Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes

The development of selective histone deacetylase (HDAC) inhibitors with anti-cancer and anti-inflammatory properties remains challenging in large part owing to the difficulty of probing the interaction of small molecules with megadalton protein complexes. A combination of affinity capture and quantitative mass spectrometry revealed the selectivity with which 16 HDAC inhibitors target multiple HDAC complexes scaffolded by ELM-SANT domain subunits, including a novel mitotic deacetylase complex (MiDAC). Inhibitors clustered according to their target profiles with stronger binding of aminobenzamides to the HDAC NCoR complex than to the HDAC Sin3 complex. We identified several non-HDAC targets for hydroxamate inhibitors. HDAC inhibitors with distinct profiles have correspondingly different effects on downstream targets. We also identified the anti-inflammatory drug bufexamac as a class IIb (HDAC6, HDAC10) HDAC inhibitor. Our approach enables the discovery of novel targets and inhibitors and suggests that the selectivity of HDAC inhibitors should be evaluated in the context of HDAC complexes and not purified catalytic subunits.

开发具有抗癌和抗炎特性的选择性组蛋白去乙酰化酶（HDAC）抑制剂在很大程度上仍然具有挑战性，这主要是因为探究小分子与百万道尔顿蛋白质复合物的相互作用存在困难。亲和捕获和定量质谱联用揭示了16种HDAC抑制剂对由ELM - SANT结构域亚基构成支架的多种HDAC复合物的选择性，包括一种新的有丝分裂去乙酰化酶复合物（MiDAC）。抑制剂根据其靶点特征聚类，氨基苯甲酰胺与HDAC NCoR复合物的结合比与HDAC Sin3复合物的结合更强。我们确定了几种异羟肟酸抑制剂的非HDAC靶点。具有不同特征的HDAC抑制剂对下游靶点有相应不同的影响。我们还确定抗炎药丁苯羟酸是一种IIb类（HDAC6，HDAC10）HDAC抑制剂。我们的方法能够发现新的靶点和抑制剂，并表明应在HDAC复合物的背景下而不是纯化的催化亚基中评估HDAC抑制剂的选择性。