Blockade of Neuronal α7-nAChR by α-Conotoxin ImI Explained by Computational Scanning and Energy Calculations

α-Conotoxins potently inhibit isoforms of nicotinic acetylcholine receptors (nAChRs), which are essential for neuronal and neuromuscular transmission. They are also used as neurochemical tools to study nAChR physiology and are being evaluated as drug leads to treat various neuronal disorders. A number of experimental studies have been performed to investigate the structure-activity relationships of conotoxin/nAChR complexes. However, the structural determinants of their binding interactions are still ambiguous in the absence of experimental structures of conotoxin-receptor complexes. In this study, the binding modes of α-conotoxin ImI to the α7-nAChR, currently the best-studied system experimentally, were investigated using comparative modeling and molecular dynamics simulations. The structures of more than 30 single point mutants of either the conotoxin or the receptor were modeled and analyzed. The models were used to explain qualitatively the change of affinities measured experimentally, including some nAChR positions located outside the binding site. Mutational energies were calculated using different methods that combine a conformational refinement procedure (minimization with a distance dependent dielectric constant or explicit water, or molecular dynamics using five restraint strategies) and a binding energy function (MM-GB/SA or MM-PB/SA). The protocol using explicit water energy minimization and MM-GB/SA gave the best correlations with experimental binding affinities, with an R2 value of 0.74. The van der Waals and non-polar desolvation components were found to be the main driving force for binding of the conotoxin to the nAChR. The electrostatic component was responsible for the selectivity of the various ImI mutants. Overall, this study provides novel insights into the binding mechanism of α-conotoxins to nAChRs and the methodological developments reported here open avenues for computational scanning studies of a rapidly expanding range of wild-type and chemically modified α-conotoxins. Author Summary: Conotoxins are peptide toxins extracted from the venom of carnivorous marine cone snails. Members of the α-conotoxin subfamily potently block nicotinic acetylcholine receptors (nAChRs), which are involved in signal transmission between two neurons or between neurons and muscle fibers. nAChRs are important pharmacological targets due to their involvement in the transmission of pain stimuli and also in numerous neurone diseases and disorders. Their potency and specificity have led to the development of α-conotoxins as drug leads, and also to their use in the investigation of the role of nAChRs in various physiological processes. The most studied conotoxin/nAChR system, ImI/α7, was modeled in this study, and several computational methods were tested for their ability to explain the perturbations observed experimentally after introducing single point mutations into either ImI or the α7 receptor. The aim of this study was to establish a theoretical basis to rapidly identify new α-conotoxin mutants that might have improved specificity and affinity for a given receptor subtype. Furthermore, hundreds of thousands of conotoxins are predicted to exist, and computational methods are needed to help streamline the discovery of their molecular targets.