Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-β-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry

Journal of Computational Chemistry

Volumn 26, Issue 11, 2005, Pages 1131-1147

  Antony, Jens ^a   Piquemal, Jean Philip ^b   Gresh, Nohad ^c  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^c CNRS   (France)

Author keywords

Mercaptocarboxylate inhibitors; Metallo lactamase; Polarizable molecular mechanics; Quantum chemistry; Validation

Indexed keywords

MERCAPTOCARBOXYLATE INHIBITORS; METALLO-Β-LACTAMASE; POLARIZABLE MOLECULAR MECHNAICS; QUANTUM CHEMISTRY; VALIDATION;

BACTERIA; CHEMICAL BONDS; ENZYMES; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; QUANTUM THEORY; X RAY DIFFRACTION ANALYSIS;

COMPLEXATION;

BETA LACTAMASE; CAPTOPRIL; ENZYME INHIBITOR; MANDELIC ACID DERIVATIVE; METALLOPROTEIN; THIOL DERIVATIVE; THIOMANDELIC ACID;

ALGORITHM; ARTICLE; BACTEROIDES FRAGILIS; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DRUG ANTAGONISM; ENZYMOLOGY; METABOLISM; PROTEIN BINDING;

ALGORITHMS; BACTEROIDES FRAGILIS; BETA-LACTAMASES; BINDING SITES; CAPTOPRIL; ENZYME INHIBITORS; MANDELIC ACIDS; METALLOPROTEINS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; PROTEIN BINDING; SULFHYDRYL COMPOUNDS;

EID: 22844443933     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20245     Document Type: Article

References (78)

