Title: Homology modelling and identification of active site residue in the nucleoprotein of influenza virus through in silico strategy for drug target

Authors: Pallavi Somvanshi, Vijai Singh

Addresses: Bioinformatics Centre, Biotech Park, Sector-G Jankipuram, Lucknow-226021, Uttar Pradesh, India. ' Synth Bio Group, Epigenomics Project, Universite d'Evry Val d'Essonne-Genopole (R), Tour Evry2, etage 10, 523 Terrasses de l'Agora, 91034 Evry Cedex, France

Abstract: Influenza A virus poses a serious threat towards public health globally. Its genome encodes a nucleoprotein (NP) (498-amino acid) which plays a vital role in viral RNA replication and host specificity. Homology modelling was used to generate the 3-D structure of four different strains (H5N1, H6N1, H3N2 and H7N1) using a known protein template crystal structure (PDB code No. 2IQH). The validation of 3-D structure was done with the help of PROCHECK encompassing amino acid residues in the most favoured region of all strains. The identification of catalytic amino acid residue in the active site domain in 3-D structure of NP was also done. The structure and catalytic amino acid residue present in the NP may help to target and design the antiviral drugs against influenza.

Keywords: influenza virus; nucleoprotein; NP; homology modelling; antiviral drugs; active site residue; flu virus; drug targets; amino acid residues.

DOI: 10.1504/IJMEI.2010.029802

International Journal of Medical Engineering and Informatics, 2010 Vol.2 No.1, pp.26 - 36

Published online: 02 Dec 2009 *

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