garcia, Joana; Moriyama, Hideaki; Weber, Roy E.; Storz, Jay F.; Fago, Angela

    2013-01-01

    SUMMARY Semi-fossorial ground squirrels face challenges to respiratory gas transport associated with the chronic hypoxia and hypercapnia of underground burrows, and such challenges are compounded in species that are native to high altitude. During hibernation, such species must also contend with vicissitudes of blood gas concentrations and plasma pH caused by episodic breathing. Here, we report an analysis of hemoglobin (Hb) function in six species of marmotine ground squirrels with different altitudinal distributions. Regardless of their native altitude, all species have high Hb–O2 affinities, mainly due to suppressed sensitivities to allosteric effectors [2,3-diphosphoglycerate (DPG) and chloride ions]. This suppressed anion sensitivity is surprising given that all canonical anion-binding sites are conserved. Two sciurid species, the golden-mantled and thirteen-lined ground squirrel, have Hb–O2 affinities that are characterized by high pH sensitivity and low thermal sensitivity relative to the Hbs of humans and other mammals. The pronounced Bohr effect is surprising in light of highly unusual amino acid substitutions at the C-termini that are known to abolish the Bohr effect in human HbA. Taken together, the high O2 affinity of sciurid Hbs suggests an enhanced capacity for pulmonary O2 loading under hypoxic and hypercapnic conditions, while the large Bohr effect should help to ensure efficient O2 unloading in tissue capillaries. In spite of the relatively low thermal sensitivities of the sciurid Hbs, our results indicate that the effect of hypothermia on Hb oxygenation is the main factor contributing to the increased blood–O2 affinity in hibernating ground squirrels. PMID:24172889

  12. Negative Allosteric Modulators of Metabotropic Glutamate Receptors Subtype 5 in Addiction: a Therapeutic Window

    Science.gov (United States)

    2016-01-01

    Background: Abundant evidence at the anatomical, electrophysiological, and molecular levels implicates metabotropic glutamate receptor subtype 5 (mGluR5) in addiction. Consistently, the effects of a wide range of doses of different mGluR5 negative allosteric modulators (NAMs) have been tested in various animal models of addiction. Here, these studies were subjected to a systematic review to find out if mGluR5 NAMs have a therapeutic potential that can be translated to the clinic. Methods: Literature on consumption/self-administration and reinstatement of drug seeking as outcomes of interest published up to April 2015 was retrieved via PubMed. The review focused on the effects of systemic (i.p., i.v., s.c.) administration of the mGluR5 NAMs 3-((2-Methyl-4-thiazolyl)ethynyl)pyridine (MTEP) and 2-Methyl-6-(phenylethynyl)pyridine (MPEP) on paradigms with cocaine, ethanol, nicotine, and food in rats. Results: MTEP and MPEP were found to reduce self-administration of cocaine, ethanol, and nicotine at doses ≥1mg/kg and 2.5mg/kg, respectively. Dose-response relationship resembled a sigmoidal curve, with low doses not reaching statistical significance and high doses reliably inhibiting self-administration of drugs of abuse. Importantly, self-administration of cocaine, ethanol, and nicotine, but not food, was reduced by MTEP and MPEP in the dose range of 1 to 2mg/kg and 2.5 to 3.2mg/kg, respectively. This dose range corresponds to approximately 50% to 80% mGluR5 occupancy. Interestingly, the limited data found in mice and monkeys showed a similar therapeutic window. Conclusion: Altogether, this review suggests a therapeutic window for mGluR5 NAMs that can be translated to the treatment of substance-related and addictive disorders. PMID:26802568

  13. Substrate specificity changes for human reticulocyte and epithelial 15-lipoxygenases reveal allosteric product regulation.

    Science.gov (United States)

