Aza-SAHA Derivatives Are Selective Histone Deacetylase 10 Chemical Probes That Inhibit Polyamine Deacetylation and Phenocopy HDAC10 Knockout

We report the first well-characterized selective chemical
probe
for histone deacetylase 10 (HDAC10) with unprecedented selectivity
over other HDAC isozymes. HDAC10 deacetylates polyamines and has a
distinct substrate specificity, making it unique among the 11 zinc-dependent
HDAC hydrolases. Taking inspiration from HDAC10 polyamine substrates,
we systematically inserted an amino group (“aza-scan”)
into the hexyl linker moiety of the approved drug Vorinostat (SAHA).
This one-atom replacement (C→N) transformed SAHA from an unselective
pan-HDAC inhibitor into a specific HDAC10 inhibitor. Optimization
of the aza-SAHA structure yielded the HDAC10 chemical probe DKFZ‑748, with
potency and selectivity demonstrated by cellular and biochemical target
engagement, as well as thermal shift assays. Cocrystal structures
of our aza-SAHA derivatives with HDAC10 provide a structural rationale
for potency, and chemoproteomic profiling confirmed exquisite cellular
HDAC10-selectivity of DKFZ‑748 across the target
landscape of HDAC drugs. Treatment of cells with DKFZ‑748, followed by quantification of selected polyamines, validated for
the first time the suspected cellular function of HDAC10 as a polyamine
deacetylase. Finally, in a polyamine-limiting in vitro tumor model, DKFZ‑748 showed dose-dependent growth inhibition of
HeLa cells. We expect DKFZ‑748 and related probes
to enable further studies on the enigmatic biology of HDAC10 and acetylated
polyamines in both physiological and pathological settings.