1. Cricco, J. A.; Orellano, E. G.; Rasia, R. M.; Vila, A. J. Coord Chem Rev 1999, 190-192, 519.
2. Wang, Z.; Fast, W.; Valentine, A. M.; Benkovic, S. J. Curr Opin Chem Biol 1999, 3, 614.
3. (a) Salsbury, F. R., Jr.; Crowly, M. F.; Brooks, C. L., III. Proteins 2001, 44, 448;
4. (b) Suarez, D.; Merz, K. M., Jr. J Am Chem Soc 2001, 123, 3759;
5. (c) Diaz, N.; Suarez, D.; Merz, K. M., Jr. J Am Chem Soc 2001, 123, 9867;
6. (d) Suarez, D.; Brothers, E. N.; Merz, K. M., Jr. Biochemistry 2002, 41, 6615;
7. (e) Suarez, D.; Diaz, N.; Merz, K. M., Jr. J Comput Chem 2002, 23, 1587;
8. (f) Oelschlaeger, P.; Schmid, R. D.; Pleiss, J. Protein Eng 2003, 16, 341;
9. (g) Oelschlaeger, P.; Schmid, R. D.; Pleiss, J. Biochemistry 2003, 42, 8945;
10. (h) Dal Peraro, M.; Vila, A. J.; Carloni, P. Proteins 2004, 54, 412.
11. (a) Gilson, H. S. R.; Krauss, M. J Am Chem Soc 1999, 121, 6984;
12. (b) Diaz, N.; Suarez, D.; Merz, K. M., Jr. J Am Chem Soc 2000, 122, 4197;
13. (c) Krauss, M.; Gilson, H. S. R.; Gresh, N. J Phys Chem B 2001, 105, 8040;
14. (d) Olsen, L.; Antony, J.; Hemmingsen, L.; Mikkelsen, K. J Phys Chem A 2002, 106, 1046;
15. (e) Dal Peraro, M.; Vila, A. J.; Carloni, P. J Biol Inorg Chem 2002, 7, 704;
16. (f) Krauss, M.; Gresh, N.; Antony, J. J Phys Chem B 2003, 108, 1215;
17. (g) Olsen, L.; Antony, J.; Ryde, U.; Adolph, H.-W.; Hemmingsen, L. J Phys Chem B 2003, 107, 2366;
18. (h) Dal Peraro, M.; Vila, A. J.; Carloni, P. Inorg Chem 2003, 42, 45.
19. Concha, N. O.; Rasmussen, B. A.; Bush, K.; Herzberg, O. Structure 1996, 4, 823.
20. Concha, N. O.; Janson, P. A.; Rowling, P.; Pearson, S.; Cheaver, C. A.; Clarke, B. P.; Lewis, C.; Galleni, M.; Frère, J.-M.; Payne, D. J.; Bateson, J. H.; Abdel-Meguid, S. S. Biochemistry 2000, 39, 4288.
21. Garcia-Saez, I.; Mercuri, P. S.; Papamicael, C.; Kahn, R.; Frère, J.-M.; Galleni, M.; Rossolini, G. M.; Dideberg, O. J Mol Biol 2003, 325, 651.
22. (a) Carfi, A.; Pares, S.; Duee, E.; Galleni, M.; Duez, C.; Frere, J.-M.; Dideberg, O. EMBO J 1995, 14, 4914.
23. (b) Carfi, A.; Duee, E.; Paul-Soto, R.; Galleni, M.; Frère, J.-M.; Dideberg, O. Acta Crystallogr D 1998, 54, 47.
24. Fabiane, S. M.; Sohi, M. K.; Wan, T.; Payne, D. J.; Bateson, J. H.; Mitchell, T.; Sutton, B. J. Biochemistry 1998, 37, 12404.
25. Toney, J. H.; Fitzgerald, P. M. D.; Grover-Sharma, N.; Olson, S. H.; May, W. H.; Sundelof, J. G.; Vanderwall, D. E.; Cleary, K. A.; Grant, S. K.; Wu, J. K.; Kozarich, J. W.; Pompliano, D. I.; Hammond, G. C. Chem Biol 1998, 5, 185.
26. Ullah, J. H.; Walsh, T. R.; Taylor, I. A.; Emery, D. C.; Verma, C. S.; Gamblin, S. J.; Spencer, J. J Mol Biol 1998, 284, 125.
27. Toney, J. H.; Hammond, G. G.; Fitzgerald, P. M. D.; Sharma, N.; Balkovec, J. M.; Rouen, G. P.; Olson, S. H.; Hammond, M. L.; Greenlee, M. L.; Gao, Y.-D. J Biol Chem 2001, 276, 31913.
28. Siemann, S.; Evanoff, D. P.; Marrone, L.; Clarke, A. J.; Viswanatha, T.; Dmitrienko, G. I. Antimicrob Agents Chemother 2002, 46, 2450.
29. Damblon, C.; Jensen, M.; Ababou, A.; Barsukov, I.; Papamicael, C.; Schofield, C. J.; Olsen, L.; Bauer, R.; Roberts, G. C. K. I Biol Chem 2003, 278, 29240.
30. Mollard, C. C.; Papamicael, C.; Damblon, C.; Vessilier, S.; Amicosante, G.; Schofield, C. I.; Galleni, M.; Frère, J. M.; Roberts, G. C. K. J Biol Chem 2001, 276, 45015.
31. Antony, J.; Gresh, N.; Olsen, L.; Hemmingsen, L.; Schofield, C. S.; Bauer, R. J Comput Chem 2002, 23, 1281.
32. Faerman, C. H.; Price, S. L. J Am Chem Soc 1990, 112, 4915.
33. (a) Rogalewicz, F.; Ohanessian, G.; Gresh, N. J Comput Chem 2000, 21, 963;
34. (b) Tiraboschi, G.; Fournie-Zaluski, M.-C.; Roques, B.-P.; Gresh, N. J Comput Chem 2001, 22, 103;
