Physical and Functional Analysis of the Putative Rpn13 Inhibitor RA190

Dickson, Paige; Abegg, Daniel; Vinogradova, Ekaterina V.; Takaya, Junichiro; An, Hongchan; Simanski, Scott; Cravatt, Benjamin F.; Adibekian, Alexander; Kodadek, Thomas

doi:10.1016/j.chembiol.2020.08.007

Cited by 21 publications

(29 citation statements)

References 42 publications

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“…Altogether, these experiments led to two conclusions; 1) the level of hRpn13 directly correlates with induction of apoptosis by XL5-VHL-2 and 2) substantial reduction in hRpn13 level retains of its role in induced apoptosis by XL5-VHL-2. This data thus highlights limitations of earlier studies that relied on incomplete knockdown by siRNA 31,32 .…”

Section: Structure Validation By Chemical Probing Reveals a Site For Protac Additionmentioning

confidence: 62%

“…Specific targeting of hRpn13 Pru preferentially to hRpn13 full length protein may be an effective therapeutic strategy, with less expected toxicity. The mechanism of action for previous hRpn13 targeting compounds failed to be elucidated as interference was not observed for any known hRpn13 activity, including interaction with proteasomes, ubiquitin or UCHL5 20,27,31,32,35,60 . This study provides a viable mechanism of action for future investigations of hRpn13 as a therapeutic target.…”

Section: Discussionmentioning

confidence: 99%

“…CRISPR-based gene editing indicated hRpn13-binding compounds (RA190 and RA183) 27,28 to induce apoptosis in an hRpn13-dependent manner 29,30 , albeit knockdown experiments suggest little dependency 31 , including for an hRpn13-binding peptoid 32,33 .…”

Section: Introductionmentioning

confidence: 99%

“…The C-terminal end of proteasome subunit hRpn2 extends across the hRpn13 Nterminal Pru (Pleckstrin-like receptor for ubiquitin) domain [34][35][36] which also binds ubiquitin 6,7 dynamically, maintaining it in an extended conformation, with interactions at the ubiquitin linker region that cause preference for chains linked by K48 37,38 . RA190 and RA183 react with hRpn13 C88 at the periphery of the hRpn2-binding region 27,28 , but are generally reactive with exposed cysteines, impairing specificity 28,31,35 . Aided by a pipeline extending from in silico and biophysical integrated screening to high resolution structure determination, we generated bifunctional PROTAC-fused hRpn13-targeting compounds that require an intact hRpn13 Pru domain to induce apoptosis in multiple myeloma cells.…”

Section: Introductionmentioning

confidence: 99%

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Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma

Sabbasani

Osei-Amponsa

et al. 2021

Preprint

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Proteasome substrate receptor hRpn13 is a promising anti-cancer target. By integrated in silico and biophysical screening, we identified a chemical scaffold that binds hRpn13 with non-covalent interactions that mimic the proteasome and a weak electrophile for Michael addition. hRpn13 Pru domain binds proteasomes and ubiquitin whereas its DEUBAD domain binds deubiquitinating enzyme UCHL5. NMR revealed lead compound XL5 to interdigitate into a hydrophobic pocket created by lateral movement of a Pru β-hairpin with an exposed end for Proteolysis Targeting Chimeras (PROTACs). Implementing XL5-PROTACs as chemical probes identified a DEUBAD-lacking hRpn13 species (hRpn13Pru) present naturally with cell type-dependent abundance. XL5-PROTACs preferentially target hRpn13Pru, causing its ubiquitination. Gene-editing and rescue experiments established hRpn13 requirement for XL5-PROTAC-triggered apoptosis and increased p62 levels. These data establish hRpn13 as an anti-cancer target for multiple myeloma and introduce an hRpn13-targeting scaffold that can be optimized for preclinical trials against hRpn13Pru-producing cancer types.

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Section: Structure Validation By Chemical Probing Reveals a Site For Protac Additionmentioning

confidence: 62%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma

Sabbasani

Osei-Amponsa

et al. 2021

Preprint

View full text Add to dashboard Cite

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“…Loss of cell viability, however, by either of these two hRpn13‐targeting compounds does not seem to require hRpn13 according to hRpn13‐knockdown experiments [165,166] and a cell line with a defective hRpn13 Pru domain [164], although conflicting data on this matter exist [163]. These compounds are able to interact with other cellular components, which likely contribute to the induction of apoptosis [165,166]. Nonetheless, these findings collectively suggest that hRpn13 is a promising therapeutic target.…”

Section: Proteasome As a Therapeutic Targetmentioning

confidence: 99%

Proteasome interaction with ubiquitinated substrates: from mechanisms to therapies

et al. 2020

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The 26S proteasome is responsible for regulated proteolysis in eukaryotic cells. Its substrates are diverse in structure, function, sequence length, and amino acid composition, and are targeted to the proteasome by post-translational modification with ubiquitin. Ubiquitination occurs through a complex enzymatic cascade and can also signal for other cellular events, unrelated to proteasome-catalyzed degradation. Like other post-translational protein modifications, ubiquitination is reversible, with ubiquitin chain hydrolysis catalyzed by the action of deubiquitinating enzymes (DUBs), ~90 of which exist in humans and allow for temporal events as well as dynamic ubiquitin-chain remodeling. DUBs have been known for decades to be an integral part of the proteasome, as deubiquitination is coupled to substrate unfolding and translocation into the internal degradation chamber. Moreover, the proteasome also binds several ubiquitinating enzymes as well as shuttle factors that recruit ubiquitinated substrates. The role of this intricate machinery and how ubiquitinated substrates interact with proteasomes remains an area of active investigation. Here, we review what has been learned about the mechanisms used by the proteasome to bind ubiquitinated substrates, substrate shuttle factors, ubiquitination machinery, and DUBs. We also discuss many open questions that require further study or the development of innovative approaches to be answered. Finally, we address the promise of expanded therapeutic targeting that could benefit from such new discoveries.

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Ubiquitin receptors play redundant roles in the proteasomal degradation of the p53 repressor MDM2

2022

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Much remains to be determined about the participation of ubiquitin receptors in proteasomal degradation and their potential as therapeutic targets. Suppression of the ubiquitin receptor S5A/PSMD4/hRpn10 alone stabilises p53/ TP53 but not the key p53 repressor MDM2. Here, we observed S5A and the ubiquitin receptors ADRM1/PSMD16/hRpn13 and RAD23A and B functionally overlap in MDM2 degradation. We provide further evidence that degradation of only a subset of ubiquitinated proteins is sensitive to S5A knockdown because ubiquitin receptor redundancy is commonplace. p53 can be upregulated by S5A modulation while degradation of substrates with redundant receptors is maintained. Our observations and analysis of Cancer Dependency Map (DepMap) screens show S5A depletion/loss substantially reduces cancer cell line viability. This and selective S5A dependency of proteasomal substrates make S5A a target of interest for cancer therapy.

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Physical and Functional Analysis of the Putative Rpn13 Inhibitor RA190

Cited by 21 publications

References 42 publications

Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma

Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma

Proteasome interaction with ubiquitinated substrates: from mechanisms to therapies

Ubiquitin receptors play redundant roles in the proteasomal degradation of the p53 repressor MDM2

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