Small Molecule Screen Identifies Non-catalytic USP3 Chemical Handle
Mandeep K Mann1,2, Esther Wolf3, Madhushika Silva1
1Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, Suite 700, Toronto, Ontario M5G 1L7, Canada.
ACS Omega
|January 15, 2024
Summary
Researchers identified a novel small molecule targeting the USP3 zinc-finger ubiquitin-binding domain (ZnF-UBD). This compound is a starting point for developing deubiquitylase-targeting chimeras (DUBTACs) to control protein deubiquitylation.
Area of Science:
- Biochemistry
- Molecular Biology
- Drug Discovery
Background:
- Zinc-finger ubiquitin-binding domains (ZnF-UBDs) are key components of deubiquitylases (DUBs).
- ZnF-UBDs are underexplored for developing deubiquitylase-targeting chimeras (DUBTACs).
- Previous work demonstrated the ligandability of ZnF-UBDs.
Purpose of the Study:
- To identify small molecules that bind to the ZnF-UBD of USP3.
- To develop chemical tools for interrogating USP3 function and DUBTACs.
Main Methods:
- Small molecule library screening against 11 ZnF-UBDs.
- Biochemical assays to determine binding affinity (KD).
- Hydrogen-deuterium exchange mass spectrometry (HDX-MS) to confirm binding site.
Main Results:
- Compound 59 was identified, binding the USP3 ZnF-UBD with a KD of 14 μM.
- HDX-MS confirmed compound 59 binds the ubiquitin-binding pocket of USP3.
- Compound 59 did not inhibit USP3's cleavage of K48-linked diubiquitin.
Conclusions:
- Compound 59 is a valuable starting point for developing USP3-specific chemical probes.
- This research opens avenues for creating DUBTACs to modulate protein deubiquitylation.
- Further studies can explore the functional consequences of recruiting USP3 to ubiquitylated proteins.
