3601
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Bhatia S, Bharatam PV. Possibility of the Existence of Donor–Acceptor Interactions in Bis(azole)amines: An Electronic Structure Analysis. J Org Chem 2014; 79:4852-62. [DOI: 10.1021/jo402862r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Sonam Bhatia
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S. A. S.
Nagar, Punjab 160 062, India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S. A. S.
Nagar, Punjab 160 062, India
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3602
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Guo Z, Streu K, Krilov G, Mohanty U. Probing the Origin of Structural Stability of Single and Double Stapled p53 Peptide Analogs Bound to MDM2. Chem Biol Drug Des 2014; 83:631-42. [DOI: 10.1111/cbdd.12284] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/06/2013] [Accepted: 01/06/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Zuojun Guo
- Department of Chemistry; Boston College; 2609 Beacon Street Chestnut Hill MA 02467 USA
- Genomics Institute of the Novartis Research Foundation; 10675 John Jay Hopkins Dr. San Diego CA 92121 USA
| | - Kristina Streu
- Department of Chemistry; Boston College; 2609 Beacon Street Chestnut Hill MA 02467 USA
| | - Goran Krilov
- Schrödinger, Inc.; 120 W 45th Street, 17th Fl. New York NY 10036 USA
| | - Udayan Mohanty
- Department of Chemistry; Boston College; 2609 Beacon Street Chestnut Hill MA 02467 USA
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3603
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Xing J, Li Q, Zhang S, Liu H, Zhao L, Cheng H, Zhang Y, Zhou J, Zhang H. Identification of dipeptidyl peptidase IV inhibitors: virtual screening, synthesis and biological evaluation. Chem Biol Drug Des 2014; 84:364-77. [PMID: 24674599 DOI: 10.1111/cbdd.12327] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/14/2014] [Accepted: 03/14/2014] [Indexed: 12/20/2022]
Abstract
Inhibition of dipeptidyl peptidase IV is an important approach for the treatment of type-2 diabetes. In this study, we reported a multistage virtual screening workflow that integrated 3D pharmacophore models, structural consensus docking, and molecular mechanics/generalized Born surface area binding energy calculation to identify novel dipeptidyl peptidase IV inhibitors. After screening our in-house database, two hit compounds, HWL-405 and HWL-892, having persistent high performance in all stages of virtual screening were identified. These two hit compounds together with several analogs were synthesized and evaluated for in vitro inhibition of dipeptidyl peptidase IV. The experimental data indicated that most designed compounds exhibited significant dipeptidyl peptidase IV inhibitory activity. Among them, compounds 35f displayed the greatest potency against dipeptidyl peptidase IV in vitro with the IC50 value of 78 nm. In an oral glucose tolerance test in normal male Kunming mice, compound 35f reduced blood glucose excursion in a dose-dependent manner.
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Affiliation(s)
- Junhao Xing
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
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3604
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Hosseini A, Brouk M, Lucas MF, Glaser F, Fishman A, Guallar V. Atomic picture of ligand migration in toluene 4-monooxygenase. J Phys Chem B 2014; 119:671-8. [PMID: 24798294 DOI: 10.1021/jp502509a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Computational modeling combined with mutational and activity assays was used to underline the substrate migration pathways in toluene 4-monooxygenase, a member of the important family of bacterial multicomponent monooxygenases (BMMs). In all structurally defined BMM hydroxylases, several hydrophobic cavities in the α-subunit map a preserved path from the protein surface to the diiron active site. Our results confirm the presence of two pathways by which different aromatic molecules can enter/escape the active site. While the substrate is observed to enter from both channels, the more hydrophilic product is withdrawn mainly from the shorter channel ending at residues D285 and E214. The long channel ends in the vicinity of S395, whose variants have been seen to affect activity and specificity. These mutational effects are clearly reproduced and rationalized by the in silico studies. Furthermore, the combined computational and experimental results highlight the importance of residue F269, which is located at the intersection of the two channels.
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Affiliation(s)
- Ali Hosseini
- Department of Life Sciences, Barcelona Supercomputing Center , Nexus II Building, 08034 Barcelona, Spain
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3605
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Salam NK, Adzhigirey M, Sherman W, Pearlman DA. Structure-based approach to the prediction of disulfide bonds in proteins. Protein Eng Des Sel 2014; 27:365-74. [PMID: 24817698 DOI: 10.1093/protein/gzu017] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Protein engineering remains an area of growing importance in pharmaceutical and biotechnology research. Stabilization of a folded protein conformation is a frequent goal in projects that deal with affinity optimization, enzyme design, protein construct design, and reducing the size of functional proteins. Indeed, it can be desirable to assess and improve protein stability in order to avoid liabilities such as aggregation, degradation, and immunogenic response that may arise during development. One way to stabilize a protein is through the introduction of disulfide bonds. Here, we describe a method to predict pairs of protein residues that can be mutated to form a disulfide bond. We combine a physics-based approach that incorporates implicit solvent molecular mechanics with a knowledge-based approach. We first assign relative weights to the terms that comprise our scoring function using a genetic algorithm applied to a set of 75 wild-type structures that each contains a disulfide bond. The method is then tested on a separate set of 13 engineered proteins comprising 15 artificial stabilizing disulfides introduced via site-directed mutagenesis. We find that the native disulfide in the wild-type proteins is scored well, on average (within the top 6% of the reasonable pairs of residues that could form a disulfide bond) while 6 out of the 15 artificial stabilizing disulfides scored within the top 13% of ranked predictions. Overall, this suggests that the physics-based approach presented here can be useful for triaging possible pairs of mutations for disulfide bond formation to improve protein stability.
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Affiliation(s)
- Noeris K Salam
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - Matvey Adzhigirey
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - Woody Sherman
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - David A Pearlman
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
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3606
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Li H, Kasam V, Tautermann CS, Seeliger D, Vaidehi N. Computational method to identify druggable binding sites that target protein-protein interactions. J Chem Inf Model 2014; 54:1391-400. [PMID: 24762202 DOI: 10.1021/ci400750x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein-protein interactions are implicated in the pathogenesis of many diseases and are therefore attractive but challenging targets for drug design. One of the challenges in development is the identification of potential druggable binding sites in protein interacting interfaces. Identification of interface surfaces can greatly aid rational drug design of small molecules inhibiting protein-protein interactions. In this work, starting from the structure of a free monomer, we have developed a ligand docking based method, called "FindBindSite" (FBS), to locate protein-protein interacting interface regions and potential druggable sites in this interface. FindBindSite utilizes the results from docking a small and diverse library of small molecules to the entire protein structure. By clustering regions with the highest docked ligand density from FBS, we have shown that these high ligand density regions strongly correlate with the known protein-protein interacting surfaces. We have further predicted potential druggable binding sites on the protein surface using FBS, with druggability being defined as the site with high density of ligands docked. FBS shows a hit rate of 71% with high confidence and 93% with lower confidence for the 41 proteins used for predicting druggable binding sites on the protein-protein interface. Mining the regions of lower ligand density that are contiguous with the high scoring high ligand density regions from FBS, we were able to map 70% of the protein-protein interacting surface in 24 out of 41 structures tested. We also observed that FBS has limited sensitivity to the size and nature of the small molecule library used for docking. The experimentally determined hotspot residues for each protein-protein complex cluster near the best scoring druggable binding sites identified by FBS. These results validate the ability of our technique to identify druggable sites within protein-protein interface regions that have the maximal possibility of interface disruption.
