Biomimetic Synthesis and Chemical Proteomics Reveal the Mechanism of Action and Functional Targets of Lysine-Reactive Phloroglucinol Meroterpenoids

ABSTRACT: Natural products have long been an enduring source of drug leads and chemical probes that have led to the development of numerous medicines. Despite their scarcity, the discovery of natural products that modulate protein function through covalent interactions with lysine residues holds immense potential to unlock new therapeutic interventions and advance our understanding of the intricate biological processes governed by these modifications. Phloroglucinol meroterpenoids comprise one of the largest classes of natural products displaying a vast array of biological activities. However, their mechanism of action and molecular targets have remained largely unexplored. In this study, we present an in-depth experimental and computational investigation into the synthesis, physicochemical and kinetic parameters, molecular mechanism of action, and functional cellular targets of selected phloroglucinol meroterpenoids. We leverage synthetic clickable analogues of natural products to observe disparate proteome-wide reactivity by in-gel fluorescence scanning and cell imaging. By implementing sample multiplexing and a redesigned desthiobiotin-based probe, we streamline a quantitative activity-based protein profiling protocol for mapping proteome-wide reactivity and ligandability of proteinaceous lysines directly in human cells. Using this platform, we identify numerous lysine-phloroglucinol meroterpenoid interactions in breast cancer cells that occur at functional sites on proteins from diverse structural and functional classes. Lastly, we demonstrate that phloroglucinol meroterpenoids perturb diverse biochemical functions through stereoselective and site-specific modification of lysines in proteins involved in glycolysis, lipid metabolism, and mitochondrial respiration. These findings underscore the broad potential of phloroglucinol meroterpenoids for targeting functional lysines in the human proteome.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Breast Cancer

SUBMITTER: Mikail Abbasov  

LAB HEAD: Mikail E. Abbasov

PROVIDER: PXD045370 | Pride | 2024-05-23

REPOSITORIES: Pride