Protein-ligand NOE matching: A high-throughput method for binding pose evaluation that does not require protein NMR resonance assignments

Journal of the American Chemical Society

Volumn 128, Issue 22, 2006, Pages 7252-7263

  Constantine, Keith L ^a   Davis, Malcolm E ^a   Metzler, William J ^a   Mueller, Luciano ^a   Claus, Brian L ^a  

^a BRISTOL MYERS SQUIBB   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL ENGINEERING; DATA ACQUISITION; FATTY ACIDS; MOLECULAR STRUCTURE; MUSCLE; NUCLEAR MAGNETIC RESONANCE;

COMPUTATIONAL DOCKING; FORTUITOUS DISTRIBUTION; MUSCLE FATTY ACID-BINDING PROTEIN (MFABP); NUCLEAR OVERHAUSER EFFECTS (NOE); THREE-DIMENSIONAL (3D) STRUCTURE;

PROTEINS;

FATTY ACID BINDING PROTEIN; LIGAND; LIPID BINDING PROTEIN; LYMPHOCYTE FUNCTION ASSOCIATED ANTIGEN 1; PROTEIN;

ACCURACY; ARTICLE; BINDING SITE; CARBON NUCLEAR MAGNETIC RESONANCE; HIGH THROUGHPUT SCREENING; LIGAND BINDING; MATHEMATICAL MODEL; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CARBON ISOTOPES; FATTY ACID-BINDING PROTEINS; LIGANDS; LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN-1; MODELS, CHEMICAL; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; PROTEINS;

EID: 33744913530     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja060356w     Document Type: Article

References (67)

