Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 reverse transcriptase

Journal of the American Chemical Society

Volumn 127, Issue 49, 2005, Pages 17253-17260

  Zhou, Zhigang ^a   Madrid, Marcela ^b   Evanseck, Jeffrey D ^a   Madura, Jeffry D ^a  

^a DUQUESNE UNIVERSITY   (United States)

^b PITTSBURGH SUPERCOMPUTING CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; DISEASES; DRUG PRODUCTS; ENZYMES; MOLECULAR DYNAMICS; MUTAGENESIS; PRINCIPAL COMPONENT ANALYSIS;

MOLECULAR MECHANICS; MUTATIONS; REVERSE TRANSCRIPTASE (RT);

ENZYME INHIBITION;

NEVIRAPINE; RNA DIRECTED DNA POLYMERASE; RNA DIRECTED DNA POLYMERASE INHIBITOR;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; AMINO ACID ANALYSIS; ARTICLE; BINDING AFFINITY; BINDING KINETICS; CALCULATION; CONTROLLED STUDY; DRUG INTERACTION; DRUG PROTEIN BINDING; DRUG RESISTANCE; ENZYME INHIBITION; HUMAN IMMUNODEFICIENCY VIRUS 1; INHIBITION KINETICS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MECHANICS; NONHUMAN; POISSON DISTRIBUTION; PRINCIPAL COMPONENT ANALYSIS; SIMULATION; STRUCTURE ACTIVITY RELATION; SURFACE PROPERTY; TRANSCRIPTION REGULATION;

AMINO ACID SUBSTITUTION; ANTI-HIV AGENTS; BINDING SITES; DRUG RESISTANCE, VIRAL; HIV-1 REVERSE TRANSCRIPTASE; MODELS, MOLECULAR; MUTATION; NEVIRAPINE; PRINCIPAL COMPONENT ANALYSIS; PROTEIN CONFORMATION; REVERSE TRANSCRIPTASE INHIBITORS; THERMODYNAMICS;

EID: 29144436035     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja053973d     Document Type: Article

References (77)

