Binding affinities for a series of selective inhibitors of gelatinase-A using molecular dynamics with a linear interaction energy approach

Journal of Physical Chemistry B

Volumn 105, Issue 22, 2001, Pages 5304-5315

  Hou, T J ^a   Zhang, W ^a   Xu, X J ^a  

^a PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GELATINASE; HYDROXYMATE; LINEAR INTERACTION ENERGY;

BINDING ENERGY; COMPUTER SIMULATION; CORROSION INHIBITORS; ELECTROSTATICS; ENTROPY; FREE ENERGY; GELS; HYDROGEN BONDS; HYDROPHOBICITY; VAN DER WAALS FORCES;

MOLECULAR DYNAMICS;

EID: 0035822178     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0044476     Document Type: Article

References (52)

1. Hou, T. J.; Wang, J. M.; Chen L. R.; Xu, X. J. Protein Eng. 1999, 12, 639.
2. van Gunsteren, W. F. Protein Eng. 1988, 2, 5.
3. Jorensen, W. L. Acc. Chem. Res. 1989, 22, 184.
4. Kollman, P. Chem. Rev. 1993, 93, 2395.
5. Tomioka, N.; Itai, A.; Iitaka, Y. J. Comput.-Aided Mol. Design 1987, 1, 197.
6. Novotny, J.; Bruccoleri, R. E.; Saul, F. A. Biochemistry 1989, 28, 4735.
7. Williams, D. H.; Cox, J. P. L.; Doig, A. J.; Gardner, M.; Gerhard, U.; Kaye, P. T.; Lal, A. R.; Nicholls, I. A.; Salter, C. J.; Mitchell, R. C. J. Am. Chem. Soc. 1991, 113, 7020.
8. Searle, M. S.; Williams, D. H.; Gerhard, U. J. Am. Chem. Soc. 1992, 114, 10697.
9. Horton, N.; Lewis, M. Protein Sci. 1992, 1, 169.
10. Bohacek, R. S.; McMartin, C. J. Med. Chem. 1992, 35, 1671.
11. Krystek, S.; Stouch, T.; Novotny, J. J. Mol. Biol. 1993, 234, 661.
12. Böhn, H. J. J. Comput-Aided Mol. Design 1994, 8, 243.
13. Head, R. D.; Smythe, M. L.; Oprea, T. I.; Waller, C. L.; Greene, S. M.; Marshall, G. R. J. Am. Chem. Soc. 1996, 118, 3959.
14. Matthew, D. E.; Christopher, W. M.; Timoghy, R. A.; Gaia, V. P.; Roger, P. M. J. Comput.-Aided Mol. Design 1997, 11, 425.
15. Åqvist, J.; Medina, C.; Samuelsson, J. E. Protein Eng. 1994, 7, 385.
16. Åqvist, J.; Mowbray, S. M. J. Biol. Chem. 1995, 270, 9978.
17. Hansson, T.; Åqvist, J. Protein Eng. 1995, 8, 1137.
18. Åqvist, J.; Hansson, T. J. Phys. Chem. 1996, 100, 9512.
19. Hansson, T.; Marelius, J.; Åqvist, J. J. Comput.-Aided Mol. Design 1998, 12, 27.
20. Paulsen, M. D.; Ornstein, R. L. Protein Eng. 1996, 9, 567.
21. Wang, J.; Dixon, R.; Kollman, P. A. Proteins: Struct., Funct., Genet. 1999, 34, 69.
22. Jones-Hertzog, D. K.; Jougensen, W. L. J. Med. Chem. 1997, 40, 1539.
23. Woessner, J. F. FASBE J. 1991, 5, 2145.
24. Nagase, H.; Fields, G. B. Biopolymer 1996, 40, 399.
25. Bottomley, K. M. K.; Bradshaw, D.; Nixon, J. S. Metalloproteinases as Targets for Antiinflammatory Drugs; Birkhäuser Verlag: Switzerland, 1999.
