Inhibition Mechanism of Lecithin-Dependent Hemolysin from Vibrio parahaemolyticus by Flavonoids: An Enzyme Kinetic and Structural Approach

Vibrio parahaemolyticus is a pathogenic bacterium that threatens food safety by infecting humans and marine organisms. Among its virulence factors, lecithin-dependent hemolysin (vpLDH) has been identified as a promising target for attenuating its pathogenicity. This study explores the inhibitory mechanisms of three natural flavonoids—quercetin, morin, and EGCG—on LDH using enzyme kinetics, fluorescence quenching, and molecular dynamics simulations. The flavonoids quercetin, morin, and EGCG inhibited vpLDH phospholipase A2 activity via a competitive mechanism with inhibition constants of 17.1, 17.27, and 24.24 µM, respectively. Fluorescence quenching experiments confirmed that the evaluated flavonoids formed a stable, non-fluorescent complex (1:1 stoichiometry) with vpLDH. Also, via Stern–Volmer plots, the dissociation constant was calculated (Kd); quercetin showed the highest affinity, followed by morin and EGCG. Molecular dynamics simulations revealed that all evaluated ligands bind to the vpLDH active site vicinity with oscillations < 1.7 nm (100 ns), indicating that both the flavonoids and substrate vpLDH complexes are stable. These findings demonstrate that quercetin, morin, and EGCG are stable competitive inhibitors, highlighting their potential as natural anti-virulence agents against V. parahaemolyticus.