Identifying the CmbT substrates specificity by using a quantitative structure-activity relationship (QSAR) study

Journal of the Taiwan Institute of Chemical Engineers

Volumn 45, Issue 3, 2014, Pages 764-771

  Filipic, Brankica ^a   Nikolic, Katarina ^a   Filipic, Slavica ^a   Jovcic, Branko ^a   Agbaba, Danica ^a   Antic Stankovic, Jelena ^a   Kojic, Milan ^a   Golic, Natasa ^a  

^a UNIVERSITY OF BELGRADE   (Serbia)

Author keywords

CmbT; Lactococcus lactis; MFS general substrate transporter; Multidrug resistance; QSAR

Indexed keywords

ANTIBIOTICS; COMPUTATIONAL CHEMISTRY; MOLECULAR GRAPHICS; PROTEINS; THREE DIMENSIONAL;

CMBT; LACTOCOCCUS LACTIS; MFS GENERAL SUBSTRATE TRANSPORTER; MULTIDRUG RESISTANCE; QSAR;

SUBSTRATES;

EID: 84895918570     PISSN: 18761070     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jtice.2013.09.033     Document Type: Article

References (46)

1. Levy S.B. Active efflux mechanisms for antimicrobial resistance. Antimicrob Agents Chemother 1992, 36:695-703.
2. Nikaido H. Multidrug efflux pumps of gram-negative bacteria. J Bacteriol 1996, 178:5853-5859.
3. Lawrence L.E., Barrett J.F. Efflux pumps in bacteria: overview, clinical relevance, and potential pharmaceutical target. Exp Opin Investig Drugs 1998, 7:199-217.
4. Sutcliffe J. Resistance to macrolides mediated by efflux mechanisms. Curr Opin Anti-Infect Investig Drugs 1999, 1:403-412.
5. Dushi R., Gutmann D.A., Khoo Y.S., Fagg L.A., van Veen H.W. The choreography of multidrug export. Biochem Soc Trans 2011, 39:807-811.
6. Putman M., van Veen H.W., Konings W.N. Molecular properties of bacterial multidrug transporters. Microbiol Mol Biol Rev 2000, 64:672-693.
7. Rouch D.A., Cram D.S., DiBerardino D., Littlejohn T.G., Skurray R.A. Efflux-mediated antiseptic resistance gene qacA from Staphylococcus aureus: common ancestry with tetracycline- and sugar-transport proteins. Mol Microbiol 1990, 4:2051-2062.
8. Lomovskaya O., Lewis K., Emr An Escherichia coli locus for multidrug resistance. Proc Natl Acad Sci USA 1992, 89:8938-8942.
9. Marger M.D., Saier M.H. A major superfamily of transmembrane facilitators that catalyse uniport, symport and antiport. Trends Biochem Sci 1993, 18:13-20.
10. Paulsen I.T., Skurray R.A. Topology, structure and evolution of two families of proteins involved in antibiotic and antiseptic resistance in eukaryotes and prokaryotes-an analysis. Gene 1993, 124:1-11.
11. Lewis K. Multidrug resistance pumps in bacteria: variations on a theme. Trends Biochem Sci 1994, 19:119-123.
12. Bradley S.F. Staphylococcus aureus infections and antibiotic resistance in older adults. Clin Infect Dis 2002, 34:211-216.
13. Garau J. Treatment of drug-resistant pneumococcal pneumonia. Lancet Infect Dis 2002, 2:404-415.
14. Bolhuis H., Molenaar D., Poelarends G., van Veen H.W., Poolman B., Driessen A.J., et al. Proton motive force-driven and ATP-dependent drug extrusion systems in multidrug-resistant Lactococcus lactis. J Bacteriol 1994, 176:6957-6964.
15. Bolhuis H., Poelarends G., van Veen H.W., Poolman B., Driessen A.J., Konings W.N. The lactococcal lmrP gene encodes a proton motive force dependent drug transporter. J Biol Chem 1995, 270:26092-26098.
16. Lubelski J., Mazurkiewicz P., van Merkerk R., Konings W.N., Driessen A.J. ydaG and ydbA of Lactococcus lactis encode a heterodimeric ATP-binding cassette-type multidrug transporter. J Biol Chem 2004, 279:34449-34455.
17. Filipic B., Golic N., Jovcic B., Tolinacki M., Bay D.C., Turner R.J., et al. The cmbT gene encodes a novel major facilitator multidrug resistance transporter in Lactococcus lactis. Res Microbiol 2013, 164:46-54.
18. Mazurkiewicz P., Sakamoto K., Poelarends G.J., Konings W.N. Multidrug transporters in lactic acid bacteria. Mini Rev Med Chem 2005, 5:173-181.
19. Lubelski J., van Merkerk R., Konings W.N., Driessen A.J.M. Nucleotide-binding sites of the heterodimeric LmrCD abc-multidrug transporter of Lactococcus lactis are asymmetric. Biochemistry 2006, 45:648-656.
20. Xue Y., Yap C.W., Sun L.Z., Cao Z.W., Wang J.F., Chen Y.Z. Prediction of P-glycoprotein substrates by a support vector machine approach. J Chem Inf Comput Sci 2004, 44:1497-1505.
