Quantitative structure-activity relationship and classification analysis of diaryl ureas against vascular endothelial growth factor receptor-2 kinase using linear and non-linear models

Chemical Biology and Drug Design

Volumn 73, Issue 6, 2009, Pages 644-654

  Sun, Min ^a   Chen, Junqing ^a   Wei, Hongtao ^a   Yin, Shuangqing ^a   Yang, Yan ^a   Ji, Min ^a  

^a SOUTHEAST UNIVERSITY   (China)

Author keywords

Classification; Enhanced replacement method; Multivariate linear regression; Quantitative structure activity relationship; Support vector machine; Vascular endothelial growth factor receptor 2 kinase inhibitors

Indexed keywords

AMINOBENZOISOXAZOLE UREA; AMINOINDAZOLE UREA; ANTINEOPLASTIC AGENT; DIARYL UREA; ENZYME INHIBITOR; PROTEIN TYROSINE KINASE; UNCLASSIFIED DRUG; UREA; VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 INHIBITOR; VASCULOTROPIN RECEPTOR 2;

ACCURACY; ARTICLE; BIOLOGICAL ACTIVITY; COMPUTER PROGRAM; DRUG DESIGN; DRUG STRUCTURE; ENHANCED REPLACEMENT METHOD; ENZYME INHIBITION; GENETIC ALGORITHM; LINEAR REGRESSION ANALYSIS; MULTIVARIATE ANALYSIS; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STATISTICAL MODEL; SUPPORT VECTOR MACHINE; TECHNIQUE;

ALGORITHMS; DISCRIMINANT ANALYSIS; LINEAR MODELS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SOFTWARE; UREA; VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR-2;

EID: 65649131871     PISSN: 17470277     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2009.00814.x     Document Type: Article

References (38)

