Prediction of binding affinity for estrogen receptor α modulators using statistical learning approaches

Molecular Diversity

Volumn 12, Issue 2, 2008, Pages 93-102

  Wang, Yonghua ^a   Li, Yan ^b   Ding, Jun ^a   Wang, Yuan ^a   Chang, Yaqing ^a  

^a DALIAN OCEAN UNIVERSITY   (China)

^b DALIAN UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Estrogen receptor modulators; Neural networks; Prediction; QSAR

Indexed keywords

ESTROGEN RECEPTOR ALPHA; FLAVONOID; LIGAND; SELECTIVE ESTROGEN RECEPTOR MODULATOR; XANTHINE DERIVATIVE;

ARTICLE; BAYESIAN LEARNING; BINDING AFFINITY; BIOLOGICAL ACTIVITY; COMPUTER MODEL; CORRELATION COEFFICIENT; DRUG BINDING; DRUG DESIGN; DRUG EFFICACY; DRUG POTENCY; EXPERIMENTATION; IC 50; MOLECULAR INTERACTION; MULTIPLE LINEAR REGRESSION ANALYSIS; PREDICTION; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; RELIABILITY; STATISTICAL ANALYSIS;

BAYES THEOREM; COMPUTER SIMULATION; ESTROGEN RECEPTOR ALPHA; ESTROGEN RECEPTOR MODULATORS; INHIBITORY CONCENTRATION 50; LIKELIHOOD FUNCTIONS; MODELS, CHEMICAL; NEURAL NETWORKS (COMPUTER); PRINCIPAL COMPONENT ANALYSIS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 50849144643     PISSN: 13811991     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11030-008-9080-1     Document Type: Article

References (44)

