Investigation of Molecular Modeling And Molecular Dynamics Simulation In BRCA-1 And BRCA-2 Genes of Amygdalin Ligand

Abstract Breast cancer is the most common type of cancer and the most fatal type among women. BRCA-1 and BRCA-2 are tumor suppressor genes known to cause breast cancer. Drug studies have become very important to target the production of more accurate drugs by reducing the cost with the previous designs of drugs in this field. Amygdalin is used in the treatment of especially cancer, characterized by the loss of red blood cell production. In this study, which was conducted for the first time, it was aimed to examine the use of amygdalin in breast cancer treatment by coupling to the active regions of BRCA-1 and BRCA-2 genes by molecular docking method. The best attachment scores were selected. Amygdalin was taken from PubChem database in sdf format. According to the molecular insertion results, the free energy of the amygdalin ligand for binding to the BRCA-1 protein was -4.8 kcal/mol and the free energy for binding to the BRCA-2 protein was -7.2 kcal/mol also include Ki values. MD simulation was performed using Desmond. Insertion results show that the amygdalin ligand binds more strongly to the BRCA-2 protein than to the BRCA-1 protein. MD simulation for the highly active inhibitor Amigydalin in complex with protein BRCA-2 revealed that the stabilization of ligand was achieved due to the formation of uninterrupted hydrophobic interactions. Due to the binding power of amygdalin ligand, it reveals a unique structure for breast cancer and it is thought to be a reference for designing new molecules with the same structure against cancer and applying these molecules in vivo and in vitro studies.