Polyethylene terephthalate (PET) has been widely used to make disposable bottles, among others, leading to massive PET waste accumulation in the environment. The discovery of the Ideonella sakaiensis PETase and MHETase enzymes, which hydrolyze PET into its constituting monomers, opened the possibility of a promising route for PET biorecycling. We describe an atomistic and thermodynamic interpretation of the catalytic reaction mechanism of PETase using umbrella sampling simulations at the robust PBE/MM MD level with a large QM region. The reaction mechanism takes place in two stages, acylation and deacylation, each of which occurs through a single, associative, concerted and asynchronous step. Acylation consists of proton transfer from Ser131 to His208, concerted with a nucleophilic attack by Ser131 on the substrate, leading to a tetrahedral transition state, which subsequently results in the release of MHET after the breaking of the ester bond. Deacylation is driven by deprotonation of an active site water molecule by His208, with the resulting hydroxide attacking the acylated Ser131 intermediate and breaking its bond to the substrate. Subsequently, His208 transfers the water proton to Ser131, with ensuant formation of MHET and enzyme regeneration. The rate-limiting acylation has a free energy barrier of 20.0 kcal·mol–1, consistent with the range of experimental values of 18.0–18.7 kcal·mol–1. Finally, we identify residues whose mutation should increase the enzyme turnover. Specifically, mutation of Asp83, Asp89, and Asp157 by nonpositive residues is expected to decrease the barrier of the rate-limiting step. This work led to the understanding of the catalytic mechanism of PETase and opened the way for additional rational enzyme engineering.

The COVID-19 has been creating a global crisis, causing countless deaths and unbearable panic. Despite the progress made in the development of the vaccine, there is an urge need for the discovery of antivirals that may better work at different stages of SARS-CoV-2 reproduction. The main protease (M pro ) of the SARS-CoV-2 is a crucial therapeutic target due to its critical function in virus replication. The α-ketoamide derivatives represent an important class of inhibitors against the M pro of the SARS-CoV. While there is 99% sequence similarity between SARS-CoV and SARS-CoV-2 main proteases, anti-SARS-CoV compounds may have a huge demonstration's prospect of their effectiveness against the SARS-CoV-2. In this study, we applied various computational approaches to investigate the inhibition potency of novel designed α-ketoamide-based compounds. In this regard, a set of 21 α-ketoamides was employed to construct a QSAR model, using the genetic algorithm-multiple linear regression (GA-MLR), as well as a pharmacophore fit model. Based on the GA-MLR model, 713 new designed molecules were reduced to 150 promising hits, which were later subject to the established pharmacophore fit model. Among the 150 compounds, the best selected compounds (3 hits) with greater pharmacophore fit score were further studied via molecular docking, molecular dynamic simulations along with the Absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Our approach revealed that the three hit compounds could serve as potential inhibitors against the SARS-CoV-2 M pro target.

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