Thermal shift engagement assay for Class IIA histone deacetylase inhibitor screening

Histone deacetylase (HDAC) proteins are the targets of several anti-cancer clinical drugs, which motivates future inhibitor development. Class IIA HDAC proteins, HDAC4, HDAC5, HDAC7, and HDAC9, are pseudodeacetylases that lack a key catalytic amino acid residue resulting in low deacetylase activity. Yet enzymatic deacetylase activity assays are typically used to assess inhibitor potency. A ligand binding assay is needed for a more relevant assessment of inhibitor engagement by class IIA HDAC proteins. As an efficient method to directly assess inhibitor binding, thermal shift assays were developed for HDAC4, 5, and 7. Consistent with prior activity assays, thermal shift analysis reproduced the expected binding of various inhibitors to HDAC1, HDAC4, HDAC5, and HDAC7. Additionally, a higher throughput thermal shift format was developed using dot blot analysis. Thermal shift analysis offers a useful complement to enzyme activity assays for characterization of HDAC inhibitors.