Natural products perennially serve
as prolific sources of drug
leads and chemical probes, fueling the development of numerous therapeutics.
Despite their scarcity, natural products that modulate protein function
through covalent interactions with lysine residues hold immense potential
to unlock new therapeutic interventions and advance our understanding
of the biological processes governed by these modifications. Phloroglucinol
meroterpenoids constitute one of the most expansive classes of natural
products, displaying a plethora of biological activities. However,
their mechanism of action and cellular targets have, until now, remained
elusive. In this study, we detail the concise biomimetic synthesis,
computational mechanistic insights, physicochemical attributes, kinetic
parameters, molecular mechanism of action, and functional cellular
targets of several phloroglucinol meroterpenoids. We harness synthetic
clickable analogues of natural products to probe their disparate proteome-wide
reactivity and subcellular localization through in-gel fluorescence
scanning and cell imaging. By implementing sample multiplexing and
a redesigned lysine-targeting probe, we streamline a quantitative
activity-based protein profiling, enabling the direct mapping of global
reactivity and ligandability of proteinaceous lysines in human cells.
Leveraging this framework, we identify numerous lysine–meroterpenoid
interactions in breast cancer cells at tractable protein sites across
diverse structural and functional classes, including those historically
deemed undruggable. We validate that phloroglucinol meroterpenoids
perturb biochemical functions through stereoselective and site-specific
modification of lysines in proteins vital for breast cancer metabolism,
including lipid signaling, mitochondrial respiration, and glycolysis.
These findings underscore the broad potential of phloroglucinol meroterpenoids
for targeting functional lysines in the human proteome.