In Silico Evaluation of PETase Binding Affinity toward PET Degradation Intermediates

Poly(ethylene terephthalate) (PET) is one of the most widely used synthetic plastics and poses significant environmental challenges due to its persistence in nature. Enzymatic degradation of PET by PETase has emerged as a promising biological approach for sustainable plastic recycling. In this study, an in silico molecular docking approach was employed to investigate the binding affinity and interaction patterns of key PET degradation intermediates—terephthalic acid (TPA), bis(2-hydroxyethyl) terephthalate (BHET), mono(2-hydroxyethyl) terephthalate (MHET), and ethylene glycol (EG)—with PETase. Molecular docking was performed using AutoDock Vina to evaluate binding energies and ligand orientations within the enzyme’s active site. The docking results revealed a clear hierarchy in binding affinities following the order TPA > BHET > MHET > EG. Larger aromatic intermediates exhibited stronger interactions and deeper binding within the catalytic pocket, while smaller hydrolysis products showed weaker interactions and shallow binding modes. These findings provide molecular-level insights into PETase–substrate specificity and support the sequential nature of PET degradation. This preprint presents computational evidence supporting enzyme–substrate interactions involved in PET biodegradation and serves as a foundational study for future work involving molecular dynamics simulations, enzyme engineering, and structure-based optimization.