ClpP-based MtPTAC technology enables targeted degradation of inner mitochondrial membrane proteins

Mitochondrial proteostasis is essential for tumorigenesis, and mitochondrial inner membrane proteins have emerged as meaningful targets due to their crucial functions in regulating apoptosis, maintaining oxidative phosphorylation, and influencing tumor initiation and progression. Targeted protein degradation (TPD) has garnered significant attention as a promising therapeutic approach. However, conventional TPD platforms relying on the ubiquitin-proteasome system or lysosomal pathways encounter inherent obstacles in targeting proteins sequestered within the mitochondrial compartment and cannot degrade mitochondrial inner membrane proteins. Utilizing our previously established MtPTAC system, we selected dihydroorotate dehydrogenase (DHODH), the rate-limiting enzyme in de novo pyrimidine biosynthesis, as a model substrate. We designed and synthesized a series of degraders, with 3D-2 achieving over 50 % degradation efficiency of DHODH via the ClpP protease. This degrader can form a stable ternary complex with DHODH and ClpP, and it exhibits significant inhibitory effects across various tumor cell lines. This technological innovation is the first to successfully degrade endogenous mitochondrial inner membrane proteins. It provides a diverse toolkit for investigating mitochondrial protein functions and paving the way for novel anticancer therapies.