Protein flexibility and species specificity in structure-based drug discovery: Dihydrofolate reductase as a test system

Journal of the American Chemical Society

Volumn 129, Issue 12, 2007, Pages 3634-3640

  Bowman, Anna L ^a   Lerner, Michael G ^a   Carlson, Heather A ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG PRODUCTS; ENZYME INHIBITION; ENZYME KINETICS; FUNGI; X RAY CRYSTALLOGRAPHY;

DIHYDROFOLATE REDUCTASE (DHFR); MULTIPLE PROTEIN STRUCTURE (MPS); PNEUMOCYSTIS CARINII; PROTEIN FLEXIBILITY;

PROTEIN FOLDING;

DIHYDROFOLATE REDUCTASE;

ARTICLE; CRYSTAL STRUCTURE; HUMAN; NONHUMAN; PHARMACOPHORE; PNEUMOCYSTIS CARINII; PROTEIN ANALYSIS; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

ANIMALS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; FOLIC ACID ANTAGONISTS; HUMANS; MODELS, MOLECULAR; PLIABILITY; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY; TETRAHYDROFOLATE DEHYDROGENASE;

EID: 33947662384     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja068256d     Document Type: Article

References (53)

1. Viudes, A.; Peman, J.; Canton, E.; Ubeda, P.; Lopez-Ribot, J. L.; Gobernado, M. Eur. J. Clin. Microbiol. Infect. Dis. 2002, 21, 767-774.
2. Sullivan, D. J.; Moran, G. P.; Pinjon, E.; Al-Mosaid, A.; Stokes, C.; Vaughan, C.; Coleman, D. C. FEMS Yeast Res. 2004, 4, 369-376.
3. Edwards, J. E. N. Engl. J. Med. 1991, 324, 1060-1062.
4. Morris, A.; Lundgren, J. D.; Masur, H.; Walzer, P. D.; Hanson, D. L.; Frederick, T.; Huang, L.; Beard, C. B.; Kaplan, J. E. Emerg. Infect. Dis. 2004, 10, 1713-1720.
5. Schweitzer, B. I.; Dicker, A. P.; Bertino, J. R. FASEB J. 1990, 4, 2441-2452.
6. Chan, J. H.; Hong, J. S.; Kuyper, L. F.; Baccanari, D. P.; Joyner, S. S.; Tansik, R. L.; Boytos, C. M.; Rudolph, S. K. J. Med. Chem. 1995, 38, 3608-3616.
7. Whitlow, M.; Howard, A. J.; Stewart, D.; Hardman, K. D.; Kuyper, L. F.; Baccanari, D. P.; Fling, M. E.; Tansik, R. L. J. Biol. Chem. 1997, 272, 30289-30298.
8. Gschwend, D. A.; Good, A. C.; Kuntz, I. D. J. Mol. Recognit. 1996, 9, 175-186.
9. Wong, K. F.; Selzer, T.; Benkovic, S. J.; Hammes-Schiffer, S. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6807-6812.
10. Rajagopalan, P. T. R.; Lutz, S.; Benkovic, S. J. Biochemistry 2002, 41, 12618-12628.
11. Gschwend, D. A.; Sirawaraporn, W.; Santi, D. V.; Kuntz, I. D. Proteins: Struct., Fund., Genet. 1997, 29, 59-67.
12. Baccanari, D. P.; Daluge, S.; King, R. W. Biochemistry 1982, 21, 5068-5075.
13. Delves, C. J.; Ballantine, S. P.; Tansik, R. L.; Baccanari, D. P.; Stammers, D. K. Protein Expression Purif. 1993, 4, 16-23.
14. Medina, I.; Mills, J.; Leoung, G.; Hopewell, P. C.; Lee, B.; Modin, G.; Benowitz, N.; Wofsy, C. B. N. Engl. J. Med. 1990, 323, 776-782.
15. Lee, S. A. J. Pharm. Pract. 2006, 19, 5-9.
16. Rosowsky, A.; Forsch, R. A.; Queener, S. F. J. Med. Chem. 2002, 45, 233-241.
17. Sternberg, S. Science 1994, 266, 1632-1634.
18. Carlson, H. A.; McCammon, J. A. Mol. Pharmacol. 2000, 57, 213-218.
19. Carlson, H. A.; Masukawa, K. M.; McCammon, J. A. J. Phys. Chem. A 1999, 103, 10213-10219.
20. 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.
21. Meagher, K. L.; Carlson, H. A. J. Am. Chem. Soc. 2004, 126, 13276-13281.
22. Meagher, K. L.; Lerner, M. G.; Carlson, H. A. J. Med. Chem. 2006, 49, 3478-3484.
23. 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; http://www.rcsb.org/pdb/.