26. Willenbrock, F.; Murphy, G. Am. J. Respir. Crit. Car. Med. 1994, 150, 5165.
27. Green, J.; Wang, M.; Liu, Y. E.; Raymond, L. A.; Rosen, C.; Shi, Y. E. J. Biol. Chem. 1996, 271, 30375.
28. Murphy, G. J. P.; Murphy, G.; Reynolds, J. J. FEBS Lett. 1991, 289, 4.
29. Muller, D.; Quantin, B.; Gesnel, M. C.; Millon-Collard, R.; Abecossis, J.; Breathnach, R. Biochem. J. 1988, 253, 187-912.
30. Liotta, L. A.; Steeg, P. S.; Stetler-Stevenson, W. G. Cell 1991, 64, 327.
31. Whittaker, M.; Floyd, C. D; Brown, P.; Gearing, A. J. H. Chem. Rev. 1999, 99, 2735.
32. Stetler-Stevenson, W. G.; Aznavoorian, S.; Liotta, L. A. Annu. Rev. Cell. Biol. 1993, 9, 541.
33. Beckett, R. P.; Davidson, A. H.; Drummond, A. H. Drug Discov. Today 1996, 1, 16.
34. Morgunova, E.; Tuuttila, A.; Bergmann, U.; Isupov, M.; Lindqvist, Y.; Schneider, G.; Tryggvason, K. Science 1999, 284, 1667.
35. Toba, S.; Damodaran, K. V.; Merz, K. M., Jr. J. Med. Chem. 1999, 42, 1225.
36. Hoops, S. C.; Anderson, K. W.; Merz, K. M., Jr. J. Am. Chem. Soc. 1991, 113, 8262.
37. Natchus, M. G.; Cheng, M. Y.; Wahl, C. T. Bioorg. Med. Chem. Lett. 1998, 8, 2077.
38. Porter, J. R.; Beeley, N. R. A.; Boyce, B. A.; Mason, B.; Millican, A.; Millar, K.; Leonard, J.; Morphy, J. R.; O'Connell, J. P. Bioorg. Med. Chem. Lett. 1994, 4, 2741.
39. Broadhurst, M. J.; Brown, P. A.; Lawton, G.; Ballantyne, N.; Borkakoti, N.; Bottomley, K. M. K.; Cooper, M. I.; Eatherton, A. J.; Kilford, I. R.; Malsher, P. J.; Nixon, J. S.; Lewis, E. J.; Sutton, B. M.; Johnson, W. H. Bioorg. Med. Chem. Lett. 1997, 7, 2299.
40. Alpegiani, M.; Bissolino, P.; Absate, F.; Perrone, E.; Corigli, R.; Jabes, D. Chem. Abstr. 1999, 130, 139360.
41. InsightII User Guide, Molecular Simulations Inc., San Diego, 1999.
42. Ryde, U. Proteins: Struct., Funct., Genet. 1995, 21, 40.
43. Wang, J. M.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049.
44. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117 (7), 5179.
45. MOPAC 7.0 User Guide Quantum Chemistry Program Exchange (QCPE), Indiana University, 1993.
46. Gaussian 98 User Guide, Gaussian, Inc., Pittsburgh, 1998.
47. Cleplak, P.; Cornell, W. D.; Bayly, C.; Kollman, P. A. J. Comput. Chem. 1994, 16, 1357.
48. Keil, M.; Exner, T.; Brickmann, J. J. Mol. Model. 1998, 4, 335.
49. SYBYL ver. 6.5, Tripos Associates, St. Louis, MO., 1999.
50. Janin, J. Proteins: Struct., Funct., Genet. 1994, 24, R1.
51. Carlson, H. A.; Jorgensen, W. L. J. Phys. Chem. 1995, 99, 10667.
52. McDonald, N. A.; Carlson, H. A.; Jorgensen, W. L. J. Phys. Org. Chem. 1997, 10, 563.