Genipin, a natural compound from Gardenia jasminoides, is a well-known compound in Chinese medicine that is used for the treatment of cancer, inflammation, and diabetes. The use of genipin in classical medicine is hindered because of its unknown molecular mechanisms of action apart from its strong cross-linking ability. Genipin is increasingly applied as a specific inhibitor of proton transport mediated by mitochondrial uncoupling protein 2 (UCP2). However, its specificity for UCP2 is questionable, and the underlying mechanism behind its action is unknown. Here, we investigated the effect of genipin in different systems, including neuroblastoma cells, isolated mitochondria, isolated mitochondrial proteins, and planar lipid bilayer membranes reconstituted with recombinant proteins. We revealed that genipin activated dicarboxylate carrier and decreased the activity of UCP1, UCP3, and complex III of the respiratory chain alongside with UCP2 inhibition. Based on competitive inhibition experiments, the use of amino acid blockers, and site-directed mutagenesis of UCP1, we propose a mechanism of genipin's action on UCPs. At low concentrations, genipin binds to arginine residues located in the UCP funnel, which leads to a decrease in UCP's proton transporting function in the presence of long chain fatty acids. At concentrations above 200 mM, the inhibitory action of genipin on UCPs is overlaid by increased nonspecific membrane conductance due to the formation of protein-genipin aggregates. Understanding the concentration-dependent mechanism of genipin action in cells will allow its targeted application as a drug in the above-mentioned diseases. SIGNIFICANCE Genipin is a well-known natural cross-linking agent for proteins, collagen, gelatin, and chitosan. However, the mechanism of its multiple effects on cells and mitochondria is under dispute. Mitochondrial UCP2 was previously revealed as an important target for genipin. We show that inhibition of UCP2 by genipin at submillimolar concentrations depends on the presence of three positively charged arginines in the funnel of the protein. This mechanism is similar to the UCP inhibition by purine nucleotides such as ATP/ADP and GTP/GDP. The effect of genipin is not specific to UCP2, which can be explained by the presence of arginines in homologous UCP1 and UCP3. This insight is crucial for the design of specific inhibitors of UCPs. FIGURE 9 Extracted ion chromatograms of genipin-modified UCP1 tryptic peptides. Signals at m/z 919.47 and 914.14 correspond to UCP1 tryptic peptide 184 NVIICTELVTYDLMKGALVNNK 206 carrying K198 (919.47; tR ¼ 21.4) and C188 (919.14; tR ¼ 24.2), respectively, modified with genipin adduct of 158 amu after incubation with 50 mM (A) and 1 mM (B) genipin. Corresponding CID spectra are provided in Fig. S1. (C) Positions of cysteine C188 and lysine K198 in UCP1, at which genipin modifications were detected. Three-dimensional structure of UCP1 was computed based on the crystallographic structure of ANT (PDB: 1OKC) using PyMol. To see this figure in color, go...