The effect of Phenol Hydroxylase enzyme on some phenolic compounds by molecular docking and simulation study

سال انتشار: 1400
محل انتشار: اولین همایش بین المللی و دهمین همایش ملی بیوانفورماتیک ایران
کد COI اختصاصی: IBIS10_214
زبان مقاله: انگلیسی
تعداد مشاهده: 181

نویسندگان

Faculty of Agriculture and Environment, Islamic Azad University, Meybod, Yazd,Iran

Department of Environment, College of Agriculture and Natural Resources, Islamic Azad University of

Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran

چکیده

Pseudomonas phenol hydroxylase is a bacterial enzyme with hydroxylase activity that can add the hydroxylgroup to chemical compounds and increases their water solubility. This in-silico study investigated the effectof pseudomonas phenol hydroxylase enzyme on some phenolic compounds by simulation and moleculardocking study. In this study, after obtaining the FASTA file sequencing of phenol hydroxylase from Uniprotserver, the production of its PDB file was performed by i-tasser server. Then the confirmation of ۳D structurewas performed by Ramachandran Plot Server. Also, the structure of phenolic compounds were obtained frompubchem server and converted to PDB files by Avogadro V۱.۲ software. The molecular dynamic of phenolhydroxylase was done by Gromacs ۲۰۲۱ software. Then the molecular docking of phenolic compounds onphenol hydroxylase enzyme was done by Autodock v.۴.۲ software after stabilization of RMSD parameter.The ramachandran plot showed that more than ۹۸% of total residues are in preferred and highly preferredregions. According to RMSD results, the simulation system was stabilized after ۵۰ nanoseconds of simulationtime. The results of docking study showd that some phenolic compounds such as Bisphenol(-۷.۱۷ kj/mol),Dinoseb(-۶.۲۰ kj/mol), ۴-Nonylphenol(-۶.۰۳ kj/mol), ۴-Octylphenol(-۵.۹۳ kj/mol), ۴-Chlorophenol(-۴.۹۲kj/mol), Catechol(-۴.۲۳ kj/mol), Phenole(-۴.۱۸ kj/mol) have the high tendency to interact with phenolhydroxylase enzyme. These interactions occurred via some hydrogen and hydrophobic bounds at the bindingsite of phenol hydroxylase. This simulation and molecular docking study showed that phenolic compoundshave the high tendency to interact with Pseudomonas phenol hydroxylase enzyme. These results confirm thatthis enzyme can be effective on phenolic compounds.

کلیدواژه ها

Docking, Phenol Hydroxylase, Phenolic compounds, Simulation

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