Molecular Docking Analysis of Chamazulene as COX-2 Potential Inhibitor
Molecular Docking Analysis of Chamazulene as COX-2 Potential Inhibitor
Ali Firouzmand,1,*Vida Hasanvand,2Maryam Soveyni,3
1. Department of Biology, Faculty of Science, Bu-Ali Sina University, Hamedan, Iran 2. Department of Biology, Faculty of Science, Bu-Ali Sina University, Hamedan, Iran 3. Department of Biology, Faculty of Science, Bu-Ali Sina University, Hamedan, Iran
Introduction: In this research article, we investigated the interaction between Chamazulene and COX-2 protein. For this purpose, we used the molecular docking method.
COX-2 inhibitors (coxibs) are a type of nonsteroidal anti-inflammatory drug (NSAID) that directly target cyclooxygenase-2, COX-2, an enzyme responsible for inflammation and pain. Targeting selectivity for COX-2 reduces the risk of peptic ulceration and is the main feature of celecoxib, rofecoxib, and other members of this drug class.
in this paper, the interaction between ligand and target protein has been investigated on in-silico step using bioinformatics methods. According to the obtained results, Chamazulene compound have a good interaction with COX-2 protein.
Methods: In this study, at first, we used uniport website and PDB website to extract protein's 3D structure as pdb file.
After this, we made the protein ready for the project by making changes using Chimera software.
COX-2(5KIR) had two chains, so we decided to keep all chains because there are cavities between the chains.
Also, by using this software, water molecules were removed from the protein and hydrogen molecules were added to its structure.
After this changes, we used pubchem website and drugbank website to extract 3D Structure of drugs as sdf file.
finally, everything is ready for the molecular docking process by using PyRx software.
In this research, the blind docking method was used. Therefore, the defined grid box includes the entire two chains of the protein.
At the end, we used molegro virtual docker to check the results of different models.
Results: according to the numbers, Chamazulene has suitable interaction with COX-2 protein. So, it's clear that our compound can be docked to COX-2 protein.
the numbers of binding affinity are suitable. also, we have normal range of numbers on RMSD
Conclusion: Therefore, we conclude that Chamazulene has analgesic and anti-inflammatory properties.
however, in this article we just worked on in-silico. to prove these conclusions, in-vitro and in-vivo steps should be done