Biological and Medicinal Chemistry

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

Authors

Abstract

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. Co-crystal structures of our aza-SAHA derivatives with HDAC10 provide a structural rationale for potency, and chemoproteomic profiling con-firmed 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, confirmed for the first time the suspected cellular function of HDAC10 as a polyamine deacetylase. Finally, in a polyamine-limited 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.

Version notes

Added chemoproteomic profiling of DKFZ-748 with an HDACi affinity matrix. Added docking of HDACi into HDAC6 and HDAC10 to help explain selectivity. Added cell proliferation data of HeLa cells under polyamine-limiting conditions. Overall revised the text and data representation.

Content

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Supplementary material

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Supporting Information
Supplementary schemes, tables, and figures, detailed experimental procedures, compound characterization, and 1H and 13C NMR spectra of newly synthesized substances
Thumbnail image of Helmholtz Drug Repurposing Cotreatment Screen with DKFZ-757.xlsx
Helmholtz Drug Repurposing Library Screen
Screening data from co-treatment of the Helmholtz Drug Repurposing Library with DKFZ-757 in BE(2)-C cells.
Thumbnail image of NCI-60 Screen DKFZ-711.xlsx
NCI-60 Screen with DKFZ-711
Outcome of a screen against the NCI-60 cancer cell line panel with HDAC10 inhibitor DKFZ-711
Thumbnail image of HDAC10-728_complex_docked_748.pdb
Docking of DKFZ-748 into HDAC10
PDB model of DKFZ-748 docked into the crystal structure of the HDAC10-DKFZ-728 complex (PDB: 7SGK).
Thumbnail image of HDAC6_5edu_docked_SAHA.pdb
Docking of SAHA into HDAC6
PDB model of SAHA docked into the crystal structure of the HDAC6-trichostatin A complex (PDB: 5EDU).
Thumbnail image of HDAC6_5edu_docked_711.pdb
Docking of DKFZ-711 into HDAC6
PDB model of DKFZ-711 docked into the crystal structure of the HDAC6-trichostatin A complex (PDB: 5EDU).