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Affiliation(s)
- Hubert Li
- Division of Immunology, Beckman Research Institute of the City of Hope , 1500 E Duarte Road, Duarte, California 91010, United States
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3607
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Zhu K, Day T, Warshaviak D, Murrett C, Friesner R, Pearlman D. Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction. Proteins 2014; 82:1646-55. [PMID: 24619874 DOI: 10.1002/prot.24551] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/04/2014] [Accepted: 03/06/2014] [Indexed: 01/21/2023]
Abstract
We present the blinded prediction results in the Second Antibody Modeling Assessment (AMA-II) using a fully automatic antibody structure prediction method implemented in the programs BioLuminate and Prime. We have developed a novel knowledge based approach to model the CDR loops, using a combination of sequence similarity, geometry matching, and the clustering of database structures. The homology models are further optimized with a physics-based energy function (VSGB2.0), which improves the model quality significantly. H3 loop modeling remains the most challenging task. Our ab initio loop prediction performs well for the H3 loop in the crystal structure context, and allows improved results when refining the H3 loops in the context of homology models. For the 10 human and mouse derived antibodies in this assessment, the average RMSDs for the homology model Fv and framework regions are 1.19 Å and 0.74 Å, respectively. The average RMSDs for five non-H3 CDR loops range from 0.61 Å to 1.05 Å, and the H3 loop average RMSD is 2.91 Å using our knowledge-based loop prediction approach. The ab initio H3 loop predictions yield an average RMSD of 1.28 Å when performed in the context of the crystal structure and 2.67 Å in the context of the homology modeled structure. Notably, our method for predicting the H3 loop in the crystal structure environment ranked first among the seven participating groups in AMA-II, and our method made the best prediction among all participants for seven of the ten targets.
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Affiliation(s)
- Kai Zhu
- Schrodinger, LLC, New York, New York, 10036
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3608
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Inhibition and biochemical characterization of methicillin-resistant Staphylococcus aureus shikimate dehydrogenase: an in silico and kinetic study. Molecules 2014; 19:4491-509. [PMID: 24727420 PMCID: PMC6270726 DOI: 10.3390/molecules19044491] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/03/2014] [Accepted: 04/04/2014] [Indexed: 12/19/2022] Open
Abstract
Methicillin-resistant Staphylococcus auerus (MRSA) strains are having a major impact worldwide, and due to their resistance to all β-lactams, an urgent need for new drugs is emerging. In this regard, the shikimate pathway is considered to be one of the metabolic features of bacteria and is absent in humans. Therefore enzymes involved in this route, such as shikimate dehydrogenase (SDH), are considered excellent targets for discovery of novel antibacterial drugs. In this study, the SDH from MRSA (SaSDH) was characterized. The results showed that the enzyme is a monomer with a molecular weight of 29 kDa, an optimum temperature of 65 °C, and a maximal pH range of 9–11 for its activity. Kinetic studies revealed that SDH showed Michaelis-Menten kinetics toward both substrates (shikimate and NADP+). Initial velocity analysis suggested that SaSDH catalysis followed a sequential random mechanism. Additionally, a tridimensional model of SaSDH was obtained by homology modeling and validated. Through virtual screening three inhibitors of SaSDH were found (compounds 238, 766 and 894) and their inhibition constants and mechanism were obtained. Flexible docking studies revealed that these molecules make interactions with catalytic residues. The data of this study could serve as starting point in the search of new chemotherapeutic agents against MRSA.
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3609
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Zhang K, Zhang J, Gao ZG, Zhang D, Zhu L, Han GW, Moss SM, Paoletta S, Kiselev E, Lu W, Fenalti G, Zhang W, Müller CE, Yang H, Jiang H, Cherezov V, Katritch V, Jacobson KA, Stevens RC, Wu B, Zhao Q. Structure of the human P2Y12 receptor in complex with an antithrombotic drug. Nature 2014; 509:115-8. [PMID: 24670650 DOI: 10.1038/nature13083] [Citation(s) in RCA: 291] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 01/27/2014] [Indexed: 02/06/2023]
Abstract
P2Y receptors (P2YRs), a family of purinergic G-protein-coupled receptors (GPCRs), are activated by extracellular nucleotides. There are a total of eight distinct functional P2YRs expressed in human, which are subdivided into P2Y1-like receptors and P2Y12-like receptors. Their ligands are generally charged molecules with relatively low bioavailability and stability in vivo, which limits our understanding of this receptor family. P2Y12R regulates platelet activation and thrombus formation, and several antithrombotic drugs targeting P2Y12R--including the prodrugs clopidogrel (Plavix) and prasugrel (Effient) that are metabolized and bind covalently, and the nucleoside analogue ticagrelor (Brilinta) that acts directly on the receptor--have been approved for the prevention of stroke and myocardial infarction. However, limitations of these drugs (for example, a very long half-life of clopidogrel action and a characteristic adverse effect profile of ticagrelor) suggest that there is an unfulfilled medical need for developing a new generation of P2Y12R inhibitors. Here we report the 2.6 Å resolution crystal structure of human P2Y12R in complex with a non-nucleotide reversible antagonist, AZD1283. The structure reveals a distinct straight conformation of helix V, which sets P2Y12R apart from all other known class A GPCR structures. With AZD1283 bound, the highly conserved disulphide bridge in GPCRs between helix III and extracellular loop 2 is not observed and appears to be dynamic. Along with the details of the AZD1283-binding site, analysis of the extracellular interface reveals an adjacent ligand-binding region and suggests that both pockets could be required for dinucleotide binding. The structure provides essential insights for the development of improved P2Y12R ligands and allosteric modulators as drug candidates.
