Assigning functionality to cysteines by base editing of cancer dependency genes
Open accessPublished version of a preprint
Abstract
Covalent chemistry represents an attractive strategy for expanding the ligandability of the proteome, and chemical proteomics has revealed numerous electrophile-reactive cysteines on diverse human proteins. Determining which of these covalent binding events affect protein function, however, remains challenging. Here we describe a base-editing strategy to infer the functionality of cysteines by quantifying the impact of their missense mutation on cancer cell proliferation. The resulting atlas, which covers more than 13,800 cysteines on more than 1,750 cancer dependency proteins, confirms the essentiality of cysteines targeted by covalent drugs and, when integrated with chemical proteomic data, identifies essential, ligandable cysteines in more than 160 cancer dependency proteins. We further show that a stereoselective and site-specific ligand targeting an essential cysteine in TOE1 inhibits the nuclease activity of this protein through an apparent allosteric mechanism. Our findings thus describe a versatile method and valuable resource to prioritize the pursuit of small-molecule probes with high function-perturbing potential.
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- Authors
- Li, H., Ma, T., Remsberg, J. R., Won, S. J., DeMeester, K. E., Njomen, E., Ogasawara, D., Zhao, K. T., Huang, T. P., Lu, B., Simon, G. M., Melillo, B., Schreiber, S. L., Lykke-Andersen, J., Liu, D. R., & Cravatt, B. F.
- Affiliations
- Scripps Research Institute (US)
- University of California San Diego (US)
- Broad Institute (US)
- Vividion Therapeutics (United States) (US)
- Corresponding author
- Li, Haoxin
- Cravatt, Benjamin F.
- ORCID
- Venue
- Nature Chemical Biology
- Published
- 2023-10-02
- Volume
- 19
- Issue
- 11
- Pages
- 1320-1330
- ISSN
- 1552-4450 (ISSN-L)
- 1552-4469
- PMC
- PMC10698195
- OpenAlex
- W4387252290
- Cited by
- 62
- References
- 20
- Citations by year
- 2026: 17 · 2025: 17 · 2024: 18 · 2023: 10
- FWCI
- 6.34
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Chemical Biology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- U.S. Department of Health & Human Services | NIH | National Cancer Institute (R35 CA231991)
- U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R35 GM118069, GM118062)
- Topics
- Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Keywords
- base editing, missense mutations, tumor cell proliferation, chemoproteomics, TOE1, allosteric inhibition, chemical probes, covalent binding
- MeSH terms
- Gene Editing, Cysteine, Humans, Neoplasms, Nuclear Proteins, Proteome, Proteomics
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