If you are strictly talking about affinity, not efficacy, one way that affinity between a ligand and a receptor could be modified is through the presence of an allosteric modulator. So far, there are but few known endogenous allosteric modulators at GPCR and I do not know if concentration of such compounds might change in some neurological pathologies. I doubt though that an allosteric compound, by binding to a receptor and thus changing it's conformation, might purely change the affinity for orthosteric ligands without somehow altering its signalling pathways compared to what you would expect the orthosteric ligand to activate by itself.

eg. muscarinic receptors (and most class A GPCRs) have a higher affnity for ACh once bound to the endogenous G-proteins.