Biophysics and Physicobiology 13, 173-180 (2016)

ISSN: 2189-4779

In silico studies for the interaction of tumor necrosis factor-alpha (TNF-α) with different saponins from Vietnamese ginseng (Panax vietnamesis)

Oanh T. P. Kim, Manh D. Le, Hoang X. Trinh and Hai V. Nong

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 effi- cient inhibitors of TNF-α. But the interactions between TNF-α and the saponins are still unclear. In this study, molecular docking and molecular dynamics simula- tions 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 structur- ally stable during 100 ns molecular dynamics simula- tion. The predicted binding sites would help to subse- quently investigate the inhibitory mechanism of triterpene saponins.

URL: https://www.jstage.jst.go.jp/article/biophysico/13/0/13_173/_article

DOI: 10.2142/biophysico.13.0_173

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