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

Dopamine-modified hyaluronic acid (DA-HA) as a novel dopamine-mimetics with minimal autoxidation and cytotoxicity

Dopamine-modified hyaluronic acid (DA-HA) has been initially developed as an efficient coating and adhesion material for industrial uses. However, the biological activity and safety of DA-HA in the brain have not been explored yet. Here, we report a series of evidence that DA-HA exhibits similar functionality as dopamine (DA), but with much lower toxicity arising from autoxidation. DA-HA shows very little autoxidation even after 48-h incubation. This is profoundly different from DA and its derivatives including l-DOPA, which all induce severe neuronal death after pre-autoxidation, indicating that autoxidation is the cause of neuronal death. Furthermore, in vivo injection of DA-HA induces significantly lower toxicity compared to 6-OHDA, a well-known oxidized and toxic form of DA, and alleviates the apomorphine-induced rotational behavior in the 6-OHDA animal model of Parkinson's disease. Our study proposes that DA-HA with DA-like functionalities and minimal toxicity has a great potential to treat DA-related disease.

Neuroprotective Activity of Enantiomers of Salsolinol and N-Methyl-(R)-salsolinol: In Vitro and In Silico Studies

Salsolinol (1-methyl-1,2,3,4-tetrahydroisoquinoline-6,7-diol) is a close structural analogue of dopamine with an asymmetric center at the C1 position, and its presence in vivo, both in humans and rodents, has already been proven. Yet, given the fact that salsolinol colocalizes with dopamine-rich regions and was first detected in the urine of Parkinson's disease patients, its direct role in the process of neurodegeneration has been proposed. Here, we report that R and S enantiomers of salsolinol, which we purified from commercially available racemic mixture by means of high-performance liquid chromatography, exhibited neuroprotective properties (at the concentration of 50 μM) toward the human dopaminergic SH-SY5Y neuroblastoma cell line. Furthermore, within the study, we observed no toxic effect of N-methyl-(R)-salsolinol on SH-SY5Y neuroblastoma cells up to the concentration of 750 μM, either. Additionally, our molecular docking analysis showed that enantiomers of salsolinol should exhibit a distinct ability to interact with dopamine D2 receptors. Thus, we postulate that our results highlight the need to acknowledge salsolinol as an active dopamine metabolite and to further explore the neuroregulatory role of enantiomers of salsolinol.

Structural and expression analysis of the dopamine receptors reveals their crucial roles in regulating the insulin signaling pathway in oysters

Dopamine performs its critical role upon binding to receptors. Since dopamine receptors are numerous and versatile, understanding their protein structures and evolution status, and identifying the key receptors involved in the modulation of insulin signaling will provide essential clues to investigate the molecular mechanism of neuroendocrine regulating the growth in invertebrates. In this study, seven dopamine receptors were identified in the Pacific oysters (Crassostrea gigas) and were classified into four subtypes according to their protein secondary and tertiary structures, and ligand-binding activities. Of which, DR2 (dopamine receptor 2) and D(2)RA-like (D(2) dopamine receptor A-like) were considered the invertebrate-specific type 1 and type 2 dopamine receptors, respectively. Expression analysis indicated that the DR2 and D(2)RA-like were highly expressed in the fast-growing oyster "Haida No.1". After in vitro incubation of ganglia and adductor muscle with exogenous dopamine and dopamine receptor antagonists, the expression of these two dopamine receptors and ILPs (insulin-like peptides) was also significantly affected. Dual-fluorescence in situ hybridization results showed that D(2)RA-like and DR2 were co-localized with MIRP3 (molluscan insulin-related peptide 3) and MIRP3-like (molluscan insulin-related peptide 3-like) in the visceral ganglia, and were co-localized with ILP (insulin-like peptide) in the adductor muscle. Furthermore, the downstream components of dopamine signaling, including PKA, ERK, CREB, CaMKK1, AKT, and GSK3β were also significantly affected by the exogenous dopamine and dopamine receptor antagonists. These findings confirmed that dopamine might affect the secretion of ILPs through the invertebrate-specific dopamine receptors D(2)RA-like and DR2, and thus played crucial roles in the growth regulation of the Pacific oysters. Our study establishes the potential regulatory relationship between the dopaminergic system and insulin-like signaling pathway in marine invertebrates.

