Enrichment factor analyses on g-protein coupled receptors with known crystal structure

Journal of Chemical Information and Modeling

Volumn 53, Issue 4, 2013, Pages 739-743

  Anighoro, Andrew ^a   Rastelli, Giulio ^a  

^a UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; PROTEINS;

BINDING MODES; DRUG SCREENING; DRUG TARGETS; ENRICHMENT FACTORS; G PROTEIN COUPLED RECEPTORS; MULTITARGET; STRUCTURE-BASED; VIRTUAL SCREENING;

CRYSTAL STRUCTURE;

G PROTEIN COUPLED RECEPTOR;

ARTICLE; BINDING SITE; CHEMISTRY; CRYSTALLIZATION; DRUG ANTAGONISM; DRUG DATABASE; DRUG SCREENING; FACTORIAL ANALYSIS; HUMAN; MOLECULAR DOCKING; MOLECULAR LIBRARY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DATABASE; STATISTICS;

BINDING SITES; CRYSTALLIZATION; DATABASES, PHARMACEUTICAL; DATABASES, PROTEIN; DRUG EVALUATION, PRECLINICAL; FACTOR ANALYSIS, STATISTICAL; HUMANS; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; RECEPTORS, G-PROTEIN-COUPLED; SMALL MOLECULE LIBRARIES;

EID: 84876551012     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci4000745     Document Type: Article

References (30)

