3551
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Tochowicz A, Dalziel S, Eidam O, O'Connell JD, Griner S, Finer-Moore JS, Stroud RM. Development and binding mode assessment of N-[4-[2-propyn-1-yl[(6S)-4,6,7,8-tetrahydro-2-(hydroxymethyl)-4-oxo-3H-cyclopenta[g]quinazolin-6-yl]amino]benzoyl]-l-γ-glutamyl-D-glutamic acid (BGC 945), a novel thymidylate synthase inhibitor that targets tumor cells. J Med Chem 2013; 56:5446-55. [PMID: 23710599 DOI: 10.1021/jm400490e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
N-[4-[2-Propyn-1-yl[(6S)-4,6,7,8-tetrahydro-2-(hydroxymethyl)-4-oxo-3H-cyclopenta[g]quinazolin-6-yl]amino]benzoyl]-l-γ-glutamyl-d-glutamic acid 1 (BGC 945, now known as ONX 0801), is a small molecule thymidylate synthase (TS) inhibitor discovered at the Institute of Cancer Research in London. It is licensed by Onyx Pharmaceuticals and is in phase 1 clinical studies. It is a novel antifolate drug resembling TS inhibitors plevitrexed and raltitrexed that combines enzymatic inhibition of thymidylate synthase with α-folate receptor-mediated targeting of tumor cells. Thus, it has potential for efficacy with lower toxicity due to selective intracellular accumulation through α-folate receptor (α-FR) transport. The α-FR, a cell-surface receptor glycoprotein, which is overexpressed mainly in ovarian and lung cancer tumors, has an affinity for 1 similar to that for its natural ligand, folic acid. This study describes a novel synthesis of 1, an X-ray crystal structure of its complex with Escherichia coli TS and 2'-deoxyuridine-5'-monophosphate, and a model for a similar complex with human TS.
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Affiliation(s)
- Anna Tochowicz
- Department of Biochemistry and Biophysics, University of California-San Francisco , 600 16th Street, San Francisco, California 94158, United States
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3552
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Li Z, Li T, Dai S, Xie X, Ma X, Zhao W, Zhang W, Li J, Wang PG. New Insights into the Pharmacological Chaperone Activity of C2-Substituted Glucoimidazoles for the Treatment of Gaucher Disease. Chembiochem 2013; 14:1239-47. [DOI: 10.1002/cbic.201300197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Indexed: 12/23/2022]
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3553
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Study of the interaction of Huperzia saururus Lycopodium alkaloids with the acetylcholinesterase enzyme. J Mol Graph Model 2013; 44:136-44. [PMID: 23827878 DOI: 10.1016/j.jmgm.2013.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/14/2013] [Accepted: 05/27/2013] [Indexed: 11/22/2022]
Abstract
In the present study, we describe and compare the binding modes of three Lycopodium alkaloids (sauroine, 6-hydroxylycopodine and sauroxine; isolated from Huperzia saururus) and huperzine A with the enzyme acetylcholinesterase. Refinement and rescoring of the docking poses (obtained with different programs) with an all atom force field helped to improve the quality of the protein-ligand complexes. Molecular dynamics simulations were performed to investigate the complexes and the alkaloid's binding modes. The combination of the latter two methodologies indicated that binding in the active site is favored for the active compounds. On the other hand, similar binding energies in both the active and the peripheral sites were obtained for sauroine, thus explaining its experimentally determined lack of activity. MM-GBSA predicted the order of binding energies in agreement with the experimental IC50 values.
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3554
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Gewald R, Grunwald C, Egerland U. Discovery of triazines as potent, selective and orally active PDE4 inhibitors. Bioorg Med Chem Lett 2013; 23:4308-14. [PMID: 23806553 DOI: 10.1016/j.bmcl.2013.05.099] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 05/27/2013] [Accepted: 05/31/2013] [Indexed: 01/21/2023]
Abstract
Expanding on HTS hit 4 afforded a series of [1,3,5]triazine derivatives as novel PDE4 inhibitors. The SAR development and optimization process with the emphasis on ligand efficiency and physicochemical properties led to the discovery of compound 44 as a potent, selective and orally active PDE4 inhibitor.
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Affiliation(s)
- Rainer Gewald
- BioCrea GmbH, Meissner Strasse 191, 01445 Radebeul, Germany.
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3555
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Caner S, Nguyen N, Aguda A, Zhang R, Pan YT, Withers SG, Brayer GD. The structure of the Mycobacterium smegmatis trehalose synthase reveals an unusual active site configuration and acarbose-binding mode. Glycobiology 2013; 23:1075-83. [PMID: 23735230 DOI: 10.1093/glycob/cwt044] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Trehalose synthase (TreS) catalyzes the reversible conversion of maltose into trehalose in mycobacteria as one of three biosynthetic pathways to this nonreducing disaccharide. Given the importance of trehalose to survival of mycobacteria, there has been considerable interest in understanding the enzymes involved in its production; indeed the structures of the key enzymes in the other two pathways have already been determined. Herein, we present the first structure of TreS from Mycobacterium smegmatis, thereby providing insights into the catalytic machinery involved in this intriguing intramolecular reaction. This structure, which is of interest both mechanistically and as a potential pharmaceutical target, reveals a narrow and enclosed active site pocket within which intramolecular substrate rearrangements can occur. We also present the structure of a complex of TreS with acarbose, revealing a hitherto unsuspected oligosaccharide-binding site within the C-terminal domain. This may well provide an anchor point for the association of TreS with glycogen, thereby enhancing its role in glycogen biosynthesis and degradation.
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Affiliation(s)
- Sami Caner
- Department of Biochemistry and Molecular Biology, University of British Columbia, British Columbia, Canada
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3556
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Krieger IV, Freundlich JS, Gawandi VB, Roberts JP, Gawandi VB, Sun Q, Owen JL, Fraile MT, Huss SI, Lavandera JL, Ioerger TR, Sacchettini JC. Structure-guided discovery of phenyl-diketo acids as potent inhibitors of M. tuberculosis malate synthase. ACTA ACUST UNITED AC 2013; 19:1556-67. [PMID: 23261599 DOI: 10.1016/j.chembiol.2012.09.018] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/14/2012] [Accepted: 09/19/2012] [Indexed: 11/16/2022]
Abstract
The glyoxylate shunt plays an important role in fatty acid metabolism and has been shown to be critical to survival of several pathogens involved in chronic infections. For Mycobacterium tuberculosis (Mtb), a strain with a defective glyoxylate shunt was previously shown to be unable to establish infection in a mouse model. We report the development of phenyl-diketo acid (PDKA) inhibitors of malate synthase (GlcB), one of two glyoxylate shunt enzymes, using structure-based methods. PDKA inhibitors were active against Mtb grown on acetate, and overexpression of GlcB ameliorated this inhibition. Crystal structures of complexes of GlcB with PDKA inhibitors guided optimization of potency. A selected PDKA compound demonstrated efficacy in a mouse model of tuberculosis. The discovery of these PDKA derivatives provides chemical validation of GlcB as an attractive target for tuberculosis therapeutics.
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Affiliation(s)
- Inna V Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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3557
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Ariza A, Moroz OV, Blagova EV, Turkenburg JP, Waterman J, Roberts SM, Vind J, Sjøholm C, Lassen SF, De Maria L, Glitsoe V, Skov LK, Wilson KS. Degradation of phytate by the 6-phytase from Hafnia alvei: a combined structural and solution study. PLoS One 2013; 8:e65062. [PMID: 23741456 PMCID: PMC3669009 DOI: 10.1371/journal.pone.0065062] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 04/20/2013] [Indexed: 11/19/2022] Open
Abstract
Phytases hydrolyse phytate (myo-inositol hexakisphosphate), the principal form of phosphate stored in plant seeds to produce phosphate and lower phosphorylated myo-inositols. They are used extensively in the feed industry, and have been characterised biochemically and structurally with a number of structures in the PDB. They are divided into four distinct families: histidine acid phosphatases (HAP), β-propeller phytases, cysteine phosphatases and purple acid phosphatases and also split into three enzyme classes, the 3-, 5- and 6-phytases, depending on the position of the first phosphate in the inositol ring to be removed. We report identification, cloning, purification and 3D structures of 6-phytases from two bacteria, Hafnia alvei and Yersinia kristensenii, together with their pH optima, thermal stability, and degradation profiles for phytate. An important result is the structure of the H. alvei enzyme in complex with the substrate analogue myo-inositol hexakissulphate. In contrast to the only previous structure of a ligand-bound 6-phytase, where the 3-phosphate was unexpectedly in the catalytic site, in the H. alvei complex the expected scissile 6-phosphate (sulphate in the inhibitor) is placed in the catalytic site.
