Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases

Journal of the American Chemical Society

Volumn 130, Issue 8, 2008, Pages 2639-2648

  Stoica, Ileana ^a   Sadiq, S Kashif ^a   Coveney, Peter V ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BOLTZMANN EQUATION; DRUG PRODUCTS; ENTHALPY; ENTROPY; HYDROGEN BONDS; MOLECULAR DYNAMICS; POISSON DISTRIBUTION;

BINDING AFFINITIES; DRUG RESISTANCE; DRUG-PROTEASE INTERACTIONS; MOLECULAR LEVEL; VIBRATIONAL ENTROPY;

ENZYME ACTIVITY;

HIV 1 PROTEASE; PROTEINASE; SAQUINAVIR; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; BINDING AFFINITY; BIOENERGY; COMPUTER SIMULATION; DRUG PROTEIN BINDING; ENTHALPY; ENTROPY; HYDROGEN BOND; INTERNAL CONSISTENCY; LIGAND BINDING; MOLECULAR DYNAMICS; POISSON DISTRIBUTION; PREDICTION;

EID: 39749152456     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0779250     Document Type: Article

References (56)

1. Alfano, M.; Poli, G. Drug. Des. ReV.-Online 2004, 1, 83-92.
2. Wlodawer, A.; Miller, M.; Jaskolski, M.; Sathyanarayana, B. K.; Baldwin, E.; Weber, I. T.; Selk, L. M.; Clawson, L.; Schneider, J.; Kent, S. B. Science 1989, 245, 616-621.
3. Wang, W.; Donini, O.; Reyes, C. M.; Kollman, P. A. Annu. ReV. Biophys Biomol. Struct. 2001, 30, 211-243.
4. Wan, S.; Coveney, P. V.; Flower, D. R. Philos. Trans. R. Soc. A 2005, 363, 2037-2053.
5. Kollman, P. A.; et al. Acc. Chem. Res. 2000, 33, 889-897.
6. Rizzo, R. C.; Toba, S.; Kuntz. I. D. J. Med. Chem. 2004, 47, 3065-3074.
7. Page, C. S.; Bates, P. A. J. Comput. Chem. 2006, 27, 1990-2007.
8. Ode, H.; Neya, S.; Hata, M.; Sugiura, W.; Hoshino, T. J. Am. Chem. Soc. 2006, 24, 7887-7895.
9. Ode, H.; Matsuyama, S.; Hata, M.; Hoshino, T.; Kakizawa, J.; Sugiura, W. J. Med. Chem. 2007, 50, 1768-1777.
10. Hou, T.; Yu, R. J. Med. Chem. 2007, 50, 1177-1188.
11. Wang, W.; Kollman, P. A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 14937-14942.
12. Lepsik, M.; Kriz, Z.; Havlas, Z. Proteins: Struct., Funct. Bioinf. 2004, 57, 279-293.
13. Kalra, P.; Reddy, T.; Jayaram, B. J. Med. Chem. 2001, 44, 4325-4338.
14. Krohn, A.; Redshaw, S.; Ritchie, J. C.; Graves, B. J.; Hatada, M. H. J. Med. Chem. 1991, 34, 3340-3342.
15. Hong, L.; Zhang, X. C.; Hartsuck, J. A.; Tang, J. Protein Sci. 2004, 9, 1898-1904.
16. Maschera, B.; Darby, G.; Palu, G.; Wright, L.; Tisdale, M.; Myers, R.; Blair, E. D.; Furfine, E. S. J. Biol. Chem. 1996, 271, 33231-33235.
17. Ermolieff, J.; Lin, X.; Tang, J. Biochemistry 1997, 36, 12364-12370.
18. Shenderovich, M. D.; Kagan, R. M.; Heseltine, P. N.; Ramnarayan, K. K. Protein Sci. 2004, 12, 1706-1718.
19. Kovalskyy, D.; Dubyna, V.; Mark, A. E.; Korenelyuk, A. Proteins: Struct., Funct. Bioinf. 2005, 58, 450-458.
20. Wittayanarakul, K.; Aruksakunwong, O.; Saen-oon, S.; Chantratita, W.; Parasuk, V.; Sompornpisut, P.; Hannongbua, S. Biophys. J. 2005, 88, 867-879.
21. Wittayanarakul, K.; Hannongbua, S.; Feig, M. J. Comput. Chem. 2007, DOI: 10.1002/jcc.20821 (published online Sept 11, 2007).
22. Sadiq, S. K.; Wan, S.; Coveney, P. V. Biochemistry 2007, 46, 14865-14877.
23. Frisch, M. J.; et al. Gaussian 98; Gaussian Inc.: Pittsburgh, PA, 2001.
