Binding of Isoflurane to a Bacterial Voltage-Gated Sodium Channel: Structure and Accessibility of Distinct Interaction Sites

Abstract

The most likely targets for volatile anesthetics (VA) are ion channels. The mechanism of volatile anesthetic action is not completely understood. Identifying the molecular pathway for drug binding is crucial to understand the effect of VA on voltage gated sodium channels. We use Molecular Dynamics simulations to identify the binding sites for a hydrophobic general anesthetic isoflurane, on voltage gated bacterial sodium channel NaChBac. Apart from the voltage sensing domain (S1-S4), linker and the pore domain (S5-S6), bacterial sodium channels also have fenestrations, which provide a hydrophobic tunnel through the lipid-embedded portion of the channel to the central cavity, where the known local anesthetic site is located. Unbiased “flooding” simulations were performed on the activated open confirmation of NaChBac. We performed a cluster analysis to identify all the possible binding sites of isoflurane. The three most important ones among them are: a region near the selectivity filter, called the extracellular site, a region near the S4-S5 linker, called the linker site, and a region within the cavity, called the cavity site. The most important observation is that isoflurane enters the central cavity through the fenestrations. Free energy perturbation method was employed to calculate the binding affinities of isoflurane for each of these sites. We also studied the interactions between isoflurane and the amino acids in these three binding sites.