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Affiliation(s)
- Antonio Ariza
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Olga V. Moroz
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Elena V. Blagova
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Johan P. Turkenburg
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Jitka Waterman
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Shirley M. Roberts
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | | | | | | | | | | | | | - Keith S. Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
- * E-mail:
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3558
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Engineering the meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum by site saturation mutagenesis for D-phenylalanine synthesis. Appl Environ Microbiol 2013; 79:5078-81. [PMID: 23728814 DOI: 10.1128/aem.01049-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to enlarge the substrate binding pocket of the meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum to accommodate larger 2-keto acids, four amino acid residues (Phe146, Thr171, Arg181, and His227) were targeted for site saturation mutagenesis. Among all mutants, the single mutant H227V had a specific activity of 2.39 ± 0.06 U · mg(-1), which was 35.1-fold enhancement over the wild-type enzyme.
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3559
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Aguirre C, ten Brink T, Walker O, Guillière F, Davesne D, Krimm I. BcL-xL conformational changes upon fragment binding revealed by NMR. PLoS One 2013; 8:e64400. [PMID: 23717610 PMCID: PMC3662666 DOI: 10.1371/journal.pone.0064400] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 04/12/2013] [Indexed: 11/19/2022] Open
Abstract
Protein-protein interactions represent difficult but increasingly important targets for the design of therapeutic compounds able to interfere with biological processes. Recently, fragment-based strategies have been proposed as attractive approaches for the elaboration of protein-protein surface inhibitors from fragment-like molecules. One major challenge in targeting protein-protein interactions is related to the structural adaptation of the protein surface upon molecular recognition. Methods capable of identifying subtle conformational changes of proteins upon fragment binding are therefore required at the early steps of the drug design process. In this report we present a fast NMR method able to probe subtle conformational changes upon fragment binding. The approach relies on the comparison of experimental fragment-induced Chemical Shift Perturbation (CSP) of amine protons to CSP simulated for a set of docked fragment poses, considering the ring-current effect from fragment binding. We illustrate the method by the retrospective analysis of the complex between the anti-apoptotic Bcl-xL protein and the fragment 4′-fluoro-[1,1′-biphenyl]-4-carboxylic acid that was previously shown to bind one of the Bcl-xL hot spots. The CSP-based approach shows that the protein undergoes a subtle conformational rearrangement upon interaction, for residues located in helices 2, 3 and the very beginning of 5. Our observations are corroborated by residual dipolar coupling measurements performed on the free and fragment-bound forms of the Bcl-xL protein. These NMR-based results are in total agreement with previous molecular dynamic calculations that evidenced a high flexibility of Bcl-xL around the binding site. Here we show that CSP of protein amine protons are useful and reliable structural probes. Therefore, we propose to use CSP simulation to assess protein conformational changes upon ligand binding in the fragment-based drug design approach.
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Affiliation(s)
- Clémentine Aguirre
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Tim ten Brink
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Olivier Walker
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Florence Guillière
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Dany Davesne
- UMR5822/IN2P3/F-69622 Lyon, Université de Lyon, IPNL, Villeurbanne, France
| | - Isabelle Krimm
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
- * E-mail:
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3560
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Lu DL, Ding DJ, Yan WJ, Li RR, Dai F, Wang Q, Yu SS, Li Y, Jin XL, Zhou B. Influence of glucuronidation and reduction modifications of resveratrol on its biological activities. Chembiochem 2013; 14:1094-104. [PMID: 23703900 DOI: 10.1002/cbic.201300080] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Indexed: 12/18/2022]
Abstract
Resveratrol (3,5,4'-trihydroxystilbene, RES), a star among dietary polyphenols, shows a wide range of biological activities, but it is rapidly and extensively metabolized into its glucuronide and sulfate conjugates as well as to the corresponding reduced products. This begs the question of whether the metabolites of RES contribute to its in vivo biological activity. To explore this possibility, we synthesized its glucuronidation (3-GR and 4'-GR) and reduction (DHR) metabolites, and evaluated the effect of these structure modifications on biological activities, including binding ability with human serum albumin (HSA), antioxidant activity in homogeneous solutions and heterogeneous media, anti-inflammatory activity, and cytotoxicity against various cancer cell lines. We found that 1) 4'-GR, DHR and RES show nearly equal binding to HSA, mainly through hydrogen bonding, whereas 3-GR adopts a quite different orientation mode upon binding, thereby resulting in reduced ability; 2) 3-GR shows comparable (even equal) ability to RES in FRAP- and AAPH-induced DNA strand breakage assays; DHR, 3-GR, and 4'-GR exhibit anti-hemolysis activity comparable to that of RES; additionally, 3-GR and DHR retain some degree activity of the parent molecule in DPPH.-scavenging and cupric ion-initiated oxidation of LDL assays, respectively; 3) compared to RES, 4'-GR displays equipotent ability in the inhibition of COX-2, and DHR presents comparable activity in inhibiting NO production and growth of SMMC-7721 cells. Relative to RES, its glucuronidation and reduction metabolites showed equal, comparable, or some degree of activity in the above assays, depending on the specific compound and test model, which probably supports their roles in contributing to the in vivo biological activities of the parent molecule.
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Affiliation(s)
- Dong-Liang Lu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, 222 Tianshui Street S., Lanzhou 730000, China
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3561
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Wang YM, Lin W, Chai SC, Wu J, Ong SS, Schuetz EG, Chen T. Piperine activates human pregnane X receptor to induce the expression of cytochrome P450 3A4 and multidrug resistance protein 1. Toxicol Appl Pharmacol 2013; 272:96-107. [PMID: 23707768 DOI: 10.1016/j.taap.2013.05.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/24/2013] [Accepted: 05/10/2013] [Indexed: 11/28/2022]
Abstract
Activation of the pregnane X receptor (PXR) and subsequently its target genes, including those encoding drug transporters and metabolizing enzymes, while playing substantial roles in xenobiotic detoxification, might cause undesired drug-drug interactions. Recently, an increased awareness has been given to dietary components for potential induction of diet-drug interactions through activation of PXR. Here, we studied, whether piperine (PIP), a major component extracted from the widely-used daily spice black pepper, could induce PXR-mediated expression of cytochrome P450 3A4 (CYP3A4) and multidrug resistance protein 1 (MDR1). Our results showed that PIP activated human PXR (hPXR)-mediated CYP3A4 and MDR1 expression in human hepatocytes, intestine cells, and a mouse model; PIP activated hPXR by recruiting its coactivator SRC-1 in both cellular and cell-free systems; PIP bound to the hPXR ligand binding domain in a competitive ligand binding assay in vitro. The dichotomous effects of PIP on induction of CYP3A4 and MDR1 expression observed here and inhibition of their activity reported elsewhere challenges the potential use of PIP as a bioavailability enhancer and suggests that caution should be taken in PIP consumption during drug treatment in patients, particularly those who favor daily pepper spice or rely on certain pepper remedies.
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Affiliation(s)
- Yue-Ming Wang
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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3562
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Lepore R, Tramontano A, Via A. TiPs: a database of therapeutic targets in pathogens and associated tools. Bioinformatics 2013; 29:1821-2. [PMID: 23698860 PMCID: PMC3702258 DOI: 10.1093/bioinformatics/btt289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
MOTIVATION The need for new drugs and new targets is particularly compelling in an era that is witnessing an alarming increase of drug resistance in human pathogens. The identification of new targets of known drugs is a promising approach, which has proven successful in several cases. Here, we describe a database that includes information on 5153 putative drug-target pairs for 150 human pathogens derived from available drug-target crystallographic complexes. AVAILABILITY AND IMPLEMENTATION The TiPs database is freely available at http://biocomputing.it/tips. CONTACT anna.tramontano@uniroma1.it or allegra.via@uniroma1.it.