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Affiliation(s)
- Kaihua Zhang
- 1] CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China [2]
| | - Jin Zhang
- 1] CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China [2]
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Dandan Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Lan Zhu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Gye Won Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Steven M Moss
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Silvia Paoletta
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Evgeny Kiselev
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Weizhen Lu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Gustavo Fenalti
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Wenru Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, An der Immenburg 4, D-53121 Bonn, Germany
| | - Huaiyu Yang
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Vadim Cherezov
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Vsevolod Katritch
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Raymond C Stevens
- 1] Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA [2] iHuman Institute, ShanghaiTech University, 99 Haike Road, Pudong, Shanghai 201203, China
| | - Beili Wu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Qiang Zhao
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
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3610
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Waiker DK, Karthikeyan C, Poongavanam V, Kongsted J, Lozach O, Meijer L, Trivedi P. Synthesis, biological evaluation and molecular modelling studies of 4-anilinoquinazoline derivatives as protein kinase inhibitors. Bioorg Med Chem 2014; 22:1909-15. [DOI: 10.1016/j.bmc.2014.01.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 12/18/2022]
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3611
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Zimmer MH, Li B, Shahid RS, Peshkepija P, Zimmer M. Structural Consequences of Chromophore Formation and Exploration of Conserved Lid Residues amongst Naturally Occurring Fluorescent Proteins. Chem Phys 2014; 429:5-11. [PMID: 24465077 PMCID: PMC3899699 DOI: 10.1016/j.chemphys.2013.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Computational methods were used to generate the lowest energy conformations of the immature precyclized forms of the 28 naturally occurring GFP-like proteins deposited in the pdb. In all 28 GFP-like proteins, the beta-barrel contracts upon chromophore formation and becomes more rigid. Our prior analysis of over 260 distinct naturally occurring GFP-like proteins revealed that most of the conserved residues are located in the top and bottom of the barrel in the turns between the β-sheets.(1) Structural analyses, molecular dynamics simulations and the Anisotropic Network Model were used to explore the role of these conserved lid residues as possible folding nuclei. Our results are internally consistent and show that the conserved residues in the top and bottom lids undergo relatively less translational movement than other lid residues, and a number of these residues may play an important role as hinges or folding nuclei in the fluorescent proteins.
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Affiliation(s)
- Matthew H. Zimmer
- Chemistry Department, Connecticut College, New London, CT06320, USA
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Binsen Li
- Chemistry Department, Connecticut College, New London, CT06320, USA
| | - Ramza S. Shahid
- Chemistry Department, Connecticut College, New London, CT06320, USA
| | - Paola Peshkepija
- Chemistry Department, Connecticut College, New London, CT06320, USA
| | - Marc Zimmer
- Chemistry Department, Connecticut College, New London, CT06320, USA
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3612
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Integration of methods in cheminformatics and biocalorimetry for the design of trypanosomatid enzyme inhibitors. Future Med Chem 2014; 6:17-33. [DOI: 10.4155/fmc.13.185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: The enzyme GAPDH, which acts in the glycolytic pathway, is seen as a potential target for pharmaceutical intervention of Chagas disease. Results: Herein, we report the discovery of new Trypanosoma cruzi GAPDH (TcGAPDH) inhibitors from target- and ligand-based virtual screening protocols using isothermal titration calorimetry (ITC) and molecular dynamics. Molecular dynamics simulations were used to gain insight on the binding poses of newly identified inhibitors acting at the TcGAPDH substrate (G3P) site. Conclusion: Nequimed125, the most potent inhibitor to act upon TcGAPDH so far, which sits on the G3P site without any contact with the co-factor (NAD+) site, underpins the result obtained by ITC that it is a G3P-competitive inhibitor. Molecular dynamics simulation provides biding poses of TcGAPDH inhibitors that correlate with mechanisms of inhibition observed by ITC. Overall, a new class of dihydroindole compounds that act upon TcGAPDH through a competitive mechanism of inhibition as proven by ITC measurements also kills T. cruzi.
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3613
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Poongavanam V, Narayana Moorthy NSH, Kongsted J. Dual mechanism of HIV-1 integrase and RNase H inhibition by diketo derivatives – a computational study. RSC Adv 2014. [DOI: 10.1039/c4ra05728g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Dual inhibition of HIV-1 integrase and RNase H by the diketo derivatives is investigated through ligand and structure based computational methods.
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Affiliation(s)
| | | | - Jacob Kongsted
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- Odense M, Denmark
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3614
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Lagunin AA, Goel RK, Gawande DY, Pahwa P, Gloriozova TA, Dmitriev AV, Ivanov SM, Rudik AV, Konova VI, Pogodin PV, Druzhilovsky DS, Poroikov VV. Chemo- and bioinformatics resources for in silico drug discovery from medicinal plants beyond their traditional use: a critical review. Nat Prod Rep 2014; 31:1585-611. [DOI: 10.1039/c4np00068d] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
An overview of databases andin silicotools for discovery of the hidden therapeutic potential of medicinal plants.
