Molecular modeling studies of yersinia pestis dihydrofolate reductase

Journal of Biomolecular Structure and Dynamics

Volumn 29, Issue 2, 2011, Pages 351-367

  Oliveira, Aline A ^a   Rennó, Magdalena N ^b   de Matos, César A S ^c   Bertuzzi, Morena D ^a   Ramalho, Teodorico C ^d   Fraga, Carlos A M ^b   França, Tanos C C ^a  

^a MILITARY INSTITUTE OF ENGINEERING   (Brazil)

^b FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^c Schlumberger Oilfield Services   (Brazil)

^d FEDERAL UNIVERSITY OF LAVRAS   (Brazil)

Author keywords

Docking; Homology Modeling; Molecular Dynamics; Plague; Selective inhibition; Yp DHFR; Yersinia pestis

Indexed keywords

DIHYDROFOLATE REDUCTASE; METHOTREXATE; PIRITREXIM; TRIMETOPRIME; TRIMETOPRIME 5' CBP; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CONTROLLED STUDY; DRUG PROTEIN BINDING; DRUG STRUCTURE; ENERGY TRANSFER; ENZYME ACTIVE SITE; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN INTERACTION; VALIDATION PROCESS; YERSINIA PESTIS;

YERSINIA PESTIS;

EID: 80052188062     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2011.10507390     Document Type: Article

References (93)

