Effects of Esculin as an antimicrobial compound on pectatelyase enzyme of Pectobacterium carotovorum by molecular dynamicssimulation

Background and Aim : Esculin, a coumarin glucoside ingredient, has a wide range of roles. Ithas also shown anti-inflammatory, anti-oxidant. Pectobacterium carotovorum and pectate lyase(PL) as its major pathogenic factor cause a great amount of harm to products such as potatoes andonions annually. This enzyme has also proven to be the cause of methanol production in storedfruits.Methods : Esculin as ligand and PL as receptor were downloaded from Pubchem and rcsb server,respectively. Molecular docking was done using Autodock ۴.۲. And also, molecular dynamicssimulation was performed by Gromacs software (ver. ۲۰۲۱.۱).Results : The docking results determined their ?G to be -۵.۵۴ kcal.mol-۱ and also demonstratedamino acids that bonded. Besides, the result of molecular dynamic simulation determined theaverage and standard deviations of the radius of gyration, area per residue, Root Mean-SquareDeviation, Root mean square fluctuation, H-bond, and secondary structure. Pectate lyase-waterinteraction was considered as the control group.Conclusion : Based on the results of current study, the effect of esculin on inhibiting the pectatelyase enzyme was concluded. And as a result, its potential to be used in industries against PLenzyme and Pectobacterium carotovorum.

کلیدواژه ها:

Pectobacterium carotovorum ، pectate lyase ، Esculin ، Simulation