title: Classification of cytochrome P450 1A2 inhibitors and noninhibitors by machine learning techniques.
abstract: The cytochrome P450 (P450) superfamily plays an important role in the metabolism of drug compounds, and it is therefore highly desirable to have models that can predict whether a compound interacts with a specific isoform of the P450s. In this work, we provide in silico models for classification of CYP1A2 inhibitors and noninhibitors. Training and test sets consisted of approximately 400 and 7000 compounds, respectively. Various machine learning techniques, such as binary quantitative structure activity relationship, support vector machine (SVM), random forest, kappa nearest neighbor (kNN), and decision tree methods were used to develop in silico models, based on Volsurf and Molecular Operating Environment descriptors. The best models were obtained using the SVM, random forest, and kNN methods in combination with the BestFirst variable selection method, resulting in models with 73 to 76% of accuracy on the test set prediction (Matthews correlation coefficients of 0.51 and 0.52). Finally, a decision tree model based on Lipinski's Rule-of-Five descriptors was also developed. This model predicts 67% of the compounds correctly and gives a simple and interesting insight into the issue of classification. All of the models developed in this work are fast and precise enough to be applicable for virtual screening of CYP1A2 inhibitors or noninhibitors or can be used as simple filters in the drug discovery process.
authors.affiliation: Biostructural Research, Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.
authors.forename: Poongavanam
authors.initials: P
authors.lastname: Vasanthanathan
authors.forename: Olivier
authors.initials: O
authors.lastname: Taboureau
authors.forename: Chris
authors.initials: C
authors.lastname: Oostenbrink
authors.forename: Nico P E
authors.initials: NP
authors.lastname: Vermeulen
authors.forename: Lars
authors.initials: L
authors.lastname: Olsen
authors.forename: Flemming Steen
authors.initials: FS
authors.lastname: Jørgensen
mesh_terms: D001185:Artificial Intelligence; D065609:Cytochrome P-450 CYP1A2 Inhibitors; D004791:Enzyme Inhibitors / Q000145:classification*; D008962:Models, Theoretical; D021281:Quantitative Structure-Activity Relationship
chemical_list: D065609:Cytochrome P-450 CYP1A2 Inhibitors; D004791:Enzyme Inhibitors