Allosteric inhibition of human mitochondrial ClpP by hijacking the dordaviprone (ONC201) binding site

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. ClpP is a mitochondrial protease and a validated cancer target. Here, the authors develop quinazolinone compounds that bind to the same site as the FDA-approved activator ClpP dordaviprone, yet they inhibit ClpP, reducing tumor burden in leukemia mouse models.

Authors

Institutions

Publication Details

Journal
Nature Communications
Published
2026-09-28
DOI
https://doi.org/10.1038/s41467-026-78140-5
Primary Topic
Mitochondrial Function and Pathology
Type
article
Field-Weighted Citation Impact
0.00
Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
article

Allosteric inhibition of human mitochondrial ClpP by hijacking the dordaviprone (ONC201) binding site

Algirdas Vėlyvis, Taira Kiyota, Matthew Diamandas, Evelyne Lima Fernandes et al.
Nature Communications
Mitochondrial Function and Pathology
article

Allosteric inhibition of human mitochondrial ClpP by hijacking the dordaviprone (ONC201) binding site

Algirdas Vėlyvis, Taira Kiyota, Matthew Diamandas, Evelyne Lima Fernandes, Mark A. Reed, Benson Wan, Rose Hurren, Monica M. Goncalves, Ross S. Mancini, Natalie Zeytuni, Neil C. Pomroy, Aaron David Schimmer, Shiva Kalhor‐Monfared, Ahmed M. Aman, Siavash Vahidi, Iain D. G. Watson, Marcela Gronda, Anh M. Chau, Dakai Ling, Matias Casás‐Selves, Andrei K. Yudin, Ratheesh Subramaniam, Yongran Yan, Adwaith B. Uday, Yue Feng, Methvin Isaac, David Uehling, Mary Ma, Richard Marcellus, Gil Prive, Zhezhou Wang, S. Quinn W. Currie, Dhananjay Joshi, Yulia Jitkova, Mohammed Mohammed
article en

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. ClpP is a mitochondrial protease and a validated cancer target. Here, the authors develop quinazolinone compounds that bind to the same site as the FDA-approved activator ClpP dordaviprone, yet they inhibit ClpP, reducing tumor burden in leukemia mouse models.

Nature Communications
Ontario Institute for Cancer Research (CA), University Health Network (CA), University of Toronto (CA), Princess Margaret Cancer Centre (CA), Krembil Brain Institute, McGill University (CA), University of Guelph (CA)
Good health and well-being
Openalex Percentile: Top 19%
Mitochondrial Function and Pathology
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.