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Medicinal plants are a vast repository of natural compounds with therapeutic effects against various ailments. Bioactive compounds of these plants have shown to possess anticancer activities. Cancer is one of the fatal diseases causing premature deaths across the world. Two important metabolites, serpentine, a major secondary metabolite of Rauwolfia serpentina, and amarogentin, isolated from Swertia chirata, are found to possess anticancer properties. A comparable in silico analysis of the two anticancer agents serpentine and amarogentin has been done to evaluate their ability to inhibit two potential molecular targets for cancer, nuclear factor-κB (NF-κB) and cyclo-oxygenase-2 (COX-2). The least binding energies of amarogentin with NF-κB and COX-2 are −7·173 and −7·649, respectively, which are better than that of serpentine. The molecular simulation of amarogentin and serpentine suggests that amarogentin has better binding affinities with both cancer targets. Amarogentin is thermodynamically more stable with COX-2 than with NF-κB. Amarogentin is a potent anticancer agent as evidenced by the inhibition of COX-2. This finding would be beneficial to people with cancer.

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