Small-molecule binding-site discovery using silyl ether-enabled chemoproteomics

For chemical probe and drug discovery campaigns, the pairing of mass spectrometry-based chemoproteomics with photoaffinity labelling has emerged as a favoured approach for target discovery and mode of action assignment. However, photocrosslinked peptide-compound adducts raise analytic challenges for quantitative binding site discovery. Here, to address these challenges, we establish the Silyl Ether Enables Chemoproteomic Interaction and Target Engagement (SEE-CITE) method. SEE-CITE incorporates a fully functionalized chemically cleavable photocrosslinking handle that enables precise site-of-labelling identification and head-to-head comparisons of relative binding site engagement by chemically diverse compounds. To ensure high-confidence localization of labelled residues, we extended the MSFragger algorithm of the FragPipe computational platform to report localization scores customized for photoaffinity labelling and SEE-CITE data. When applied to scout fragments and analogues of select FDA-approved kinase inhibitors, SEE-CITE delineates known drug binding sites and uncovers small-molecule binding sites that affect the protein activity of RTN4 and COX5A.

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Publication Details

Journal
Nature Chemistry
Published
2026-04-27
DOI
https://doi.org/10.1038/s41557-026-02127-4
Primary Topic
Click Chemistry and Applications
Type
article
Field-Weighted Citation Impact
0.00
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article

Small-molecule binding-site discovery using silyl ether-enabled chemoproteomics

Nikolas R. Burton, Fengchao Yu, Ajit S. Divakaruni, Miranda Villanueva et al.
Nature Chemistry
Click Chemistry and Applications
article

Small-molecule binding-site discovery using silyl ether-enabled chemoproteomics

Nikolas R. Burton, Fengchao Yu, Ajit S. Divakaruni, Miranda Villanueva, Alexandra C. Turmon, Sho Takechi, Keriann M. Backus, Marc Liesa, Lisa M. Boatner, Andréa B Ball, Nithesh Perumal, Javier Rubio, Elijah Biletch, Aditya Sivakumar, Chau Ngo, Alexey I. Nesvizhskii, Phillip Kim
article en

Abstract

For chemical probe and drug discovery campaigns, the pairing of mass spectrometry-based chemoproteomics with photoaffinity labelling has emerged as a favoured approach for target discovery and mode of action assignment. However, photocrosslinked peptide-compound adducts raise analytic challenges for quantitative binding site discovery. Here, to address these challenges, we establish the Silyl Ether Enables Chemoproteomic Interaction and Target Engagement (SEE-CITE) method. SEE-CITE incorporates a fully functionalized chemically cleavable photocrosslinking handle that enables precise site-of-labelling identification and head-to-head comparisons of relative binding site engagement by chemically diverse compounds. To ensure high-confidence localization of labelled residues, we extended the MSFragger algorithm of the FragPipe computational platform to report localization scores customized for photoaffinity labelling and SEE-CITE data. When applied to scout fragments and analogues of select FDA-approved kinase inhibitors, SEE-CITE delineates known drug binding sites and uncovers small-molecule binding sites that affect the protein activity of RTN4 and COX5A.

Nature Chemistry
University of California, Los Angeles (US), Daiichi Sankyo (Germany) (DE), University of Michigan (US), UCLA Health (US), Instituto de Salud Carlos III (ES), UCLA Medical Center (US), Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas (ES), Abterra Biosciences (United States) (US), Daiichi-Sankyo (Japan) (JP), Broad Center (US), Institut de Biologia Molecular de Barcelona (ES)
Openalex Percentile: Top 10%
Click Chemistry and Applications
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