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Affiliation(s)
- Rosalba Lepore
- Department of Physics, Sapienza University, 00185 Rome, Italy
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3563
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Haapalainen AM, Thomas K, Tyler PC, Evans GB, Almo SC, Schramm VL. Salmonella enterica MTAN at 1.36 Å resolution: a structure-based design of tailored transition state analogs. Structure 2013; 21:963-74. [PMID: 23685211 DOI: 10.1016/j.str.2013.04.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 04/08/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
Abstract
Accumulation of 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH) in bacteria disrupts the S-adenosylmethionine pool to alter biological methylations, synthesis of polyamines, and production of quorum-sensing molecules. Bacterial metabolism of MTA and SAH depends on MTA/SAH nucleosidase (MTAN), an enzyme not present in humans and a target for quorum sensing because MTAN activity is essential for synthesis of autoinducer-2 molecules. Crystals of Salmonella enterica MTAN with product and transition state analogs of MTA and SAH explain the structural contacts causing pM binding affinity for the inhibitor and reveal a "water-wire" channel for the catalytic nucleophile. The crystal structure shows an extension of the binding pocket filled with polyethylene glycol. We exploited this discovery by the design and synthesis of tailored modifications of the currently existing transition state analogs to fill this site. This site was not anticipated in MTAN structures. Tailored inhibitors with dissociation constants of 5 to 15 pM are characterized.
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Affiliation(s)
- Antti M Haapalainen
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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3564
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Molecular dynamics simulation of tryptophan hydroxylase-1: binding modes and free energy analysis to phenylalanine derivative inhibitors. Int J Mol Sci 2013; 14:9947-62. [PMID: 23665899 PMCID: PMC3676822 DOI: 10.3390/ijms14059947] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 04/27/2013] [Accepted: 05/06/2013] [Indexed: 02/05/2023] Open
Abstract
Serotonin is a neurotransmitter that modulates many central and peripheral functions. Tryptophan hydroxylase-1 (TPH1) is a key enzyme of serotonin synthesis. In the current study, the interaction mechanism of phenylalanine derivative TPH1 inhibitors was investigated using molecular dynamics (MD) simulations, free energy calculations, free energy decomposition analysis and computational alanine scanning. The predicted binding free energies of these complexes are consistent with the experimental data. The analysis of the individual energy terms indicates that although the van der Waals and electrostatics interaction contributions are important in distinguishing the binding affinities of these inhibitors, the electrostatic contribution plays a more crucial role in that. Moreover, it is observed that different configurations of the naphthalene substituent could form different binding patterns with protein, yet lead to similar inhibitory potency. The combination of different molecular modeling techniques is an efficient way to interpret the interaction mechanism of inhibitors and our work could provide valuable information for the TPH1 inhibitor design in the future.
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3565
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Activation of Nucleotide-Binding Oligomerization Domain 1 (NOD1) Receptor Signaling in Labeo rohita by iE-DAP and Identification of Ligand-Binding Key Motifs in NOD1 by Molecular Modeling and Docking. Appl Biochem Biotechnol 2013; 170:1282-309. [DOI: 10.1007/s12010-013-0263-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/22/2013] [Indexed: 01/01/2023]
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3566
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Thakur PK, Kumar J, Ray D, Anjum F, Hassan MI. Search of potential inhibitor against New Delhi metallo-beta-lactamase 1 from a series of antibacterial natural compounds. J Nat Sci Biol Med 2013; 4:51-6. [PMID: 23633835 PMCID: PMC3633303 DOI: 10.4103/0976-9668.107260] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background: New Delhi metallo-β-lactamase-1 (NDM-1)-producing Gram-negative bacteria are today's major worldwide health concern. The enzyme NDM-1 provides bacterial resistance by its hydrolytic activity against the β-lactam ring of antibiotics. Inhibition of NDM-1 may prevent the hydrolysis of β-lactam ring of the antibiotics, and therefore, plays an important role against antibacterial resistance. Materials and Methods: Here we made an attempt to design suitable inhibitors against NDM-1 from different natural antibacterial compounds using molecular docking approach. Results: We observed that natural compounds such as Nimbolide and Isomargololone are showing an appreciable IC50 value as well as significant binding energy value for NDM-1. We further observed these compounds showing better affinity to NDM-1 on comparison with 14 β-lactam antibiotics. Conclusion: Finally, our study provides a platform for the development of a potent inhibitor of NDM-1, which may be considered as a potential drug candidate against bacterial resistance.
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3567
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Ichiyama K, Gopala Reddy SB, Zhang LF, Chin WX, Muschin T, Heinig L, Suzuki Y, Nanjundappa H, Yoshinaka Y, Ryo A, Nomura N, Ooi EE, Vasudevan SG, Yoshida T, Yamamoto N. Sulfated polysaccharide, curdlan sulfate, efficiently prevents entry/fusion and restricts antibody-dependent enhancement of dengue virus infection in vitro: a possible candidate for clinical application. PLoS Negl Trop Dis 2013; 7:e2188. [PMID: 23658845 PMCID: PMC3636050 DOI: 10.1371/journal.pntd.0002188] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 03/20/2013] [Indexed: 11/18/2022] Open
Abstract
Curdlan sulfate (CRDS), a sulfated 1→3-β-D glucan, previously shown to be a potent HIV entry inhibitor, is characterized in this study as a potent inhibitor of the Dengue virus (DENV). CRDS was identified by in silico blind docking studies to exhibit binding potential to the envelope (E) protein of the DENV. CRDS was shown to inhibit the DENV replication very efficiently in different cells in vitro. Minimal effective concentration of CRDS was as low as 0.1 µg/mL in LLC-MK2 cells, and toxicity was observed only at concentrations over 10 mg/mL. CRDS can also inhibit DENV-1, 3, and 4 efficiently. CRDS did not inhibit the replication of DENV subgenomic replicon. Time of addition experiments demonstrated that the compound not only inhibited viral infection at the host cell binding step, but also at an early post-attachment step of entry (membrane fusion). The direct binding of CRDS to DENV was suggested by an evident reduction in the viral titers after interaction of the virus with CRDS following an ultrafiltration device separation, as well as after virus adsorption to an alkyl CRDS-coated membrane filter. The electron microscopic features also showed that CRDS interacted directly with the viral envelope, and caused changes to the viral surface. CRDS also potently inhibited DENV infection in DC-SIGN expressing cells as well as the antibody-dependent enhancement of DENV-2 infection. Based on these data, a probable binding model of CRDS to DENV E protein was constructed by a flexible receptor and ligand docking study. The binding site of CRDS was predicted to be at the interface between domains II and III of E protein dimer, which is unique to this compound, and is apparently different from the β-OG binding site. Since CRDS has already been tested in humans without serious side effects, its clinical application can be considered. There is no specific approved antiviral and vaccine for treatment or prevention of dengue, an acute mosquito-transmitted viral disease that affects more than 50 million people each year. Dengue virus (DENV) entry is a critical step that establishes the infection and enables virus replication. Curdlan sulfate (CRDS) is known to inhibit the entry and propagation of HIV-1 in the laboratory. Here we applied a computational binding site identification strategy, which suggested that CRDS could be a probable entry inhibitor of the viral surface E protein. CRDS potently blocked DENV infection at an early stage of the virus lifecycle in vitro. In addition, CRDS prevented antibody dependent enhancement, which is considered to be one of the most important clinical observations in DENV-infected patients. CRDS shows a favorable selectivity index against all serotypes of DENV. Further computational docking indicates that the compound binds to a pocket on the DENV E protein. Since CRDS has already been tested in humans without serious side effects, it can be a good candidate for clinical application.
