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Targeted activation in localized protein environments via deep red photoredox catalysis

Nature Chemistry volume 15, pages 101–109 (2023)Cite this article

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Abstract

State-of-the-art photoactivation strategies in chemical biology provide spatiotemporal control and visualization of biological processes. However, using high-energy light (λ < 500 nm) for substrate or photocatalyst sensitization can lead to background activation of photoactive small-molecule probes and reduce its efficacy in complex biological environments. Here we describe the development of targeted aryl azide activation via deep red-light (λ = 660 nm) photoredox catalysis and its use in photocatalysed proximity labelling. We demonstrate that aryl azides are converted to triplet nitrenes via a redox-centric mechanism and show that its spatially localized formation requires both red light and a photocatalyst-targeting modality. This technology was applied in different colon cancer cell systems for targeted protein environment labelling of epithelial cell adhesion molecule (EpCAM). We identified a small subset of proteins with previously known and unknown association to EpCAM, including CDH3, a clinically relevant protein that shares high tumour-selective expression with EpCAM.

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Fig. 1: Selective and targeted uses of aryl azides in chemical biology require low-energy light.
Fig. 2: DR photoredox catalysis overcomes fundamental photolytic limitations of aryl azides.
Fig. 3: Computational analysis reveals a redox-neutral, electron-transfer pathway for triplet nitrene formation.
Fig. 4: Mechanistic differences exist between singlet and triplet perfluoroaryl nitrenes.
Fig. 5: DR-light-mediated protein labelling.
Fig. 6: DR-light-mediated photocatalytic labelling of cellular environments.

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Data availability

Data supporting the main findings of this study are available in the Article, Supplementary Information and Source Data. All Supplementary figures, experimental details and synthesis information are included in the Supplementary Information. Unprocessed proteomics results are available in the Supplementary Data Table. Raw proteomics data are deposited on MassIVE (public data access: ftp://massive.ucsd.edu/MSV000088973/). Source data are provided with this Paper.

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Acknowledgements

Research was supported by the NIH National Institute of General Medical Sciences (R01-GM125206) and gifts from Merck & Co., Inc. J.L.W was funded in part by the Columbia Center for Computational Electrochemistry (CCCE). This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant no. ACI-154856246. In particular, we used San Diego Computing Center’s Expanse resources under allocation ID COL151.

Author information

Author notes

  1. Rob C. Oslund & Olugbeminiyi O. Fadeyi

    Present address: InduPro, Cambridge, MA, USA

  2. These authors contributed equally: Nicholas Eng Soon Tay, Keun Ah Ryu.

Authors and Affiliations

  1. Department of Chemistry, Columbia University, New York, NY, USA

    Nicholas Eng Soon Tay, John L. Weber, David C. Cabanero, David R. Reichman & Tomislav Rovis

  2. Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA

    Keun Ah Ryu, Rob C. Oslund & Olugbeminiyi O. Fadeyi

  3. Genetics and Pharmacogenomics, Merck & Co., Inc., San Francisco, CA, USA

    Aleksandra K. Olow

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Contributions

N.E.S.T., K.A.R., R.C.O., O.O.F. and T.R. conceived the work. N.E.S.T., K.A.R., A.K.O., D.C.C., R.C.O., O.O.F. and T.R. designed and executed experiments. N.E.S.T., K.A.R., D.C.C., R.C.O., O.O.F. and T.R. interpreted results. J.L.W. and D.R.R. designed and executed chemistry-based computations. J.L.W. and D.R.R. interpreted chemistry-based computational results. N.E.S.T., K.A.R., R.C.O., O.O.F. and T.R. wrote the manuscript, with input from all authors.

Corresponding authors

Correspondence to Rob C. Oslund, Olugbeminiyi O. Fadeyi or Tomislav Rovis.

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Competing interests

K.A.R., A.K.O., R.C.O. and O.O.F. were employed by Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., during the experimental planning, execution and/or preparation of this manuscript. The remaining authors declare no competing interests.

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Nature Chemistry thanks Robin Bon and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–44, NMR and HRMS data of all new compounds, uncropped western blot images of Supplementary figures.

Reporting Summary

Supplementary Table 1

Excel-based table listing processed proteomics data for EpCAM-targeted proximity labelling.

Supplementary Table 2

Excel-based table listing pre-processed proteomics data for EpCAM-targeted proximity labelling.

Supplementary Data 1

Source data for Supplementary figures.

Supplementary Data 2

Computational cartesian coordinates.

Source data

Source Data Fig. 2B

UV-vis source data for Fig 2b.

Source Data Fig. 5

Statistical source data for Fig. 5b,c.

Source Data Fig. 5_2

Unprocessed western blots for Fig. 5b,c.

Source Data Fig. 6

Unprocessed western blot for Fig. 6b.

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Tay, N.E.S., Ryu, K.A., Weber, J.L. et al. Targeted activation in localized protein environments via deep red photoredox catalysis. Nat. Chem. 15, 101–109 (2023). https://doi.org/10.1038/s41557-022-01057-1

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