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Prediction of the interaction of HIV-I Integrase and Raltegravir through molecular modeling approach

Author(s): Marudamuthu Balakrishnan1*, Thangaraj Sindhu2, Sundarraj Rajamanikandan2

Journal: Journal of Pharmacy Research
ISSN 0974-6943

Volume: 4;
Issue: 5;
Start page: 1391;
Date: 2011;
Original page

Keywords: Docking | HIV-I integrase | Molecular modeling | Molsoft ICM-pro 3.5 | Raltegravir.

The present study was designed to investigate the binding mode of the drug Raltegravir with the newly modeled protein HIV-I integrase. The 3-D structure model of HIV-I integrase was constructed from the putative sequence using homology modeling techniques. Target sequence possessed sequence identity 80.181% with the template. Structural refinement and energy minimization of the built HIV-I integrase model was done. The structural quality and accuracy of the predicted model was verified using Procheck, WHAT IF, Errat and Verify 3D showed thatthe modeled structure is satisfactory and suited for analysis of the substrate binding pocket and docking studies. Validity of the structural model was assessed by docking simulation with theHIV-I integrase inhibitor Raltegravir. Detailed analyses of HIV-I integrase and Raltegravir interactions were done in Molsoft ICM-pro 3.5. Based on the RMSD and energy values, the best docking orientation was selected. The residues in binding domain responsible for binding to the inhibitor with high binding affinity were identified.
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