1. Achtman, M., Zurth, K., Morelli, G., Torrea, G., Guiyoule, A., and Carniel, E., 1999. Proc Natl Acad Sci USA, 96:14043–14048. Erratum in:Proc Natl Acad Sci USA 97, 8192 (2000)
2. Perry, R. D., and Fetherston, J. D., 1997. Clin Microbiol Rev, 10:35–66.
3. Kukkonen, M., Lahteenmaki, K., Suomalainen, M., Kalkkinen, N., Emody, L., Lang, H., and Korhonen, T. K., 2001. Mol Microbiol, 40:1097–1111.
4. Bitam, I., Baziz, B., Rolain, J., Belkaid, M., and Raoult, D., 2006. Emerg Infect Dis, 12:1975–1976.
5. Bitam, I., Dittmar, K., Parola, P., Whiting, M. F., and Raoult, D., 2010. Int J Infect Dis, 14:e667–e676.
6. Eisen, R. J., Borchert, J. N., Holmes, J. L., Amatre, G., Wyk, K. V., Enscore, R. E., Babi, N., Atiku, L. A., Wilder, A. P., Vetter, S. M., Bearden, S. W., Montenieri, J. A., and Gage, K. L., 2008. Am J Trop Med Hyg, 78:949–956.
7. Lahteenmaki, K., Virkola, R., Saren, A., Emody, L., and Korhonen, T. K., 1998. Infect Immun, 66:5755–5762.
8. Lahteenmaki, K., Kuuselam, P., and Korhonen, T. K., 2001. FEMS Microbiol Rev, 25:531–552.
9. Achtman, M., Morelli, G., Zhu, P., Wirth, T., Diehl, I., Kusecek, B., Vogler, A. J., Wagner, D. M., Allender, C. J., Easterday, W. R., Chenal-Francisque, V., Worsham, P., Thomson, N. R., Parkhill, J., Lindler, L. E., Carniel, E., and Keim, P., 2004. Proc Natl Acad Sci USA, 101:17837–17842.
10. Galimand, M., Guiyoule, A., Gerbaud, G., Rasoamanana, B., Chanteau, S., Carniel, E., and Courvalin, P., 1997. New Eng J of Med, 337:677–680.
11. Welch, T. J., Fricke, W. F., McDermott, P. F., White, D. G., Rosso, M. L., Rasko, D. A., Mammel, M. K., Eppinger, M., Rosovitz, M. J., Wagner, D., Rahalison, L., LeClerc, J. E., Hinshaw, J. M., Lindler, L. E., Cebula, T. A., Carniel, E., and Ravel, J., 2007. PloS ONE, 2:e309
12. Huennekens, F. M., Duffy, T. H., and Vitols, K. S., 1987. NCI Monogr, 5:1–8.
13. Ingraham, H. A., Dickey, L., and Goulian, M., 1986. Biochemistry, 25:3225–3230.
14. Yoshida, A., Tanaka, S., Hiraoka, O., Koyama, Y., Hirota, Y., Ayusawa, D., Seno, T., Garrett, C., and Wataya, Y., 1987. J Biol Chem, 262:8235–8241.
15. Roth, B., Rauckman, B. S., Ferone, R., Baccanari, D. P., Champness, J. N., and Hyde, R. M., 1987. J Med Chem, 30:348–356.
16. Rosowsky, A., Forsch, R. A., and Queener, S. F., 2002. J Med Chem, 45:233–241.
17. Kuyper, L. F., Roth, B., Baccanari, D. P., Ferone, R., Beddell, C. R., Champness, J. N., Stammers, D. K., Dann, J., Norrington, F. E., Baker, D. J., and Goodford, P. J., 1985. J Med Chem, 28:303–311.
18. Akten, E. D., Cansu, S., and Doruker, P., 2009. J Biomol Struct Dyn, 27:13–25.
19. Andrianov, A. M., 2009. J Biomol Struct Dyn, 26:445–454.
20. Andrianov, A. M., and Anishchenko, I. V., 2009. J Biomol Struct Dyn, 27:179–193.
21. Borkar, A., Ghosh, I., and Bhattacharyya, D., 2010. J Biomol Struct Dyn, 27:695–712.
22. Cambria, M. T., Di Marino, D., Falconi, M., Garavaglia, S., and Cambria, A., 2010. J Biomol Struct Dyn, 27:501–509.
23. da Cunha, E. F.F., Barbosa, E. F., Oliveira, A. A., and Ramalho, T. C., 2010. J Biomol Struct Dyn, 27:619–625.
24. Meynier, C., Guerlesquin, F., and Roche, P., 2009. J Biomol Struct Dyn, 27:49–57.
25. Mohan, S., Perry, J. J. P., Poulose, N., Nair, B. G., and Anilkumar, G., 2009. J Biomol Struct Dyn, 26:455–464.
26. Ramalho, T. C., Caetano, M. S., da Cunha, E. F.F., Souza, T. C. S., and Rocha, M. V. J., 2009. J Biomol Struct Dyn, 27:195–207.
27. Sille, J., and Remko, M., 2009. J Biomol Struct Dyn, 26:431–444.
28. Bairagya, H. R., Mukhopadhyay, B. P., and Sekar, K., 2009. J Biomol Struct Dyn, 27:149–158.
