Molecular Dynamics Simulation Framework to Probe the Binding Hypothesis of CYP3A4 Inhibitors

Abstract

The Cytochrome P450 family of heme-containing proteins plays a major role in catalyzing phase I metabolic reactions, and the CYP3A4 subtype is responsible for the metabolism of many currently marketed drugs. Additionally, CYP3A4 has an inherent affinity for a broad spectrum of structurally diverse chemical entities, often leading to drug-drug interactions mediated by the inhibition or induction of the metabolic enzyme. The current study explores the binding of selected highly efficient CYP3A4 inhibitors by docking and molecular dynamics (MD) simulation protocols and their binding free energy calculated using the WaterSwap method. The results indicate the importance of binding pocket residues including Phe57, Arg105, Arg106, Ser119, Arg212, Phe213, Thr309, Ser312, Ala370, Arg372, Glu374, Gly481 and Leu483 for interaction with CYP3A4 inhibitors. The residue-wise decomposition of the binding free energy from the WaterSwap method revealed the importance of binding site residues Arg106 and Arg372 in the stabilization of all the selected CYP3A4-inhibitor complexes. The WaterSwap binding energies were further complemented with the MM(GB/PB)SA results and it was observed that the binding energies calculated by both methods do not differ significantly. Overall, our results could guide towards the use of multiple computational approaches to achieve a better understanding of CYP3A4 inhibition, subsequently leading to the design of highly specific and efficient new chemical entities with suitable ADMETox properties and reduced side effects.

Keywords: CYP3A4; CYP3A4 inhibitors; WaterSwap; docking; molecular dynamics simulation; residue-wise energy decomposition.

Figure 1

Superposition of chain A in CYP3A4 crystal structures (a) 1TQN (red), 3UA1 (cyan), 3NXU (green) and 4K9W (pink); (b) positioning of Arg212 within 1TQN (red), 3UA1 (cyan), 3NXU (green) and 4K9W (pink); and (c) the structural organization of 1TQN.

Figure 2

The chemical structures and experimental biological activity (IC₅₀) values of the selected CYP3A4 inhibitors fulfilling the drug efficiency criteria. For structural analogues the common scaffold is shown in black and the R groups are presented in red. The selected CYP3A4 inhibitors YK1–5 have the following ChEMBL IDs CHEMBL1683444 (YK1), CHEMBL520419 (YK2), CHEMBL1683445 (YK3), CHEMBL482102 (YK4) and CHEMBL3145341 (YK5) and are highlighted yellow in Table S1.

Figure 3

The time dependent distance analysis of (a) CYP3A4-YK1; (b) CYP3A4-YK2; (c) CYP3A4-YK3; (d) CYP3A4-YK4; and (e) CYP3A4-YK5 residues and inhibitor groups involved in hydrogen bonding. The distances are measured in Angstrom (Å) and the time is shown along the x-axis.

Figure 4

(a) The correlation between the binding free energy of the complex predicted by WaterSwap and the IC₅₀ values for YK1–5. (b) The correlation between the binding free energy of the complex predicted by WaterSwap and the IC₅₀ values with the data for YK5 removed as it is a significant outlier compared to the other compounds. Note that the values for YK4 and YK5 are the average of WaterSwap calculations using two different starting structures to ensure that the structures were representative of the entire MD trajectory.

Figure 5

The decomposition of the WaterSwap binding free energy into residue-wise components. The values for the selected CYP3A4 inhibitors are shown, where negative values indicate that the residue stabilizes the inhibitor–protein complex and positive values indicates stabilization of the water cluster rather than the inhibitor.