A Complete Assessment of Dopamine Receptor- Ligand Interactions Through Computational Methods

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A Complete Assessment of Dopamine Receptor- Ligand Interactions Through Computational Methods molecules Article A Complete Assessment of Dopamine Receptor- Ligand Interactions through Computational Methods Beatriz Bueschbell 1 , Carlos A. V. Barreto 2 , António J. Preto 2, Anke C. Schiedel 1 and Irina S. Moreira 2,3,* 1 PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, D-53121 Bonn, Germany; [email protected] (B.B.); [email protected] (A.C.S.) 2 Center for Neuroscience and Cell Biology, UC- Biotech Parque Tecnológico de Cantanhede, Núcleo 04, Lote B, 3060-197 Cantanhede, Portugal; [email protected] (C.A.V.B.); [email protected] (A.J.P.) 3 Institute for Interdisciplinary Research, University of Coimbra, 3004-531 Coimbra, Portugal * Correspondence: [email protected]; Tel.: +351-231-249-730 Received: 5 February 2019; Accepted: 23 March 2019; Published: 27 March 2019 Abstract: Background: Selectively targeting dopamine receptors (DRs) has been a persistent challenge in the last years for the development of new treatments to combat the large variety of diseases involving these receptors. Although, several drugs have been successfully brought to market, the subtype-specific binding mode on a molecular basis has not been fully elucidated. Methods: Homology modeling and molecular dynamics were applied to construct robust conformational models of all dopamine receptor subtypes (D1-like and D2-like). Fifteen structurally diverse ligands were docked. Contacts at the binding pocket were fully described in order to reveal new structural findings responsible for selective binding to DR subtypes. Results: Residues of the aromatic microdomain were shown to be responsible for the majority of ligand interactions established to all DRs. Hydrophobic contacts involved a huge network of conserved and non-conserved residues between three transmembrane domains (TMs), TM2-TM3-TM7. Hydrogen bonds were mostly mediated by the serine microdomain. TM1 and TM2 residues were main contributors for the coupling of large ligands. Some amino acid groups form electrostatic interactions of particular importance for D1R-like selective ligands binding. Conclusions: This in silico approach was successful in showing known receptor-ligand interactions as well as in determining unique combinations of interactions, which will support mutagenesis studies to improve the design of subtype-specific ligands. Keywords: dopamine receptors; molecular docking; molecular dynamics; receptor-ligand interactions 1. Introduction 1.1. Dopamine Receptors The dopaminergic system has been intensively studied over the past 75 years due to the (patho)physiological role in modulating cognitive and motor behaviour [1,2]. The importance of dopamine has dramatically emerged from being just an intermediate in the formation of noradrenaline to having a celebrity status as the most important mammalian neurotransmitter [3]. Dopamine binds to five distinct dopamine receptors (DRs; D1–5 Receptor), grouped into two classes —D1-like and D2-like receptors— that differ in their physiological effects and signal transduction. The D1-like receptors, D1R and D5R, are principally coupled to Gs proteins and enhance the activity of adenylyl-cyclase, whereas D2-like receptors, D2–4R, are primarily coupled to inhibitory Gi proteins and suppress the activity of adenylyl cyclases [1,4]. The DRs belong to the G Protein-Coupled Receptor family (GPCRs), the largest and most diverse protein family in humans with approximately 800 members [5,6]. Molecules 2019, 24, 1196; doi:10.3390/molecules24071196 www.mdpi.com/journal/molecules Molecules 2019, 24, x FOR PEER REVIEW 2 of 26 adenylyl-cyclase, whereas D2-like receptors, D2–4R, are primarily coupled to inhibitory Gi proteins andMolecules suppress2019, 24 ,the 1196 activity of adenylyl cyclases [1,4]. The DRs belong to the G Protein-Coupled2 of 26 Receptor family (GPCRs), the largest and most diverse protein family in humans with approximately 800 members [5,6]. GPCRs share a conserved overall fold of seven transmembrane helices (TMs) GPCRs share a conserved overall fold of seven transmembrane helices (TMs) linked by three linked by three intracellular loops (ICLs) and three extracellular loops (ECLs). Around 30–40% of all intracellular loops (ICLs) and three extracellular loops (ECLs). Around 30–40% of all available available pharmacotherapeutics target this protein family [7]. pharmacotherapeutics target this protein family [7]. Many severe neuropsychiatric and neurodegenerative disorders such as Tourette’s syndrome, Many severe neuropsychiatric and neurodegenerative disorders such as Tourette’s syndrome, schizophrenia, Parkinson’s disease and Huntington’s disease are believed to occur as a result of schizophrenia, Parkinson’s