Efficient Elimination of Nonstoichiometric Enzyme Inhibitors from HTS Hit Lists

High-throughput screening often identifies not only specific, stoichiometrically binding inhibitors but also undesired com- pounds that unspecifically interfere with the targeted activity by nonstoichiometrically binding, unfolding, and/or inactivat- ing proteins. In this study, the effect of such unwanted inhibitors on several different enzyme targets was assessed based on screening results for over a million compounds. In particular, the shift in potency on variation of enzyme concentration was used as a means to identify nonstoichiometric inhibitors among the screening hits. These potency shifts depended on both compound structure and target enzyme. The approach was confirmed by statistical analysis of thousands of dose-response curves, which showed that the potency of competitive and therefore clearly stoichiometric inhibitors was not affected by increasing enzyme concentration. Light-scattering measurements of thermal protein unfolding further verified that com- pounds that stabilize protein structure by stoichiometric binding show the same potency irrespective of enzyme concentra- tion. In summary, measuring inhibitor IC 50 values at different enzyme concentrations is a simple, cost-effective, and reliable method to identify and eliminate compounds that inhibit a specific target enzyme via nonstoichiometric mechanisms. (Journal of Biomolecular Screening 2009:679-689)