0% Complete
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 Eskandari
1
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.
لیست مقالات
لیست مقالات بایگانی شده
Identification of Antigenic Proteins of Acinetobacter baumannii as Potential Novel Vaccine Candidates Through a Reverse Vaccinology Approach
Amirhossein Ghadiri - Abbas Doosti - Mostafa Shakhsi-Niaei
Identification of circRNA-miRNA-mRNA Interaction in Myocardial Infarction
Amir Hesam Pahlevani - Ashkan Nazari - Kiarash Zare - Mohammad Ghorbani - Abdolhakim Aalkamel - Mohammad Mehdi Naghizadeh
A novel approach to find Biomarkers affecting Autism Spectrum Disorder (ASD) Using Machine Learning
Amir Zarghami - Milad Besharatifard - Fatemeh Zare-Mirakabad
Modeling and Predicting the Use of Medications Antiplatelets and ARBs Using Logistic Regression
Ahmad Aliyari Boroujeni - Pouya Joze Soleimani - Shima Soltani - Farzaneh Karamitanha
Upregulation of IL6 as a Hub Gene in Metastatic Breast Cancer: Insights from Gene Expression and Network Analysis
Roxana Tajdini - Farinaz Behfarjam - Maryam Shahhoseini - Mostafa Rafiepour
An efficient method based on transformers for antimicrobial peptide prediction
Alireza Khorramfard - Jamshid Pirgazi - Ali Ghanbari Sorkhi
Comprehensive Gene and Protein Catalog for Antimicrobial Environments: A Metagenomic Approach to Mitigate Antimicrobial Resistance
Donya Afshar Jahanshahi - Arad Ariaeenejad - Arman Hasannejad - Mohammad Reza Zabihi - Shohreh Ariaeenejad - Kaveh Kavousi
Prediction of E8 mpox virus protein structure: a potential to design inhibitor
Mahsa Kazemi - Saeide Karimi - Maryam Kheirani nasab - Maryam Kazemi - Mahboobeh Nazari
Designing Guide RNAs Considering Essential Genes for Genome Editing of Yarrowia lipolytica Using Deep Learning in the CRISPR System
Zahra Vahdani - Farshad Darvishi - Fatemeh Zare-Mirakabad
New inhibitors of the Toxoplasmosis by in-silico drug repurposing
Milad Jaberi - Masoud Aliyar - Mosleh Kadkhodamohammadi - Parva Karimimousivandi
بیشتر
ثمین همایش، سامانه مدیریت کنفرانس ها و جشنواره ها - نگارش 42.7.0