Binding affinity of hydroxamate inhibitors of matrix metalloproteinase-2

Journal of Molecular Modeling

Volumn 10, Issue 2, 2004, Pages 112-120

  Zhang, Wei ^a   Hou, Ting Jun ^a   Qiao, Xue Bin ^a   Huai, Sun ^b   Xu, Xiao Jie ^a  

^a PEKING UNIVERSITY   (China)

^b Aeon Inc   (United States)

Author keywords

AMBER force field; FEP; Gelatinase A; Hydroxamate; MMP 2

Indexed keywords

FUNCTIONAL GROUP; GELATINASE A; HYDROXAMIC ACID DERIVATIVE; MATRIX METALLOPROTEINASE INHIBITOR; STROMELYSIN; ZINC;

ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; CONTROLLED STUDY; DRUG PROTEIN BINDING; DRUG STRUCTURE; ELECTRIC FIELD; ELECTRICITY; ENERGY YIELD; ENZYME CONFORMATION; FORCE; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; PHARMACODYNAMICS; PRIORITY JOURNAL; SIMULATION; SURFACE CHARGE;

AMIDES; BINDING SITES; CATALYSIS; COMPUTER SIMULATION; ELECTROSTATICS; ENZYME INHIBITORS; HYDROXAMIC ACIDS; MATRIX METALLOPROTEINASE 2; MODELS, MOLECULAR; MOLECULAR STRUCTURE; ZINC;

EID: 2542448200     PISSN: 16102940     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00894-004-0181-1     Document Type: Article

References (33)

1. Whittaker M, Floyd CD, Brown P, Gearing AJH (1999) Chem Rev 99:2735-2776
2. Buisson AC, Gilles C, Polette M, Zahm JM, Birembaut P, Tournier JM (1996) Lab Invest 74:658-669
3. Lafeur M, Underwood JL, Rappolee DA, Werb Z (1996) J Exp Med 184:2311-2326
4. Cawston TE (1996) Pharm Theor 70:163-182
5. Johnson LL, Dyer R, Hupe DJ (1998) Curr Opin Chem Biol 2:466-471
6. Massova I, Kotra LP, Fridman R, Mobashery S (1998) FASEB J 12:1075-1095
7. Liotta LA, Tryggvason K, Garbisa S, Robey PG, Abe S (1981) Biochemistry-US 20:100-104
8. Senior RM, Griffin GL, Fliszar CJ, Shapiro SD, Goldberg GI, Welgus HG (1991) J Biol Chem 266:7870-7875
9. Morgunova E, Tuuttila A, Bergmann U, Isupov M, Lindqvist Y, Schneider G, Tryggvason K (1999) Science 284:1667-1670
10. Lovejoy B, Hassell AM, Luther MA, Weigl D, Jordan SR (1994) Biochemistry 33:8207-8217
11. Bode W, Gomis-Ruth FX, Stocker W (1993) FEBS Lett 331:134-140
12. Chen LY, Rydel TJ, Dunaway CM, Pikul S, Dunham KM (1999) J Mol Biol 293:545-557
13. Hoops SC, Anderson KW, Merz KMJ (1991) J Am Chem Soc 113:8262-8270
14. Toba S, Damodaran KV, Merz KM (1999) J Med Chem 42:1225-1234
15. Hou TJ, Zhang W, Xu XJ (2001) J Phys Chem B 105:5304-5315
16. Hou TJ, Zhang W, Xu XJ (2002) J Comput Aid Mol Des 16:27-41
17. Zhang W, Hou TJ, Xu XJ (2001) Acta Chim Sinica 59:2116-2121
18. Hou TJ, Zhang W, Xu XJ (2001) Acta Chim Sinica 59:1184-1189
19. Vedani A, Huhta DW (1990) J Am Chem Soc 112:4759-4767
20. Stote RH, Karplus M (1995) Proteins 23:12-31
21. Hou TJ, Zhang, W, Xu XJ (2002) Acta Chim Sinica 60:221-227
22. Hou TJ, Guo SL, Xu XJ (2002) J Phys Chem B 106:5527-5535
23. Donini OAT, Kollman PA (2000) J Med Chem 43:4180-4188
24. Dhanaraj V, Williams MG, Ye QZ, Molina F, Johnson LL, Ortwine DF, Pavlovsky A, Rubin JR, Skeean RW, White AD, Humblet C, Hupe DJ, Blundell TL (1999) Croatica Chemica Acta 72:575-591
25. Poter JR, Beeley NRA, Boyce BA (1994) Bioorg Med Chem Lett 4:2741-2746
26. Insight II 95.0 User Guide (1995) Accelrys Inc, San Diego, Calif.
27. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA, Stratman RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Baboul AG, Stefanov BB, Liu C, Liashenko A, Piskorz P, Komaromi, I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Gonzalez C, Challacombe M, Gill PMW, Johnson BG, Chen W, Wong MW, Andres JL, Gonzales C, Head-Gordon M, Replogle ES, Pople JA (1998) Gaussian 98. Gaussian, Pittsburgh, Pa.
28. Direct Force Field 1.0 User Guide (2001) Aeon Inc, San Diego, USA
29. Bayly CI, Cieplak P, Cornell WD, Kollman PA (1993) J Phys Chem 97:10269-10280
30. Cerius 2 User Guide (1995) Acceloys Inc, San Diego, USA
31. MOPAC 7.0 User Guide (1993) Quantum Chemistry Program Exchange (QCPE). Indiana University, USA
32. Case DA, Pearlman DA, Caldwell JW, Cheatham III TE, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsui, V, Radmer RJ, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner P, Kollman PA (1999) AMBER 6.0. University of California, San Francisco, Calif.
33. Levy DE, Lapierre F, Liang W, Ye W, Lange CW, Li X, Grobelny D, Casabonne M, Tyrrell D, Holme K, Nadzan A, Galardy RE (1998) J Med Chem 41:199-223