Molecular electrostatic potential analysis for enzymatic substrates, competitive inhibitors, and transition-state inhibitors

Journal of the American Chemical Society

Volumn 118, Issue 37, 1996, Pages 8825-8836

  Bagdassarian, Carey K ^a   Schramm, Vern L ^a   Schwartz, Steven D ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE; ADENOSINE DEAMINASE; ADENOSINE MONOPHOSPHATE DEAMINASE; ADENOSINE PHOSPHATE; COFORMYCIN; FORMYCIN PHOSPHATE; NUCLEOTIDASE; TUBERCIDIN PHOSPHATE; UNCLASSIFIED DRUG;

ARTICLE; ENANTIOMER; ENZYME BINDING; ENZYME INHIBITION; ENZYME STRUCTURE; MATHEMATICS; MOLECULAR DYNAMICS; STEREOCHEMISTRY;

EID: 0029788667     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja952781n     Document Type: Article

References (52)

1. Wolfenden, R. Acc. Chem. Res. 1972, 5, 10-18.
2. Schramm, V. L.; Horenstein, B. A.; Kline, P. C. J. Biol. Chem. 1994, 269, 18259-18262.
3. Perelson, A. S.; Oster, G. F. J. Theor. Biol. 1979, 81, 645-670.
4. Tasi, G.; Palinko, I. Topics Curr. Chem. 1995, 174, 45-71.
5. Carbó, R.; Leyda, L.; Arnau, M. Int. J. Quantum Chem. 1980, 17, 1185-1189.
6. Bowen-Jenkins, P. E.; Cooper, D. L.; Richards, W. G. J. Phys. Chem. 1985, 89, 2195-2197.
7. Hodgkin, E. E.; Richards, W. G. Int. J. Quantum Chem.: Quantum Biol. Symp. 1987, 14, 105-110.
8. Richards, W. G.; Hodgkin, E. E. Chem. Br. 1988, 24, 1141-1144.
9. Petke, J. D. J. Comput. Chem. 1993, 14, 928-933.
10. Richard, A. M. J. Comput. Chem. 1991, 12, 959-969.
11. Sjoberg, P.; Politzer, P. J. Phys. Chem. 1990, 94, 3959-3961.
12. Politzer, P., Truhlar, D. G., Eds. Chemical Applications of Atomic and Molecular Electrostatic Potentials; Plenum Press: New York, 1981.
13. Weiner, P. K.; Langridge, R.; Blaney, J. M.; Schaefer, R.; Kollman, P. A. Proc. Natl. Acad. Sci. U.S.A. 1982, 79, 3754-3758.
14. Novotny, J.; Sharp, K. Prog. Biophys. Molec. Biol. 1992, 58, 203-224.
15. Warshel, A.; Naray-Szabo, G.; Sussman, F.; Hwang, J.-K. Biochemistry 1989, 28, 3629-3637.
16. Chau, P.-L.; Dean, P. M. J. Mol. Graph. 1987, 5, 97-100.
17. Dean, P. M.; Chau, P.-L. J. Mol. Graph. 1987, 5, 152-158.
18. Gasteiger, J.; Li, X.; Rudolph, C.; Sadowski, J.; Zupan, J. J. Am. Chem. Soc. 1994, 116, 4608-4620.
19. Wagener, M.; Sadowski, J.; Gasteiger, J. J. Am. Chem. Soc. 1995, 117, 7769-7775.
20. Heiden, W.; Moeckel, G.; Brickmann, J. J. Comput.-Aided Mol. Des. 1993, 7, 503-514.
21. Mezey, P. G. Int. J. Quantum. Chem.: Quant. Biol. Symp. 1987, 14, 127-132.
22. Mezey, P. G. Shape in Chemistry: An Introduction to Molecular Shape and Topology; VCH Publishers: New York, 1993.
23. Arteca, G. A.; Hernandez-Laguna, A.; Randez, J. J.; Smeyers, Y. G.; Mezey, P. G. J. Comput. Chem. 1991, 12, 705-716.
24. Alkorta, I.; Villar, H. O.; Arteca, G. A. J. Comput. Chem. 1993, 14, 530-540.