24. Wang, J.; Wolf, R. M.; Case, D. A.; Kollman, P. A. J. Comput. Chem. 2004, 25, 1157-1174.
25. Wang, J. M.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074.
26. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
27. Kale, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. J. Comput. Phys. 1999, 151, 283-312.
28. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T. J. Chem. Phys. 1995, 103, 8577-9593.
29. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
30. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak. J. R. J. Chem. Phys. 1984, 81, 3684-3690.
31. Meagher, K. L.; Carlson, H. A. Proteins: Struct., Funct. Bioinf. 2005, 58, 119-125.
32. Sanner, M. F.; Olson, A. J.; Spehner, J. C. Biopolymers 1996, 38, 305-320.
33. Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A.; Brooks, C. L., III. J. Comput. Chem. 2004, 25, 265-284.
34. Naim, M.; et al. J. Chem. Inf. Modell. 2007, 47, 122-133.
35. Chen, W.; Chang, C. E.; Gilson, M. K. Biophys. J. 2004, 87, 3035-3049.
36. Onufriev, A.; Bashford, D.; Case, D. A. Proteins: Struct., Funct. Bioinf. 2004, 55, 383-394.
37. Rocchia, W.; Sridharan, S.; Nicholls, A.; Alexov, E.; Chiabrera, A.; Honig, B. J. Comput. Chem. 2002, 23, 128-137.
38. Sitkoff, D.; Sharp, K. A.; Honig, B. J. Phys. Chem. 1994, 98, 1978-1988.
39. Cornell, W. D.; et al. J. Am. Chem. Soc. 1995, 117, 5179-5197.
40. Gohlke, H.; Case, D. A. J. Comput. Chem. 2004, 25, 238-250.
41. Lu, Y.; Yang, C.-Y.; Wang, S. J. Am. Chem. Soc. 2005, 128, 11830-11839.
42. Coveney, P. V.; Saksena, R. S.; Zasada, S. J.; McKeown, M.; Pickles, S. Comput. Phys. Commun. 2007, 176, 406-418.
43. Sadiq, S. K.; Zasada, S. J.; Wright, D.; Stoica, I.; Coveney, P. V. A molecular simulation based automated binding affinity calculator for ligandbound HIV-1 proteases. Preprint, 2008.
44. Pearlman, D. A. J. Med. Chem. 2005, 48, 7796-7807.
45. Chang, C. E.; Chen, W.; Gilson, M. K. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 1534-1539.
46. Liu, T.; Wen, Y.; Jorrisen, R. N.; Gilson, M. K. Nucleic Acids Res. 2006, 35, D198-D201.
47. Lafont, V.; Armstrong, A. A.; Ohtaka, H.; Kiso, Y.; Amzel, L. M.; Freire, E. Chem. Biol. Drug Des. 2007, 69, 413-422.
48. Velazquez-Campoy, A.; Muzammil, S.; Ohtaka, H.; Schon, A.; Vega, A.; Freire, E. Curr. Drug Targets Infect. Dis. 2003, 3, 311-328.
49. Gohlke, H.; Klebe, G. Angew. Chem., Int. Ed. 2002, 41, 2644-2676.
50. Ohtaka, H.; Schon, A.; Freire, E. Biochemistry 2003, 42, 13659-13666.
51. Gilson, M. K.; Zhou, H.-X. Annu. ReV. Biophys. Biomol. Struct. 2007, 36, 21-42.
52. Muzammil, S.; Armstrong, A. A.; Kang, L. M.; Jakalian, A.; Bonneau, P. R.; Schmelmer, V.; Amzel, M. L.; Freire, E. J. Virol. 2007, 81, 5144-5154.
53. Hornak, V.; Okur, A.; Rizzo, R. C.; Simmerling, C. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 915-920.
54. Deveraux, H. L.; Emery, V. C.; Johnson, M. A.; Loveday, C. J. Med. Virol. JA0779250 2001, 65, 218-224.
55. Gulnik, S. V.; Suvorov, L. I.; Liu, B.; Yu, B.; Anderson, B.; Mitsuya, H.; Erickson, J. W. Biochemistry 1995, 34, 9282-9287.
56. Prabu-Jeyabalan, M.; Nalivaika, E.; King, N. M.; Schiffer, C. A. J. Virol. 2005, 78, 12446-12454.