CovET: A covariation-evolutionary trace method that identifies protein structure-function modules

Measuring the relative effect that any two sequence positions have on each other may improve protein design or help better interpret coding variants. Current approaches use statistics and machine learning but rarely consider phylogenetic divergences which, as shown by Evolutionary Trace studies, provide insight into the functional impact of sequence perturbations. Here, we reframe covariation analyses in the Evolutionary Trace framework to measure the relative tolerance to perturbation of each residue pair during evolution. This approach (CovET) systematically accounts for phylogenetic divergences: at each divergence event, we penalize covariation patterns that belie evolutionary coupling. We find that while CovET approximates the performance of existing methods to predict individual structural contacts, it performs significantly better at finding structural clusters of coupled residues and ligand binding sites. For example, CovET found more functionally critical residues when we examined the RNA recognition motif and WW domains. It correlates better with large-scale epistasis screen data. In the dopamine D2 receptor, top CovET residue pairs recovered accurately the allosteric activation pathway characterized for Class A G protein-coupled receptors. These data suggest that CovET ranks highest the sequence position pairs that play critical functional roles through epistatic and allosteric interactions in evolutionarily relevant structure-function motifs. CovET complements current methods and may shed light on fundamental molecular mechanisms of protein structure and function.

Modulatory effects of phytol on the antiemetic property of domperidone, possibly through the D2 receptor interaction pathway: in vivo and in silico studies

The current study is designed to evaluate the antiemetic effect of the diterpenoid phytol (PHY) using in vivo and in silico studies. For this, emesis was induced in 4-day-old chicks by the oral administration of copper sulfate (CuSO4.5H2O) at 50 mg/kg. To see the possible antiemetic mechanism of PHY, we used a number of reference drugs such as domperidone (80 mg/kg), ondansetron (24 mg/kg) and hyoscine (100 mg/kg) as positive controls, while the vehicle served as a negative control group. PHY was administered orally at the doses of 50 and 75 mg/kg. Both PHY and reference drugs were given alone or in combined groups to evaluate their synergistic or antagonistic effects on the chicks. Molecular docking of PHY and reference drugs was carried out against 5HT3, D2, D3, H1, NK1, and mAChRs (M1-M5) receptors for estimating binding affinity to the receptors. Drug-receptor interactions and active sites of the receptors were observed with the aid of different computational tools. The drug-likeness and pharmacokinetics of all the drugs were predicted through the SwissADME online database. The results suggest that PHY reduces the mean number of retches and increases latency dose-dependently in the birds. In the combination groups, PHY75 showed better antiemetic effects with domperidone and ondansetron. In addition, PHY exhibited the highest binding affinity with the D2 receptor (6CM4) (- 7.3 kcal/mol). In conclusion, PHY showed an antiemetic activity in chicks, possibly through the D2 receptor interaction pathway.

Location of dopamine in lipid bilayers and its relevance to neuromodulator function

Dopamine (DA) is a neurotransmitter that also acts as a neuromodulator, with both functions being essential to brain function. Here, we present the first experimental measurement of DA location in lipid bilayers using x-ray diffuse scattering, solid-state deuterium NMR, and electron paramagnetic resonance. We find that the association of DA with lipid headgroups as seen in electron density profiles leads to an increase of intermembrane repulsion most likely due to electrostatic charging. DA location in the lipid headgroup region also leads to an increase of the cross-sectional area per lipid without affecting the bending rigidity significantly. The order parameters measured by solid-state deuterium NMR decrease in the presence of DA for the acyl chains of PC and PS lipids, consistent with an increase in the area per lipid due to DA. Most importantly, these results support the hypothesis that three-dimensional diffusion of DA to target membranes could be followed by relatively more efficient two-dimensional diffusion to receptors within those membranes.

