The structure of active opsin as a basis for identification of GPCR agonists by dynamic homology modelling and virtual screening assays

FEBS Letters

Volumn 585, Issue 22, 2011, Pages 3587-3592

  Schneider, Michael ^a,c   Wolf, Steffen ^a,b   Schlitter, Jürgen ^a   Gerwert, Klaus ^a,b  

^a RUHR UNIVERSITY BOCHUM   (Germany)

^b MAX PLANCK INSTITUTE   (Germany)

^c TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

Author keywords

Beta(2) adrenoreceptor; Dynamic homology model; GPCR; Molecular dynamics simulations; Opsin; Virtual ligand screening

Indexed keywords

ADRENALIN; BETA 2 ADRENERGIC RECEPTOR; CARAZOLOL; G PROTEIN COUPLED RECEPTOR; OPSIN;

ARTICLE; BINDING AFFINITY; CHEMICAL BOND; CONTROLLED STUDY; CRYSTAL STRUCTURE; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; SCREENING; SEQUENCE HOMOLOGY;

BINDING SITES; LIGANDS; MOLECULAR DYNAMICS SIMULATION; OPSINS; PROTEIN CONFORMATION; RECEPTORS, ADRENERGIC, BETA-2; RECEPTORS, G-PROTEIN-COUPLED;

EID: 80855148236     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2011.10.027     Document Type: Article

References (39)

