Molecular Dynamics Approach in the Comparison of Wild-Type andMutants of D-hydantoinase

Pregabalin (PGB), has already shown great potential in clinical applications as an analgesic,anticonvulsant, and anxiolytic drug [۱]. A suitable reaction for the production of PGB is theenzymatic desymmetrization of ۳-isobutyl glutarimide (IBI) to R-۳-isobutyl glutaric acidmonoamide (R-IBM), which can be converted to S-PGB by the Hofmann rearrangement. PGB isa chiral compound and S-PGB exhibited a much greater level of anticonvulsant activity than RPGB[۲]. Therefore, R-selective enzymes are being researched for the asymmetric hydrolysis ofIBI to yield R-IBM. An enzyme that can be used is D-hydantoinase, which belongs to the familyof cyclic amidohydrolases and hydrolyzes bulky cyclic imides into their corresponding halfamides[۳]. Molecular docking indicated that three residues, Met-۶۳, Leu-۶۵, and Cys-۳۱۷, mayaffect the substrate binding [۴]. In this work, we did molecular dynamics (MD) simulations onboth wild-type and mutant enzymes (cf. Table ۱) to determine the effects of the mutations on thelocal structure of the active site and the overall structure of the enzyme, as well as whether thereis a relationship between these changes and ee and kcat. Based on the RMSD, RMSF, and Rganalysis of MD simulations results, M۶۳AL۶۵AC۳۱۷T was determined to be the best mutant ofthis enzyme. This result is in good agreement with the experimental results, which indicate thatthis mutation has ۹۶.۵۲% eep [۵].

Keywords:

Pregabalin , D-hydantoinase , Molecular docking , MD simulations