Variations of the canonical triad of IsPETase: In silico insights with molecular dynamics simulation

Plastic waste causes severe environmental problems worldwide, and biological recycling is an eco-friendly method to deal with it. The discovery of IsPETase has attracted interest in the scientific community. Its mesophilic nature is an exciting characteristic for new perspectives into PET degradation research. Here, we used a molecular dynamics approach and discussed the possibility of variations for the canonical catalytic triad at pH 7 and 300 K. We prepared three variants and performed a comparative molecular docking protocol of BHET in these three and the wild type. We performed molecular dynamics focusing on the nucleophilic distance and the protonation states of the residues chosen on our mutations. In all simulations, the ligand remained bound to the active site. The total binding energy on the variants diminished but always remained favorable for interaction. Upon analysis of the interaction contribution of each residue, the simulations with the wild type and D206E presented a more stable bond with basically the same binding energy pattern. However, the lysine variants showed a reduction in the unfavorable contributions - while D206E/H237K did not present any unfavorability whatsoever. The new charge distribution and side chains conformation for both lysine variants kept the nucleophilic distance while pushing the ligand away from the oxyanion hole. The single mutants studied here did not show promising results. However, the peculiar behavior of D206E/H237K provokes curiosity about what consequences may arise with empirical data. We believe the discussion here may benefit future efforts regarding PET degradation efficiency at ambient conditions.