Molecular Docking and Molecular Dynamics Study of a Local Lipase: Insights into Substrate Specificity and Thermostability for Biodiesel Biocatalyst Development

Abstract

Lipase enzymes are widely utilized as biocatalysts in biodiesel production due to their specificity and environmentally friendly characteristics. This study aims to evaluate the interaction between a locally isolated lipase enzyme and fatty acids with varying carbon chain lengths (C2–C18) using molecular docking and molecular dynamics simulations. Docking results revealed that the highest binding affinity was observed for palmitic acid (C14) with a value of -7.986 kJ/mol, indicating a preference toward long-chain fatty acids. Molecular dynamics analysis, including root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (Rg), demonstrated that the enzyme exhibits greater structural stability at 50°C compared to temperatures below 30°C, suggesting its thermostable nature. Comparative analysis showed that the studied enzyme shares 95.44% sequence similarity with Lipase ITB1.1, yet exhibits higher binding affinity toward similar substrates. Considering that lipase ITB1.1 has been experimentally reported to catalyze transesterification reactions for biodiesel and biolubricant production, the enzyme investigated in this study is predicted to possess similar catalytic potential. These findings indicate that the local lipase enzyme is a promising candidate for biocatalytic applications in biodiesel production, although further experimental validation is required