The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists

Abstract

Dopamine neurotransmitter and its receptors play a critical role in the cell signaling process responsible for information transfer in neurons functioning in the nervous system. Development of improved therapeutics for such disorders as Parkinson's disease and schizophrenia would be significantly enhanced with the availability of the 3D structure for the dopamine receptors and of the binding site for dopamine and other agonists and antagonists. We report here the 3D structure of the long isoform of the human D2 dopamine receptor, predicted from primary sequence using firstprinciples theoretical and computational techniques (i.e., we did not use bioinformatic or experimental 3D structural information in predicting structures). The predicted 3D structure is validated by comparison of the predicted binding site and the relative binding affinities of dopamine, three known dopamine agonists (antiparkinsonian), and seven known antagonists (antipsychotic) in the D2 receptor to experimentally determined values. These structures correctly predict the critical residues for binding dopamine and several antagonists, identified by mutation studies, and give relative binding affinities that correlate well with experiments. The predicted binding site for dopamine and agonists is located between transmembrane (TM) helices 3, 4, 5, and 6, whereas the best antagonists bind to a site involving TM helices 2, 3, 4, 6, and 7 with minimal contacts to TM helix 5. We identify characteristic differences between the binding sites of agonists and antagonists.W ith the implication of G protein-coupled receptor (GPCR) in many diseases (1, 2), the need to solve the highresolution 3D structure of this class of integral membrane proteins to enable structure-based drug design is an important problem in structural biology. Despite the importance of solving the structure of the GPCRs, the only experimental 3D structure available for a GPCR is bovine rhodopsin. This lack of structures is because the GPCRs are bound to the membrane, making it difficult to express in sufficient quantities for crystallization.To provide structural and ligand binding information on GPCRs, we have been developing first-principles computational techniques for predicting the 3D structure of GPCRs using only the amino acid sequence (MembStruk) and for predicting binding site and binding energy of various ligands to GPCRs (HierDock). Using these techniques, we have reported the structure of olfactory receptors (3, 4), bovine rhodopsin (4, 5), and other GPCRs (4). Dopamine neurotransmitter plays a critical role in cellular signaling processes responsible for information transfer in neurons functioning in the nervous system (6, 7). Dopamine receptors (DR) belong to the superfamily of GPCRs, and to date there are five reported sequences for the human DR with multiple isoforms for each. The DRs may be subdivided based on their pharmacological behavior into the D1-like and the D2-like subfamilies, and these are ideal targets for treating schizophrenia and Parkinson's disease; th...

Molecular cloning, expression and variation analyses of the dopamine D2 receptor gene in pig breeds in China

“…Here the SNP frequency of the pDRD2 gene is one per 80 bp, similar to previous results before correction for sample size (Jungerius et al, 2005). Structure analysis of the human DRD2 showed that, Asp114 in TM III and Phe390 in TM VI were essential for its binding to dopamine (Shi and Javitch, 2002;Kalani et al, 2004). In this study, the mutation Phe390Tyr might have altered the affinity of pig DRD2 to its ligand.…”

Prediction of the 3-D structure of rat MrgA G protein-coupled receptor and identification of its binding site

“…The MembStruk and HierDock protocols have also been applied to other GPCRs including bovine rhodopsin receptor [10], human dopamine D2 receptor [13], human β2 adrenergic receptor [14] and several olfactory receptors [15][16][17]. In each case the key interactions observed in the experiments are identified from our prediction, validating that these methods can predict the 3D structures of the proteins and the binding sites of strongly bound ligands to these sites.…”

“…This protocol has been used for several GPCRs [9,10,13,14,16,27,28], outer membrane protein A [29], and globular proteins [15,[30][31][32][33][34]. In this paper we used the modified HierDock protocol (MSCdock) described in Cho et al 2005 [35].…”

Biospectra Analysis: Model Proteome Characterizations for Linking Molecular Structure and Biological Response

“…Bioassay composition, in turn, was based on achieving representation of a wide range of functionally diverse proteins (Supporting Information) reflecting major constituents of the drugable proteome. These selection criteria provided a bioassay array configuration containing receptors for dopamine subtypes D 1 -D 4 , as well as other biogenic-amine receptors. Assessment of functional response capacity of molecules relied on published reports by others documenting the functional activity of specific dopamine ligands.…”

“…4 Alteration in biological signal transduction through these receptors is implicated in neurological and psychiatric disorders and normal aging. Targeting these sites with agonists or antagonists has been a longstanding focus in therapeutic intervention.…”