Determination of species-specific allosteric binding sites in pyruvate kinase and its use in drug design studies

Abstract

Knowledge of structural and sequential differences in allosteric regions and con formational changes occurring in catalytic sites as a result of allosteric coupling had a great impact in the design of species-specific allosteric inhibitors. It is the most critical strategy to design effective drugs by targeting the disease-causing organism only without harming the infected organism. Glycolytic pathway is the most essential metabolic pathway in almost all living organisms which converts glucose into pyruvate to produce energy, thus it is often targeted in drug design studies. The objective of this study was to develop a new approach to identify all possible species-specific allosteric binding sites that will inhibit the activity of critical allosteric enzyme in the glycolytic pathway which was Pyruvate Kinase (PK) . The ultimate goal was to propose drug molecules that will bind to the proposed allosteric sites and inhibit the activity of bac terial/parasitic PK without effecting human PK. In addition to sequence and structural comparisons, the computational approach con sists of several steps; computational solvent-mapping to identify all possible ligand binding sites, identification of interface regions, elastic network modeling (ENM) to predict the regions which would have the highest effect on global or essential dynamics upon ligand binding; screening approved drug molecules via docking studies using GOLD tool to propose possible drug candidates. Accordingly, several FDA approved and world - wide used molecules were identified that bind to bacterial PK with high binding affinities without much effect on human PK.