QSAR model of the quorum-quenching N-acyl-homoserine lactone lactonase activity

Journal of Biological Systems

Volumn 16, Issue 2, 2008, Pages 279-293

  Nantasenamat, Chanin ^a   Piacham, Theeraphon ^a   Tantimongcolwat, Tanawut ^a   Naenna, Thanakorn ^a   Isarankura Na Ayudhya, Chartchalerm ^a   Prachayasittikul, Virapong ^a  

^a MAHIDOL UNIVERSITY   (Thailand)

Author keywords

N acyl homoserine lactone; PLS; QSAR; Quorum quenching; Quorum sensing

Indexed keywords

EID: 44849097809     PISSN: 02183390     EISSN: None     Source Type: Journal    
DOI: 10.1142/S021833900800254X     Document Type: Article

References (44)

1. Camara M, Williams P, Hardman A, Controlling infection by turning in and turning down the volume of bacterial small-talk, Lancet Infect Dis 2:667-676, 2002.
2. Whitehead NA, Barnard AML, Slater H, Simpson NJL, Salmond GPC, Quorum-sensing in Gram-negative bacteria, FEMS Microbiol Rev 25:365-404, 2001.
3. Winzer K, Williams P, Quorum sensing and the regulation of virulence gene expression in pathogenic bacteria, Int J Med Microbiol 291:131-143, 2001.
4. Fuqua C, Parsek MR, Greenberg EP, Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing, Annu Rev Genet 35:439-468, 2001.
5. Bassler BL, How bacteria talk to each other: regulation of gene expression by quorum sensing, Curr Opin Microbiol 2:582-587, 1999.
6. Reading NC, Sperandio V, Quorum sensing: the many languages of bacteria, FEMS Microbiol Lett 254:1-11, 2006.
7. Miller MB, Bassler BL, Quorum sensing in bacteria, Annu Rev Microbiol 55:165-199, 2001.
8. Yates EA, Philipp B, Buckley C, Atkinson S, Chhabra SR, Sockett RE, Goldner M, Dessaux Y, Camara M, Smith H, Williams P, N-acylhomoserine lactones undergo lactonolysis in a pH-, temperature-, and acyl chain length-dependent manner during growth of Yersinia pseudotuberculosis and Pseudomonas aeruginosa, Infect Immun 70:5635-5646, 2002.
9. Persson T, Givskov M, Nielsen J, Quorum sensing inhibition: targeting chemical communication in Gram-negative bacteria, Curr Med Chem 12:3103-3115, 2005.
10. Rasmussen TB, Givskov M, Quorum sensing inhibitors: a bargain of effects, Microbiology 152:895-904, 2006.
11. Suga H, Smith KM, Molecular mechanisms of bacterial quorum sensing as a new drug target, Curr Opin Chem Biol 7:586-591, 2003.
12. Williams P, Quorum sensing: an emerging target for antibacterial chemotherapy? Expert Opin Ther Targets 6:257-274, 2002.
13. Kim MH, Choi WC, Kang HO, Lee JS, Kang BS, Kim KJ, Derewenda ZS, Oh TK, Lee CH, Lee JK, The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase, Proc Natl Acad Sci USA 102:17606-17611, 2005.
14. Dong YH, Wang LH, Xu JL, Zhang HB, Zhang XF, Zhang LH, Quenching quorumsensing-dependent bacterial infection by an N-acyl homoserine lactonase, Nature 411:813-817, 2001.
15. Reimmann C, Ginet N, Michel L, Keel C, Michaux P, Krishnapillai V, Zala M, Heurlier K, Triandafillu K, Harms H, Defago G, Haas D, Genetically programmed autoinducer destruction reduces virulence gene expression and swarming motility in Pseudomonas aeruginosa PA O1, Microbiology 148:923-932, 2002.
16. Vlachos C, Paton RC, Saunders JR, Wu QH, A rule-based approach to the modelling of bacterial ecosystems, Biosystems 84:49-72, 2006.
17. Anguige K, King JR, Ward JP, Modelling antibiotic- and anti-quorum sensing treatment of a spatially-structured Pseudomonas aeruginosa population, J Math Biol 51:557-594, 2005.
18. Anguige K, King JR, Ward JP, Williams P, Mathematical modeling of therapies targeted at bacterial quorum sensing, Math Biosci 192:39-83, 2004.
19. Fagerlind MG, Nilsson P, Harlen M, Karlsson S, Rice SA, Kjelleberg S, Modeling the effect of acylated homoserine lactone antagonists in Pseudomonas aeruginosa, Biosystems 80:201-213, 2005.
20. Riedel K, Kothe M, Kramer B, Saeb W, Gotschlich A, Ammendola A, Eberl L, Computer-aided design of agents that inhibit the cep quorum-sensing system of Burkholderia cenocepacia, Antimicrob Agents Chemother 50:318-323, 2006.
