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Updated: Dec 1, 2025
Profiling Ubiquitin and Ubiquitin-like Dependent Post-translational Modifications and Identification of Significant Alterations
Published on: November 7, 2019
Identification of proteasome inhibitors using analysis of gene expression profiles
Arjan Mofers1, Karthik Selvaraju1, Johannes Gubat1
1Biomedical and Clinical Sciences, Linköping University, SE-58183, Linköping, Sweden.
Abstract:
Inhibitors of the 20S proteasome such as bortezomib (Velcade®) and carfilzomib (Kypriolis®) are in clinical use for the treatment of patients with multiple myeloma and mantle cell lymphoma. In an attempt to identify novel inhibitors of the ubiquitin-proteasome system (UPS) we used the connectivity map (CMap) resource, based on alterations of gene expression profiles by perturbagens, and performed COMPARE analyses of drug sensitivity patterns in the NCI60 panel. Cmap analysis identified a large number of small molecules with strong connectivity to proteasome inhibition, including both well characterized inhibitors of the 20S proteasome and molecules previously not described to inhibit the UPS. A number of these compounds have been reported to be cytotoxic to tumor cells and were tested for their ability to decrease processing of proteasome substrates. The antibiotic thiostrepton and the natural products celastrol and curcumin induced strong accumulation of polyubiquitinated proteasome substrates in exposed cells. Other compounds elicited modest increases of proteasome substrates, including the protein phosphatase inhibitor BCI-Cl and the farnesyltransferase inhibitor manumycin A, suggesting that these compounds inhibit proteasome function. Induction of chaperone expression in the absence of proteasome inhibition was observed by a number of compounds, suggesting other effects on the UPS. We conclude that the combination of bioinformatic analyses and cellular assays resulted in the identification of compounds with potential to inhibit the UPS.
Insights
Researchers identified novel ubiquitin-proteasome system (UPS) inhibitors using bioinformatics and cellular assays. This approach revealed compounds like thiostrepton, celastrol, and curcumin that effectively inhibit proteasome function, offering potential new cancer therapies.
Area of Science:
- Pharmacology
- Molecular Biology
- Bioinformatics
Background:
- The ubiquitin-proteasome system (UPS) is crucial for cellular protein homeostasis.
- Current UPS inhibitors, such as bortezomib, are used to treat multiple myeloma and mantle cell lymphoma.
- There is a need for novel UPS inhibitors to overcome resistance and improve therapeutic outcomes.
Purpose of the Study:
- To identify novel small molecules that inhibit the ubiquitin-proteasome system (UPS).
- To leverage the Connectivity Map (CMap) resource and COMPARE analyses for drug discovery.
- To validate potential UPS inhibitors through cellular assays measuring proteasome substrate processing.
Main Methods:
- Utilized the Connectivity Map (CMap) database to analyze gene expression profiles.
- Performed COMPARE analyses on the NCI-60 drug sensitivity panel.
- Assessed the accumulation of polyubiquitinated proteasome substrates in cells treated with identified compounds.
Main Results:
- CMap analysis identified numerous small molecules connected to proteasome inhibition.
- The antibiotic thiostrepton and natural products celastrol and curcumin strongly increased proteasome substrate accumulation.
- Other compounds, including BCI-Cl and manumycin A, showed modest inhibition, suggesting diverse mechanisms of UPS interaction.
Conclusions:
- The integrated approach of bioinformatic analysis and cellular assays is effective for discovering UPS inhibitors.
- Identified compounds like thiostrepton, celastrol, and curcumin warrant further investigation as potential therapeutics.
- This study expands the repertoire of known UPS-modulating compounds and provides a framework for future drug discovery in this area.
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