Structurally Diverse Histone Deacetylase Photoreactive Probes: Design, Synthesis, and Photolabeling Studies in Live Cells and Tissue

Histone deacetylase (HDAC) activity is modulated in vivo by post‐translational modifications and formation of multiprotein complexes. Novel chemical tools to study how these factors affect engagement of HDAC isoforms by HDAC inhibitors (HDACi) in cells and tissues are needed. In this study, a synthetic strategy to access chemically diverse photoreactive probes (PRPs) was developed and used to prepare seven novel HDAC PRPs 9–15. The class I HDAC isoform engagement by PRPs was determined in biochemical assays and photolabeling experiments in live SET‐2, HepG2, HuH7, and HEK293T cell lines and in mouse liver tissue. Unlike the HDAC protein abundance and biochemical activity against recombinant HDACs, the chemotype of the PRPs and the type of cells were key in defining the engagement of HDAC isoforms in live cells. Our findings suggest that engagement of HDAC isoforms by HDACi in vivo may be substantially modulated in a cell‐ and tissue‐type‐dependent manner. Engaged by inhibitors? The identity of the histone deacetylase isoforms engaged by inhibitors in vivo is one of the unresolved mysteries in epigenetic drug discovery. Using newly designed photoreactive probes, we show that their relative histone deacetylase isoform engagement in live cells in culture and mouse liver tissue is chemotype‐ and cell‐type dependent and is substantially different from the isoform selectivity determined in the biochemical assays.