A combined molecular modeling study on gelatinases and their potent inhibitors

Journal of Computational Chemistry

Volumn 31, Issue 1, 2010, Pages 24-42

  Xi, Lili ^a   Du, Juan ^a   Li, Shuyan ^a   Li, Jiazhong ^a   Liu, Huanxiang ^a   Yao, Xiaojun ^a  

^a LANZHOU UNIVERSITY   (China)

Author keywords

CoMFA; CoMSIA; Docking; Genetic algorithm (GA); Matrix metalloproteinase 2 (MMP 2); Matrix metalloproteinase 9 (MMP 9)

Indexed keywords

BINDING MODES; COMFA; COMPARATIVE-MOLECULAR-SIMILARITY-INDICES ANALYSIS; GELATINASE; MATRIX METALLOPROTEINASE-2; MATRIX METALLOPROTEINASE-9; MATRIX METALLOPROTEINASES; MOLECULAR FIELDS; MOLECULAR MODELING STUDIES; MULTIPLE LINEAR REGRESSIONS; NEW SERIES; PATHOLOGICAL PROCESS; POTENT INHIBITOR; POTENTIAL INHIBITORS; PREDICTIVE ABILITIES; QSAR MODEL; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS; SEQUENCE ALIGNMENTS; SIMILARITIES AND DIFFERENCES; STRUCTURAL FEATURE;

BINDING ENERGY; BINDING SITES; DOCKING; ENZYME INHIBITION; ETHERS; FEATURE EXTRACTION; GENETIC ALGORITHMS; LIGANDS; LINEAR REGRESSION; MOLECULAR GRAPHICS; MOLECULAR MODELING; PROTEINS; SULFUR COMPOUNDS; ZINC;

ULSI CIRCUITS;

GELATINASE A; GELATINASE B; HYDROXAMIC ACID; PROTEINASE INHIBITOR; SULFONAMIDE;

ARTICLE; CHEMICAL STRUCTURE; DRUG ANTAGONISM; HUMAN; METABOLISM; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

HUMANS; HYDROXAMIC ACIDS; MATRIX METALLOPROTEINASE 2; MATRIX METALLOPROTEINASE 9; MODELS, MOLECULAR; PROTEASE INHIBITORS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SULFONAMIDES;

EID: 72449157094     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21279     Document Type: Article

References (101)