disease and Huntington’s disease are believed to occur as a result imbalances and alterations in dopamine signaling [8–10]. Moreover, also a wide array of psychiatric of imbalances and alterations in dopamine signaling [8–10]. Moreover, also a wide array of disorders such as hallucinations, paranoia, bipolar disorder, gambling, alcoholism, mania, psychiatric disorders such as hallucinations, paranoia, bipolar disorder, gambling, alcoholism, mania, depression, eating disorders, movement and hyperactivity disorders are linked to malfunctioning depression, eating disorders, movement and hyperactivity disorders are linked to malfunctioning dopaminergic transmission [3,11–13]. The discovery of chlorpromazine, the first antipsychotic drug, dopaminergic transmission [3,11–13]. The discovery of chlorpromazine, the first antipsychotic in the 1950s, was the hallmark of the development of a collection of antipsychotics [14] which were drug, in the 1950s, was the hallmark of the development of a collection of antipsychotics [14] later reported to commonly bind to the D2R subtype (with different affinity) [4,11]. The “first- which were later reported to commonly bind to the D2R subtype (with different affinity) [4,11]. generation/classical” antipsychotics came along with significant motor side effects such as tardive The “first-generation/classical” antipsychotics came along with significant motor side effects such dyskinesia, extrapyramidal symptoms and related conditions. These problems were not eliminated as tardive dyskinesia, extrapyramidal symptoms and related conditions. These problems were not in “second-generation/atypical” antipsychotics, and others such as weight gain and the “metabolic eliminated in “second-generation/atypical” antipsychotics, and others such as weight gain and the syndrome” also appeared [11,15–17]. It was then later discovered that these multiple clinical and “metabolic syndrome” also appeared [11,15–17]. It was then later discovered that these multiple clinical adverse effects of several antipsychotics depended on the combination of occupied receptors from and adverse effects of several antipsychotics depended on the combination of occupied receptors from other systems such as cholinergic, histaminergic and serotoninergic receptors (but always including other systems such as cholinergic, histaminergic and serotoninergic receptors (but always including the the D2R) resulting in non-selective profiles and therefore in an insufficient explanation of the D R) resulting in non-selective profiles and therefore in an insufficient explanation of the mechanism mechanism2 of action [11,15]. Until today, no drug has yet been identified with antipsychotic action of action [11,15]. Until today, no drug has yet been identified with antipsychotic action without without a significant affinity for the D2R [15]. However, antipsychotics remain a necessary first-line a significant affinity for the D R[15]. However, antipsychotics remain a necessary first-line treatment treatment for the management2 of a variety of the already mentioned psychiatric disorders (Figure 1). for the management of a variety of the already mentioned psychiatric disorders (Figure1). In fact, In fact, it is difficult to directly target one of these diseases with one specific antipsychotic, since there it is difficult to directly target one of these diseases with one specific antipsychotic, since there are are also numerous cases of non-responding patients to first-line or any antipsychotic treatment or also numerous cases of non-responding patients to first-line or any antipsychotic treatment or which which become resistant to treatment over time [11,18]. become resistant to treatment over time [11,18]. Figure 1. Examples for first-line treatments of neurological diseases and selective dopamine receptor Figure 1. Examples for first-line treatments of neurological diseases and selective dopamine receptor ligands. Drugs are classified in typical and atypical antipsychotics [19]. The targets of the selective ligands.ligands haloperidole,Drugs are classified 7-OH-DPAT, in typical SCH23390 and atypical and SKF38393 antipsychotics were colored [19]. The in blue. targets of the selective ligands haloperidole, 7-OH-DPAT, SCH23390 and SKF38393 were colored in blue. The search for DR subtype selective (foremost D2R-selective) therapeutics is an ongoing field of research [15] as current drugs have D2R/D3R-affinity or affinity for all DRs [19,20]. It has been proposed Molecules 2019, 24, 1196 3 of 26 that substituted 4-phenylpiperazine compounds distinguish between D3R and D2R selectivity [21,22]. In addition, the aminotetraline derivative 7-OH-DPAT was identified as a selective D3R agonist [23,24], whereas it was shown that most D4R available therapeutics are not selective [22], with only one exception, haloperidole [25]
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