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Using sulfuramidimidoyl fluorides that undergo sulfur(vi) fluoride exchange for inverse drug discovery

Nature Chemistry volume 12, pages 906–913 (2020)Cite this article

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Abstract

Drug candidates that form covalent linkages with their target proteins have been underexplored compared with the conventional counterparts that modulate biological function by reversibly binding to proteins, in part due to concerns about off-target reactivity. However, toxicity linked to off-target reactivity can be minimized by using latent electrophiles that only become activated towards covalent bond formation on binding a specific protein. Here we study sulfuramidimidoyl fluorides, a class of weak electrophiles that undergo sulfur(vi) fluoride exchange chemistry. We show that equilibrium binding of a sulfuramidimidoyl fluoride to a protein can allow nucleophilic attack by a specific amino acid side chain, which leads to conjugate formation. We incubated small molecules, each bearing a sulfuramidimidoyl fluoride electrophile, with human cell lysate, and the protein conjugates formed were identified by affinity chromatography–mass spectrometry. This inverse drug discovery approach identified a compound that covalently binds to and irreversibly inhibits the activity of poly(ADP-ribose) polymerase 1, an important anticancer target in living cells.

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Fig. 1: SAFs 1–16 react with proteins in HEK293T cell lysate.
Fig. 2: Proteins targeted by SAFs 1–16 identified using isobaric MS/MS tagging in conjunction with proteomic mass spectrometry.
Fig. 3: Validation of reactions between SAFs and selected recombinant proteins.
Fig. 4: Analysis of PARP1 inhibitory activity of a subset of SAFs.
Fig. 5: SAF 2 irreversibly inhibits the activity of PARP1 in HeLa cells.

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Data availability

Additional methods and data are provided in the Supplementary Information. All data generated or analysed during this study are included in this published article (and its supplementary files). Source data are provided with this paper.

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Acknowledgements

This work was supported by the Skaggs Institute for Chemical Biology, the Lita Annenberg Hazen Foundation and National Institutes of Health grants DK046335 (J.W.K.). R.C.B. was supported by a grant from the American Cancer Society. D.E.M. was supported by a grant from the George E. Hewitt Foundation for Medical Research. This work was supported in part by the National Institute of Environmental Health Sciences (NIEHS) Grant R35 ES030443, and NIEHS Superfund Research Program P42 ES004699.

Author information

Author notes

  1. Rachel C. Botham

    Present address: Codexis, Redwood City, CA, USA

  2. Suhua Li

    Present address: School of Chemistry, Sun Yat-Sen University, Guangzhou, P. R. China

  3. David E. Mortenson

    Present address: Gilead Sciences Inc., Foster City, CA, USA

  4. Hua Wang

    Present address: Sorrento Therapeutics, Inc., San Diego, CA, USA

  5. These authors contributed equally: Gabriel J. Brighty, Rachel C. Botham, Suhua Li.

Authors and Affiliations

  1. Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA

    Gabriel J. Brighty, Rachel C. Botham, Suhua Li, Luke Nelson, David E. Mortenson, Gencheng Li, Hua Wang, K. Barry Sharpless & Jeffery W. Kelly

  2. Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA

    Gabriel J. Brighty, Rachel C. Botham, David E. Mortenson & Jeffery W. Kelly

  3. Department of Entomology and Nematology, University of California Davis, Davis, CA, USA

    Christophe Morisseau & Bruce D. Hammock

  4. UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, USA

    Christophe Morisseau & Bruce D. Hammock

  5. The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA

    K. Barry Sharpless & Jeffery W. Kelly

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Contributions

G.J.B., R.C.B. and J.W.K. conceived and designed the experiments G.J.B., R.C.B., S.L., L.N., D.E.M., G.L., C.M. and H.W. carried out the experiments and performed the data analysis G.J.B., R.C.B., S.L., C.M., B.D.H., K.B.S. and J.W.K. co-wrote the paper.

Corresponding authors

Correspondence to K. Barry Sharpless or Jeffery W. Kelly.

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Supplementary information

Supplementary Information

Supplementary Figs, 1–9, biological methods, synthetic protocol for the sulfuramidimidoyl fluorides, references and NMR spectra.

Reporting Summary

Supplementary Dataset 1

Excel spreadsheet of mass spectrometry proteomics data.

Supplementary Dataset 2

Excel spreadsheet of peptide mapping data.

Supplementary Dataset 3

Excel spreadsheet of Gene Ontology data.

Source data

Source Data Fig. 1

Unprocessed gel.

Source Data Fig. 3

Unprocessed gels.

Source Data Fig. 3

Statistical source data.

Source Data Fig. 4

Unprocessed gels.

Source Data Fig. 4

Statistical source data.

Source Data Fig. 5

Unprocessed gels.

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Brighty, G.J., Botham, R.C., Li, S. et al. Using sulfuramidimidoyl fluorides that undergo sulfur(vi) fluoride exchange for inverse drug discovery. Nat. Chem. 12, 906–913 (2020). https://doi.org/10.1038/s41557-020-0530-4

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