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Affiliation(s)
- Koji Ichiyama
- Translational ID Lab, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Human Sciences, Musashino University, Tokyo, Japan
| | - Sindhoora Bhargavi Gopala Reddy
- Translational ID Lab, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biotechnology, Sri Jayachamarajendra College of Engineering, Mysore, Karnataka, India
| | - Li Feng Zhang
- Translational ID Lab, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wei Xin Chin
- Translational ID Lab, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tegshi Muschin
- Department of Bio and Environmental Chemistry, Kitami Institute of Technology, Kitami, Japan
| | - Lars Heinig
- Translational ID Lab, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Youichi Suzuki
- Translational ID Lab, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Haraprasad Nanjundappa
- Department of Biotechnology, Sri Jayachamarajendra College of Engineering, Mysore, Karnataka, India
| | - Yoshiyuki Yoshinaka
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Nobuo Nomura
- Department of Human Sciences, Musashino University, Tokyo, Japan
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Subhash G. Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Takashi Yoshida
- Department of Bio and Environmental Chemistry, Kitami Institute of Technology, Kitami, Japan
| | - Naoki Yamamoto
- Translational ID Lab, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- * E-mail:
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3568
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Hancock R, Schaap M, Pfister H, Wells G. Peptide inhibitors of the Keap1-Nrf2 protein-protein interaction with improved binding and cellular activity. Org Biomol Chem 2013; 11:3553-7. [PMID: 23615671 DOI: 10.1039/c3ob40249e] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Inhibitors of the Keap1-Nrf2 protein-protein interaction (PPI) have been proposed as potential anti-inflammatory and cancer chemopreventive agents. Such compounds have the potential to increase the intracellular concentrations of Nrf2 in a reversible manner and consequently increase the expression of a battery of gene products with antioxidant response elements (AREs) in their promoter region. In this manuscript we describe the development of peptide inhibitors with modified C- and N-termini and reduced overall charge. The activity of the compounds in inhibiting the PPI and in cellular assays of Nrf2 function are described. Compound 10 has potent activity (IC50 = 22 nM) in a cell-free fluorescence polarisation assay and induced the expression of Nrf2 dependent gene products in cells, suggesting that it has potential as a lead molecule for the development of peptidomimetic inhibitors.
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Affiliation(s)
- Rowena Hancock
- UCL School of Pharmacy, University College London, London, United Kingdom
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3569
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Ali I, Haque A, Saleem K, Hsieh MF. Curcumin-I Knoevenagel's condensates and their Schiff's bases as anticancer agents: synthesis, pharmacological and simulation studies. Bioorg Med Chem 2013; 21:3808-20. [PMID: 23643901 DOI: 10.1016/j.bmc.2013.04.018] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 12/15/2022]
Abstract
Pyrazolealdehydes (4a-d), Knoevenagel's condensates (5a-d) and Schiff's bases (6a-d) of curcumin-I were synthesized, purified and characterized. Hemolysis assays, cell line activities, DNA bindings and docking studies were carried out. These compounds were lesser hemolytic than standard drug doxorubicin. Minimum cell viability (MCF-7; wild) observed was 59% (1.0 μg/mL) whereas the DNA binding constants ranged from 1.4×10(3) to 8.1×10(5) M(-1). The docking energies varied from -7.30 to -13.4 kcal/mol. It has been observed that DNA-compound adducts were stabilized by three governing forces (Van der Wall's, H-bonding and electrostatic attractions). It has also been observed that compounds 4a-d preferred to enter minor groove while 5a-d and 6a-d interacted with major grooves of DNA. The anticancer activities of the reported compounds might be due to their interactions with DNA. These results indicated the bright future of the reported compounds as anticancer agents.
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Affiliation(s)
- Imran Ali
- Department of Chemistry, Jamia Millia Islamia (Central University), New Delhi 110025, India.
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3570
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Pathania S, Randhawa V, Bagler G. Prospecting for novel plant-derived molecules of Rauvolfia serpentina as inhibitors of Aldose Reductase, a potent drug target for diabetes and its complications. PLoS One 2013; 8:e61327. [PMID: 23613832 PMCID: PMC3629236 DOI: 10.1371/journal.pone.0061327] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 03/07/2013] [Indexed: 12/23/2022] Open
Abstract
Aldose Reductase (AR) is implicated in the development of secondary complications of diabetes, providing an interesting target for therapeutic intervention. Extracts of Rauvolfia serpentina, a medicinal plant endemic to the Himalayan mountain range, have been known to be effective in alleviating diabetes and its complications. In this study, we aim to prospect for novel plant-derived inhibitors from R. serpentina and to understand structural basis of their interactions. An extensive library of R. serpentina molecules was compiled and computationally screened for inhibitory action against AR. The stability of complexes, with docked leads, was verified using molecular dynamics simulations. Two structurally distinct plant-derived leads were identified as inhibitors: indobine and indobinine. Further, using these two leads as templates, 16 more leads were identified through ligand-based screening of their structural analogs, from a small molecules database. Thus, we obtained plant-derived indole alkaloids, and their structural analogs, as potential AR inhibitors from a manually curated dataset of R. serpentina molecules. Indole alkaloids reported herein, as a novel structural class unreported hitherto, may provide better insights for designing potential AR inhibitors with improved efficacy and fewer side effects.
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Affiliation(s)
- Shivalika Pathania
- Biotechnology Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur, Himachal Pradesh, India
| | - Vinay Randhawa
- Biotechnology Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur, Himachal Pradesh, India
| | - Ganesh Bagler
- Biotechnology Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur, Himachal Pradesh, India
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3571
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Kjær S, Linch M, Purkiss A, Kostelecky B, Knowles PP, Rosse C, Riou P, Soudy C, Kaye S, Patel B, Soriano E, Murray-Rust J, Barton C, Dillon C, Roffey J, Parker PJ, McDonald NQ. Adenosine-binding motif mimicry and cellular effects of a thieno[2,3-d]pyrimidine-based chemical inhibitor of atypical protein kinase C isoenzymes. Biochem J 2013; 451:329-42. [PMID: 23418854 DOI: 10.1042/bj20121871] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The aPKC [atypical PKC (protein kinase C)] isoforms ι and ζ play crucial roles in the formation and maintenance of cell polarity and represent attractive anti-oncogenic drug targets in Ras-dependent tumours. To date, few isoform-specific chemical biology tools are available to inhibit aPKC catalytic activity. In the present paper, we describe the identification and functional characterization of potent and selective thieno[2,3-d]pyrimidine-based chemical inhibitors of aPKCs. A crystal structure of human PKCι kinase domain bound to a representative compound, CRT0066854, reveals the basis for potent and selective chemical inhibition. Furthermore, CRT0066854 displaces a crucial Asn-Phe-Asp motif that is part of the adenosine-binding pocket and engages an acidic patch used by arginine-rich PKC substrates. We show that CRT0066854 inhibits the LLGL2 (lethal giant larvae 2) phosphorylation in cell lines and exhibits phenotypic effects in a range of cell-based assays. We conclude that this compound can be used as a chemical tool to modulate aPKC activity in vitro and in vivo and may guide the search for further aPKC-selective inhibitors.
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Affiliation(s)
- Svend Kjær
- Structural Biology, Cancer Research UK, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
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3572
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Bacarizo J, Camara-Artigas A. Atomic resolution structures of the c-Src SH3 domain in complex with two high-affinity peptides from classes I and II. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:756-66. [PMID: 23633584 DOI: 10.1107/s0907444913001522] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 01/15/2013] [Indexed: 12/20/2022]
Abstract
The atomic resolution crystal structures of complexes between the SH3 domain of the c-Src tyrosine kinase and two high-affinity peptides belonging to class I and class II have been solved. The crystals of the Thr98Asp and Thr98Glu mutants in complex with the APP12 peptide (APPLPPRNRPRL) belonged to the trigonal space group P3121 and in both cases the asymmetric unit was composed of one molecule of the SH3-APP12 complex. The crystals of the Thr98Glu mutant in complex with the VSL12 peptide (VSLARRPLPLP) belonged to the trigonal space group P3221 and the asymmetric unit was also composed of a single molecule of the SH3-VSL12 complex. All crystals were obtained in the presence of PEG 300 under the same conditions as reported for the intertwined dimeric structure of the c-Src SH3 domain, but the presence of the peptide stabilizes the monomeric form of the domain. These structures allow a detailed analysis of the role of salt bridges, cation-π interactions and hydrogen bonds in the binding of proline-rich motifs to the c-Src SH3 domain. Moreover, these crystallographic structures allow the role of water molecules in the binding of these motifs to the c-Src SH3 domain to be studied for the first time.
