Cyanopyrrolidine inhibitors of ubiquitin specific protease 7 mediate desulfhydration of the active-site cysteine.
Abstract
Ubiquitin specific protease 7 (USP7) regulates the protein stability of key cellular regulators in pathways ranging from apoptosis to neuronal development, making it a promising therapeutic target. Here we used an engineered, activated variant of the USP7 catalytic domain to perform structure–activity studies of electrophilic peptidomimetic inhibitors. Employing this USP7 variant, we found that inhibitors with a cyanopyrrolidine warhead unexpectedly promoted a β-elimination reaction of the initial covalent adducts, thereby converting the active-site cysteine residue to dehydroalanine. We determined that this phenomenon is specific for the USP7 catalytic cysteine and that structural features of the inhibitor and protein microenvironment impact elimination rates. Using comprehensive docking studies, we propose that the characteristic conformational dynamics of USP7 allow access to conformations that promote the ligand-induced elimination. Unlike in conventional reversible-covalent inhibition, the compounds described here irreversibly destroy a catalytic residue while simultaneously converting the inhibitor to a nonelectrophilic byproduct. Accordingly, this unexpected finding expands the scope of covalent inhibitor modalities and offers intriguing insights into enzyme–inhibitor dynamics.
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A new class of GNE cyanopyrrolidine-based inhibitors has been described.
“Recently, a new class of GNE cyanopyrrolidine-based inhibitors has been described.”
From USP7 Is a Master Regulator of Genome Stability (2020) · cites this paper as Bashore et al., 2020
The ability of C223 to act as a nucleophile for bond hydrolysis is eliminated by its conversion to DHA.
“Therefore, the ability of C223 to act as a nucleophile for bond hydrolysis is eliminated (Bashore et al., 2020).”
From USP7 Is a Master Regulator of Genome Stability (2020) · cites this paper as Bashore et al., 2020
GNE Compound 11 specifically targets C223.
“These inhibitors, including GNE Compound 11, specifically target C223.”
From USP7 Is a Master Regulator of Genome Stability (2020) · cites this paper as Bashore et al., 2020
GNE cyanopyrrolidine inhibitors cause desulfhydration of the active-site cysteine of USP7, converting it to dehydroalanine (DHA).
“Interestingly, these novel inhibitors cause desulfhydration of the active-site cysteine of USP7, converting it to dehydroalanine (DHA).”
From USP7 Is a Master Regulator of Genome Stability (2020) · cites this paper as Bashore et al., 2020
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USP7 Is a Master Regulator of Genome Stability
Valles, G. J., Bezsonova, I., Woodgate, R., & Ashton, N. W. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.00717 · Cited by 114 · see citing works
“Therefore, the ability of C223 to act as a nucleophile for bond hydrolysis is eliminated (Bashore et al., 2020).”
Background
- Authors
- Bashore, C., Jaishankar, P., Skelton, N. J., Fuhrmann, J., Hearn, B. R., Liu, P. S., Renslo, A. R., & Dueber, E. C.
- Affiliations
- Genentech (US)
- University of California, San Francisco (US)
- Corresponding author
- Renslo, Adam R.
- Dueber, Erin C.
- ORCID
- Venue
- ACS Chemical Biology
- Publisher
- American Chemical Society (ACS)
- Published
- 2020-04-17
- Volume
- 15
- Issue
- 6
- Pages
- 1392-1400
- ISSN
- 1554-8929 (ISSN-L)
- 1554-8937
- OpenAlex
- W3016342679
- Cited by
- 34
- References
- 44
- Citations by year
- 2026: 5 · 2025: 3 · 2024: 4 · 2023: 2 · 2022: 6 · 2021: 9 · 2020: 5
- FWCI
- 2.03
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- ACS Chemical Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (AI105106)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Protease and Inhibitor Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Keywords
- USP7, active site cysteine, dehydroalanine, β-elimination, covalent inhibitors, irreversible inhibition, protein conformational dynamics, structure-activity relationship
- MeSH terms
- Ubiquitin-Specific Peptidase 7, Cysteine, Enzyme Inhibitors, Humans, Pyrrolidines, Catalytic Domain, Peptidomimetics, Molecular Docking Simulation
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