Benzimidazole derivatives. 3. 3D-QSAR/CoMFA model and computational simulation for the recognition of 5-HT4 receptor antagonists

Journal of Medicinal Chemistry

Volumn 45, Issue 22, 2002, Pages 4806-4815

  López Rodríguez, María L ^a   Murcia, Marta ^a   Benhamú, Bellinda ^a   Viso, Alma ^a   Campillo, Mercedes ^b   Pardo, Leonardo ^b  

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARAGINE; ASPARTIC ACID; BENZIMIDAZOLE 4 CARBOXAMIDE DERIVATIVE; BENZIMIDAZOLE 4 CARBOXYLATE DERIVATIVE; CARBON; CARBONYL DERIVATIVE; CARBOXYLIC ACID DERIVATIVE; LIGAND; MEMBRANE PROTEIN; OXYGEN; RHODOPSIN; SERINE; SEROTONIN 4 ANTAGONIST; SEROTONIN 4 RECEPTOR; UCM 21195; UCM 26995; UNCLASSIFIED DRUG;

ARTICLE; ATOM; BINDING AFFINITY; CHEMICAL INTERACTION; COMPUTER SIMULATION; CRYSTAL STRUCTURE; DRUG BINDING; DRUG STRUCTURE; DRUG SYNTHESIS; ELECTRICITY; ELECTRON TRANSPORT; ENERGY; HYDROGEN BOND; ION TRANSPORT; LIGAND BINDING; MOLECULAR RECOGNITION; PROTEIN DOMAIN; PROTEIN INTERACTION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SOLVATION; STEREOCHEMISTRY;

ANIMALS; BENZIMIDAZOLES; BINDING SITES; COMPUTER SIMULATION; LIGANDS; MALE; MODELS, MOLECULAR; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RADIOLIGAND ASSAY; RATS; RATS, SPRAGUE-DAWLEY; RECEPTORS, SEROTONIN; RECEPTORS, SEROTONIN, 5-HT4; SEROTONIN ANTAGONISTS;

EID: 0037168074     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm020807x     Document Type: Article

References (60)

1. 4 receptors: an update. In Serotoninergic Neurons and 5-HT Receptors in the CNS; Baumgarten, H. G., Göthert, M., Eds.; Springer-Verlag: Berlin, 1997; pp 439-474.
2. Hoyer, D.; Martin, G. 5-HT receptor classification and nomenclature: towards a harmonization with the human genome. Neuropharmacology 1997, 36, 419-428.
3. Uphouse, L. Multiple serotonin receptors: too many, not enough, or just the right number? Neurosci. Biobehav. Rev. 1997, 21, 679-698.
4. Murphy, D. L.; Andrews, A. M.; Wichems, C. H.; Li, Q.; Tohda, M.; Greenberg, B. Brain serotonin neurotransmission: an overview and update with an emphasis on serotonin subsystem heterogeneity, multiple receptors, interactions with other neurotransmitter systems, and consequent implications for understanding the actions of serotonergic drugs. J. Clin. Psychiatry 1988, 59 (Suppl. 15), 4-12.
5. 1-like receptors: a time to bid goodbye. Trends Pharmacol. Sci. 1998, 19, 311-316.
6. + current in colliculi neurones via activation of a cyclic AMP-dependent protein kinase. Br. J. Pharmacol. 1992, 105, 973-979.
7. 3 and "atypical" 5-HT receptors mediating guinea-pig ileal contractions in vitro. Br. J. Pharmacol. 1990, 101, 513-520.
8. 4 receptors in human colon, rat oesophagus and rat ileum. Br. J. Pharmacol. 1995, 115, 47-56.
9. 4) receptors in guinea pig stomach: The effect of TKS159, a novel agonist, on gastric motility and acetylcholine release. J. Pharmacol. Exp. Ther. 1996, 276, 989-995.
10. 4 receptor. Br. J. Pharmacol. 1990, 100, 665-667.
11. 4 receptors in the human isolated detrusor muscle: effects of indole, benzimidazolone and substituted benzamide agonists and antagonists. Br. J. Pharmacol. 1996, 118, 1965-1970.
12. Briejer, M. R.; Akkermans, L. M.; Schuurkes, J. A. Gastrointestinal prokinetic benzamides: the pharmacology underlying stimulation of motility. Pharmacol. Rev. 1995, 47, 631-651.
13. 4 receptors in motility disorders: New therapeutic agents. In Drug development: molecular targets for GI diseases; Gagiella, T. S., Guglietta, A., Eds.; Humana Press Inc.: Totowa, NJ, 2000; pp 177-202.
14. 4 receptors in 5-hydroxytryptophan-induced diarrhea in mice. J. Pharmacol. Exp. Ther. 1994, 271, 741-747.
15. Farthing, M. J. G. New drugs in the management of the irritable bowel syndrome. Drugs 1998, 56, 11-21.
16. Farthing, M. J. G. Irritable bowel syndrome: new pharmaceutical approaches to treatment. Best Pract. Res. Clin. Gastroenterol. 1999, 13, 461-471.
17. 4 receptors mediate arrhythmias? Trends Pharmacol. Sci. 1994, S15, 451-455.
18. 4 receptor agonists and bladder disorders. Trends Pharmacol. Sci. 1996, 17, 314-316.
19. Ferguson, D.; Christopher, N. Urinary bladder function and drug development. Trends Pharmacol. Sci. 1996, 17, 161-165.
20. 4 receptors. Trends Pharmacol. Sci. 1995, 16, 391-398.
21. 4 receptor antagonists. Med. Res. Rev. 1997, 17, 163-214.
22. 4 binding sites. J. Comput.-Aided Mol. Des. 1997, 11, 589-599.
23. 4. Patent PCT/ES97/00068, WO 97/35860, 1997; Chem. Abstr. 1997, 127 (4), 331485n.
24. 4 receptor antagonists. Bioorg. Med. Chem. 1999, 7, 2271-2281.
25. 4 receptor by site-directed mutagenesis and molecular modeling. Br. J. Pharmacol. 2000, 130, 527-538.
26. 4 receptor guided by sitedirected mutagenesis and the crystal structure of rhodopsin. J. Comput.-Aided Mol. Des. 2001, 15, 1025-1033.
27. Ballesteros, J. A.; Weinstein, H. Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. Methods Neurosci. 1995, 25, 366-428.
28. 4 receptor. Bioorg. Med. Chem. Lett. 2001, 11, 2807-2811.
29. Green, S. M.; Marshall, G. R. 3D-QSAR: a current perspective. Trends Pharmacol. Sci. 1995, 16, 285-291.
30. Cramer, R. D.; Patterson, D. E.; Bunce, J. D. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
31. Clark, M.; Cramer, R. D. I.; Jones, D. M.; Patterson, D. E.; Simeroth, P. E. Comparative molecular field analysis (CoMFA). 2. Toward its use with 3D-structural databases. Tetrahedron Comput. Methodol. 1990, 3, 47-59.
32. 4 receptor ligands: influence of an intramolecular hydrogen bond. Tetrahedron 2001, 57, 6745-6749.
33. 3 receptors. J. Med. Chem. 1999, 42, 5020-5028.