1. Shuker, S. B.; Hajduk, P. J.; Meadows, R. P.; Fesik, S. W. Science 1996, 274, 1531-1534.
2. Coles, M.; Heller, M.; Kessler, H. Drug Discovery Today 2003, 8, 803-810.
3. Pellecchia, M.; Sem, D. S.; Wüthrich, K. Nat. Rev. Drug Discovery 2002, 11, 211-219.
4. Stockman, B. J.; Dalvit, C. Prog. NMR Spectrosc. 2002, 41, 187-231.
5. Roberts, G. C. K. Drug Discovery Todav 2000, 5, 230-240.
6. Homans, S. W. Angew. Chem., Int. Ed. 2004, 43, 290-300.
7. Ferentz, A. E.; Wagner, G. Q. Rev. Biophys. 2000, 33, 29-65.
8. Riek, R.; Pervushin, K.; Wüthrich, K. Trends Biochem. Sci. 2000, 25, 462-468.
9. Tugarinov, V.; Muhandiram, R.; Ayed, A.; Kay, L. E. J. Am. Chem. Soc. 2002, 124, 10025-10035.
10. Clore, G. M.; Schwieters, C. D. Curr. Opin. Struct. Biol. 2002, 12, 146-153.
11. Güntert, P. Prog. NMR Spectrosc. 2003, 43, 105-125.
12. Gronwald, W.; Kalbitzer, H. R. Prog. NMR Spectrosc. 2004, 44, 33-96.
13. Medek, A.; Olejniczak, E. T.; Meadows, R. P.; Fesik, S. W. J. Biomol. NMR 2000, 18, 229-238.
14. Hillisch, A.; Pineda, L. F.; Hilgenfeld, R. Drug Discovery Today 2004, 9, 659-669.
15. Clore, G. M.; Gronenborn, A. M. J. Magn. Reson. 1982, 48, 402-418.
16. Clore, G. M.; Gronenborn, A. M. J. Magn. Reson. 1983, 53, 423-442.
17. Campbell, A. P.; Sykes, B. D. Annu. Rev. Biophys. Biomol. Struct. 1993, 22, 99-122.
18. Ni, F.; Scheraga, H. A. Acc. Chem. Res. 1994, 27, 257-264.
19. Constantine, K. L. Biophys. J. 2001, 8l, 1275-1284.
20. Mayer, M.; Meyer, B. Angew. Chem., Int. Ed. 1999, 38, 1784-1788.
21. Hajduk, P. J.; Mack, J. C.; Olejniczak, E. T.; Park, C.; Dandliker, P. J.; Beutel, B. A. J. Am Chem. Soc. 2004, 126, 2390-2398.
22. Wang, B.; Raha, K.; Merz, K. M., Jr. J. Am. Chem. Soc. 2004, 126, 11430-11432.
23. Farmer, B. T., II; Constantine, K. L.; Goldfarb, V.; Friedrichs, M. S.; Wittekind, M.; Yanchunas, J., Jr.; Robertson, J. G.; Mueller, L. Nat. Struct. Biol. 1996, 3, 995-997.
24. Medek, A.; Hajduk, P. J.; Mack, J.; Fesik, S. W. J. Am. Chem. Soc. 2000, 122, 1241-1242.
25. McCoy, M. A.; Wyss, D. F. J. Biomol. NMR 2000, 18, 189-198.
26. Schieborr, U.; Vogtherr, M.; Elshorst, B.; Betz, M.; Grimme, S.; Pescatore, B.; Langer, T.; Saxena, K.; Schwalbe, H. ChemBioChem 2005, 6, 1891-1898.
27. Pellecchia, M.; Meininger, D.; Dong, Q.; Chang, E.; Jack, R.; Sem, D. S. J. Biomol. NMR 2002, 22, 165-173.
28. Bertini, I.; Fragai, M.; Giachetti, A.; Luchinat, C.; Maletta, M.; Parigi, G.; Yeo, K. J. J. Med. Chem. 2005, 48, 7544-7559.
29. Breeze, A. L. Prog. NMR Spectrosc. 2000, 36, 323-372.
30. Petros, A. M.; Kawai, M.; Luly, J. R.; Fesik, S. W. FEBS Lett. 1992, 308, 309-314.
31. Seavy, B.; Farr, E.; Westler, W.; Markley, J. J. Biomol NMR 1991, 1, 217-236.
32. Potin, D.; et al. Bioorg. Med. Chem. Lett. 2005, 15, 1161-1164.
33. Ewing, T. J.; Makino, S.; Skillman, A. G.; Kuntz, I. D. J. Comput.-Aided Mol. Des. 2000, 15, 411-428.
34. Nilges, M.; Gronenborn, A. M.; Brünger, A. T.; Clore, G. M. Protein Eng. 1988, 2, 27-38.
35. Sheriff, S. Unpublished results.
36. Kallen, J.; Weizenbach, K.; Ramage, P.; Geyl, D.; Kriwacki, R.; Legge, G.; Cottens, S.; Weitz-Schmidt, G.; Hommel, U. J. Mol. Biol. 1999, 292, 1-9.
