Exploring experimental sources of multiple protein conformations in structure-based drug design

Journal of the American Chemical Society

Volumn 129, Issue 26, 2007, Pages 8225-8235

  Damm, Kelly L ^a   Carlson, Heather A ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG DESIGN; IMMUNODEFICIENCY; PHARMACOPHORE MODELS; STRUCTURE BASED DESIGN;

CONFORMATIONS; CRYSTAL STRUCTURE; DRUG PRODUCTS; IMMUNOLOGY; LIGANDS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

PROTEINS;

PROTEINASE; SOLVENT;

ACCURACY; ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; DRUG DESIGN; LIGAND BINDING; MODEL; NUCLEAR MAGNETIC RESONANCE; PHARMACOPHORE; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

ANTI-HIV AGENTS; DRUG DESIGN; HIV PROTEASE; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 34447271743     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0709728     Document Type: Article

References (76)

1. Hardy, L. W.; Malikayil, A. Curr. Drug Discovery 2003, December, 15-20.
2. Jorgensen, W. L. Science 2004, 303, 1813-1818.
3. Carlson, H. A.; McCammon, J. A. Mol. Pharmacol. 2000, 57, 213-218.
4. Luque, I.; Freire, E. Proteins: Struct., Funct., Bioinf. 2000, Suppl. 4, 63-71.
5. Ma, B.; Shatsky, M.; Wolfson, H. J.; Nussinov, R. Protein Sci. 2002, 11, 184-197.
6. Carlson, H. A. Curr. Pharm. Des. 2002, 8, 1571-1578.
7. Teague, S. J. Nat. Rev. Drug Discovery 2003, 2, 527-541.
8. Teodoro, M. L.; Kavraki, L. E. Curr. Pharm. Des. 2003, 9, 1635-1648.
9. Wong, C. F.; McCammon, J. A. Annu. Rev. Pharmacol. Toxicol. 2003, 43, 31-45.
10. Jiang, F.; Kim, S. H. J. Mol. Biol. 1991, 219, 79-102.
11. Ferrari, A. M.; Wei, B. Q.; Costantino, L.; Shoichet, B. K. J. Med. Chem. 2004, 47, 5076-5084.
12. Knegtel, R. M.; Kuntz, I. D.; Oshiro, C. M. J. Mol. Biol. 1997, 266, 424-440.
13. Erickson, J. A.; Jalaie, M.; Robertson, D. H.; Lewis, R. A.; Vieth, M. J. Med. Chem. 2004, 47, 45-55.
14. Frimurer, T. M.; Peters, G. H.; Iversen, L. F.; Andersen, H. S.; Moller, N. P.; Olsen, O. H. Biophys. J. 2003, 84, 2273-2281.
15. Kallblad, P.; Dean, P. M. J. Mol. Biol. 2003, 326, 1651-1665.
16. Carlson, H. A.; Masukawa, K. M.; Rubins, K.; Bushman, F. D.; Jorgensen, W. L.; Lins, R. D.; Briggs, J. M.; McCammon, J. A. J. Med. Chem. 2000, 43, 2100-2114.
17. Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. J. Mol. Biol. 2001, 308, 377-395.
18. Cavasotto, C. N.; Abagyan, R. A. J. Mol. Biol. 2004, 337, 209-225.
19. Fernandes, M. X.; Kairys, V.; Gilson, M. K. J. Chem. Inf. Comput. Sci. 2004, 44, 1961-1970.
20. Meagher, K. L.; Carlson, H. A. J. Am. Chem. Soc. 2004, 126, 13276-13281.
21. Meagher, K. L.; Lerner, M. G.; Carlson, H. A. J. Med. Chem. 2006, 49, 3478-3484.
22. Philippopoulos, M.; Lim, C. Proteins: Struct., Funct., Bioinf 1999, 36, 87-110.
