Structural distortions induced by Kinase Inhibiting RNase Attenuator (KIRA) compounds prevent the formation of face-to-face dimers of Inositol Requiring Enzyme 1α

Abstract

Inositol-Requiring Enzyme 1 (IRE1) is a transmembrane dual kinase/ribonuclease protein involved in propagation of the unfolded protein response (UPR). IRE1 is currently explored as a potential drug target due to growing evidence of its role in variety of disease conditions. Upon activation, IRE1 cleaves X-box Binding Protein 1 (XBP1) mRNA through its RNase domain. Small molecules targeting the kinase site are known to either increase or decrease RNase activity, but the allosteric relationship between the kinase and RNase domains of IRE1 is poorly understood. Subsets of IRE1 kinase inhibitors (known as \"KIRA\" compounds) bind to the ATP-binding site and allosterically impede the RNase activity. KIRA compounds are able to regulate the RNase activity by stabilizing monomeric form of IRE1.\n\nIn the present work, computational analysis, protein-protein and protein-ligand docking studies, and molecular dynamics simulations were applied to different IRE1 dimer systems to provide structural insights into the perturbation of IRE1 dimers by small molecules kinase inhibitors that regulate the RNase activity. By analyzing structural deviations, energetic components and number of hydrogen bonds in the interface region, we propose that the KIRA inhibitors act at an early stage of IRE1 activation by interfering with IRE1 face-to-face dimer formation, thus disabling the activation of the RNase domain. The work sheds light on the mechanism of action of KIRA compounds and may assist in development of further compounds in e.g. cancer therapeutics. The work also provides information on the sequence of events and protein-protein interactions initiating the unfolded protein response.\n\nNon-technical SummaryThe unfolded protein response is a protective feedback mechanism whereby cells regulate high levels of misfolded proteins in the endoplasmic reticulum. Due to its significance in cell survival, the UPR has become an interesting target in cancer therapy. A key pathway of the UPR is initiated by the activation of inositol requiring enzyme 1 (IRE1), which must first dimerise in order to mediate the stress signal. Different inhibitors have been proposed in order to block the UPR at the level of IRE1. We here unveil, through detailed computational studies, the mode of action of a set of IRE1 inhibitors targeting the kinase domain, which in turn helps us to further understand the mechanism of activation and progression of the UPR.