25. Johnson, M. A.; Maggiora, G. M., Eds. Concepts and Applications of Molecular Similarity; Wiley-Interscience: New York, 1990.
26. Dean, P. M. BioEssays 1994, 16, 683-687.
27. Hopfinger, A. J. J. Am. Chem. Soc. 1980, 102, 7196-7206.
28. Kline, P. C.; Schramm, V. L. J. Biol. Chem. 1994, 269, 22385-22390.
29. Ehrlich, J. I.; Schramm, V. L. Biochemistry 1994, 33, 8890-8896.
30. (a) Horenstein, B. A.; Schramm, V. L. Biochemistry 1993, 32, 7089-7097.
31. (b) Horenstein, B. A.; Schramm, V. L. Biochemistry 1993, 32, 9917-9925.
32. Kline, P. C.; Schramm, V. L. Biochemistry 1995, 34, 1153-1162.
33. Merkler, D. J.; Kline, P. C.; Weiss, P.; Schramm, V. L. Biochemistry 1993, 32, 12993-13001.
34. Mentch, F.; Parkin, D. W.; Schramm, V. L. Biochemistry 1987, 26, 921-930.
35. Parkin, D. W.; Mentch, F.; Banks, G. A.; Horenstein, B. A.; Schramm, V. L. Biochemistry 1991, 30, 4586-4594.
36. Merkler, D. J.; Brenowitz, M.; Schramm, V. L. Biochemistry 1990, 29, 8358-8364.
37. Merkler, D. J.; Schramm, V. L. Biochemistry 1993, 32, 5792-5799.
38. Merkler, D. J.; Wali, A. S.; Taylor, J.; Schramm, V. L. J. Biol. Chem. 1989, 264, 21422-21430.
39. Radzicka, A.; Wolfenden, R. Methods Enzymol. 1995, 249, 284-312.
40. Shih, P.; Wolfenden, R. Biochemistry 1996, 35, 4697-4703.
41. Wilson, D. K.; Rudolph, F. B.; Quiocho, F. A. Science 1991, 252, 1278-1284.
42. Wilson, D. K.; Quiocho, F. A. Biochemistry 1993, 32, 1689-1694.
43. DeWolf, W. E., Jr.; Fullin, F. A.; Schramm, V. L. J. Biol. Chem. 1979, 254, 10868-10875.
44. Schramm, V. L.; Baker, D. L. Biochemistry 1985, 24, 641-646.
45. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Johnson, B. G.; Robb, M. A.; Cheeseman, J. R.; Keith, T.; Petersson, G. A.; Montgomery, J. A.; Raghavachari, K.; Al-Laham, M. A.; Zakrzewski, V. G.; Ortiz, J. V.; Foresman, J. B.; Cioslowski, J.; Stefanov, B. B.; Nanayakkara, A.; Challacombe, M.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J. L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Binkley, J. S.; DeFrees, D. J.; Baker, J.; Stewart, J. P.; Head-Gordon, M.; Gonzalez, C.; Pople, J. A. Gaussian 94, Revision C.2; Gaussian, Inc.: Pittsburgh, PA, 1995.
46. Betts, L.; Xiang, S.; Short, S. A.; Wolfenden, R.; Carter, C. W., Jr. J. Mol. Biol. 1994, 235, 635-656.
47. Kearsley, S. K.; Smith, G. M. Tetrahedron Comput. Methodol. 1990, 3, 615-633.
48. Klebe, G.; Mietzner, T.; Weber, F. J. Comput.-Aided Mol. Des. 1994, 8, 751-778.
49. Indeed, the surface topologies are more easily appreciated when physically rotating the molecules with the visualization package.
50. 3. Visualization uncovered it, and it was deleted. This point corresponded to a region of low electron density in the molecular core close to a nucleus.
51. Xiang, S.; Short, S. A.; Wolfenden, R.; Carter, C. W., Jr. Biochemistry 1995, 34, 4516-4523.
52. Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P. Science 1983, 220, 671-683.