23. Hornak, V.; Okur, A.; Rizzo, R. C.; Simmerling, C. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 915-920.
24. Toth, G.; Borics, A. J. Mol. Graphics Modell. 2006, 24, 465-474.
25. Garbuzynskiy, S. O.; Melnik, B. S.; Lobanov, M. Y.; Finkelstein, A. V.; Galzitskaya, O. V. Proteins: Struct., Funct., Bioinf. 2005, 60, 139-147.
26. Lee, M. R.; Kollman, P. A. Structure 2001, 9, 905-916.
27. Spronk, C. A. E. M.; Linge, J. P.; Hilbers, C. W.; Vuister, G. W. J. Biomol. NMR 2002, 22, 281-289.
28. Billeter, M. Q. Rev. Biophys. 1992, 25, 325-377.
29. Snyder, D. A.; Chen, Y.; Denissova, N. G.; Acton, T.; Aramini, J. M.; Ciano, M.; Karlin, R.; Liu, J.; Manor, P.; Rajan, P. A.; Rossi, P.; Swapna, G. V.; Xiao, R.; Rost, B.; Hunt, J.; Montelione, G. T. J. Am. Chem. Soc. 2005, 127, 16505-16511.
30. Yee, A. A.; Savchenko, A.; Ignachenko, A.; Lukin, J.; Xu, X.; Skarina, T.; Evdokimova, E.; Liu, C. S.; Semesi, A.; Guido, V.; Edwards, A. M.; Arrowsmith, C. H. J. Am. Chem. Soc. 2005, 127, 16512-16517.
31. Thomas, M. P.; McInnes, C.; Fischer, P. M. J. Med. Chem. 2006, 49, 92-104.
32. Subramanian, J.; Sharma, S.; B-Rao, C. J. Med. Chem. 2006, 49, 5434-5441.
33. Davis, A. M.; Teague, S. J.; Kleywegt, G. J. Angew. Chem., Int. Ed. 2003, 42, 2718-2736.
34. Barril, X.; Morley, S. D. J. Med. Chem. 2005, 48, 4432-4443.
35. Spronk, C. A. E. M.; Nabuurs, S. B.; Bonvin, A. M.; Krieger, E.; Vuister, G. W.; Vriend, G. J. Biomol. NMR 2003, 25, 225-234.
36. Huang, S-Y.; Zou, X. Protein Sci. 2007, 16, 43-51.
37. Fesik, S. W. J. Biomol. NMR 1993, 3, 261-269.
38. McCoy, M. A.; Wyss, D. F. J. Am. Chem. Soc. 2002, 124, 2104-2105.
39. Zabell, A. P. R.; Post, C. B. Proteins: Struct., Funct., Bioinf. 2002, 46, 295-307.
40. Hicks, R. P. Curr. Med. Chem. 2001, 8, 627-640.
41. Hajduk, P. J. Mol. Interventions 2006, 6, 266-272.
42. Zartler, E. R.; Shapiro, M. J. Curr. Pharm. Des. 2006, 12, 3963-3972.
43. Babine, R. E.; Bender, S. L. Chem. Rev. 1997, 97, 1359-1472.
44. Ala, P. J.; Huston, E. E.; Klabe, R. M.; Jadhav, P. K.; Lam, P. Y.; Chang, C. H. Biochemistry 1998, 37, 15042-15049.
45. Wlodawer, A.; Gustchina, A. Biochim. Biophys. Acta 2000, 1477, 16-34.
46. Eder, J.; Hommel, U.; Cumin, F.; Martoglio, B.; Gerhartz, B. Curr. Pharm. Des. 2007, 13, 271-285.
47. Yamazaki, T.; Hinck, A. P.; Wang, Y. X.; Nicholson, L. K.; Torchia, D. A.; Wingfield, P.; Stahl, S. J.; Kaufman, J. D.; Chang, C. H.; Domaille, P. J.; Lam, P. Y. Protein Sci. 1996, 5, 495-506.
48. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235-242.
49. Hu, L.; Benson, M. L.; Smith, R. D.; Lerner, M. G.; Carlson, H. A. Proteins: Struct., Funct., Bioinf. 2006, 60, 333-340.
50. Rutenber, E.; Fauman, E. B.; Keenan, R. J.; Fong, S.; Furth, P. S.; Ortiz de Montellano, P. R.; Meng, E.; Kuntz, I. D.; DeCamp, D. L.; Salto, R.; Rose, J. R.; Craik, C. S.; Stroud, R. M. J. Biol. Chem. 1993, 238, 15343-15346.
