General Stepwise Approach to Optimize a TR-FRET Assay for Characterizing the BRD/PROTAC/CRBN Ternary Complex

Proteolysis-targeting chimeras (PROTACs) degrade target proteins by engaging the ubiquitin-proteasome system. Assays detecting target-PROTAC-E3 ligase ternary complexes are critical for PROTAC development. Both time-resolved fluorescence energy transfer (TR-FRET) assays and amplified luminescent proximity homogeneous assays can characterize ternary complexes and assess PROTAC efficacy; stepwise optimization protocols for these assays are lacking. To identify assay conditions that can be applied to various targets and PROTACs, we used a stepwise approach to optimize a TR-FRET assay of BRD2(BD1)/PROTACs/CRBN ternary complexes. This assay is sensitive and specific and responds to the bivalent PROTACs dBET1, PROTAC BET Degrader-1, and PROTAC BET Degrader-2 but not to non-PROTAC ligands of BRD2(BD1) or CRBN. The activity rank order of dBET1, PROTAC BET Degrader-1, and PROTAC BET Degrader-2 in the TR-FRET assay corresponded with previously reported cell growth inhibition assays, indicating the effectiveness of our assay for predicting PROTAC cellular activity. The TR-FRET ternary complex formation assay for BRD2(BD1)/PROTAC/CRBN can be configured to characterize the binding activities of BRD2(BD1) and CRBN ligands with the same compound activity rank order as that of previously reported binary binding assays for individual targets but with the advantage of simultaneously assessing the ligand activities for both targets. Our assay is modular in nature, as BRD2(BD1) can be replaced with other BRDs and successfully detect ternary complexes without modifying other assay conditions. Therefore, the TR-FRET ternary complex assay for BRDs provides a general assay protocol for establishing assays for other targets and bivalent molecules.