Identification of a novel small molecule that inhibits deacetylase but not defatty-acylase reaction catalysed by SIRT2

• Published in: Philosophical transactions of the Royal Society of London. Series B. Biological sciences Vol. 373; no. 1748; p. 20170070
• Main Authors: Kudo, Norio, Ito, Akihiro, Arata, Mayumi, Nakata, Akiko, Yoshida, Minoru
• Format: Journal Article
• Language: English
• Published: England The Royal Society 05.06.2018; The Royal Society Publishing
• Subjects: Acetylation; Acetylation - drug effects; Anti-Cancer Drug Development; Anticancer properties; Binding; Biological activity; Cancer; Carcinogenesis; Carcinogens; Catalytic Domain; Cell Proliferation - drug effects; Crystal Structure; Crystallography; Deacylase; Dependent Lysine Deacetylase; Epigenetics; High-Throughput Screening; Histidine; Humans; Hydrogen bonds; Hydrophobicity; Leukemia; Lysine; Mode of action; NAD; Pancreatic cancer; Physiological effects; Proteins; Sirt2; Sirtuin 2 - antagonists & inhibitors; Sirtuins; Substrates; Zinc; crystal structure; NAD+-dependent lysine deacetylase; deacylase; SIRT2; high-throughput screening; anti-cancer drug development
• ISSN: 0962-8436; 1471-2970
• DOI: 10.1098/rstb.2017.0070

SIRT2 is a member of the human sirtuin family of proteins and possesses NAD+-dependent lysine deacetylase/deacylase activity. SIRT2 has been implicated in carcinogenesis in various cancers including leukaemia and is considered an attractive target for cancer therapy. Here, we identified NPD11033, a selective small-molecule SIRT2 inhibitor, by a high-throughput screen using the RIKEN NPDepo chemical library. NPD11033 was largely inactive against other sirtuins and zinc-dependent deacetylases. Crystallographic analysis revealed a unique mode of action, in which NPD11033 creates a hydrophobic cavity behind the substrate-binding pocket after a conformational change of the Zn-binding small domain of SIRT2. Furthermore, it forms a hydrogen bond to the active site histidine residue. In addition, NPD11033 inhibited cell growth of human pancreatic cancer PANC-1 cells with a concomitant increase in the acetylation of eukaryotic translation initiation factor 5A, a physiological substrate of SIRT2. Importantly, NPD11033 failed to inhibit defatty-acylase activity of SIRT2, despite its potent inhibitory effect on its deacetylase activity. Thus, NPD11033 will serve as a useful tool for both developing novel anti-cancer agents and elucidating the role of SIRT2 in various cellular biological processes. This article is part of a discussion meeting issue ‘Frontiers in epigenetic chemical biology’.