Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel

Significance Voltage-gated sodium (Nav) channels control neuronal signaling and are key targets for local anesthetics, antiepileptics, and therapeutics for a range of disorders. Multimicrosecond Anton simulations have provided completely unbiased molecular-level views of the interactions of lipophilic drugs with the recently solved bacterial channel, NavAb from Arcobacter butzleri. Newly parameterized benzocaine and phenytoin molecules exhibit different membrane partition coefficients, crossing rates and distributions around the channel, leading to the identification of distinct high- and low-affinity sites. We observe a minimum free energy pathway through membrane-bound fenestrations to a pore-blocking location, or from aqueous solution directly through the (closed) intracellular gate. These observations help explain experimental data and provide insight into Nav inhibition processes that will assist future drug development. Voltage-gated sodium (Nav) channels are important targets in the treatment of a range of pathologies. Bacterial channels, for which crystal structures have been solved, exhibit modulation by local anesthetic and anti-epileptic agents, allowing molecular-level investigations into sodium channel-drug interactions. These structures reveal no basis for the “hinged lid”-based fast inactivation, seen in eukaryotic Nav channels. Thus, they enable examination of potential mechanisms of use- or state-dependent drug action based on activation gating, or slower pore-based inactivation processes. Multimicrosecond simulations of NavAb reveal high-affinity binding of benzocaine to F203 that is a surrogate for FS6, conserved in helix S6 of Domain IV of mammalian sodium channels, as well as low-affinity sites suggested to stabilize different states of the channel. Phenytoin exhibits a different binding distribution owing to preferential interactions at the membrane and water–protein interfaces. Two drug-access pathways into the pore are observed: via lateral fenestrations connecting to the membrane lipid phase, as well as via an aqueous pathway through the intracellular activation gate, despite being closed. These observations provide insight into drug modulation that will guide further developments of Nav inhibitors.