Docking-based virtual screening for ligands of G protein-coupled receptors: Not only crystal structures but also in silico models

Journal of Molecular Graphics and Modelling

Volumn 29, Issue 5, 2011, Pages 614-623

  Vilar, Santiago ^a   Ferino, Giulio ^a   Phatak, Sharangdhar S ^b   Berk, Barkin ^a   Cavasotto, Claudio N ^b   Costanzi, Stefano ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b UNIVERSITY OF TEXAS   (United States)

Author keywords

Beta adrenergic receptors; Docking; G protein coupled receptors; Homology modeling; Virtual screening

Indexed keywords

ADRENERGIC RECEPTORS; COMPUTATIONAL EXPERIMENT; COMPUTER-AIDED TECHNIQUES; DATA SETS; G PROTEIN COUPLED RECEPTORS; HOMOLOGY MODELING; HOMOLOGY MODELS; IN-SILICO MODELS; PHYSIOLOGICAL FUNCTIONS; PRIORITIZATION; SCREENING PERFORMANCE; VIRTUAL SCREENING;

COMPUTER AIDED ANALYSIS; ENZYME INHIBITION; PROTEINS;

LIGANDS;

BETA 2 ADRENERGIC RECEPTOR; BETA 2 ADRENERGIC RECEPTOR BLOCKING AGENT; BETA 2 ADRENERGIC RECEPTOR STIMULATING AGENT; CARAZOLOL; GUANINE NUCLEOTIDE BINDING PROTEIN;

ARTICLE; COMPUTER MODEL; CRYSTAL STRUCTURE; MOLECULAR DOCKING; PERFORMANCE; PRIORITY JOURNAL; SCREENING; STRUCTURAL HOMOLOGY;

ADRENERGIC BETA-2 RECEPTOR AGONISTS; ADRENERGIC BETA-2 RECEPTOR ANTAGONISTS; COMPUTER SIMULATION; DRUG DESIGN; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; RECEPTORS, ADRENERGIC, BETA-2; RECEPTORS, G-PROTEIN-COUPLED;

EID: 79751525956     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2010.11.005     Document Type: Article

References (50)

