8I7X

Crystal structure of human ClpP in complex with ZG36

Summary for 8I7X

• Entry DOI: 10.2210/pdb8i7x/pdb
• Descriptor: ATP-dependent Clp protease proteolytic subunit, mitochondrial, (6S,9aS)-N-[(4-bromophenyl)methyl]-6-[(2S)-butan-2-yl]-8-[(4-methoxynaphthalen-1-yl)methyl]-4,7-bis(oxidanylidene)-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide (3 entities in total)
• Functional Keywords: mitochondrial protease, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 14
• Total formula weight: 347164.30

Authors

Wang, P.Y.,Gan, J.H.,Yang, C.-G. (deposition date: 2023-02-02, release date: 2023-07-19, Last modification date: 2024-05-29)

Primary citation

Zhang, R.,Wang, P.,Wei, B.,Chen, L.,Song, X.,Pan, Y.,Li, J.,Gan, J.,Zhang, T.,Yang, C.G.
Assessment of the structure-activity relationship and antileukemic activity of diacylpyramide compounds as human ClpP agonists.
Eur.J.Med.Chem., 258:115577-115577, 2023

PubMed Abstract: Human caseinolytic protease P (ClpP) is required for the regulatory hydrolysis of mitochondrial proteins. Allosteric ClpP agonists dysfunctionally activate mitochondrial ClpP in antileukemic therapies. We previously developed ZG111, a potent ClpP agonist derived from ICG-001, inhibits the proliferation of pancreatic ductal adenocarcinoma cell lines in vitro and in vivo by degrading respiratory chain complex proteins. Herein, we studied the structure-activity relationships of ICG-001 analogs as antileukemia agents. Compound ZG36 exhibited improved stabilization effects on the thermal stability of ClpP in acute myeloid leukemia (AML) cell lines compared with the stabilization effects of ZG111, indicating a direct binding between ZG36 and ClpP. Indeed, the resolved ZG36/ClpP structural complex reveals the mode of action of ZG36 during ClpP binding. Compound ZG36 nonselectively degrades respiratory chain complexes and decreases the mitochondrial DNA, eventually leading to the collapse of mitochondrial function and leukemic cell death. Finally, ZG36 treatment inhibited 3-D cell growth in vitro and suppressed the tumorigenesis of AML cells in xenografted mice models. Collectively, we developed a new class of human ClpP agonists that can be used as potential antileukemic therapies.

PubMed: 37352796
DOI: 10.1016/j.ejmech.2023.115577

Experimental method

X-RAY DIFFRACTION (1.99 Å)