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Affiliation(s)
- Julio Bacarizo
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence, Carretera de Sacramento, 04120 Almería, Spain
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3573
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Shi J, Chen J, Serradji N, Xu X, Zhou H, Ma Y, Sun Z, Jiang P, Du Y, Yang J, Dong C, Wang Q. PMS1077 sensitizes TNF-α induced apoptosis in human prostate cancer cells by blocking NF-κB signaling pathway. PLoS One 2013; 8:e61132. [PMID: 23593410 PMCID: PMC3621893 DOI: 10.1371/journal.pone.0061132] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 03/05/2013] [Indexed: 01/05/2023] Open
Abstract
Our previous studies have demonstrated that PMS1077, a platelet-activating factor (PAF) antagonist, could induce apoptosis of Raji cells. However, the mechanism of action has not yet been determined. The nuclear transcription factor-kappa B (NF-κB) signaling pathway plays a critical role in tumor cell survival, proliferation, invasion, metastasis, and angiogenesis, so we determined the effects of PMS1077 and its structural analogs on tumor necrosis factor-α (TNF-α) induced activation of NF-κB signaling. In this study, we found that PMS1077 inhibited TNF-α induced expression of the NF-κB regulated reporter gene in a dose dependent manner. Western blot assay indicated that PMS1077 suppressed the TNF-α induced inhibitor of κB-α (IκB-α) phosphorylation, IκB-α degradation, and p65 phosphorylation. PMS1077 consistently blocked TNF-α induced p65 nuclear translocation as demonstrated in the immunofluorescence assay used. Docking studies by molecular modeling predicted that PMS1077 might interact directly with the IκB kinase-β (IKK-β) subunit. These results suggested that PMS1077 might suppress the activation of NF-κB by targeting IKK-β involved in the NF-κB signaling pathway. Finally, we showed that PMS1077 sensitized cells to TNF-α induced apoptosis by suppressing the expression of NF-κB regulated anti-apoptotic genes. Our results reveal a novel function of PMS1077 on the NF-κB signaling pathway and imply that PMS1077 can be considered as an anti-tumor lead compound.
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Affiliation(s)
- Jie Shi
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jing Chen
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Nawal Serradji
- Université Paris Diderot, Sorbonne Paris Cité, ITODYS, CNRS UMR 7086, Paris, France
| | - Ximing Xu
- Université Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative, CNRS EAC4413, Paris, France
| | - Heng Zhou
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yinxing Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhihong Sun
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Peng Jiang
- Université Paris Diderot, Sorbonne Paris Cité, UMR S-698, Paris, France
| | - Yuping Du
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jinbo Yang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Changzhi Dong
- Université Paris Diderot, Sorbonne Paris Cité, ITODYS, CNRS UMR 7086, Paris, France
- * E-mail: (CD); (QW)
| | - Qin Wang
- School of Life Sciences, Lanzhou University, Lanzhou, China
- * E-mail: (CD); (QW)
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3574
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Non-canonical H-bonds in β-lactamases: importance of C–H···π interactions. J Biol Inorg Chem 2013; 18:539-45. [DOI: 10.1007/s00775-013-0998-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 03/17/2013] [Indexed: 10/27/2022]
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3575
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Salmon RC, Cliff MJ, Rafferty JB, Kelly DJ. The CouPSTU and TarPQM transporters in Rhodopseudomonas palustris: redundant, promiscuous uptake systems for lignin-derived aromatic substrates. PLoS One 2013; 8:e59844. [PMID: 23555803 PMCID: PMC3610893 DOI: 10.1371/journal.pone.0059844] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 02/21/2013] [Indexed: 11/18/2022] Open
Abstract
The biodegradation of lignin, one of the most abundant carbon compounds on Earth, has important biotechnological applications in the derivation of useful products from lignocellulosic wastes. The purple photosynthetic bacterium Rhodopseudomonas palustris is able to grow photoheterotrophically under anaerobic conditions on a range of phenylpropeneoid lignin monomers, including coumarate, ferulate, caffeate, and cinnamate. RPA1789 (CouP) is the periplasmic binding-protein component of an ABC system (CouPSTU; RPA1789, RPA1791–1793), which has previously been implicated in the active transport of this class of aromatic substrate. Here, we show using both intrinsic tryptophan fluorescence and isothermal titration calorimetry that CouP binds a range of phenylpropeneoid ligands with Kd values in the nanomolar range. The crystal structure of CouP with ferulate as the bound ligand shows H-bond interactions between the 4-OH group of the aromatic ring with His309 and Gln305. H-bonds are also made between the carboxyl group on the ferulate side chain and Arg197, Ser222, and Thr102. An additional transport system (TarPQM; RPA1782–1784), a member of the tripartite ATP-independent periplasmic (TRAP) transporter family, is encoded at the same locus as rpa1789 and several other genes involved in coumarate metabolism. We show that the periplasmic binding-protein of this system (TarP; RPA1782) also binds coumarate, ferulate, caffeate, and cinnamate with nanomolar Kd values. Thus, we conclude that R. palustris uses two redundant but energetically distinct primary and secondary transporters that both employ high-affinity periplasmic binding-proteins to maximise the uptake of lignin-derived aromatic substrates from the environment. Our data provide a detailed thermodynamic and structural basis for understanding the interaction of lignin-derived aromatic substrates with proteins and will be of use in the further exploitation of the flexible metabolism of R. palustris for anaerobic aromatic biotransformations.
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Affiliation(s)
- Robert C. Salmon
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - John B. Rafferty
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
- * E-mail: (JR); (DJK)
| | - David J. Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
- * E-mail: (JR); (DJK)
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3576
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Ji Q, Zhang L, Jones MB, Sun F, Deng X, Liang H, Cho H, Brugarolas P, Gao YN, Peterson SN, Lan L, Bae T, He C. Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR. Proc Natl Acad Sci U S A 2013; 110:5010-5. [PMID: 23479646 PMCID: PMC3612684 DOI: 10.1073/pnas.1219446110] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Quinone molecules are intracellular electron-transport carriers, as well as critical intra- and extracellular signals. However, transcriptional regulation of quinone signaling and its molecular basis are poorly understood. Here, we identify a thiol-stress-sensing regulator YodB family transcriptional regulator as a central component of quinone stress response of Staphylococcus aureus, which we have termed the quinone-sensing and response repressor (QsrR). We also identify and confirm an unprecedented quinone-sensing mechanism based on the S-quinonization of the essential residue Cys-5. Structural characterizations of the QsrR-DNA and QsrR-menadione complexes further reveal that the covalent association of menadione directly leads to the release of QsrR from operator DNA following a 10° rigid-body rotation as well as a 9-Å elongation between the dimeric subunits. The molecular level characterization of this quinone-sensing transcriptional regulator provides critical insights into quinone-mediated gene regulation in human pathogens.
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Affiliation(s)
- Quanjiang Ji
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Liang Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Marcus B. Jones
- Infectious Disease Group, Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, MD 20850
| | - Fei Sun
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Xin Deng
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Haihua Liang
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Hoonsik Cho
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN 46408; and
| | - Pedro Brugarolas
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Yihe N. Gao
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Scott N. Peterson
- Infectious Disease Group, Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, MD 20850
| | - Lefu Lan
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN 46408; and
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
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3577
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Agostino M, Mancera RL, Ramsland PA, Yuriev E. AutoMap: A tool for analyzing protein–ligand recognition using multiple ligand binding modes. J Mol Graph Model 2013; 40:80-90. [DOI: 10.1016/j.jmgm.2013.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 01/01/2013] [Indexed: 10/27/2022]
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3578
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The crystal structure of Sporosarcina pasteurii urease in a complex with citrate provides new hints for inhibitor design. J Biol Inorg Chem 2013; 18:391-9. [DOI: 10.1007/s00775-013-0983-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 01/29/2013] [Indexed: 11/26/2022]
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3579
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Yadav PK, Singh G, Gautam B, Singh S, Yadav M, Srivastav U, Singh B. Molecular modeling, dynamics studies and virtual screening of Fructose 1, 6 biphosphate aldolase-II in community acquired- methicillin resistant Staphylococcus aureus (CA-MRSA). Bioinformation 2013; 9:158-64. [PMID: 23423142 PMCID: PMC3569604 DOI: 10.6026/97320630009158] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 01/15/2013] [Indexed: 11/23/2022] Open
Abstract
Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) has recently emerged as a nosocomial pathogen to the
community which commonly causes skin and soft-tissue infections (SSTIs). This strain (MW2) has now become resistant to the
most of the beta-lactam antibiotics; therefore it is the urgent need to identify the novel drug targets. Recently fructose 1,6
biphosphate aldolase-II (FBA) has been identified as potential drug target in CA-MRSA. The FBA catalyses the retro-ketolic
cleavage of fructose-1,6-bisphosphate (FBP) to yield dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P)
in glycolytic pathway. In the present research work the 3D structure of FBA was predicted using the homology modeling method
followed by validation. The molecular dynamics simulation (MDS) of the predicted model was carried out using the 2000 ps time
scale and 1000000 steps. The MDS results suggest that the modeled structure is stable. The predicted model of FBA was used for
virtual screening against the NCI diversity subset-II ligand databases which contain 1364 compounds. Based on the docking energy
scores, it was found that top four ligands i.e. ZINC01690699, ZINC13154304, ZINC29590257 and ZINC29590259 were having lower
energy scores which reveal higher binding affinity towards the active site of FBA. These ligands might act as potent inhibitors for
the FBA so that the menace of antimicrobial resistance in CA-MRSA can be conquered. However, pharmacological studies are
required to confirm the inhibitory activity of these ligands against the FBA in CA-MRSA.
