Structural Perspectives of the CYP3A Family and Their Small Molecule Modulators in Drug Metabolism

Abstract

Cytochrome P450 enzymes function to catalyze a wide range of reactions, many of which are critically important for drug response. Members of the human cytochrome P450 3A (CYP3A) family are particularly important in drug clearance, and they collectively metabolize more than half of all currently prescribed medications. The ability of these enzymes to bind a large and structurally diverse set of compounds increases the chances of their modulating or facilitating drug metabolism in unfavorable ways. Emerging evidence suggests that individual enzymes in the CYP3A family play discrete and important roles in catalysis and disease progression. Here we review the similarities and differences among CYP3A enzymes with regard to substrate recognition, metabolism, modulation by small molecules, and biological consequence, highlighting some of those with clinical significance. We also present structural perspectives to further characterize the basis of these comparisons.

Keywords: CYP3A family; CYP3A4; CYP3A5; crystal structure; drug metabolism; small molecule modulators.

Fig. 1.

Protein sequence homology among CYP3A enzymes. Members of the human CYP3A family were aligned and colored by protein sequence homology, with blue indicating a complete match and white indicating a residue deviation.

Fig. 2.

Effects of various compounds on CYP3A. Several relevant endogenous compounds, pharmaceuticals, or tool compounds are indicated as substrates (gray curved arrows), inhibitors (orange flattened arrows), enzymatic activators (green double arrows), or inducers (purple arrow) of CYP3A. Known selectivity information is indicated along the circle as red (CYP3A5-selective), blue (CYP3A4-selective), yellow (CYP3A7-selective), or black (unknown or non-selective). Abbreviations: PXR, Pregnane X Receptor; 2α-OHT, 2α-hydroxytestosterone; 6β-OHT, 6β-hydroxytestosterone; 4β-HC, 4β-hydroxycholesterol; 4OH-MDZ, 4-hydroxymidazolam; 1OH-MDZ, 1-hydroxymidazolam; 13-O-DMT, 13-O-desmethyltacrolimus; M1, Vincristine metabolite 1.

Fig. 3.

Promiscuity of the CYP3A4 ligand -binding pocket. The crystal structures of CYP3A4 were obtained from PDB and aligned to illustrate the structural diversity of ligands capable of binding to CYP3A4. Progesterone (PDB : 5A1P) is shown in light green, Eerythromycin (PDB: 2J0D) in orange, Kketoconazole (PDB : 2V0M) in blue, Rritonavir analog (PDB : 4K9U) in pink, Bbromoergocryptine (PDB: 3UA1) in yellow, and Mmidazolam (PDB : 5TE8) in green. Asterisks (*) indicates that two molecules of the same ligand are bound in the respective structures.

Fig. 4.

Structural differences in CYP3A conformations. (A) CYP3A4 demonstrates flexibility in the active site. Ketoconazole-bound (PDB : 2V0M) (blue), water-bound (PDB : 4I3Q) (purple), or ligand-free (PDB : 1TQN) (gray) structures of CYP3A4 are overlaid. The flexibility of the F–F′ region at the roof of the binding pocket in the ketoconazole-bound structure is indicated by the yellow arrow. (B) Differences in key active-site residues in CYP3A4 and CYP3A5 contribute to the differential binding modes of ritonavir. Ritonavir-bound CYP3A4 (PDB : 3NXU) (blue) superimposed with ritonavir-bound CYP3A5 (PDB : 5VEU) (raspberry) demonstrates slightly different ligand-binding poses. The magnified panel shows the residues responsible for this difference in CYP3A4 (cyan) versus CYP3A5 (red).