Conformational properties and energetic analysis of aliskiren in solution and receptor site

Molecular Informatics

Volumn 30, Issue 11-12, 2011, Pages 973-985

  Politi, Aggeliki ^a,b   Leonis, Georgios ^b   Tzoupis, Haralambos ^a,b   Ntountaniotis, Dimitrios ^c   Papadopoulos, Manthos G ^b   Grdadolnik, Simona Golic ^d,e   Mavromoustakos, Thomas ^a,b  

^a UNIVERSITY OF ATHENS   (Greece)

^b INSTITUTE OF BIOLOGY   (Greece)

^c UNIVERSITY OF PATRAS   (Greece)

^d NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^e EN FIST CENTRE OF EXCELLENCE   (Slovenia)

Author keywords

Aliskiren; Conformational analysis; Molecular dynamics; NMR spectroscopy; Renin

Indexed keywords

BINDING ENERGY; CONFORMATIONS; FREE ENERGY; HYDROGEN BONDS; MOLECULAR DYNAMICS; VAN DER WAALS FORCES;

ALISKIREN; BINDING CAVITY; CONFORMATIONAL ANALYSIS; CONFORMATIONAL PROPERTIES; ENERGETIC ANALYSIS; NMR-SPECTROSCOPY; ORALLY ACTIVE; PROPERTY ANALYSIS; RECEPTOR SITES; RENIN;

NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

ALISKIREN; RENIN;

AMINO ACID SEQUENCE; ARTICLE; CALCULATION; DRUG CONFORMATION; DRUG RECEPTOR BINDING; DRUG STRUCTURE; ENERGY TRANSFER; HUMAN; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; PRIORITY JOURNAL; SOLVATION; STRUCTURE ANALYSIS;

EID: 83455163883     PISSN: 18681743     EISSN: 18681751     Source Type: Journal    
DOI: 10.1002/minf.201100077     Document Type: Article

References (58)