1. Lappano, R.; Maggiolini, M. G protein-coupled receptors: novel targets for drug discovery in cancer Nat. Rev. Drug Discov. 2011, 10, 47-60
2. Lagerström, M. C.; Schiöth, H. B. Structural diversity of G protein-coupled receptors and significance for drug discovery Nat. Rev. Drug Discov. 2008, 7, 339-357
3. Stevens, R. C.; Cherezov, V.; Katritch, V.; Abagyan, R.; Kuhn, P.; Rosen, H.; Wüthrich, K. The GPCR Network: a large-scale collaboration to determine human GPCR structure and function Nat. Rev. Drug Discov. 2012, 12, 25-34
4. Shoichet, B. K.; Kobilka, B. K. Structure-based drug screening for G-protein-coupled receptors Trends Pharmacol. Sci. 2012, 33, 268-272
5. McRobb, F. M.; Capuano, B.; Crosby, I. T.; Chalmers, D. K.; Yuriev, E. Homology modelling and docking evaluation of aminergic G protein-coupled receptors J. Chem. Inf. Model. 2010, 50, 626-637
6. Okuno, Y.; Tamon, A.; Yabuuchi, H.; Niijima, S.; Minowa, Y.; Tonomura, K.; Kunimoto, R.; Feng, C. GLIDA: GPCR -ligand database for chemical genomics drug discovery -database and tools update Nucleic Acids Res. 2008, 36, 907-912
7. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shaw, D. E.; Shelley, M.; Perry, J. K.; 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
8. 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
9. Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew, R. K.; Goodsell, D. S.; Olson, A. J. Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity J. Comput. Chem. 2009, 16, 2785-2791
10. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function J. Comput. Chem. 1998, 19, 1639-1662
11. Huey, R.; Morris, G. M.; Olson, A. J.; Goodsell, D. S. A Semiempirical Free Energy Force Field with Charge-Based Desolvation J. Comput. Chem. 2007, 28, 1145-1152
12. Rastelli, G.; Degliesposti, G.; Del Rio, A.; Sgobba, M. Binding estimation after refinement, a new automated procedure for the refinement and rescoring of docked ligands in virtual screening Chem. Biol. Drug Des. 2009, 73, 283-286
13. Rastelli, G.; Del Rio, A.; Degliesposti, G.; Sgobba, M. Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA J. Comput. Chem. 2010, 31, 797-810
14. Parenti, M. D.; Rastelli, G. Advances and applications of binding affinity prediction methods in drug discovery Biotechnol. Adv. 2012, 30, 244-250
15. Cherezov, V.; Rosenbaum, D. M.; Hanson, M. A.; Rasmussen, S. G.; Thian, F. S.; Kobilka, T. S.; Choi, H. J.; Kuhn, P.; Weis, W. I.; Kobilka, B. K.; Stevens, R. C. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor Science 2007, 318, 1258-1265
16. Jaakola, V. P.; Griffith, M. T.; Hanson, M. A.; Cherezov, V.; Chien, E. Y.; Lane, J. R.; Ijzerman, A. P.; Stevens, R. C. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist Science 2008, 322, 1211-1217
17. Liu, W.; Chun, E.; Thompson, A. A.; Chubukov, P.; Xu, F.; Katritch, V.; Han, G. W.; Roth, C. B.; Heitman, L. H.; IJzerman, A. P.; Cherezov, V.; Stevens, R. C. Structural basis for allosteric regulation of GPCRs by sodium ions Science 2012, 337, 232-236
18. Chien, E. Y.; Liu, W.; Zhao, Q.; Katritch, V.; Han, G. W.; Hanson, M. A.; Shi, L.; Newman, A. H.; Javitch, J. A.; Cherezov, V.; Stevens, R. C. Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist Science 2010, 330, 1091-1095
19. Shimamura, T.; Shiroishi, M.; Weyand, S.; Tsujimoto, H.; Winter, G.; Katritch, V.; Abagyan, R.; Cherezov, V.; Liu, W.; Han, G. W.; Kobayashi, T.; Stevens, R. C.; Iwata, S. Structure of the human histamine H1 receptor complex with doxepin Nature 2011, 475, 65-70
20. Jaakola, V. P.; Ijzerman, A. P. The crystallographic structure of the human adenosine A2A receptor in a high-affinity antagonist-bound state: implications for GPCR drug screening and design Curr. Opin. Struct. Biol. 2010, 20, 401-414
21. Lebon, G.; Warne, T.; Edwards, P. C.; Bennett, K.; Langmead, C. J.; Leslie, A. G.; Tate, C. G. Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation Nature 2011, 18, 521-525
22. Pieper, U.; Webb, B. M.; Barkan, D. T.; Schneidman-Duhovny, D.; Schlessinger, A.; Braberg, H.; Yang, Z.; Meng, E. C.; Pettersen, E. F.; Huang, C. C.; Datta, R. S.; Sampathkumar, P.; Madhusudhan, M. S.; Sjölander, K.; Ferrin, T. E.; Burley, S. K.; Sali, A. ModBase, a database of annotated comparative protein structure models, and associated resources Nucleic Acids Res. 2011, 39, 465-474
23. Fiser, A.; Do, R. K.; Sali, A. Modeling of loops in protein structures Protein Sci. 2000, 9, 1753-1773
24. Fiser, A.; Sali, A. ModLoop: automated modeling of loops in protein structures Bioinformatics 2003, 19, 2500-2501
25. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossvary, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. AMBER 10; University of California: San Francisco, 2008.
26. Jain, A. Bias reporting, and sharing: computational evaluations of docking methods J. Comput. -Aided Mol. Des. 2008, 22, 201-212
27. Sgobba, M.; Caporuscio, F.; Anighoro, A.; Portioli, C.; Rastelli, G. Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations Eur. J. Med. Chem. 2012, 58, 431-40
28. Gurevich, E. V.; Bordelon, Y.; Shapiro, R. M.; Arnold, S. E.; Gur, R. E.; Joyce, J. N. Mesolimbic dopamine D3 receptors and use of antipsychotics in patients with schizophrenia. A postmortem study Arch. Gen. Psychiatry 1997, 54, 225-232
29. Burstein, E. S.; Ma, J.; Wong, S.; Gao, Y.; Pham, E.; Knapp, A. E.; Nash, N. R.; Olsson, R.; Davis, R. E.; Hacksell, U.; Weiner, D. M.; Brann, M. R. Intrinsic efficacy of antipsychotics at human D2, D3, and D4 dopamine receptors: identification of the clozapine metabolite N-desmethylclozapine as a D2/D3 partial agonist J. Pharmacol. Exp. Ther. 2005, 315, 1278-1287
30. Stahl, S. M. Selective histamine H1 antagonism: novel hypnotic and pharmacologic actions challenge classical notions of antihistamines CNS Spectr. 2008, 13, 1027-1038