    Wecksler, Aaron T; Kenyon, Victor; Deschamps, Joshua D; Holman, Theodore R

    2008-07-15

    Human reticulocyte 15-lipoxygenase (15-hLO-1) and epithelial 15-lipoxygenase (15-hLO-2) have been implicated in a number of human diseases, with differences in their substrate specificity potentially playing a central role. In this paper, we present a novel method for accurately measuring the substrate specificity of the two 15-hLO isozymes and demonstrate that both cholate and specific LO products affect substrate specificity. The linoleic acid (LA) product, 13-hydroperoxyoctadienoic acid (13-HPODE), changes the ( k cat/ K m) (AA)/( k cat/ K m) (LA) ratio more than 5-fold for 15-hLO-1 and 3-fold for 15-hLO-2, while the arachidonic acid (AA) product, 12-( S)-hydroperoxyeicosatetraenoic acid (12-HPETE), affects only the ratio of 15-hLO-1 (more than 5-fold). In addition, the reduced products, 13-( S)-hydroxyoctadecadienoic acid (13-HODE) and 12-( S)-hydroxyeicosatetraenoic acid (12-HETE), also affect substrate specificity, indicating that iron oxidation is not responsible for the change in the ( k cat/ K m) (AA)/( k cat/ K m) (LA) ratio. These results, coupled with the dependence of the 15-hLO-1 k cat/ K m kinetic isotope effect ( (D) k cat/ K m) on the presence of 12-HPETE and 12-HETE, indicate that the allosteric site, previously identified in 15-hLO-1 [Mogul, R., Johansen, E., and Holman, T. R. (1999) Biochemistry 39, 4801-4807], is responsible for the change in substrate specificity. The ability of LO products to regulate substrate specificity may be relevant with respect to cancer progression and warrants further investigation into the role of this product-feedback loop in the cell.

  14. Orthosteric and Allosteric Ligands of Nicotinic Acetylcholine Receptors for Smoking Cessation

    Directory of Open Access Journals (Sweden)

    Tasnim S. Mohamed

    2015-11-01

    Full Text Available Nicotine addiction, the result of tobacco use, leads to over six million premature deaths world-wide, a number that is expected to increase by a third within the next two decades. While more than half of smokers want and attempt to quit, only a small percentage of smokers are able to quit without pharmacological interventions. Therefore, over the past decades, researchers in academia and the pharmaceutical industry have focused their attention on the development of more effective smoking cessation therapies, which is now a growing 1.9 billion dollar market. Because the role of neuronal nicotinic acetylcholine receptors (nAChR in nicotine addiction is well established, nAChR based therapeutics remain the leading strategy for smoking cessation. However, the development of neuronal nAChR drugs that are selective for a nAChR subpopulation is challenging, and only few neuronal nAChR drugs are clinically available. Among the many neuronal nAChR subtypes that have been identified in the brain, the α4β2 subtype is the most abundant and plays a critical role in nicotine addiction. Here, we review the role of neuronal nAChRs, especially the α4β2 subtype, in the development and treatment of nicotine addiction. We also compare available smoking cessation medications and other nAChR orthosteric and allosteric ligands that have been developed with emphasis on the difficulties faced in the development of clinically useful compounds with high nAChR subtype selectivity.

  15. Identification of potential small molecule allosteric modulator sites on IL-1R1 ectodomain using accelerated conformational sampling method.

    Directory of Open Access Journals (Sweden)

    Chao-Yie Yang

    Full Text Available The interleukin-1 receptor (IL-1R is the founding member of the interleukin 1 receptor family which activates innate immune response by its binding to cytokines. Reports showed dysregulation of cytokine production leads to aberrant immune cells activation which contributes to auto-inflammatory disorders and diseases. Current therapeutic strategies focus on utilizing antibodies or chimeric cytokine biologics. The large protein-protein interaction interface between cytokine receptor and cytokine poses a challenge in identifying binding sites for small molecule inhibitor development. Based on the significant conformational change of IL-1R type 1 (IL-1R1 ectodomain upon binding to different ligands observed in crystal structures, we hypothesized that transient small molecule binding sites may exist when IL-1R1 undergoes conformational transition and thus suitable for inhibitor development. Here, we employed accelerated molecular dynamics (MD simulation to efficiently sample conformational space of IL-1R1 ectodomain. Representative IL-1R1 ectodomain conformations determined from the hierarchy cluster analysis were analyzed by the SiteMap program which leads to identify small molecule binding sites at the protein-protein interaction interface and allosteric modulator locations. The cosolvent mapping analysis using phenol as the probe molecule further confirms the allosteric modulator site as a binding hotspot. Eight highest ranked fragment molecules identified from in silico screening at the modulator site were evaluated by MD simulations. Four of them restricted the IL-1R1 dynamical motion to inactive conformational space. The strategy from this study, subject to in vitro experimental validation, can be useful to identify small molecule compounds targeting the allosteric modulator sites of IL-1R and prevent IL-1R from binding to cytokine by trapping IL-1R in inactive conformations.

