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Worldwide, breast cancer is the most life-threatening disease among women. There is always high search to find a cure for cancer. Plant compounds have been identified that they have anti-cancer properties. Therefore, phyto-compounds can be potential for the development of new drugs. In this research, three-dimensional (3-D) structure of breast cancer cell line proteins, tumor suppressor gene (p53), caspase-3 and retinoblastoma-1 were generated and docking with plant compounds (garcinone E, triterpenoid and gallic acid respectively) was studied. The three-dimensional models of proteins were built using SWISS model. Then, the physical and chemical characters of the protein models were determined using ExPASy-ProtParam tool. Next, the proteins were assessed using validation tools such as PROCHECK, ProQ, ERRAT and Verify 3D programs. The results show that the proteins were stable. Lastly, the protein models were docked successfully with garcinone E, triterpenoid and gallic acid respectively using BSP-slim server. The docking scores of the protein-phyto-compound complexes (p53-garcinone E, caspase-3-triterpenoid and Rb1-gallic acid) were 3.873, 4.321 and 3.051 respectively. The proteins had a stable bond with phyto-compounds. The study of the protein-phyto-compound complex interaction will aid in designing new clinical drugs.