• Docking Simulation of Umbelliprenin as a Potential Lead Inhibitor against 5-Lipoxygenase Enzyme
  • Maryam Pakarha,1,* Ali Firouzmand,2
    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


  • Introduction: 5-Lipoxygenase (5-LOX) is a key enzyme in the metabolism of unsaturated fatty acids, particularly arachidonic acid. It catalyzes the synthesis of leukotrienes (potent inflammatory mediators) and is implicated in inflammatory, allergic, and neoplastic diseases. Umbelliprenin Binds the active site of 5-LOX, blocking arachidonic acid metabolism and reducing LTB4/cysteinyl-LT production. it also Neutralizes reactive oxygen species (ROS) generated by 5-LOX. Umbelliprenin (C₂₄H₃₀O₃; MW: 366) is abundant in Ferula species such as F. szowitsiana F. sinkiangensis, and F. qazvinica. It is also present in food-related plants like celery, coriander, and citrus.
  • Methods: In this study, at first uniport website and RCSB website was used to extract protein's 3D structure as pdb file. After this, protein was made ready for the project by making changes using Chimera software. 5-lox enzyme (receptor, PDB: 6n2w) has two chains. every two chains are kept because of the cavity which exist between them. Also, using chimera software, water molecules were removed from the protein and hydrogen molecules were added to its structure. After this changes, pubchem website was used to extract 2D Structure of compound as sdf file. At the end, everything was ready for the molecular docking process using PyRx software.
  • Results: according to numbers, there are 9 various conformation which ligand is docked to protein. in best model, binding affinity is -8.3. in weakest conformation this number is -7.2 so it is acceptable too. however, primary analyzing was done on the first model due to its suitable results.
  • Conclusion: According to docking studies, the compound has suitable interaction with 5-lox protein. Because it has suitable binding affinity (x<-5) and also in at least one of the conformations, it has RMSD lower bond and RMSD upper bond close to each other or equal. Therefore, it is concluded that this compound has the potential to become an inhibitor for the protein. However, this conclusion is based on in-silico studies. In the next stages and to prove this conclusion, in-vitro and in-vivo research should be done.
  • Keywords: 5-Lipoxygenase, Umbelliprenin, molecular docking, inhibitor, protein