29. Jin, B., Lee, H. M., and Kim, S. K., 2010. J Biomol Struct Dyn, 27:457–464.
30. Koshy, C., Parthiban, M., and Sowdhamini, R., 2010. J Biomol Struct Dyn, 28:71–83.
31. Mehrnejad, F., and Zarei, M., 2010. J Biomol Struct Dyn, 27:551–559.
32. Roy, S., and Thakur, A. R., 2010. J Biomol Struct Dyn, 27:443–455.
33. Sharadadevi, A., and Nagaraj, R., 2010. J Biomol Struct Dyn, 27:541–550.
34. Sharma, S., Sonavane, U. B., and Joshi, R. R., 2010. J Biomol Struct Dyn, 27:663–676.
35. Tao, Y., Rao, Z. H., and Liu, S. Q., 2010. J Biomol Struct Dyn, 28:143–157.
36. Timofeyeva, N. A., Koval, V. V., Knorre, D. G., Zharkov, D. O., Saparbaev, M. K., Ishchenko, A. A., and Fedorova, O. S., 2009. J Biomol Struct Dyn, 26:637–652.
37. Varughese, J. F., Chalovich, J. M., and Li, Y., 2010. J Biomol Struct Dyn, 28:159–173.
38. Zhang, J. P., 2009. J Biomol Struct Dyn, 27:159–162.
39. Zhong, L. H., and Xie, J. M., 2009. J Biomol Struct Dyn, 26:525–533.
40. Cordomi, A., and Perez, J. J., 2009. J Biomol Struct Dyn, 27:127–147.
41. Hage-Melim, L. I. D., da Silva, C. H.T.D., Semighini, E. P., Taft, C. A., and Sampaio, S. V., 2009. J Biomol Struct Dyn, 27:27–35.
42. Kahlon, A. K., Roy, S., and Sharma, A., 2010. J Biomol Struct Dyn, 28:201–210.
43. Chen, C. Y. C., 2009. J Biomol Struct Dyn, 27:271–282.
44. Chen, C. Y., 2010. J Biomol Struct Dyn, 27:627–640.
45. Chen, C. Y., Chang, Y. H., Bau, D. T., Huang, H. J., Tsai, F. J., Tsai, C. H., and Chen, C. Y. C., 2009. J Biomol Struct Dyn, 27:171–178.
46. Huang, H. J., Lee, K. J., Yu, H. W., Chen, C. Y., Hsu, C. H., Chen, H. Y., Tsai, F. J., and Chen, C. Y. C., 2010. J Biomol Struct Dyn, 28:23–37.
47. Huang, H. J., Lee, K. J., Yu, H. W., Chen, H. Y., Tsai, F. J., and Chen, C. Y., 2010. J Biomol Struct Dyn, 28:187–200.
48. Likhatskaya, G. N., Solov'eva, T. F., Novikova, O. D., Issaeva, M. P., Gusev, K. V., Kryzhko, I. B., Trifonov, E. V., and Nurminski, E. A., 2005. J Biom Struc Dyn, 23:163–174.
49. da Cunha, E. F.F., Ramalho, T. C., Maia, E. R., and Alencastro, R. B., 2005. Expert Opin Ther Patents, 15:967–986.
50. Cody, V., Pace, J., Chisum, K., and Rosowsky, A., 2006. Prot Struc Func Bioinf, 65:959–969.
51. Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. E., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M., 1977. J Mol Biol, 112:535–542.
52. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E., 2000. Nucleic Acids Res, 28:235–242.
53. Summerfield, R. L., Daigle, D. M., Mayer, S., Mallik, D., Hughes, D. W., Jackson, S. G., Sulek, M., Organ, M. G., Brown, E. D., and Junop, M. S., 2006. J Med Chem, 49:6977–6986.
54. Guex, N., and Peitsch, M. C., 1997. Electrophoresis, 18:2714–2723.
55. Schwede, T., Kopp, J., Guex, N., and Peitsch, M. C., 2003. Nucleic Acid Res, 31:3381–3385.
56. Arnold, K., Bordoli, L., Kopp, J., and Schwede, T., 2006. Bioinformatics, 22:195–201.
57. Cody, V., Galitsky, N., Rak, D., Luft, J. R., Pangborn, W., and Queener, S. F., 1999. Biochemistry, 38:4303–4312.
58. van der Spoel, D., Lindahl, E., Hess, B., van Buuren, A. R., Apol, E., Meulenhoff, P. J., Tieleman, D. P., Sijbers, A. L.T. M., Feenstra, K. A., van Drunen, R., and Berendsen, H. J. C., 2005. GROMACS user manual version 4.0. Groningen:University of Groningen, Department of Biophysical Chemistry.
59. Berendsen, H. J. C., Van der Spoel, D., and Van Drunen, R., 1995. Comput Phys Commun, 91:43–56.
60. Schuettelkopf, A. W., and van Aalten, D. M.F., 2004. Acta Crystallogr, SectD:BiolCrystallogr, 60:1355–1363.
