Molecular Dynamics Insights into the Biodegradation of Synthetic Polymers by <i>Moniliophthora roreri</i> Cutinases

The natural degradation of synthetic polymers is an extremely slow process, often taking hundreds to thousands of years. The fungus <i>Moniliophthora roreri</i> produces cutinase enzymes, such as <i>Mr</i>Cut1, <i>Mr</i>Cut2, and <i>Mr</i>Cut3, which are capable of depolymerizing synthetic polymers. Although experimental studies have demonstrated that the <i>Mr</i>Cut1 enzyme can degrade polyethylene succinate (PES), polycaprolactone (PCL), and polyethylene terephthalate (PET), its three-dimensional structure and the atomistic details underlying the binding process with these polymers remain elusive. Here, we present the first atomistic simulations of <i>Mr</i>Cut1 in complex with PES, PCL, and PET oligomers, providing structural insights into substrate recognition, binding modes, and key interactions driving polymer degradation. Additionally, we evaluated the structural differences among <i>Mr</i>Cut1, <i>Mr</i>Cut2, and <i>Mr</i>Cut3 to assess how these variations affect their affinity for forming enzyme-polymer complexes. Through Free Energy Landscape (FEL) and active site volume analyses, we demonstrate the structural similarity between <i>Mr</i>Cut1 and <i>Mr</i>Cut3, as well as their respective volumes for polymer binding at the active site. Our results indicate that the binding affinities of PES, PCL, and PET for <i>Mr</i>Cut1 are -9.17 ± 0.49, -9.00 ± 0.56, and -8.40 ± 0.49 kcal/mol, respectively. In contrast, these ligands exhibit lower affinities for <i>Mr</i>Cut3, with values of -7.99 ± 0.43, -7.95 ± 0.60, and -7.30 ± 0.42 kcal/mol, respectively. Furthermore, our findings suggest that the absence of the catalytic triad in <i>Mr</i>Cut2, together with the lack of a well-formed active site cavity, may result in its inefficient catalytic activity. Finally, we demonstrate, for the first time, the potential of <i>Mr</i>Cut3 as a biocatalyst, similar to <i>Mr</i>Cut1, and explore its applicability in the biodegradation of certain synthetic polymers.