Comparative chemometric and QSAR/SAR study of structurally unrelated substrates of a MATE efflux pump VmrA from V. parahaemolyticus: Prediction of multidrug resistance

QSAR and Combinatorial Science

Volumn 27, Issue 3, 2008, Pages 314-329

  Kiralj, Rudolf ^a   Ferreira, Márcia M C ^a  

^a UNIVERSITY OF CAMPINAS   (Brazil)

Author keywords

Agent receptor interactions; Molecular descriptors; Multidrug resistance; Regression models; Semiempirical methods

Indexed keywords

AROMATIC COMPOUNDS; AROMATIZATION; CLUSTER ANALYSIS; COMPUTATIONAL CHEMISTRY; ESCHERICHIA COLI; HIERARCHICAL SYSTEMS; HYDROGEN BONDS; HYDROPHOBICITY; LEAST SQUARES APPROXIMATIONS; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS;

AGENT - RECEPTOR INTERACTION; DESCRIPTORS; EFFLUX PUMPS; HYDROPHOBICS; MOLECULAR DESCRIPTORS; MULTIDRUG RESISTANCE; RECEPTOR INTERACTION; REGRESSION MODELLING; SEMI-EMPIRICAL METHODS; V. PARAHAEMOLYTICUS;

FORECASTING;

4',6 DIAMIDINO 2 PHENYLINDOLE; ACRIFLAVINE; AMPICILLIN; AZASERINE; BUTYLATED HYDROXYANISOLE; CEFOTAXIME; CHLORAMPHENICOL; CIPROFLOXACIN; CLAVULANIC ACID; DEOXYCHOLATE SODIUM; DODECYL SULFATE SODIUM; DOXORUBICIN; DOXYCYCLINE; ELLIPTICINE; ERYTHROMYCIN; ETHIDIUM BROMIDE; MULTIDRUG RESISTANCE PROTEIN; NORFLOXACIN; OXYTETRACYCLINE; PHENOLPHTHALEIN; PIPERACILLIN; RHODAMINE 6G; SORBIC ACID; STREPTOMYCIN; TAZOBACTAM; TETRACYCLINE; TETRAPHENYLPHOSPHONIUM; TICARCILLIN; UNCLASSIFIED DRUG; UNINDEXED DRUG; VIBRIO MULTIDRUG RESISTANCE PROTEIN A;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; AROMATIZATION; ARTICLE; BACTERIAL STRAIN; CHEMOMETRIC ANALYSIS; COMPARATIVE STUDY; DRUG STRUCTURE; ESCHERICHIA COLI; HYDROGEN BOND; HYDROPHILICITY; HYDROPHOBICITY; MINIMUM INHIBITORY CONCENTRATION; MULTIDRUG RESISTANCE; NONHUMAN; PARTIAL LEAST SQUARES REGRESSION; PRIORITY JOURNAL; PROTEIN TRANSPORT; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STATISTICAL MODEL; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; VIBRIO PARAHAEMOLYTICUS;

VIBRIO; VIBRIO PARAHAEMOLYTICUS;

EID: 49149086789     PISSN: 1611020X     EISSN: 16110218     Source Type: Journal    
DOI: 10.1002/qsar.200630164     Document Type: Article

References (36)

