Yi-Han Zhou

Mechanism of CYP2C9 Inhibition by Flavones and Flavonols

This article describes an in vitro investigation of the inhibition of cytochrome P450 (P450) 2C9 by a series of flavonoids made up of flavones (flavone, 6-hydroxyflavone, 7-hydroxyflavone, chrysin, baicalein, apigenin, luteolin, scutellarein, and wogonin) and flavonols (galangin, fisetin, kaempferol, morin, and quercetin). With the exception of flavone, all flavonoids were shown to inhibit CYP2C9-mediated diclofenac 4′-hydroxylation in the CYP2C9 RECO system, with Ki value ≤2.2 μM. In terms of the mechanism of inhibition, 6-hydroxyflavone was found to be a noncompetitive inhibitor of CYP2C9, whereas the other flavonoids were competitive inhibitors. Computer docking simulation and constructed mutants substituted at residue 100 of CYP2C9.1 indicate that the noncompetitive binding site of 6-hydroxyflavone lies beside Phe100, similar to the reported allosteric binding site of warfarin. The other flavonoids exert competitive inhibition through interaction with the substrate binding site of CYP2C9 accessed by flurbiprofen. These results suggest flavonoids can participate in interactions with drugs that act as substrates for CYP2C9 and provide a possible molecular basis for understanding cooperativity in human P450-mediated drug-drug interactions.

The metabolism of CYP2C9 and CYP2C19 for gliclazide by homology modeling and docking study.

With homology modeling techniques, a 3D structure model of CYP2C19 was built and refined with molecular mechanics and molecular dynamics simulations. The refined model was assessed to be reasonable by Profile-3D and PROCHECK programs. With the aid of the automatic molecular docking, one substrate and two inhibitors were docked to CYP2C19 by InsightII/Affinity program. The docking results, which are in well agreement with the reported results, demonstrate that the refined model of CYP2C19 is reliable. Then, with the refined model of CYP2C19 and the crystal structure of CYP2C9, the metabolisms of them for gliclazide in two different metabolic pathways were studied and the results show that both enzymes have more favorable interaction energies and stronger affinity with gliclazide in methylhydroxylation pathway than in 6beta-hydroxylation pathway. It is exciting that substrate inhibition phenomenon can be found in metabolisms of CYP2C9 and CYP2C19 for gliclazide in two metabolic pathways. Gliclazide can change the conformation of the active sites and decrease obviously the affinities between gliclazide in the active site and enzymes when it is docked in the second active sites in CYP2C9 and CYP2C19. These results are in well agreement with the kinetic experimental results.

CATALYTIC REACTION MECHANISM OF HUMAN PHOTORECEPTOR RETINOL DEHYDROGENASE: A THEORETICAL STUDY

Human photoreceptor retinol dehydrogenase (hRDH8) catalyzes the reduction of all-trans-retinal to all-trans-retinol with NADPH as a rate-limiting step in the visual cycle. Based on the docking results of the substrate to the 3D structure of hRDH8 which is generated by homology modeling method, three quantum chemical calculation models with different sizes were used to investigate the catalytic reaction mechanism of hRDH8 with the aid of density functional theory. The calculations indicate that hRDH8 employs a general acid/base mechanism that a proton is transferred to the keto oxygen of the substrate after the pro-S hydride of NADPH transfer to keto carbon of the substrate. The H-transfer order is converse to that in the proposed mechanism of 17s-hydroxysteroid dehydrogenase 1, which is highly related to the hRDH8 sequence. Tyr155 always provides the proton to the keto oxygen of the substrate whether unprotonated Lys159 is considered or not in the calculation models. However, protonated Lys159 changes the...

Molecular docking study of the affinity of CYP2C9 and CYP2D6 for imrecoxib

With the aid of the automatic molecular docking, the affinity of CYP2C9 and CYP2D6 for imrecoxib was studied by InsightII/Affinity program. The results indicate that CYP2C9–imrecoxib complex has higher stability and stronger affinity because CYP2C9 has more favorable interaction energy (-62.72 kcal/mol) and higher Ludi score (610) with imrecoxib than CYP2D6 (-50.22 kcal/mol and 551) and this is consistent with the results of the kinetic experiments by Li et al. By analyzing the theoretical results combined with the experimental ones, we suggest that the affinity difference is caused by the difference of the structure between CYP2C9 and CYP2D6, and the most important residues for enzyme–substrate complexes, such as Phe476, Asn204, Phe100, Leu366 and Arg108 of CYP2C9 and Phe120, Glu216, and Phe483 of CYP2D6 were also identified.

The 3D structure of the defense-related rice protein Pir7b predicted by homology modeling and ligand binding studies

AbstractTo better understand the ligand-binding mechanism of protein Pir7b, important part in detoxification of a pathogen-derived compound against Pyricularia oryzae, a 3D structure model of protein Pir7b was constructed based on the structure of the template SABP2. Three substrates were docking to this protein, two of them were proved to be active, and some critical residues are identified, which had not been confirmed by the experiments. His87 and Leu17 considered as ‘oxyanion hole’ contribute to initiating the Ser86 nucleophilic attack. Gln187 and Asp139 can form hydrogen bonds with the anilid group to maintain the active binding orientation with the substrates. The docking model can well interpret the specificity of protein Pir7b towards the anilid moiety of the substrates and provide valuable structure information about the ligand binding to protein Pir7b. FigureLigand binding analysis based on the refined Pir7b model. Magenta dash line, hydrogen bond; Red dash line, distance label. (a) Docking of 2-naphthol AS-acetate to Pir7b model. A 3D figure of 2-naphthol AS-acetate-Pir7b complex is also attached (b) Docking of 2-naphthol AS-2-chlor-propionate to Pir7b model. (c) Docking of 2-naphthol-acetate to Pir7b model.