PMID- 27924272
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20200929
IS  - 2189-4779 (Print)
IS  - 2189-4779 (Electronic)
IS  - 2189-4779 (Linking)
VI  - 13
DP  - 2016
TI  - In silico studies for the interaction of tumor necrosis factor-alpha (TNF-alpha) with 
      different saponins from Vietnamese ginseng (Panax vietnamesis).
PG  - 173-180
AB  - Tumor necrosis factor-alpha (TNF-alpha) 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-alpha. 
      But the interactions between TNF-alpha and the saponins are still unclear. In this 
      study, molecular docking and molecular dynamics simulations of TNF-alpha 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-alpha. The saponins were docked to the pore at the top of the "bell" or 
      "cone" shaped TNF-alpha 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.
FAU - Kim, Oanh T P
AU  - Kim OT
AD  - Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, 
      10000 Vietnam.
FAU - Le, Manh D
AU  - Le MD
AD  - Center for Computational Physics, Institute of Physics, Vietnam Academy of 
      Science and Technology, Hanoi, 10000 Vietnam.
FAU - Trinh, Hoang X
AU  - Trinh HX
AD  - Center for Computational Physics, Institute of Physics, Vietnam Academy of 
      Science and Technology, Hanoi, 10000 Vietnam.
FAU - Nong, Hai V
AU  - Nong HV
AD  - Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, 
      10000 Vietnam.
LA  - eng
PT  - Journal Article
DEP - 20160714
PL  - Japan
TA  - Biophys Physicobiol
JT  - Biophysics and physicobiology
JID - 101675089
EIN - Biophys Physicobiol. 2016 Aug 24;13:207. PMID: 27924275
PMC - PMC5042174
OTO - NOTNLM
OT  - TNF-alpha inhibitor
OT  - ginsenosides
OT  - molecular docking
OT  - molecular dynamics simulation
EDAT- 2016/12/08 06:00
MHDA- 2016/12/08 06:01
PMCR- 2016/07/14
CRDT- 2016/12/08 06:00
PHST- 2016/01/08 00:00 [received]
PHST- 2016/05/12 00:00 [accepted]
PHST- 2016/12/08 06:00 [entrez]
PHST- 2016/12/08 06:00 [pubmed]
PHST- 2016/12/08 06:01 [medline]
PHST- 2016/07/14 00:00 [pmc-release]
AID - 13_173 [pii]
AID - 10.2142/biophysico.13.0_173 [doi]
PST - epublish
SO  - Biophys Physicobiol. 2016 Jul 14;13:173-180. doi: 10.2142/biophysico.13.0_173. 
      eCollection 2016.