1. FDA/CFSAN Bad Bug Book: Vibrio parahaemolyticus. http://vm.cfsan.fda.gov/~mow/chap9.html (last access 7/9/2005).
2. CDC/DBMD Disease Information: Vibrio parahaemolyticus. http://www.cdc.gov/neidod/dbmd/diseaseinfo/vibrioparahaemolyticu-g.htm (last access 7/9/2005).
3. NZFSA Data Sheet: Vibrio parahaemolyticus. http://www.nzfsa.govt.nz/science/data_sheets/vibrio-parahaemolyticus.pdf (last access 8/9/2005).
4. H. Ho, H. Amin, H.-R. Lee. e-Medicine.com. Vibrio Infections. http://www.emedicine.com/med/topic2375.htm (last access 8/9/2005).
5. J. Chen, Y. Morita, M. N. Huda, T. Kuroda, T. Mizushima, T. Tsuchiya, J. Bacteriol. 2002, 184, 572-576.
6. Y. Morita, K. Kodama, S. Shiota, T. Mine, A. Kataoka, T. Mizusima, T. Tsuchiya, Antimicrob. Agents Chemother. 1998, 42, 1778-1782.
7. M. H. Brown, I. T. Paulsen, R. A. Skurray, Mol. Microbiol. 1999, 31, 394-395.
8. Genome composition of V. parahaemolyticus RIND2210633. http://www.membranetransport.org (last access 12/7/2005).
9. K. Makin, K. Oshima, K. Kurokawa, K. Yokoyama, T. Uda, K. Tagomori, Y. Iijima, M. Najima, M. Nakano, A. Yamashita, Y. Kubota, S. Kimura, T. Yasunaga, T. Honda, H. Shinagawa, M. Hattori, T. Iida, Lancet 2003, 361, 743-749.
10. R. N. Hvorup, B. Winnen, A. B. Chang, Y. Jiang, X.-F. Zhou, M. H. Saier, Jr., Eur. J. Biochem. 2003, 270, 799-813.
11. K. Poole, Antimicrob. Agents Chemother. 2000, 44, 2233-2241.
12. V. Cattoir, Pathol. Biol. 2004, 52, 607-616.
13. D. Ma, D. N. Cook, M. Alberti, N. G. Pon, H. Nikaido, J. E. Hearst, Mol. Microbiol 1995, 16, 45-55.
14. Titan 1.0.8, Wavefunction, Inc., Irvine, CA 2001.
15. F. H. Allen, Acta Cryst. B 2002, 38, 380-388.
16. Cambridge Structural Database 5.26, Release November 2004 - Update February 2005, The Cambridge Structural Data Centre, University of Cambridge, Cambridge, UK 2004.
17. I. J. Bruno, J. C. Cole, P. R. Edgington, M. Kessler, C. F. Macrae, P. McCabe, J. Pearson, R. Taylor, Acta Cryst. B 2002, 58, 389-397.
18. I. Piantanida, V. Tomisic, M. Zinic, J. Chem. Soc. Perkin Trans. 2000, 375-383.
19. C.-P. Hsiao, K. J. Siebert, Int. J. Food Microbiol. 1999, 47, 189-201.
20. R. Kiralj, B. Kojic-Prodic, I. Piantanida, M. Zinic, Acta Cryst. B 1999, 55, 55-69.
21. V. Vrabel, J. Sivy, S. Marchalin, Acta Cryst. C 1997, 53, 1926-1927.
22. A. Fizgerald, L. H. Jensen, Acta Cryst. B 1978, 34, 828-836.
23. V. S. Lobanov, MOPAC 6.0 for Microsoft Windows, University of Florida 1996.
24. Chem3Dultra 6.0, CambridgeSoft.Com, Cambridge, MA 2000.
25. S. Wold, L. Eriksson, Statistical Validation of QSAR Results, in: H. van de Waterbeemd (Ed.), Chemometric Methods in Molecular Design, VCH, Weinheim 1995, pp. 309-318.
26. K. R. Beebe, R. Pell, M. B. Seasholtz, Chemometrics: A Practical Guide, Wiley, New York 1998.
27. M. M. C. Ferreira, J. Braz. Chem. Soc. 2002, 13, 742-753.
28. R. Kiralj, M. M. C. Ferreira, Croat. Chem. Acta 2005, 78, 541-549.
29. Matlab 5.2, Mathworks, Inc., Natick, MA 2001.
30. Pirouette 3.02, Infometrix, Woodinville, WA 2001.
31. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne, Nucl. Acid. Res. 2000, 28, 235-242.
32. LPC/CSU: Ligand-Protein Contacts & Contacts of Structural Units, SPACE servers at the Weizmann Institute of Science, Rehovot, Israel. http://atlantis.weizmann.ac.il/space/servers/ (last access 05/01/ 2006)
33. V. Sobolev, A. Sorokine, J. Prilusky, E. E. Abola, M. Edelman, Bioinformatics 1999, 15, 327-332.
34. A. Galbraikh, A. Tropsha, J. Mol. Graph. Mod. 2002, 20, 269-276.
35. A. Tropsha, P. Gramatica, V. K. Gombar, QSAR Comb. Sci. 2003, 22, 69-77.
36. R. Kiralj, Structural studies of 4,9-diazapyrene derivatives. PhD Thesis, University of Zagreb, Zagreb, Croatia 1999.