1. Koup, R. A.; Merluzzi, V. J.; Margrave, K. D.; Adems, J.; Grozinger, K.; Eckner, R. J.; Saivan, J. L. J. Infect. Dis. 1991, 163, 966-970.
2. Richman, D.; Rosenthal, A. S.; Shoog, M.; Eckner, R. J.; Chou, T. C.; Sabo, J. P.; Merluzzi, V. J. Antimicrob. Agents Chemother. 1991, 35, 305-308.
3. De Clercq, E. Clin. Microbiol. Rev. 1995, 8, 200-239.
4. Tantillo, C.; Ding, J.; Jacobo-Molina, A.; Nanni, R. G.; Boyer, P. L.; Hughes, S. H.; Pauwels, R.; Andries, K.; Janssen, P. A. J.; Arnold, E. J. Mol. Biol. 1994, 243, 369-387.
5. Kohlstaedt, L. A.; Wang, J.; Friedman, J. M.; Rice. P. A.; Steitz, T. A. Science 1992, 256, 1783-1790.
6. Smerdon, S. J.; Jager, J.; Wang, J.; Kohlstaedt, L. A.; Chirino, A. J.; Friedman, J. M.; Rice, P. A.; Steitz, T. A. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 3911-3915.
7. Ding, J.; et al. Structure 1995, 3, 365-379.
8. Ding, J.; Das, K.; Moereels, H.; Koynians, L.; Andries, K.; Janssen, P. A.; Hughes, S. H.; Arnold, E. Nat. Struct. Biol. 1995, 2, 407-415.
9. Jacobo-Molina, A.; Ding, J.; Nanni, R. G.; Jr., A. D. C.; Lu, X.; Tamtilo, C.; Williams, R. L.; Kamer, G.; Ferris, A. L.; Clark, P.; Hizi, A.; Hughes, S. H.; Arnold, E. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 6320-6324.
10. Huang, H.; Chopra, R.; Verdine, G. L.; Harrison, S. C. Science 1998, 282, 1669-1675.
11. Larder, B. A. In Reverse transcriptase; Skalka, A. M., G. S., Eds.; Cold spring Harbor Laboratory Press: Plainview, NY. 1993: pp 205-222.
12. Larder, B. A. In Reverse Transcriptase; Skalka, A. M., G. S., Eds.; Cold spring Harbor Laboratory Press: Plainview, NY. 1993; pp 163-191.
13. Ding, J.; Das, K.; Hsiou, Y.; Zhang, W.; Arnold. E.; Yadav, P. N. S.; Hughes, S. H. Struct.-Based Drug Des. 1997, 41-82.
14. Pedersen, O. S.; Pedersen, E. B. Antiviral Chem. Chemother. 1999, 10, 285-314.
15. Wang, J.; Smerdon, S. J.; Jager, J.; Kohlstaedt, L. A.; Rice, P. A.; Friedman, J. M.; Steitz, T. A. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 7242.
16. Ren, J.; Esnouf, R.; Garman, E.; Somers, D.; Ross, C.; Kirby, I.; Keeling, J.; Darby, G.; Jones, Y.; Stuart, D.; Stammers, D.; et al. Nat. Struct. Biol. 1995, 2, 293.
17. Das, K.; Ding, J.; Hsiou, Y.; Clark, A. J.; Moereels, H.; Koymans, L.; Andries, K.; Pauwels, R.; Janssen, P.; Boyer, P.; Clark, P.; Smith, R. J.; Kroeger, S. M.; Michejda, C.; Hughes, S.; Arnold, E. J. Mol. Biol. 1996, 264, 1085-1100.
18. Ding, J.; Das, K.; Ydev, P. N. S.; Hsiou, Y.; Zhang, W.; Hughes, S. H.; Arnold, E. In Structure Based Drug Design; P., W., Ed.; Marcel Dekker: New York, 1997; pp41-82.
19. Zhou, Z.; Madrid, M.; Madura, J. D. Proteins: Struct., Fund., Genet. 2002, 49, 529-542.
20. Hsiou, Y.; Ding, J.; Das, K.; Jr., A. D. C.; Hughes, S. H.; Arnold, E. Structure 1996, 4, 853-860.
21. Jager, J.; Smerdon, S. J.; Wang, J.; Boisvert, D. C.; Steitz, T. A. Structure 1994, 2, 869-876.
22. Ding, J.; Hughes, S. H.; Arnold, E. Biopolymers 1997, 44, 125-138.
23. Sarafianos, S. G.; Das, K.; Ding, J.; Hsiou, Y.; Hughes, S. H.; Arnold, E. Current perspectives on mechanisms of HIV-1 reverse transcriptase inhibition by nonnucleoside inhibitors. In Anti-Infectives: Recent Advances in Chemistry and Structure-Activity Relationships; Bentley, P. H., O'Hanlon, P. J., Eds.; 1997; Vol. 198, pp 328-334.
24. Rodgers, D. W.; Gamblin, S. J.; Harris, B. A.; Ray, S.; Culp, J. S.; Hellmig, B.; Woolf, D. J.; Debouck, C.; Harrison, S. C.; Ray, S. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 1222-1226.
25. Kroeger Smith, M. B.; Hose, B. M.; Hawkins, A.; Lipchock, J.; Farnsworth, D. W.; Rizzo, R. C.; Tirado-Rives, J.; Arnold, E.; Zhang, W.; Hughes, S. H.; Jorgensen, W. L.; Michejda, C. J.; Smith, R. H., Jr. J. Med. Chem. 2003, 46, 1940-1947.
26. Ren, J.; Esnouf, R.; Hopkins, A.; Ross, C.; Jones, Y.; Stammers, D.; Stuart. D. Structure 1995, 3, 915-926.
27. Rittinger, K.; Divita, G.; Goody, R. Proc. Natl. Acad. Sci. U.S.A. 1995. 92, 8046-8049.
28. Spence, R. A.; Kati, W. M.; Anderson, K. S.; Johnson, K. A. Science 1995. 267, 988-993.
29. Spence, R. A.; Anderson, K. S.; Johnson, K. A. Biochemistry 1996, 35, 1054-1063.
30. Kensch, O.; Resile, T.; Wohrl, B. M.; Goody, R. S.; Steinhoff, H.-J. J. Mol. Biol. 2000, 301, 1029-1039.
31. Hermann, T.; Heumann, H. Eur. J. Biochem. 1996, 242, 98-103.
32. Madrid, M.; Jacobo-Molina, A.; Ding, J.; Arnold, E. Protein: Struct., Fund., Genet. 1999, 35, 332-337.
