Integrated Biochemical Characterization and Computational Dynamics of Carbohydrate-Active Enzymes from the Plant-Parasitic Nematode, Ditylenchus destructor for Industrial Biocatalysis

Abstract

This study characterized cellulase and -Amylase from the plant-parasitic nematode Ditylenchus destructor using integrated computational and experimental approaches to identify reliable industrial biocatalysts. Wet-lab validation via Bradford assay, DNS assay, and Filter Paper Assay (FPA) confirmed enzyme presence and catalytic activity. Molecular docking yielded strong Glide XP scores, indicating high substrate affinity for cellulose and starch. Subsequent 100 ns explicit-solvent MD simulations confirmed remarkable dynamic stability, evidenced by consistently low C-RMSD values (4.0–4.8 Å) and stable radius of gyration profiles (3.68–3.84 nm). Persistent hydrogen bonds and hydrophobic contacts with key active-site residues GLN-131 and ASN-98 in cellulase, GLU-274 and HIS-242 in -Amylase underpin complex stability. These findings collectively position D. destructor enzymes as promising next-generation industrial biocatalyst candidates for food processing and biofuel applications. However, further biochemical validation and empirical kinetic testing under industrially relevant conditions remain necessary to confirm scalability, while the identified residues provide a molecular blueprint for future enzyme engineering initiatives.