Cationic polyamines such as spermidine and spermine are critical in all forms of life, as they regulate the function of biological macromolecules. Intracellular polyamine metabolism is regulated by reversible acetylation and dysregulated polyamine metabolism is associated with neoplastic diseases such as colon cancer, prostate cancer and neuroblastoma. Here we report that histone deacetylase 10 (HDAC10) is a robust polyamine deacetylase, using recombinant enzymes from Homo sapiens (human) and Danio rerio (zebrafish). The 2.85 Å-resolution crystal structure of zebrafish HDAC10 complexed with a transition-state analogue inhibitor reveals that a glutamate gatekeeper and a sterically constricted active site confer specificity for N⁸-acetylspermidine hydrolysis and disfavour acetyllysine hydrolysis. Both HDAC10 and spermidine are known to promote cellular survival through autophagy. Accordingly, this work sets a foundation for studying the chemical biology of autophagy through the structure-based design of inhibitors that may also serve as new leads for cancer chemotherapy.

Significance: Histone deacetylase 6 (HDAC6) is a zinc metalloenzyme that serves as the tubulin deacetylase in the cell cytosol. Inhibition of tubulin deacetylase activity leads to suppression of microtubule dynamics, causing cell cycle arrest and apoptosis, which is a validated strategy for cancer chemotherapy. Selective inhibition of HDAC6 is clinically preferable, since unwanted inhibition of other HDAC isozymes can lead to undesirable off-target effects. Here, X-ray crystal structures of HDAC6-inhibitor complexes reveal molecular features responsible for the isozyme selectivity measured in inhibition assays, including an unusual monodentate hydroxamate-Zn ²⁺ coordination mode as well as intermolecular interactions of bulky inhibitor substituents. These observations will inform the design of HDAC6-selective inhibitors with improved properties.