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Online Journal of Bioinformatics©

Established 1995

ISSN 1443-2250


Volume 21 (3):271-273, 2020.

In Silico 3D Polymerase PB2 protein target docking for influenza A virus


Suchitru Kunurri, Balaji SRN, Ankit Gupta, Narayana Murthy Lalam and Krishna Kant Gupta


Department of Bioinformatics, NTHRYS Biotech Labs., Hyderabad. 500044. Andhra Pradesh, India.




Kunurri S, Balaji SRN, Gupta A, Lalam NM, Gupta KK., In Silico 3D Polymerase PB2 protein target docking for influenza A virus , Onl J Bioinform., 21 (3):271-273, 2020. Avian influenza virus is highly contagious variable widespread in birds. We found 60 virus proteins but selected only polymerase PB2 by Database of Essential Genes (DEG) for growth reproduction and survival and Non-homology with Human BLASTP. Structure was retrieved from PDB and ligands from 66 analogs for bioactivity, stereochemistry and Lipinskiís rule. Analogs of Amantadine, Oseltamivir. Rimantadine and zanamivir ligands were used for docking with Polymerase PB2 scores. Optimal conformation of the docked complex with least energy and most fitness were determined with Gold, iGemdock and MVD software by virtual screening of ligands against target protein. Results suggested that CID7505949 IUPAC 2R, 3R, 4S, 3-acetamido-4-diaminomethylideneamino-2-(dibutylcarbamoyl)-3.4-dihydro-2H-pyran-6-carboxylic-acid exhibited optimal GOLD docking score of 48.42. Docking with iGemdock for fitness, ligands were minimized and docked with the target. Again CID7505949 showed the best fitness score with 9 hydrogen bonds. MVD confirmed RMSD hydrogen bond interaction and torsion values. Amino acid residues Gln 602, Ser 741. Thr 598, Arg 692, Gln 632, Ser 529, Arg 630. Ser714, Lys 738, Phe 694, Asp 740 and Gly 693 were present in the interaction region. We find zanamivir analog CID7505949 exhibited most efficient docking with polymerase PB2.


Keywords: Avian influenza; Polymerase P132; Docking; ligand; drug-design.