Proteasome-based Proteome Profiling (PBPP) for tracking protein/small molecules interactions in living cells

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In recent years, powerful chemoproteomic methods such as thermal proteome profiling (TPP) or limited proteolysis mass spectrometry (LIP-MS), have been developed for chemical biology and drug discovery to decipher interactions between proteins and small molecules without altering their chemical structure. These methodologies have successfully identified proteins with affinity for the small molecules of interest, but without indicating whether the interaction is sufficient to induce target misfolding and degradation. We introduced a methodology to decipher the contaminants interactions with proteins without chemical modification, based on the co-exposure of eukaryotic cells to compounds and proteasome inhibitors. By combining 2 experimental conditions (compound +/- MG132) and proteomics, the interactions that induce sufficient disruption of the target to address it to the proteasome were rapidly deciphered, while observing the effects of contaminants. Proteins were considered as potential targets disrupted by small molecules when their decreased abundance was completely or partially abolished upon co-exposure with the proteasomal inhibitor. We previously applied this methodology to the pesticide chlordecone (CLD) on hepatocytes and identified that it induced septin degradation, triggering toxicity and fibrosis. As proof-of concept, we applied this methodology to HepaRG cells exposed to three contaminants: CLD (pesticide), staurosporine (alkaloid) and deoxynivalenol (mycotoxin).

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