Structure and mechanism of action of the hydroxy–aryl–aldehyde class of IRE1 endoribonuclease inhibitors

Abstract

Endoplasmic reticulum (ER) stress activates the unfolded protein response and its dysfunction is linked to multiple diseases. The stress transducer IRE1α is a transmembrane kinase endoribonuclease (RNase) that cleaves mRNA substrates to re-establish ER homeostasis. Aromatic ring systems containing hydroxy-aldehyde moieties, termed hydroxy aryl aldehydes (HAA), selectively inhibit IRE1α RNase and thus represent a novel chemical series for therapeutic development. We solved crystal structures of murine IRE1α in complex with three HAA inhibitors. HAA inhibitors engage a shallow pocket at the RNase active site through pi-stacking interactions with His910 and Phe889, an essential Schiff base with Lys907 and a H-bond with Tyr892. Structure activity studies and mutational analysis of contact residues define the optimal chemical space of inhibitors and validate the inhibitor binding site. These studies lay the foundation for understanding both the biochemical and cellular functions of IRE1α using small molecule inhibitors and suggest new avenues for inhibitor design.

Long-Range Inhibitor-Induced Conformational Regulation of Human IRE1αEndoribonuclease Activity

“…3). Consistent with previously published structures, the kinase active sites are facing each other and are in an orientation and proximity favorable for transautophosphorylation [3P23 (Ali et al, 2011) and 4PL3 (Sanches et al, 2014)]. The present structure may possibly represent an early postphosphoryl-transfer dimer, while the face-to-face structure of dephosphorylated human IRE1a may represent a state just prior to phosphoryl transfer.…”

“…In this structure, the kinase active sites are facing each other and are in a suitable orientation and proximity for transautophosphorylation, but the RNase domains are far from each other and inactive. A similar "face-to-face" structure was recently reported for mouse IRE1a, but this structure was phosphorylated (PDB ID 4PL3; Sanches et al, 2014). More recently, a few other dephosphorylated human crystal structures were reported.…”

Physiological/pathological ramifications of transcription factors in the unfolded protein response

“…MKC-3946, a salicylaldehydes derivative, inhibits chemically induced XBP1 splicing in multiple myeloma cell lines as well as patient-derived samples without affecting IRE1α phosphorylation in this context (Mimura et al 2012). In addition, other small molecules, including MKC9989, OICR464, and OICR573, block XBP1 splicing with minimal effect on IRE1α kinase activity, suggesting a direct effect on XBP1 (Sanches et al 2014).…”

Endoplasmic reticulum proteostasis in glioblastoma—From molecular mechanisms to therapeutic perspectives

“…The current therapeutic and pharmacological strategies that target ER proteostasis in cancer focus either on exacerbating ER stress to a level with which tumor cells cannot cope and therefore die or on decreasing the adaptive capacity of the tumor cells, leading to loss of selective advantage and tumor death. Over the past 5 years, several inhibitors of the three UPR sensors have been developed (Table 1) (44,58,(126)(127)(128)(129)(130)(131)(132)(133)(134)(135)(136)(137)(138)(139)(140). Some new drugs are now tested to specifically target particular UPR sensors to kill cancer cells or sensitize them to commonly used treatments.…”