Docking covalent inhibitors: A parameter free approach to pose prediction and scoring

Journal of Chemical Information and Modeling

Volumn 54, Issue 7, 2014, Pages 1932-1940

  Zhu, Kai ^a   Borrelli, Kenneth W ^a   Greenwood, Jeremy R ^a   Day, Tyler ^a   Abel, Robert ^a   Farid, Ramy S ^a   Harder, Edward ^a  

^a SCHRÖDINGER INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; LARGE SCALE SYSTEMS; LIGANDS; PROTEINS;

BINDING GEOMETRIES; COVALENT ATTACHMENT; COVALENT REACTION; PARAMETER FITTING; PROTEIN STRUCTURES; PROTEIN-LIGAND COMPLEXES; STRUCTURAL REFINEMENT; VIRTUAL SCREENING;

MOLECULAR MODELING;

ENZYME INHIBITOR; LIGAND;

CHEMISTRY; DRUG DEVELOPMENT; METABOLISM; MOLECULAR DOCKING; PROCEDURES; PROTEIN CONFORMATION; STRUCTURE ACTIVITY RELATION; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DRUG DISCOVERY; ENZYME INHIBITORS; LIGANDS; MOLECULAR DOCKING SIMULATION; PROTEIN CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84904966114     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci500118s     Document Type: Article

References (25)

1. Singh, J.; Petter, R. C.; Baillie, T. A.; Whitty, A. The Resurgence of Covalent Drugs Nat. Rev. Drug Discovery 2011, 10, 307-317
2. Lin, C.; Kwong, A. D.; Perni, R. B. Discovery and Development of VX-950, a Novel, Covalent, and Reversible Inhibitor of Hepatitis C Virus NS3.4A Serine Protease Infect. Disord.: Drug Targets 2006, 6, 3-16
3. Njoroge, F. G.; Chen, K. X.; Shih, N.-Y.; Piwinski, J. J. Challenges in Modern Drug Discovery: a Case Study of Boceprevir, an HCV Protease Inhibitor for the Treatment of Hepatitis C Virus Infection Acc. Chem. Res. 2008, 41, 50-59
4. Honigberg, L. A.; Smith, A. M.; Sirisawad, M.; Verner, E.; Loury, D.; Chang, B.; Li, S.; Pan, Z.; Thamm, D. H.; Miller, R. A.; Buggy, J. J. The Bruton Tyrosine Kinase Inhibitor PCI-32765 Blocks B-Cell Activation and Is Efficacious in Models of Autoimmune Disease and B-Cell Malignancy Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 13075-13080
5. Perni, R. B.; Chandorkar, G.; Cottrell, K. M.; Gates, C. A.; Lin, C.; Lin, K.; Luong, Y.-P.; Maxwell, J. P.; Murcko, M. A.; Pitlik, J.; Rao, G.; Schairer, W. C.; Van Drie, J.; Wei, Y. Inhibitors of Hepatitis C Virus NS3.4A Protease. Effect of P4 Capping Groups on Inhibitory Potency and Pharmacokinetics Bioorg. Med. Chem. Lett. 2007, 17, 3406-3411
6. Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. a; Sanschagrin, P. C.; Mainz, D. T. Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes J. Med. Chem. 2006, 49, 6177-6196
7. Goodsell, D. S.; Olson, A. J. Automated Docking of Substrates to Proteins by Simulated Annealing Proteins 2009, 8, 195-202
8. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and Validation of a Genetic Algorithm for Flexible Docking J. Mol. Biol. 1997, 267, 727-748
9. Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew, R. K.; Goodsell, D. S.; Olson, A. J. Software News and Updates AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility 2009, 30, 2785-2791
10. Ouyang, X.; Zhou, S.; Su, C. T. T.; Ge, Z.; Li, R.; Kwoh, C. K. CovalentDock: Automated Covalent Docking with Parameterized Covalent Linkage Energy Estimation and Molecular Geometry Constraints J. Comput. Chem. 2013, 34, 326-336
11. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: a New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy J. Med. Chem. 2004, 47, 1739-1749
12. Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: a New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening J. Med. Chem. 2004, 47, 1750-1759
13. Jacobson, M. P.; Pincus, D. L.; Rapp, C. S.; Day, T. J. F.; Honig, B.; Shaw, D. E.; Friesner, R. A. A Hierarchical Approach to All-Atom Protein Loop Prediction Proteins 2004, 55, 351-367
14. Jacobson, M. P.; Friesner, R. A.; Xiang, Z.; Honig, B. On the Role of the Crystal Environment in Determining Protein Side-Chain Conformations J. Mol. Biol. 2002, 320, 597-608
15. Zhu, K.; Pincus, D. L.; Zhao, S.; Friesner, R. A. Long Loop Prediction Using the Protein Local Optimization Program Proteins 2006, 65, 438-452
16. Zhu, K.; Shirts, M. R.; Friesner, R. A. Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program: Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects J. Chem. Theory Comput. 2007, 3, 2108-2119
17. Zhao, S.; Zhu, K.; Li, J.; Friesner, R. A. Progress in Super Long Loop Prediction Proteins 2011, 79, 2920-2935
18. Li, J.; Abel, R.; Zhu, K.; Cao, Y.; Zhao, S.; Friesner, R. A. The VSGB 2.0 Model: a Next Generation Energy Model for High Resolution Protein Structure Modeling Proteins 2011, 79, 2794-2812
19. Watts, K. S.; Dalal, P.; Murphy, R. B.; Sherman, W.; Friesner, R. A.; Shelley, J. C. ConfGen: a Conformational Search Method for Efficient Generation of Bioactive Conformers J. Chem. Inf. Model. 2010, 50, 534-546
20. Sastry, G. M.; Adzhigirey, M.; Day, T.; Annabhimoju, R.; Sherman, W. Protein and Ligand Preparation: Parameters, Protocols, and Influence on Virtual Screening Enrichments J. Comput.-Aided. Mol. Des. 2013, 27, 221-234
21. Schrodinger, Inc.: Maestro v9.5, 2013.
22. Shelley, J. C.; Cholleti, A.; Frye, L. L.; Greenwood, J. R.; Timlin, M. R.; Uchimaya, M. Epik: a Software Program for pK(a) Prediction and Protonation State Generation for Drug-Like Molecules J. Comput.-Aided. Mol. Des. 2007, 21, 681-691
23. Greenwood, J. R.; Calkins, D.; Sullivan, A. P.; Shelley, J. C. Towards the Comprehensive, Rapid, and Accurate Prediction of the Favorable Tautomeric States of Drug-Like Molecules in Aqueous Solution J. Comput.-Aided. Mol. Des. 2010, 24, 591-604
24. Blair, J. A.; Rauh, D.; Kung, C.; Yun, C.-H.; Fan, Q.-W.; Rode, H.; Zhang, C.; Eck, M. J.; Weiss, W. A.; Shokat, K. M. Structure-Guided Development of Affinity Probes for Tyrosine Kinases Using Chemical Genetics Nat. Chem. Biol. 2007, 3, 229-238
25. Colarusso, S.; Gerlach, B.; Koch, U.; Muraglia, E.; Conte, I.; Stansfield, I.; Matassa, V. G.; Narjes, F. Evolution, Synthesis and SAR of Tripeptide Alpha-Ketoacid Inhibitors of the Hepatitis C Virus NS3/NS4A Serine Protease Bioorg. Med. Chem. Lett. 2002, 12, 705-708