Development of 1,2,4-Oxadiazoles as Potent and Selective Inhibitors of the Human Deacetylase Sirtuin 2: Structure–Activity Relationship, X-ray Crystal Structure, and Anticancer Activity

Abstract

Sirt2 is a target for the treatment of neurological, metabolic, and age-related diseases including cancer. Here we report a series of Sirt2 inhibitors based on the 1,2,4-oxadiazole scaffold. These compounds are potent Sirt2 inhibitors active at single-digit μM level by using the Sirt2 substrate α-tubulin-acetylLys40 peptide and inactive up to 100 μM against Sirt1, -3, and -5 (deacetylase and desuccinylase activities). Their mechanism of inhibition is uncompetitive toward both the peptide substrate and NAD, and the crystal structure of a 1,2,4-oxadiazole analog in complex with Sirt2 and ADP-ribose reveals its orientation in a still unexplored subcavity useful for further inhibitor development. Tested in leukemia cell lines, 35 and 39 induced apoptosis and/or showed antiproliferative effects at 10 or 25 μM after 48 h. Western blot analyses confirmed the involvement of Sirt2 inhibition for their effects in NB4 and in U937 cells. Our results provide novel Sirt2 inhibitors with a compact scaffold and structural insights for further inhibitor improvement.

SIRT2 and lysine fatty acylation regulate the transforming activity of K-Ras4a

“…Thus SIRT2 may provide an additional link between K-Ras4a signaling and cellular metabolism. Given that Ras proteins play critical roles in many human cancers, SIRT2, as a Ras regulator, may be an important therapeutic target for cancer, which is consistent with several recent reports ( Jing et al, 2016 ; Moniot et al, 2017 ; Shah et al, 2016 ; Wang et al, 2014 ; Wilking-Busch et al, 2017 ; Xu et al, 2016 ; Zhao et al, 2013 , 2016 ). The physiological and pathophysiological roles of SIRT2 thus merit further investigation.…”

SIRT2 and lysine fatty acylation regulate the oncogenic activity of K-Ras4a

“…Thus SIRT2 may provide an additional link between K-Ras4a signaling and cellular metabolism. Given that Ras proteins play critical roles in many human cancers, SIRT2, as a Ras regulator, may be an important therapeutic target for cancer, which is consistent with several recent reports 50,53, 54,57,58,85–87 . The physiological and pathophysiological roles of SIRT2 thus merit further investigation.…”

Identification of Bichalcones as Sirtuin Inhibitors by Virtual Screening and <em>in Vitro </em>Testing

“…In the crystal structures of sirt1, it was shown that substrates make H-bond interactions with the backbone of a conserved valine residue (sirt1 numbering Val412) which is crucial for the correct orientation of the acyl-lysine in the active site [44]. In case of sirt2, we first examined the binding interactions of the native ligands including both the peptide substrates, the cofactor fragments and the co-crystallized inhibitors with the protein [31][32][33][34][35][36][37][38][39][40][41][42][43]. In the hit selection process, a special importance was given to compounds that were able to interact with residues Phe234, Phe235, Phe190 and Glu237 in the catalytic pocket.…”

“…Within the last two decades, several sirt1 and sirt2 crystal structures have been solved in both apo and holo forms [31][32][33][34][35][36][37][38][39][40][41][42][43]. Ternary structures of sirt1 and sirt2 in complex with cofactor analogues, peptide-based and structurally diverse inhibitors revealed a high conformational flexibility in the catalytic pocket, especially in the extended C-pocket region.…”