1. S Nilsson J-A Gustafsson 2002 Biological role of estrogen and estrogen receptors Crit Rev Biochem Mol Biol 37 1 28 10.1080/10409230290771438
2. S Green P Walter V Kumar A Krust JM Bornert P Argos 1986 Human estrogen receptor cDNA: sequence, expression and homology to v-erb-A Nature 320 134 139 10.1038/320134a0
3. P Ascenzi A Bocedi M Marino 2006 Structure-function relationship of estrogen receptor α and β: impact on human health Mol Aspects Med 27 299 402 10.1016/j.mam.2006.07.001
4. INH White 1999 The tamoxifen dilemma Carcinogenesis 20 1153 1160 10.1093/carcin/20.7.1153
5. M Maricic O Gluck 2002 Review of raloxifene and its clinical applications in osteoporosis Expert Opin Pharmacother 3 767 775 10.1517/14656566.3.6.767
6. CP Miller 2002 SERMs: evolutionary chemistry, revolutionary biology Curr Pharm Des 8 2089 2111 10.2174/1381612023393404
7. H Fang W Tong LM Shi R Blair R Perkins W Branham 2001 Structure-activity relationships for a large diverse set of natural, synthetic, and environmental estrogens Chem Res Toxicol 14 280 294 10.1021/tx000208y
8. F Eertmans W Dhooge S Stuyvaert F Comhaire 2003 Comhaire endocrine disruptors: effects on male fertility and screening tools for their assessment Toxicol In Vitro 17 515 524 10.1016/S0887-2333(03)00121-8
9. D Ibarreta A Daxenberger HH Meyer 2001 Possible health impact of phytoestrogens and xenoestrogens in food APMIS 109 161 184 10.1034/j.1600-0463. 2001.090301.x
10. HU Bryant 2002 Selective estrogen receptor modulators Rev Endocr Metab Disord 3 231 241 10.1023/A:1020076426727
11. VC Jordan 2003 Antiestrogens and selective estrogen receptor modulators as multifunctional medicines. 2. Clinical considerations and new agents J Med Chem 46 1081 1111 10.1021/jm020450x
12. MJ Meegan DG Lloyd 2003 Advances in the science of estrogen receptor modulation Curr Med Chem 10 181 210
13. AM Brzozowski AC Pike Z Dauter RE Hubbard T Bonn O Engstrom 1997 Molecular basis of agonism and antagonism in the oestrogen receptor Nature 389 753 758 10.1038/39645
14. JI MacGregor VC Jordan 1998 Basic guide to the mechanisms of antiestrogen action Pharmacol Rev 50 151 196
15. H Hong W Tong H Fang L Shi Q Xie J Wu 2002 Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts Environ Health Perspect 110 29 36
16. JJ Chen C-A Tsai H Moon H Ahn JJ Young CH Chen 2006 Decision threshold adjustment in class prediction SAR QSAR Environ Res 17 337 352 10.1080/10659360600787700
17. A Asikainen M Kolehmainen J Ruuskanen K Tuppurainen 2006 Structure-based classification of active and inactive estrogenic compounds by decision tree, LVQ and kNN methods Chemosphere 62 658 673 10.1016/j.chemosphere.2005.04.115
18. H Li CY Ung CW Yap Y Xue ZR Li YZ Chen 2006 Prediction of estrogen receptor agonists and characterization of associated molecular descriptors by statistical learning methods J Mol Graph Model 25 313 323 10.1016/j.jmgm.2006. 01.007
19. LB Salum I Polikarpov AD Andricopulo 2007 Structural and chemical basis for enhanced affinity and potency for a large series of estrogen receptor ligands: 2D and 3D QSAR studies J Mol Graph Model 26 34 42 10.1016/j.jmgm.2007. 02.001
20. HY Chen KD Dykstra ET Birzin K Frisch W Chan YT Yang 2004 Estrogen receptor ligands. Part 1. The discovery of flavanoids with subtype selectivity Bioorg Med Chem Lett 14 1417 1421 10.1016/j.bmcl.2004.01.031
21. HY Chen S Kim JY Wu ET Birzin W Chan YT Yang 2004 Estrogen receptor ligands. Part 3. The SAR of dihydrobenzoxathiin SERMs Bioorg Med Chem Lett 14 3 2551 2554 10.1016/j.bmcl.2004.02.084
22. S Kim J Wu HY Chen ET Birzin W Chan YT Yang 2004 Estrogen receptor ligands. Part 4. The SAR of the syn-dihydrobenzoxathiin SERAMs Bioorg Med Chem Lett 14 2741 2745 10.1016/j.bmcl.2004.03.074
23. S Kim JY Wu ET Birzin K Frisch W Chan LY Pai 2004 Estrogen receptor ligands II, Discovery of benzoxathiins as potent, selective estrogen receptor α modulators J Med Chem 47 2171 2175 10.1021/jm034243o
24. Q Tan ET Birzin W Chan YT Yang LY Pai EC Hayes 2004 Estrogen receptor ligands. Part 6. Synthesis and binding affinity of dihydrobenzodithiins Bioorg Med Chem Lett 14 3753 3755 10.1016/j.bmcl.2004.04.101
25. Q Tan ET Birzin W Chan YT Yang LY Pai EC Hayes 2004 Estrogen receptor ligands. Part 5. The SAR of dihydrobenzoxathiins containing modified basic side chains Bioorg Med Chem Lett 14 3747 3751 10.1016/j.bmcl.2004.04.100
26. Q Tan TA Blizzard JD Morgan II ET Birzin W Chan YT Yang 2005 Estrogen receptor ligands. Part 10. Chromanes: old scaffolds for new SERAMs Bioorg Med Chem Lett 15 1675 1681 10.1016/j.bmcl.2005.01.046
27. TA Blizzard F DiNinno JD Morgan II JY Wu HY Chen S Kim 2004 Estrogen receptor ligands. Part 8. Dihydrobenzoxathiin SERAMs with heteroatomsubstituted side chains Bioorg Med Chem Lett 14 3865 3868 10.1016/j.bmcl.2004.05.073
28. TA Blizzard F DiNinno JD Morgan HY Chen II JY Wu C Gude 2004 Estrogen receptor ligands. Part 7. Dihydrobenzoxathiin SERAMs with bicyclic amine side chains Bioorg Med Chem Lett 14 3664 3861
29. TA Blizzard F DiNinno HY Chen S Kim JY Wu W Chan 2005 Estrogen receptor ligands. Part 13. Dihydrobenzoxathiin SERAMs with an optimized antagonist side chain Bioorg Med Chem Lett 15 3912 3916 10.1016/j.bmcl.2005.05.089
30. TA Blizzard F Dininno JD Morgan II HY Chen JY Wu S Kim 2005 Estrogen receptor ligands. Part 9. Dihydrobenzoxathiin SERAMs with alkyl substituted pyrrolidine side chains and linkers Bioorg Med Chem Lett 15 107 113 10.1016/j.bmcl.2004.10.036
31. Y Wang Y Li S-L Yang L Yang 2005 An in silico approach for screening flavonoids as P-glycoprotein inhibitors based on bayesian-regularized neural network J Comput Aided Mol Des 19 137 147 10.1007/s10822-005-3321-5
32. Y Wang Y Li S-L Yang L Yang 2005 Classification of substrates and inhibitors of P-Glycoprotein using unsupervised machine learning approach J Chem Inf Comput Sci 45 750 757 10.1021/ci050041k
33. Y Wang Y Li B Wang 2007 An in Silico method for screening nicotine derivatives as cytochrome P450 2A6 selective inhibitors based on kernel partial least squares Int J Mol Sci 8 166 179
34. Kier LB, Hall LH (1999) Molecular structure description: the electrotopological state. Academic Press, San Diego
35. I Moriguchi S Hirono I Nakagome H Hirano 1994 Comparison of reliability of log P values for drugs calculated by several methods Chem Pham Bull 42 976 978
36. Hansch C, Leo A (1979) Substituent constants for correlation analysis in chemistry and biology. Wiley, New York
37. CN Alves JC Pinheiro AJ Camargo MMC Ferreira RAF Romero ABF da Silva 2001 A multiple linear regression and partial least squares study of flavonoid compounds with anti-HIV activity J Mol Struct THEOCHEM 541 81 88 10.1016/S0166-1280(00)00755-7
38. DJC MacKay 1992 Bayesian interpolation Neural Comput 4 415 447 10.1162/neco.1992.4.3.415
39. DJC MacKay 1992 A practical bayesian framework for backprop networks Neural Comput 4 448 472 10.1162/neco.1992.4.3.448
40. DJC MacKay 1995 Probable networks and plausible predictions-a review of practical Bayesian methods for supervised neural networks Netw Comput Neural Syst 6 469 505 10.1088/0954-898X/6/3/011
41. FD Foresee MT Hagan 1997 Gauss-Newton approximation to Bayesian regularization Proceedings of the 1997 International Joint Conference on neural network 3 1930 1935
42. MT Hagan MB Menhaj 1994 Training feed forward networks with Marquardt algorithm IEEE Trans Neural Netw 5 989 993 10.1109/72.329697
43. D Nguyen B Widrow 1990 Improving the learning speed of 2-layer neural networks by choosing initial values of the adaptive weights Proc Int Joint Conf Neural Netw 3 21 26 10.1109/IJCNN.1990.137819
44. S Wold K Esbensen P Geladi 1987 Principal component analysis Chemom Intell Lab Syst 2 37 52 10.1016/0169-7439(87)80084-9