Comprehensive profiling of degrader-protein interactions

Targeted protein degradation and induced proximity refer to strategies that leverage the recruitment of proteins to facilitate their modification, regulation or degradation. As the complexity of degraders becomes apparent, advances in unbiased methodology are needed to unveil hidden chemical targets. Here we establish a high throughput affinity purification mass spectrometry workflow in cell lysates for the unbiased identification of degrader interactomes. We map the targets of 20 IMiD analogs identifying 298 proteins as chemically recruited to cereblon and demonstrate the power of enrichment methods for identifying novel protein targets that are overlooked using global whole cell screening methods. We use a computational workflow to estimate target confidence and perform a biochemical screen to identify a lead compound for novel non-ZF target PPIL4. Our study provides a comprehensive inventory of targets chemically recruited to cereblon and delivers a robust and scalable workflow for identifying new drug-induced protein interactions in cell lysates.