In Silico Study on the Ligand-Binding and Activation Mechanisms of the Human Dopamine D3 Receptor

Abstract

G-protein coupled receptors (GPCRs), one of the largest protein families in the human genome, are responsible for a vast majority of physiological responses. Activation of dopamine G-protein-coupled receptors in the central nervous system (CNS) regulates movement, cognition, and emotion. Dysfunction of these receptors may lead to diseases such as attention-deficit hyperactivity disorder (ADHD), Tourette's syndrome, Parkinson's disease, and schizophrenia.Due to lack of the hD3R N-terminal domain and in hope of better understanding its role in ligand binding, homology modeling was utilized by using sphingosine 1-phosphate receptor 1 (S1P1) as a template (32.3% similarity). The modeled N-terminus was then combined with the previously resolved hD3R to form a new hD3R. Docking different types of ligands, 7-OH-DPAT, dopamine, Eticlopride, and Haloperidol, with hD3R, we attempted to stimulate conformational alterations to the receptor's active/inactive forms. Each system was run for more than 500 ns molecular dynamics (MD) simulations to study conformational changes accordant with receptor activation. For the dopamine-hD3R complex, significant structural changes were observed. Including the ∼8A outward tilt of TM6, measured by the distance between Arg1283.50 and Thr3286.34 Cα atoms, as well as the ∼5A gradual nearing of Tyr2085.58 and Tyr3837.53 Cα atoms, both of which are consistent with previous studies and may potentially demonstrate the tendency of receptor activation. MM/PBSA binding free energy calculations showed the best affinity for Haloperidol, followed by Eticlopride, 7-OH-DPAT, and then dopamine. Interestingly, during MD simulations, we found that for agonist bound systems, the N-terminus of hD3R lay flat on the binding site opening, whereas for antagonist and inverse agonist bound systems, the N-terminus of hD3R stood upright. Elucidating the molecular mechanisms of ligand-binding and receptor activation may aid in structure-based drug and nano-medicine design.