biostudies-literatureUnknown13Kim OTTumor necrosis factor-alpha (TNF-α) is a cytokine that plays an important role in inflammatory process and tumor development. Recent studies demonstrate that triterpene saponins from Vietnamese ginseng are efficient inhibitors of TNF-α. But the interactions between TNF-α and the saponins are still unclear. In this study, molecular docking and molecular dynamics simulations of TNF-α with three different triterpene saponins (majonoside R2, vina-ginsenoside R1 and vina-ginsenoside R2) were performed to evaluate their binding ability. Our results showed that the triterpene saponins have a good binding affinity with protein TNF-α. The saponins were docked to the pore at the top of the "bell" or "cone" shaped TNF-α trimer and the complexes were structurally stable during 100 ns molecular dynamics simulation. The predicted binding sites would help to subsequently investigate the inhibitory mechanism of triterpene saponins.Biophysics and physicobiology173-180https://www.ebi.ac.uk/biostudies/studies/S-EPMC5042174biostudies-literature<i>In silico</i> studies for the interaction of tumor necrosis factor-alpha (TNF-α) with different saponins from Vietnamese ginseng (<i>Panax vietnamesis</i>).PMC5042174Kim OTLe MDTrinh HXNong HVfalse<i>In silico</i> studies for the interaction of tumor necrosis factor-alpha (TNF-α) with different saponins from Vietnamese ginseng (<i>Panax vietnamesis</i>).Tumor necrosis factor-alpha (TNF-α) is a cytokine that plays an important role in inflammatory process and tumor development. Recent studies demonstrate that triterpene saponins from Vietnamese ginseng are efficient inhibitors of TNF-α. But the interactions between TNF-α and the saponins are still unclear. In this study, molecular docking and molecular dynamics simulations of TNF-α with three different triterpene saponins (majonoside R2, vina-ginsenoside R1 and vina-ginsenoside R2) were performed to evaluate their binding ability. Our results showed that the triterpene saponins have a good binding affinity with protein TNF-α. The saponins were docked to the pore at the top of the "bell" or "cone" shaped TNF-α trimer and the complexes were structurally stable during 100 ns molecular dynamics simulation. The predicted binding sites would help to subsequently investigate the inhibitory mechanism of triterpene saponins.2016-01-01T00:00:00Z20162024-10-15T09:00:33.495Z2019-03-27T02:25:31ZS-EPMC50421742792427210.2142/biophysico.13.0_173