In Silico Study of the Effect of Thymoquinone on Three Pre-apoptotic Factors of Bad, Bak, and Bim
محل انتشار: مجله تحقیقات دارویی ابن سینا، دوره: 1، شماره: 1
سال انتشار: 1399
نوع سند: مقاله ژورنالی
زبان: انگلیسی
مشاهده: 152
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شناسه ملی سند علمی:
JR_AJPR-1-1_002
تاریخ نمایه سازی: 30 مرداد 1401
چکیده مقاله:
Background: 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 andproliferation of cancer cells by inducing apoptosis. This study intended to evaluate the effect of thethymoquinone (TQ) on the three pre-apoptotic factors Bad, Bak, and Bim in the simulation environment.Methods: The Protein Data Bank (PDB) files of three pre-apoptotic proteins Bad, Bak, and Bim wereobtained from PDB database and the molecular structure of TQ from PubChem database. The optimization,simulation, molecular docking, and molecular dynamics (MD) computation were performed usingAutoDock, VMD, and GROMACS packages on each one of the proteins in free mode and ligand bindingmode.Results: The number and type of hydrogen and hydrophobic bonds at the binding site of TQ and preapoptoticfactors Bad, Bak, and Bim were detected at the lowest level of energy. The lowest bindingenergy level of TQ had the highest tendency to bind to the BAD molecule. After the binding of TQ toproteins, 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.Conclusion: The variations of binding energy indicated that TQ can affect the three pre-apoptotic factorsBad, Bak, and Bim. This bond seems to increase their activity by variation in the secondary structure ofthe Bim specific residues.
کلیدواژه ها:
نویسندگان
Javad Saffari Chaleshtori
Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
Sayed Hesamoddin Mortazavi
Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences,Shahrekord, Iran
Ehsan Heidari Sureshjani
Young Researchers and Elites Club, Islamic Azad University, Shahrekord Branch, Shahrekord, Iran
Keyhan Ghatre Samani
Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran