Conformational studies of two bradykinin antagonists by using two-dimensional nmr techniques and molecular dynamics simulations

Journal of Biomolecular Structure and Dynamics

Volumn 23, Issue 2, 2005, Pages 125-134

 

^a nee Trzepalka) E   (Poland)

Author keywords

BK antagonists; Cis trans isomerization; Conformational studies; Molecular dynamics; N methylation; NMR spectroscopy

Indexed keywords

ADAMANTANEACETIC ACID DEXTRO ARGINYLBRADYKININ[1 ARGININE 2 PROLINE 3 HYDROXYPROLINE 4 GLYCINE 5 [3 (2 THIENYL)ALANINE] 6 SERINE 7 (2 NAPHTHYLALANINE) 8 [3 (2 THIENYLALANINE] 9 ARGININE; ADAMANTANECARBOXYLIC ACID DEXTRO ARGINYLBRADYKININ[1 ARGININE 2 PROLINE 3 HYDROXYPROLINE 4 GLYCINE 5 [3 (2 THIENYL)ALANINE] 6 SERINE 7 DEXTRO PHENYLALANINE N BENZYL 8 GLYCINE 9 ARGININE; ARGININE; BRADYKININ ANTAGONIST; CARBOXYL GROUP; DIMETHYL SULFOXIDE; GUANIDINE; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL BOND; DRUG STRUCTURE; ISOMER; ISOMERIZATION; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN STRUCTURE; SIMULATION;

BRADYKININ; COMPUTER SIMULATION; HUMANS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; RECEPTORS, BRADYKININ; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 25144485431     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2005.10507053     Document Type: Article

References (63)

1. Bhoola, K. D., Figueroa, C. D., and Worthy, K., 1992. Pharmacol. Rev., 44:1–80.
2. Marceau, F., and Regoli, D., 2004. Nat. Rev. Drug Discov., 3:845–852.
3. Coture, R., Harrisson, M., Vianna, R. M., and Cloutier, F., 2001. Eur. J. Pharmacol., 429:161–76.
4. Vellani, V., Zachrisson, O., and McNaughton, P. A., 2004. J. Physiol., 560:391–401.
5. Regoli, D., and Barabé, J., 1988. Methods Enzymol., 163:210–230.
6. Philips, E., Conder, M. J., Bevan, S., McIntyre, P., and Webb, M., 1992. J.Neurochem., 58:243–249.
7. Farmer, S. G., and Burch, R. M., 1991. Bradykinin Antagonists. Basic and Clinical Research Edited by:Burch, R. M., 1–31. NY-Basel-Hong Kong:Marcel Dekker Inc. The Pharmacology of Bradykinin Receptors. In
8. Vavrek, R. J., and Stewart, J. M., 1985. Peptides, 6:161–164.
9. Schachter, L. R., Uchida, Y., Longridge, D. J., Labedz, T., Whalley, E. T., Vavrek, R. J., and Stewart, J. M., 1987. Br. J. Pharmacol., 92:851–855.
10. Stewart, J. M., and Vavrek, R. J., 1986. Adv. Exp. Med. Biol., 198:537–542.
11. Dawidowska, O., Wierzba, T. H., Prahl, A., Kowalczyk, W., Derdowska, I., Neubert, K., Zabrocki, J., Olejniczak, B., Juzwa, W., and Lammek, B., 2004. J. Pept. Res., 63:29–35.
12. Vitoux, B., Aubry, A., Cung, M. T., and Marrad, M., 1986. J. Pept. Protein Res., 27:617–632.
13. Lee, S. C., Russell, A. F., and Laidig, W. D., 1990. Int. J. Pept. Protein Res., 35:367–377.
14. Kotovych, G., Cann, J. R., Stewart, J. M., and Yamamoto, H., 1998. Biochem. Cell Biol., 76:257–266.
15. Liu, X., Stewart, M., Gera, L., and Kotovych, G., 1993. Biopolymers, 33:1237–1247.
16. Kyle, D. J., Blake, P. R., Smithwick, D., Green, L. M., Martin, J. A., Sinsko, J. A., and Summers, M. F., 1993. J. Med. Chem., 36:1450–1460.
17. Otter, A., Bigler, P., Stewart, J. M., and Kotovych, G., 1993. Biopolymers, 33:769–780.
18. Sejbal, J., Cann, J. R., Stewart, J. M., Gera, L., and Kotovych, G., 1996. J. Med. Chem., 39:1281–1292.
19. Chou, P. Y., and Fasman, G. D., 1979. Biophys. J., 26:367–384.
20. Wilmot, C. M., and Thornton, J. M., 1988. J. Mol. Biol., 203:221–232.
21. Rose, G. D., Gierasch, L. M., and Smith, J. A., 1985. Adv. Protein Chem., 37:1–109.
22. Hutchinson, E. G., and Thornton, J. M., 1994. Protein Science, 3:2207–2216.
23. Kuroda, Y., Ueda, H., Nozawa, H., and Ogoshi, H., 1997. Tetrahedron Letters, 38:7901–7904.
24. Bax, A., and Freeman, R., 1985. J. Magn. Reson., 65:355–360.
25. Braunschweiler, L., and Ernst, R. R., 1983. J. Magn. Reson., 53:521–528.
26. Bax, A., and Davis, D. G., 1985. J. Magn. Reson., 63:207–213.
27. Kay, L. E., Keifer, P., and Saarinen, T., 1992. J. Am. Chem. Soc., 114:10663–10665.
28. Bax, A., and Summers, M. F., 1986. J. Am. Chem. Soc., 108:2093–2094.
29. Palmer, A. G., III, Cavanagh, J., Wright, P. E., and Rance, M., 1991. J. Magn. Reson., 93:151–170.
30. Delaglio, F., Grzesiek, S., Geerten, W. V., Zhu, G., Pfeifer, J., and Bax, A., 1995. J. Biomol. NMR, 6:277–293.
31. Varian. Nuclear Magnetic Resonance Instruments, VnmrTM Software, Revision 5.3B 1/97.
32. Bartles, T. Xia, Billeter, M., Günter, P., and Wütrich, K., 1995. J. Biomol. NMR, 5:1–10.
33. Hoffman, R. E., and Davies, D. B., 1998. Magn. Reson. Chem., 26:523–525.
34. Koźminski, W., 1998. J. Magn. Reson., 134:189–193.
35. Rance, M., Sorensen, O. W., Bodenhausen, G., Wagner, G., Ernst, R. R., and Wütrich, K., 1983. Biochem. Biophys. Res. Commun., 117:479–485.
36. Weiner, S. J., Kollman, P. A., Nguyen, D. T., and Case, D. A., 1986. J. Comput. Chem., 7:230–252.
37. Case, D. A., Pearlman, D. A., Caldwell, J. W., Cheatham, T. E., III, Ross, W. S., Simmerling, C., Darden, T., Merz, K. M., Stanton, R. V., Cheng, A., Vincent, J. J., Crowley, M., Ferguson, D. M., Radmer, R., Seibel, G. L., Singh, U. C., Wiener, P., and Kollman, P. A., 2002. Amber 7.0. San Francisco:University of California.
38. Allen, F. H., Davies, J. E., Galloy, J. J., Johnson, O., Kennard, O., Macrae, C. F., Mitchell, E. M., Mitchell, G. F., Smith, J. M., and Watson, D. G., 1991. J. Chem. Inf. Comp. Sci., 31:187–204.
39. Schmidt, M. W., Baldridge, K. K., Boatz, J. A., Elbert, S. T., Gordon, M. S., Jensen, J. H., Koseki, S., Matsunaga, N., Nguyen, K. A., Su, S., Windus, T. L., Dupuis, M., and Montgomery, J. A., 1993. J. Comput. Chem., 14:1347–1363.
40. Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A., 1993. J. Phys. Chem., 97:10269–10280.
41. Case, D. A., Pearlman, D. A., Caldwell, J. W., Cheatham, T. E., III, Ross, W. S., Simmerling, C., Darden, T., Merz, K. M., Stanton, R. V., Cheng, A., Vincent, J. J., Crowley, M., Ferguson, D. M., Radmer, R., Seibel, G. L., Singh, U. C., Weiner, P. K., and Kollman, P. A., 1997. Amber 5.0. San Francisco:University of California.
42. Meadows, R., Post, C. B., Luxon, B. A., and Gorenstein, D. G., 1994. MORASS 2.1 Program. W. Lafayette:Purdue University.
43. Massefski, W., Jr and Bolton, P. H., 1985. J. Magn. Reson., 65:526–530.
44. Bystrov, V. F., 1976. Progr. NMR Spectrosc., 10:41–81.
45. Yu, C., Yang, T. H., Yeh, C. J., and Chuang, L. C., 1999. Can. J. Chem., 70:1950–1955.
46. Marquard, D. W., 1963. J. Soc. Industr. Appl. Math., 11:431–441.
47. Sikorska, E., and Lammek, B., 2004. Peptides, In Press
48. Fox, T., and Kollman, P. A., 1998. J. Phys. Chem. B., 102:8070–8079.
49. Riddick, J. A., Bunger, W. B., and Sakand, T. K., 1986. Organic Solvents:Physical Properties and Methods of Purification. New York, NY:Wiley.
50. Elber, R., and Karplus, M., 1990. J. Am. Chem. Soc., 112:9161–9175.
51. Ewald, P. P., 1921. Ann. Phys., 64:253–287.
52. Darden, T., York, D., and Pedersen, L., 1993. J. Chem. Phys., 98:10089–10092.
53. Ryckeart, J. P., Ciccotti, G., and Berendsen, H. J. C., 1977. J. Comput. Phys., 23:327–341.
54. Dorman, D. E., and A, F., 1973. J. Org. Chem., 38:2379–2383.
55. Bach, A. C., III, Eyerman, C. Y., Gross, J. D., Bower, M. J., Haflow, R. L., Weber, P. C., and Degrado, W. F., 1994. J. Am. Chem. Soc., 116:3207–3219.
56. Andersen, N. H., Neidigh, J. W., Harris, S. M., Lee, G. M., Liu, Z., and Tong, H., 1997. J. Am. Chem. Soc., 119:8547–8561.
57. Dyson, H. J., Rance, M., Houghten, R. A., Lerner, R. A., and Wright, P. E., 1988. J. Mol. Biol., 201:161–200.
58. Richardson, J. S., 1981. Advan. Protein Chem., 34:167–339.
59. Pellegrini, M., Mammi, S., Gobbo, M., Rocchi, R., and Peggion, E., 1995. Biopolymers, 6:461–472.
60. Pardi, A., Billeter, M., and Wütrich, K., 1984. J. Mol. Biol., 180:741–751.
61. Evans, J. N. S., 1995. Biomolecular NMR Spectroscopy. Oxford, New York, Tokyo:Oxford University Press.
62. Lewis, P. N., Mamony, F. A., and Scheraga, H. A., 1973. Biochim. Biophys. Acta, 303:211–229.
63. McDonald, I. K., and Thornton, J. M., 1994. J. Mol. Biol., 238:777–793.