Metabolic ménages à trois: what does it mean for drug design?

Allosteric modulation of substrate motion in cytochrome P450 3A4-mediated xylene oxidation

Many cytochrome P450 enzymes (CYPs) exhibit allosteric behavior reflecting a complex ligand-binding process involving numerous factors: conformational selection, protein-protein interactions, substrate/effector/protein structure, and multiple-ligand binding. The interplay of CYP plasticity and rigidity contributes to substrate/product selectivity and to allosterism. Detailed evidence describing how protein motion modulates product selectivity is incomplete as are descriptions of effector-induced modulation of substrate dynamics. Our intent was to discover details of allosteric behavior and CYP3A4 flexibility and rigidity by investigating substrate motion using low-molecular weight ligands. Steady state kinetics and product ratios were measured for oxidation of m-xylene-(2)H3 and p-xylene; intramolecular isotope effects were measured for m-xylene-(2)H3 oxidation as a function of m-xylene-(2)H3 and p-xylene concentration. Biphasic kinetic plots indicated homotropic cooperative behavior with xylene isomers. Selectivity for aromatic hydroxylation over benzylic hydroxylation of m-xylene-(2)H3 supports a model in which the region near the CYP3A4 active oxidizing species limits substrate dynamics. p-Xylene impedes the motion of m-xylene-(2)H3 substrates that have access to the active oxidizing species: (kH/kD)obs values for m-xylene-(2)H3 decreased with p-xylene concentration. m-Xylene-(2)H3 and p-xylene do not have simultaneous access to the active oxidizing species: deuterium-labeled and unlabeled p-xylene exhibited similar effects on the (kH/kD)obs values for m-xylene-(2)H3 oxidation. p-Xylene and m-xylene-(2)H3 bind at different sites: m-xylene-(2)H3 oxidation rates and product selectivity were consistent across the p-xylene concentration range. Overall, this study indicates that the intramolecular isotope effect experimental design provides a unique opportunity to investigate allosteric mechanisms as it provides information about substrate motion when the enzyme is primed to oxidize substrates.

Evidence of CYP3A allosterism in vivo: analysis of interaction between fluconazole and midazolam

The allosteric effect of fluconazole (effector) on the formation of 1’-hydroxymidazolam (1’-OH-MDZ) and 4-hydroxymidazolam (4-OH-MDZ) from the CYP3A4/5 substrate, midazolam (MDZ), was examined in healthy volunteers. Following pre-treatment of fluconazole, AUC_4-OH/AUC_MDZ increased 35–62%, while AUC_1’-OH/AUC_MDZ decreased 5–37%; AUC_1’-OH/AUC_4-OH ratio decreased 46–58% by fluconazole and had no association with CYP3A5 genotype. 1’-OH-MDZ formation in vitro was more susceptible than 4-OH-MDZ formation to inhibition by fluconazole. Fluconazole decreased the intrinsic formation clearance ratio of 1’-OH-MDZ/4-OH-MDZ to an extent that was quantitatively comparable to in vivo observations. The elimination clearance of midazolam metabolites appeared unaffected by fluconazole. This study demonstrated that fluconazole alters midazolam product formation both in vivo and in vitro in a manner consistent with an allosteric interaction. The 1'-OH-MDZ/4-OH-MDZ ratio may serve as a biomarker of such interactions between midazolam, CYP3A4/5 and other putative effectors.