Abstract
Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels mediating fundamental physiological activities in the nervous system and have become important targets for drug design. For a long time, the acetylcholine binding protein (AChBP) has been used as a surrogate to study the nAChR structure-function. Taking advantage of more than 100 AChBP crystal structures in the Protein DataBank (PDB), we explored the relationship between the size, efficiency, and efficacy of nAChR ligands and the C-loop movement. We found that the size of the ligand is correlated with the opening of the C-loop, which can be used in selecting AChBP crystal structures with appropriate C-loop opening to be used for nAChR ligand docking. Ligand size and C-loop opening are reversely correlated with the ligand efficiency rather than the binding affinity. Ligand efficiency could be accurately predicted using simple computational docking, giving a correlation coefficients (R2) up to 0.73. The efficacy of nAChR ligands might be related to ligand size, C-loop opening, and ligand efficiency. Results from this study are useful for engineering the binding affinity and efficacy of nAChR ligands.
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