همایش ملی بیوانفورماتیک ایران

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

Molecular docking and bioinformatics study of active compounds of thyme) Thymus vulgaris( in inhibiting COX-2 enzyme related to inflammatory diseases

نویسندگان :

Razieh Biglari Farash¹ Azizollah Kheiry² Najmaddin Mortazavi³ Mohsen Sani khani⁴

1- دانشگاه زنجان 2- دانشگاه زنجان 3- دانشگاه زنجان 4- دانشگاه زنجان

کلمات کلیدی :

thyme،molecular binding،bioinformatics،prostaglandin

چکیده :

Inflammation is a natural response of the body to injury or infection that, if chronic, can lead to diseases such as rheumatoid arthritis, cancer, and heart disease. The cyclooxygenase-2 enzyme plays a key role in the production of prostaglandins and inflammatory processes, and its inhibition is recognized as a therapeutic target. Molecular docking is a method often used in drug design because it can predict how small molecule ligands will bind to target binding sites. Molecular docking can be used to identify potential compounds that inhibit the COX-2 enzyme. thyme )Thymus vulgaris( has proven anti-inflammatory effects with its bioactive compounds such as thymol, carvacrol, and linalool. In this study, bioinformatics methods including molecular docking and molecular dynamics simulations were used to investigate the interaction of these compounds with COX-2. Initially, information related to thymol and carvacrol was extracted from the PubChem database (PubChem Database, 2024). The crystal structure of the COX-2 enzyme was obtained from the Protein Data Bank (Protein Data Bank, 2024). AutoDock Vina software was used for docking simulation (Trott and Olson, 2010). The compounds were placed in the active site of COX-2 and their binding energies were calculated. GROMACS software was used for dynamic simulation. The stability of the complexes was evaluated by indices such as the difference between the crystal structure of the ligand compound and the predicted binding (RMSD) and kinetic energy. The pharmacokinetic properties and toxicity of the compounds were predicted using the SwissADME tool. The docking results showed that carvacrol has a lower binding energy than thymol, indicating its stronger interaction with the COX-2 active site. The hydrogen bond binding energy of thymol with the active site of the COX-2 enzyme was negative 8.6 kcal/mol, while the binding energy of carvacrol was negative 1.7 kcal/mol, making this compound a better option than thymol for pharmaceutical use. The RMSD of the thymol-COX-2 and carvacrol-COX-2 complexes were about 1.2 and 1.8 Å, respectively, indicating the high stability of these interactions during the 50 ns simulation. Kinetic energy changes of the compounds also showed that the carvacrol complex is more stable. Drug absorption, distribution, metabolism and excretion (ADMET) analysis (Dhanaraj and Asok, 2017) showed that carvacrol has high permeability through the blood-brain barrier (BBB) and thymol has lower permeability, making carvacrol a potential candidate for the treatment of nervous system inflammation. This study showed that the carvacrol compound from Shiraz thyme plant interacts strongly with the COX-2 enzyme and can be investigated as a drug candidate for inhibiting this enzyme. Molecular dynamics simulation and ADMET analysis showed low hepatotoxicity for both compounds, confirming the stability and safety of these compounds. It is suggested that further experimental tests be performed to confirm these results.

لیست مقالات

لیست مقالات بایگانی شده

Dysregulated genes in the fat tissue of children confer a risk of cancer

Armita Kakavand Hamidi - Mahsa Mohammad Amoli

Development of Novel Cellulose Crystal-Hyaluronic Acid Anti-Cancer Carriers for Targeting

Yeganeh Abbasian Bajgiran - Maryam Azimzadeh Irani

Molecular docking study of some herbal compounds as potential inhibitors of SARS-CoV-2 spike receptor

Mohammad Satari - Alireza Karami - Samin Saleh

ATIC as a Theranostic Biomarker in Gastrointestinal Cancers: Insights from Autophagy Pathway Analysis

Pooya Jalali - Maryam Eghbali - Zahra Eghabli - Yasaman Gholinezhad - Zahra Salehi

Identifying Key Genes, miRNAs, and lncRNAs in Lennert Lymphoma Through Comprehensive Network Analysis of Diverse Omics Data

Fatemeh Shadvar

Investigation of the interaction between 2-aminothiazole and bovine serum albumin (BSA), using the methods of molecular docking calculations and density functional theory (DFT)

Forough Pakzadi - Yaghub Pazhang - Ebrahim Nemati-Kande

Molecular docking and bioinformatics study of active compounds of thyme) Thymus vulgaris( in inhibiting COX-2 enzyme related to inflammatory diseases

Razieh Biglari Farash - Azizollah Kheiry - Najmaddin Mortazavi - Mohsen Sani khani

Prediction of E8 mpox virus protein structure: a potential to design inhibitor

Mahsa Kazemi - Saeide Karimi - Maryam Kheirani nasab - Maryam Kazemi - Mahboobeh Nazari

BIRC5: The Silent Architect of Tumor Persistence and Senescence in Hepatocellular Carcinoma

Amirhosein Farrokhzad - Maryam Kaboli - Elahe Hoseinnia - Elham Rismani - Massoud Vosough

Novel Anti-ageing Strategy Via Targeting CST With Vitamin B1

SeyedMobin Mousavi Ghomi - Maryam Azimzadeh Irani - Aida Arezoumandchafi

ثمین همایش، سامانه مدیریت کنفرانس ها و جشنواره ها - نگارش 40.4.1