Potent ClpP agonists with anticancer properties bind with improved structural complementarity and alter the mitochondrial N-terminome

• Published in: Structure (London) 2023-02, Vol.31 (2), p.185-200.e10
• Main Authors: Mabanglo, Mark F., Wong, Keith S., Barghash, Marim M., Leung, Elisa, Chuang, Stephanie H.W., Ardalan, Afshan, Majaesic, Emily M., Wong, Cassandra J., Zhang, Shen, Lang, Henk, Karanewsky, Donald S., Iwanowicz, Andrew A., Graves, Lee M., Iwanowicz, Edwin J., Gingras, Anne-Claude, Houry, Walid A.
• Format: Article
• Language: English
• Subjects: cancer; ClpP agonist; ClpP protease; drug design; Endopeptidase Clp - genetics; Endopeptidase Clp - metabolism; HYTANE mass spectrometry; imipridones; mitochondria; Mitochondria - metabolism; N-terminome; Proteolysis; Proteomics; TR compounds; X-ray crystallography
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2022.12.002

The mitochondrial ClpP protease is responsible for mitochondrial protein quality control through specific degradation of proteins involved in several metabolic processes. ClpP overexpression is also required in many cancer cells to eliminate reactive oxygen species (ROS)-damaged proteins and to sustain oncogenesis. Targeting ClpP to dysregulate its function using small-molecule agonists is a recent strategy in cancer therapy. Here, we synthesized imipridone-derived compounds and related chemicals, which we characterized using biochemical, biophysical, and cellular studies. Using X-ray crystallography, we found that these compounds have enhanced binding affinities due to their greater shape and charge complementarity with the surface hydrophobic pockets of ClpP. N-terminome profiling of cancer cells upon treatment with one of these compounds revealed the global proteomic changes that arise and identified the structural motifs preferred for protein cleavage by compound-activated ClpP. Together, our studies provide the structural and molecular basis by which dysregulated ClpP affects cancer cell viability and proliferation. [Display omitted] •TR compounds have nanomolar binding affinity for human mitochondrial ClpP protease•TR compounds have great shape and charge complementary with their binding sites•TR compounds target ClpP and exhibit antiproliferative activity on cancer cells•N-terminome analysis reveals cellular changes caused by TR-induced ClpP activation Mabanglo et al. describe compounds, named TRs, targeting human mitochondrial ClpP protease with nanomolar affinity. Co-crystal structures with ClpP demonstrate excellent shape and charge complementarity of TR compounds with their binding site on ClpP. The compounds activate ClpP, resulting in nonspecific protein degradation leading to antiproliferative activity on cancer cells.