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Affiliation(s)
- Alexey A. Lagunin
- Orekhovich Institute of Biomedical Chemistry of Rus. Acad. Med. Sci
- Moscow, Russia
- Russian National Research Medical University
- Medico-Biologic Faculty
- Moscow, Russia
| | - Rajesh K. Goel
- Department of Pharmaceutical Sciences and Drug Research
- Punjabi University
- Patiala-147002, India
| | - Dinesh Y. Gawande
- Department of Pharmaceutical Sciences and Drug Research
- Punjabi University
- Patiala-147002, India
| | - Priynka Pahwa
- Department of Pharmaceutical Sciences and Drug Research
- Punjabi University
- Patiala-147002, India
| | | | | | - Sergey M. Ivanov
- Orekhovich Institute of Biomedical Chemistry of Rus. Acad. Med. Sci
- Moscow, Russia
| | - Anastassia V. Rudik
- Orekhovich Institute of Biomedical Chemistry of Rus. Acad. Med. Sci
- Moscow, Russia
| | - Varvara I. Konova
- Orekhovich Institute of Biomedical Chemistry of Rus. Acad. Med. Sci
- Moscow, Russia
| | - Pavel V. Pogodin
- Orekhovich Institute of Biomedical Chemistry of Rus. Acad. Med. Sci
- Moscow, Russia
- Russian National Research Medical University
- Medico-Biologic Faculty
- Moscow, Russia
| | | | - Vladimir V. Poroikov
- Orekhovich Institute of Biomedical Chemistry of Rus. Acad. Med. Sci
- Moscow, Russia
- Russian National Research Medical University
- Medico-Biologic Faculty
- Moscow, Russia
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3615
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Levit A, Beuming T, Krilov G, Sherman W, Niv MY. Predicting GPCR Promiscuity Using Binding Site Features. J Chem Inf Model 2013; 54:184-94. [DOI: 10.1021/ci400552z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Anat Levit
- Institute
of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty
of Agriculture Food and Environment, The Hebrew University, Rehovot 76100, Israel
- Fritz
Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 91904, Israel
| | - Thijs Beuming
- Schrodinger Inc., 120 West Forty-Fifth Street, 17th Floor, New York, New York 10036, United States
| | - Goran Krilov
- Schrodinger Inc., 120 West Forty-Fifth Street, 17th Floor, New York, New York 10036, United States
| | - Woody Sherman
- Schrodinger Inc., 120 West Forty-Fifth Street, 17th Floor, New York, New York 10036, United States
| | - Masha Y. Niv
- Institute
of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty
of Agriculture Food and Environment, The Hebrew University, Rehovot 76100, Israel
- Fritz
Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 91904, Israel
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3616
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Zauhar RJ, Gianti E, Welsh WJ. Fragment-based Shape Signatures: a new tool for virtual screening and drug discovery. J Comput Aided Mol Des 2013; 27:1009-36. [PMID: 24366428 PMCID: PMC3880490 DOI: 10.1007/s10822-013-9698-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 12/03/2013] [Indexed: 12/13/2022]
Abstract
Since its introduction in 2003, the Shape Signatures method has been successfully applied in a number of drug design projects. Because it uses a ray-tracing approach to directly measure molecular shape and properties (as opposed to relying on chemical structure), it excels at scaffold hopping, and is extraordinarily easy to use. Despite its advantages, a significant drawback of the method has hampered its application to certain classes of problems; namely, when the chemical structures considered are large and contain heterogeneous ring-systems, the method produces descriptors that tend to merely measure the overall size of the molecule, and begin to lose selective power. To remedy this, the approach has been reformulated to automatically decompose compounds into fragments using ring systems as anchors, and to likewise partition the ray-trace in accordance with the fragment assignments. Subsequently, descriptors are generated that are fragment-based, and query and target molecules are compared by mapping query fragments onto target fragments in all ways consistent with the underlying chemical connectivity. This has proven to greatly extend the selective power of the method, while maintaining the ease of use and scaffold-hopping capabilities that characterized the original implementation. In this work, we provide a full conceptual description of the next generation Shape Signatures, and we underline the advantages of the method by discussing its practical applications to ligand-based virtual screening. The new approach can also be applied in receptor-based mode, where protein-binding sites (partitioned into subsites) can be matched against the new fragment-based Shape Signatures descriptors of library compounds.
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Affiliation(s)
- Randy J Zauhar
- Department of Chemistry and Biochemistry, University of the Sciences, 600 S. 43rd Street, Philadelphia, PA, 19104, USA,
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3617
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Thomas T, McLean KC, McRobb FM, Manallack DT, Chalmers DK, Yuriev E. Homology modeling of human muscarinic acetylcholine receptors. J Chem Inf Model 2013; 54:243-53. [PMID: 24328076 DOI: 10.1021/ci400502u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We have developed homology models of the acetylcholine muscarinic receptors M₁R-M₅R, based on the β₂-adrenergic receptor crystal as the template. This is the first report of homology modeling of all five subtypes of acetylcholine muscarinic receptors with binding sites optimized for ligand binding. The models were evaluated for their ability to discriminate between muscarinic antagonists and decoy compounds using virtual screening using enrichment factors, area under the ROC curve (AUC), and an early enrichment measure, LogAUC. The models produce rational binding modes of docked ligands as well as good enrichment capacity when tested against property-matched decoy libraries, which demonstrates their unbiased predictive ability. To test the relative effects of homology model template selection and the binding site optimization procedure, we generated and evaluated a naïve M₂R model, using the M₃R crystal structure as a template. Our results confirm previous findings that binding site optimization using ligand(s) active at a particular receptor, i.e. including functional knowledge into the model building process, has a more pronounced effect on model quality than target-template sequence similarity. The optimized M₁R-M₅R homology models are made available as part of the Supporting Information to allow researchers to use these structures, compare them to their own results, and thus advance the development of better modeling approaches.
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Affiliation(s)
- Trayder Thomas
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) , 381 Royal Parade, Parkville, VIC 3052 Australia
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3618
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Abstract
Docking methodology aims to predict the experimental binding modes and affinities of small molecules within the binding site of particular receptor targets and is currently used as a standard computational tool in drug design for lead compound optimisation and in virtual screening studies to find novel biologically active molecules. The basic tools of a docking methodology include a search algorithm and an energy scoring function for generating and evaluating ligand poses. In this review, we present the search algorithms and scoring functions most commonly used in current molecular docking methods that focus on protein-ligand applications. We summarise the main topics and recent computational and methodological advances in protein-ligand docking. Protein flexibility, multiple ligand binding modes and the free-energy landscape profile for binding affinity prediction are important and interconnected challenges to be overcome by further methodological developments in the docking field.
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3619
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Beard H, Cholleti A, Pearlman D, Sherman W, Loving KA. Applying physics-based scoring to calculate free energies of binding for single amino acid mutations in protein-protein complexes. PLoS One 2013; 8:e82849. [PMID: 24340062 PMCID: PMC3858304 DOI: 10.1371/journal.pone.0082849] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/28/2013] [Indexed: 11/18/2022] Open
Abstract
Predicting changes in protein binding affinity due to single amino acid mutations helps us better understand the driving forces underlying protein-protein interactions and design improved biotherapeutics. Here, we use the MM-GBSA approach with the OPLS2005 force field and the VSGB2.0 solvent model to calculate differences in binding free energy between wild type and mutant proteins. Crucially, we made no changes to the scoring model as part of this work on protein-protein binding affinity--the energy model has been developed for structure prediction and has previously been validated only for calculating the energetics of small molecule binding. Here, we compare predictions to experimental data for a set of 418 single residue mutations in 21 targets and find that the MM-GBSA model, on average, performs well at scoring these single protein residue mutations. Correlation between the predicted and experimental change in binding affinity is statistically significant and the model performs well at picking "hotspots," or mutations that change binding affinity by more than 1 kcal/mol. The promising performance of this physics-based method with no tuned parameters for predicting binding energies suggests that it can be transferred to other protein engineering problems.