  16. In search of allosteric modulators of a7-nAChR by solvent density guided virtual screening.

    Science.gov (United States)

    Dey, Raja; Chen, Lin

    2011-04-01

    Nicotinic acetylcholine receptors (nAChR) are pentameric ligand gated ion channels whose activity can be modulated by endogenous neurotransmitters as well as by synthetic ligands that bind the same or distinct sites from the natural ligand. The subtype of α7 nAChR has been considered as a potenial therapeutic target for Alzheimer's disease, schizophrenia and other neurological and psychiatric disorders. Here we have developed a homology model of α7 nAChR based on two high resolution crystal structures with Brookhaven Protein Data Bank (PDB) codes 2QC1 and 2WN9 for threading on one monomer and then for building a pentamer, respectively. A number of small molecule binding sites are identified using Pocket Finder (J. An, M. Tortov, and R. Abagyan, Molecular & Cellular Proteomics, 4.6, 752-761 (2005)) of Internal Coordinate Mechanics (ICM). Remarkably, these computer-identified sites match perfectly with ordered solvent densities found in the high-resolution crystal structure of α1 nAChR, suggesting that the surface cavities in the α7 nAChR model are likely binding sites of small molecules. A high throughput virtual screening by flexible ligand docking of 5008 small molecule compounds was performed at three potential allosteric modulator (AM) binding sites of α7 nAChR using Molsoft ICM software (R. Abagyan, M. Tortov and D. Kuznetsov, J Comput Chem 15, 488-506, (1994)). Some experimentally verified allosteric modulators of α7 like CCMI comp-6, LY 7082101, 5-HI, TQS, PNU-120596, genistein, and NS-1738 ranked among top 100 compounds, while the rest of the compounds in the list could guide further search for new allosteric modulators.

  17. Positive allosteric modulation of mGluR5 accelerates extinction learning but not relearning following methamphetamine self-administration

    Directory of Open Access Journals (Sweden)

    Peter R Kufahl

    2012-11-01

    Full Text Available Recent studies have implicated glutamate neurotransmission as an important substrate for the extinction of conditioned behaviors, including responding for drug reinforcement. Positive allosteric modulation of the type-5 metabotropic glutamate receptor (mGluR5 in particular has emerged as a treatment strategy for the enhancement of extinction of drug-motivated behaviors. Here, we investigated the effects of the mGluR5 positive allosteric modulator CDPPB, a compound known for its cognitive enhancing effects in rodents, on extinction learning in rats with different histories of methamphetamine (METH training. Rats were trained to self-administer METH under two conditions: 16 daily sessions of short access (90 min/day, ShA, or 8 daily sessions of short access followed by 8 sessions of long access (6 hr/day, LgA. Control rats self-administered sucrose pellets in daily 30 min sessions. Next, rats were administered vehicle or 30 mg/kg CDPPB prior to 7 consecutive daily extinction sessions, subjected to additional extinction sessions to re-establish a post-treatment baseline, and then tested for reinstatement of behavior in the presence of METH- or sucrose-paired cues. Rats were then subjected to a second series of extinction sessions, preceded by vehicle or 30 mg/kg CDPPB, and an additional test for cue-triggered reinstatement. CDPPB treatment resulted in a more rapid extinction of responding on the active lever, especially in the early sessions of the first extinction sequence. However, treatment effects were minimal during subsequent cue reinstatement tests and nonexistent during the second series of extinction sessions. Rats with histories of ShA, LgA and sucrose training expressed similar behavioral sensitivities to CDPPB, with LgA rats demonstrating a modestly higher treatment effect. Positive allosteric modulation of mGluR5 may therefore have some beneficial effects on efforts to facilitate extinction learning and reduce methamphetamine seeking.

  18. Vestigialization of an allosteric switch: genetic and structural mechanisms for the evolution of constitutive activity in a steroid hormone receptor.

    Directory of Open Access Journals (Sweden)

    Jamie T Bridgham

    2014-01-01

    Full Text Available An important goal in molecular evolution is to understand the genetic and physical mechanisms by which protein functions evolve and, in turn, to characterize how a protein's physical architecture influences its evolution. Here we dissect the mechanisms for an evolutionary shift in function in the mollusk ortholog of the steroid hormone receptors (SRs, a family of biologically essential transcription factors. In vertebrates, the activity of SRs allosterically depends on binding a hormonal ligand; in mollusks, however, the SR ortholog (called ER, because of high sequence similarity to vertebrate estrogen receptors activates transcription in the absence of ligand and does not respond to steroid hormones. To understand how this shift in regulation evolved, we combined evolutionary, structural, and functional analyses. We first determined the X-ray crystal structure of the ER of the Pacific oyster Crassostrea gigas (CgER, and found that its ligand pocket is filled with bulky residues that prevent ligand occupancy. To understand the genetic basis for the evolution of mollusk ERs' unique functions, we resurrected an ancient SR progenitor and characterized the effect of historical amino acid replacements on its functions. We found that reintroducing just two ancient replacements from the lineage leading to mollusk ERs recapitulates the evolution of full constitutive activity and the loss of ligand activation. These substitutions stabilize interactions among key helices, causing the allosteric switch to become "stuck" in the active conformation and making activation independent of ligand binding. Subsequent changes filled the ligand pocket without further affecting activity; by degrading the allosteric switch, these substitutions vestigialized elements of the protein's architecture required for ligand regulation and made reversal to the ancestral function more complex. These findings show how the physical architecture of allostery enabled a few large

