Defining how ligands engage proteins in their native biological context remains a major challenge in modern biology and drug discovery. This challenge is especially acute for compounds emerging from phenotypic screens, which often produce strong biological effects despite acting through unknown targets and poorly resolved mechanisms of action. Thermal Proteome Profiling has emerged as a powerful solution to this problem by exploiting ligand- and state-dependent changes in protein thermal stability that can be monitored in an untargeted and unbiassed manner on the proteome-level. However, despite their considerable promise, conventional stability-proteomics workflows remain limited by technical complexity, substantial resource requirements and sensitivity to experimental variability, which have collectively restricted their widespread adoption and prevented broad deployment.
This seminar presents DIA Thermal PISA, a next-generation thermal-proteomics approach developed at WEHI to increase thermal proteomics sensitivity, throughput and experimental accessibility. Using a panel of diverse antimalarial compounds, we demonstrate that the method enables efficient identification of drug-protein interactions in complex proteomic backgrounds in both lysate and live-cell settings, across diverse target classes including enzymes, proteases, transporters and chaperones. Proteome-wide stability signatures in live cells additionally reveal direct downstream effects of drug action and pathway-level perturbations, providing mechanistic insight into compound mechanisms of action.