Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes

Abstract

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.

Plants Release Precursors of Histone Deacetylase Inhibitors to Suppress Growth of Competitors

“…In contrast to APO, we did not observe a correlation between TSA-induced changes in gene expression and H3 acetylation, even though all tested HDAC inhibitors led to a global increase in H3ac and to growth inhibition. This discrepancy suggests that TSA and APO act on different HDACs in the plant, similar to clinically applied HDAC inhibitors, which display characteristic target profiles in humans (Bantscheff et al, 2011;West and Johnstone, 2014). Specificity for the target HDAC might also result in the deacetylation of different histones and/or histone residues, a notion supported by the observation that TSA and APO affected acetylation patterns in different genomic contexts and in different epigenetic states ( Figure 3G; Supplemental Figure 14).…”

A Role for Widely Interspaced Zinc Finger (WIZ) in Retention of the G9a Methyltransferase on Chromatin

“…In addition to G9a and GLP, CDYL1 co-purified with WIZ, HDAC1 and HDAC2, and MIER1 (81). HDAC2 was shown by mass spectrometry to associate with G9a, GLP, WIZ, MIER1 and MIER2, and the reciprocal purification with G9a bait yielded both HDAC2 and MIER1 (82).…”

A Quantitative Proteomic Analysis of In Vitro Assembled Chromatin

“…We have shown in the past that TSA treatment results in a moderate increase of histone acetylation on assembled chromatin in contrast to what is observed in tissue culture cells where TSA treatment results in a strong hyperacetylation of histones (53)(54)(55). During in vitro assembly, the histones are deposited in a preacetylated form, which will not get deacetylated when TSA is present (41).…”

“…3B, panels (a) and (c)). Upon retention time calibration using ten conserved peptides that were distributed over the entire LC gradient we could quantify 1035 proteins in the SWATH runs performed on triplicate samples 54 of chromatin assemblies after 15, 60, and 240 min (Fig. 3B, panel (d)).…”