Rapid labelling and covalent inhibition of intracellular native proteins using ligand-directed N-acyl-N-alkyl sulfonamide
Open accessAbstract
Selective modification of native proteins in live cells is one of the central challenges in recent chemical biology. As a unique bioorthogonal approach, ligand-directed chemistry recently emerged, but the slow kinetics limits its scope. Here we successfully overcome this obstacle using N-acyl-N-alkyl sulfonamide as a reactive group. Quantitative kinetic analyses reveal that ligand-directed N-acyl-N-alkyl sulfonamide chemistry allows for rapid modification of a lysine residue proximal to the ligand binding site of a target protein, with a rate constant of ~10 4 M−1 s−1, comparable to the fastest bioorthogonal chemistry. Despite some off-target reactions, this method can selectively label both intracellular and membrane-bound endogenous proteins. Moreover, the unique reactivity of N-acyl-N-alkyl sulfonamide enables the rational design of a lysine-targeted covalent inhibitor that shows durable suppression of the activity of Hsp90 in cancer cells. This work provides possibilities to extend the covalent inhibition approach that is currently being reassessed in drug discovery.
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In 2021, Hamachi et al. developed a small molecule covalent inhibitor (compound 76) based on NASA reaction group that prevents HDM2-p53 interaction.
“In 2021, Hamachi et al. developed a small molecule covalent inhibitor, compound (76), based on the N-acyl-N-alkyl sulfonamide (NASA) reaction group, which can prevent the interaction between HDM2 and p53.”
From Recent advances in targeting the “undruggable” proteins: from drug discovery to clinical trials (2023) · cites this paper as [220]
That study yielded more broadly reactive electrophiles, such as dicarboxaldehydes, for further lysine profiling, and identified less-reactive electrophiles, including N-acyl-N-alkyl sulfonamides, previously used as bioconjugation tools in cells.
“This study yielded more broadly reactive electrophiles, such as dicarboxaldehydes, that could be used for further lysine profiling experiments, but also identified less-reactive electrophiles, including N-acyl-N-alkyl sulfonamides, which had been previously used as tools for bioconjugation in cells202,203.”
From Advances in covalent drug discovery (2022) · cites this paper as [203]
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- Authors
- Tamura, T., Ueda, T., Goto, T., Tsukidate, T., Shapira, Y., Nishikawa, Y., Fujisawa, A., & Hamachi, I.
- Affiliations
- Kyoto University (JP)
- Weizmann Institute of Science (IL)
- Corresponding author
- Hamachi, Itaru
- Venue
- Nature Communications
- Published
- 2018-05-14
- Volume
- 9
- Issue
- 1
- Pages
- 1870-1870
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC5951806
- OpenAlex
- W2806557186
- Cited by
- 242
- References
- 51
- Citations by year
- 2026: 21 · 2025: 52 · 2024: 34 · 2023: 30 · 2022: 31 · 2021: 32 · 2020: 25 · 2019: 14 · 2018: 3
- FWCI
- 7.78
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Institutional Repositories DataBase (IRDB) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Kyoto University Research Information Repository (Kyoto University) (submittedVersion, cc-by)
- Funders
- Kyoto University Foundation
- Japan Society for the Promotion of Science (15K17884, 18J14502, 16J10316, CREST, 17H06348)
- Japan Science and Technology Agency (CREST, 17H06348)
- Core Research for Evolutional Science and Technology (17H06348)
- Topics
- Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Biotin and Related Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Keywords
- bioorthogonal labeling, covalent inhibition, lysine modification, membrane proteins, HSP90, cancer cells, covalent inhibitors, reaction kinetics
- MeSH terms
- Animals, Chemistry Techniques, Analytical, HeLa Cells, Heterocyclic Compounds, 1-Ring, Humans, Kinetics, Lysine, Staining and Labeling, Sulfanilamides, Tetrahydrofolate Dehydrogenase, HSP90 Heat-Shock Proteins, Myoblasts, Cell Line, Tumor, Mice, TOR Serine-Threonine Kinases
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