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

Abstract

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.