Peer-reviewedCC BY-NC-ND 4.0Nature Communications
Allosteric inhibition of human mitochondrial ClpP by hijacking the dordaviprone (ONC201) binding site
9 affiliations
- 1Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON Canada
- 2Department of Anatomy and Cell Biology, McGill University, Montréal, QC Canada
- 3Ontario Institute for Cancer Research, Toronto, ON Canada
- 4Princess Margaret Cancer Centre, University Health Network, Toronto, ON Canada
- 5Department of Chemistry, University of Toronto, Toronto, ON Canada
- 6UHN Therapeutics, Krembil Brain Institute, University Health Network, Toronto, ON Canada
- 7Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON Canada
- 8Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON Canada
- 9Centre de Recherche en Biologie Structurale (CRBS), Montréal, QC Canada
Abstract
ClpP protease maintains proteostasis in human mitochondria and is overexpressed in cancers such as acute myeloid leukemia (AML). While activators such as dordaviprone (ONC201) have reached the clinic, the development of ClpP inhibitors has been hampered by paradoxical activation upon orthosteric inhibitor binding. Here, we report a series of quinazolinone-based compounds that allosterically inhibit human ClpP with nanomolar potency. Cryo-EM and H/D exchange mass spectrometry reveal that our lead compound binds sub-stoichiometrically to a distal hydrophobic pocket ~30 Å from the active sites, disrupts a conserved inter-subunit cluster, and induces a conformational change that misaligns the catalytic triad, thereby inactivating ClpP. The binding site of our quinazolinone-based inhibitors partially overlaps with that of the activator dordaviprone. In a xenograft mouse model of leukemia, our lead compound significantly reduced tumor burden following short-term oral administration. Our findings identify a regulatory hotspot in human ClpP and a mechanistically distinct inhibition strategy.
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BibTeX
@article{goncalves2026allosteric,
title = {{Allosteric inhibition of human mitochondrial ClpP by hijacking the dordaviprone (ONC201) binding site}},
author = {Monica M. Goncalves and Adwaith B. Uday and Iain D. G. Watson and Anh M. Chau and Shiva Kalhor-Monfared and Benson Wan and Taira Kiyota and S. Quinn W. Currie and Yulia Jitkova and Yue Feng and Matthew Diamandas and Dakai Ling and Mary Ma and Ross S. Mancini and Zhezhou Wang and Matias Casás-Selves and Dhananjay Joshi and Mohammed Mohammed and Ratheesh Subramaniam and Evelyne Lima Fernandes and Yongran Yan and Neil Pomroy and Rose Hurren and Marcela Gronda and Algirdas Velyvis and Andrei K. Yudin and Mark A. Reed and Gil Prive and Ahmed Aman and Methvin Isaac and Richard Marcellus and David Uehling and Aaron D. Schimmer and Natalie Zeytuni and Siavash Vahidi},
journal = {Nature Communications},
year = {2026},
month = sep,
doi = {10.1038/s41467-026-78140-5},
url = {https://doi.org/10.1038/s41467-026-78140-5},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Allosteric inhibition of human mitochondrial ClpP by hijacking the dordaviprone (ONC201) binding site
AU - Monica M. Goncalves
AU - Adwaith B. Uday
AU - Iain D. G. Watson
AU - Anh M. Chau
AU - Shiva Kalhor-Monfared
AU - Benson Wan
AU - Taira Kiyota
AU - S. Quinn W. Currie
AU - Yulia Jitkova
AU - Yue Feng
AU - Matthew Diamandas
AU - Dakai Ling
AU - Mary Ma
AU - Ross S. Mancini
AU - Zhezhou Wang
AU - Matias Casás-Selves
AU - Dhananjay Joshi
AU - Mohammed Mohammed
AU - Ratheesh Subramaniam
AU - Evelyne Lima Fernandes
AU - Yongran Yan
AU - Neil Pomroy
AU - Rose Hurren
AU - Marcela Gronda
AU - Algirdas Velyvis
AU - Andrei K. Yudin
AU - Mark A. Reed
AU - Gil Prive
AU - Ahmed Aman
AU - Methvin Isaac
AU - Richard Marcellus
AU - David Uehling
AU - Aaron D. Schimmer
AU - Natalie Zeytuni
AU - Siavash Vahidi
PY - 2026
DA - 2026/09/28
JO - Nature Communications
DO - 10.1038/s41467-026-78140-5
UR - https://doi.org/10.1038/s41467-026-78140-5
AB - ClpP protease maintains proteostasis in human mitochondria and is overexpressed in cancers such as acute myeloid leukemia (AML). While activators such as dordaviprone (ONC201) have reached the clinic, the development of ClpP inhibitors has been hampered by paradoxical activation upon orthosteric inhibitor binding. Here, we report a series of quinazolinone-based compounds that allosterically inhibit human ClpP with nanomolar potency. Cryo-EM and H/D exchange mass spectrometry reveal that our lead compound binds sub-stoichiometrically to a distal hydrophobic pocket ~30 Å from the active sites, disrupts a conserved inter-subunit cluster, and induces a conformational change that misaligns the catalytic triad, thereby inactivating ClpP. The binding site of our quinazolinone-based inhibitors partially overlaps with that of the activator dordaviprone. In a xenograft mouse model of leukemia, our lead compound significantly reduced tumor burden following short-term oral administration. Our findings identify a regulatory hotspot in human ClpP and a mechanistically distinct inhibition strategy.
SN - 2041-1723
ER -