Development of High-Efficiency Mitochondrial Protease Targeting Chimeras (MtPTACs) for Targeted Degradation of POLRMT and Beyond

Abstract Despite the broad success of targeted protein degradation (TPD), achieving efficient degradation within mitochondria remains a challenge. Herein, we report a highly active degrader targeting human mitochondrial RNA polymerase (POLRMT) based on the Mitochondrial Protease Targeting Chimeras (MtPTACs) strategy. The lead compound, MTP-B1, is a highly potent MtPTAC to achieve essentially complete target degradation (Dmax > 98%) within 24 h at sub-micromolar concentrations. Mechanistically, MTP-B1 circumvents the compensatory transcriptional upregulation induced by POLRMT inhibitors and sustains downstream signaling suppression in washout assays. Remarkably, under the dosing regimens tested, MTP-B1 exhibited greater in vivo antitumor efficacy than the co-administration of a POLRMT inhibitor and a ClpP activator, highlighting the therapeutic potential of targeted protein degradation in mitochondria. These findings, further supported by the extension to a second target, dihydroorotate dehydrogenase (DHODH), provide high-efficiency MtPTACs as a powerful and generalizable modality for mitochondrial medicine.