همایش ملی بیوانفورماتیک ایران

صفحه اصلی / 4th international edition and 13th Iranian Conference on Bioinformatics

Molecular Docking Studies of Natural Organic Compounds against Urease of Helicobacter Pylori

نویسندگان :

Vajiheh Eskandari¹

1- Department of Biology, Faculty of Science, University of Zanjan, Zanjan, Iran

کلمات کلیدی :

Helicobacter pylori،natural organic compounds،Urease،Molecular docking simulation

چکیده :

Helicobacter pylori exploited urease to infect the highly acidic human stomach (Graham, and Miftahussurur, 2018). Clinically drug therapies in the treatment of H. pylori are associated with many adverse effects; therefore, there is a need for replacing pharmaceutical compounds with less harmful and preferably natural compounds as novel drugs to treat Helicobacter pylori infection. The purpose of this study was to investigate the molecular docking studies of oxadiazole natural compounds (1000 molecules) as potential urease inhibitors of H. pylori The 3-D of Urease (PDB ID. 1e9y) was retrieved from the Protein Data Bank (Berman and Westbrook, 2000), and clead with Discovery Studio 4.1, then minimized and changed using MGLTools to pdbqt format. 1000 approved natural organic compounds were obtained from Selleckchem Inc web site. The docking process of all compounds to important residues of the urease enzyme was performed using Autodock Vina (Trott and Olson, 2010) and Autodock 4 in pyRx program (Dallakyan and Olson, 2015) and AutoDock Vina software. Finally, ligand and junction interactions were analyzed and evaluated by Discovery Studio 4.5 Client software. According to this study, the organic natural compounds exhibited powerful inhibitory activity against the human pathogen H.pylori. All affinities of the compounds were calculated, and the best compounds with low ΔG (-ΔG) were obtained as follow; Sclareolide with Binding energy -8.5, Rutaecarpine with Binding energy -8.2, Cryptotanshinone with Binding energy -8.1, Chrysin with Binding energy -8.0, Tanshinone IIA with Binding energy -7.9, Indirubin with Binding energy -7.9, Vitamin K1 Tanshinone I with Binding energy -8.0 and Kinetin with Binding energy -8. That above mentioned ligands have occupied and interact with the substrate binding site and also active site of the urease i.e: His136, His138, Ala169, KCX219, His221, His248, and Asp362. The present findings revealed the inhibitory effect of the natural organic compounds on the urea enzyme of Helicobacter pylori and can be a very good alternative to chemical drugs.