Structure-guided design of ISOX-DUAL-based Degraders targeting BRD4 and CBP/EP300. A case of Degrader collapse

Degraders with dual activity against BRD4 and CBP/EP300 were designed. A structure-guided design approach was taken to assess and test potential exit vectors on the dual BRD4 and CBP/EP300 inhibitor, ISOX-DUAL. Candidate Degrader panels revealed that VHL-recruiting moieties could mediate dose-responsive ubiquitination of BRD4. A panel of CRBN-recruiting thalidomide-based Degraders were unable to induce ubiquitination or degradation of target proteins. High-resolution protein co-crystal structures revealed an unexpected interaction between the thalidomide moiety and Trp81 on the first bromodomain of BRD4. The inability to form a ternary complex provides a potential rationale for the lack of Degrader activity with these compounds, some of which have remarkable affinities close to those of (+)-JQ1, as low as 65 nM in a biochemical assay, vs 1.5 M for their POI ligand, ISOX-DUAL. Such a “Degrader collapse” may represent an under-reported mechanism by which some putative Degrader molecules are inactive with respect to target protein degradation.