Neurotransmitter and psychostimulant recognition by the dopamine transporter

Abstract

Na+/Cl−-coupled biogenic amine transporters are the primary targets of therapeutic and abused drugs, ranging from antidepressants to the psychostimulants cocaine and amphetamines, and to their cognate substrates. Here we determine x-ray crystal structures of the Drosophila melanogaster dopamine transporter (dDAT) bound to its substrate dopamine (DA), a substrate analogue 3,4-dichlorophenethylamine, the psychostimulants D-amphetamine, methamphetamine, or to cocaine and cocaine analogues. All ligands bind to the central binding site, located approximately halfway across the membrane bilayer, in close proximity to bound sodium and chloride ions. The central binding site recognizes three chemically distinct classes of ligands via conformational changes that accommodate varying sizes and shapes, thus illustrating molecular principles that distinguish substrates from inhibitors in biogenic amine transporters.

Combined in vitro and in silico approaches to the assessment of stimulant properties of novel psychoactive substances – The case of the benzofuran 5-MAPB

“…These observations are similar to those reported from the recent dDAT crystal structures (Wang et al, 2015). In fact all reported poses of these docked compounds preserve ~3Å-4Å separation between Y156 and D79.…”

“…We augment our ligand binding and functional data with structural results from computational molecular modelling, docking studies and atomistic molecular dynamics simulations, which have been previously shown to be robust methods for predicting the binding sites of various psychostimulants at human DAT (hDAT) in relation to the substrate binding site (Beuming et al, 2008;Bisgaard et al, 2011). We present here, on the basis of the crystal structure from Drosophila melanogaster dopamine transporter (dDAT) (PDB ID: 4XP1) (Wang et al, 2015), a molecular model of 5-MAPB bound to rat DAT (rDAT), in comparison with that of dopamine, amphetamine, 5-APB, MDMA, cocaine and RTI-121 also bound to rDAT. Our studies compare the structural changes produced by various ligands binding to rDAT to the already ongoing work in hDAT models (Hamilton et al, 2013;Hansen et al, 2014;Khelashvili et al, 2015aKhelashvili et al, , 2015b since it is the primary animal model used in functional studies and pre-clinical drug abuse testing.…”

“…The construction of the homology model of rDAT (rDAT dDAT ) in complex with dopamine uses established protocols previously described for the construction of a human DAT (hDAT) model (Hamilton et al, 2013;Hansen et al, 2014;Khelashvili et al, 2015aKhelashvili et al, , 2015b. Briefly, as the template, the homology model uses the recent crystal structure of the neurotransmitter sodium symporter (NSS) DAT from Drosophila melanogaster (dDAT) bound to dopamine (PDB ID: 4XP1) (Wang et al, 2015). www.schrodinger.com.…”

“…These models were based on the high-resolution structure of the Drosophila melanogaster dopamine transporter, dDAT, bound to the neurotransmitter dopamine (PDB ID: 4XP1) (Wang et al, 2015) and a refined structure-based sequence alignment of neurotransmitter…”

“…The chemical structures of cocaine and amphetamine were extracted from the crystallographic structures of dDAT (Wang et al, 2015); hydrogen atoms were added and the most favorable protonation state was calculated with Protein Preparation Wizard. The cocaine scaffold was manipulated in the Build module of Schrödinger Release 2016-2, to add and remove atoms to produce RTI-121, followed by the same treatment in the Protein Preparation…”