QSAR study of oxazolidinone antibacterial agents using artificial neural networks

Molecular Simulation

Volumn 33, Issue 6, 2007, Pages 517-530

  Zou, C ^a   Zhou, L ^a  

^a SICHUAN UNIVERSITY   (China)

Author keywords

Artificial neural network; Oxazolidinone; Partial least square regression; QSAR

Indexed keywords

BACTERIA; LEAST SQUARES APPROXIMATIONS; MOLECULAR STRUCTURE; NEURAL NETWORKS;

OXAZOLIDINONE; PARTIAL LEAST SQUARE REGRESSION;

KETONES;

EID: 34548139737     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020601188528     Document Type: Article

References (41)

1. B.H. Yagi, G.E. Zurenko. In vitro activity of linezolid and eperezolid, two novel oxazolidinone antimicrobial agents, against anaerobic bacteria. Anaerobe, 3, 301 (1997).
2. G. Corti, R. Cinelli, F. Paradisi. Clinical and microbiologic efficacy and safety profile of linezolid, a new oxazolidinone antibiotic. Int. J. Antimicrob. Agents, 16, 527 (2000).
3. B. Bozdogan, P.C. Appelbaum. Oxazolidinones: activity, mode of action, and mechanism of resistance. Int. J. Antimicrob. Agents, 23, 113 (2004).
4. C.H. Park, D.R. Brittelli, C.L.J. Wang, F.D. Marsh, W.A. Gregory, M.A. Wuonola, R.J. McRipley, V.S. Eberly, A.M. Slee, M. Forbes. Antibacterials. Synthesis and structure-activity studies of 3-aryltoxooxazolidines. 4. multiply-substituted aryl derivatives. J. Med. Chem., 35, 1156 (1992).
5. B. Das, S. Rudra, A. Yadav, A. Ray, A.V.S.R. Rao, A.S.S.V. Srinivas, A. Soni, S. Saini, S. Shukla, M. Pandya, P. Bhateja, S. Malhotra, T. Mathur, S.K. Arora, A. Rattan, A. Mehta. Synthesis and SAR of novel oxazolidinones: discovery of ranbezolid. Bioorg. Med. Chem. Lett., 15, 4261 (2005).
6. B.B. Lohray, V.B. Lohray, B.K. Srivastava, S. Gupta, M. Solanki, P. Kapadnis, V. Takale, P. Pandya. Oxazolidinone: search for highly potent antibacterial. Bioorg. Med. Chem. Lett, 14, 3139 (2004).
7. M.R. Barbachyn, C.W. Ford. Oxazolidinone structure-activity relationships leading to linezolid. Angew. Chem. Int. Ed., 42, 2010 (2003).
8. A.R. Renslo, P. Jaishankar, R. Venkatachalam, C. Hackbarth, S. Lopez, D.V. Patel, M.F. Gordeev. Conformational constraint in oxazolidinone antibacterials. synthesis and structure-activity studies of (azabicyclo[3.1.0] hexylphenyl) oxazolidinones. J. Med. Chem., 48, 5009 (2005).
9. A.R. Renslo, H. Gao, P. Jaishankar, R. Venkatachalam, M. Go'mez, J. Blais, M. Huband, J.V.N.V. Prasadb, M.F. Gordeev. Conformational constraint in oxazolidinone antibacterials. Part 2: synthesis and structure-activity studies of oxa-, aza-, and thiabicyclo[3.1.0]-hexylphenyl oxazolidinones. Bioorg. Med. Chem. Lett., 16, 1126 (2006).
10. A.N. Pae, S.Y. Kim, H.Y. Kim, H.J. Joo, Y.S. Cho, K. Choi, J.H. Choi, H.Y. Koh. 3D QSAR studies on new oxazolidinone antibacterial agents by comparative molecular field analysis. Bioorg. Med. Chem. Lett., 9, 2685 (1999).
11. B. Gopalakrishnan, A. Khanderwal, S.N. Selvakumar, J. Das, S. Trehan, M.S. Kumarb. Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies of tricyclic oxazolidinones as antibacterial agents. Bioorg. Med. Chem., 11, 2569 (2003).
12. D.T. Manallack, D.J. Livingstone. Neural networks in drug discovery: have they lived up to their promise? Eur. J. Med. Chem., 34, 195 (1999).
13. G. Schneider, P. Wrede. Artificial neural networks for computer-based molecular design. Prog. Biophys. Mol. Biol., 70, 175 (1998).
14. K.L.E. Kaiser. The use of neural networks in QSARs for acute aquatic toxicological endpoints. J. Mol. Struct. (Theochem), 622, 85 (2003).
15. A.P. Borosy, K. Keseru, P. Matyus. Application of nonlinear and local modeling methods for 3D QSAR study of class I antiarrhythmics. Chemometr. Intell. Lab. Syst., 54, 107 (2000).
16. D.G. Arjona, G.L. Perez, A.G. Gonzalez. Non-linear QSAR modeling by using multilayer perceptron feedforward neural networks trained by back-propagation. Talanta, 56, 79 (2002).
17. K. Hasegawa, T. Deushi, O. Yargashi, Y. Miyashita, S. Sasaki. Artificial neural network studies in quantitative structure-activity relationships of antifungal azoxy compounds. Eur. J. Med. Chem., 30, 569 (1995).
