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Prediction of Aromatic Hydroxylation Sites for Human CYP1A2 Substrates Using Condensed Graph of Reactions

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Abstract

In this paper, support vector machine and condensed graph of reaction (CGR) approaches have been used to predict the regioselectivity of aromatic hydroxylation for human CYP1A2 substrates. Experimental data on aromatic hydroxylation for human cytochrome CYP1A2 (observed molecular or “real” transformations) used in the modeling were extracted from the Metabolite database and the XenoSite database. In addition, all potential but unobserved (“unreal”) transformations were generated. The dataset containing “real” and “unreal” transformations was converted into an ensemble of CGRs representing pseudomolecules with conventional (single, double, aromatic, etc.) bonds and dynamic bonds characterizing chemical transformations. ISIDA fragment descriptors generated for CGRs were used for the modeling. The models have been validated in three times repeated fivefold cross-validation on the training set and then on an external set. The final model was constructed by consensus over models built on different descriptors sets. Predictive performance of our model on the external test set was similar to that of XenoSite and Way2Drug tools. Unlike previously used atom labeling-based approaches, the proposed CGR-based representation of metabolic transformations could be applied to different types of reactions catalyzed by the same enzyme and therefore, it is more suitable for automatized handling of metabolic data.

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Acknowledgements

We thank Prof. Vladimir Poroikov for providing us with the experimental data set and useful discussion. ChemAxon is acknowledged for the software tools used in this study for data storage and standardization. The study was supported by Russian Science Foundation (Contract 14-43-00024).

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Authors and Affiliations

  1. Kazan Federal University, 18 Kremlyovskaya Str., Kazan, Russia, 420008

    T. I. Madzhidov, A. A. Khakimova, R. I. Nugmanov & A. Varnek

  2. Université de Strasbourg, 4 rue B. Pascal, 67000, Strasbourg, France

    C. Muller, G. Marcou & A. Varnek

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  1. T. I. Madzhidov
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  2. A. A. Khakimova
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  3. R. I. Nugmanov
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Correspondence to T. I. Madzhidov or A. Varnek.

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Madzhidov, T.I., Khakimova, A.A., Nugmanov, R.I. et al. Prediction of Aromatic Hydroxylation Sites for Human CYP1A2 Substrates Using Condensed Graph of Reactions. BioNanoSci. 8, 384–389 (2018). https://doi.org/10.1007/s12668-017-0499-7

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