Molecular simulation study of the unbinding of alpha-conotoxin [Upsilon 4E]GID at the alpha 7 and alpha 4 beta 2 neuronal nicotinic acetylcholine receptors

The alpha 7 and alpha 4 beta 2 neuronal nicotinic receptors belonging to the family of ligand-gated ion channels are most prevalent in the brain, and are implicated in various neurodegenerative disorders. alpha-conotoxin GID (and its analogue [Upsilon 4E]GID) specifically inhibits these subtypes, with more affinity towards the human alpha 7 (h alpha 7) subtype, and is valuable in understanding the physiological roles of these receptors. In this study, we use umbrella-sampling molecular dynamics simulations to understand the mechanism of interaction between [Upsilon 4E]GID and the agonist binding pockets of the alpha 4 beta 2 and the h alpha 7 receptors, and to estimate their relative binding affinities (Delta G(bind)). The obtained Delta G(bind) values indicate stronger interaction with the h alpha 7 receptor, in agreement with previous experimental studies. Simulations also revealed different unbinding pathways between the two receptor subtypes, enabling identification of a number of interactions at locations far from the orthosteric binding site which may explain the difference in [Upsilon 4E]GID potency. The pathways identified will help in the design of novel conotoxins with increased potency at alpha 4 beta 2, for which there is currently no known highly potent conotoxin inhibitor. Computational mutational free energy analyses also revealed a number of possible single-site mutations to GID which might enhance its selective binding to alpha 4 beta 2 over alpha 7.