Structure-Guided Design of a “Bump-and-Hole” Bromodomain-Based Degradation Tag

Chemical biology tools to modulate protein levels in cells are critical to decipher complex biology. Targeted protein degradation offers the potential for rapid and dose-dependent protein depletion through the use of protein fusion tags toward which protein degraders have been established. Here, we present a newly developed protein degradation tag BRD4BD1L94V along with the corresponding cereblon (CRBN)-based heterobifunctional degrader based on a “bump-and-hole” approach. The resulting compound XY-06-007 shows a half-degradation concentration (DC50, 6 h) of 10 nM against BRD4BD1L94V with no degradation of off-targets, as assessed by whole proteome mass spectrometry, and demonstrates suitable pharmacokinetics for in vivo studies. We demonstrate that BRD4BD1L94V can be combined with the dTAG approach to achieve simultaneous degrader-mediated depletion of their respective protein fusions. This orthogonal system complements currently available protein degradation tags and enables investigation into the consequences resulting from rapid degradation of previously undruggable disease codependencies.

用于调控细胞内蛋白质水平的化学生物学工具，是解析复杂生命活动的核心手段。靶向蛋白质降解技术可借助已开发适配的蛋白质融合标签，实现快速且剂量依赖性的蛋白质耗竭。本研究报道了一种全新开发的蛋白质降解标签BRD4BD1L94V，以及基于cereblon（CRBN）构建、采用凸凹适配（bump-and-hole）策略的对应双功能降解剂。所得化合物XY-06-007对BRD4BD1L94V的6小时降解半数有效浓度（DC50）为10 nM；经全蛋白质组质谱分析验证，该化合物无脱靶降解现象，且其药代动力学特性适配体内研究需求。本研究证实，BRD4BD1L94V可与dTAG技术联用，实现降解剂介导的对应蛋白质融合体的同步耗竭。该正交系统可弥补现有蛋白质降解标签的局限性，为探究既往不可成药的疾病共依赖蛋白快速降解所引发的生物学效应提供了全新研究范式。