34. 4 receptors in guinea-pig and rat brain. Br. J. Pharmacol. 1993, 109, 618-624.
35. 50) of an enzymatic reaction. Biochem. Pharmacol. 1973, 22, 3099-3108.
36. Singh, U. C.; Kollman, P. A. An approach to computing electrostatic charges for molecules. J. Comput. Chem. 1984, 5, 129-145.
37. Cornell, W. D.; Cieplak, P.; Bayly, C.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
38. Dunn, W. J.; Wold, S.; Edlund, U.; Hellberg, S.; Gasteiger, J. Multivariate structure-activity relationships between data from a battery of biological tests and an ensemble of structure descriptors: the PLS method. Quant. Struct. - Act. Relat. 1984, 3, 131-137.
39. Wold, S.; Ruhe, A.; Wold, H.; Dunn, W. J. I. The covariance problem in linear regression. The partial least squares (PLS) approach to generalized inverses. SIAM J. Sci. Stat. Comput. 1984, 5, 735-743.
40. Cramer, R. D.; Bunce, J. D.; Patterson, D. E. Crossvalidation, bootstrapping and partial least squares compared with multiple regression in conventional QSAR studies. Quant. Struct. - Act. Relat. 1988, 7, 18-25.
41. Wold, S.; Albano, C.; Dunn, W. J. I.; Edlund, U.; Esbensen, W.; Geladi, P.; Hellberg, S.; Johansson, E.; Lindberg, W.; Sjöstrom, M. Multivariate data analysis in chemistry. In Chemometrics: mathematics and statistics in chemistry; Kowwalsky, B. R., Ed.; Reidel: Dordrecht, The Netherlands, 1984; pp 17-95.
42. SYBYL, version 6.6: Tripos Inc., 1699 South Hanley Road, St. Louis, MO 63144.
43. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98; Gaussian, Inc.: Pittsburgh, PA, 1998.
44. Palczewski, K.; Kumasaka, T.; Hori, T.; Behnke, C. A.; Motoshima, H.; Fox, B. A.; Le Trong, I.; Teller, D. C.; Okada, T.; Stenkamp, R. E.; Yamamoto, M.; Miyano, M. Crystal structure of rhodopsin: A G protein-coupled receptor. Science 2000, 289, 739-745.
45. Dunbrack, R. L.; Cohen, F. E. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 1997, 6, 1661-1681.
46. - conformation. Biophys. J. 2000, 79, 2754-2760.
47. 1A receptor ligands to explore the three-dimensional structure of the receptor. Mol. Pharmacol. 2002, 62, 15-21.
48. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E.; Ross, W. S.; Simmerling, T. A.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vicent, J. J.; Crowley, M.; Ferguson, D. M.; Radmer, R. J.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 5; University of California, San Francisco, 1997.
49. Cieplak, P.; Cornell, W. D.; Bayly, C.; Kollman, P. A. Application of the multimolecule and multiconformational RESP methodology to biopolymers: charge derivation for DNA, RNA, and proteins J. Comput. Chem. 1995, 16, 1357-1377.
50. Levitt, M.; Perutz, M. F. Aromatic rings act as hydrogen bond acceptors. J. Mol. Biol. 1988, 201, 751-754.
51. Suzuki, S.; Green, P. G.; Bumgarner, R. E.; Dasgupta, S.; Goddard, W. A. I.; Blake, G. A. Benzene forms hydrogen bonds with water. Science 1992, 257, 942-945.
52. Rodham, D. A.; Suzuki, S.; Suenram, R. D.; Lovas, F. J.; Dasgupta, S.; Goddard, W. A. I.; Blake, G. A. Hydrogen bonding in the benzene-ammonia dimer. Nature 1993, 362, 735-737.
53. Steiner, T.; Koellner, G. Hydrogen bonds with π-acceptors in proteins: frequencies and role in stabilizing local 3D structures. J. Mol. Biol. 2001, 305, 535-557.
54. Burley, S. K.; Petsko, G. A. Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science 1985, 229, 23-28.
55. O'Neil, K. T.; DeGrado, W. F. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 1990, 250, 646-651.
56. Monne, M.; Hermansson, M.; von Heijne, G. A turn propensity scale for transmembrane helices. J. Mol. Biol. 1999, 288, 141-145.
57. Horn, F.; Weare, J.; Beukers, M. W.; Horsch, S.; Bairoch, A.; Chen, W.; Edvardsen, O.; Campagne, F.; Vriend, G. GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res. 1998, 26, 275-279.
58. Lowry, O. H.; Rosebrough, N. J.; Farr, A. L.; Randall, R. J. Protein measurement with the folin phenol reagent. J. Biol. Chem. 1951, 193, 265-275.
59. Kraulis, P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 1991, 24, 945-950.
60. Merritt, E. A.; Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 1997, 277, 505-524.