Computer-assisted scanning of ligand interactions: Analysis of the fructose 1,6-bisphosphatase - AMP complex using free energy calculations [5]

Journal of the American Chemical Society

Volumn 122, Issue 25, 2000, Pages 6114-6115

  Erion, Mark D ^a   Van Poelje, Paul D ^a   Reddy, M Rami ^a  

^a Metabasis Therapeutics Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE PHOSPHATE; FRUCTOSE BISPHOSPHATASE;

BINDING AFFINITY; COMPLEX FORMATION; HYDROGEN BOND; LETTER; LIGAND BINDING; MOLECULAR INTERACTION;

EID: 0034725411     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja000651v     Document Type: Letter

References (25)

1. (a) Fersht, A. R. Trends Biochem. Sci. 1987, 12, 301-304.
2. (b) Erion, M. D.; Takabayashi, K.; Smith, H. B.; Kessi, J.; Wagner, S.; Honger, S.; Shames, S. L.; Ealick, S. E. Biochemistry 1997, 36, 11725-11734.
3. (a) Kati, W. M.; Wolfenden, R. Science 1989, 243, 1591-1593.
4. (b) Straus, D.; Raines, R.; Kawashima, E.; Knowles, J. R.; Gilbert, W. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 2272-2276.
5. (a) Erion, M. D., Stoeckler, J. D.; Guida, W. C.; Walter, R. L.; Ealick, S. E. Biochemistry 1997, 36, 11735-11748.
6. (b) Stoeckler, J. D.; Poirot, A. F.; Smith, R. M., Parks, R. E., Jr.; Ealick, S. E.; Takabayashi, K.; Erion, M. D. Biochemistry 1997, 36, 11749-11756.
7. Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A. Science 1987, 235, 574-576.
8. For a recent review of free energy calculations in ligand design see: Reddy, M. R.; Erion, M. D.; Agarwal, A. In Reviews in Computational Chemistry; Wiley: New York, 2000, Vol. 16, pp 217-304.
9. (a) Daggett, V.; Brown, F.; Kollman, P. J. Am. Chem. Soc 1989, 111, 8247-8256.
10. (b) Pearlman, D. A.; Rao, B. G. In Encyclopedia of Computational Chemistry, Wiley: New York, 1999; Vol. 2, 1036-1061.
11. Thermodynamic cycles used to calculate relative binding and solvation free energies are described in the Supporting Information.
12. (a) Mitchell, M. J.; McCammon, J. A. J. Comput. Chem. 1991, 12, 271-275.
13. (b) Pearlman, D. A.; Kollman, P. A. J. Chem. Phys. 1991, 94, 4532-4545.
14. (c) Reddy, M. R.; Erion, M. D. J. Comput. Chem. 1999, 20, 1018-1027.
15. (a) Ke, H. M.; Zhang, Y. P.; Lipscomb, W. N. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 5243-5247.
16. (b) Iversen, L. F.; Brzozowski, M.; Hastrup, S.; Hubbard, R.; Kastrup, J. S.; Larsen, I. K.; Naerum, L.; Norskov-Lauridsen, L.; Rasmussen, P. B.; Thim, L.; Wiberg, F. C.; Lundgren, K. Protein Sci. 1997, 6, 971-982.
17. Erion, M. D.; Kasibhatla, S. R.; Bookser, B. C.; van Poelje, P. D.; Reddy, M. R.; Gruber, H. E.; Appleman, J. R. J. Am. Chem. Soc. 1999, 121, 308-319.
18. Computational details are similar to those used previously, see: Erion, M. D.; Reddy, M. R. J. Am. Chem. Soc. 1998, 120, 3295-3304.
19. Gidh-Jain, M.; Zhang, Y.; van Poelje, P. D.; Liang, J. Y.; Huang, S.; Kim, J.; Elliott, J. T.; Erion, M. D.; Pilkis, S. J.; Raafat El-Maghrabi, M.; Lipscomb, W. N. J. Biol. Chem. 1994, 269, 27732-27738.
20. Ealick, S. E.; Babu, Y. S.; Bugg, C. E.; Erion, M. D.; Guida, W. C.; Montgomery, J. A.; Secrist, J. A. 3rd. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 11540-11544.
21. Morales, J. C.; Kool, E. T. Nat. Struct. Biol. 1998, 5, 950-954.
22. (a) Pattabiraman, N. J. Med. Chem. 1999, 42, 3821 -3854.
23. (b) Bohacek, R. S.; McMartin, C. J. Med. Chem. 1992, 35, 1671.
24. (c) Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Venkataraghavan, R. J. Med. Chem. 1986, 29, 2149-2153.
25. (d) Goodford, P. J. J. Med. Chem. 1985, 28, 849-857.