1st International and 10th National Iranian Conference on Bioinformatics

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

Paper ID : 1179-ICB10

Authors:

Mohamad Hosein Najafi chaleshtori, Hadi Zarei Mahmoud Abadi¹, Javad Saffari-Chaleshtori *²

¹میبد دانشگاه آزاد اسلامی

²گروه آموزشی بیوشیمی/مرکزتحقیقات بیوشیمی بالینی

Abstract:

Pseudomonas phenol hydroxylase is a bacterial enzyme with hydroxylase activity that can add the hydroxyl group to chemical compounds and increases their water solubility. This in-silico study investigated the effect of pseudomonas phenol hydroxylase enzyme on some phenolic compounds by simulation and molecular docking study. In this study, after obtaining the FASTA file sequencing of phenol hydroxylase from Uniprot server, the production of its PDB file was performed by i-tasser server. Then the confirmation of 3D structure was performed by Ramachandran Plot Server. Also, the structure of phenolic compounds were obtained from pubchem server and converted to PDB files by Avogadro V1.2 software. The molecular dynamic of phenol hydroxylase was done by Gromacs 2021 software. Then the molecular docking of phenolic compounds on phenol hydroxylase enzyme was done by Autodock v.4.2 software after stabilization of RMSD parameter. The ramachandran plot showed that more than 98% of total residues are in preferred and highly preferred regions. According to RMSD results, the simulation system was stabilized after 50 nanoseconds of simulation time. The results of docking study showd that some phenolic compounds such as Bisphenol(-7.17 kj/mol), Dinoseb(-6.20 kj/mol), 4-Nonylphenol(-6.03 kj/mol), 4-Octylphenol(-5.93 kj/mol), 4-Chlorophenol(-4.92 kj/mol), Catechol(-4.23 kj/mol), Phenole(-4.18 kj/mol) have the high tendency to interact with phenol hydroxylase enzyme. These interactions occurred via some hydrogen and hydrophobic bounds at the binding site of phenol hydroxylase. This simulation and molecular docking study showed that phenolic compounds have the high tendency to interact with Pseudomonas phenol hydroxylase enzyme. These results confirm that this enzyme can be effective on phenolic compounds.

Keywords:

Docking, Phenol Hydroxylase, Phenolic compounds, Simulation

Status : Paper Accepted (Poster Presentation)