1. Burzlaff, N. Concepts Model Biginorg Chem 2006, 17, 397.
2. Sternlicht, M. D.; Werb, Z. Annu Rev Cell Dev Biol 2001, 17, 463.
3. Whittaker, M.; Floyd, C. D.; Brown, P.; Gearing, A. J. H. Chem Rev 1999, 99, 2735.
4. Overall, C. M.; Lopez-Otin, C. Nature Rev Cancer 2002, 2, 657.
5. Fingleton, B. Curr Pharm. Des 2004, 13, 333.
6. Visse, R.; Nagase, H. Cire Res 2003, 92, 827.
7. Galis, Z. S.; Khatri, J. J. Circ Res 2002, 90, 251.
8. Liu, Y. E.; Wang, M.; Greene, J.; Su, J.; Ullrich, S.; Li, H.; Sheng, S.; Alexander, P.; Sang, Q. A.; Shi, Y. E. J Biol Chem 1997, 272, 20479.
9. Johnso, G.; Galis, Z. S. Arterioscler Thromb Vase Biol 2004, 24, 54.
10. Raffetto, J. D.; Khalil, R. A. Biochem Pharmacol. 2008, 75, 346.
11. Fingleton, B. Expert Opin Ther Tar 2003, 7, 385.
12. Vihinen, P.; Ala-aho, R.; Kahari, V. M. Curr Cancer Drug Targets 2005, 5, 203.
13. George, S. J. Expert Opin. Inv Drug 2000, 9, 993.
14. Yong, V. W. Expert Opin Inv Drug 1999, 8, 255.
15. Yong, V. W.; Power, C.; Forsyth, P.; Edwards, D. R. Nat Rev Neurosci 2001, 2, 502.
16. Begers, G.; Brekken, R.; McMahon, G.; Vu, T. H.; Itoh, T.; Tamaki, K.; Tanzawa, K.; Thorpe, P.; Itohara, S.; Werb, Z.; Hanahan, D. Nat Cell Boil 2000, 2, 737.
17. Allan, J. A.; Docherty, A. J.; Barker, P. J.; Huskisson, N. S.; Reynolds, J. J.; Murphy, G. Biochem J 1995, 309, 299.
18. Hu, J.; Steen, P. E. V. D.; Sang, Q. X.; Opdenakker, G. Nat Rev Drug Discov 2007, 6, 480.
19. Sang, Q. X.; Jin, Y.; Newcomer, R. G.; Monroe, S. C.; Fang, X.; Hurst, D. R.; Lee, S.; Cao, Q.; Schwartz, M. A. Curr Top Med Chem 2006, 6, 289.
20. Skiles, J. W.; Gonnella, N. C.; Jeng, A. Y. Curr Med Chem 2004, 11,2911.
21. Tu, G.; Xu, W.; Huang, H.; Li, S. Curr Med Chem 2008, 15, 1388.
22. Fisher, J. F.; Mobashery, S. Cancer Metastasis Rev 2006, 25, 115.
23. Verma, R. P.; Hansen, C. Bioorg Med Chem 2007, 15, 2223.
24. Matter, H.; Schudok, M. Curr Opin Drug Discov Dev 2004, 7, 513.
25. Cuniasse, P.; Devel, L.; Makaritis, A.; Beau, F.; Georgiadis, D.; Matziari, M.; Yiotakis, A.; Dive, V. Biochimie 2005, 87, 393.
26. Jani, M.; Tordai, H.; Trexler, M.; Banyai, L.; Patthy, L. Biochimie 2005, 87, 385.
27. Kontogiorgis, C. A. Curr Med Chem 2005, 12, 339.
28. Mannello, F.; Tonti, G.; Papa, S. Curr Cancer Drug Targets 2005, 5, 285.
29. Maskos, K. Biochimie 2005, 87, 249.
30. Rao, B. G. Curr Pharm Des 2005, 11, 295.
31. Tyndall, J. D.; Nail, T.; Fairlie, D. P. Chem Rev 2005, 105, 973.
32. Wasserman, Z. R. Chem Biol 2005, 12, 143.
33. Pirard, B. Drug Discov Today 2007, 12, 640.
34. Cheng, X.; Wang, Q.; Fang, H.; Xu., W. Curr Med Chem 2008, 15, 368.
35. Supuran, C. T.; Casini, A.; Scozzafave, A. Med Res Rev 2003, 23, 535.
36. Yang, S.-M.; Scannevin, R. H.; Wang, B.; Burke, S. L.; Wilson, L. J.; Karnachi, P.; Rhodes, K. J.; Lagu, B.; Murray, W. V. Bioorg Med. Chem Lett 2008, 18, 1135.
