Small-Molecule Inhibitors Targeting Proteasome-Associated Deubiquitinases

Abstract

The 26S proteasome is the principal protease for regulated intracellular proteolysis. This multi-subunit complex is also pivotal for clearance of harmful proteins that are produced throughout the lifetime of eukaryotes. Recent structural and kinetic studies have revealed a multitude of conformational states of the proteasome in substrate-free and substrate-engaged forms. These conformational transitions demonstrate that proteasome is a highly dynamic machinery during substrate processing that can be also controlled by a number of proteasome-associated factors. Essentially, three distinct family of deubiquitinases–USP14, RPN11, and UCH37–are associated with the 19S regulatory particle of human proteasome. USP14 and UCH37 are capable of editing ubiquitin conjugates during the process of their dynamic engagement into the proteasome prior to the catalytic commitment. In contrast, RPN11-mediated deubiquitination is directly coupled to substrate degradation by sensing the proteasome’s conformational switch into the commitment steps. Therefore, proteasome-bound deubiquitinases are likely to tailor the degradation events in accordance with substrate processing steps and for dynamic proteolysis outcomes. Recent chemical screening efforts have yielded highly selective small-molecule inhibitors for targeting proteasomal deubiquitinases, such as USP14 and RPN11. USP14 inhibitors, IU1 and its progeny, were found to promote the degradation of a subset of substrates probably by overriding USP14-imposed checkpoint on the proteasome. On the other hand, capzimin, a RPN11 inhibitor, stabilized the proteasome substrates and showed the anti-proliferative effects on cancer cells. It is highly conceivable that these specific inhibitors will aid to dissect the role of each deubiquitinase on the proteasome. Moreover, customized targeting of proteasome-associated deubiquitinases may also provide versatile therapeutic strategies for induced or repressed protein degradation depending on proteolytic demand and cellular context.

Research Progress of DUB Enzyme in Hepatocellular Carcinoma

“…The research group of Finley et al identified more than two hundred inhibitors of USP14 based on high-throughput screening of Ub-AMC hydrolysis assays; IU1 is the first specific inhibitor targeting USP14, named IU1 (194). In addition, other inhibitors have been developed: IU1 analogs, such as IU1-206 and IU1-248 and IU2 series (195); spautin-1 is a small molecule inhibitor of USP10 and also inhibits USP13 (196). Recent research reports identify Wu-5 as a novel USP10 inhibitor that induces degradation of the FLT3 mutant protein (197).…”

“…A leukemia drug, 6-thioguanine, was found to be a potent inhibitor of USP2, exhibiting a non-competitive and slow-binding inhibitory mechanism for USP2 (199). Studies have reported that inhibitors of USP8 include RA- (195). Although UCH37 lacks specific inhibitors, the developed multi-target inhibitors can also provide new strategies and ideas for clinical drug development.…”

Mitochondrially-Targeted Therapeutic Strategies for Alzheimer’s Disease

“…Finally, since activating Nuclear factor erythroid-derived 2 -like 2 (Nrf2) increases proteasome activity, the antioxidant 3H-1,2-dithiole-3-thione (D3T), which upregulates both 20S and 19S proteasome subunits, are promising therapeutic targets [ 185 , 186 ]. As a proof of concept, genetic activation of the proteasome ameliorates the aging process and elongates lifespan in different models, including C. elegans, human fibroblasts and yeast cells [ 187 , 188 ].…”

Advances in Proteasome Enhancement by Small Molecules

“…The main function of these DUBs is to remove monoubiquitin and polyubiquitin chains from substrates tagged for proteasomal degradation [ 202 , 203 , 204 , 205 ]. USP14, a DUB of the cysteine protease class, interacts reversibly with the proteasome [ 124 , 206 , 207 , 208 ] and it cleaves the ubiquitin chain off the targeted protein before degradation by the proteasome [ 209 , 210 ], thereby inhibiting the degradation of ubiquitin-protein conjugates in vitro and in vivo [ 124 ]. Unlike USP14, the RPN11, a DUB of the metalloprotease class, is part of the 19S RP and cleaves the ubiquitin chain after degradation has been initiated by the proteasome [ 200 ].…”

“…Further optimization of IU1 has led to the discovery of more potent analogues such as IU1-47 (IC 50 of 0.6 µM) ( Figure 3 , compound 2 ) [ 213 ], IU1-248 (IC 50 of 0.83 µM) ( Figure 3 , compound 3 ) [ 214 ], and 1B10 and 1D18 ( Figure 3 , compound 4 & 5 respectively) which have better membrane permeability [ 215 ]. A recent review by Moon et al [ 210 ], is focused on small molecules that inhibit proteasome-associated deubiquitinase and can be consulted for more information on DUB inhibitors.…”