Molecular docking and molecular dynamic simulations of apoptosis proteins with potential anticancer compounds present in Clinacanthus nutans extract using gas chromatography–mass spectrometry

Abstract

Clinacanthus nutans is a medicinal plant recognised for its anticancer properties. We previously discovered that the C. nutans extract had the most potent inhibitory effect on MCF7 breast cancer cell and significantly induced apoptosis. However, there is a scarcity of studies demonstrating the molecular interactions of C. nutans-derived chemical compounds associated with apoptosis-related proteins. Therefore, the objective of this study was to determine the potential chemical compounds found in the C. nutans extract and examine their interactions with the targeted apoptotic proteins using molecular docking and molecular dynamic simulations. To address this objective, the compounds found in the SF2 extract of C. nutans were analysed using Gas Chromatography-Mass Spectrometry (GC-MS). The molecular interaction of the compounds with the targeted apoptotic proteins were determined using molecular docking and molecular dynamic simulations. GC-MS analysis revealed a total of 32 compounds in the SF2 extract. Molecular docking analysis showed that compound β-amyrenol had the highest binding affinity for MDM2-P53 (−7.26 kcal/mol), BCL2 (−11.14 kcal/mol), MCL1-BAX (−6.42 kcal/mol), MCL1-BID (−6.91 kcal/mol), and caspase-9 (−12.54 kcal/mol), whereas campesterol had the highest binding affinity for caspase-8 (−10.11 kcal/mol) and caspase-3 (−10.14 kcal/mol). These selected compounds were subjected to molecular dynamic simulation at 310 K for 100 ns. The results showed that the selected protein-ligand conformation complexes were stable, compact, and did not alter much when compared to the protein references. The findings indicate that β-amyrenol and campesterol are potentially significant compounds that might provide insight into the molecular interactions of the compounds with the apoptosis-related proteins. Communicated by Ramaswamy H. Sarma