System-Wide Profiling by Proteome Integral Solubility Alteration Assay of Drug Residence Times for Target Characterization

[Image: see text] Most drugs are used in the clinic and drug candidate target multiple proteins, and thus detailed characterization of their efficacy targets is required. While current methods rely on quantitative measurements at thermodynamic equilibrium, kinetic parameters such as the residence time of a drug on its target provide a better proxy for efficacy in vivo. Here, we present a residence time proteome integral solubility alteration (ResT-PISA) assay, which facilitates monitoring temporal protein solubility profiles after drug removal (“off-curve”) in cell lysates or intact cells, quantifying the lifetime of drug–target interaction. A compressed version of the assay measures the integral under the off-curve enabling the multiplexing of binding affinity and residence time assessments into a single proteomic analysis. We introduce a combined scoring system for three parametric dimensions to improve prioritization of targets. By providing complementary information to other characteristics of drug–target interaction, the ResT-PISA approach will be useful in drug development and precision medicine.