21. Cabrera M.A., González I., Fernández C., Navarro C., Bermejo M. A topological substructural approach for the prediction of P-glycoprotein substrates. J Pharm Sci 2006, 95:589-606.
22. de Cerqueira Lima P., Golbraikh A., Oloff S., Xiao Y., Tropsha A. Combinatorial QSAR modeling of P-glycoprotein substrates. J Chem Inf Model 2006, 46:1245-1254.
23. Huang J., Ma G., Muhammad I., Cheng Y. Identifying P-glycoprotein substrates using a support vector machine optimized by a particle swarm. J Chem Inf Model 2007, 47:1638-1647.
24. Kuipers O.P., de Ruyter P.G.G.A., Kleerebezem M., de Vos W.M. Quorum sensing-controlled gene expression in lactic acid bacteria. J Biotechnol 1998, 64:15-21.
25. Sakamoto K., Margolles A., van Veen H.W., Konings W.N. Hop resistance in the beer spoilage bacterium Lactobacillus brevis is mediated by the ATP-binding cassette multidrug transporter HorA. J Bacteriol 2001, 183:5371-5375.
26. Madera M., Vogel C., Kummerfeld S.K., Chothia C., Gough J. The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res 2004, 32:235-239.
27. Kelley L.A., Sternberg M.J.E. Protein structure prediction on the web: a case study using the Phyre server. Nat Protoc 2009, 4:363-371.
28. Bennett-Lovsey R.M., Herbert A.D., Sternberg M.J.E., Kelley L.A. Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins 2008, 70:611-625.
29. Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
30. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat.F T.N., Weissig H., et al. The protein data bank. Nucleic Acids Res 2000, 28:235-242.
31. Tress M.L., Jones D.T., Valenica A. Predicting reliable regions in protein alignments from sequence profiles. J Mol Biol 2003, 330:705-718.
32. Duan Y., Wu C., Chowdhury S., Lee M.C., Xiong G., Zhang W., et al. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 2003, 24:1999-2012.
33. Ryckaert J.P., Ciccotti G., Berendsen H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977, 23:327-341.
34. Wass M.N., Kelley L.A., Sternberg M.J. 3DLigandSite: predicting ligand-binding sites using similar structures. Nucleic Acids Res 2010, 38:W469-W473. 10.1093/nar/gkq406.
35. Stewart J.J.P. Optimization of parameters for semiempirical methods. I. Method. J Comput Chem 1989, 10:209-220.
36. Stewart J.J.P. Optimization of parameters for semiempirical methods. II. Applications. J Comput Chem 1989, 10:221-264.
37. Fischer C.F.F. The Hartree-Fock method for atoms: a numerical approach 1977, John Wiley and Sons, New York.
38. Barone V., Biczysko M., Bloino J., Puzzarini C. Characterization of the elusive conformers of glycine from state-of-the-art structural, thermodynamic, and spectroscopic computations: theory complements experiment. J Chem Theory Comput 2013, 9:1533-1547.
39. Nikolic K., Ivković B., Bešović Ž, Marković S., Agbaba D. A validated enantiospecific method for determination and purity assay of clopidogrel. Chirality 2009, 21:878-885.
40. Pastor M., Cruciani G., McLay I., Pickett S., Clementi S. GRid-INdependent. Descriptors (GRIND): a novel class of alignment-independent three-dimensional molecular descriptors. J Med Chem 2000, 43:3233-3243.
41. Eriksson L., Johansson E., Kettaneh-Wold N., Trygg J., Wikstrom C., Wold S. Multi-and megavariate data analysis. Basic principles and applications I 2001, Umetrics Academy, Umeå. 2nd ed.
42. Allen D.M. The relationship between variable selection and data augmentation and a method for prediction. Technometrics 1974, 16:125-127.
43. Wold S., Johansson E., Cocchi M. PLS-partial least-squares projections to latent structures. 3D-QSAR in drug design, theory, methods, and applications 1993, 523-550. ESCOM, Leiden. H. Kubinyi (Ed.).
44. Filipic B., Jovcic B., Uzelac G., Miljkovic M., Antic-Stankovic J., Topisirovic L., et al. Over-expressed CmbT multidrug resistance transporter improves the fitness of Lactococcus lactis. Genetika 2013, 45:197-206.
45. Bolhuis H., van Veen H.W., Brands J.R., Putman M., Poolman B., Driessen A.J., et al. Energetics and mechanism of drug transport mediated by the Lactococcal multidrug transporter LmrP. J Biol Chem 1996, 271:24123-24128.
46. Mazurkiewicz P., Konings W.N., Poelarends G.J. Acidic residues in the Lactococcal multidrug efflux pump lmrp play critical roles in transport of lipophilic cationic compounds. J Biol Chem 2002, 277:26081-26088.