Activity-based protein profiling reveals deubiquitinase and aldehyde dehydrogenase targets of a cyanopyrrolidine
Nattawadee Panyain1, Aurélien Godinat1, Aditya Raymond Thawani1
1Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London W12 0BZ UK nattawadee.panyain@epfl.ch e.tate@imperial.ac.uk.
Abstract:
Ubiquitin carboxy-terminal hydrolase L1 (UCHL1), a deubiquitinating enzyme (DUB), is a potential drug target in various cancers, and liver and lung fibrosis. However, bona fide functions and substrates of UCHL1 remain poorly understood. Herein, we report the characterization of UCHL1 covalent inhibitor MT16-001 based on a thiazole cyanopyrrolidine scaffold. In combination with chemical proteomics, a closely related activity-based probe (MT16-205) was used to generate a comprehensive quantitative profile for on- and off-targets at endogenous cellular abundance. Both compounds are selective for UCHL1 over other DUBs in intact cells but also engage a range of other targets with good selectivity over the wider proteome, including aldehyde dehydrogenases, redox-sensitive Parkinson's disease related protein PARK7, and glutamine amidotransferase. Taken together, these results underline the importance of robust profiling of activity-based probes as chemical tools and highlight the cyanopyrrolidine warhead as a versatile platform for liganding diverse classes of protein with reactive cysteine residues which can be used for further inhibitor screening, and as a starting point for inhibitor development.
Insights
Researchers characterized MT16-001, a novel UCHL1 inhibitor, revealing its potential and off-target effects. This study emphasizes the importance of comprehensive profiling for chemical probes in drug discovery.
Area of Science:
- Biochemistry
- Chemical Biology
- Drug Discovery
Background:
- Ubiquitin carboxy-terminal hydrolase L1 (UCHL1) is a deubiquitinating enzyme (DUB) implicated as a drug target in cancers and fibrotic diseases.
- The precise functions and substrates of UCHL1 are not fully elucidated, hindering therapeutic development.
Purpose of the Study:
- To characterize a novel UCHL1 covalent inhibitor, MT16-001, based on a thiazole cyanopyrrolidine scaffold.
- To comprehensively profile the on- and off-targets of MT16-001 and a related activity-based probe (MT16-205) using chemical proteomics.
Main Methods:
- Synthesis and characterization of UCHL1 inhibitor MT16-001 and activity-based probe MT16-205.
- Application of chemical proteomics to quantitatively profile on- and off-targets at endogenous levels.
- Assessment of compound selectivity against other DUBs and the broader proteome.
Main Results:
- MT16-001 and MT16-205 exhibit selectivity for UCHL1 over other DUBs in cellular assays.
- These compounds engage additional targets, including aldehyde dehydrogenases, PARK7, and glutamine amidotransferase, with notable selectivity over the wider proteome.
- The cyanopyrrolidine scaffold demonstrates versatility for targeting proteins with reactive cysteine residues.
Conclusions:
- Robust profiling of activity-based probes is crucial for understanding chemical tool behavior.
- The cyanopyrrolidine warhead serves as a valuable platform for developing inhibitors against diverse cysteine-containing proteins.
- This work provides a foundation for further inhibitor screening and development targeting UCHL1 and related enzymes.
