Cooperative Aldehyde Chemistry Maps an Orthogonal Lysine Reactivity Landscape

Reactive aldehyde metabolites are commonly viewed as drivers of nonspecific protein damage and stochastic cross-linking. Here, we show that cooperative aldehyde chemistry can generate multicomponent, mass-consistent electrophilic intermediates in water with strong lysine bias and site selectivity. Specifically, malondialdehyde (MDA) couples with monoaldehydes (e.g., acetaldehyde and benzaldehyde) to form a cooperative intermediate that channels reactivity toward lysine, yielding chemically stable dihydropyridine (DHP) adducts under aqueous conditions. Across peptides, purified proteins, and complex lysates, this pathway produces nonrandom, lysine-selective labeling. Comparison with NHS-ester chemoproteomic data sets suggests a distinct selectivity regime: whereas NHS acylation broadly tracks nucleophile accessibility with weak context dependence, cooperative MDA-monoaldehyde chemistry preferentially labels lysines in acidic microenvironments, consistent with an electrostatically influenced association-and-capture model that promotes productive cyclization to stable DHP adducts. Finally, electronic tuning of the DHP scaffold affords red-shifted emission compatible with live-cell imaging. Together, these results establish a tunable cooperative aldehyde platform that expands selective lysine bioconjugation chemistry and enables proteome-scale mapping of lysine microenvironment reactivity not captured by conventional acylating reagents.