other عمومى General پژوهشي Research <div class="rounded" style="background: rgb(238, 238, 238); border: 1px solid rgb(204, 204, 204); padding: 5px 10px; text-align: justify;"><span style="line-height:2;"><span style="font-family:Times New Roman;"><span style="font-size:14px;"><span style="color:#2980b9;"><strong>Background</strong>:</span> Apoptosis is one of the most vital mechanisms in the removal of old and damaged cells, especially cancer cells. Many polyphenolic and antioxidant compounds can inhibit the growth and proliferation of cancer cells by inducing apoptosis. This study intended to evaluate the effect of the thymoquinone (TQ) on the three pre-apoptotic factors Bad, Bak, and Bim in the simulation environment.</span></span><br> <span style="font-family:Times New Roman;"><span style="font-size:14px;"><span style="color:#2980b9;"><strong>Methods</strong>:</span> The Protein Data Bank (PDB) files of three pre-apoptotic proteins Bad, Bak, and Bim were obtained from PDB database and the molecular structure of TQ from PubChem database. The optimization, simulation, molecular docking, and molecular dynamics (MD) computation were performed using AutoDock, VMD, and GROMACS packages on each one of the proteins in free mode and ligand binding mode.</span></span><br> <span style="font-family:Times New Roman;"><span style="font-size:14px;"><span style="color:#2980b9;"><strong>Results</strong>:</span> The number and type of hydrogen and hydrophobic bonds at the binding site of TQ and pre-apoptotic factors Bad, Bak, and Bim were detected at the lowest level of energy. The lowest binding energy level of TQ had the highest tendency to bind to the BAD molecule. After the binding of TQ to proteins, the radius of gyration (Rg) of Bim increased while the Rg of Bad and Bak decreased. However, the secondary structures (Turn, Coil, Helix, and Bend) were greatly affected in the binding of TQ to Bad, Bak, and Bim.</span></span><br> <span style="font-family:Times New Roman;"><span style="font-size:14px;"><span style="color:#2980b9;"><strong>Conclusion</strong>:</span> The variations of binding energy indicated that TQ can affect the three pre-apoptotic factors Bad, Bak, and Bim. This bond seems to increase their activity by variation in the secondary structure of the Bim specific residues.</span></span></span></div> Apoptosis, Pre-apoptotic factors, Thymoquinone, Molecular dynamics 5 9 http://ajpr1.umsha.ac.ir/browse.php?a_code=A-10-2-2&slc_lang=other&sid=1 Javad Saffari Chaleshtori 10031947532846003 10031947532846003 No Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran Sayed Hesamoddin Mortazavi 10031947532846004 10031947532846004 No Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran Ehsan Heidari Sureshjani 10031947532846005 10031947532846005 No Young Researchers and Elites Club, Islamic Azad University, Shahrekord Branch, Shahrekord, Iran Keyhan Ghatreh Samani kgsamani@yahoo.com 10031947532846006 10031947532846006 Yes Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran