Recent mutagenesis experiments have identified some of the functional amino acids that are essential in the interaction of nicotinic agents with the binding site of the neural nicotinic acetylcholine receptor (nAChR). Although this receptor is one of the best studied and characterized the lack of detailed experimental information regarding its quaternary structure has turned it into a challenge for computational chemistry. We have previously reported [J. Comput. Aided Mol. Design 13 (1999) 57-68] a computational protocol based on molecular mechanics and molecular dynamics (MD) where SER82, ASP83, TRP86, ASP89, TYR93, TYR190, TYR198 and ARG209 were placed around selected agonists and antagonists aided by stereoelectronic criteria. Explicit water molecules were used with the double goal of simulating aqueous environment and keeping the system from falling apart. The protocol was stable enough to allow the ligands to evolve to their thermodynamically most probable structure while maintaining the key interactions. In this communication we use the average model for the agonists (one average structure for each agonist) to calculate quantum mechanically the interactions of the binding site with one neurotransmitter acetylcholine (ACh, 1), as well as with two of the most potent agonists described so far [nicotine (2) and epibatidine (3)] and the modeled binding site. A wide variety of methods as well as basis sets were used in order to rationalise the best way to treat the problem. In this limited set of compounds, a good correlation between total interaction energies and biological affinity is observed. © 2002 Elsevier Science Inc. All rights reserved.
- Density functional