Discovery and Characterization of a Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6

Histone deacetylase 6 (HDAC6) inhibition is an attractive
strategy
for treating numerous cancers, and HDAC6 catalytic inhibitors are
currently in clinical trials. The HDAC6 zinc-finger ubiquitin-binding
domain (UBD) binds free C-terminal diglycine motifs of unanchored
ubiquitin polymer chains and protein aggregates, playing an important
role in autophagy and aggresome assembly. However, targeting this
domain with small molecule antagonists remains an underdeveloped avenue
of HDAC6-focused drug discovery. We report SGC-UBD253 (25), a chemical probe potently targeting HDAC6-UBD
in vitro with selectivity over nine other UBDs, except for weak USP16
binding. In cells, 25 is an effective antagonist of HDAC6-UBD
at 1 μM, with marked proteome-wide selectivity. We identified SGC-UBD253N (32), a methylated derivative of 25 that is 300-fold less active, serving as a negative control.
Together, 25 and 32 could enable further
exploration of the biological function of the HDAC6-UBD and investigation
of the therapeutic potential of targeting this domain.