Protein Modelling and Rational Drug Designing

In order to better understand the structural and Chemical features of HIV-1 protease, in the pathogenesis of HIV, the docking, QSAR (MFA and 2D QSAR ) pharmacophore studies have been conducted on recently explored N-phenyloxazolidinone based carbamate Compounds with known HIV protease inhibitory activities.Docking analysis of the analogue compounds suggest the role of hydrogen bonding and other weak interactions in enzyme selectivity and their docking scores are well correlated with activity. Quantitative structure activity relationship (QSAR) models weere developed for N-phenyloxazolidinone basedcarbamate derivatives. It includes molecular field analysis (MFA) and 2D-QSAR. The models were developed using 38 compounds and their predictive ability was assesssed using a test set of 10 compounds. The predictive 3-D QSAR models have conventional r2 values of 0.98 for MFA and 2-QSAR respectively respectively Pharmacophore models for these inhibitors were generated using HipHop module of Catalyst software. HipHopgenerated 2-featured pharmacophore model and Hypogen generated 2-featured pharmacophore model and Hypogen generated 5-featured pharmacophore model. Further these results were supported with structure based drug design, using Ligand fit., Autodock, Affinity. The results of docking, QSAR and pharmacophore methodologies provide a powerful tool directed to the design of novel and selective HIV protease inhibitors. On the bassis of these studies and with Ludi, a new molecule was designed which shows promising estimated acivity. In ligand fit The highly active molecule sdmol_5 with IC50 value shows the docking score 70.462 where as the lydi ligand showed the activity of 124.20.