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Affiliation(s)
- Pramod Kumar Yadav
- Department of Computational Biology & Bioinformatics, Sam Higginbottom Institute of Agriculture, Technology & Sciences (Deemed University), Allahabad-211007, India
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3580
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Pozharski E, Weichenberger CX, Rupp B. Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:150-67. [PMID: 23385452 DOI: 10.1107/s0907444912044423] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/26/2012] [Indexed: 11/10/2022]
Abstract
As a result of substantial instrumental automation and the continuing improvement of software, crystallographic studies of biomolecules are conducted by non-experts in increasing numbers. While improved validation almost ensures that major mistakes in the protein part of structure models are exceedingly rare, in ligand-protein complex structures, which in general are most interesting to the scientist, ambiguous ligand electron density is often difficult to interpret and the modelled ligands are generally more difficult to properly validate. Here, (i) the primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) the most common categories of building errors or overinterpretation are classified; (iii) a few instructive and specific examples are discussed in detail, including an electron-density-based analysis of ligand structures that do not contain any ligands; (iv) means of avoiding such mistakes are suggested and the implications for database validity are discussed and (v) a user-friendly software tool that allows non-expert users to conveniently inspect ligand density is provided.
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Affiliation(s)
- Edwin Pozharski
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA.
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3581
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Computational study and peptide inhibitors design for the CDK9 - cyclin T1 complex. J Mol Model 2013; 19:1711-25. [PMID: 23296566 DOI: 10.1007/s00894-012-1735-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 12/13/2012] [Indexed: 01/08/2023]
Abstract
Cyclin dependent kinase 9 (CDK9) is a protein that belongs to the cyclin-dependent kinases family, and its main role is in the regulation of the cell transcription processes. Since the increased activity of CDK9 is connected with the development of pathological processes such as tumor growth and survival and HIV-1 replication, inhibition of the CDK9 could be of particular interest for treating such diseases. The activation of CDK9 is initiated by the formation of CDK9/cyclin T1 complex, therefore disruption of its formation could be a promising strategy for the design of CDK9 inhibitors. In order to assist in the design of potential inhibitors of CDK9/cyclin T1 complex formation, a computational study of the CDK9/cyclin T1 interface was conducted. Ten peptides were designed using the information from the analysis of the complex, hot spot residues and fragment based design. The designed peptides were docked to CDK9 structures obtained by molecular dynamics simulations of CDK9/cyclin T1 complex and the CDK9 alone and their binding affinities were evaluated using molecular mechanics Poisson Boltzman surface area (MM-PBSA) method and steered molecular dynamics (SMD). Designed peptide sequences LQTLGF and ESIILQ, both derived from the surface of cyclin T1, as well as the peptide sequence PRWPE, derived from fragment based design, showed the most favorable binding properties and were selected for our further studies.
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3582
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Ruiz FX, Cousido-Siah A, Mitschler A, Farrés J, Parés X, Podjarny A. X-ray structure of the V301L aldo-keto reductase 1B10 complexed with NADP(+) and the potent aldose reductase inhibitor fidarestat: implications for inhibitor binding and selectivity. Chem Biol Interact 2013; 202:178-85. [PMID: 23295227 DOI: 10.1016/j.cbi.2012.12.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 12/12/2012] [Accepted: 12/18/2012] [Indexed: 01/03/2023]
Abstract
Only one crystal structure is currently available for tumor marker AKR1B10, complexed with NADP(+) and tolrestat, which is an aldose reductase inhibitor (ARI) of the carboxylic acid type. Here, the X-ray structure of the complex of the V301L substituted AKR1B10 holoenzyme with fidarestat, an ARI of the cyclic imide type, was obtained at 1.60Å resolution by replacement soaking of crystals containing tolrestat. Previously, fidarestat was found to be safe in phase III trials for diabetic neuropathy and, consistent with its low in vivo side effects, was highly selective for aldose reductase (AR or AKR1B1) versus aldehyde reductase (AKR1A1). Now, inhibition studies showed that fidarestat was indeed 1300-fold more selective for AR as compared to AKR1B10, while the change of Val to Leu (found in AR) caused a 20-fold decrease in the IC50 value with fidarestat. Structural analysis of the V301L AKR1B10-fidarestat complex displayed enzyme-inhibitor interactions similar to those of the AR-fidarestat complex. However, a close inspection of both the new crystal structure and a computer model of the wild-type AKR1B10 complex with fidarestat revealed subtle changes that could affect fidarestat binding. In the crystal structure, a significant motion of loop A was observed between AR and V301L AKR1B10, linked to a Phe-122/Phe-123 side chain displacement. This was due to the presence of the more voluminous Gln-303 side chain (Ser-302 in AR) and of a water molecule buried in a subpocket located at the base of flexible loop A. In the wild-type AKR1B10 model, a short contact was predicted between the Val-301 side chain and fidarestat, but would not be present in AR or in V301L AKR1B10. Overall, these changes could contribute to the difference in inhibitory potency of fidarestat between AR and AKR1B10.
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Affiliation(s)
- Francesc Xavier Ruiz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
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3583
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Cao J, Ma X, Wang X, Wang X, Zhang Z, Geng Z, Wang Z. Azole derivatives as novel non-iron-chelating inhibitors of prolyl hydroxylase 3 for HIF-1 activation. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00117b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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3584
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Characterization and application of a newly synthesized 2-deoxyribose-5-phosphate aldolase. J Ind Microbiol Biotechnol 2012. [PMID: 23179467 DOI: 10.1007/s10295-012-1213-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A codon-optimized 2-deoxyribose-5-phosphate aldolase (DERA) gene was newly synthesized and expressed in Escherichia coli to investigate its biochemical properties and applications in synthesis of statin intermediates. The expressed DERA was purified and characterized using 2-deoxyribose-5-phosphate as the substrate. The specific activity of recombinant DERA was 1.8 U/mg. The optimum pH and temperature for DERA activity were pH 7.0 and 35 °C, respectively. The recombinant DERA was stable at pH 4.0-7.0 and at temperatures below 50 °C. The enzyme activity was inhibited by 1 mM of Ni(2+), Ba(2+) and Fe(2+). The apparent K (m) and V (max) values of purified enzyme for 2-deoxyribose-5-phosphate were 0.038 mM and 2.9 μmol min(-1) mg(-1), for 2-deoxyribose were 0.033 mM and 2.59 μmol min(-1) mg(-1), respectively, which revealed that the enzyme had similar catalytic efficiency towards phosphorylated and non-phosphorylated substrates. To synthesize statin intermediates, the bioconversion process for production of (3R, 5S)-6-chloro-2,4,6-trideoxyhexose from chloroacetaldehyde and acetaldehyde by the recombinant DERA was developed and a conversion of 94.4 % was achieved. This recombinant DERA could be a potential candidate for application in production of (3R, 5S)-6-chloro-2,4,6-trideoxyhexose.
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3585
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Guerrero L, Castillo J, Quiñones M, Garcia-Vallvé S, Arola L, Pujadas G, Muguerza B. Inhibition of angiotensin-converting enzyme activity by flavonoids: structure-activity relationship studies. PLoS One 2012. [PMID: 23185345 PMCID: PMC3504033 DOI: 10.1371/journal.pone.0049493] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Previous studies have demonstrated that certain flavonoids can have an inhibitory effect on angiotensin-converting enzyme (ACE) activity, which plays a key role in the regulation of arterial blood pressure. In the present study, 17 flavonoids belonging to five structural subtypes were evaluated in vitro for their ability to inhibit ACE in order to establish the structural basis of their bioactivity. The ACE inhibitory (ACEI) activity of these 17 flavonoids was determined by fluorimetric method at two concentrations (500 µM and 100 µM). Their inhibitory potencies ranged from 17 to 95% at 500 µM and from 0 to 57% at 100 µM. In both cases, the highest ACEI activity was obtained for luteolin. Following the determination of ACEI activity, the flavonoids with higher ACEI activity (i.e., ACEI >60% at 500 µM) were selected for further IC50 determination. The IC50 values for luteolin, quercetin, rutin, kaempferol, rhoifolin and apigenin K were 23, 43, 64, 178, 183 and 196 µM, respectively. Our results suggest that flavonoids are an excellent source of functional antihypertensive products. Furthermore, our structure-activity relationship studies show that the combination of sub-structures on the flavonoid skeleton that increase ACEI activity is made up of the following elements: (a) the catechol group in the B-ring, (b) the double bond between C2 and C3 at the C-ring, and (c) the cetone group in C4 at the C-ring. Protein-ligand docking studies are used to understand the molecular basis for these results.
