Merits and pitfalls of conventional and covalent docking in identifying new hydroxyl aryl aldehyde like compounds as human IRE1 inhibitors

Antonio Carlesso,Leif A Eriksson,Adrienne M Gorman,Afshin Samali,Chetan Chintha

doi:10.1038/s41598-019-39939-z

Antonio Carlesso, Leif A Eriksson + Show 3 more

Open Access

https://doi.org/10.1038/s41598-019-39939-z

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Abstract

IRE1 is an endoplasmic reticulum (ER) bound transmembrane bifunctional kinase and endoribonuclease protein crucial for the unfolded protein response (UPR) signaling pathway. Upon ER stress, IRE1 homodimerizes, oligomerizes and autophosphorylates resulting in endoribonuclease activity responsible for excision of a 26 nucleotide intron from the X-box binding protein 1 (XBP1) mRNA. This unique splicing mechanism results in activation of the XBP1s transcription factor to specifically restore ER stress. Small molecules targeting the reactive lysine residue (Lys907) in IRE1α’s RNase domain have been shown to inhibit the cleavage of XBP1 mRNA. Crystal structures of murine IRE1 in complex with covalently bound hydroxyl aryl aldehyde (HAA) inhibitors show that these molecules form hydrophobic interactions with His910 and Phe889, a hydrogen bond with Tyr892 and an indispensable Schiff-base with Lys907. The availability of such data prompted interest in exploring structure-based drug design as a strategy to develop new covalently binding ligands. We extensively evaluated conventional and covalent docking for drug discovery targeting the catalytic site of the RNase domain. The results indicate that neither computational approach is fully successful in the current case, and we highlight herein the potential and limitations of the methods for the design of novel IRE1 RNase binders.

Highlights

The unfolded protein response (UPR) is a cellular stress response related to the folding of proteins in the endoplasmic reticulum (ER)
In order to decipher the mode of action of the hydroxy aryl aldehyde (HAA) inhibitors, we investigated through visual inspection, the proximity of the ligand binding site to the catalytic residues involved in site-specific cleavage of X-box binding protein 1 (XBP1) mRNA
We have investigated a series of covalent HAA inhibitors of the Inositol-requiring enzyme 1 (IRE1) RNase domain

Summary

Introduction

The unfolded protein response (UPR) is a cellular stress response related to the folding of proteins in the endoplasmic reticulum (ER). The UPR has two purposes: initially restoring normal cell function by interrupting protein synthesis, and increasing the production of molecular chaperones involved in protein folding. Under ER stress, IRE1 dimerizes, trans-autophosphorylates and activates its endoribonuclease domain[5,6]. The direct RNase inhibitors known to date share a common hydroxy aryl aldehyde (HAA) moiety, which reacts selectively with a specific lysine residue (Lys907) through Schiff base formation in the RNase domain[7]. Besides formation of a reversible Schiff base with Lys[907], the inhibitors establish hydrophobic contacts with His[910] and Phe[889] and a hydrogen bond with Tyr[892] in the IRE1 RNase domain. Details regarding IRE1 RNase activation and the mechanism of mRNA recognition and cleavage still remain unresolved

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Results

Conclusion