In Silico Prediction of the Metabolic Resistance of Vitamin D Analogs against CYP3A4 Metabolizing Enzyme

• Published in: International journal of molecular sciences Vol. 23; no. 14; p. 7845
• Main Authors: Żołek, Teresa, Yasuda, Kaori, Brown, Geoffrey, Sakaki, Toshiyuki, Kutner, Andrzej
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 16.07.2022; MDPI
• Subjects: Amino acids; Analogs; Binding; Binding sites; Calciferol; Cancer; Conversion; Crystal structure; CYP3A4 protein; Cytochrome; Cytochrome P450; cytochrome P450 24A1; cytochrome P450 3A4; Cytochromes P450; Drug development; Enzymes; in silico prediction; Ligands; Metabolism; Metabolites; Mitochondria; Molecular docking; Molecular dynamics; Prostate; Proteins; Severe acute respiratory syndrome coronavirus 2; Simulation; Vitamin D; vitamin D analogs
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms23147845

The microsomal cytochrome P450 3A4 (CYP3A4) and mitochondrial cytochrome P450 24A1 (CYP24A1) hydroxylating enzymes both metabolize vitamin D and its analogs. The three-dimensional (3D) structure of the full-length native human CYP3A4 has been solved, but the respective structure of the main vitamin D hydroxylating CYP24A1 enzyme is unknown. The structures of recombinant CYP24A1 enzymes have been solved; however, from studies of the vitamin D receptor, the use of a truncated protein for docking studies of ligands led to incorrect results. As the structure of the native CYP3A4 protein is known, we performed rigid docking supported by molecular dynamic simulation using CYP3A4 to predict the metabolic conversion of analogs of 1,25-dihydroxyvitamin D2 (1,25D2). This is highly important to the design of novel vitamin D-based drug candidates of reasonable metabolic stability as CYP3A4 metabolizes ca. 50% of the drug substances. The use of the 3D structure data of human CYP3A4 has allowed us to explain the substantial differences in the metabolic conversion of the side-chain geometric analogs of 1,25D2. The calculated free enthalpy of the binding of an analog of 1,25D2 to CYP3A4 agreed with the experimentally observed conversion of the analog by CYP24A1. The metabolic conversion of an analog of 1,25D2 to the main vitamin D hydroxylating enzyme CYP24A1, of unknown 3D structure, can be explained by the binding strength of the analog to the known 3D structure of the CYP3A4 enzyme.