1. G. Muller Towards 3D structures of G protein-coupled receptors: a multidisciplinary approach Curr. Med. Chem. 7 2000 861 888
2. S. Costanzi, J. Siegel, I.G. Tikhonova, and K.A. Jacobson Rhodopsin and the others: a historical perspective on structural studies of G protein-coupled receptors Curr. Pharm. Des. 15 2009 3994 4002
3. M.A. Hanson, and R.C. Stevens Discovery of new GPCR biology: one receptor structure at a time Structure 17 2009 8 14
4. V. Cherezov, D.M. Rosenbaum, M.A. Hanson, S.G.F. Rasmussen, F.S. Thian, T.S. Kobilka, H.J. Choi, P. Kuhn, W.I. Weis, B.K. Kobilka, and R.C. Stevens High-resolution crystal structure of an engineered human beta(2)-adrenergic G protein-coupled receptor Science 318 2007 1258 1265 (Pubitemid 350172884)
5. D.M. Rosenbaum, V. Cherezov, M.A. Hanson, S.G.F. Rasmussen, F.S. Thian, T.S. Kobilka, H.J. Choi, X.J. Yao, W.I. Weis, R.C. Stevens, and B.K. Kobilka GPCR engineering yields high-resolution structural insights into beta(2)-adrenergic receptor function Science 318 2007 1266 1273 (Pubitemid 350172885)
6. S. Costanzi On the applicability of GPCR homology models to computer-aided drug discovery: a comparison between in silico and crystal structures of the beta(2)-adrenergic receptor J. Med. Chem. 51 2008 2907 2914 (Pubitemid 351706019)
7. S. Vilar, J. Karpiak, and S. Costanzi Ligand and structure-based models for the prediction of ligand-receptor affinities and virtual screenings: development and application to the beta(2)-adrenergic receptor J. Comput. Chem. 31 2010 707 720
8. J.J. Irwin, and B.K. Shoichet ZINC - a free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 45 2005 177 182 (Pubitemid 40736970)
9. http://zinc.docking.org/
10. MOE, Version 2008.10 2008 Chemical Computing Group, Inc. www.chemcomp.com
11. Maestro, Version 8.5 2008 Schrödinger, LLC New York, NY
12. Glide, Version 5.0 2008 Schrödinger, LLC New York, NY
13. C.N. Cavasotto, A.J.W. Orry, N.J. Murgolo, M.F. Czarniecki, S.A. Kocsi, B.E. Hawes, K.A. O'Neill, H. Hine, M.S. Burton, J.H. Voigt, R.A. Abagyan, M.L. Bayne, and F.J. Monsma Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening J. Med. Chem. 51 2008 581 588 (Pubitemid 351252286)
14. P. Diaz, S.S. Phatak, J. Xu, F. Astruc-Diaz, C.N. Cavasotto, and M. Naguib 6-Methoxy-N-alkyl isatin acylhydrazone derivatives as a novel series of potent selective cannabinoid receptor 2 inverse agonists: design, synthesis, and binding mode prediction J. Med. Chem. 52 2009 433 444
15. P. Diaz, S.S. Phatak, J.J. Xu, F.R. Fronczek, F. Astruc-Diaz, C.M. Thompson, C.N. Cavasotto, and M. Naguib 2,3-Dihydro-1-benzofuran derivatives as a series of potent selective cannabinoid receptor 2 agonists: design, synthesis, and binding mode prediction through ligand-steered modeling ChemMedChem 4 2009 1615 1629
16. S.S. Phatak, E.A. Gatica, C.N. Cavasotto, Ligand-steered modeling and docking: a benchmarking study in class A G-protein-coupled receptors, J. Chem. Inf. Model., Article ASAP, http://dx.doi.org/10.1021/ci100285f.
17. ICM, Molsoft, LLC, www.molsoft.com.
18. Prime, Version 2.0 2008 Schrödinger, LLC New York, NY
19. C.N. Cavasotto, and R.A. Abagyan Protein flexibility in ligand docking and virtual screening to protein kinases J. Mol. Biol. 337 2004 209 225 (Pubitemid 38270258)
20. S. Engel, A.P. Skoumbourdis, J. Childress, S. Neumann, J.R. Deschamps, C.J. Thomas, A.O. Colson, S. Costanzi, and M.C. Gershengorn A virtual screen for diverse ligands: discovery of selective G protein-coupled receptor antagonists J. Am. Chem. Soc. 130 2008 5115 5123 (Pubitemid 351537071)
21. C.N. Cavasotto, J.A. Kovacs, and R.A. Abagyan Representing receptor flexibility in ligand docking through relevant normal modes J. Am. Chem. Soc. 127 2005 9632 9640 (Pubitemid 40934775)
22. W. Sherman, T. Day, M.P. Jacobson, R.A. Friesner, and R. Farid Novel procedure for modeling ligand/receptor induced fit effects J. Med. Chem. 49 2006 534 553 (Pubitemid 43157487)
23. P. Kolb, D.M. Rosenbaum, J.J. Irwin, J.J. Fung, B.K. Kobilka, and B.K. Shoichet Structure-based discovery of beta(2)-adrenergic receptor ligands Proc. Natl. Acad. Sci. U.S.A. 106 2009 6843 6848
24. V. Katritch, V.P. Jaakola, J.R. Lane, J. Lin, A.P. Ijzerman, M. Yeager, I. Kufareva, R.C. Stevens, and R. Abagyan Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists J. Med. Chem. 53 2010 1799 1809
25. 2A adenosine receptors ligands J. Med. Chem. 2010 doi:10.1021/jm100240h
26. A.A. Ivanov, D. Barak, and K.A. Jacobson Evaluation of homology modeling of G-protein-coupled receptors in light of the A(2A) adenosine receptor crystallographic structure J. Med. Chem. 52 2009 3284 3292
27. C.N. Cavasotto, and N. Singh Docking and high throughput docking: successes and the challenge of protein flexibility Curr. Comput. Aided Drug Des. 4 2008 221 234