61. Klon, A. E., Heroux, A., Ross, L. J., Pathak, V., Johnson, C. A., Piper, J. R., Borhani, D. W., and Mol, J., 2002. Biol, 320:677–693.
62. Pontius, J., Richelle, J., and Wodak, S. J., 1996. J MolBiol, 264:121–136.
63. Laskowski, R. A., Macarthur, M. W., Moss, D. S., and Thornton, J. M., 1993. J Appl Crystallogr, 26:283–291.
64. Vriend, G. J., 1990. Mol Graph, 8:52–56.
65. Bowie, J. U., Luthy, R., and Eisenberg, D., 1991. Science, 253:164–170.
66. Luthy, R., Bowie, J. U., and Eisenberg, D., 1992. Nature, 356:83–85.
67. 2008. http://nihserver.mbi.ucla.edu/Verify_3D/accessed in May
68. Sippl, M. J., 1993. Proteins, 17:355–362.
69. Hehre, W. J., Deppmeier, B. J., and Klunzinger, P. E., 1999. PC SPARTAN Pro. Irvine, CA:Wavefunction.
70. Dewar, M. J. S., Zoebisch, E. G., Healy, E. F., and Stewart, J. J. P., 1985. J Am Chem Soc, 107:3902–3909.
71. Thomsen, R., and Christensen, M. H., 2006. J Med Chem, 49:3315–3332.
72. Oostenbrink, C., Villa, A., Mark, A. E., and van Gunsteren, W. F., 2004. J Comput Chem, 25:1656–1676.
73. Humphrey, W., Dalke, A., and Schulten, K., 1996. J Mol Graph, 14:33–38.
74. Edwards, P. M., 2002. J Chem Inf Comput Sci, 42:1270–1271.
75. Koradi, R., Billeter, M., and Wüthrich, K., 1996. J Mol Graph, 14:51–55.
76. Warren, D., 2002. The PyMOL molecular graphics system San Carlos, CA:DeLano Scientific.
77. Ramachandran, G. N., and Sasisekharan, V., 1968. Adv Protein Chem, 23:283–437.
78. Oefner, C., D'arcy, A., and Winkler, F. K., 1988. Eur J Biochem, 174:377–385.
79. Davies, J. F., Delcamp, T. J., Prendergad, N. J., Ashford, V. A., Freisheim, J. H., and Kraut, J., 1990. Biochemistry, 29:9467–9479.
80. Polshakov, V. I., 2001. Russ Chem Bull Int Ed50,:1733–1752.
81. Wright, J. E., Yurasek, G. K., Chen, Y., and et al. 2003. Biochem Pharmacol, 65:1427–1433. Further studies on the interaction of nonpolyglutamatable aminopterin analogs with dihydrofolate reductase and the reduced folate carrier as determinants of in vitro antitumor activity
82. Warren, G. L., Webster, A. C., Capelli, A. M., Clarke, B., LaLonde, J., Lambert, M. H., Lindvall, M., Nevins, N., Semus, S. F., Senger, S., Tedesco, G., Wall, I. D., Woolven, J. M., Peishoff, C. E., and Head, M. S., 2006. J Med Chem, 49:5912–5931.
83. Leach, A. R., Shoichet, B. K., and Peishoff, C. E., 2006. J Med Chem, 49:5851–5855.
84. Kontoyanni, M., McClellan, L. M., and Sokol, G. S., 2004. J Med Chem, 47:558–565.
85. Gonçalves, A. S., França, T. C.C., Villar, J. D. F., and Pascutti, P. G., 2011. J Braz Chem Soc, 22:155–165.
86. Guimarães, A. P., Oliveira, A. A., Cunha, E. F. F., Ramalho, T. C., and França, T. C.C., 2011. J Biom Struc Dyn, 28:455–469.
87. Guimarães, A. P., Oliveira, A. A., Cunha, E. F. F., Ramalho, T. C., and França, T. C.C., 2011. J Mol Model, 17:1–13.
88. da Silva, M. L., da Silva, A. G., Batista, P. R., Figueroa-Villar, J. D., Pascutti, P. G., and França, T. C.C., 2010. Mol Sim, 36:5–14.
89. França, T. C.C., Rocha, M. R. M., Reboredo, B. M., Renno, M. N., Tinoco, L. W., and Figueroa-Villar, J. D., 2008. J Braz Chem Soc, 19:64–73.
90. Gonçalves, A. S., França, T. C.C., Wilter, A., and Villar, J. D. F., 2006. J Braz Chem Soc, 17:968–975.
91. França, T. C.C., Wilter, A., Pascutti, P. G., Ramalho, T. C., and Figueroa-Villar, J. D., 2006. J Braz Chem Soc, 17:1383–1392.
92. França, T. C.C., Pascutti, P. G., Ramalho, T. C., and Figueroa-Villar, J. D., 2005. Biophys Chem, 115:1–10.
93. França, T. C.C., Medeiros, A. L., Santos Filho, O. A., Santos, E. C. P., and Figueroa-Villar, J. D., 2004. J Braz Chem Soc, 15:450–454.