37. Yang, S.-M.; Scannevin, R. H.; Wang, B.; Burke, S. L.; Huang, Z.; Karnachi, P.; Wilson, L. J.; Rhodes, K. J.; Lagu, B.; Murray, W. V. Bioorg Med Chem Lett 2008, 18, 1140.
38. Chou, K. C. Curr Med Chem 2004, 11, 2105.
39. Chou, K. C.; Wei, D. Q.; Zhong, W. Z. Biochem Biophys Res Comm 2003, 308, 148.
40. Li, Y.; Wei, D. Q.; Gao, W. N.; Gao, H.; Liu, B. N.; Huang, C. J.; Xu, W. R.; Liu, D. K.; Chen, H. F.; Chou, K. C. Med Chem 2007, 3, 576.
41. Wang, J. F.; Wei, D. Q.; Chen, C.; Li, Y.; Chou, K. C. Protein Pept Lett 2008, 15, 27.
42. Sirois, S.; Wei, D. Q.; Du, Q. S.; Chou, K. C. J Chem Inf Comput Sci 2004, 44, 1111.
43. Prado-Prado, F. J.; González-Díaz, H.; de la Vega, O. M.; Ubeira, F. M.; Chou, K. C. Bioorg Med Chem 2008, 16, 5871.
44. Du, Q. S.; Huang, R, B.; Wei, Y. T.; Du, L. Q.; Chou, K. C. J Comput Chem 2008, 29, 211.
45. Du, Q. S.; Mezey, P. G.; Chou, K. C. J Comput Chem 2005,26,461.
46. Chou, K. C.; Shen, H. B. Nat Protocols 2008, 3, 153.
47. Chou, K. C.; Shen, H. B. Anal Biochem 2007, 370, 1.
48. Chou, K. C.; Shen, H. B. Biophys Res Comm 2007, 360, 339.
49. Shen, H. B.; Chou, K. C. Biochem Biophys Res Comm. 2007,364,53.
50. Chou, K. C.; Shen, H. B. Biochem Biophys Res Comm 2008, 376, 321,
51. Chou, K. C. Anal Biochem 1996, 233, 1.
52. Shen, H. B.; Chou, K. C. Anal Biochem 2008, 375, 388.
53. Chou, K. C.; Shen, H. B. Biochem. Biophys Res Coram 2007, 357, 633.
54. Shen, H. B.; Chou, K, C. Biochem Biophys Res Comm 2007, 363, 297.
55. Nicolotti, O.; Miscioscia, T. F.; Leonetti, F.; Muncipinto, G.; Carotti, A. J Chem. Inf Model. 2007, 47, 2439.
56. Hansch, C.; Robert, M. M.; Fujita, T.; Maloney, P. P.; Geiger, F.; Streich, M. J Am Chem Soc 1963, 85, 2817.
57. Hansen, C. Drug Design; Aeademin Press: New York 1971, Vol.1, p. 271.
58. Hansch, C.; Leo, A. J. Substitute Constants for Correlation Analysis in Chemistry and Biology; Wiley: New York, 1979.
59. Marshall, G. R.; Cramer, R. D., III. Trends Pharmacol Sci 1988, 9, 285.
60. Gramer, R. D., III; Patterson, D. E.; Bunce, J. D. Prog Clin Biol Res 1989, 291, 161.
61. Klebe, G.; Mietzner, T. J Comput Aided Mol. Des 1994, 8, 583.
62. Klebe, G.; Abraham, U. J Comput Aided Mol Des 1999, 13, 1.
63. Hopfinger, A. J.; Wang, S.; Tokarski, J. S.; Jin, B.; Albuquerque, M.; Madhav, P. J.; Duraiswami, C. J Am Chem Soc 1997, 119, 10509.
64. Tong, W.; Lowis, D. R.; Perkins, R.; Chen, Y.; Welsh, W. J.; Goddette, D. W.; Heritage, T. W.; Sheehan, D. M. J Chem Inf Comput Sci 1998, 38, 669.
65. Du, Q. S.; Huang, R. B.; Chou, K. C. Curr Protein Pept Sci 2008, 9, 248.
66. Du, Q. S.; Huang, R. B.; Wei, Y. T.; Pang, Z. W.; Du, L. Q.; Chou, K. C. J Comput Chem 2009, 30, 295.
67. Du, Q. S.; Huang, R. B.; Wei, Y. T.; Wang, C. H.; Chou, K. C. J Comput Chem 2007, 28, 2043.
