A Deep Dive into the Conformational Dynamics of CYP3A4: Understanding the Binding of Homotropic and Non-homotropic Ligands for Mitigating Drug-Drug interaction (DDI)

Cytochrome P450 (CYP) enzymes are well known for metabolism of drugs. The present study attempts to understand the homotropic cooperativity of CYP3A4 inhibitor Ketoconazole (KLN) and the plasticity of the active site upon binding to different drug chemotypes. To understand this, molecular dynamic (MD) simulation studies of four systems of CYP3A4 have been undertaken followed by structural analysis of the crystallographic structures bound to five drug molecules. Unlike earlier reports, our study revealed that the region following helix F and G - helix H and preceding I- exhibited RMSF values in the range of 4-6 angstrom. The binding pattern of inhibitors may involve an initial binding at the peripheral site followed by their coordination with heme. Binding of KLN at the heme binding site was energetically more stable as compared to the KLN bound at other positions. The number of non-bonded interactions appeared to increase between the ligands and the CYP3A4 residues when both the sites were occupied. Involvement of hydrophobic residues (I300, I301, F304, A305, T309) increased during the homotropic cooperativity of ligands. Binding of the ligand at the heme binding site followed by binding at the peripheral site induces homo cooperativity effect. We also report here that 3D volume occupancy of ligands determines the phenomenon of homotropic versus non-homotropic effect which was observed from the binding mode analysis of KLN (homotropic ligand) and Ritonavir (non-homotropic ligand).

Automated summary

This study investigates the homotropic cooperativity of CYP3A4 inhibitor Ketoconazole (KLN) and the plasticity of the active site upon binding to different drug chemotypes using molecular dynamic simulation studies and structural analysis. The results demonstrate that binding of KLN at the heme binding site is energetically more stable, and involvement of hydrophobic residues increases during the homotropic cooperativity of ligands. The 3D volume occupancy of ligands determines the phenomenon of homotropic versus non-homotropic effect, as observed from the binding mode analysis of KLN (homotropic ligand) and Ritonavir (non-homotropic ligand).