35. (c) Gresh, N.; Shi, G.-B. J Comput Chem 2004, 25, 160;
36. (d) Gresh, N.; Kafafi, S. A.; Truchon, J.-F.; Salahub, D. R. J Comput Chem 2004, 25, 823.
37. Ren, P.; Ponder, J. W. J Comput Chem 2002, 23, 1497.
38. Stevens, W. J.; Basch, H.; Krauss, M. J Chem Phys 1984, 81, 6026.
39. Hay, P. J.; Hadt, W. R. J Chem Phys 1985, 82, 299.
40. Pople, J. A.; Binkley, J. S.; Seeger, R. Int J Quantum Chem 1976, Symp. 10, 1.
41. (a) Lee, C.; Yang, W.; Parr, R. G. Phys Rev 1988, B37, 785;
42. (b) Becke, A. J Chem Phys 1993, 98, 5648.
43. (a) Saebo, S.; Pulay, P. J Chem Phys 1987, 86, 914;
44. (b) Saebo, S.; Pulay, P. J Chem Phys 1988, 88, 1884;
45. (c) Saebo, S.; Tong, W.; Pulay, P. J Chem Phys 1993, 98, 2170.
46. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Sttatmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision B.05; Gaussian, Inc.: Pittsburgh, PA, 2003.
47. Jaguar 5.0. Schrodinger Inc., Portland, Oregon, 2002.
48. Murphy, R. B.; Beachy, M. D.; Friesner, R. A. J Chem Phys 1995, 103, 1481.
49. Tannor, D. K.; Marten, B.; Murphy, R.; Friesner, R. A.; Sitkoff, D.; Ringnalda, M.; Goddard, W. A., Ill; Honig, B. J Am Chem Soc 116, 11875.
50. Vigné-Maeder, F.; Claverie, P. J Chem Phys 1988, 88, 4934.
51. Garmer, D. R.; Stevens, W. J. J Phys Chem 1989, 93, 8263.
52. (a) Gresh, N.; Claverie, P.; Pullman, A. Int J Quantum Chem 1986, 29, 101;
53. (b) Gresh, N. J Comput Chem 1995, 16, 856;
54. (c) Gresh, N. J Phys Chem A 1997, 101, 8680;
55. (d) Gresh, N.; Guo, H.; Salahub, D. R.; Roques, B.-P.; Kafafi, S. A. J Am Chem Soc 1999, 121, 7885.
56. Piquemal, J.-P.; Gresh, N.; Giessner-Prettre, C. J Phys Chem A 2003, 107, 10353.
57. Murrell, J. N.; Teixeiras-Dias, J. J. C. Mol Phys 1970, 19, 521.
58. Piquemal J. P.; Merging, A.; Parioel, O.; Giessner-Prettre, C. J Comput Chem 2005, 26, 1052.
59. Gresh, N.; Piquemal, J.-P.; Krauss, M. J Comput Chem 2005, 26, 1113.
60. Stevens, W. J.; Fink, W. Chem Phys Letts 1987, 139, 15.
61. (a) Tiraboschi, G.; Gresh, N.; Roques, B.-P. J Comput Chem 1999, 20, 1979;
62. (b) Tiraboschi, G.; Gresh, N.; Giessner-Prettre, C.; Pedersen, L. G.; Deerfield, D. W. J Comput Chem 2000, 21, 1011.
63. Langlet, J.; Claverie, P.; Caillet, J.; Pullman, A. J Phys Chem 1988, 92, 1631.
64. Langlet, J.; Gresh, N.; Giessner-Prettre, C. Biopolymers 1995, 36, 765.
65. (a) Gresh, N.; Sponer, J. E.; Spackova, N.; Leszczynski, J.; Sponer, J. J Phys Chem B 107, 8669;
66. (b) Ledecq, M.; Lebon, F.; Durant, F.; Giessner-Prettre, C.; Marquez, A.; Gresh, N. J Phys Chem B 2003, 107, 10640.
67. Gresh, N.; Derreumaux, P. J Phys Chem B 2003, 107, 4862.
68. Gresh, N.; Claverie, P.; Pullman, A. Theoret Chim Acta 1984, 66, 1.
69. Evangelakis, G.; Rizos, J.; Lagaris, I.; Demetropoulos, G. N. Comput Phys Commun 1987, 46, 401.
70. Force-Field Cff91. Discover Software, Accelrys Inc., San Diego, CA.
71. Garcia-Saez, I.; Hopkins, J.; Papamicael, C.; Franceschini, N.; Amicosante, G.; Rossolini, G. M.; Galleni, M.; Frere, J.-M; Dideberg, O. J Biol Chem 2003, 26, 23868.
72. (a) Scrofani, S. D.; Chung, J.; Huntley, J. J.; Benkovic, S. J.; Wright, P. E.; Dyson, H. J. Biochemistry 1999, 38, 14507;
73. (b) Huntley, J. J.; Scrofani, S. D.; Osborne, M. J.; Wright, P. E.; Dyson, H. J. Biochemistry 2000, 39, 13356;
74. (c) Moali, C.; Anne, C.; Lamotte-Brasseur, J.; Groslambert, S.; Devreese, B.; Van Beeumen, J.; Galleni, M.; Frere, J.-M. Chem Biol 2003, 10, 319;
75. (d) Huntley, J. J.; Fast, W.; Benkovic, S. J.; Wright, P. E.; Dyson, H. J. Protein Sci 2003, 12, 1368.
76. Garmer, D. R.; Gresh, N.; Roques, B.-P. Proteins 1998, 31, 42.
77. (a) Gresh, N. J Phys Chem A 1997, 8680;
78. Masella, M.; Gresh, N.; Flament, J.-P. J Chem Soc Faraday Trans 1998, 94, 2745.