Selective Inhibition of Histone Deacetylase 10: Hydrogen Bonding to the Gatekeeper Residue is Implicated

Abstract

The discovery of isozyme-selective histone deacetylase (HDAC) inhibitors is critical for understanding the biological functions of individual HDACs and for validating HDACs as clinical drug targets. The isozyme HDAC10 contributes to chemotherapy resistance via inhibition of autophagic flux and has recently been described to be a polyamine deacetylase, but no studies directed toward selective HDAC10 inhibitors have been published. Herein, we disclose that the use of two complementary ligand-displacement assays has revealed unexpectedly potent HDAC10 binding of tubastatin A, which has been previously described as a highly selective HDAC6 inhibitor. We synthesized a targeted selection of tubastatin A derivatives and found that a basic amine in the cap group was required for strong HDAC10, but not HDAC6, binding. Only potent HDAC10 binders mimicked HDAC10 knockdown by causing dose-dependent accumulation of acidic vesicles in the BE(2)-C neuroblastoma cell line. Docking of inhibitors into human HDAC10 homology models indicated that a hydrogen-bond between a basic cap group nitrogen and the HDAC10 gatekeeper residue Glu272 was responsible for potent HDAC10 binding. Taken together, the presented assays and homology models provide an optimal platform for the development of HDAC10-selective inhibitors, as exemplified with the tubastatin A scaffold.<br>

Target deconvolution of HDAC pharmacopoeia highlights MBLAC2 as common off-target

“…Since no highly selective HDAC10 probes have been reported yet according to ChemicalProbes.org, our data designates TH65, with at least 30-fold selectivity (limit of our assay) over other HDACs, as novel promising chemical probe for HDAC10. Interestingly, we found the HDAC6 inhibitor Tubastatin A to be the second most selective HDAC10 inhibitor (CATDS = 0.67), contrasting the original and recent reports 34,35 but agreeing with results of in-cell nano-BRET binding assays 36 . Furthermore, the pan-HDAC inhibitor Abexinostat had the highest HDAC10 a nity in the panel of drugs (pK d app HDAC10 = 7.8 vs.…”

First Fluorescent Acetylspermidine Deacetylation Assay for HDAC10 Identifies Inhibitors of Neuroblastoma Cell Colony Growth That Increase Lysosome Accumulation

“…For this purpose, we chose Quisinostat which was recently determined to bind tightly to hHDAC10 with an EC50 of 10 nM in time-resolved fluorescence resonance energy transfer experiments. 60…”

“…73 Figure S3). 60 We compared the activity based potency with the recently published HDAC10 binding assay as mentioned above. This assay system was already used to show HDAC10 binding for Tubastatin A, Quisinostat and Abexinostat.…”

First Fluorescent Acetylspermidine Deacetylation Assay for HDAC10 Identifies Inhibitors of Neuroblastoma Cell Colony Growth That Increase Lysosome Accumulation

“…73 Figure S3). 60 We compared the activity based potency with the recently published HDAC10 binding assay as mentioned above. This assay system was already used to show HDAC10 binding for Tubastatin A, Quisinostat and Abexinostat.…”