Selective Sirt2 inhibition by ligand-induced rearrangement of the active site.

Tobias Rumpf,Matthias Schiedel,Karin Schmidtkunz,Stefan Gerhardt,Wolfgang Sippl,Martin Pannek,David A Sinclair,Judit Oláh,Oliver Einsle,Attila Lehotzky,Brian J North,Kathrin I Ladwein,Berin Karaman,Mike Schutkowski,Judit Ovádi,Manfred Jung,Claudia Roessler,Clemens Steegborn,Markus Gajer

doi:10.1038/ncomms7263

Abstract

Sirtuins are a highly conserved class of NAD+-dependent lysine deacylases. The human isotype Sirt2 has been implicated in the pathogenesis of cancer, inflammation and neurodegeneration, which makes the modulation of Sirt2 activity a promising strategy for pharmaceutical intervention. A rational basis for the development of optimized Sirt2 inhibitors is lacking so far. Here we present high-resolution structures of human Sirt2 in complex with highly selective drug-like inhibitors that show a unique inhibitory mechanism. Potency and the unprecedented Sirt2 selectivity are based on a ligand-induced structural rearrangement of the active site unveiling a yet-unexploited binding pocket. Application of the most potent Sirtuin-rearranging ligand, termed SirReal2, leads to tubulin hyperacetylation in HeLa cells and induces destabilization of the checkpoint protein BubR1, consistent with Sirt2 inhibition in vivo. Our structural insights into this unique mechanism of selective sirtuin inhibition provide the basis for further inhibitor development and selective tools for sirtuin biology.

Highlights

Sirtuins are a highly conserved class of NAD þ -dependent lysine deacylases
We found that treatment with NCA leads to an increase in the acetylation of mitochondrial proteins, whereas treatment with SirReal[2] did not, suggesting that SirReal[2] is unable to regulate Sirt[3] activity in cells (Supplementary Fig. 10b)
There are many indications that sirtuins play an important role in neurodegeneration, cancer, bacterial infections and inflammation and that a modulation of Sirt[2] activity could be a new strategy for pharmaceutical intervention

Summary

Introduction

Sirtuins are a highly conserved class of NAD þ -dependent lysine deacylases. The human isotype Sirt[2] has been implicated in the pathogenesis of cancer, inflammation and neurodegeneration, which makes the modulation of Sirt[2] activity a promising strategy for pharmaceutical intervention. We present high-resolution structures of human Sirt[2] in complex with highly selective drug-like inhibitors that show a unique inhibitory mechanism. Potency and the unprecedented Sirt[2] selectivity are based on a ligand-induced structural rearrangement of the active site unveiling a yet-unexploited binding pocket. NAD þ -dependent protein deacylases (sirtuins) constitute a unique class of enzymes that are conserved from bacteria to humans. The physiological studies of Sirt[2] have so far been hampered by the lack of potent and isotype-specific modulators of sirtuin activity. The first X-ray structure of Sirt[2] in complex with a potent macrocyclic peptidic inhibitor was reported, but this inhibitor lacked the desired isotype selectivity[28] and, due to its physicochemical properties, might be of limited use for drug discovery. The relevance of the observed biochemical activity is further supported by cellular studies

Methods

Results

Conclusion