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OJBTM
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.
ABSTRACT
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 Lipinski’s 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.
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