A rational computer-aided drug discovery approach to target IRE1 and PERK: Insights into structural dynamics and selectivity

Abstract

Cells constantly monitor the number of misfolded proteins they accumulate. The accumulation of misfolded proteins in the endoplasmic reticulum (ER) triggers an evolutionarily conserved signaling pathway called the unfolded protein response (UPR). Inositol-requiring enzyme 1 (IRE1), PKR-like endoplasmic reticulum kinase (PERK), and activating transcription factor 6 (ATF6) are the main UPR signal transducers. IRE1α and PERK were characterized using a chemical biology approach. Primarily, computational analysis of druggable sites of IRE1α and PERK was carried out. We performed docking studies to understand the selectivity of PERK kinase inhibitors. Additionally, KIT was identified as a common non-specific target of UPR kinase inhibitors kinase inhibiting RNase attenuator 6 (KIRA6) and GSK2606414 (GSK414). We analyzed the IRE1α RNase pocket for the suitability of structure-based drug screening. Further, we looked at how an IRE1α kinase inhibitor impacted the different dimer forms using in silico methods. Finally, virtual screening was performed for the IRE1α kinase active site. Novel lead compound NUIG10 was identified and validated in in vitro direct binding assay and RNase activity assay. Collectively, we highlighted various aspects of IRE1α and PERK drug discovery. In particular, our approaches provided structural insights into hit-identification and hit-to- lead optimization of novel IRE1 inhibitors.