The molecular basis of resilience to the effect of the Lys103Asn mutation in non-nucleoside HIV-1 reverse transcriptase inhibitors studied by targeted molecular dynamics simulations

Journal of the American Chemical Society

Volumn 127, Issue 20, 2005, Pages 7570-7578

  Rodríguez Barrios, Fátima ^a   Balzarini, Jan ^b   Gago, Federico ^a  

^a UNIVERSITY OF ALCALÁ   (Spain)

^b REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; COMPUTER SIMULATION; CONFORMATIONS; DRUG PRODUCTS; ENZYME INHIBITION; ENZYMES; HYDROGEN BONDS; MOLECULAR DYNAMICS; VIRUSES;

BINDING POCKETS; DRUG DESIGN; SIDE CHAINS;

MUTAGENESIS;

ASPARAGINE; EFAVIRENZ; ETRAVIRINE; LYSINE; NEVIRAPINE; RNA DIRECTED DNA POLYMERASE; RNA DIRECTED DNA POLYMERASE INHIBITOR; TYROSINE;

AMINO ACID SUBSTITUTION; ARTICLE; CALCULATION; CRYSTAL STRUCTURE; DRUG BINDING SITE; DRUG PROTEIN BINDING; DRUG STRUCTURE; ENERGY; ENZYME CONFORMATION; GENE MUTATION; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROGEN BOND; MOLECULAR DYNAMICS; NONHUMAN; SIMULATION; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

ANTI-HIV AGENTS; BINDING SITES; COMPUTER SIMULATION; HIV-1 REVERSE TRANSCRIPTASE; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; NEVIRAPINE; OXAZINES; PYRIDAZINES; REVERSE TRANSCRIPTASE INHIBITORS; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 19744364217     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja042289g     Document Type: Article

References (56)

