Chemoproteomics Enabled Discovery of Selective Probes for NuA4 Factor BRD8

Bromodomain-containing
proteins frequently reside in multisubunit
chromatin complexes with tissue or cell state-specific compositions.
Recent studies have revealed tumor-specific dependencies on the BAF
complex bromodomain subunit BRD9 that are a result of recurrent mutations
afflicting the structure and composition of associated complex members.
To enable the study of ligand engaged complex assemblies, we established
a chemoproteomics approach using a functionalized derivative of the
BRD9 ligand BI-9564 as an affinity matrix. Unexpectedly, in addition
to known interactions with BRD9 and associated BAF complex proteins,
we identify a previously unreported interaction with members of the
NuA4 complex through the bromodomain-containing subunit BRD8. We apply
this finding, alongside a homology-model-guided design, to develop
chemical biology approaches for the study of BRD8 inhibition and to
arrive at first-in-class selective and cellularly active probes for
BRD8. These tools will empower further pharmacological studies of
BRD9 and BRD8 within respective BAF and NuA4 complexes.

含溴结构域（bromodomain）的蛋白质通常存在于具有组织或细胞状态特异性组成的多亚基染色质复合物中。近期研究表明，肿瘤细胞对BAF复合物的溴结构域亚基BRD9存在肿瘤特异性依赖，该依赖源于复发性突变干扰了相关复合物组分的结构与组成。为开展配体结合的复合物组装体相关研究，我们构建了一种化学蛋白质组学方法：以BRD9配体BI-9564的功能化衍生物作为亲和基质。出乎意料的是，除了与BRD9及相关BAF复合物蛋白的已知相互作用外，我们还发现了一种此前未被报道的相互作用——通过含溴结构域亚基BRD8与NuA4复合物成员结合。基于该发现并结合同源建模指导的设计策略，我们开发了用于研究BRD8抑制作用的化学生物学方法，并获得了针对BRD8的首创选择性且具备细胞活性的探针。这些研究工具将为BAF与NuA4复合物中BRD9和BRD8的后续药理学研究提供有力支撑。