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Targeting the Spliceosomal Protein USP39 Through Allosteric Ligands and PROTAC-Induced Degradation
Daniel Schäfer1,2,3, Cristian Prieto-Garcia4, Jianhui Wang1,2
1Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University Frankfurt am Main, Max-von-Laue-Str. 15, D-60438, Frankfurt am Main, Germany.
Angewandte Chemie (International Ed. in English)
|December 22, 2025
Summary
Researchers developed novel PROTACs targeting USP39, a key spliceosome protein implicated in diseases. These molecules efficiently degrade USP39, offering a new therapeutic strategy for splicing-related disorders like cancer and retinitis pigmentosa.
Area of Science:
- Molecular Biology
- Biochemistry
- Pharmacology
Background:
- Precise gene expression regulation is vital for cell function; splicing dysregulation links to diseases like cancer.
- Ubiquitin-specific protease 39 (USP39), a non-enzymatic spliceosome factor, is a challenging drug target.
Purpose of the Study:
- To discover small-molecule ligands targeting USP39.
- To develop proteolysis-targeting chimeras (PROTACs) for USP39 degradation.
- To validate USP39 as a therapeutic target for splicing-associated diseases.
Main Methods:
- Discovery of thiazole-based USP39 ligands.
- Structure-activity relationship studies using AlphaFold.
- Design and optimization of USP39-targeting PROTACs (e.g., USP39_PROTAC_V1) utilizing the VHL E3 ligase.
- Biophysical and biochemical assays for ternary complex formation and binding affinity.
- Cellular assays for USP39 degradation and proteome-wide profiling.
- Mechanistic studies involving proteasome and neddylation inhibition.
Main Results:
- Small-molecule ligands selectively engage USP39 via its zinc finger domain.
- USP39_PROTAC_V1 efficiently degrades USP39 in cells (1 nM) with minimal off-target effects.
- Degradation is VHL-dependent and sensitive to proteasome/neddylation inhibition.
- USP39 depletion mimics known 5'-splice-site-specific splicing patterns.
Conclusions:
- Targeted protein degradation via PROTACs is effective for USP39.
- USP39 modulation offers a promising therapeutic avenue for splicing-related diseases, including cancer and retinitis pigmentosa.
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