# Rapireon, a new macrocycle molecular glue that selectively activates the nuclease activity of IRE1

> **NIH NIH RF1** · JOHNS HOPKINS UNIVERSITY · 2024 · $1,830,581

## Abstract

The unfolded protein response (UPR) pathway plays an essential role in health and
diseases from cancer to neurodegeneration. Of the three UPR pathway branches, the
IRE1-XBP1 pathway is the most highly conserved in comparison with the PERK and
ATF6 pathways. It has been shown that selective genetic activation of XBP1 in the IRE1
pathway is effective in multiple neurodegenerative disorders from Alzheimer’s disease
(AD) to Parkinson’s disease (PD). Using an XBP1-driven luciferase reporter system, we
screened a library of newly designed macrocycles called rapafucins that are modeled after
the immunosuppressive and anticancer drug rapamycin and identified an activator of
XBP1 named Rapireon. Further characterization of Rapireon revealed that it acts as a
molecule glue by recruiting FKBP12 to form a ternary complex with the cytosolic
domain of IRE1. Moreover, the FKBP12-Rapireon complex was found to selectively
activate the nuclease activity of IRE1 without affecting its kinase activity. In this
application, we propose to carry out in-depth characterization of the mode of action of
Rapireon using both biochemical and structural biology approaches. In preliminary
studies, we already obtained a low-resolution cryo-EM structural model of the FKBP12-
Rapireon-IRE1 ternary complex. We will continue to collect more data and refine the the
structure to better than 2.5 Å resolution. In parallel, we will build on our existing high-
resolution (below 2 Å) FKBP12-Rapireon binary complex x-ray crystal structure and
attempt to obtain the crystal structure of the ternary complex. To improve the potency
and specificity of the existing Rapireon lead, we will design and synthesize a DNA-
encoded library (DEL) of Rapireon analogs and develop a solution-phase proximity
ligation/deep sequencing platform to identify new analogs of Rapireon from the DEL.
Once a potent lead compound is identified, we will attempt to improve the
pharmacokinetic property and bioavailability of Rapireon through structural optimization
of Raprieon, giving rise to a Rapireon analog that can serve as a tool compound for
exploring its potential in treating neurodegenerative diseases.

## Key facts

- **NIH application ID:** 10944301
- **Project number:** 1RF1NS138343-01
- **Recipient organization:** JOHNS HOPKINS UNIVERSITY
- **Principal Investigator:** Jun O. Liu
- **Activity code:** RF1 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $1,830,581
- **Award type:** 1
- **Project period:** 2024-09-17 → 2027-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10944301

## Citation

> US National Institutes of Health, RePORTER application 10944301, Rapireon, a new macrocycle molecular glue that selectively activates the nuclease activity of IRE1 (1RF1NS138343-01). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10944301. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*