Recent Developments in Cell Permeable Deubiquitinating Enzyme Activity-Based Probes

Overview

Journal Front Chem

Specialty Chemistry

Date 2020 Jan 11

PMID 31921788

Citations 14

Authors

Daniel Conole

Milon Mondal

Jaimeen D Majmudar

Edward W Tate

Affiliations

Soon will be listed here.

Abstract

Deubiquitinating enzymes (DUBs) function to remove or cleave ubiquitin from post-translationally modified protein substrates. There are about 100 known DUBs in the proteome, and their dysregulation has been implicated a number of disease states, but the specific function of many subclass members remains poorly understood. Activity-based probes (ABPs) react covalently with an active site residue to report on specific enzyme activity, and thus represent a powerful method to evaluate cellular and physiological enzyme function and dynamics. Ubiquitin-based ABPs, such as HA-Ub-VME, an epitope-tagged ubiquitin carrying a C-terminal reactive warhead, are the leading tool for "DUBome" activity profiling. However, these probes are generally cell membrane impermeable, limiting their use to isolated enzymes or lysates. Development of cell-permeable ABPs would allow engagement of DUB enzymes directly within the context of an intact live cell or organism, refining our understanding of physiological and pathological function, and greatly enhancing opportunities for translational research, including target engagement, imaging and biomarker discovery. This mini-review discusses recent developments in small molecule activity-based probes that target DUBs in live cells, and the unique applications of cell-permeable DUB activity-based probes vs. their traditional ubiquitin-based counterparts.

Citing Articles

Genetic Code Expansion Approaches to Decipher the Ubiquitin Code.

Wanka V, Fottner M, Cigler M, Lang K Chem Rev. 2024; 124(20):11544-11584.

PMID: 39311880 PMC: 11503651. DOI: 10.1021/acs.chemrev.4c00375.

Discovery of potent and selective activity-based probes (ABPs) for the deubiquitinating enzyme USP30.

Mondal M, Cao F, Conole D, Auner H, Tate E RSC Chem Biol. 2024; 5(5):439-446.

PMID: 38725909 PMC: 11078216. DOI: 10.1039/d4cb00029c.

Deciphering non-canonical ubiquitin signaling: biology and methodology.

van Overbeek N, Aguirre T, van der Heden van Noort G, Blagoev B, Vertegaal A Front Mol Biosci. 2024; 10:1332872.

PMID: 38414868 PMC: 10897730. DOI: 10.3389/fmolb.2023.1332872.

Fluorometric Characterization of DUB Activity: From Single-Enzyme Reactions to Live Intact Cells.

Rahnama A, Melvin A Methods Mol Biol. 2022; 2591:25-44.

PMID: 36350541 DOI: 10.1007/978-1-0716-2803-4_3.

On the Study of Deubiquitinases: Using the Right Tools for the Job.

Caba C, Mohammadzadeh A, Tong Y Biomolecules. 2022; 12(5).

PMID: 35625630 PMC: 9139131. DOI: 10.3390/biom12050703.

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