Conformational analysis, molecular shape comparison, and pharmacophore identification of different allosteric modulators of muscarinic receptors

Structurally dissimilar compounds such as alcuronium and the newly synthesized substances derived from the bisbenzyl ether TMB4 and from hexamethonium stabilize antagonist binding to M(2)-cholinoceptors which is indicative of an allosteric action. in order to propose a hypothesis for the common pharmacophore and the corresponding active conformations, seven flexible compounds in a data set were individually aligned onto the most active and, additionally, rigid alcuronium molecule using a torsional angle flexible fit. An S-shape conformation was found to be a plausible general active conformation. In a subsequent molecular shape analysis the overlap and the nonoverlap steric volumes, RMS alignment as well as electrostatic field potentials were employed as possible structure-activity correlation descriptors. The corresponding 3D-QSAR formulation exhibits a correlation between allosteric modulation potency and the nonoverlap steric volume as well as the proton and oxygen anion probe electrostatic field potentials. Because of large structural diversity among the small number of compounds studied, the apparent 3D-QSAR is best thought of as a convenient representation of the common spatial pharmacophore hypothesis.