Linked Life Data

17064917

Source:http://linkedlifedata.com/resource/pubmed/id/17064917

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
2006-11-20
pubmed:abstractText
In the study, molecular dynamics simulations combined with MM-PBSA (Molecular Mechanics and Poisson-Boltzmann Surface Area) technique were applied to predict the binding mode of the polyphenol inhibitor in the binding pocket of the HCV NS3 serine protease for which the ligand-protein crystal structure is not available. The most favorable geometry of three candidates from molecular docking had a binding free energy about 3 and 6kcal/mol more favorable than the other two candidates, respectively, and was identified as the correct binding mode. In the mode, the correlation of the calculated and experimental binding affinities of all five polyphenol compounds is satisfactory indicated by r(2)=0.92. The most favorable binding mode suggests that two galloyl residues at 3 and 4 positions of the glucopyranose ring of the inhibitors interact with SER139, GLY137, ALA157, and ASP81 by hydrogen bond interaction and with ALA156 and HIE57 by hydrophobic interaction and are essential for the activities of the studied inhibitors.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jan
pubmed:issn
0968-0896
pubmed:author
pubmed:issnType
Print
pubmed:day
1
pubmed:volume
15
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
220-6
pubmed:dateRevised
2011-11-17
pubmed:meshHeading
pubmed-meshheading:17064917-Binding Sites, pubmed-meshheading:17064917-Computer Simulation, pubmed-meshheading:17064917-Crystallography, X-Ray, pubmed-meshheading:17064917-Drugs, Chinese Herbal, pubmed-meshheading:17064917-Flavonoids, pubmed-meshheading:17064917-Hydrogen Bonding, pubmed-meshheading:17064917-Ligands, pubmed-meshheading:17064917-Models, Biological, pubmed-meshheading:17064917-Models, Molecular, pubmed-meshheading:17064917-Molecular Structure, pubmed-meshheading:17064917-Phenols, pubmed-meshheading:17064917-Polyphenols, pubmed-meshheading:17064917-Quantitative Structure-Activity Relationship, pubmed-meshheading:17064917-Serine Endopeptidases, pubmed-meshheading:17064917-Serine Proteinase Inhibitors, pubmed-meshheading:17064917-Stereoisomerism, pubmed-meshheading:17064917-Viral Nonstructural Proteins
pubmed:year
2007
pubmed:articleTitle
Prediction of binding for a kind of non-peptic HCV NS3 serine protease inhibitors from plants by molecular docking and MM-PBSA method.
pubmed:affiliation
College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't