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Affiliation(s)
- Hege Beard
- Schrödinger, New York, New York, United States of America
| | | | - David Pearlman
- Schrödinger, New York, New York, United States of America
| | - Woody Sherman
- Schrödinger, New York, New York, United States of America
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3620
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Sheftel S, Muratore KE, Black M, Costanzi S. Graph analysis of β2 adrenergic receptor structures: a "social network" of GPCR residues. In Silico Pharmacol 2013; 1:16. [PMID: 25505660 PMCID: PMC4230308 DOI: 10.1186/2193-9616-1-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 11/25/2013] [Indexed: 02/07/2023] Open
Abstract
Purpose G protein-coupled receptors (GPCRs) are a superfamily of membrane proteins of vast pharmaceutical interest. Here, we describe a graph theory-based analysis of the structure of the β2 adrenergic receptor (β2 AR), a prototypical GPCR. In particular, we illustrate the network of direct and indirect interactions that link each amino acid residue to any other residue of the receptor. Methods Networks of interconnected amino acid residues in proteins are analogous to social networks of interconnected people. Hence, they can be studied through the same analysis tools typically employed to analyze social networks – or networks in general – to reveal patterns of connectivity, influential members, and dynamicity. We focused on the analysis of closeness-centrality, which is a measure of the overall connectivity distance of the member of a network to all other members. Results The residues endowed with the highest closeness-centrality are located in the middle of the seven transmembrane domains (TMs). In particular, they are mostly located in the middle of TM2, TM3, TM6 or TM7, while fewer of them are located in the middle of TM1, TM4 or TM5. At the cytosolic end of TM6, the centrality detected for the active structure is markedly lower than that detected for the corresponding residues in the inactive structures. Moreover, several residues acquire centrality when the structures are analyzed in the presence of ligands. Strikingly, there is little overlap between the residues that acquire centrality in the presence of the ligand in the blocker-bound structures and the agonist-bound structures. Conclusions Our results reflect the fact that the receptor resembles a bow tie, with a rather tight knot of closely interconnected residues and two ends that fan out in two opposite directions: one toward the extracellular space, which hosts the ligand binding cavity, and one toward the cytosol, which hosts the G protein binding cavity. Moreover, they underscore how interaction network is by the conformational rearrangements concomitant with the activation of the receptor and by the presence of agonists or blockers. Electronic supplementary material The online version of this article (doi:10.1186/2193-9616-1-16) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samuel Sheftel
- Department of Chemistry, American University, 4400 Massachusetts Ave, Northwest, Washington, DC 20016 USA
| | - Kathryn E Muratore
- Department of Chemistry, American University, 4400 Massachusetts Ave, Northwest, Washington, DC 20016 USA
| | - Michael Black
- Department of Computer Science, American University, Northwest, Washington, DC 20016 USA
| | - Stefano Costanzi
- Department of Chemistry, American University, 4400 Massachusetts Ave, Northwest, Washington, DC 20016 USA ; Center for Behavioral Neuroscience, American University, Northwest, Washington, DC 20016 USA
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3621
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Frączek T, Siwek A, Paneth P. Assessing Molecular Docking Tools for Relative Biological Activity Prediction: A Case Study of Triazole HIV-1 NNRTIs. J Chem Inf Model 2013; 53:3326-42. [DOI: 10.1021/ci400427a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Tomasz Frączek
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, Zeromskiego
116, 90-924 Lodz, Poland
| | - Agata Siwek
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, Zeromskiego
116, 90-924 Lodz, Poland
- Department
of Organic Chemistry, Faculty of Pharmacy, Medical University, Chodzki 4a, 20-093 Lublin, Poland
| | - Piotr Paneth
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, Zeromskiego
116, 90-924 Lodz, Poland
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3622
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Felts B, Pramod AB, Sandtner W, Burbach N, Bulling S, Sitte HH, Henry LK. The two Na+ sites in the human serotonin transporter play distinct roles in the ion coupling and electrogenicity of transport. J Biol Chem 2013; 289:1825-40. [PMID: 24293367 DOI: 10.1074/jbc.m113.504654] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Neurotransmitter transporters of the SLC6 family of proteins, including the human serotonin transporter (hSERT), utilize Na(+), Cl(-), and K(+) gradients to induce conformational changes necessary for substrate translocation. Dysregulation of ion movement through monoamine transporters has been shown to impact neuronal firing potentials and could play a role in pathophysiologies, such as depression and anxiety. Despite multiple crystal structures of prokaryotic and eukaryotic SLC transporters indicating the location of both (or one) conserved Na(+)-binding sites (termed Na1 and Na2), much remains uncertain in regard to the movements and contributions of these cation-binding sites in the transport process. In this study, we utilize the unique properties of a mutation of hSERT at a single, highly conserved asparagine on TM1 (Asn-101) to provide several lines of evidence demonstrating mechanistically distinct roles for Na1 and Na2. Mutations at Asn-101 alter the cation dependence of the transporter, allowing Ca(2+) (but not other cations) to functionally replace Na(+) for driving transport and promoting 5-hydroxytryptamine (5-HT)-dependent conformational changes. Furthermore, in two-electrode voltage clamp studies in Xenopus oocytes, both Ca(2+) and Na(+) illicit 5-HT-induced currents in the Asn-101 mutants and reveal that, although Ca(2+) promotes substrate-induced current, it does not appear to be the charge carrier during 5-HT transport. These findings, in addition to functional evaluation of Na1 and Na2 site mutants, reveal separate roles for Na1 and Na2 and provide insight into initiation of the translocation process as well as a mechanism whereby the reported SERT stoichiometry can be obtained despite the presence of two putative Na(+)-binding sites.
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Affiliation(s)
- Bruce Felts
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203 and
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3623
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Zheng Z, Ucisik MN, Merz KM. The Movable Type Method Applied to Protein-Ligand Binding. J Chem Theory Comput 2013; 9:5526-5538. [PMID: 24535920 DOI: 10.1021/ct4005992] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurately computing the free energy for biological processes like protein folding or protein-ligand association remains a challenging problem. Both describing the complex intermolecular forces involved and sampling the requisite configuration space make understanding these processes innately difficult. Herein, we address the sampling problem using a novel methodology we term "movable type". Conceptually it can be understood by analogy with the evolution of printing and, hence, the name movable type. For example, a common approach to the study of protein-ligand complexation involves taking a database of intact drug-like molecules and exhaustively docking them into a binding pocket. This is reminiscent of early woodblock printing where each page had to be laboriously created prior to printing a book. However, printing evolved to an approach where a database of symbols (letters, numerals, etc.) was created and then assembled using a movable type system, which allowed for the creation of all possible combinations of symbols on a given page, thereby, revolutionizing the dissemination of knowledge. Our movable type (MT) method involves the identification of all atom pairs seen in protein-ligand complexes and then creating two databases: one with their associated pairwise distant dependent energies and another associated with the probability of how these pairs can combine in terms of bonds, angles, dihedrals and non-bonded interactions. Combining these two databases coupled with the principles of statistical mechanics allows us to accurately estimate binding free energies as well as the pose of a ligand in a receptor. This method, by its mathematical construction, samples all of configuration space of a selected region (the protein active site here) in one shot without resorting to brute force sampling schemes involving Monte Carlo, genetic algorithms or molecular dynamics simulations making the methodology extremely efficient. Importantly, this method explores the free energy surface eliminating the need to estimate the enthalpy and entropy components individually. Finally, low free energy structures can be obtained via a free energy minimization procedure yielding all low free energy poses on a given free energy surface. Besides revolutionizing the protein-ligand docking and scoring problem this approach can be utilized in a wide range of applications in computational biology which involve the computation of free energies for systems with extensive phase spaces including protein folding, protein-protein docking and protein design.
