Unraveling Lysine Deacetylase Inhibitor Specificities for Endogenous Acetylation Sites

Lysine deacetylases (KDACs) are important regulators of biological processes. KDAC inhibitors (KDACIs) are important tools for basic research and attractive therapeutic candidates, yet their effects on in-vivo acetylation sites are poorly known. Here we obtained acetylation signatures for 19 different KDACIs that cover all known deacetylases. Most KDACIs targeting non-sirtuin deacetylases increased acetylation of a small, but specific, subset of the acetylome, and included sites on histone and other chromatin-associated proteins. Using a combination of genetic deletion and inhibitor treatment we found that the sirtuin inhibitor nicotinamide increased acetylation via SIRT1 inhibition, whereas tubacin and bufexamac affected cytoplasmic proteins through inhibition of HDAC6. Bufexamac additionally triggered an HDAC6-independent hypoxia-like response by stabilizing HIF1-α, providing a potential mechanistic basis for its adverse pro-inflammatory effects. Our results provide a systematic view of the scope and specificities of KDACIs for acetylation sites, and uncovered unexpected acetylation profiles for several of commonly used inhibitors.