  19. Vestigialization of an Allosteric Switch: Genetic and Structural Mechanisms for the Evolution of Constitutive Activity in a Steroid Hormone Receptor

    Science.gov (United States)

    Bridgham, Jamie T.; Keay, June; Ortlund, Eric A.; Thornton, Joseph W.

    2014-01-01

    An important goal in molecular evolution is to understand the genetic and physical mechanisms by which protein functions evolve and, in turn, to characterize how a protein's physical architecture influences its evolution. Here we dissect the mechanisms for an evolutionary shift in function in the mollusk ortholog of the steroid hormone receptors (SRs), a family of biologically essential transcription factors. In vertebrates, the activity of SRs allosterically depends on binding a hormonal ligand; in mollusks, however, the SR ortholog (called ER, because of high sequence similarity to vertebrate estrogen receptors) activates transcription in the absence of ligand and does not respond to steroid hormones. To understand how this shift in regulation evolved, we combined evolutionary, structural, and functional analyses. We first determined the X-ray crystal structure of the ER of the Pacific oyster Crassostrea gigas (CgER), and found that its ligand pocket is filled with bulky residues that prevent ligand occupancy. To understand the genetic basis for the evolution of mollusk ERs' unique functions, we resurrected an ancient SR progenitor and characterized the effect of historical amino acid replacements on its functions. We found that reintroducing just two ancient replacements from the lineage leading to mollusk ERs recapitulates the evolution of full constitutive activity and the loss of ligand activation. These substitutions stabilize interactions among key helices, causing the allosteric switch to become “stuck” in the active conformation and making activation independent of ligand binding. Subsequent changes filled the ligand pocket without further affecting activity; by degrading the allosteric switch, these substitutions vestigialized elements of the protein's architecture required for ligand regulation and made reversal to the ancestral function more complex. These findings show how the physical architecture of allostery enabled a few large-effect mutations

  20. The Enzyme Function Initiative†

    Science.gov (United States)

    Gerlt, John A.; Allen, Karen N.; Almo, Steven C.; Armstrong, Richard N.; Babbitt, Patricia C.; Cronan, John E.; Dunaway-Mariano, Debra; Imker, Heidi J.; Jacobson, Matthew P.; Minor, Wladek; Poulter, C. Dale; Raushel, Frank M.; Sali, Andrej; Shoichet, Brian K.; Sweedler, Jonathan V.

    2011-01-01

    The Enzyme Function Initiative (EFI) was recently established to address the challenge of assigning reliable functions to enzymes discovered in bacterial genome projects; in this Current Topic we review the structure and operations of the EFI. The EFI includes the Superfamily/Genome, Protein, Structure, Computation, and Data/Dissemination Cores that provide the infrastructure for reliably predicting the in vitro functions of unknown enzymes. The initial targets for functional assignment are selected from five functionally diverse superfamilies (amidohydrolase, enolase, glutathione transferase, haloalkanoic acid dehalogenase, and isoprenoid synthase), with five superfamily-specific Bridging Projects experimentally testing the predicted in vitro enzymatic activities. The EFI also includes the Microbiology Core that evaluates the in vivo context of in vitro enzymatic functions and confirms the functional predictions of the EFI. The deliverables of the EFI to the scientific community include: 1) development of a large-scale, multidisciplinary sequence/structure-based strategy for functional assignment of unknown enzymes discovered in genome projects (target selection, protein production, structure determination, computation, experimental enzymology, microbiology, and structure-based annotation); 2) dissemination of the strategy to the community via publications, collaborations, workshops, and symposia; 3) computational and bioinformatic tools for using the strategy; 4) provision of experimental protocols and/or reagents for enzyme production and characterization; and 5) dissemination of data via the EFI’s website, enzymefunction.org. The realization of multidisciplinary strategies for functional assignment will begin to define the full metabolic diversity that exists in nature and will impact basic biochemical and evolutionary understanding, as well as a wide range of applications of central importance to industrial, medicinal and pharmaceutical efforts. PMID