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

Abstract

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'.

Mechanism-based inhibitors of SIRT2: structure–activity relationship, X-ray structures, target engagement, regulation of α-tubulin acetylation and inhibition of breast cancer cell migration

“…Numerous SIRT2 inhibitors have been reported recently ( Fig. 1), 24,[30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48] some of which are commercially available (e.g., SirReal2, AGK-2, tenovin-6). However, all of these compounds are endowed with limitations such as lack of isozyme selectivity, lack of potency (revealed by limited ability to inhibit demyristoylase activity), and/or poor solubility.…”

“…Efforts of numerous groups over the last two decades have led to almost 30 X-ray crystal structures, including several co-crystal structures with ligands and inhibitors. [34][35][36][37][38][39][40][49][50][51][52][53][54][55][56] This has provided insight into the binding mechanism and substrate scope of SIRT2 at the molecular level. In the present work, we have built on this knowledge to develop the most potent and selective SIRT2 inhibitors reported to date.…”

A Small‐Molecule SIRT2 Inhibitor That Promotes K‐Ras4a Lysine Fatty‐Acylation

“…[2a, 6] Recent studies suggest that among these compounds,o nly TM can weakly inhibit the demyristoylation activity of SIRT2. [7] TM is a thiomyristoyl lysine compound, and is am echanism-based SIRT2 inhibitor. [2a] TM has been shown to possess ab road anticancer effect.…”

Direct Comparison of SIRT2 Inhibitors: Potency, Specificity, Activity‐Dependent Inhibition, and On‐Target Anticancer Activities

“…SirReal2 inhibits the deacetylation activity of SIRT2 with a relatively low IC 50 value of 0.23 μM, however, consistent with a recent report it was unable to inhibit the demyristoylation activity of SIRT2 at the highest concentration tested. [11] AGK2 and Tenovin-6 inhibited both SIRT1 and SIRT2 deacetylation with similar IC 50 values, suggesting that these two inhibitors are not very selective. Like SirReal2, these compounds did not inhibit the demyristoylation activity of SIRT2 at the highest concentration tested.…”