Harnessing indole scaffolds to identify small-molecule IRE1α inhibitors modulating XBP1 mRNA splicing

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• Inositol-requiring enzyme 1 alpha (IRE1α) is a crucial sensor protein regulating endoplasmic reticulum (ER) stress.
• IRE1α controls X-box binding protein 1 (XBP1) mRNA splicing and downstream unfolded protein response (UPR) pathways.
• Dysregulation of IRE1α is linked to various human diseases, highlighting its therapeutic potential.

Purpose of the Study:

• To identify and characterize novel small molecules targeting IRE1α.
• To investigate the inhibition mechanism and therapeutic potential of these compounds.

Main Methods:

• Synthesis and screening of substituted indoles as IRE1α inhibitors.
• Co-crystal structure determination to elucidate the inhibition mode.
• Cellular assays to evaluate inhibition of ER stress-induced XBP1 mRNA splicing.

Main Results:

• A series of potent and selective substituted indole-based IRE1α inhibitors were identified, including IA107.
• The co-crystal structure revealed IA107 allosterically inhibits IRE1α RNase activity by binding the kinase domain without affecting dimerization.
• IA107 demonstrated concentration-dependent inhibition of cellular XBP1 mRNA splicing, with a prodrug showing a ~50-fold enhancement in activity.

Conclusions:

• Substituted indoles represent a promising chemotype for developing potent and selective IRE1α inhibitors.
• These compounds modulate RNA splicing and offer expanded therapeutic applications for IRE1α-targeted therapies.
• The findings support the development of small molecules for treating IRE1α-dysregulated diseases.