Advances in Discovering Deubiquitinating Enzyme (DUB) Inhibitors

Abstract

Deubiquitinating enzymes, or DUBs, comprise a family of proteases that regulate ubiquitination dynamics. Since their discovery, genetic and functional studies have nominated DUBs as a promising class for drug discovery across diverse therapeutic areas. Consequent probe and drug discovery efforts over the past 15 years have resulted in over 50 reported inhibitors and advances in DUB structural studies, assay formats, and chemical biology tools. Accumulating knowledge from these studies has enabled several important recent breakthroughs. In this review, we highlight recent successes in solving DUB-ligand co-structures and the development of rigorously characterized potent and selective inhibitors. We posit that these advances in pharmacological targeting of DUBs establish the enzyme family as targetable and provide a framework for other DUBs programs. Accordingly, we envision increasingly rapid progress in the development of potent and selective inhibitors for a wide range of DUBs and advancement of DUB-targeting drugs to the clinic.

High-throughput matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry–based deubiquitylating enzyme assay for drug discovery

“…The linkage between ubiquitin and the TAMRA moiety in the Ub-KG(TAMRA) substrate is an isopeptide bond 91 , but Ub-KG(TAMRA) lacks the presence of a proximal ubiquitin or substrate and is therefore no closer to a genuine DUB substrate than Ub-AMC or Ub-Rho. Ub-AMC and Ub-Rho have been successfully used with many of the USP family members in HTS campaigns 42 and to determine cleavage kinetics. However, many DUBs, belonging to the JAMM, OTU, MINDY, MJD and ZUP1 families, are incompatible with these substrates.…”

“…This can result in different outcomes, from preventing proteasomal degradation of a specific substrate to switching off signaling events triggered by ubiquitin conjugation. Given the relevance of ubiquitylation in several human diseases, the interest in manipulating specific diseaserelated DUBs constitutes an expanding research area in the drug discovery field 42,43 . Of particular interest are those DUBs that stabilize proto-oncogene proteins whose abundance cannot be otherwise regulated by using currently available drugs.…”

USP30 sets a trigger threshold for PINK1–PARKIN amplification of mitochondrial ubiquitylation

“…Early academic efforts to obtain specific small molecule inhibitors were only partially successful (Ritorto et al, 2014). More recently, industry-led efforts have generated some highly specific inhibitors, exemplified by compounds targeting USP7, an enzyme linked to the p53/MDM2 signalling axis (Kategaya et al, 2017;Lamberto et al, 2017;Turnbull et al, 2017;Gavory et al, 2018;Schauer et al, 2019). Some N-cyano pyrrolidines, which resemble known cathepsin C covalent inhibitors, have been reported in the patent literature to be dual inhibitors of UCHL1 and USP30 (Laine et al, 2011).…”

A novel USP30 inhibitor recapitulates genetic loss of USP30 and sets the trigger for PINK1-PARKIN amplification of mitochondrial ubiquitylation

“…Early academic efforts to obtain specific small molecule inhibitors were only partially successful (30). More recently industryled efforts have generated some highly specific inhibitors, exemplified by compounds targeting USP7, an enzyme linked to the p53/MDM2 signaling axis (31)(32)(33)(34)(35). Some Ncyano pyrrolidines, which resemble known cathepsin C covalent inhibitors, have been reported in the patent literature to be dual inhibitors of UCHL1 and USP30 (36).…”