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Affiliation(s)
- Zheng Zheng
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435
| | - Melek N Ucisik
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435
| | - Kenneth M Merz
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435
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3624
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Ozen A, Sherman W, Schiffer CA. Improving the Resistance Profile of Hepatitis C NS3/4A Inhibitors: Dynamic Substrate Envelope Guided Design. J Chem Theory Comput 2013; 9:5693-5705. [PMID: 24587770 DOI: 10.1021/ct400603p] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Drug resistance is a principal concern in the treatment of quickly evolving diseases. The viral protease NS3/4A is a primary drug target for the hepatitis C virus (HCV) and is known to evolve resistance mutations in response to drug therapy. At the molecular level, drug resistance reflects a subtle change in the balance of molecular recognition by NS3/4A; the drug resistant protease variants are no longer effectively inhibited by the competitive active site inhibitors but can still process the natural substrates with enough efficiency for viral survival. In previous works we have developed the "substrate envelope" hypothesis, which posits that inhibitors should be less susceptible to drug resistance if they better mimic the natural substrate molecular recognition features. In this work, we perform molecular dynamics simulations on four native substrates bound to NS3/4A and discover a clearly conserved dynamic substrate envelope. We show that the most severe drug resistance mutations in NS3/4A occur at residues that are outside the substrate envelope. Comparative analysis of three NS3/4A inhibitors reveals structural and dynamic characteristics of inhibitors that could lead to resistance. We also suggest inhibitor modifications to improve resistance profiles based on the dynamic substrate envelope. This study provides a general framework for guiding the development of novel inhibitors that will be more robust against resistance by mimicking the static and dynamic binding characteristics of natural substrates.
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Affiliation(s)
- Ayşegül Ozen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Woody Sherman
- Schrödinger, Inc., 120 West 45th Street, New York, NY 10036, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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3625
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Yilmaz OG, Olmez EO, Ulgen KO. Targeting the Akt1 allosteric site to identify novel scaffolds through virtual screening. Comput Biol Chem 2013; 48:1-13. [PMID: 24291487 DOI: 10.1016/j.compbiolchem.2013.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/20/2013] [Accepted: 10/21/2013] [Indexed: 11/28/2022]
Abstract
Preclinical data and tumor specimen studies report that AKT kinases are related to many human cancers. Therefore, identification and development of small molecule inhibitors targeting AKT and its signaling pathway can be therapeutic in treatment of cancer. Numerous studies report inhibitors that target the ATP-binding pocket in the kinase domains, but the similarity of this site, within the kinase family makes selectivity a major problem. The sequence identity amongst PH domains is significantly lower than that in kinase domains and developing more selective inhibitors is possible if PH domain is targeted. This in silico screening study is the first time report toward the identification of potential allosteric inhibitors expected to bind the cavity between kinase and PH domains of Akt1. Structural information of Akt1 was used to develop structure-based pharmacophore models comprising hydrophobic, acceptor, donor and ring features. The 3D structural information of previously identified allosteric Akt inhibitors obtained from literature was employed to develop a ligand-based pharmacophore model. Database was generated with drug like subset of ZINC and screening was performed based on 3D similarity to the selected pharmacophore hypotheses. Binding modes and affinities of the ligands were predicted by Glide software. Top scoring hits were further analyzed considering 2D similarity between the compounds, interactions with Akt1, fitness to pharmacophore models, ADME, druglikeness criteria and Induced-Fit docking. Using virtual screening methodologies, derivatives of 3-methyl-xanthine, quinoline-4-carboxamide and 2-[4-(cyclohexa-1,3-dien-1-yl)-1H-pyrazol-3-yl]phenol were proposed as potential leads for allosteric inhibition of Akt1.
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Affiliation(s)
- Oya Gursoy Yilmaz
- Bogazici University, Department of Chemical Engineering, 34342 Istanbul, Turkey.
| | - Elif Ozkirimli Olmez
- Bogazici University, Department of Chemical Engineering, 34342 Istanbul, Turkey.
| | - Kutlu O Ulgen
- Bogazici University, Department of Chemical Engineering, 34342 Istanbul, Turkey.
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3626
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Haider K, Huggins DJ. Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules. J Chem Inf Model 2013; 53:2571-86. [PMID: 24070451 PMCID: PMC3840717 DOI: 10.1021/ci4003409] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Intermolecular interactions in the aqueous phase must compete with the interactions between the two binding partners and their solvating water molecules. In biological systems, water molecules in protein binding sites cluster at well-defined hydration sites and can form strong hydrogen-bonding interactions with backbone and side-chain atoms. Displacement of such water molecules is only favorable when the ligand can form strong compensating hydrogen bonds. Conversely, water molecules in hydrophobic regions of protein binding sites make only weak interactions, and the requirements for favorable displacement are less stringent. The propensity of water molecules for displacement can be identified using inhomogeneous fluid solvation theory (IFST), a statistical mechanical method that decomposes the solvation free energy of a solute into the contributions from different spatial regions and identifies potential binding hotspots. In this study, we employed IFST to study the displacement of water molecules from the ATP binding site of Hsp90, using a test set of 103 ligands. The predicted contribution of a hydration site to the hydration free energy was found to correlate well with the observed displacement. Additionally, we investigated if this correlation could be improved by using the energetic scores of favorable probe groups binding at the location of hydration sites, derived from a multiple copy simultaneous search (MCSS) method. The probe binding scores were not highly predictive of the observed displacement and did not improve the predictivity when used in combination with IFST-based hydration free energies. The results show that IFST alone can be used to reliably predict the observed displacement of water molecules in Hsp90. However, MCSS can augment IFST calculations by suggesting which functional groups should be used to replace highly displaceable water molecules. Such an approach could be very useful in improving the hit-to-lead process for new drug targets.