Rational design, synthesis, and pharmacological evaluation of a cohort of novel beta-adrenergic receptors ligands enables an assessment of structure-activity relationships

Biomedical applications of molecules that are able to modulate β-adrenergic signaling have become increasingly attractive over the last decade, revealing that β-adrenergic receptors (β-ARs) are key targets for a plethora of therapeutic interventions, including cancer. Despite successes in β-AR drug discovery, identification of β-AR ligands that are useful as selective chemical tools in pharmacological studies of the three β-AR subtypes, or lead compounds for drug development is still a highly challenging task. This is mainly due to the intrinsic plasticity of β-ARs as G protein-coupled receptors in conjunction with the requirement for functional receptor subtype selectivity, tissue specificity and minimal off-target effects. With the aim to provide insight into structure-activity relationships for the three β-AR subtypes, we have synthesized and obtained the pharmacological profile of a series of structurally diverse compounds (named MC) that were designed based on the aryloxy-propanolamine scaffold of SR59230A. Comparative analysis of their predicted binding mode within the active and inactive states of the receptors in combination with their pharmacological profile revealed key structural elements that control their activity as agonists or antagonists, in addition to clues about substituents that mediate selectivity for one receptor subtype over the others. We anticipate that these results will facilitate selective β-AR drug development efforts.

Dynamic and thermodynamic impact of L94A, W100A, and W100L mutations on the D2 dopamine receptor bound to risperidone

DRD2 is an important receptor in the mediation of antipsychotic drugs but also in Parkinson medication, hyperprolactinemia, nausea and vomiting. Recently, crystallographic studies of the DRD2-risperidone complex have provided important information about risperidone recognition in wild-type and different stabilizing DRD2-risperidone residues. Using the crystallographic structure of the DRD2-risperidone complex as a starting point, we undertook molecular dynamics (MD) simulations to investigate the structural and thermodynamic basis of molecular recognition by risperidone at the ligand-binding sites of wild-type and mutant DRD2. A solvated phospholipid bilayer was used to construct DRD2-risperidone complexes, which were then subjected to several microsecond (μs) MD simulations in order to obtain realistic receptor-ligand conformations under the equilibrated simulation time. Risperidone had a higher affinity for wild-type and L94A mutant DRD2 than the W100L and W100A mutants, according to binding free energy calculations using the Molecular Mechanics Generalized-Born Surface Area (MMGBSA) method, explaining the experimental differences in ligand residence times. Principal component (PC) analysis revealed important conformational mobility upon molecular recognition of risperidone for the L94A mutant compared to the wild type, indicating an unfavorable entropic component that may contribute to improving risperidone affinity in the L94A DRD2 mutant.

Anticancer efficacy of endo- and exogenous potent ligands acting at dopaminergic receptor-expressing cancer cells

Cancer is one of the most common and dreaded diseases affecting the vastness of society. Unfortunately, still some people die especially when cancer is not diagnosed and thus caught early enough. On the other hand, using available chemo- or radiotherapy may result in serious side effects. Therefore, cancer-specific medications seem to be the most desired and safe therapy. Knowing that some cancers are characterized by overexpression of specific receptors on the cell surface, target-mediated drugs could serve as a unique and effective form of therapy. In line with this, recently dopaminergic receptors were presented important in cancer therapy as several dopaminergic ligands revealed their efficacy in tumor growth reduction as well as in apoptosis mediation. Unfortunately, the indication of whether DA receptor agonists or antagonists are the best choices in cancer treatment is quite difficult, since both of them may exert either pro- or anticancer effects. In this review, we analyze the therapeutic efficacy of compounds, both of exogenous and endogenous origin, targeting dopaminergic receptor-expressing cancers.

Identification of Novel Dopamine D2 Receptor Ligands—A Combined In Silico/In Vitro Approach

Diseases of the central nervous system are an alarming global problem showing an increasing prevalence. Dopamine receptor D2 (D2R) has been shown to be involved in central nervous system diseases. While different D2R-targeting drugs have been approved by the FDA, they all suffer from major drawbacks due to promiscuous receptor activity leading to adverse effects. Increasing the number of potential D2R-targeting drug candidates bears the possibility of discovering molecules with less severe side-effect profiles. In dire need of novel D2R ligands for drug development, combined in silico/in vitro approaches have been shown to be efficient strategies. In this study, in silico pharmacophore models were generated utilizing both ligand- and structure-based approaches. Subsequently, different databases were screened for novel D2R ligands. Selected virtual hits were investigated in vitro, quantifying their binding affinity towards D2R. This workflow successfully identified six novel D2R ligands exerting micro- to nanomolar (most active compound KI = 4.1 nM) activities. Thus, the four pharmacophore models showed prospective true-positive hit rates in between 4.5% and 12%. The developed workflow and identified ligands could aid in developing novel drug candidates for D2R-associated pathologies.

