In silico investigation of the lignin polymer biodegradation by two actinomycetal peroxidase enzymes

Abstract

Lignin is the generic term of a large group of aromatic polymers. During the manufacturing chain of paper production, lignin is cleaved by chemical reagents, which leads to the production of numerous phenolic and chlorinated intermediates, that is ultimately ejected into the wastewater, leading to environmental pollution and possible toxicological risks. It is therefore important to find a safer lignin degradation pathway that must be more respectful of the environment and health. Dye-decolorizing peroxidase (DyP) are enzymes that play a crucial role in the biodegradation of lignin. In this study, we have carried out in-silico research aimed at evaluating the biodegradation activity of the lignin polymer by two actinomycetal DyP peroxidases, belonging to the species Streptomyces coelicolor and Amycolatopsis sp. A molecular docking study of the degradation potential of the lignin trimer Coniferyl sinapyl p-coumaryl alcohol by the two peroxidases was performed. The results show a strong molecular interaction of the lignin polymer with the DyP peroxidase of Streptomyces coelicolor and Amycolatopsis sp, showing a low binding energy of −9.4, and −9.3 Kcal/mol, respectively; with the involvement of the key amino acids of the enzyme active site. A 10 ns MD simulation analysis was also performed. The results of this analysis confirm the stability of the peroxidase-lignin complexes of the two bacterial species, indicating the catalytic efficiency of these enzymes toward the lignin polymer.