Stabilizing HDAC11 with SAHA to assay slow-binding benzamide inhibitors

• Published in: Bioorganic & medicinal chemistry letters 2017-07, Vol.27 (13), p.2943-2945
• Main Authors: Tian, Yinping, Lv, Wenhui, Li, Xuewei, Wang, Congying, Wang, Dayuan, Wang, Peng G., Jin, Jin, Shen, Jie
• Format: Article
• Language: English
• Subjects: Benzamides - chemistry; Benzamides - pharmacology; Chaperone molecule; Dose-Response Relationship, Drug; Enzyme Stability - drug effects; HDAC11; Histone Deacetylase Inhibitors - chemistry; Histone Deacetylase Inhibitors - pharmacology; Histone Deacetylases - chemistry; Histone Deacetylases - metabolism; Inhibitor screening; Molecular Structure; Slow-binding; Structure-Activity Relationship; Unstable protein
• ISSN: 0960-894X; 1464-3405
• DOI: 10.1016/j.bmcl.2017.05.004

[Display omitted] Among 18 human histone deacetylases (HDAC), HDAC11 is least studied. MS275, a benzamide HDAC inhibitor (HDACi), was stereotypically considered to selectively target Class I HDACs. We verified this slow-binding inhibitor also targeted HDAC11. In a traditional enzyme based assay, MS275 at low concentrations surprisingly behaved as an agonist. This was attributed to the poor stability of HDAC11 which lost 40% activity in 3h at 37°C. By adding 0.2μM SAHA, HDAC11 activity was stabilized during the 3-h assay period. Since 0.2μM SAHA inhibited 50% HDAC11 activity, the apparent IC50′ of MS275 was adjusted to the true IC50=0.65μM. Finally, the new method demonstrated its superiority in one-dose-screening assays by decreasing false negative results. This work highlighted an optimized strategy to assay slow-binding inhibitors of unstable proteins with known fast-binding inhibitors. It should be especially useful in a hit-discovery stage to find moderate potent compounds.