A compound-based proteomic approach discloses 15-ketoatractyligenin methyl ester as a new PPARγ partial agonist with anti-proliferative ability

Proteomics based approaches are emerging as useful tools to identify the targets of bioactivecompounds and elucidate their molecular mechanisms of action. Here, we applied a chemical proteomicstrategy to identify the peroxisome proliferator-activated receptor γ (PPARγ) as a molecular targetof the pro-apoptotic agent 15-ketoatractyligenin methyl ester (compound 1). We demonstrated thatcompound 1 interacts with PPARγ, forms a covalent bond with the thiol group of C285 and occupiesthe sub-pocket between helix H3 and the β-sheet of the ligand-binding domain (LBD) of the receptorby Surface Plasmon Resonance (SPR), mass spectrometry-based studies and docking experiments. 1displayed partial agonism of PPARγ in cell-based transactivation assays and was found to inhibit theAKT pathway, as well as its downstream targets. Consistently, a selective PPARγ antagonist (GW9662)greatly reduced the anti-proliferative and pro-apoptotic effects of 1, providing the molecular basisof its action. Collectively, we identified 1 as a novel PPARγ partial agonist and elucidated its mode ofaction, paving the way for therapeutic strategies aimed at tailoring novel PPARγ ligands with reducedundesired harmful side effects.