Novel application of 2D and 3D-similarity searches to identify substrates among cytochrome P450 2C9, 2D6, and 3A4.
Cytochrome P450 (CYP450) is a class of enzymes where the substrate identification is particularly important to know. It would help medicinal chemists to design drugs with lower side effects due to drug-drug interactions and to extensive genetic polymorphism. Herein, we discuss the application of the 2D and 3D-similarity searches in identifying reference structures with higher capacity to retrieve substrates of three important CYP enzymes (CYP2C9, CYP2D6, and CYP3A4). On the basis of the complementarities of multiple reference structures selected by different similarity search methods, we proposed the fusion of their individual Tanimoto scores into a consensus Tanimoto score (T(consensus)). Using this new score, true positive rates of 63% (CYP2C9) and 81% (CYP2D6) were achieved with false positive rates of 4% for the CYP2C9-CYP2D6 data set. Extended similarity searches were carried out on a validation data set, and the results showed that by using the T(consensus) score, not only the area of a ROC graph increased, but also more substrates were recovered at the beginning of a ranked list.
Freitas
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Grupo de Estudos em Quimica Medicinal de Produtos Naturais, NEQUIMED-PN, Instituto de Quimica de Sao Carlos, Universidade de Sao Paulo, 13560-970 Sao Carlos, SP, Brazil.
Bauab
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Montanari
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CA
D019540:Area Under Curve; D019389:Cytochrome P-450 CYP2D6 / Q000378:metabolism; D051544:Cytochrome P-450 CYP3A / Q000378:metabolism; D003577:Cytochrome P-450 Enzyme System / Q000378:metabolism*; D055808:Drug Discovery / Q000379:methods*; D007527:Isoenzymes / Q000378:metabolism; D011485:Protein Binding; D012372:ROC Curve; D015203:Reproducibility of Results
D007527:Isoenzymes; D003577:Cytochrome P-450 Enzyme System; D019389:Cytochrome P-450 CYP2D6; D051544:Cytochrome P-450 CYP3A