21. McDowell P, Affas Z, Reynolds C, Holden MTG, Wood SJ, Saint S, Cockayne A, Hill PJ, Dodd CER, Bycroft BW, Chan WC, Williams P, Structure, activity and evolution of the group I thiolactone peptide quorum-sensing system of Staphylococcus aureus, Mol Microbiol 41:503-512, 2001.
22. Welch M, Dutton JM, Glansdorp FG, Thomas GL, Smith DS, Coulthurst SJ, Barnard AM, Salmond GP, Spring DR, Structure-activity relationships of Erwinia carotovora quorum sensing signaling molecules, Bioorg Med Chem Lett 15:4235-4238, 2005.
23. Persson T, Hansen TH, Rasmussen TB, Skinderso ME, Givskov M, Nielsen J, Rational design and synthesis of new quorum-sensing inhibitors derived from acylated homoserine lactones and natural products from garlic, Org Biomol Chem 3:253-262, 2005.
24. Wang LH, Weng LX, Dong YH, Zhang LH, Specificity and enzyme kinetics of the quorum-quenching N-acyl homoserine lactone lactonase (AHL-lactonase), J Biol Chem 279:13645-13651, 2004.
25. Dennington II R, Keith T, Millam J, Eppinnett K, Hovell WL, Gilliland R, GaussView, Version 3.09, Semichem, Inc., Shawnee Mission, KS, 2003.
26. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery J, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, 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 JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA, Gaussian 03, Revision C.02, Gaussian, Inc., Wallingford, CT, 2004.
27. Thanikaivelan P, Subramanian V, Raghava Rao J, Unni Nair B, Application of quantum chemical descriptor in quantitative structure activity and structure property relationship, Chem Phys Lett 323:59-70, 2000.
28. Karelson M, Lobanov VS, Katritzky AR, Quantum-chemical descriptors in QSAR/QSPR studies, Chem Rev 96:1027-1044, 1996.
29. Nantasenamat C, Isarankura-Na-Ayudhya C, Tansila N, Naenna T, Prachayasittikul V, Prediction of GFP spectral properties using artificial neural network, J Comput Chem 28:1275-1289, 2007.
30. Wold S, Sjostrom M, Eriksson L, PLS-regression: a basic tool of chemometrics, Chemometr Intell Lab 58:109-130, 2001.
31. Haaland DM, Thomas EV, Partial least-squares methods for spectral analyses. 1. Relation to other quantitative calibration methods and the extraction of qualitative information, Anal Chem 60:1193-1202, 1988.
32. Cedeno W, Agrafiotis DK, Using particle swarms for the development of QSAR models based on K-nearest neighbor and kernel regression, J Comput Aided Mol Des 17: 255-263, 2003.
33. Gasteiger J, Engel T, Cheminformatics: A Textbook, Wiley-VCH, Weinheim, 2003.
34. Tetko IV, The WWW as a tool to obtain molecular parameters, Mini Rev Med Chem 3:809-820, 2003.
35. Tetko IV, Computing chemistry on the Web, Drug Discov Today 10:1497-1500, 2005.
36. Tetko IV, Gasteiger J, Todeschini R, Mauri A, Livingstone D, Ertl P, Palyulin VA, Radchenko EV, Zefirov NS, Makarenko AS, Tanchuk VY, Prokopenko VV, Virtual computational chemistry laboratory - design and description, J Comput Aided Mol Des 19:453-463, 2005.
37. Todeschini R, Consonni V, Mannhold R, Kubinyi H, Timmerman H, Handbook of Molecular Descriptors, Wiley-VCH, Weinheim, 2000.
38. Nantasenamat C, Isarankura-Na-Ayudhya C, Naenna T, Prachayasittikul V, Quantitative structure-imprinting factor relationship of molecularly imprinted polymers, Biosens Bioelectron 22:3309-3317, 2007.
39. Agrafiotis DK, Cedeno W, Lobanov VS, On the use of neural network ensembles in QSAR and QSPR, J Chem Inf Comput Sci 42:903-911, 2002.
40. Livingstone DJ, Manallack DT, Tetko IV, Data modelling with neural networks: advantages and limitations, J Comput Aided Mol Des 11:135-142, 1997.
41. Witten IH, Frank E, Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations, Morgan Kaufmann Publishers, San Francisco, 2000.
42. nd ed., Wiley-VCH, Weinheim, 1999.
43. Gu CG, Jiang X, Ju XH, Yang XL, Yu GF, DFT study on the structure-toxicity relationship of dioxin compounds using PLS analysis, SAR QSAR Environ Res 18:603-619, 2007.
44. Zhou YP, Cai CB, Huan S, Jiang JH, Wu HL, Shen GL, Yu RQ, QSAR study of angiotensin II antagonists using robust boosting partial least squares regression, Anal Chim Acta 593:68-74, 2007.