1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Molecular docking and molecular dynamic simulation of Curcumin on three pre-apoptotic factors of Bad, Bak, and Bim
Paper ID : 1156-ICB10
Authors:
Fateme Davarani Asl1, Pegah Khosravian2, Mehdi Rezaee1, Javad Saffari-Chaleshtori *3
1Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
2Medical plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
3Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
Abstract:
Curcumin, a polyphenol compound, is derived from the plant Curcuma longa. This antioxidant with apoptotic effects can lead cells to death especially in cancer cells. This molecular dynamic and molecular docking simulation study investigated the effects of curcumin on three pre-apoptotic factors of Bad, Bak, and Bim. The PDB files of these three factors were obtained from www.rcsb.org and the 3D structure of curcumin was obtained from PubChem and converted to a PDB file by Avogadro v.1.2 software. Via GROMACS 2018, studies on molecular dynamic simulation were conducted in water and ion environment. Furthermore, AutoDock v.4.2.6 software performed the docking of curcumin as a ligand to these pre-apoptotic proteins. Also, LigPlot+ v.4.5.3 was used to determine the hydrogen and hydrophobic bonds at the binding sites. Curcumin with the highest tendency could bind to Bad by -6.58 kcal/mol of binding energy. In addition, the binding of curcumin to the other proteins induced some changes in molecular dynamic factors such as radius of gyration (Rg), root-mean-square deviation (RMSD), and root-mean-square fluctuation (RMSF). A significant increase in Rg and RMSD was seen in Bad and Bak after docking with curcumin. Moreover, curcumin induced some variations in RMSF and secondary structure in these factors. According to this study, curcumin could bind to Bad, Bak, and Bim directly, induce conformational changes, and increase their likelihood of dimerization that can lead to activating apoptotic pathways. These results confirmed the apoptotic effects of curcumin on cancer cells.
Keywords:
Bad, Bak, Bim, Curcumin, Molecular dynamics
Status : Paper Accepted (Poster Presentation)