Mechanistic Insight into the Enantioselective Degradation of Esterase QeH to (R)/(S)–Quizalofop–Ethyl with Molecular Dynamics Simulation Using a Residue-Specific Force Field

The enantioselective mechanism of the esterase QeH against the two enantiomers of quizalofop-ethyl (QE) has been primitively studied using computational and experimental approaches. However, it is still unclear how the esterase QeH adjusts its conformation to adapt to substrate binding and promote enzym<i>e-substrate interactions in the catalytic kinetics. The equilibrium processes of enzyme-subst</i>rate interactions and catalytic dynamics were reproduced by performing independent molecular dynamics (MD) runs on the QeH-(<i>R</i>)/(<i>S</i>)-QE complexes with a newly developed residue-specific force field (RSFF2C). Our results indicated that the benzene ring of the (<i>R</i>)-QE structure can simultaneously form anion-π and cation-π interactions with the side-chain group of Glu328 and Arg384 in the binding cavity of the QeH-(<i>R</i>)-QE complex, resulting in (<i>R</i>)-QE being closer to its catalytic triplet system (Ser78-Lys81-Tyr189) with the distances measured for the hydroxyl oxygen atom of the catalytic Ser78 of QeH and the carbonyl carbon atom of (<i>R</i>)-QE of 7.39 Å, compared to the 8.87 Å for (S)-QE, whereas the (<i>S</i>)-QE structure can only form an anion-π interaction with the side chain of Glu328 in the QeH-(<i>S</i>)-QE complex, being less close to its catalytic site. The computational alanine scanning mutation (CAS) calculations further demonstrated that the π-π stacking interaction between the indole ring of Trp351 and the benzene ring of (<i>R</i>)/(<i>S</i>)-QE contributed a lot to the binding stability of the enzyme-substrate (QeH-(<i>R</i>)/(<i>S</i>)-QE). These results facilitate the understanding of their catalytic processes and provide new theoretical guidance for the directional design of other key enzymes for the initial degradation of aryloxyphenoxypropionate (AOPP) herbicides with higher catalytic efficiencies.