BINDING-SITE MODELING OF THE MUSCARINIC M1 RECEPTOR - A COMBINATION OF HOMOLOGY-BASED AND INDIRECT APPROACHES

A model of the muscarinic ml receptor has been constructed on the basi s of the putative three-dimensional structural similarity between bact eriorhodopsin and G-protein coupled receptors. The homology-based ml r eceptor model takes into account hydrophobicity and conserved amino ac ids and information from site-directed mutagenesis studies and from hy dropathy plots. The resulting model was used in conjunction with an in direct model which describes a proposed active agonist conformation of acetylcholine and a number of related compounds. A receptor-excluded volume was constructed by superimposing these muscarinic agonists and calculating their combined van der Waals volume. The resulting m1 rece ptor excluded volume was used to define the agonist binding site, whic h consists of nine amino acids and which binds agonists primarily thro ugh interaction with Asp105 (ionic interaction), Thr192 and Asn382 (hy drogen bonds). The model is flexible since the conformation of the nin e amino acids may change in response to the agonist structure. The com bination of indirect and homology-based approaches is particularly att ractive since it utilizes more experimental data than a purely homolog y-based model and since a binding-site model might be more realistic a nd general in terms of applicability than indirect models. Docking of the ligands was performed by optimizing attractive interactions and mi nimizing repulsive interactions. In addition to the agonists used to d efine the binding site, structurally different agonists are also accom modated by the binding-site model. Furthermore, the m1 receptor bindin g-site model is able to reproduce experimentally determined stereosele ctivities.