Journal
COMPUTATIONAL BIOLOGY AND CHEMISTRY
Volume 53, Issue -, Pages 308-317Publisher
ELSEVIER SCI LTD
DOI: 10.1016/j.compbiolchem.2014.11.001
Keywords
p7?of HCV; Antivirals; Docking; MD simulations
Funding
- National Science Council, Taiwan, Taiwan [NSC-101-2112-M-010-002-MY3]
- Deutscher Akademischer Austausch Dienst (DAAD)
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Protein p7 of HCV is a 63 amino acid channel forming membrane protein essential for the progression of viral infection. With this momentousness, p7 emerges as an important target for antiviral therapy. A series of small molecule drugs, such as amantadine, rimantadine, amiloride, hexamethylene amiloride, NN-DNJ and BIT225 have been found to affect the channel activity. These compounds are docked against monomeric and hexameric structures of p7 taken at various time steps from a molecular dynamics simulation of the protein embedded in a hydrated lipid bilayer. The energetics of binding identifies the guanidine based ligands as the most potent ligands. The adamantanes and NN-DNJ show weaker binding energies. The lowest energy poses are those at the site of the loop region for the monomer and hexamer. For the latter, the poses show a tendency of the ligand to face the lumen of the pore. The mode of binding is that of a balance between hydrophobic interactions and hydrogen bond formation with backbone atoms of the protein. (C) 2014 Elsevier Ltd. All rights reserved.
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