Molecular docking studies of novel thiazolidinedione analogs as HIV-1-RT inhibitors

Molecular docking studies were performed on 280 novel thiazolidinediones by Glide, FlexX, and Scigress Explorer Ultra programs and the X-ray crystallographic structure of HIV-1 Reverse transcriptase (PDB code 1RT2) to study the binding mode of these analogs. The experimental conformation of the bound ligand TNK 651 was precisely reproduced by the docking procedures as demonstrated by low (<3.00 Å) root mean square deviations. Results of this study indicated that most of the compounds dock into the active site of 1RT2 enzyme with good docking scores comparable to the bound compound TNK 651. The docking analysis of the highest active molecule 232 (Glide XP score −12.47) and 55 (FlexX score −29.71) shows significant interaction with active site amino acid residues and H-bond interactions with the key amino acid residues.