Differences in the binding of Local Anaesthetics and Anti-Epileptics in the inactivated state of the human sodium channel Nav1.4.

Voltage-gated sodium channels play a vital role in nerve and muscle cells, enabling them to encode and transmit electrical signals. Currently, there exist several classes of drugs that aim to inhibit these channels for therapeutic purposes, including local anaesthetics, anti-epileptics and anti-arrhythmics. However, sodium channel inhibiting drugs lack subtype specificity; instead, they inhibit all sodium channels in the human body. Improving understanding of the mechanisms of binding of existing non-selective drugs is important in providing insight into how subtype-selective drugs could be developed. This study used molecular dynamics simulations to investigate the binding of the anti-epileptics carbamazepine and lamotrigine, and the local anaesthetic lidocaine in neutral and charged states, to the recently resolved human Nav1.4 channel. Replica exchange solute tempering was used to enable greater sampling of each compound within the pore. It was found that all four compounds show similarities in their binding sites within the pore. However, the positions of the carbamazepine and lamotrigine did not occlude the centre of the pore, but preferentially bound to DII and DIII. The charged and neutral forms of lidocaine positioned themselves more centrally in the pore, with more common interactions to DIV. The best localised binding site was for charged lidocaine, whose aromatic moiety interacted with Y1593 while the amine projected toward the selectivity filter. Comparisons to our previous simulations and published structures highlight potential differences between tonic and use-dependent block related to conformational changes occurring in the pore.