Development of BODIPY FL Thalidomide As a High-Affinity Fluorescent Probe for Cereblon in a Time-Resolved Fluorescence Resonance Energy Transfer Assay

Ligands for Cereblon, a component of a functional E3 ligase complex that targets proteins for proteolysis, are critical for developing Molecular Glues and proteolysis-targeting chimeras (PROTACs), which have therapeutic implications for various diseases. However, the lack of sensitivity of previously reported assays limits characterization of Cereblon ligands. To address this shortcoming, we developed BODIPY FL thalidomide (10) as a high-affinity fluorescent probe for the human Cereblon protein, with a K_d value of 3.6 nM. We then used BODIPY FL thalidomide (10) to develop a Cereblon time-resolved fluorescence resonance energy transfer (TR-FRET) binding assay. The IC₅₀ values of the Cereblon ligand pomalidomide (8) were 6.4 nM in our Cereblon TR-FRET binding assay, 264.8 nM in a previously reported Cy5-conjugated thalidomide (7)-mediated fluorescence polarization (FP) assay, and 1.2 μM in a previously reported Cy5-conjugated Cereblon Modulator (compound 7) (9)-mediated TR-FRET assay, indicating that our Cereblon TR-FRET binding assay is 41- and 187-fold more sensitive than these two previously published assays. With our Cereblon TR-FRET binding assay, we detected binding of Cereblon ligands but not binding of bromodomain-containing protein 4 or von Hippel-Lindau ligands, thereby demonstrating its selectivity. Our Cereblon TR-FRET binding assay was very stable and detected changes in phthalimide activity due to thalidomide isomerization. Therefore, the BODIPY FL thalidomide (10)-mediated Cereblon TR-FRET binding assay we designed is highly sensitive, selective, and stable and will aid the development and characterization of novel Cereblon ligands.