Monitoring Target Engagement of Deubiquitylating Enzymes Using Activity Probes: Past, Present, and Future

Methods Mol Biol. 2016;1449:395-410. doi: 10.1007/978-1-4939-3756-1_26.


Deubiquitylating enzymes or DUBs are a class of enzymes that selectively remove the polypeptide posttranslational modification ubiquitin from a number of substrates. Approximately 100 DUBs exist in human cells and are involved in key regulatory cellular processes, which drive many disease states, making them attractive therapeutic targets. Several aspects of DUB biology have been studied through genetic knock-out or knock-down, genomic, or proteomic studies. However, investigation of enzyme activation and regulation requires additional tools to monitor cellular and physiological dynamics. A comparison between genetic ablation and dominant-negative target validation with pharmacological inhibition often leads to striking discrepancies. Activity probes have been used to profile classes of enzymes, including DUBs, and allow functional and dynamic properties to be assigned to individual proteins. The ability to directly monitor DUB activity within a native biological system is essential for understanding the physiological and pathological role of individual DUBs. We will discuss the evolution of DUB activity probes, from in vitro assay development to their use in monitoring DUB activity in cells and in animal tissues, as well as recent progress and prospects for assessing DUB inhibition in vivo.

Keywords: ABP; Activity-based probe; Acyloxymethyl ketone; DUB; Deubiquitylating enzyme; Hemagglutinin; JAB1/Mov34/Mpr1 Pad1 N-terminal + protease; JAMM; MACHADO-Josephin domain proteas; MJD; MP; Mpr1/Pad1 N-terminal+; OTU; Ovarian tumor protease; PA; Propargy; SENP; Sentrin-specific protease; UCH; USP; Ubiquitin C-terminal hydrolase; Ubiquitin-like protein; Ubiquitin-specific protease; Ubl; VME; VMS; Vinyl methyl ester; Vinyl methyl sulfone.

MeSH terms

  • Animals
  • Deubiquitinating Enzymes / genetics
  • Deubiquitinating Enzymes / metabolism
  • Endopeptidases / genetics
  • Endopeptidases / metabolism
  • Enzyme Activation / genetics
  • Enzyme Activation / physiology
  • Humans
  • Protein Processing, Post-Translational / genetics
  • Proteomics / methods*
  • Ubiquitin / genetics
  • Ubiquitin / metabolism*


  • Ubiquitin
  • Endopeptidases
  • Deubiquitinating Enzymes