Identification of kinase inhibitors that rule out the CYP27B1-mediated activation of vitamin D: an integrated machine learning and structure-based drug designing approach

CYP27B1, a cytochrome P450-containing hydroxylase enzyme, converts vitamin D precursor calcidiol (25-hydroxycholecalciferol) to its active form calcitriol (1α,25(OH)2D3). Tyrosine kinase inhibitor such as imatinib is reported to interfere with the activation of vitamin D3 by inhibiting CYP27B1 enzyme. Consequently, there is a decrease in the serum levels of active vitamin D that in turn may increase the relapse risk among the cancer patients treated with imatinib. Within this framework, the current study focuses on identifying other possible kinase inhibitors that may affect the calcitriol level in the body by inhibiting CYP27B1. To achieve this, we explored multiple machine learning approaches including support vector machine (SVM), random forest (RF), and artificial neural network (ANN) to identify possible CYP27B1 inhibitors from a pool of kinase inhibitors database. The most reliable classification model was obtained from the SVM approach with Matthews correlation coefficient of 0.82 for the external test set. This model was further employed for the virtual screening of kinase inhibitors from the binding database (DB), which tend to interfere with the CYP27B1-mediated activation of vitamin D. This screening yielded around 4646 kinase inhibitors that were further subjected to structure-based analyses using the homology model of CYP27B1, as the 3D structure of CYP27B1 complexed with heme was not available. Overall, five kinase inhibitors including two well-known drugs, i.e., AT7867 (Compound-2) and amitriptyline N-oxide (Compound-3), were found to interact with CYP27B1 in such a way that may preclude the conversion of vitamin D to its active form and hence testify the impairment of vitamin D activation pathway.