Database searching using protein crystal structures and molecular docking procedures

摘要

The objective for this computational exercise is to select compounds from a 3D database of commercially available compounds a set of molecules to be biologically assayed for inhibitory activity against the proteolytic enzyme Rhinovirus 3C protease (RVP). It is expected that this database searching procedure will produce "active" compounds at a greater rate than simple random selection. We have performed this operation by using the docking program EPDOCK on a set of molecules selected from the All Chemicals Directory (ACD) based on a 3D pharmacophore search. Several molecules were found with Ki values in the 1-10 uM range. The docking and analysis procedure is outlined and future prospects for this methodology are discussed.