Profiling the proteome-wide selectivity of diverse electrophiles

Zanon, P.R.A.; Yu, F.; Musacchio, P.Z.; Lewald, L.; Zollo, M.; Krauskopf, K.; ... ; Hacker, S.M. (2025)

Article / Letter to editor

Covalent inhibitors that do not rely on hijacking enzymatic activity have mainly been limited to those targeting cysteine residues. The development of such cysteine-directed covalent inhibitors has greatly profited from the use of competitive residue-specific proteomics to determine their proteome-wide selectivity. Several probes have been developed to monitor other amino acids using this technology, and many more electrophiles exist to modify proteins. Nevertheless, there has been a lack of direct, proteome-wide comparisons of the selectivity of diverse electrophiles. Here we developed an unbiased workflow to analyse electrophile selectivity proteome-wide and used it to directly compare 56 alkyne probes containing diverse reactive groups. In this way, we verified and identified probes to monitor a total of nine different amino acids, as well as the protein amino terminus, across the proteome.

• All authors: Zanon, P.R.A.; Yu, F.; Musacchio, P.Z.; Lewald, L.; Zollo, M.; Krauskopf, K.; Mrdović, D.; Raunft, P.; Maher, T.E.; Cigler, M.; Chang, C.J.; Lang, K.; Toste, F.D.; Nesvizhskii, A.I.; Hacker, S.M.
• Date: 2025-10-30
• Journal: Nature Chemistry
• Volume: 17
• Issue: 11
• Pages: 1712 - 1721
• DOI: doi:10.1038/s41557-025-01902-z
• Link: https://www.nature.com/articles/s41557-025-01902-z