Proanthocyanidins inhibit CYP1B1 through mixed-type kinetics and stable binding in molecular dynamics simulations

Abstract

Cytochrome P450 1B1 (CYP1B1) is a heme-containing enzyme involved in procarcinogen activation and estrogen metabolism, contributing to tumor progression. This study investigates the inhibitory effects of proanthocyanidin (PA) on CYP1B1-catalyzed reactions and its underlying mechanisms. Enzyme kinetics revealed that PA exerts mixed-type inhibition with an IC₅₀ of 2.53 ± 0.01 μM. Molecular docking demonstrated that PA binds to key residues (Phe231, Gly329, Ala330, Asn228, Asn265) and the heme cofactor through hydrogen bonding and π-π stacking, interfering with substrate binding and electron transfer. Molecular dynamics simulations over 200 ns confirmed the stability of the PA-CYP1B1 complex. To validate the stability and inhibitory relevance of the simulation results, berberine, a known CYP1B1 inhibitor, was used as a positive control in parallel analyses. In silico ADMET prediction indicated high intestinal absorption and a favorable safety profile, with no significant CYP inhibition or mutagenicity. However, low membrane permeability and multiple drug-likeness violations suggest limited oral bioavailability. These findings support the potential of PA as a natural CYP1B1 inhibitor for cancer prevention and treatment. Further structural optimization or formulation strategies may enhance its pharmacokinetic properties and clinical applicability.

Keywords: ADMET; CYP1B1; Inhibition kinetics; Molecular dynamics; Proanthocyanidin.

Fig. 1

Dose–response curve of proanthocyanidin (PA) inhibiting CYP1B1 activity.

Fig. 2

Michaelis–Menten kinetics of ethoxyresorufin catalysis by CYP1B1 with and without PA.

Fig. 3

Lineweaver-Burk plot showing mixed-type inhibition of CYP1B1 by PA.

Fig. 4

Heatmap of interaction between CYP1B1 key residues and known inhibitors.

Fig. 5

Docking pose of proanthocyanidin in CYP1B1 active site.

Fig. 6

RMSD profiles of CYP1B1 in complex with proanthocyanidin (A) and berberine (B) during 200 ns molecular dynamics simulations.

Fig. 7

RMSF comparison of CYP1B1 residues over 200 ns MD simulations in complex with proanthocyanidin and berberine. (A) RMSF of CYP1B1 in complex with proanthocyanidin. (B) RMSF of CYP1B1 in complex with berberine.

Fig. 8

RMSF of ligand atoms during 200 ns MD simulation within the CYP1B1 binding site. (A) RMSF of proanthocyanidin atoms in the CYP1B1 binding pocket. (B) RMSF of berberine atoms in the CYP1B1 binding pocket.

Fig. 9

Rg profiles of CYP1B1 in complex with different ligands over 200 ns MD simulations. (A) CYP1B1–proanthocyanidin complex; (B) CYP1B1–berberine complex.

Fig. 10

Solvent Accessible Surface Area (SASA) of CYP1B1 in complex with proanthocyanidin (A) and berberine (B) over a 200 ns molecular dynamics simulation. Both systems exhibit similar fluctuation ranges (20,000–21,800 Ų), indicating stable protein surface exposure under simulated conditions.