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Affiliation(s)
- Kamran Haider
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences , Lahore, 54792, Pakistan
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3627
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List NH, Curutchet C, Knecht S, Mennucci B, Kongsted J. Toward Reliable Prediction of the Energy Ladder in Multichromophoric Systems: A Benchmark Study on the FMO Light-Harvesting Complex. J Chem Theory Comput 2013; 9:4928-38. [DOI: 10.1021/ct400560m] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Nanna Holmgaard List
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Carles Curutchet
- Departament
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Stefan Knecht
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
- Laboratory
of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Straße 10, 8093 Zürich, Switzerland
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Risorgimento
35, 56126 Pisa, Italy
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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3628
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Poongavanam V, Kongsted J. Virtual screening models for prediction of HIV-1 RT associated RNase H inhibition. PLoS One 2013; 8:e73478. [PMID: 24066050 PMCID: PMC3774690 DOI: 10.1371/journal.pone.0073478] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/19/2013] [Indexed: 11/28/2022] Open
Abstract
The increasing resistance to current therapeutic agents for HIV drug regiment remains a major problem for effective acquired immune deficiency syndrome (AIDS) therapy. Many potential inhibitors have today been developed which inhibits key cellular pathways in the HIV cycle. Inhibition of HIV-1 reverse transcriptase associated ribonuclease H (RNase H) function provides a novel target for anti-HIV chemotherapy. Here we report on the applicability of conceptually different in silico approaches as virtual screening (VS) tools in order to efficiently identify RNase H inhibitors from large chemical databases. The methods used here include machine-learning algorithms (e.g. support vector machine, random forest and kappa nearest neighbor), shape similarity (rapid overlay of chemical structures), pharmacophore, molecular interaction fields-based fingerprints for ligands and protein (FLAP) and flexible ligand docking methods. The results show that receptor-based flexible docking experiments provides good enrichment (80–90%) compared to ligand-based approaches such as FLAP (74%), shape similarity (75%) and random forest (72%). Thus, this study suggests that flexible docking experiments is the model of choice in terms of best retrieval of active from inactive compounds and efficiency and efficacy schemes. Moreover, shape similarity, machine learning and FLAP models could also be used for further validation or filtration in virtual screening processes. The best models could potentially be use for identifying structurally diverse and selective RNase H inhibitors from large chemical databases. In addition, pharmacophore models suggest that the inter-distance between hydrogen bond acceptors play a key role in inhibition of the RNase H domain through metal chelation.
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Affiliation(s)
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
- * E-mail:
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3629
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Integrating virtual and biochemical screening for protein tyrosine phosphatase inhibitor discovery. Methods 2013; 65:219-28. [PMID: 23969317 DOI: 10.1016/j.ymeth.2013.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 08/09/2013] [Accepted: 08/13/2013] [Indexed: 12/14/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) represent an important class of enzymes that mediate signal transduction and control diverse aspects of cell behavior. The importance of their activity is exemplified by their significant contribution to disease etiology with over half of all human PTP genes implicated in at least one disease. Small molecule inhibitors targeting individual PTPs are important biological tools, and are needed to fully characterize the function of these enzymes. Moreover, potent and selective PTP inhibitors hold the promise to transform the treatment of many diseases. While numerous methods exist to develop PTP-directed small molecules, we have found that complimentary use of both virtual (in silico) and biochemical (in vitro) screening approaches expedite compound identification and drug development. Here, we summarize methods pertinent to our work and others. Focusing on specific challenges and successes we have experienced, we discuss the considerable caution that must be taken to avoid enrichment of inhibitors that function by non-selective oxidation. We also discuss the utility of using "open" PTP structures to identify active-site directed compounds, a rather unconventional choice for virtual screening. When integrated closely, virtual and biochemical screening can be used in a productive workflow to identify small molecules targeting PTPs.
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3630
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Design of e-pharmacophore models using compound fragments for the trans-sialidase of Trypanosoma cruzi: screening for novel inhibitor scaffolds. J Mol Graph Model 2013; 45:84-97. [PMID: 24012872 DOI: 10.1016/j.jmgm.2013.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/31/2013] [Accepted: 08/06/2013] [Indexed: 11/23/2022]
Abstract
Chagas' is a fatal disease that affects millions of people worldwide. The lack of safe and effective treatments for Chagas' highlights the need for the discovery of new drugs to fight the disease. Trypanosoma cruzi, the parasitic cause of Chagas' disease, synthesizes a trans-sialidase (TcTS) enzyme responsible for the transfer of sialic acids from the host cell surface to glycoconjugates on the parasitic cell surface. TcTS has no human analogs and is vital to the life cycle of T. cruzi, making TcTS an important enzyme for drug design against Chagas' disease. We use fragment docking to generate various e-pharmacophore hypotheses depicting protein residues important for ligand binding. Virtual screening of the ZINC Clean Leads database with more than 4 million compounds using the e-pharmacophore models found 82 potential inhibitors of TcTS. Molecular dynamics and free energy of binding calculations were used to rank the compounds based on their affinity for TcTS. Two compounds-ZINC13359679 and ZINC02576132-were found to be the most promising lead candidates for TcTS inhibition, and their binding modes are analyzed in detail.
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3631
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Tóth G, Baska F, Schretner A, Rácz Á, Noszál B. Site-specific basicities regulate molecular recognition in receptor binding: in silico docking of thyroid hormones. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:721-30. [DOI: 10.1007/s00249-013-0921-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/09/2013] [Accepted: 07/16/2013] [Indexed: 12/20/2022]
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3632
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Durrant JD, Friedman AJ, Rogers KE, McCammon JA. Comparing neural-network scoring functions and the state of the art: applications to common library screening. J Chem Inf Model 2013; 53:1726-35. [PMID: 23734946 PMCID: PMC3735370 DOI: 10.1021/ci400042y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Indexed: 11/29/2022]
Abstract
We compare established docking programs, AutoDock Vina and Schrödinger's Glide, to the recently published NNScore scoring functions. As expected, the best protocol to use in a virtual-screening project is highly dependent on the target receptor being studied. However, the mean screening performance obtained when candidate ligands are docked with Vina and rescored with NNScore 1.0 is not statistically different than the mean performance obtained when docking and scoring with Glide. We further demonstrate that the Vina and NNScore docking scores both correlate with chemical properties like small-molecule size and polarizability. Compensating for these potential biases leads to improvements in virtual screen performance. Composite NNScore-based scoring functions suited to a specific receptor further improve performance. We are hopeful that the current study will prove useful for those interested in computer-aided drug design.
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Affiliation(s)
- Jacob D Durrant
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA.
