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Reversible lysine-targeted probes reveal residence time-based kinase selectivity

Abstract

The expansion of the target landscape of covalent inhibitors requires the engagement of nucleophiles beyond cysteine. Although the conserved catalytic lysine in protein kinases is an attractive candidate for a covalent approach, selectivity remains an obvious challenge. Moreover, few covalent inhibitors have been shown to engage the kinase catalytic lysine in animals. We hypothesized that reversible, lysine-targeted inhibitors could provide sustained kinase engagement in vivo, with selectivity driven in part by differences in residence time. By strategically linking benzaldehydes to a promiscuous kinase binding scaffold, we developed chemoproteomic probes that reversibly and covalently engage >200 protein kinases in cells and mice. Probe–kinase residence time was dramatically enhanced by a hydroxyl group ortho to the aldehyde. Remarkably, only a few kinases, including Aurora A, showed sustained, quasi-irreversible occupancy in vivo, the structural basis for which was revealed by X-ray crystallography. We anticipate broad application of salicylaldehyde-based probes to proteins that lack a druggable cysteine.

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Fig. 1: Benzaldehyde probe 1 reversibly labels cellular proteins.
Fig. 2: Salicylaldehyde probes exhibit prolonged kinase residence time in cells.
Fig. 3: Quasi-irreversible engagement of AURKA in cells.
Fig. 4: Cocrystal structure of AURKA bound to salicylaldehyde 3.
Fig. 5: Quantifying kinase occupancy by salicylaldehyde 3 in mice.
Fig. 6: Salicylaldehyde probe 3 reveals PF-06873600 target engagement in vivo.

Data availability

All mass spectrometry raw files have been deposited into the MassIVE database (http://massive.ucsd.edu) and can be downloaded by the identifier MSV000088924, as well as in ProteomeXchange (http://www.proteomexchange.org) with accession number PXD031899. Source data are provided in a source data file or in the Supplementary Datasets. Coordinates and structure factors have been deposited in the PDB under accession code 7FIC. Source data are provided with this paper.

Code availability

The script used for LFQ quantification is available upon request.

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Acknowledgements

Funding for this study was provided by the National Cancer Institute (NCI) (NIH NCI F31CA214028, A.C.), Ono Pharma Foundation (J.T.) and Pfizer. Mass spectrometry was supported in part by the University of California, San Francisco (UCSF) Program for Breakthrough Biomedical Research and the Adelson Medical Research Foundation (A.L.B.).

Author information

Authors and Affiliations

Authors

Contributions

T.Y. and J.T. conceived the project, designed the experiments and analyzed the data. T.Y. synthesized the aldehyde probes, evaluated the probes in biochemical and chemoproteomics experiments, and acquired and analyzed LFQ and TMT proteomics data. A.C. acquired and analyzed LFQ proteomics data. X.W. crystallized and determined the structure of AURKA–probe 3. G.B.C. refined the X-ray structure. B.H., P.K. and J.R.M. performed mouse pharmacology experiments. J.D.C. analyzed TMT proteomics data. T.Y. and J.T. wrote the manuscript with input from all of the authors. J.C.K., J.D.L., S.N. and A.L.B. edited the manuscript.

Corresponding author

Correspondence to Jack Taunton.

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Competing interests

T.Y., B.H., P.K., J.R.M., J.C.K., J.D.L., S.N. and J.D.C. are current or former employees of Pfizer. J.T. is a founder of Global Blood Therapeutics, Principia Biopharma, Kezar Life Sciences, Cedilla Therapeutics and Terremoto Biosciences, and is a scientific advisor to Entos.

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Nature Chemical Biology thanks Benjamin Cravatt and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Reversible protein labeling by benzaldehyde probe 2.

(a) Chemical structures of 1 and 2. (b) Jurkat cells were treated with 1 or 2 (2 μM, 30 min), followed by compound washout for the indicated times. Cells were lysed in the presence of 25 mM sodium cyanoborohydride, except as indicated (#). After copper-promoted click conjugation with TAMRA-azide, samples were analyzed by in-gel fluorescence and Coomassie blue staining. Data are representative of two independent experiments.

Source data

Extended Data Fig. 2 Probe 3 modification of overexpressed Src.

(a) COS-7 cells were transfected with WT or K295Q (#) Flag-Src, or not transfected (*), and then treated with the indicated concentrations of probe 3 (30 min). After lysis in the presence of sodium borohydride and TAMRA-azide conjugation, samples were analyzed by in-gel fluorescence and western blotting. Data are representative of two independent experiments. (b) Concentration-dependent labeling of Flag-Src (n = 2, mean values from two independently performed experiments were plotted).

Source data

Extended Data Fig. 3 Rapid dissociation of probe 3 from overexpressed Src.

(a) COS-7 cells were transfected with Flag-Src, or not transfected (*), and treated with probe 3 (2 μM, 30 min), followed by washout for the indicated times. After lysis in the presence of sodium borohydride and TAMRA-azide conjugation, samples were analyzed by in-gel fluorescence and western blotting. (b) Normalized fluorescence intensity of ~65 kDa band corresponding to Flag-Src (mean ± SD, n = 3).

Source data

Extended Data Fig. 4 Dissociation of probe 3 from recombinant AURKA and Src.

AURKA or Src (5 μM) was treated with probe 3 (5.1 μM) in 50 mM HEPES, pH 8.0 at RT for 5 min, followed by 20-fold dilution into buffer containing 10 μM XO44. The percentage of XO44-modified and unmodified kinase was quantified by LC-MS at the indicated time points, and % unmodified kinase (corresponding to probe 3-bound kinase) was plotted vs. time (n = 2, mean values from two independently performed experiments were plotted).

Extended Data Fig. 5 Related to Fig. 5.

Volcano plot showing log2 fold-change and significance (−log10 p-value; two tailed t-test assuming unequal variance) of proteins enriched by probe 3 (t = 3 h post-dose) vs. vehicle. Red, kinases; gray, non-kinases.

Supplementary information

Supplementary Information

Supplementary Figs. 1 and 2, Supplementary Tables 1 and 2, and Supplementary Note.

Reporting Summary

Supplementary Datasets 1–12

Chemoproteomics dataset.

Source data

Source Data Fig. 1

Uncropped gel.

Source Data Fig. 2

Uncropped gels.

Source Data Fig. 3

Uncropped gels and western blots.

Source Data Extended Data Fig. 1

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Source Data Extended Data Fig. 2

Uncropped gel and blots.

Source Data Extended Data Fig. 3

Uncropped gel and blots.

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Yang, T., Cuesta, A., Wan, X. et al. Reversible lysine-targeted probes reveal residence time-based kinase selectivity. Nat Chem Biol (2022). https://doi.org/10.1038/s41589-022-01019-1

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