Mitochondria‐Targeting Moieties Based on N‐Tethered Pyridinium Cations

Mitochondria‐targeting moieties (MTMs) are molecular fragments designed to deliver covalently tethered functional cargo to mitochondria, providing a modular strategy for chemical biology tools, imaging agents, and mitochondria‐targeted therapies. Phosphonium‐ or nitrogen cation‐based MTMs are not inert vectors and exhibit intrinsic bioactivity on mitochondrial and cellular levels to various extents. Here, we systematically evaluated a panel of N + ‐based cations to determine how structural features influence subcellular distribution and inherent bioactivity. Live‐cell imaging of fluorescent dye conjugates revealed that 3,5‐diphenylpyridinium (DPPy + ) exhibits cellular uptake and mitochondrial targeting comparable to the benchmark triphenylphosphonium (TPP + ), whereas conjugates with unsubstituted pyridinium preferentially accumulate in lysosomes. Profiling of inert cargo derivatives showed that DPPy + has lower intrinsic activity on mitochondrial membrane potential and oxidative phosphorylation, as well as on cellular respiration and viability than TPP + . The combination of efficient mitochondrial delivery and low intrinsic bioactivity translated to bioactive cargo: a Kv1.3 inhibitor conjugate with DPPy + induced apoptosis in cancer cell lines and demonstrated improved cancer selectivity relative to the TPP + conjugate in pancreatic organoid models. These results position lipophilic pyridinium cations as effective TPP + surrogates with enhanced biocompatibility for mitochondria‐targeted therapeutic and diagnostic agents, while revealing the structure‐dependent competing lysosomal accumulation of permanent nitrogen cations.