1. J. Ballesteros, S. Kitanovic, F. Guarnieri, P. Davies, B.J. Fromme, K. Konvicka, L. Chi, R.P. Millar, J.S. Davidson, H. Weinstein, and S.C. Sealfon Functional microdomains in G-protein-coupled receptors. The conserved arginine-cage motif in the gonadotropin-releasing hormone receptor J. Biol. Chem. 273 1998 10445 10453 (Pubitemid 28227654)
2. J. Drews Drug discovery: a historical perspective Science 287 2000 1960 1964 (Pubitemid 30158662)
3. T. Okada, M. Sugihara, A.-N. Bondar, M. Elstner, P. Entel, and V. Buss The retinal conformation and its environment in rhodopsin in light of a new 2.2 crystal structure J. Mol. Biol. 342 2004 571 583 (Pubitemid 39149759)
4. 1-adrenergic G-protein-coupled receptor Nature 454 2008 486 491
5. 2- adrenergic G protein-coupled receptor Science 318 2007 1258 1265 (Pubitemid 350172884)
6. V.-P. Jaakola, M.T. Griffith, M.A. Hanson, V. Cherezov, E.Y.T. Chien, J.R. Lane, A.P. Ijzerman, and R.C. Stevens The 2.6 crystal structure of a human A2A adenosine receptor bound to an antagonist Science 322 2008 1211 1217
7. B. Wu, E.Y.T. Chien, C.D. Mol, G. Fenalti, W. Liu, V. Katritch, R. Abagyan, A. Brooun, P. Wells, F.C. Bi, D.J. Hamel, P. Kuhn, T.M. Handel, V. Cherezov, and R.C. Stevens Structures of the CXCR4 Chemokine GPCR with small-molecule and cyclic peptide antagonists Science 330 2010 1066 1071
8. E.Y.T. Chien, W. Liu, Q. Zhao, V. Katritch, G. Won Han, M.A. Hanson, L. Shi, A.H. Newman, J.A. Javitch, V. Cherezov, and R.C. Stevens Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist Science 330 2010 1091 1095
9. S. Wolf, M. Böckmann, U. Höweler, J. Schlitter, and K. Gerwert Simulations of a G protein-coupled receptor homology model predict dynamic features and a ligand binding site FEBS Lett. 582 2008 3335 3342
10. M. Michino, E. Abola, C.L. Brooks, J.S. Dixon, J. Moult, and R.C. Stevens Community-wide assessment of GPCR structure modeling and docking understanding Nat. Rev. Drug Discov. 8 2009 455 463
11. T.P. Kenakin Pharmacological onomastics: What's in a name? Br. J. Pharmacol. 153 2008 432 438 (Pubitemid 351199005)
12. D.M. Rosenbaum, S.G.F. Rasmussen, and B.K. Kobilka The structure and function of G-protein-coupled receptors Nature 459 2009 356 363
13. 2-adrenergic receptor ligands Proc. Natl. Acad. Sci. USA 106 2009 6843 6848
14. E. Archer, B. Maigret, C. Escrieut, L. Pradayrol, and D. Fourmy Rhodopsin crystal: new template yielding realistic models of G-protein-coupled receptors? Trends Pharmacol. Sci. 24 2003 36 40 (Pubitemid 36009288)
15. P. Scheerer, J.H. Park, P.W. Hildebrand, Y.J. Kim, N. Krausz, H.-W. Choe, K.P. Hofmann, and O.P. Ernst Crystal structure of opsin in its G-protein-interacting conformation Nature 455 2008 497 502
16. 2 adrenoceptor Nature 469 2011 175 180
17. 2 adrenoceptor complex Nature 469 2011 236 240
18. S.G.F. Rasmussen, B.T. DeVree, Y. Zou, A.C. Kruse, K.Y. Chung, T.S. Kobilka, F.S. Thian, P.S. Chae, E. Pardon, D. Calinski, J.M. Mathiesen, S.T.A. Shah, J.A. Lyons, M. Caffrey, S.H. Gellman, J. Steyaert, G. Skiniotis, W.I. Weis, R.K. Sunahara, and B.K. Kobilka Crystal structure of the β2 adrenergic receptor-Gs protein complex Nature 477 2011 549 555
19. 1-adrenergic receptor Nature 469 2011 241 244
20. J. Standfuss, P.C. Edwards, A. D'Antona, M. Fransen, G. Xie, D.D. Oprian, and G.F.X. Schertler The structural basis of agonist-induced activation in constitutively active rhodopsin Nature 471 2011 656 660
21. K.L. Pierce, R.T. Premont, and R.J. Lefkowitz Seven-transmembrane receptors Nat. Rev. Mol. Cell Biol. 3 2002 639 650 (Pubitemid 34987785)
22. 2-adrenergic receptor Proteins 79 2011 1441 1457
23. Z. Deng, C. Chuaqui, and J. Singh Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions J. Med. Chem. 47 2004 337 344 (Pubitemid 38057878)
24. 2-AR and a photoactivated intermediate of rhodopsin identified by dynamic properties of GPCRs Biochemistry 47 2008 7317 7321 (Pubitemid 351991010)
25. B.K. Kobilka, and X. Deupi Conformational complexity of G-protein-coupled receptors Trends Pharmacol. Sci. 28 2007 397 406 (Pubitemid 47087966)
26. G. Marcou, and D. Rognan Optimizing fragment and Scaffold docking by use of molecular interaction fingerprints J. Chem. Inf. Model. 47 2007 195 207 (Pubitemid 46237537)
27. S. Radestock, T. Weil, and S. Renner Homology model-based virtual screening for GPCR ligands using docking and target-biased scoring J. Chem. Inf. Model. 48 2008 1104 1117
28. 2-adrenergic receptor J. Biol. Chem. 275 2000 37779 37788 (Pubitemid 32004894)
29. C.D. Strader, T.M. Fong, M.R. Tota, D. Underwood, and R.A. Dixon Structure and function of G protein-coupled receptors Annu. Rev. Biochem. 63 1994 101 132 (Pubitemid 24218630)
30. T. Huber, S. Menon, and T.P. Sakmar Structural basis for ligand binding and specificity in adrenergic receptors: implications for GPCR-targeted drug discovery Biochemistry 47 2008 11013 11023
31. 2-adrenergic receptor J. Phys. Chem. B 114 2010 8374 8386
32. C.D. Strader, M.R. Candelore, W.S. Hill, I.S. Sigal, and R.A. Dixon Identification of two serine residues involved in agonist activation of the beta-adrenergic receptor J. Biol. Chem. 264 1989 13572 13578 (Pubitemid 19198437)
33. 2-adrenergic receptor for fluorinated catecholamines Bioorg. Med. Chem. 17 2009 7987 7992
34. O. Trott, and A.J. Olson AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading J. Comput. Chem. 31 2010 455 461
35. Tanimoto, T.T. (1957). IBM Internal Report.
36. 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
37. 2-adrenergic receptor within the fourth transmembrane domain alters ligand binding and functional properties of the receptor J. Biol. Chem. 268 1993 23116 23121 (Pubitemid 23328021)
38. 2 adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators J. Comput. Aid. Mol. Des. 23 2009 273 288
39. K.H. Zou, A.J. O'Malley, and L. Mauri Receiver-operating characteristic analysis for evaluating diagnostic tests and predictive models Circulation 115 2007 654 657 (Pubitemid 46226175)