Thienopyrimidinone Based Sirtuin-2 (SIRT2)-Selective Inhibitors Bind in the Ligand Induced Selectivity Pocket

Abstract

Sirtuins (SIRTs) are NAD-dependent deacylases, known to be involved in a variety of pathophysiological processes and thus remain promising therapeutic targets for further validation. Previously, we reported a novel thienopyrimidinone SIRT2 inhibitor with good potency and excellent selectivity for SIRT2. Herein, we report an extensive SAR study of this chemical series and identify the key pharmacophoric elements and physiochemical properties that underpin the excellent activity observed. New analogues have been identified with submicromolar SIRT2 inhibtory activity and good to excellent SIRT2 subtype-selectivity. Importantly, we report a cocrystal structure of one of our compounds (29c) bound to SIRT2. This reveals our series to induce the formation of a previously reported selectivity pocket but to bind in an inverted fashion to what might be intuitively expected. We believe these findings will contribute significantly to an understanding of the mechanism of action of SIRT2 inhibitors and to the identification of refined, second generation inhibitors.

Tetrahydroindoles as Multipurpose Screening Compounds and Novel Sirtuin Inhibitors

“…As previously described, bulky aromatic substituents are necessary to fill the so‐called “selectivity pocket” in SIRT2 . It is highly probable that the biphenyl derivatives have a similar binding pose as that of the co‐crystalized thienopyrimidinone‐based inhibitors.…”

“…For ab etter understandingo ft he experimentally determined IC 50 values and their structural foundation, we used ac om-bined dockinga nd molecular dynamics approach for predicting possible binding modes.A ll compounds were docked to the substrate pocket of SIRT2 with at hienopyrimidinone-based inhibitor 19 [23] as template and visually inspected.T he docking poses of 16 q were passed to molecular dynamics simulations for post-processing and refinement. The ligand movements were monitored by its RMSD value to ensure as table final bindingp ose (see the Supporting Information).…”

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.…”

Synthesis of novel heterocyclic fused pyrimidin-4-one derivatives from imino-1,2,3-dithiazoles

“…Some thieno [2,3-d]pyrimidin-(4)-ones act as selective phosphodiesterase inhibitors for the treatment of inflammatory diseases, 8,9 antagonists of the glutamate receptors 10 whereas others were identified as highly selective SIRT2 inhibitors. 11,12 Owing to their growing use in compounds of therapeutic importance, the synthesis of various thienopyrimidinone-based molecules has been actively pursued in the last past decade and studied in detail, leading to several new developments. 3,13,14 This skeleton is usually obtained by condensation and ring closure from various 2,3-substituted thiophenes such as Gewald's amide, 15 2-aminothiophene-3-carbonitrile, 16 3-carbethoxy-2-phenylthioureathiophene, 17 2-aminothiophene-3-carboxylic ester.…”