Computational screening of walnut (Juglans regia) husk metabolites reveals Aesculin as a potential inhibitor of pectate lyase Pel3: Insights from molecular dynamics and τRAMD

Pectate lyase (Pel3), an enzyme derived from Clostridium bacteria, plays a significant role in the degradation of pectin and contributes to the spoilage of agricultural products. Pel3 can bind to pectin and break it down, a process that accelerates food decay. Aesculin, a natural compound extracted from walnut husk, has been recognized for its antibacterial and antifungal properties, making it a promising natural inhibitor. The aim of this study was to investigate the inhibitory mechanisms of Aesculin through molecular simulations and random accelerated molecular dynamics (RAMD). Molecular docking results showed that Aesculin may effectively bind to Pel3 and form a strong interaction. RMSD analysis revealed that Aesculin's binding to Pel3 reduced structural fluctuations, thereby enhancing the enzyme's structural stability. Slight changes in the radius of gyration (Rg) indicate a decrease in structural compactness in specific regions of the protein. Furthermore, SASA analysis revealed a modest increase in solvent accessibility. RAMD simulations, performed with 120 replicates, showed a short average residence time (∼0.015 ns), suggesting rapid unbinding and weak interaction at the active site. MM-PBSA analysis yielded a total binding free energy of −2.92 ± 0.44 kcal/mol, mainly driven by van der Waals and electrostatic contributions, confirming moderate and reversible binding. These findings suggest that Aesculin may form alternating interactions with Pel3 as an effective natural inhibitor and exhibit a short residence time in its active site. The molecular dynamics simulations and RAMD analysis suggest that Aesculin can enhance the structural stability of Pel3, presenting it as a potential anti-spoilage agent in the food and agricultural industries.