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 was unable to induce ubiquitination or
degradation of target proteins. High-resolution protein cocrystal
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 μM 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.

本研究设计了对BRD4与CBP/EP300具有双重活性的蛋白降解剂。
本研究采用结构导向设计策略，对双重靶点BRD4和CBP/EP300抑制剂ISOX-DUAL的潜在连接臂进行评估与测试。候选降解剂筛选结果显示，招募VHL的结构单元可介导BRD4的剂量依赖性泛素化。而一系列基于沙利度胺、招募CRBN的降解剂则无法诱导靶蛋白的泛素化与降解。
高分辨率蛋白质共晶体结构显示，沙利度胺基团与BRD4第一个溴结构域（bromodomain）上的Trp81之间存在意外的相互作用。无法形成三元复合物，为这类化合物缺乏降解活性提供了潜在解释；其中部分化合物的结合亲和力可媲美(+)-JQ1，在生化实验中的半数抑制浓度低至65 nM，而其对应的靶蛋白配体ISOX-DUAL的半数抑制浓度仅为1.5 μM。
这种“降解剂失效（degrader collapse）”现象，或许代表了一种尚未被广泛报道的机制：部分被认为具有降解活性的分子，实际上无法介导靶蛋白的降解。