Cysteine is one of the most intriguing amino acids due to its intrinsically high nucleophilicity and sensitivity to oxidation. It participates in a variety of chemical transformations catalyzed by diverse families of enzymes, including proteases, oxidoreductases and acyltransferases. Using activity-based protein profiling (ABPP), biological activities of different cysteines across the whole proteomes can be examined, and this allows for the identification of new cysteines residues and proteins associated with disease, i.e. new ligandable hotspots.

In ABPP experiments, cysteine-reactive probes are key to fishing out reactive cysteines in complex proteomes. Iodoacetamide-alkyne (IAA) is a widely-used cysteine probe, but its side reactions with other amino acids, poor
biostability, high cellular toxicity and only fair reaction kinetics with cysteines hamper its application for profiling cysteines in live cells.  

Against this backdrop, we have developed a new cysteine probe, N-acryloylindole-alkyne (NAIA). From LC-MS experiments, NAIA is found to show much faster reaction kinetics with cysteine than IAA in aqueous buffer solution. Gel-based ABPP experiments reveal better cysteine profiling by NAIA in cell lysates as well as in live cells. Mass spectrometry (MS) experiments also show a larger population of cysteines being identified by NAIA, further highlighting the potentials of NAIA for proteome-wide cysteine profiling.   

N-acryloylindole-alkyne (NAIA) as a promising scaffold for proteome-wide cysteine profiling

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