What makes subtypes of dopamine receptor different?

Purpose: Selective targeting of different subtypes of dopamine receptors is a strategy for fighting many neurological disorders such as Parkinson’s disease and drug addiction. It has been shown that simultaneous targeting of the dopamine orthosteric binding site and a nearby allosteric site with “bitropic” ligands can enhance the selectivity of ligands for a specific receptor subtype. We hypothesize that there are regions and residues in each receptor structure, which makes it targetable for selective compounds. We aim to identify these regions and residues with molecular dynamics (MD) simulations. Methods: We have generated over 360 microseconds of MD simulations of free D2 and D3 receptor subtypes and their complex with five different compounds. The structure and dynamics of the receptor and ligands, and their interactions are analyzed in atomistic level to highlight the differences. Results: The MD simulations highlighted some differences in dynamics of the receptor subtypes in free form. Also, it is shown that the binding affinities of the bitropic ligands are enhanced compared with their orthosteric counterparts with both 1) excluding more solvent from the binding sites, and 2) making interaction with more residues in the allosteric site. The first extracellular loop (ECL1) is a very important site of allosteric interaction in D2 subtype vs. the second extracellular loop (ECL2) for D3 subtype. A specific interaction that makes ligands selective for D2 receptor is the pi-stacking interaction and hydrogen bonding with a tryptophan residue located in the ECL2, whereas in D3, hydrogen bonding with a cysteine and a serine in ECL1 is important. Conclusions: We have identified important residues and regions in D2 and D3 that make these receptor subtypes respond differently to various ligands. We have also shown how two very closely related and similarly structures GPCR receptors have different dynamics in free form and in complex with drug-like compounds.