33. Madrid, M.; Lukin, J. A.; Madura, J. D.; Ding, J.; Arnold, E. Proteins: Struct., Fund., Genet. 2001, 45, 176-182.
34. Bahar, I.; Erman, B.; Jernigan, R. L.; Atilgan, A. R.; Covell, D. G. J. Mol. Biol. 1999, 285, 1023-1037.
35. Temiz, N. A.; Bahar, I. Proteins: Struct., Fund., Genet. 2002, 49, 61-70.
36. Rodriguez-Barrios, F.; Balzarini, J.; Gago, F. J. Am. Chem. Soc. 2005, 127, 7570-7578.
37. Rodriguez-Barrios, F.; Gago, F. J. Am. Chem. Soc. 2004, 126, 15386-15387.
38. Richman, D. D.; Havlir, D.; Corbeil, J.; Looney, D.; Ignacio, C.; Spector, S. A.; Sullivan, J.; Cheeseman, S.; Barringer, K.; Pauletti, D. J. Virol. 1994, 68, 1660-1666.
39. Richman, D. D. Antimicrob. Agents Chemother. 1993, 37, 1207-1213.
40. Richman, D. D. Annu. Rev. Pharmacol. Toxicol. 1993, 33, 149-164.
41. Richman, D. D. AIDS Res. Rev. 1992, 2, 237-248.
42. Richman, D. D. AIDS Res. Hum. Retroviruses 1992, 8, 1065-1071.
43. Mayers, D. L.; McCutchan, F. E.; Sanders-Buell, E. E.; Merritt, L. I.; Dilworth, S.; Fowler, A. K.; Marks, C. A.; Ruiz, N. M.; Richman, D. D.; Roberts, C. R. J. Acquired Immune Defic. Syndr. 1992, 5, 749-759.
44. Richman, D. D. Curr. Top. Microbiol. Immunol. 1992, 176, 131-142.
45. Richman, D. D. J. Enzyme Inhib. 1992, 6, 55-64.
46. Richman, D. D.; Guatelli, J. C.; Grimes, J.; Tsiatis, A.; Gingeras, T. J. Infect. Dis. 1991, 164, 1075-1081.
47. Richman, D.; Shih, C. K.; Lowy, I.; Rose, J.; Prodanovich, P.; Goff, S.; Griffin, J. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 11241-11245.
48. Mellors, J. W.; Dutschman, G. E.; Im, G. J.; Tramontano, E.; Winkler, S. R.; Cheng, Y. C. Mol. Pharmacol. 1992, 41, 446-451.
49. Mellors, J. W.; Im, G. J.; Tramontano, E.; Winkler, S. R.; Medina, D. J. Dutschman, G. E.; Bazmi, H. Z.; Piras, G.; Gonzalez, C. J.; Cheng, Y. C. Mol Pharmacol. 1993, 43, 11-16.
50. Shen, L.; Shen, J.; Luo, X.; Cheng, F.; Xu, Y.; Chen, K.; Arnold, E.; Ding J.; Jiang, H. Biophys. J. 2003, 84, 3547-3563.
51. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, I. J. P. J. Am. Chem. Soc. 1985, 107, 3902-3909.
52. Akalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. J. Comput. Chem. 2000 2l, 132-146.
53. Wang, J.; Morin, P.; Wang, W.; Kollman, P. A. J. Am. Chem. Soc. 2001 123, 5221-5230.
54. Case, D. A.; et al. AMBER7; University of Califonia: San Francisco, 2002
55. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; III. T. E. C. Debolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. A. Comput. Phys. Commun. 1995, 91, 1-41.
56. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
57. Wang, J.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074.
58. Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
59. Wang, W.; Kollman, P. A. J. Mol. Biol. 2000, 303, 567-582.
60. Kollman, P. A.; Massova, I.; Reyes, C.;Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., III. Acc. Chem. Res. 2000, 33, 889-897.
61. Schulze, B. G.; Evanseck, J. D. J. Am. Chem. Soc. 1999, 121, 6444-6454.
62. Baisera, M. A.; Wriggers, W.; Oono, Y.; Schulten, K. J. Phys. Chem. 1996, 100, 2567-2572.
63. Saarela, J. T. A.; Tuppurainen, K.; Perakyla, M.; Santa, H.; Laatikainen, R. Biophys. Chem. 2002, 95, 49-57.
64. Kitao, A.; Go, N. Curr. Opin. Struct. Biol. 1999, 9, 164-169.
65. Nolde, S. B.; Arseniev, A. S.; Orekhov, V. Y.; Billeter, M. Proteins: Struct., Fund., Genet. 2002, 46, 250-258.
66. Tournier, A. L.; Smith, J. C. Phys. Rev. Lett. 2003, 14, 208106/208101-208106/208104.
67. Caves, L. S. D.; Evanseck, J. D.; Karplus, M. Protein Sci. 1998, 7, 649-666.
68. Prompers, J. J.; Bruschweiler, R. Proteins: Struct., Fund., Genet. 2002, 46, 177-189.
69. Gower, J. C. Biometrics 1967, 23, 623-637.
70. Gower, J. C. BiometriK 1966, 53, 325-338.
71. Manly, B. F. J. Multivariale Statistical Methods: A Primer. 3rd ed.; Chapman & Hall/CRC: Boca Raton, FL 33431 USA, 2004.
72. Troyer, J. M.; Cohen, F. E. Proteins: Struct., Fund., Genet. 1995, 23. 97-110.
73. Johnson, R. A.; Wichern, D. W. Applied Multivariate Statistical Analysis. 5th ed.; Prentice Hall: Upper Saddle River, New Jersey, 2002.
74. Matlab. version 6.5 ed.: Natick, Massachusetts, 2003.
75. Smith, M. B. K.; Lamb, M. L.; Tirado-Rivcs, J.; Jorgensen, W. L.; Michejda, C. J.; Ruby, S. K.; Smith, R. H., Jr. Protein Eng. 2000, 13, 413-421.
76. Rizzo, R. C.; Wang, D.-P.; Tirado-Rives, J.; Jorgensen, W. L. J. Am. Chem. Soc. 2000, 122, 12898-12900.
77. Sarafianos, S. G.; Das, K.; Ding, J.; Boyer, P. L.; Hughes, S. H.; Arnold, E. Chem. Biol. 1999, 6, 137-146.