Molecular Modeling Insights into Metal-Organic Frameworks (MOFs) as a Potential Matrix for Immobilization of Lipase: An In Silico Study

SIMPLE SUMMARY: In recent years, a significant amount of attention has been directed toward MOFs as a potential matrix for the immobilization of enzymes. As per the literature, structures based on metal-organic frameworks (MOFs) offer hydrophobic interaction between lipases and the organic component of the MOF. To ascertain the optimal approach for enhancing the robustness and stability of biocatalysts, it is imperative to gain insights into the molecular interactions between enzymes and ligands. In this regard, the computational methodology proves to be an invaluable asset. A review of the literature reveals numerous reports discussing the interaction between lipase and various ligands. However, there is a lack of available research examining the interaction between lipase and MOF. Hence, it is imperative to comprehend the interplay between Candida rugosa lipase (CRL) and the Zeolitic imidazolate framework (ZIF-8) in order to investigate its industrial practicality. This article presents a comprehensive investigation of the utilization of molecular modeling methodologies, specifically molecular docking and molecular dynamics (MD) simulation, for the purpose of studying the interaction between CRL and ZIF-8. ABSTRACT: CRL is a highly versatile enzyme that finds extensive utility in numerous industries, which is attributed to its selectivity and catalytic efficiency, which have been impeded by the impracticality of its implementation, leading to a loss of native catalytic activity and non-reusability. Enzyme immobilization is a necessary step for enabling its reuse, and it provides methods for regulating the biocatalyst’s functional efficacy in a synthetic setting. MOFs represent a novel category of porous materials possessing distinct superlative features that make MOFs an optimal host matrix for developing enzyme-MOF composites. In this study, we employed molecular modeling approaches, for instance, molecular docking and MD simulation, to explore the interactions between CRL and a specific MOF, ZIF-8. The present study involved conducting secondary structural analysis and homology modeling of CRL, followed by docking ZIF-8 with CRL. The results of the molecular docking analysis indicate that ZIF-8 was situated within the active site pocket of CRL, where it formed hydrogen bonds with Val-81, Phe-87, Ser-91, Asp-231, Thr-132, Lue-297, Phe-296, Phe-344, Thr-347, and Ser-450. The MD simulation analysis revealed that the CRL and ZIF-8 docked complex exhibited stability over the entire simulation period, and all interactions presented in the initial docked complex were maintained throughout the simulation. The findings derived from this investigation could promote comprehension of the molecular mechanisms underlying the interaction between CRL and ZIF-8 as well as the development of immobilized CRL for diverse industrial purposes.