# Screening small molecules for rhabdomyosarcoma fusion proteins

> **NIH NIH R21** · GEORGETOWN UNIVERSITY · 2020 · $181,741

## Abstract

Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma that mainly affects young
children. Patients with the embryonal (ERMS) subtype have better survival rates and effective treatment
options. However, patients with the alveolar (ARMS) subtype have very poor outcomes and desperately need
new therapy options. Similar to some other pediatric sarcomas and leukemias, ARMS contains tumor-specific
chromosomal translocations that code for chimeric transcription factors. Approximately 60% of ARMS patients
have PAX3-FOXO1 fusion protein as the product of tumor specific chromosomal translocation. The fusion
protein represents an ideal molecular target because it is expressed only in tumor cells and it has acquired a
unique oncogenic function that is absent in parental full-length molecules, PAX3 and FOXO1. Inhibition of
fusion protein expression in experimental systems induced differentiation and chemosensitivity. We
hypothesized that small molecules, which can directly bind to PAX3-FOXO1 protein can inhibit its oncogenic
function. Small molecules with this ability may be developed as therapeutic agents in future applications. We
used surface plasmon resonance technology in a Biacore 4000 instrument to screen small molecule libraries
for compounds that can bind directly to recombinant PAX3-FOXO1 protein. We identified 119 primary hits,
which were further tested in a PAX3-FOXO1 responsive reporter assay to narrow down to 9 potential inhibitor
molecules. In this application we propose to confirm direct binding of hit compounds to the fusion protein and
validate potential lead compounds in functional assays that focus on transcriptional activity of PAX3-FOXO1.
We will also investigate the molecular mechanism of PAX3-FOXO1 inhibition based on known regulatory
processes involving PAX3-FOXO1. There have been very little advances in the treatment of ARMS in the past
35 years. Trying different combinations of existing cytotoxic agents did not significantly improve the survival.
Here we propose a novel approach with potential to discover the first targeted therapy for ARMS.

## Key facts

- **NIH application ID:** 9893458
- **Project number:** 1R21CA220087-01A1
- **Recipient organization:** GEORGETOWN UNIVERSITY
- **Principal Investigator:** AYKUT UREN
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $181,741
- **Award type:** 1
- **Project period:** 2020-02-01 → 2022-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9893458

## Citation

> US National Institutes of Health, RePORTER application 9893458, Screening small molecules for rhabdomyosarcoma fusion proteins (1R21CA220087-01A1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9893458. Licensed CC0.

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