51. Backbro, K.; Lowgren, S.; Osterlund, K.; Atepo, J.; Unge, T.; Hulten, J.; Bonham, N. M.; Schaal, W.; Karlen, A.; Hallberg, A. J. Med. Chem. 1997, 40, 898-902.
52. Hodge, C. N.; et al. Chem. Biol. 1996, 3, 301-314.
53. Lam, P. Y.; Jadhav, P. K.; Eyermann, C. J.; Hodge, C. N.; Ru, Y.; Bacheler, L. T.; Meek, J. L.; Otto, M. J.; Rayner, M. M.; Wong, Y. N.; Chang, C-H.; Weber, P. C.; Jackson, D. A.; Sharpe, T. R.; Erickson-Viitanen, S. Science 1994, 263, 380-384.
54. Sham, H. L.; et al. J. Med. Chem. 1996, 39, 392-397.
55. Jadhav, P. K.; Ala, P.; Woerner, F. J.; Chang, C. H.; Garber, S. S.; Anton, E. D.; Bacheler, L. T. J. Med. Chem. 1997, 40, 181-191.
56. Lam, P. Y.; et al. J. Med. Chem. 1996, 39, 3514-3525.
57. Huang, P. P.; Randolph, J. T.; Klein, L. L.; Vasavanonda, S.; Dekhtyar, T.; Stoll, V. S.; Kempf, D. J. Bioorg. Med. Chem. Lett. 2004, 14, 4075-4078.
58. Lovell, S. C.; Davis, I. W.; Arendall, W. B., III; de Bakker, P. I.; Word, J. M.; Prisant, M. G.; Richardson, J. S.; Richardson, D. C. Proteins: Struct., Funct., Bioinf. 2003, 50, 437-450.
59. Case, D. A.; et al. AMBER 6; University of California San Francisco: San Francisco, CA, 1996.
60. Jorgensen, W. L. BOSS, version 4.2; Yale University: New Haven, CT, 2000.
61. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236.
62. Damm, K. L.; Carlson, H. A. Biophys. J. 2006, 90, 4558-4573.
63. Molecular Operating Environment; Chemical Computing Group Inc.: Montreal, Canada, 2001.
64. Comprehensive Medicinal Chemistry; Hansch, C., Sammes, P. G., Taylor, J. B., Eds.; Pergamon Press: Oxford, 1990; Vols. 1-6.
65. Comprehensive Medicinal Chemistry Database; MDL Information Systems, Inc.: San Leandro, CA, 2003.
66. Bowman, A. L.; Lerner, M. G.; Carlson, H. A. J. Am. Chem. Soc. 2007, 129, 3634-3640.
67. Erickson, J. W. Perspect. Drug Discovery Des. 1993, 1, 109-128.
68. Wlodawer, A.; Erickson, J. W. Annu. Rev. Biochem. 1993, 62, 543-585.
69. Zoete, V.; Michielin, O.; Karplus, M. J. Mol. Biol. 2002, 315, 21-52.
70. Martin, P.; Vickrey, J. F.; Proteasa, G.; Jimenez, Y. L.; Wawrzak, Z.; Winters, M. A.; Merigan, T. C.; Kovari, L. C. Structure 2005, 13, 1887-1895.
71. Layten, M.; Hornak, V.; Simmerling, C. J. Am. Chem. Soc. 2006, 128, 13360-13361.
72. Ferrara, P.; Gohlke, H.; Price, D. J.; Klebe, G.; Brooks, C. L., III. J. Med. Chem. 2004, 47, 3032-3047.
73. Perola, E.; Walters, W. P.; Charifson, P. S. Proteins: Struct., Funct., Bioinf. 2004, 56, 235-249.
74. Joseph-McCarthy, D.; Alvarez, J. C. Proteins: Struct., Funct., Bioinf. 2003, 51, 189-202.
75. OMEGA; OpenEye Science Software: Santa Fe, NM, 2001.
76. DeLano, W. L. The PyMOL Molecular Graphics System; DeLano Scientific LLC: San Carlos, CA, 2002; http://www.pymol.org.