A physicogenetic method to assign ligand-binding relationships between 7TM receptors

Bioorganic and Medicinal Chemistry Letters

Volumn 15, Issue 16, 2005, Pages 3707-3712

  Frimurer, Thomas M ^a   Ulven, Trond ^a   Elling, Christian E ^a   Gerlach, Lars Ole ^a   Kostenis, Evi ^a   Högberg, Thomas ^a  

^a 7TM Pharma A S   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

CANDESARTAN; G PROTEIN COUPLED RECEPTOR; INDOMETACIN; RHODOPSIN;

ANALYTIC METHOD; ARTICLE; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG RECEPTOR BINDING; LIGAND BINDING; MATHEMATICAL MODEL; PHYSICAL CHEMISTRY; STRUCTURE ACTIVITY RELATION; X RAY CRYSTALLOGRAPHY;

ANIMALS; BENZIMIDAZOLES; BINDING SITES; BINDING, COMPETITIVE; CATTLE; COMPUTER SIMULATION; DRUG DESIGN; HYDROCARBONS, AROMATIC; INDOMETHACIN; LIGANDS; MODELS, BIOLOGICAL; MOLECULAR STRUCTURE; RECEPTORS, G-PROTEIN-COUPLED; RECEPTORS, IMMUNOLOGIC; RECEPTORS, PROSTAGLANDIN; RHODOPSIN; STRUCTURE-ACTIVITY RELATIONSHIP; TETRAZOLES;

BOVINAE;

EID: 22944479010     PISSN: 0960894X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmcl.2005.05.102     Document Type: Article

References (57)