1. C. M. Tice, Ann. Rep. Med. Chem. 2006, 41, 155.
2. M. Paul, A. Poyan Mehr, R. Kreutz, Physiol. Rev. 2006, 86, 747.
3. J. M. Wood, J. L. Stanton, K. G. Hofbauer, Enzyme Inhib. Med. Chem. 1987, 1, 169.
4. N. A. Powell, F. L. Ciske, C. Cai, D. D. Holsworth, K. Mennen, C. A. VanHuis, M. Jalaie, J. Day, M. Mastronardi, P. McConnell, I. Mochalkin, E. Zhang, M. J. Ryan, J. Bryant, W. Collard, S. Ferreira, C. Gu, R. Collins, J.J Edmunds, Bioorg. Med. Chem. 2007, 15, 5912.
5. H. M. Siragy, Cardiovasc. Drugs Ther. 2011, 25, 87.
6. J. Rahuel, J. P. Priestle, M. G. Grutter, J. Struct. Biol. 1991, 107, 227.
7. C. Jensen, P. Herold, H. R. Brunner, Nat. Rev. Drug Discov. 2008, 7, 399.
8. J. A. Staessen, Y. Li, T. Richart, Lancet 2006, 368(9545), 1449.
9. N. D. Fisher, N. K. Hollenberg, J Am. Soc. Nephrol. 2005, 16, 592.
10. M. Azizi, R. Webb, J. Nussberger, N. K. Hollenberg, J. Hypertens. 2006, 24, 243.
11. M. J. Brown, Circulation 2008, 118, 773.
12. A. Gradman, R. Schmieder, R. Lins, J. Nussberger, Y. Chiang, M. Bedigian, Circulation 2005, 111(8), 1012.
13. J. M. Wood, J. Maibaum, J. Rahuel, M. G. Grütter, N. C. Cohen, V. Rasetti, H. Rüger, R. Göschke, S. Stutz, W. Fuhrer, W. Schilling, P. Rigollier, Y. Yamaguchi, F. Cumin, H. P. Baum, C. R. Schnell, P. Herold, R. Mah, C. Jensen, E. O'Brien, A. Stanton, M. P. Bedigian, Biochem. Biophys. Res. Commun. 2003, 308(4), 698.
14. A. P. Politi, S. Durdagi, P. M. Minakakis, T. Mavromoustakos, G. Kokotos, J. Mol. Gr. Mod. 2010, 29, 425.
15. A. R. Leach, in Molecular Modelling: Principles and Applications. 2 nd ed., Pearson Education, Upper Saddle River, NJ, 2001.
16. W. Wang, O. Donini, C. M. Reyes, P. A. Kollman, Ann. Rev. Biophys. Biomol. Struct. 2001, 30, 211.
17. S. Wan, P. V. Coveney, D. R. Flower, Philos. Trans. Roy. Soc. A, Math., Phys. Eng. Sci. 2005, 363, 2037.
18. W. L. Jorgensen, Science 2004, 303, 1813.
19. S. A. Adcock, J. A. McCammon, Chem. Re v. 2006, 106, 1589.
20. P. A. Bash, U. C. Singh, F. K. Brown, R. Langridge, P. A. Kollman, Science 1987, 235, 574.
21. J. Gao, K. Kuczera, B. Tidor, M. Karplus, Science 1989, 244, 1069.
22. M. Lawrenz, R. Baron, J. A. McCammon, J. Chem. Theory Comput. 2009, 5, 1106.
23. W. Wang, P. A. Kollman, Proc. Natl. Acad. Sci. USA 2001, 98, 14937.
24. Y. Xu, R. Wang, Proteins 2006, 64, 1058.
25. H. Gohlke, C. Kiel, D. A. Case, J. Mol. Biol. 2003, 330, 891.
26. Quanta, Molecular Simulations Inc., San Diego, CA, 1997.
27. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, M. M. Karplus, J. Comput. Chem. 1983, 4, 187.
28. M. A. C. Preto, A. Melo, H. L. S. Maia, T. Mavromoustakos, M. J. Ramos, J. Phys. Chem. B 2005, 109(37), 17743.
29. K. P. Soteriadou, A. K. Tzinia, E. Panou-Pamonis, V. Tsikaris, M. Sakarellos-Daitsiotis, C. Sakarellos, Y. Papapoulou, R. Matsas, Biochem. J. 1996, 313, 455.
30. D. A. Case, T. Cheatham III, T. Darden, H. Gohlke, R. Luo, K. M. Merz Jr., A. Onufriev, C. Simmerling, B. Wang, R. Woods, J. Comp. Chem. 2005, 26, 1668.
31. D.A. Case, T.A. Darden, T.E. CheathamIII, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B.P. Roberts, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, P.A. Kollman, AMBER 11, University of California, San Francisco, 2010.
32. J. Rahuel, V. Rasetti, J. Maibaum, H. Rueger, R. Goschke, N. C. Cohen, S. Stutz, F. Cumin, W. Fuhrer, J. M. Wood, M. G. Grutter, Chem. Biol. 2000, 7, 493.
33. J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, D. A. Case, J. Comput. Chem. 2004, 25, 1157.
34. A. Jakalian, B. L. Bush, D. B. Jack, C. I. Bayly, J. Comput. Chem. 2000, 21, 132.
35. A. Jakalian, D. B. Jack, C. I. Bayly, J. Comput. Chem. 2002, 23, 1623.
36. T. Fox, P. A. Kollman, J. Phys. Chem. B, 1998, 102, 8070.
37. J. A. Izaguirre, D. P. Catarello, J. M. Wozniak, R. D. Skeel, J. Chem. Phys. 2001, 114, 2090.
38. J. P. Ryckaert, G. Ciccotti, H. J. C. Berendsen, J. Comput. Phys. 1977, 23, 327.
39. C. Simmerling, R. Elber, J. Zhang, Moil-view-A Program for Visualization of Structure and Dynamics of Biomolecules and STO-A Program for Computing Stochastic Paths, Kluwer, Amsterdam, The Netherlands, 1995.
40. V. A. Rassolov, M. A. Ratner, J. A. Pople, P. C. Redfern, L. A. Curtiss, J. Comp. Chem. 2001, 22, 976.
41. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J.A. Montgomery, Jr. J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M. Cossi, N. Rega, N.J. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, Ã. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, D.J. Fox
42. Z. Y. Zhang, I. M. Reardon, J. O. Hui, K. L. O'Connell, R. A. Poorman, A. G. Tomasselli, R. L. Heinrikson, Biochemistry 1991, 30(36), 8717.
43. J. S. Tokarski, A. J. Hopfinger, J. Chem. Inf. Comput. Sci. 1997, 37, 779.
44. V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, C. Simmerling, Proteins 2006, 65, 712.
45. J. M. Word, S. C. Lovell, J. S. Richardson, D. C. Richardson, J. Mol. Biol. 1999, 285, 1735.
46. R. J. Woods, J. Comput. Chem. 1990, 11, 29.
47. W. L. C. Jorgensen, J. D. Madura, R. W. Impey, M. L. Klein, J. Chem. Phys. 1983, 79, 926.
48. P. A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. H. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D. A. Case, T. E. Cheatham, Acc. Chem. Rev. 2000, 33, 889.
49. B. Honig, A. Nichols, Science 1995, 268, 1144.
50. D. Sitkoff, K. A. Sharp, B. Honig, J. Phys. Chem. 1998, 98, 1978.
51. I. Stoica, S. K. Sadiq, P. V. Coveney, J. Am. Chem. Soc. 2008, 130, 2639.
52. J. Weiser, P. S. Shenkin, W. C. Still, J. Comput. Chem. 1999, 20, 217.
53. J. Srinivasan, T. E. Cheatham, P. Cieplak, P. A. Kollman, J. Am. Chem. Soc. 1998, 120, 9401.
54. W. Wang, O. Donini, C. M. Reyes, P. A. Kollman, Ann. Rev. Biophys. Biomol. Struct. 2001, 30, 211.
55. J. Nussberger, G. Wuerzner, C. Jensen, H. R. Brunner, Hypertension 2002, 39, e 1.
56. H. Gouda, I. D. Kuntz, D. A. Case, P. A. Kollman, Biopolymers 2003, 68, 16.
57. T. Hou, J. Wang, Y. Li, W. Wang, J. Chem. Inf. Model. 2011, 51, 69.
58. Q. Zhang, T. Schlick, Biophys. J. 2006, 90(6), 1865.