Human cytochrome P450 enzymes bind drugs and other substrates mainly through conformational-selection modes

• Published in: The Journal of biological chemistry Vol. 294; no. 28; pp. 10928 - 10941
• Main Authors: Guengerich, F. Peter, Wilkey, Clayton J., Phan, Thanh T.N.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 12.07.2019; American Society for Biochemistry and Molecular Biology
• Subjects: Catalysis; conformational selection; CYP; Cytochrome P-450 CYP2D6 - metabolism; Cytochrome P-450 CYP2E1 - metabolism; Cytochrome P-450 CYP3A - metabolism; Cytochrome P-450 Enzyme Inhibitors - metabolism; Cytochrome P-450 Enzyme System - metabolism; Cytochrome P-450 Enzyme System - physiology; cytochrome P450; drug metabolism; enzyme kinetics; enzyme mechanism; Enzymology; Humans; induced fit; Kinetics; Lauric Acids; Ligands; Molecular Conformation; Oxidation-Reduction; P450; Palmitic Acid; pre-steady-state kinetics; Protein Binding - physiology; Protein Conformation - drug effects; Spiro Compounds; steroid; steroidogenesis; Substrate Specificity - physiology; pre-steady-state kinetics; drug metabolism; steroidogenesis; induced fit; P450; cytochrome P450; CYP; enzyme mechanism; enzyme kinetics; steroid; conformational selection
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.RA119.009305

Cytochrome P450 (P450) enzymes are major catalysts involved in the oxidations of most drugs, steroids, carcinogens, fat-soluble vitamins, and natural products. The binding of substrates to some of the 57 human P450s and other mammalian P450s is more complex than a two-state system and has been proposed to involve mechanisms such as multiple ligand occupancy, induced-fit, and conformational-selection. Here, we used kinetic analysis of binding with multiple concentrations of substrates and computational modeling of these data to discern possible binding modes of several human P450s. We observed that P450 2D6 binds its ligand rolapitant in a mechanism involving conformational-selection. P450 4A11 bound the substrate lauric acid via conformational-selection, as did P450 2C8 with palmitic acid. Binding of the steroid progesterone to P450 21A2 was also best described by a conformational-selection model. Hexyl isonicotinate binding to P450 2E1 could be described by either a conformational-selection or an induced-fit model. Simulation of the binding of the ligands midazolam, bromocriptine, testosterone, and ketoconazole to P450 3A4 was consistent with an induced-fit or a conformational-selection model, but the concentration dependence of binding rates for varying both P450 3A4 and midazolam concentrations revealed discordance in the parameters, indicative of conformational-selection. Binding of the P450s 2C8, 2D6, 3A4, 4A11, and 21A2 was best described by conformational-selection, and P450 2E1 appeared to fit either mode. These findings highlight the complexity of human P450-substrate interactions and that conformational-selection is a dominant feature of many of these interactions.