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3633
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Robertson JC, Hurley NC, Tortorici M, Ciossani G, Borrello MT, Vellore NA, Ganesan A, Mattevi A, Baron R. Expanding the druggable space of the LSD1/CoREST epigenetic target: new potential binding regions for drug-like molecules, peptides, protein partners, and chromatin. PLoS Comput Biol 2013; 9:e1003158. [PMID: 23874194 PMCID: PMC3715402 DOI: 10.1371/journal.pcbi.1003158] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/10/2013] [Indexed: 01/22/2023] Open
Abstract
Lysine specific demethylase-1 (LSD1/KDM1A) in complex with its corepressor protein CoREST is a promising target for epigenetic drugs. No therapeutic that targets LSD1/CoREST, however, has been reported to date. Recently, extended molecular dynamics (MD) simulations indicated that LSD1/CoREST nanoscale clamp dynamics is regulated by substrate binding and highlighted key hinge points of this large-scale motion as well as the relevance of local residue dynamics. Prompted by the urgent need for new molecular probes and inhibitors to understand LSD1/CoREST interactions with small-molecules, peptides, protein partners, and chromatin, we undertake here a configurational ensemble approach to expand LSD1/CoREST druggability. The independent algorithms FTMap and SiteMap and our newly developed Druggable Site Visualizer (DSV) software tool were used to predict and inspect favorable binding sites. We find that the hinge points revealed by MD simulations at the SANT2/Tower interface, at the SWIRM/AOD interface, and at the AOD/Tower interface are new targets for the discovery of molecular probes to block association of LSD1/CoREST with chromatin or protein partners. A fourth region was also predicted from simulated configurational ensembles and was experimentally validated to have strong binding propensity. The observation that this prediction would be prevented when using only the X-ray structures available (including the X-ray structure bound to the same peptide) underscores the relevance of protein dynamics in protein interactions. A fifth region was highlighted corresponding to a small pocket on the AOD domain. This study sets the basis for future virtual screening campaigns targeting the five novel regions reported herein and for the design of LSD1/CoREST mutants to probe LSD1/CoREST binding with chromatin and various protein partners.
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Affiliation(s)
- James C. Robertson
- Department of Medicinal Chemistry, College of Pharmacy, The University of Utah, Salt Lake City, Utah, United States of America
| | - Nate C. Hurley
- Department of Medicinal Chemistry, College of Pharmacy, The University of Utah, Salt Lake City, Utah, United States of America
| | - Marcello Tortorici
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Giuseppe Ciossani
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Maria Teresa Borrello
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Nadeem A. Vellore
- Department of Medicinal Chemistry, College of Pharmacy, The University of Utah, Salt Lake City, Utah, United States of America
| | - A. Ganesan
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- * E-mail: (AM); (RB)
| | - Riccardo Baron
- Department of Medicinal Chemistry, College of Pharmacy, The University of Utah, Salt Lake City, Utah, United States of America
- * E-mail: (AM); (RB)
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3634
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Sastry GM, Inakollu VSS, Sherman W. Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking. J Chem Inf Model 2013; 53:1531-42. [DOI: 10.1021/ci300463g] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- G. Madhavi Sastry
- Schrödinger, Sanali Infopark, 8-2-120/113, Banjara Hills,
Hyderabad 500034, Andhra Pradesh, India
| | - V. S. Sandeep Inakollu
- Schrödinger, Sanali Infopark, 8-2-120/113, Banjara Hills,
Hyderabad 500034, Andhra Pradesh, India
| | - Woody Sherman
- Schrödinger, 120 West 45th Street, New York,
New York 10036, United States
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3635
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Pearlstein RA, Sherman W, Abel R. Contributions of water transfer energy to protein-ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors. Proteins 2013; 81:1509-26. [PMID: 23468227 DOI: 10.1002/prot.24276] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 01/29/2013] [Accepted: 02/08/2013] [Indexed: 11/11/2022]
Abstract
In our previous work, we proposed that desolvation and resolvation of the binding sites of proteins can serve as the slowest steps during ligand association and dissociation, respectively, and tested this hypothesis on two protein-ligand systems with known binding kinetics behavior. In the present work, we test this hypothesis on another kinetically-determined protein-ligand system-that of p38α and eight Type II BIRB 796 inhibitor analogs. The kon values among the inhibitor analogs are narrowly distributed (10⁴ ≤ kon ≤ 10⁵ M⁻¹ s⁻¹), suggesting a common rate-determining step, whereas the koff values are widely distributed (10⁻¹ ≤ koff ≤ 10⁻⁶ s⁻¹), suggesting a spectrum of rate-determining steps. We calculated the solvation properties of the DFG-out protein conformation using an explicit solvent molecular dynamics simulation and thermodynamic analysis method implemented in WaterMap to predict the enthalpic and entropic costs of water transfer to and from bulk solvent incurred upon association and dissociation of each inhibitor. The results suggest that the rate-determining step for association consists of the transfer of a common set of enthalpically favorable solvating water molecules from the binding site to bulk solvent. The rate-determining step for inhibitor dissociation consists of the transfer of water from bulk solvent to specific binding site positions that are unfavorably solvated in the apo protein, and evacuated during ligand association. Different sets of unfavorable solvation are evacuated by each ligand, and the observed dissociation barriers are qualitatively consistent with the calculated solvation free energies of those sets.
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Affiliation(s)
- Robert A Pearlstein
- Novartis Institutes for BioMedical Research, 100 Technology Square, Cambridge, Massachusetts 02139
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3636
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Protein pocket and ligand shape comparison and its application in virtual screening. J Comput Aided Mol Des 2013; 27:511-24. [PMID: 23807262 DOI: 10.1007/s10822-013-9659-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 06/12/2013] [Indexed: 10/26/2022]
Abstract
Understanding molecular recognition is one major requirement for drug discovery and design. Physicochemical and shape complementarity between two binding partners is the driving force during complex formation. In this study, the impact of shape within this process is analyzed. Protein binding pockets and co-crystallized ligands are represented by normalized principal moments of inertia ratios (NPRs). The corresponding descriptor space is triangular, with its corners occupied by spherical, discoid, and elongated shapes. An analysis of a selected set of sc-PDB complexes suggests that pockets and bound ligands avoid spherical shapes, which are, however, prevalent in small unoccupied pockets. Furthermore, a direct shape comparison confirms previous studies that on average only one third of a pocket is filled by its bound ligand, supplemented by a 50 % subpocket coverage. In this study, we found that shape complementary is expressed by low pairwise shape distances in NPR space, short distances between the centers-of-mass, and small deviations in the angle between the first principal ellipsoid axes. Furthermore, it is assessed how different binding pocket parameters are related to bioactivity and binding efficiency of the co-crystallized ligand. In addition, the performance of different shape and size parameters of pockets and ligands is evaluated in a virtual screening scenario performed on four representative targets.
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