1. Folkman J., D'Amore P.A. (1996) Blood vessel formation: what is its molecular basis? Cell 87 : 1153 1155.
2. Risau W. (1997) Mechanisms of angiogenesis. Nature 386 : 671 674.
3. Hanahan D., Folkman J. (1996) Patterns and emerging mechanisms of the angiogenic switch during tumorigenesis. Cell 86 : 353 364.
4. Liotta L.A., Steeg P.S., Stetler-Stevenson W.G. (1991) Cancer metastasis and angiogenesis: an imbalance of positive and negative regulation. Cell 64 : 327 336.
5. Schenone S., Bondavalli F., Botta M. (2007) Antiangiogenic agents: an update on small molecule VEGFR inhibitors. Curr Med Chem 14 : 2495 2516.
6. Kuo G.H., Wang A.H., Emanuel S., DeAngelis A., Zhang R., Connolly P.J., Murray W.V., Gruninger R.H., Sechler J., Fuentes-Pesquera A., Johnson D., Middleton S.A., Jolliffe L., Chen X. (2005) Synthesis and discovery of pyrazine-pyridine biheteroaryl as a novel series of potent vascular endothelial growth factor receptor-2 inhibitors. J Med Chem 48 : 1886 1900.
7. Ji Z., Ahmed A.A., Albert D.H., Bouska J.J., Bousquet P.F., Cunha G.A., Diaz G. et al. (2008) 3-Amino-benzo[d]isoxazoles as novel multitargeted inhibitors of receptor tyrosine kinases. J Med Chem 51 : 1231 1241.
8. Dai Y.J., Hartandi K., Ji Z.Q., Ahmed A.A., Albert D.H., Bauch J.L., Bouska J.J. et al. (2007) Discovery of N-(4-(3-amino-1H-indazol-4-yl) phenyl)-N′-(2-fluoro-5-methylphenyl)urea (ABT-869), a 3-aminoindazole- based orally active multitargeted receptor tyrosine kinase inhibitor. J Med Chem 50 : 1584 1597.
9. Dai Y., Hartandi K., Soni N.B., Pease L.J., Reuter D.R., Olson A.M., Osterling D.J., Doktor S.Z., Albert D.H., Bouska J.J., Glaser K.B., Marcotte P.A., Stewart K.D., Davidsen S.K., Michaelides M.R. (2008) Identification of aminopyrazolopyridine ureas as potent VEGFR/PDGFR multitargeted kinase inhibitors. Bioorg Med Chem Lett 18 : 386 390.
10. Ruan Z.H., Wang H.M., Ren Y.R., Chen Y.W., Han J.F., Pang X.L., Liang H.J., Wu Y.Z. (2008) Pseudo receptor probes: a novel pseudo receptor-based QSAR method and application into studies on a new kind of selective vascular endothelial growth factor-2 receptor inhibitors. Chemom Intell Lab Syst 92 : 157 168.
11. Li J.Z., Qin J., Liu H.X., Yao X.J., Liu M.C., Hu Z.D. (2008) In silico prediction of inhibition activity of pyrazine-pyridine biheteroaryls as VEGFR-2 inhibitors based on least squares support vector machines. QSAR Comb Sci 27 : 157 164.
12. Sharma B.K., Sharma S.K., Singh P., Sharma S., Prabhakar Y.S. (2009) Modeling of vascular endothelial growth factor receptor 2 (VEGFR2) kinase inhibitory activity of 2-anilino-5-aryloxazoles using chemometric tools. J Enzyme Inhib Med Chem 24 : 86 93.
13. Stewart J.J.P. (1989) Optimization of parameters for semiempirical methods I. Methods J Comput Chem 10 : 209 220.
14. Tetko I.V., Gasteiger J., Todeschini R., Mauri A., Livingstone D., Ertl P., Palyulin V.A., Radchenko E.V., Zefirov N.S., Makarenko A.S., Tanchuk V.Y., Prokopenko V.V. (2005) Virtual computational chemistry laboratory - design and description. J Comput Aid Mol Des 19 : 453 463.
15. Riahi S., Pourbasheer E., Dinarvand R., Ganjali M.R., Norouzi P. (2008) Exploring QSARs for antiviral activity of 4-alkylamino-6-(2-hydroxyethyl)-2- methylthiopyrimidines by support vector machine. Chem Biol Drug Des 72 : 205 216.
16. Edraki N., Hemmateenejad B., Miri R., Khoshneviszade M. (2007) QSAR study of phenoxypyrimidine derivatives as potent inhibitors of p38 kinase using different chemometric tools. Chem Biol Drug Des 70 : 530 539.
17. Holland J.H. (1975) Adaption in Natural and Artificial Systems. Ann Arbor, MI : University of Michigan Press.
18. Robert P., Escoufier Y. (1976) A unifying tool for linear multivariate statistical methods: the RV-coefficient. Appl Stat 25 : 257 265.
19. Mercader A.G., Duchowicz P.R., Fernández F.M., Castro E.A. (2008) Modified and enhanced replacement method for the selection of molecular descriptors in QSAR and QSPR theories. Chemom Intell Lab Syst 92 : 138 144.
20. Mercader A.G., Duchowicz P.R., Fernández F.M., Castro E.A., Bennardi D.O., Autino J.C., Romanelli G.P. (2008) QSAR prediction of inhibition of aldose reductase for flavonoids. Bioorg Med Chem 16 : 7470 7476.
21. Cortes C., Vapnik V. (1995) Support-vector networks. Mach Learn 20 : 273 297.
22. Wang J., Liu H.X., Qin S., Yao X.J., Liu M.C., Hu Z.D., Fan B.T. (2007) Study on the structure-activity relationship of new anti-HIV nucleoside derivatives based on the support vector machine method. QSAR Comb Sci 26 : 161 172.
23. Chen H.F. (2008) Computational study of the binding mode of epidermal growth factor receptor kinase inhibitors. Chem Biol Drug Des 72 : 434 446.
24. Efron B. (1983) Estimating the error rate of a prediction rule: improvement on cross-validation. J Am Stat Assoc 78 : 316 331.
25. Osten D.W. (1988) Selection of optimal regression models via cross-validation. J Chemom 2 : 39 48.
26. Tropsha A., Gramatica P., Gombar V.K. (2003) The importance of being earnest: validation is the absolute essential for successful application and interpretation of QSPR models. QSAR Comb Sci 22 : 69 77.
27. 2! J Mol Graph Model 20 : 269 276.
28. Wold S., Eriksson L. (1995) Statistical validation of QSAR results. Validation tools. In : van de Waterbeemd H., editor. Chemometrics Methods in Molecular Design. Weinheim, Germany : Wiley-VCH p. 309 318.
29. Duda R.O., Hart P.E., Stork D.G. (2001) Pattern Classification. New York : Wiley & Sons.
30. Topliss J.G., Costello R.J. (1972) Chance correlations in structure-activity studies using multiple regression analysis. J Med Chem 15 : 1066 1078.
31. Topliss J.G., Edwards R.P. (1979) Chance factors in studies of quantitative structure-activity relationships. J Med Chem 22 : 1238 1244.
32. Hemmateenejad B., Yazdani M. (2009) QSPR models for half-wave reduction potential of steroids: a comparative study between feature selection and feature extraction from subsets of or entire set of descriptors. Anal Chim Acta 634 : 27 35.
33. Todeschini R., Consonni V. (2000) Handbook of Molecular Descriptors. Weinheim, Germany : Wiley-VCH.
34. Ghose A.K., Crippen G.M. (1986) Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships. I. Partition coefficients as a measure of hydrophobicity. J Comput Chem 7 : 565 577.
35. Fernandez M., Caballero J., Helguera A.M., Castro E.A., Gonzalez M.N. (2005) Quantitative structure-activity relationship to predict differential inhibition of aldose reductase by flavonoid compounds. Bioorg Med Chem 13 : 3269 3277.
36. Burden F.R. (1989) Molecular identification number for substructure searches. J Chem Inf Comput Sci 29 : 225 227.
37. Schuur J., Selzer P., Gasteiger J. (1996) The coding of three-dimensional structure of molecules by molecular transforms and its application to structure-spectra correlations and studies of biological activity. J Chem Inf Model 36 : 334 344.
38. Saiz-Urra L., Gonzalez M.P., Teijeira M. (2007) 2D-autocorrelation descriptors for predicting cytotoxicity of naphthoquinone ester derivatives against oral human epidermoid carcinoma. Bioorg Med Chem 15 : 3565 3571.