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Affiliation(s)
- Ligia Guerrero
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Spain
- Department of Research, Nutrition and Innovation, ALPINA S.A, Bogotá, Colombia
| | - Julián Castillo
- Department of Research and Development, Nutrafur S.A., Murcia, Spain
| | - Mar Quiñones
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Spain
| | - Santiago Garcia-Vallvé
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Spain
- Centre Tecnològic de Nutrició i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat, Reus, Catalonia, Spain
| | - Lluis Arola
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Spain
- Centre Tecnològic de Nutrició i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat, Reus, Catalonia, Spain
| | - Gerard Pujadas
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Spain
- Centre Tecnològic de Nutrició i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat, Reus, Catalonia, Spain
| | - Begoña Muguerza
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Spain
- Centre Tecnològic de Nutrició i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat, Reus, Catalonia, Spain
- * E-mail:
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3586
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Ahmed SM, Kruger HG, Govender T, Maguire GEM, Sayed Y, Ibrahim MAA, Naicker P, Soliman MES. Comparison of the Molecular Dynamics and Calculated Binding Free Energies for Nine FDA-Approved HIV-1 PR Drugs Against Subtype B and C-SA HIV PR. Chem Biol Drug Des 2012; 81:208-18. [DOI: 10.1111/cbdd.12063] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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3587
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Aik W, McDonough MA, Thalhammer A, Chowdhury R, Schofield CJ. Role of the jelly-roll fold in substrate binding by 2-oxoglutarate oxygenases. Curr Opin Struct Biol 2012; 22:691-700. [PMID: 23142576 DOI: 10.1016/j.sbi.2012.10.001] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 09/20/2012] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
Abstract
2-Oxoglutarate (2OG) and ferrous iron dependent oxygenases catalyze two-electron oxidations of a range of small and large molecule substrates, including proteins/peptides/amino acids, nucleic acids/bases, and lipids, as well as natural products including antibiotics and signaling molecules. 2OG oxygenases employ variations of a core double-stranded β-helix (DSBH; a.k.a. jelly-roll, cupin or jumonji C (JmjC)) fold to enable binding of Fe(II) and 2OG in a subfamily conserved manner. The topology of the DSBH limits regions directly involved in substrate binding: commonly the first, second and eighth strands, loops between the second/third and fourth/fifth DSBH strands, and the N-terminal and C-terminal regions are involved in primary substrate, co-substrate and cofactor binding. Insights into substrate recognition by 2OG oxygenases will help to enable selective inhibition and bioengineering studies.
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Affiliation(s)
- WeiShen Aik
- Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, United Kingdom
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3588
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Sennett NC, Kadirvelraj R, Wood ZA. Cofactor binding triggers a molecular switch to allosterically activate human UDP-α-D-glucose 6-dehydrogenase. Biochemistry 2012; 51:9364-74. [PMID: 23106432 DOI: 10.1021/bi301067w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Human UDP-α-D-glucose dehydrogenase (hUGDH) catalyzes the NAD(+)-dependent oxidation of UDP-α-D-glucose (UDG) to produce UDP-α-D-glucuronic acid. The oligomeric structure of hUGDH is dynamic and can form two distinct hexameric complexes in solution. The active form of hUGDH consists of dimers that undergo a concentration-dependent association to form a hexamer with 32 symmetry. In the presence of the allosteric feedback inhibitor UDP-α-D-xylose (UDX), hUGDH changes shape to form an inactive, horseshoe-shaped complex. Previous studies have identified the UDX-induced allosteric mechanism that changes the hexameric structure to inhibit the enzyme. Here, we investigate the role of the 32 symmetry hexamer in the catalytic cycle. We engineered a stable hUGDH dimer by introducing a charge-switch substitution (K94E) in the hexamer-building interface (hUGDH(K94E)). The k(cat) of hUGDH(K94E) is ~160-fold lower than that of the wild-type enzyme, suggesting that the hexamer is the catalytically relevant state. We also show that cofactor binding triggers the formation of the 32 symmetry hexamer, but UDG is needed for the stability of the complex. The hUGDH(K94E) crystal structure at 2.08 Å resolution identifies loop(88-110) as the cofactor-responsive allosteric switch that drives hexamer formation; loop(88-110) directly links cofactor binding to the stability of the hexamer-building interface. In the interface, loop(88-110) packs against the Thr131-loop/α6 helix, the allosteric switch that responds to the feedback inhibitor UDX. We also identify a structural element (the S-loop) that explains the indirect stabilization of the hexamer by substrate and supports a sequential, ordered binding of the substrate and cofactor. These observations support a model in which (i) UDG binds to the dimer and stabilizes the S-loop to promote cofactor binding and (ii) cofactor binding orders loop(88-110) to induce formation of the catalytically active hexamer.
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Affiliation(s)
- Nicholas C Sennett
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
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3589
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Nelson CA, Warren JT, Wang MW, Teitelbaum SL, Fremont DH. RANKL employs distinct binding modes to engage RANK and the osteoprotegerin decoy receptor. Structure 2012; 20:1971-82. [PMID: 23039992 PMCID: PMC3607351 DOI: 10.1016/j.str.2012.08.030] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 06/14/2012] [Accepted: 08/28/2012] [Indexed: 01/07/2023]
Abstract
Osteoprotegerin (OPG) and receptor activator of nuclear factor κB (RANK) are members of the tumor necrosis factor receptor (TNFR) superfamily that regulate osteoclast formation and function by competing for RANK ligand (RANKL). RANKL promotes osteoclast development through RANK activation, while OPG inhibits this process by sequestering RANKL. For comparison, we solved crystal structures of RANKL with RANK and RANKL with OPG. Complementary biochemical and functional studies reveal that the monomeric cytokine-binding region of OPG binds RANKL with ∼500-fold higher affinity than RANK and inhibits RANKL-stimulated osteoclastogenesis ∼150 times more effectively, in part because the binding cleft of RANKL makes unique contacts with OPG. Several side chains as well as the C-D and D-E loops of RANKL occupy different orientations when bound to OPG versus RANK. High affinity OPG binding requires a 90s loop Phe residue that is mutated in juvenile Paget's disease. These results suggest cytokine plasticity may help to fine-tune specific tumor necrosis factor (TNF)-family cytokine/receptor pair selectivity.
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Affiliation(s)
- Christopher A. Nelson
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110-1093, USA
| | - Julia T. Warren
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110-1093, USA,Department of Internal Medicine, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110-1093, USA
| | - Michael W.H. Wang
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110-1093, USA
| | - Steven L. Teitelbaum
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110-1093, USA,Department of Internal Medicine, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110-1093, USA
| | - Daved H. Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110-1093, USA,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110-1093, USA,Correspondence: DHF, , Tel: (314) 747-6547, Fax: (314) 362-8888
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3590
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Tou WI, Chen CYC. Traditional Chinese medicine as dual guardians against hypertension and cancer? J Biomol Struct Dyn 2012; 30:299-317. [PMID: 22694277 DOI: 10.1080/07391102.2012.680030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This study utilizes the comprehensive traditional Chinese medicine database TCM Database@Taiwan ( http://tcm.cmu.edu.tw/ ) in conjunction with structure-based and ligand-based drug design to identify multi-function Src inhibitors. The three potential TCM candidates identified as having suitable docking conformations and bioactivity profiles were Angeliferulate, (3R)-2'-hydroxy-3',4'-dimethoxyisoflavan-7-O-beta-D-glucoside (HMID), and 3-[2',6-dihydroxy-5'-(2-propenyl)[1,1'-biphenyl]3-yl]-(E)-2-propenoic acid (3PA). Molecular dynamics simulation demonstrated that the TCM candidates have more stable interactions with the cleft and in complex with Src kinase compared to Saracatinib. Angeliferulate and HMID, both originated from Angelica sinensis, not only interact with Lys298 and amino acids from different loops in the cleft, but also with Asp407 located on the activation loop. These interactions are important to reduce the opening of the activation loop due to phosphorylation, hence stabilize the Src kinase cleft structure and inhibit activation. The TCM candidates also exhibited high affinity to other cancer-related target proteins (EGFR, HER2, and HSP90). Our observations suggest that the TCM candidates might have multi-targeting effects in hypertension and cancer.