68. Dea-Ayuela, M. A.; Pérez-Castillo, Y.; Meneses-Marcel, A,; Ubeira, F. M.; Bolas-Fernández, F.; Chou, K.-C.; González-Díaz, H. Bioor Med Chem 2008, 16, 7770.
69. González-Díaz, H.; Olazábal, E.; Santana, L.; Uriarte, E.; González-Díaz, Y.; Castañedo, N. Bioorg Med Chem 2007, 15, 962.
70. Erhan, D.; L'Heureux, P.-J.; Yue, S. Y.; Bengio, Y. J Chem. Inf Model. 2006, 46, 626.
71. Gupta, S. P. Chem Rev 2007, 107, 3042.
72. Fernández, M.; Caballero, J.; Tundidor-Camba, A. Bioorg Med Chem 2006, 14, 4137.
73. Fernández, M.; Caballero, J. Bioorg Med. Chem 2007, 15, 6298.
74. Tsai, K. C.; Lin, T. H. J Chem Inf Comput Sci 2004, 44, 1857.
75. Smith, T. F.; Waterman, M. S. J Mol Biol 1981, 147, 195.
76. Zhang, Y.; Skolnick, J. Nucl Acids Res 2005, 33, 2302.
77. Holzhütter, H. Christoph Gille Institut für Biochemie, Charité Group for Computational Biochemistry Group Leader: available at: http://wwwcharitede/sysbio.
78. Tripos Associates, S. L. M. Sybyl version 69, 1999.
79. DRAGON for Windows Version 5.4 2006.
80. Zupan, J.; Novic, M.; Ruisánchez, I. Chemom Intell Lab Syst 1997, 38, 1.
81. Holland, J. H. In Adaptation in natural and artificial systems 1975.
82. Rogers, D.; Hopfinger, A. J. J Chem Inf Comput Sci 1994, 34, 854.
83. Li, J. Z.; Lei, B. L.; Liu, H. X,; Li, S. Y.; Yao, X. J.; Liu, M. C.; Gramatica., P. J Comput Chem 2008, 29, 2636.
84. Baliram, H.; Mohajeri, A. J Comput Chem 2008, 29, 266.
85. Chen, H.; Liu, B.; Huang, H.; Wang, S.; Ho, S. J Comput Chem. 2007, 28, 612.
86. Liu, H. X.; Papa, E.; Gramatica, P. Chem Res Toxicol 2006, 19, 1540.
87. Chou, K. C.; Zhang, C. T. Crit Rev Biochem. Mol. Biol 1995, 30, 275.
88. Chen, K.; Kurgan, L. A.; Ruan, J. J Comput Chem 2008, 29, 1596.
89. Chen, Y. L.; Li, Q. Z. J Theor Biol 2007, 248, 377.
90. Zhou, X. B.; Chen, C.; Li, Z. C.; Zou, X. Y. J Theor Biol 2007, 248, 546.
91. Chen, C.; Chen, L. X.; Zou, X. Y.; Cai, P. X. J Theor Biol 2008, 253, 388.
92. Du, P. F.; Li, Y. D. J Theor Biol. 2008, 253, 579.
93. Liu, H.; Ding, H.; Guo, F. B.; Zhang, A. Y.; Huang, J. Protein Pept Lett 2008, 15, 739.
94. Shi, M. G.; Huang, D. S.; Li, X. L. Protein Pept Lett 2008, 15, 692.
95. Gramatica, P.; Giani, E.; Papa, E. J Mol Graph Model 2007,25,755.
96. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. J Mol Biol 1996, 261,470.
97. Bernd, K.; Rarey, M.; Lengauer, T. Proteins 1999, 37, 228.
98. Pymol 0.99; Delano Scientific LLC: South San Francisco, C, 2006.
99. Consonni, V.; Todeschini, R.; Pavan, M.; Gramatica, P. J Chem Inf Comput Sci 2002, 42, 693.
100. Hemmer, M. C.; Steinhauer, V.; Gasteiger, J. Vibrat Spect 1999, 19, 151.
101. O'Brien, P. M.; Ortwine, D. F.; Pavlovsky, A. G.; Picard, J. A.; Sliskovic, D. R.; Roth, B. D.; Dyer, R. D.; Johnson, L. L.; Man, C. F.; Hallak, H. J Med Chem. 2000, 43, 156.