Chemoproteomics Reveals Time-Dependent Binding of Histone Deacetylase Inhibitors to Endogenous Repressor Complexes

Class I histone deacetylases (HDACs)
are attractive drug targets
in oncology and inflammation. However, the development of selective
inhibitors is complicated by the characteristic that the localization,
activity, and selectivity of class I HDACs are regulated by association
in megadalton repressor complexes. There is emerging evidence that
isoform and protein complex selectivity can be achieved by aminobenzamide
inhibitors. Here we present a chemoproteomics strategy for the determination
of time-dependent inhibitor binding to endogenous HDACs and HDAC complexes.
This approach enabled us to determine kinetic association and dissociation
rates for endogenously expressed repressor complexes. We found that
unlike hydroxamate type inhibitors, aminobenzamides exhibited slow
binding kinetics dependent on association within protein complexes.
These findings were in agreement with a delayed cellular response
on acetylation levels of distinct histone sites and the inability
of aminobenzamides to inhibit HDAC activity of a Sin3 complex isolated
from K562 cells.