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Affiliation(s)
- Weng Ieong Tou
- School of Medicine, China Medical University, Taichung, Taiwan
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3591
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Yang Y, Liu H, Yao X. Understanding the molecular basis of MK2-p38α signaling complex assembly: insights into protein-protein interaction by molecular dynamics and free energy studies. MOLECULAR BIOSYSTEMS 2012; 8:2106-18. [PMID: 22648002 DOI: 10.1039/c2mb25042j] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The formation of a p38 MAPK and MAPK-activated protein kinase 2 (MK2) signaling complex is physiologically relevant to cellular responses such as the proinflammatory cytokine production. The interaction between p38α isoform and MK2 is of great importance for this signaling. In this study, molecular dynamics simulation and binding free energy calculation were performed on the MK2-p38α signaling complex to investigate the protein-protein interaction between the two proteins. Dynamic domain motion analyses were performed to analyze the conformational changes between the unbound and bound states of proteins during the interaction. The activation loop, αF-I helices, and loops among α helices in the C-lobe of MK2 are found to be highly flexible and exhibit significant changes upon p38α binding. The results also show that after the binding of p38α, the N- and C-terminal domains of MK2 display an opening and twisting motion centered on the activation loop. The molecular mechanics Poisson-Boltzmann and generalized-Born surface area (MM-PB/GBSA) methods were used to calculate binding free energies between MK2 and p38α. The analysis of the components of binding free energy calculation indicates that the van der Waals interaction and the nonpolar solvation energy provide the driving force for the binding process, while the electrostatic interaction contributes critically to the specificity, rather than to MK2-p38α binding affinity. The contribution of each residue at the interaction interface to the binding affinity of MK2 with p38α was also analyzed by free energy decomposition. Several important residues responsible for the protein-protein interaction were also identified.
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Affiliation(s)
- Ying Yang
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
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3592
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Haslam NJ, Shields DC. Profile-based short linear protein motif discovery. BMC Bioinformatics 2012; 13:104. [PMID: 22607209 PMCID: PMC3534220 DOI: 10.1186/1471-2105-13-104] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 04/04/2012] [Indexed: 01/24/2023] Open
Abstract
Background Short linear protein motifs are attracting increasing attention as functionally independent sites, typically 3–10 amino acids in length that are enriched in disordered regions of proteins. Multiple methods have recently been proposed to discover over-represented motifs within a set of proteins based on simple regular expressions. Here, we extend these approaches to profile-based methods, which provide a richer motif representation. Results The profile motif discovery method MEME performed relatively poorly for motifs in disordered regions of proteins. However, when we applied evolutionary weighting to account for redundancy amongst homologous proteins, and masked out poorly conserved regions of disordered proteins, the performance of MEME is equivalent to that of regular expression methods. However, the two approaches returned different subsets within both a benchmark dataset, and a more realistic discovery dataset. Conclusions Profile-based motif discovery methods complement regular expression based methods. Whilst profile-based methods are computationally more intensive, they are likely to discover motifs currently overlooked by regular expression methods.
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Affiliation(s)
- Niall J Haslam
- Complex and Adaptive Systems Laboratory, University College Dublin, Ireland
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3593
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Feng L, Zhu W, Huang C, Li Y. Direct interaction of ONO-5046 with human neutrophil elastase through ¹H NMR and molecular docking. Int J Biol Macromol 2012; 51:196-200. [PMID: 22579959 DOI: 10.1016/j.ijbiomac.2012.04.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 03/26/2012] [Accepted: 04/23/2012] [Indexed: 11/29/2022]
Abstract
Human neutrophil elastase (HNE) has been implicated as a major contributor in the pathogenesis of diseases, such as pulmonary emphysema, acute lung injury (ALI), acute respiratory distress syndrome (ARDS), and other inflammatory diseases. Therefore, searching for appropriate and potential human neutrophil elastase inhibitors (HNEI) that would restore the balance between the free enzyme and the endogenous inhibitors would be of therapeutic interest. ONO-5046 is the first specific HNEI to improve respiratory function and protect lung tissues against various lung injuries. However, the mechanism of ONO-5046 to HNE is still unclear. In this study, the binding properties of ONO-5046 were investigated through (1)H NMR, molecular docking, and bioassay methods to understand the effect of ONO-5046 to HNE. The proton spin-lattice relaxation rate and molecular rotational correlation time results indicated that ONO-5046 has higher affinity with HNE. The molecular docking study showed that ONO-5046 is perfectly matched for the primary enzyme specificity pocket (S1 pocket), and is tightly bound to this pocket of HNE through hydrophobic and hydrogen bonding interactions. The results of both methods were validated through analysis of the HNE inhibitory activity bioassay of ONO-5046 with an IC(50) value of 87.05 nM. Our data suggested that ONO-5046 could bind to HNE through direct interaction, and that molecular docking and NMR methods are valid approaches to survey new HNEI.
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Affiliation(s)
- Li Feng
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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3594
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Venkatramani L, Johnson ES, Kolavi G, Air GM, Brouillette WJ, Mooers BHM. Crystal structure of a new benzoic acid inhibitor of influenza neuraminidase bound with a new tilt induced by overpacking subsite C6. BMC STRUCTURAL BIOLOGY 2012; 12:7. [PMID: 22559154 PMCID: PMC3416664 DOI: 10.1186/1472-6807-12-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 05/06/2012] [Indexed: 11/10/2022]
Abstract
Background Influenza neuraminidase (NA) is an important target for antiviral inhibitors since its active site is highly conserved such that inhibitors can be cross-reactive against multiple types and subtypes of influenza. Here, we discuss the crystal structure of neuraminidase subtype N9 complexed with a new benzoic acid based inhibitor (2) that was designed to add contacts by overpacking one side of the active site pocket. Inhibitor 2 uses benzoic acid to mimic the pyranose ring, a bis-(hydroxymethyl)-substituted 2-pyrrolidinone ring in place of the N-acetyl group of the sialic acid, and a branched aliphatic structure to fill the sialic acid C6 subsite. Results Inhibitor 2 {4-[2,2-bis(hydroxymethyl)-5-oxo-pyrrolidin-1-yl]-3-[(dipropylamino)methyl)]benzoic acid} was soaked into crystals of neuraminidase of A/tern/Australia/G70c/75 (N9), and the structure refined with 1.55 Å X-ray data. The benzene ring of the inhibitor tilted 8.9° compared to the previous compound (1), and the number of contacts, including hydrogen bonds, increased. However, the IC50 for compound 2 remained in the low micromolar range, likely because one propyl group was disordered. In this high-resolution structure of NA isolated from virus grown in chicken eggs, we found electron density for additional sugar units on the N-linked glycans compared to previous neuraminidase structures. In particular, seven mannoses and two N-acetylglucosamines are visible in the glycan attached to Asn200. This long, branched high-mannose glycan makes significant contacts with the neighboring subunit. Conclusions We designed inhibitor 2 with an extended substituent at C4-corresponding to C6 of sialic acid-to increase the contact surface in the C6-subsite and to force the benzene ring to tilt to maximize these interactions while retaining the interactions of the carboxylate and the pyrolidinone substituents. The crystal structure at 1.55 Å showed that we partially succeeded in that the ring in 2 is tilted relative to 1 and the number of contacts increased, but one hydrophobic branch makes no contacts, perhaps explaining why the IC50 did not decrease. Future design efforts will include branches of unequal length so that both branches may be accommodated in the C6-subsite without conformational disorder. The high-mannose glycan attached to Asn200 makes several inter-subunit contacts and appears to stabilize the tetramer.
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Affiliation(s)
- Lalitha Venkatramani
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 941 Stanton L, Young Blvd, Oklahoma City, OK 73104, USA
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