1. Reconstitution of CYP3A4 active site through assembly of ligand interactions as a grid-template: Solving the modes of the metabolism and inhibition
- Author
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Takahiro Goto, Masahiro Tohkin, and Yasushi Yamazoe
- Subjects
Pharmaceutical Science ,Ligands ,030226 pharmacology & pharmacy ,03 medical and health sciences ,Polyaromatic hydrocarbon ,0302 clinical medicine ,Catalytic Domain ,Cytochrome P-450 CYP3A ,Cytochrome P-450 Enzyme Inhibitors ,Humans ,Molecule ,Pharmacology (medical) ,Polycyclic Aromatic Hydrocarbons ,030304 developmental biology ,Pharmacology ,0303 health sciences ,Molecular Structure ,CYP3A4 ,biology ,Chemistry ,Effector ,Ligand ,Active site ,Grid ,Combinatorial chemistry ,Recombinant Proteins ,Kinetics ,biology.protein - Abstract
A hexagonal-grid based template system has been developed to a predicting tool of CYP3A4-mediated reactions through the reconstitution of the active site with the assembly of the ligands. Simultaneous interactions of flattened-shape ligands at two sites of CYP3A4, oxidizing- and triggering-sites, are essential ideas, which were supported in the simulation results of various ligands on the template. The interactions were accomplished with either uni-molecule bindings or bi-molecule bindings with ligands termed pro-metabolized and trigger molecules. The template shape was determined mainly through reciprocal comparisons of simulation results with available experiment data mainly on recombinant CYP3A4-mediated reactions of polyaromatic hydrocarbon (PAH) ligands. Through the applications of various PAH and non-PAH ligands on the template, couple region-specific interactions including mechanisms to facilitate ligand movement from the initial site to a place near heme-oxygen and to trigger of catalyses are envisioned. These are very effective tools to verify candidates of CYP3A4 ligands as the good or poor substrates. The bi-molecule binding idea also explains so called "cooperative bindings with activator/effector" as interactions with non-identical trigger molecules on this CYP3A4-template system, and also offers possible mechanisms of the non-linear kinetic behavior.
- Published
- 2019
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