37. Cavanaugh, J.; Fairbrother, W. J.; Palmer, A. G., III; Skelton, N. J. Protein NMR Spectroscopy: Principles and Practice: Academic Press: New York, 1996; pp 235-236.
38. Constantine, K. L.; Friedrichs, M. S.; Detlefson, D.; Nishio, M.; Tsunakawa, M.; Furumai, T.; Ohkuma, H.; Oki, T.; Hill, S.; Bruccoleri, R. E.; Lin, P.-F.; Mueller, L. J. Biomol. NMR 1995, 5, 271-286.
39. Fletcher, C. M.; Jones, D. N. M.; Diamond, R.; Neuhaus, D. J. Biomol. NMR 1996, 8, 292-310.
40. Osapay, K.; Case, D. A. J. Am. Chem. Soc. 1991, 113, 9436-9444.
41. Sitkoff, D.; Case, D. A. J. Am. Chem. Soc. 1997, 119, 12262-12273.
42. Iwadate, M.; Asakura, T.; Williamson, M. P. J. Biomol. NMR 1999, 13, 199-211.
43. Xu, X. P.; Case, D. A. J. Biomol. NMR 2001, 21, 321-333.
44. Wang, B.; Brothers, E. N.; Vaart, A. v. d.; Merz, K. M., Jr. J. Chem. Phys. 2004, 120, 11392-11400.
45. Papadimitriou, C. H.; Steiglitz, K. Combinatorial Optimization: Algorithms and Complexity; Dover Publications: Mineola, NY, 1982; pp 247-255.
46. Xu, Y.; Xu, D.; Kim, D.; Olman, V.; Razumovskaya, J.; Jiang, T. Comput. Sci. Eng. 2002, 4, 50-60.
47. Hus, J.-C.; Prompers, J. J.; Brüschweiler, R. J. Magn. Reson. 2002, 157, 119-123.
48. Langemeade, C.; Donald, B. R. J. Biomol. NMR 2004, 29, 111-138.
49. Bartels, C.; Güentert, P.; Billeter, M.; Wüthrich, K. J. Comput. Chem. 1997, 18, 139-149.
50. Meiler, J.; Baker, D. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 15404-15409.
51. Neuhaus, D.; Williamson, M. P. The Nuclear Overhauser Effect in Structural and Conformational Analysis; VCH Publishers: New York, 1989; p 109.
52. Jacobson, B. L. Unpublished results.
53. Constantine, K. L.; Friedrichs, M. S.; Wittekind, M.; Jamil, H.; Chu, C.-H.; Parker, R. A.; Goldfarb, V.; Mueller, L.; Farmer, B. T., II. Biochemistry 1998, 37, 7965-7980.
54. Hodsdon, M. E.; Cistola, D. P. Biochemistry 1997, 36, 2278-2290.
55. Last-Barney, K.; Davidson, W.; Cardozo, M.; Frye, L. L.; Grygon, C. A.; Hopkins, J. L.; Jeanfavre, D. D.; Pav, S.; Qian, C.; Stevenson, J. M.; Tong, L.; Zindell, R.; Kelly, T. A. J. Am. Chem. Soc. 2001, 123, 5643-5650.
56. Brünger, A. T. X-PLOR Version 3.1 Manual; Yale University Press: New Haven, CT 1992.
57. Legge, G. B.; Kriwacki, R. W.; Chung, J.; Hommel, U.; Ramage, P.; Case, D. A.; Dyson, H. J.; Wright, P. E. J. Mol. Biol. 2000, 295, 1251-1264.
58. Han, J.; Kamber, M. Data Mining: Concepts and Techniques; Morgan Kaufmann: New York, 2001; pp 335-393.
59. Hyvönen, M. T.; Hiltunen, Y.; El-Deredy, W.; Ojala, T.; Vaara, J.; Kovanen, P. T.; Ala-Korpela, M. J. Am. Chem. Soc. 2001, 123, 810-816.
60. Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Nat. Rev. Drug Discovery 2004, 3, 935-949.
61. Dobridumov, A.; Gronenborn, A. M. Proteins: Struct., Funct. Genet. 2003, 52, 18-32.
62. Lugovskoy, A. A.; Degterev, A. I.; Fahmy, A. F.; Zhou, P.; Gross, J. D.; Yuan, J.; Wagner, G. J. Am. Chem. Soc. 2002, 124, 1234-1240.
63. Matthews, S. J.; Leatherbarrow, R. J. J. Biomol. NMR 1993, 3, 597-600.
64. Lane, A. N.; Sengodagounder, A. J. Magn. Reson. 2005, 173, 339-343.
65. Grishaev. A.; Llinás, M. J. Biomol. NMR 2004, 28, 1-10.
66. Rieping, W.; Habeck, M.; Nilges, M. Science 2005, 309, 303-306.
67. Kay, L. E. J. Magn. Reson. 2005, 173, 193-207.