1. R. Fredriksson, M.C. Lagerstrom, L.G. Lundin, and H.B. Schioth Mol. Pharmacol. 63 2003 1256
2. R. Fredriksson, and H.B. Schioth Mol. Pharmacol. 67 2005 1414
3. K. Palczewski, T. Kumasaka, T. Hori, C.A. Behnke, H. Motoshima, B.A. Fox, I. Le Trong, D.C. Teller, T. Okada, R.E. Stenkamp, M. Yamamoto, and M. Miyano Science 289 2000 739
4. S. Filipek, D.C. Teller, K. Palczewski, and R. Stenkamp Annu. Rev. Biophys. Biomol. Struct. 32 2003 375
5. J.M. Baldwin EMBO J. 12 1993 1693
6. J.M. Baldwin, G.F. Schertler, and V.M. Unger J. Mol. Biol. 272 1997 144
7. For reviews on structure based drug design targeting 7TM receptors see T. Klabunde, and G. Hessler ChemBioChem 3 2002 928
8. J.A. Bikker, S. Trumpp-Kallmeyer, and C. Humblet J. Med. Chem. 41 1998 2911
9. D.R. Flower Biochim. Biophys. Acta 1422 1999 207
10. Identification of residue positions of importance for ligand binding and recognition, e.g. K. Kristiansen Pharmacol. Ther. 103 2004 21
11. tGRAP Mutant Database (http://tinygrap.uit.no/ ) containing 10,500 mutants from 1380 papers up to April 2001.
12. S.B. Needleman, and C.D. Wunsch J. Mol. Biol. 48 1970 443
13. Dayhoff, M. O.; Schwartz, R. M.; Orcutt, B. C. In Atlas of Protein Sequence and Structure; Dayhoff, M. O. Ed.; National Biochemical Research Foundation: Washington, DC, 1978; Vol. 5, pp. 345-352.
14. T.F. Smith, and M.S. Waterman J. Mol. Biol. 147 1981 195
15. W.R. Pearson, and D.J. Lipman Proc. Natl. Acad. Sci. U.S.A. 85 1988 2444
16. S. Henikoff, and J. Henikoff Proc. Natl. Acad. Sci. U.S.A. 89 1992 10915
17. S. Henikoff, and J.G. Henikoff Proteins 17 1993 49
18. S.F. Altschul J. Mol. Biol. 219 1991 555
19. S.F. Altschul J. Mol. Evol. 36 1993 290
20. J.D. Thompson, D.G. Higgins, and T. Gibson J. Nucleic Acids Res. 22 1994 4673
21. Elling, C. E. Molecular dissection of 7TM receptor structure and function. Ph.D. thesis, University of Copenhagen, Denmark, 2000.
22. E.L. Sonnhammer, G. von Heijne, and A. Krog Proc. Int. Conf. Intell. Syst. Mol. Biol. 6 1998 175
23. T.W. Schwartz Curr. Opin. Biotechnol. 5 1994 434
24. Representative papers S.P. Molnar, and J.W. King Int. J. Quant. Chem. 85 2001 662
25. A. Zaliani, and E. Gancia J. Chem. Inf. Comput. Sci. 39 1999 525
26. M. Sandberg, L. Eriksson, J. Jonsson, M. Sjöström, and S. Wold J. Med. Chem. 41 1998 2481
27. H. Matter J. Pept. Res. 52 1998 305
28. U. Norinder, and P. Svensson J. Comput. Chem. 19 1998 51
29. E.R. Collantes, and W.J. Dunn III J. Med. Chem. 38 1995 2705 and references given therein
30. U. Norinder, and T. Högberg P. Krogsgaard-Larsen T. Liljefors U. Madsen Textbook of drug design and discovery 2002 Taylor & Francis London 117
31. Various similarity scores are described in W.H. Press, B.P. Flannery, S.A. Teukolsky, and W.T. Vettering Numerical Recipes: The Art of Scientific Computing 1986 Cambridge University Press Cambridge
32. 1/2; B1 and B2 are the numbers of 1's in B1 and B2 bit maps, respectively, and BC is the number of 1's in common between B1 and B2. The resulting Cosine score CC is a value between 0 and 1. If CC = 1, B1 and B2 are identical. If CC = 0, B1 and B2 have no TRUE = 1 occasions in common.
33. H. Hirai, K. Tanaka, O. Yoshie, K. Ogawa, K. Kenmotsu, Y. Takamori, M. Ichimasa, K. Sugamura, M. Nakamura, S. Takano, and K. Nagata J. Exp. Med. 193 2001 255
34. Indomethacin effects: H. Hirai, K. Tanaka, S. Takano, M. Ichimasa, M. Nakamura, and K. Nagata J. Immunol. 168 2002 981
35. Review: S. Mitsumori Curr. Pharm. Design 10 2004 3533
36. A. Schuffenhauer, P. Floersheim, P. Acklin, and E. Jacoby J. Chem. Inf. Comput. Sci. 43 2003 391
37. M. Lapinsh, P. Prusis, T. Lundstedt, and J.E.S. Wikberg Mol. Pharmacol. 61 2002 1465
38. T.K. Attwood, M.D. Croning, and A. Gaulton Protein Eng. 15 2002 7
39. P.A. van Zwieten, and H.N. Doods Cardiovasc. Drugs Ther. 9 1995 159
40. Cf. Y.C. Martin, J.L. Kofron, and L.M. Traphagen J. Med. Chem. 45 2002 4350
41. J.-M. Receveur, E. Bjurling, T. Ulven, P.B. Little, P.K. Nørregaard, and T. Högberg Bioorg. Med. Chem. Lett. 14 2004 5075
42. Excellent review over AT1 antagonists: R.R. Wexler, W.J. Greenlee, J.D. Irvin, M.R. Goldberg, K. Prendergast, R.D. Smith, and P.B.M.W.M. Timmermans J. Med. Chem. 39 1996 625
43. Identification of AT ligand-binding sites, e.g. Y. Yamano, K. Ohyama, S. Chaki, D.F. Guo, and T. Inagami Biochem. Biophys. Res. Commun. 187 1992 1426
44. K. Noda, Y. Saad, A. Kinoshita, T.P. Boyle, R.M. Graham, A. Husain, and S.S. Karnik J. Biol. Chem. 270 1995 2284
45. H.T. Schambye, S.A. Hjorth, J. Weinstock, and T.W. Schwartz Mol. Pharmacol. 47 1995 425
46. V. Nirula, W. Zheng, R. Sothinathan, and K. Sandberg Br. J. Pharmacol. 119 1996 1505
47. B. Vianello, E. Clauser, P. Corvol, and C. Monnot Eur. J. Pharmacol. 347 1998 113
48. Homology models were constructed by use of the comparative modeling program MODELLER [(a) Sali, A.; Blundell, T. L. J. Mol. Biol. 1993, 234, 779;
49. (b) Marti-Renom, M. A.; Stuart, A.; Fiser, A.; Sańchez, R.; Melo, F.; Sali, A. Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 291.] and the structural framework of rhodopsin solved to 2.8 Å resolution (PDB Protein Database code 1F88).
50. The sequence alignment program ClustalW [Higgins, D. G.; Thompson, J. D.; Gibson, T. J. Methods Enzymol. 1996, 266, 383] was used to obtain an alignment which was in agreement with generic 7TM receptor fingerprints
51. [Baldwin, J. M. EMBO J. 1993, 12, 1693].
52. Docking of ligands was done in accordance with strategies outlined in: Rarey, M.; Kramer, B.; Lengauer, T. Bioinformatics 1999, 15, 243.
53. Grid interaction using different hydrophobic and polar probes was obtained using the SBF module of Cerius 2, Molecular Simulations Inc.: San Diego, CA.
54. Catalyst version 4.6; Molecular Simulations Inc.: San Diego, CA, 1997.
55. The 3D multi-conformational library was constructed from commercial compound collections including InterBioScreen Maybridge ChemBridge and ChemDiv to contain a maximum of 255 conformers per molecule with an energy threshold not exceeding 10 kcal/mol to the lowest energy conformation using CATALYST's conformational search module.
56. 50 values determined by non-linear regression. AT receptor binding was done according to Perlman, S.; Costa-Neto C. M.; Miyakawa, A. A.; Schambye, H.; Hjorth, S. A.; Paiva, A. C.; Rivero, R. A.; Greenlee, W. J.; Schwartz, T. W.; Mol. Pharmacol. 1997, 51, 301.
57. ® 7.0, Tripos Inc., 1699 South Hanley Rd., St. Louis, Missouri 63144, USA.