Determinants for α4β2 vs. α3β4 Subtype Selectivity of Pyrrolidine-Based nAChRs Ligands: A Computational Perspective with Focus on Recent cryo-EM Receptor Structures

The selectivity of alpha 4 beta 2 nAChR agonists over the alpha 3 beta 4 nicotinic receptor subtype, predominant in ganglia, primarily conditions their therapeutic range and it is still a complex and challenging issue for medicinal chemists and pharmacologists. Here, we investigate the determinants for such subtype selectivity in a series of more than forty alpha 4 beta 2 ligands we have previously reported, docking them into the structures of the two human subtypes, recently determined by cryo-electron microscopy. They are all pyrrolidine based analogues of the well-known alpha 4 beta 2 agonist N-methylprolinol pyridyl ether A-84543 and differ in the flexibility and pattern substitution of their aromatic portion. Indeed, the direct or water mediated interaction with hydrophilic residues of the relatively narrower beta 2 minus side through the elements decorating the aromatic ring and the stabilization of the latter by facing to the not conserved beta 2-Phe119 result as key distinctive features for the alpha 4 beta 2 affinity. Consistently, these compounds show, despite the structural similarity, very different alpha 4 beta 2 vs. alpha 3 beta 4 selectivities, from modest to very high, which relate to rigidity/extensibility degree of the portion containing the aromatic ring and to substitutions at the latter. Furthermore, the structural rationalization of the rat vs. human differences of alpha 4 beta 2 vs. alpha 3 beta 4 selectivity ratios is here proposed.