Arabian Journal of Chemistry (Jun 2023)
Anti-tumor potential and mode of action of karanjin against breast cancer; an in-silico approach
Abstract
Karanjin is a furanoflavanoid first isolated from Pongamia pinnata and has been reported to possess a cytotoxic effect on various lung, breast, leukemia, and hepatoma cancers. However, the mechanism by which karanjin persists cytotoxic effect has yet not been unleashed for breast cancer. Hence, the present study aimed to predict a possible molecular mechanism of karanjin against breast cancer and its assessment on various breast cancer cell lines. We utilized multiple system biology tools like gene set enrichment analysis, gene ontology analysis, cluster analysis, molecular docking, molecular dynamic simulations, and MMPBSA analysis to predict the lead targets. Targets for breast cancer were retrieved from DisGeNet and Therapeutic Target Prediction and matched with targets of karanjin; further, they were subjected to gene enrichment and gene ontology analysis. Molecular docking was performed on all the matched targets; the top three complexes displaying the best binding affinity and the top three hub genes predicted via gene enrichment were selected for MD simulation. Cytotoxicity assay was performed on three different cell lines T47D, MDA-MB-468, and SKBR3, at different time exposures of 24, 48, and 96 hrs. Gene enrichment analysis predicted PI3KCA, PI3KCB, and EGFR as the top 3 hub genes and the PI3K-Akt signaling pathway as the majorly modulated pathway. Molecular docking revealed CYP1A1 to possess the least binding energy (-11.7 Kcal/mol) followed by AKR1C3 (-10.2 Kcal/mol), and CYP3A4 (-10 Kcal/mol). Further, molecular dynamic simulation and MMPBSA analysis displayed the complex of karanjin with CYP1A1 and PI3KCA to be the most stable. The cytotoxicity assay revealed karanjin to possess a more significant cytotoxic effect on SKBR3 cell lines with a dose-dependent increase in efficiency and also displayed an additive/synergistic effect on the three cell lines when used in combination with a tamoxifen/gefitinib. The predictions revealed that karanjin may possess anti-breast cancer potential by the modulation of proteins CYP1A1 and PIK3CA via the PI3K-Akt signaling pathway. However, the mechanism has been proposed via in-silico tools, which need further validation using wet lab protocols; this is the future scope of the study.
