Computational study of some benzamidine-based inhibitors of thrombin-like snake venom proteinases

International Journal of Quantum Chemistry

Volumn 106, Issue 9, 2006, Pages 2107-2121

  Henriques, Elsa S ^a   Nascimento, Marco A C ^b   Ramos, Maria João ^a  

^a UNIVERSITY OF PORTO   (Portugal)

^b Depto Quim Organ Inst Quim U   (Brazil)

Author keywords

Benzamidine based inhibitors; Parameterization; Thrombin

Indexed keywords

COMPUTER SIMULATION; ENZYME INHIBITION; ENZYMES; MEDICAL APPLICATIONS; MOLECULAR DYNAMICS; NITROGEN COMPOUNDS; TOPOLOGY;

BENZAMIDINE-BASED INHIBITORS; PARAMETERIZATION; SNAKE VENOM PROTEINASES; THROMBIN;

COMPUTATIONAL METHODS;

EID: 33744485016     PISSN: 00207608     EISSN: 1097461X     Source Type: Journal    
DOI: 10.1002/qua.20999     Document Type: Article

References (27)

1. Srivastava, S.; Goswami, L. N.; Dikshit, D. K. Med Res Rev 2005, 25(1), 66.
2. Markland, F. S., Jr.; Swenson, S.; Venombin A. In Handbook of Proteolytic Enzymes; 2nd ed.; Barrett, A. J.; Rawlings, N. D.; Woessner, J. F., Eds.; Elsevier: London, 2004; p 1715.
3. Stürzebecher, J.; Stürzebecher, U.; Markwardt, F. Toxicon 1986, 24, 585.
4. Serrano, S. M. T.; Hagiwara, Y.; Murayama, N.; Highuchi, S.; Mentele, R.; Sampaio, C. A. M.; Camargo, A. C. M.; Fink, E. Eur J Biochem 1998, 251, 845.
5. Warshel, A.; Åqvist, J.; Creighton, S. Proc Natl Acad Sci USA 1989, 86, 5820.
6. McKerell, A. D., Jr.; Bashford, D.; Bellot, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J.; Stote, R.; Sträub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
7. Mackerell, A. D., Jr.; Brooks, B.; Brooks, C. L., III; Nilsson, L.; Roux, B.; Won, Y.; Karplus, M. The Encyclopaedia of Computational Chemistry; von Ragué Schleyer; Allinger, L.; Schaefer, F., Eds.; Chemistry at HARvard Macromolecular Mechanics (CHARMM) version 27b4, 2001, 1984, 1992; President and Fellows of Harvard College; John Wiley & Sons: Chichester, UK, 1998; Vol 1; p 271.
8. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; J. Millam, M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; D. Fox, J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98; Revision A.9; Gaussian: Pittsburgh, PA, 1998.
9. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J Phys Chem 1993, 97, 10269.
10. Cieplak, P.; Cornell, W. D.; Bayly, C. I.; Kollman, P. A. J Comp Chem 1995, 16, 1357.
11. Singh, U. C.; Kollman, P. A. J Comp Chem 1984, 5, 129.
12. Henriques, E. S.; Bastos, M.; Geraldes, C. F. G. C.; Ramos, M. J. Int J Quantum Chem 1999, 73, 237.
13. QUANTA™ 2000; Version 00.1110; Molecular Simulations, Inc.: San Diego, 1986-2004.
14. Darden, T.; York, D.; Pederson, L. J Chem Phys 1993, 98, 10089.
15. Foloppe, N.; MacKerell, A. D., Jr. J Comp Chem 2000, 21, 86.
16. Reynolds, C. A.; Essex, J. W.; Richards, W. G. J Am Chem Soc 1992, 114, 9075.
17. Levitt, M. Sharon, R. Proc Natl Acad Sci USA 1988, 85, 7557.
18. Banner, D. W.; Hadváry, P. J Biol Chem 1991, 266, 20085.
19. Bode, W.; Turk, D.; Sturzebecher, J. Eur J Biochem 1990, 193, 175.
20. Brandstetter, H.; Turk, D.; Hoeffken, H. W.; Grosse, D.; Sturzebecher, J.; Martin, P. D.; Edwards, B. F.; Bode, W. J Mol Biol 1992, 226, 1085.
21. Turk, D.; Sturzebecher, J.; Bode, W. FEBS Lett 1991, 287, 133.
22. Grootenhuis, P. D. J.; van Galen, P. J. M. Acta Crystallogr D 1995, 51, 560.
23. Klebe, G. J Mol Med 2000, 78, 269.
24. Gradwell, M. J.; Feeney, J. J Biomol NMR 1996, 7, 48.
25. Bourne, P. E.; Addess, K. J.; Bluhm, W. F.; Chen, L.; Deshpande, N.; Feng, Z.; Fleri, W.; Green, R.; Merino-Ott, J. C.; Townsend-Merino, W.; Weissig, H.; Westbrook, J.; Berman, H. M. Nucleic Acids Res 2004, 32 (database issue), D223.
26. Henriques, E. S.; Fonseca, N.; Ramos M. J Protein Sci 2004, 13, 2355.
27. Henriques, E. S.; Ramos M. J. (to be published).