1. Silvestri, R.; De Martino, G.; La Regina, G.; Artico, M.; Massa, S.; Vargiu, L.; Mura, M.; Loi, A. G.; Marceddu, T.; La Colla, P. J. Med. Chem. 2003, 46, 2482-2493.
2. Schinazi, R. F.; Larder, B.; Mellors, J. W. Int. Antivir. News 2000, 8, 65-92.
3. Stanford HIV sequence database 2002 (http://hivdb.Stanford.edu).
4. Hsiou, Y.; Ding, J.; Das, K.; Clark, A. D., Jr.; Boyer, P. L.; Lewi, P.; Janssen, P. A. J.; Kleim, J. P.; Rösner, M.; Hughes, S. H.; Arnold, E. J. Mol. Biol. 2001, 309, 437-445.
5. Gago, F.; et al. J. Med. Chem. 2001, 44, 1853-1865.
6. Ren, J.; Milton, J.; Weaver, K. L.; Short, S. A.; Stuart, D. I.; Stammers, D. K. Struct. Fold. Des. 2000, 8, 1089-1094.
7. Ajay; Murcko, M. A. J. Med. Chem. 1995, 38, 4953-4967.
8. Rodríguez-Barrios, F.; Gago, F. J. Am. Chem. Soc. 2004, 126, 2718-2719.
9. Esnouf, R.; Ren, J.; Ross, C.; Jones, Y.; Stammers, D.; Stuart, D. Nat. Struct. Biol. 1995, 2, 303-308.
10. Lindberg, J.; Sigurosson, S.; Löwgren, S.; Andersson, H. O.; Sahlberg, C.; Noréen, R.; Fridborg, K.; Zhang, H.; Unge, T. Eur. J. Biochem. 2002, 269, 1670-1677.
11. Maga, G.; Amacker, M.; Ruel, N.; Hubscher, U.; Spadari, S. J. Mol. Biol. 1997, 274, 738-747.
12. Rodríguez-Barrios, F.; Gago, F. J. Am. Chem. Soc. 2004, 126, 15386-15387.
13. Powels, R. Curr. Opin. Pharmacol. 2004, 4, 437-446.
14. Fujiwara, T.; Sato, A.; el-Farrash, M.; Miki, S.; Abe, K.; Isaka, Y.; Kodama, M.; Wu, Y.; Chen, L. B.; Harada, H.; Sugimoto, H.; Hatanaka, M.; Hinuma, Y. Antimicrob. Agents Chemother. 1998, 42, 1340-1345.
15. Arnold, E.; et al. J. Med. Chem. 2004, 47, 2550-2560.
16. Erickson-Viitanen, S. K.; et al. J. Med. Chem. 2000, 43, 2019-2030.
17. (a) D'Aquila, R. T.; Summers, W. C. J. Acquired Immune Defic. Syndr. 1989, 2, 579-587.
18. (b) Pelemans, H.; Esnouf, R.; Jonckheere, H.; DeClercq, E.; Balzarini, J. J. Biol. Chem. 1998, 273, 34234-34239.
19. Jonekheere, H.; Taymans, J. M.; Balzarini, J.; Velázquez, S.; Camarasa, M.-J.; Desmyter, J.; De Clercq, E.; Anné, J. J. Biol. Chem. 1994, 269, 25255-25258.
20. Pople, J. A.; et al. Gaussian 98, revision A.11.2; Gaussian, Inc.: Pittsburgh, PA, 2001.
21. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269-10280.
22. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
23. Kmunicek, J.; Luengo, S.; Gago, F.; Ortiz, A. R.; Wade, R. C.; Damborsky, J. Biochemistry 2001, 40, 8905-8917.
24. de la Fuente, J. A.; Manzanaro, S.; G. de Quesada, T.; Reymundo, I.; Luengo, S. M.; Gago, F. J. Med. Chem. 2003, 46, 5208-5221.
25. AutoDock: Automated docking of flexible ligands to receptors, Version 3.0, 1999; Morris, G. M.; Goodsell, D. S.; Huey, R.; Hart, W. E.; Halliday, S.; Belew, R.; Olson, A. J. The Scripps Research Institute, La Jolla, CA 92037-1000.
26. Hsiou, Y.; Ding, J.; Das, K.; Clark, A. D., Jr.; Hughes, S. H.; Arnold, E. Structure 1996, 4, 853-860.
27. Goodford, P. J. Med. Chem. 1985, 28, 849-857.
28. Ortiz, A. R.; Pisabarro, M. T.; Gago, F. J. Med. Chem. 1993, 36, 1866-1879.
29. Stammers, D.; et al. Nat. Struct. Biol. 1995, 2, 293-302.
30. Ma, J.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 11905-11910.
31. Ma, J. P.; Sigler, P. B.; Xu, Z. H.; Karplus, M. J. Mol. Biol. 2000, 302, 303-313.
32. http://amber.scripps.edu/doc8/amber8.pdf.
33. De Clercq, E. J. Clin. Virol. 2004, 30, 115-133.
34. Ren, J.; Nichols, C.; Bird, L. E.; Fujiwara, T.; Sugimoto, H.; Stuart, D. I.; Stammers, D. K. J. Biol. Chem. 2000, 275, 14316-14320.
35. Arnold, E.; et al. Structure 1995, 3, 365-379.
36. Shen, L.; Shen, J.; Luo, X.; Cheng, F.; Xu, Y.; Chen, K.; Arnold, E.; Ding, J.; Jiang, H. Biophys. J. 2003, 84, 3547-3563.
37. Balzarini, J.; Kleim, J. P.; Riess, G.; Camarasa, M. J.; De Clercq, E.; Karlsson, A. Biochem. Biophys. Res. Commun. 1994, 201, 1305-1312.
38. Camarasa, M. J.; San-Félix, A.; Velásquez, S.; Pérez-Pérez, M. J.; Gago, F.; Balzarini, J. Curr. Top. Med. Chem. 2004, 4, 945-963.
39. Esnouf, R. M.; Ren, J.; Hopkins, A. L.; Ross, C. K.; Jones, E. Y.; Stammers, D. K.; Stuart, D. I. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 3984-3989.
40. Sluis-Cremer, N.; Dmitrienko, G. I.; Balzarini, J.; Camarasa, M. J.; Parniak, M. A. Biochemistry 2000, 39, 1427-1433.
41. Rodgers, D. W.; Gamblin, S. J.; Harris, B. A.; Ray, S.; Culp, J. S.; Hellmig, B.; Woolf, D. J.; Debouck, C.; Harrison, S. C. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 1222-1226.
42. (a) Arnold, E.; et al. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 6320-6324.
43. (b) Huang, H.; Chopra, R.; Verdine, G. L.; Harrison, S. C. Science 1998, 282, 1669-1675.
44. Ren, J.; Stammers, D. K. Trends Pharmacol. Sci. 2005, 26, 4-7.
45. Sarafianos, S. G.; Das, K.; Hughes, S. H.; Arnold, E. Curr. Opin. Struct. Biol. 2004, 14, 716-730.
46. Sluis-Cremer, N.; Temiz, N. A.; Bahar, I. Curr. HIV Res. 2004, 2, 323-332.
47. Hendlich, M.; Bergner, A.; Günther, J.; Klebe, G. J. Mol. Biol. 2003, 326, 607-620.
48. Schinazi, R. F.; Larder, B. A.; Mellors, J. W. Int. Antivir. News 1997, 5, 129-135.
49. Ren, J.; Nichols, C. E.; Chamberlain, P. P.; Weaver, K. L.; Short, S. A.; Stammers, D. K. J. Mol. Biol. 2004, 336, 569-578.
50. (a) Bahar, I.; Erman, B.; Jernigan, R. L.; Atilgan, A. R.; Covell, D. J. Mol. Biol. 1999, 285, 1023-1037.
51. (b) Temiz, N. A.; Bahar, I. Proteins 2002, 49, 61-70.
52. (a) Madrid, M.; Jacobo-Molina, A.; Ding, J.; Arnold, E. Proteins 1999, 35, 332-337.
53. (b) Madrid, M.; Lukin, J. A.; Madura, J. D.; Ding, J.; Arnold, E. Proteins 2001, 45, 176-182.
54. Janssen, P. A. J.; et al. J. Med. Chem. 2005, 48, 1901-1909.
55. Stuart, D. I.; et al. J. Med. Chem. 1996, 39, 1589-1600.
56. Pata, J. D.; Stirtan, W. G.; Goldstein, S. W.; Steitz, T. A. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 10548-10553.