Identification and structural characterization of small-molecule inhibitors of PINK1

Abstract

Mutations in PTEN-induced putative kinase 1 (PINK1) cause early-onset autosomal recessive Parkinsons Disease (PD). PINK1 is a Ser/Thr protein kinase which functions as a mitochondrial damage sensor and initiates mitochondrial quality control by accumulating on the damaged organelle. There, it will autophosphorylate and then phosphorylate ubiquitin chains, which in turn will recruit and activate Parkin, and E3 ubiquitin ligase also implicated in PD. Ubiquitylation of mitochondrial proteins leads to the autophagic degradation of the damaged organelle. Pharmacological modulation of PINK1 constitutes an appealing avenue to study its physiological function and develop PD therapeutics. In this study, we used a thermal shift assay to identify small-molecule inhibitors of PINK1. In vitro kinase activity assays demonstrate that these molecules are ATP competitive inhibitors that block ubiquitin phosphorylation. PRT062607 (a SYK inhibitor) is the most potent inhibitor of PINK1 in our screen and has an IC50 of 2 M against insect PINK1 and 1 M in HeLa cells expressing human PINK1. The crystal structures of PINK1 in complex with PRT062607 or CYC116 reveal how the compounds interact with the ATP-binding pocket. PRT062607 notably engages with the catalytic aspartate (type-1 inhibition) and causes a destabilization of insert-2 at the autophosphorylation dimer interface. Our findings provide a scaffold for the development of more selective and potent inhibitors of PINK1 that can be used as chemical probes.