28. P. Cozzini, G.E. Kellogg, F. Spyrakis, D.J. Abraham, G. Costantino, A. Emerson, F. Fanelli, H. Gohlke, L.A. Kuhn, G.M. Morris, M. Orozco, T.A. Pertinhez, M. Rizzi, and C.A. Sotriffer Target flexibility: an emerging consideration in drug discovery and design J. Med. Chem. 51 2008 6237 6255
29. C. B-Rao, J. Subramanian, and S.D. Sharma Managing protein flexibility in docking and its applications Drug Discov. Today 14 2009 394 400
30. O. Sperandio, L. Mouawad, E. Pinto, B.O. Villoutreix, D. Perahia, and M.A. Miteva How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis Eur. Biophys. J. 2010 doi:10.1007/s00249-010-0592-0
31. J.A. Kovacs, C.N. Cavasotto, and R. Abagyan Conformational sampling of protein flexibility in generalized coordinates: application to ligand docking J. Comput. Theor. Nanosci. 2 2005 354 361 (Pubitemid 41556042)
32. A.M. Ferrari, B.Q.Q. Wei, L. Costantino, and B.K. Shoichet Soft docking and multiple receptor conformations in virtual screening J. Med. Chem. 47 2004 5076 5084 (Pubitemid 39314905)
33. C.D. Strader, T.M. Fong, M.R. Tota, D. Underwood, and R.A.F. Dixon Structure and function of G-protein-coupled receptors Annu. Rev. Biochem. 63 1994 101 132
34. M. Audet, and M. Bouvier Insights into signaling from the beta(2)-adrenergic receptor structure Nat. Chem. Biol. 4 2008 397 403 (Pubitemid 351860553)
35. G. Liapakis, J.A. Ballesteros, S. Papachristou, W.C. Chan, X. Chen, and J.A. Javitch The forgotten serine - a critical role for Ser-203(5.42) in ligand binding to and activation of the beta(2)-adrenergic receptor J. Biol. Chem. 275 2000 37779 37788 (Pubitemid 32004894)
36. P.L. Freddolino, M.Y.S. Kalani, N. Vaidehi, W.B. Floriano, S.E. Hall, R.J. Trabanino, V.W.T. Kam, and W.A. Goddard Predicted 3D structure for the human beta 2 adrenergic receptor and its binding site for agonists and antagonists Proc. Natl. Acad. Sci. U.S.A. 101 2004 2736 2741 (Pubitemid 38327680)
37. S. Bhattacharya, S.E. Hall, H. Li, and N. Vaidehi Ligand-stabilized conformational states of human beta(2) adrenergic receptor: insight into G-protein-coupled receptor activation Biophys. J. 94 2008 2027 2042
38. C. de Graaf, and D. Rognan Selective structure-based virtual screening for full and partial agonists of the beta 2 adrenergic receptor J. Med. Chem. 51 2008 4978 4985
39. K.A. Reynolds, V. Katritch, and R. Abagyan Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators J. Comput. Aided Mol. Des. 23 2009 273 288
40. I.G. Tikhonova, C.S. Sum, S. Neumann, C.J. Thomas, B.M. Raaka, S. Costanzi, and M.C. Gershengorn Bidirectional, iterative approach to the structural delineation of the functional "Chemoprint" in GPR40 for agonist recognition J. Med. Chem. 50 2007 2981 2989 (Pubitemid 47001241)
41. C.S. Sum, I.G. Tikhonova, S. Neumann, S. Engel, B.M. Raaka, S. Costanzi, and M.C. Gershengorn Identification of residues important for agonist recognition and activation in GPR40 J. Biol. Chem. 282 2007 29248 29255 (Pubitemid 350043382)
42. S. Costanzi, S. Neumann, and M.C. Gershengorn Seven transmembrane- spanning receptors for free fatty acids as therapeutic targets for diabetes mellitus: pharmacological, phylogenetic, and drug discovery aspects J. Biol. Chem. 283 2008 16269 16273
43. I.G. Tikhonova, C.S. Sum, S. Neumann, S. Engel, B.M. Raaka, S. Costanzi, and M.C. Gershengorn Discovery of novel agonists and antagonists of the free fatty acid receptor 1 (FFAR1) using virtual screening J. Med. Chem. 51 2008 625 633 (Pubitemid 351252290)
44. W. Guo, L. Shi, M. Filizola, H. Weinstein, and J.A. Javitch Crosstalk in G protein-coupled receptors: changes at the transmembrane homodimer interface determine activation Proc. Natl. Acad. Sci. U.S.A. 102 2005 17495 17500 (Pubitemid 41740894)
45. I.G. Tikhonova, R.B. Best, S. Engel, M.C. Gershengorn, G. Hummer, and S. Costanzi Atomistic insights into rhodopsin activation from a dynamic model J. Am. Chem. Soc. 130 2008 10141 10149
46. F. Deflorian, S. Engel, A.O. Colson, B.M. Raaka, M.C. Gershengorn, and S. Costanzi Understanding the structural and functional differences between mouse thyrotropin-releasing hormone receptors 1 and 2 Proteins 71 2008 783 794 (Pubitemid 351430016)
47. S. Costanzi, B.V. Joshi, S. Maddileti, L. Mamedova, M.J. Gonzalez-Moa, V.E. Marquez, T.K. Harden, and K.A. Jacobson Human P2Y(6) receptor: molecular modeling leads to the rational design of a novel agonist based on a unique conformational preference J. Med. Chem. 48 2005 8108 8111 (Pubitemid 43032518)
48. S. Bhattacharya, and N. Vaidehi Computational mapping of the conformational transitions in agonist selective pathways of a G-protein coupled receptor J. Am. Chem. Soc. 132 2010 5205 5214
49. C.S. Sum, I.G. Tikhonova, S. Costanzi, and M.C. Gershengorn Two arginine-glutamate ionic locks near the extracellular surface of FFAR1 gate receptor activation J. Biol. Chem. 284 2009 3529 3536
50. I.G. Tikhonova, and S. Costanzi Unraveling the structure and function of G protein-coupled receptors through NMR spectroscopy Curr. Pharm. Des. 15 2009 4003 4016