Identification of 3D Structure of Gag Polyprotein HIV Type 1 Group M Subtype B isolate HXB2 a Promising Drug Target by Threading Assembly Refinement

Undety Benjamin Jason¹ and Daniel Alex Anand²

¹Department of Bioinformatics, Sathyabama University, Chennai, India. ²Department of Biomedical Engineering, Sathyabama University, Chennai, India.

ABSTRACT: The discovery of potential drug to arrest the replication of HIV-1 is an ever increasing task. There are drugs mostly targeting the three enzymes reverse transcriptase, integrase and protease. Gag gene of HIV genome GAG is found to be more conserve. Functional conservation of HIV-1 Gag implicates rational drug design [1]. HIV-1 replication can be successfully blocked by targeting gag gene polyprotein, offering a promising strategy for new drug classes that complement current HIV-1 treatment options. Gag’s role being responsible forming encapsulation of the virus if disturbed the whole Virus is gone. So the challenge is now to determine the structure of Gag poly-protein as it is undetermined still. There is no crystal structure available in the PDB database. The gag polyprotein of Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) (HIV-1) is downloaded for three dimensional structure determinations. The unavailability of a close template is an added challenge for alternative structure prediction. The non availability of PDB structure and similar template with higher number of residues caused to use threading assembly refinement. This work further carries in finding active site, lead screening and docking studies of Gag poly protein.

KEYWORDS: Conservation; gag polyprotein; target; template

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