18. J.V. Turner, D.J. Maddalena, D.J. Cutler. Pharmacokinetic parameter prediction from drug structure using artificial neural networks. Int. J. Pharma., 270, 209 (2004).
19. M.J. Genin, D.A. Allwine, D.J. Anderson, M.R. Barbachyn, D.E. Emmert, S.A. Garmon, D.R. Graber, K.C. Grega, J.B. Hester, D.K. Hutchinson, J. Morris, R.J. Reischer, C.W. Ford, G.E. Zurenko, J.C. Hamel, R.D. Schaadt, D. Stapert, B.H. Yagi. Substituent effects on the antibacterial activity of nitrogen-carbon-linked (azolylphenyl) oxazolidinones with expanded activity against the fastidious gram-negative organisms Haemophilus influenzae and Moraxella catarrhalis. J. Med. Chem., 43, 953 (2000).
20. C.S. Lee, D.A. Allwine, M.R. Barbachyn, K.C. Grega, L.A. Dolak, C.W. Ford, R.M. Jensen, E.P. Seest, J.C. Hamel, R.D. Schaadt, D. Stapert, B.H. Yagi, G.E. Zurenko, M.J. Genin. Carbon-carbon-linked (pyrazolylphenyl) oxazolidinones with antibacterial activity against multiple drug resistant gram-positive and fastidious gram-negative bacteria. Bioorg. Med. Chem., 9, 3243 (2001).
21. L.M. Thomasco, R.C. Gadwood, E.A. Weaver, J.M. Ochoada, C.W. Ford, G.E. Zurenko, J.C. Hamel, D. Stapert, J.K. Moerman, R.D. Schaadt, B.H. Yagi. The synthesis and antibacterial activity of 1,3,4-phenyl oxazolidinone analogues. Bioorg. Med. Chem. Lett., 13, 4193 (2003).
22. M. Randic. On the characterization of molecular branching. J. Am. Chem. Soc., 97, 6609 (1975).
23. L.B. Kier, L.H. Hall. Molecular Connectivity in Chemistry and Drug Research, Academic Press, New York, NY (1976).
24. L.B. Kier, L.H. Hall. Molecular Connectivity in Structure Activity Analysis, John Wiley & Sons, New York, NY (1986).
25. H. Wiener. Structural determination of paraffin boiling points. J. Am. Chem. Soc., 69, 17 (1947).
26. I. Gutman, B. Russic, N. Trinajstic, C.F. Wicox Jr. Graph theory and molecular orbitals. Part 12. Acyclic polyenes. J. Chem. Phys., 62, 3399 (1975).
27. I. Gutman, M. Randic. Algebraic characterization of skeletal branching. Chem. Phys. Lett., 47, 15 (1977).
28. A.T. Balaban. Topological, index J for heteroatom-containing molecules taking into account periodicities of element properties. Math. Chem. (MATCH), 21, 115 (1986).
29. H. Hosoya. Topological index. A proposed quantity characterizing the topological nature of structural isomers of saturated hydrocarbons. Bull. Chem. Soc. Jpn., 44, 2332 (1971).
30. P. Thanikaivelan, V. Subramanian, J.R. Rao, B.U. Nair. Application of quantum chemical descriptor in quantitative structure activity and structure property relationship. Chem. Phys. Lett., 323, 59 (2000).
31. F.R. Burden. Robust QSAR models using bayesian regularized neural networks. J. Med. Chem., 42, 3183 (1999).
32. E.G. Borges, Y. Takahata. QSAR study of anti-ulcer compounds using calculated parameters. J. Mol. Struct. (Theochem), 539, 245 (2001).
33. 1A effects in vivo and in vitro via partial least squares regression. Eur. J. Med. Chem., 32, 571 (1997).
34. N.A. Kratochwil, W. Huber, F. Muller, M. Kansy, P.R. Gerber. Predicting plasma protein binding of drugs: a new approach. Biochem. Pharm., 64, 1355 (2002).
35. S. Wold, M. Sjostrom, L. Eriksson. PLS-regression: a basic tool of chemometrics. Chemometr. Intell. Lab. Syst., 58, 109 (2001).
36. G. Chong, C.H. Jun. Performance of some variable selection methods when multicollinearity is present. Chemometr. Intell. Lab. Syst., 78, 103 (2005).
37. S. Wold. In Chemometric Methods in Molecular Design, H. van de Waterbeemd (Ed.), Vol. 2, Chapter 4.4 pp. 195-218, VCH, Weinheim (1995).
38. D.E. Rummelhart, J.L. McClelland. Parallel Distributed Processing, Volume I: Foundations, MIT Press, Cambridge, MA.
39. I.V. Tetko, D.J. Livingstone, A.I. Luik. Neural network studies. 1. Comparison of overfitting and overtraining. J. Chem. Inf. Comput. Sci., 35, 826 (1995).
40. M. Smith. Neural Networks for Statistical Modeling, Van Nostrand Reinhold, New York, USA (1994).
41. J.A. Anderson. An Introduction to Neural Networks, p. 650, MIT, Cambridge, MA (1995).