24. Cody, V.; Galitsky, N.; Luft, J. R.; Pangborn, W.; Blakley, R. L.; Gangjee, A. Anti-Cancer Drug Des. 1998, 13, 307-315.
25. Cody, V.; Galitsky, N.; Luft, J. R.; Pangborn, W.; Rosowsky, A.; Blakley, R. L. Biochemistry 1997, 36, 13897-13903.
26. Cody, V.; Luft, J. R.; Pangborn, W.; Gangjee, A. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2003, 59, 1603-1609.
27. Cody, V.; Luft, J. R.; Pangborn, W.; Gangjee, A.; Queener, S. F. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 646-655.
28. Cody, V.; Luft, J. R.; Pangborn, W. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2005, 61, 147-155.
29. Klon, A. E.; Heroux, A.; Ross, L. J.; Pathak, V.; Johnson, C. A.; Piper, J. R.; Borhani, D. W. J. Mol. Biol. 2002, 320, 677-693.
30. Whitlow, M.; Howard, A. J.; Stewart, D.; Hardman, K. D.; Chan, J. H.; Baccanari, D. P.; Tansik, R. L.; Hong, J. S.; Kuyper, L. F. J. Med. Chem. 2001, 44, 2928-2932.
31. Cody, V.; Galitsky, N.; Luft, J. R.; Pangborn, W.; Gangjee, A.; Devraj, R.; Queener, S. F.; Blakley, R. L. Acta Crystallogr., Sect. D: Biol. Crystallogr. 1997, 53, 638-649.
32. Cody, V.; Galitsky, N.; Rak, D.; Luft, J. R.; Pangborn, W.; Queener, S. F. Biochemistry 1999, 38, 4303-4312.
33. Cody, V.; Galitsky, N.; Luft, J. R.; Pangborn, W.; Queener, S. F.; Gangjee, A. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2002, 58, 1393-1399.
34. Cody, V.; Luft, J. R.; Pangborn, W.; Gangjee, A.; Queener, S. F. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 646-655.
35. Cody, V.; Chan, D.; Galitsky, N.; Rak, D.; Luft, J. R.; Pangborn, W.; Queener, S. F.; Laughton, C. A.; Stevens, M. F. Biochemistry 2000, 39, 3556-3564.
36. Champness, J. N.; Achari, A.; Ballantine, S. P.; Bryant, P. K.; Delves, C. J.; Stammers, D. K. Structure 1994, 2, 915-924.
37. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E., III; Debolt, S.; Ferguson, D. M.; Seibel, G. L.; Kollman, P. A. Comput. Phys. Commun. 1995, 91, 1-41.
38. Case, D. A.; et al. AMBER 6; University of California, San Francisco, 1999.
39. Holmberg, N.; Ryde, U.; Bulow, L. Protein Eng. 1999, 12, 851-856.
40. Radkiewicz, J. L.; Brooks, C. L., III. J. Am. Chem. Soc. 2000, 122, 225-231.
41. Lerner, M. G.; Meagher, K. L.; Carlson, H. A. Unpublished results.
42. Jorgensen, W. L. BOSS, Version 4.2; Yale University, New Haven, CT, 2000.
43. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236.
44. Damm, K. L.; Carlson, H. A. Biophys. J. 2006, 90, 4558-4573.
45. MOE; Chemical Computing Group: Montreal, Canada.
46. MDDR Drug Data Report; MDL Information Systems Inc.: San Leandro, CA, 2005.
47. Sutherland, J.; O'Brien, L.; Weaver, D. J. Chem. Inf. Comput. Sci. 2003, 43, 1906-1915.
48. Comprehensive Medicinal Chemistry, MDL Information Systems Inc.: San Leandro, CA, 2005.
49. OMEGA, Version 1.8.b1; OpenEye Scientific Software, Inc.: Santa Fe, NM, 2004; www.eyesopen.com.
50. Otzen, T.; Wempe, E. G.; Kunz, B.; Bartels, R.; Lehwark-Yvetot, G.; Hansel, W.; Schaper, K.-J.; Seydel, J. K. J. Med. Chem. 2004, 47, 240-253.
51. Bolin, J. T.; Filman, D. J.; Matthews, D. A.; Hamlin, R. C.; Kraut, J. J. Biol. Chem. 1982, 257, 13650-13662.
52. Joseph-McCarthy, D.; Alvarez, J. C. Proteins: Struct., Funct., Genet. 2003, 51, 189-202.
53. Joseph-McCarthy, D.; Thomas, B. E.; Belmarsh, M.; Moustakas, D.; Alvarez, J. C. Proteins: Struct., Funct., Genet. 2003, 51, 172-188.