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.