BPS2026 – Cryo-EM structure of mammalian ATP synthase bound to the neuroprotective drug dexpramipexole

Dexpramipexole (DEX), the R-enantiomer of the antiparkinsonian drug pramipexole, was shown to improve mitochondrial function in Amyotrophic Lateral Sclerosis (ALS) and protect against brain and cardiac ischemia/reperfusion injury. It has recently been used in clinical trials for ALS, progressing through Phase II, but failed a Phase III trial despite a favorable safety profile. Here, we report the direct binding of DEX to mitochondrial ATP synthase using ligand binding affinity (microscale thermophoresis) and single-particle cryo-electron microscopy (cryo-EM) studies. We present high-resolution cryo-EM structures of the porcine heart ATP synthase bound to DEX in two rotational states, DP and E, with a nominal resolution of 2.5 Å and 2.6 Å, respectively. In both states, DEX occupies the hydrophobic pocket at the interface of α and β subunits and binds to ATP synthase only in the presence of its intrinsic inhibitory subunit IF1. Furthermore, DEX inhibits catalytic and leak channel activities of ATP synthase in a dose-dependent manner. Our structural and single-channel electrophysiology findings provide insights into the gating mechanism of the ATP synthase leak channel and will advance the development of more potent therapeutics targeting ATP synthase to treat ALS and other neurodegenerative disorders.