Structure-based identification of novel KNa1.1 inhibitors

Several types of drug-resistant epilepsies of infancy have been associated with mutations in the KCNT1 gene, which encodes the sodium-activated potassium channel subunit KNa1.1. Approximately forty different amino acid substitutions have been identified in patients, involving both transmembrane and intracellular domains of the channel subunit, and with one exception all cause gain-of-function in channel gating. Channel inhibition, therefore, is potentially a stratified approach to treat the disorder. To date, quinidine therapy has been trialled with several patients, but mostly with unsuccessful outcomes, which have been linked to its low potency and lack of specificity; effects on cardiac ion channels being a major concern. Here we describe the use of high-resolution structures of KNa1.1 channels, generated through cryo-electron microscopy, to identify novel inhibitors using computational methods. From an initial analysis of seventeen compounds identified using this approach, we found six that inhibited KNa1.1 channels. Their IC50 values ranged between 0.6 and 7.4 μM, compared to 100 μM with quinidine, and likely inhibited through pore-blocking mechanisms. The compounds delivered varying results when evaluating state-dependence and in preliminary toxicity assays, with some demonstrating negligible cellular toxicity and low levels of hERG block. These compounds may provide starting points for the development of novel pharmacophores for KNa1.1 inhibitors, with the view to treating KCNT1-associated epilepsies. Furthermore, this illustrates the potential for utilising ion channel structures generated through cryo-electron microscopy in drug discovery.