Dopamine and Dopamine-Related Ligands Can Bind Not Only to Dopamine Receptors

The dopaminergic system is one of the most important neurotransmitter systems in the central nervous system (CNS). It acts mainly by activation of the D₁-like receptor family at the target cell. Additionally, fine-tuning of the signal is achieved via pre-synaptic modulation by the D₂-like receptor family. Some dopamine drugs (both agonists and antagonists) bind in addition to DRs also to α₂-ARs and 5-HT receptors. Unfortunately, these compounds are often considered subtype(s) specific. Thus, it is important to consider the presence of these receptor subtypes in specific CNS areas as the function virtually elicited by one receptor type could be an effect of other—or the co-effect of multiple receptors. However, there are enough molecules with adequate specificity. In this review, we want to give an overview of the most common off-targets for established dopamine receptor ligands. To give an overall picture, we included a discussion on subtype selectivity. Molecules used as antipsychotic drugs are reviewed too. Therefore, we will summarize reported affinities and give an outline of molecules sufficiently specific for one or more subtypes (i.e., for subfamily), the presence of DR, α₂-ARs, and 5-HT receptors in CNS areas, which could help avoid ambiguous results.

All-Atom Molecular Dynamics Investigations on the Interactions between D2 Subunit Dopamine Receptors and Three 11C-Labeled Radiopharmaceutical Ligands

The D2 subunit dopamine receptor represents a key factor in modulating dopamine release. Moreover, the investigated radiopharmaceutical ligands used in positron emission tomography imaging techniques are known to bind D2 receptors, allowing for dopaminergic pathways quantification in the living human brain. Thus, the biophysical characterization of these radioligands is expected to provide additional insights into the interaction mechanisms between the vehicle molecules and their targets. Using molecular dynamics simulations and QM calculations, the present study aimed to investigate the potential positions in which the D2 dopamine receptor would most likely interact with the three distinctive synthetic 11C-labeled compounds (raclopride (3,5-dichloro-N-[[(2S)-1-ethylpyrrolidin-2-yl]methyl]-2-hydroxy-6-methoxybenzamide)—RACL, FLB457 (5-bromo-N-[[(2S)-1-ethylpyrrolidin-2-yl]methyl]-2,3-dimethoxybenzamide)—FLB457 and SCH23390 (R(+)-7-Chloro-8-hydroxy-3-methyl-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine)—SCH)), as well as to estimate the binding affinities of the ligand-receptor complexes. A docking study was performed prior to multiple 50 ns molecular dynamics productions for the ligands situated at the top and bottom interacting pockets of the receptor. The most prominent motions for the RACL ligand were described by the high fluctuations of the peripheral aliphatic -CH3 groups and by its C-Cl aromatic ring groups. In good agreement with the experimental data, the D2 dopamine receptor-RACL complex showed the highest interacting patterns for ligands docked at the receptor’s top position.

Interactions of a boron-containing levodopa derivative on D2 dopamine receptor and its effects in a Parkinson disease model

Levodopa is a cornerstone in Parkinson's disease treatment. Beneficial effects are mainly by binding on D₂ receptors. Docking simulations of a set of compounds including well-known D₂-ligands and a pool of Boron-Containing Compounds (BCC), particularly boroxazolidones with a tri/tetra-coordinated boron atom, were performed on the D₂ Dopamine receptor (D2DR). Theoretical results yielded higher affinity of the compound DPBX, a Dopaboroxazolidone, than levodopa on D2DR. Essential interactions with residues in the third and sixth transmembrane domains of the D2DR appear to be crucial to induce and stabilize interactions in the active receptor state. Results from a motor performance evaluation of a murine model of Parkinson's disease agree with theoretical results, as DPBX showed similar efficacy to that of levodopa for diminishing MPTP-induced parkinsonism. This beneficial effect was disrupted with prior Risperidone (D2DR antagonist) administration, supporting the role of D2DR in the biological effect of DPBX. In addition, DPBX limited neuronal loss in substantia nigra in a similar manner to that of levodopa administration.

In Vitro and In Silico Characterization of Kurarinone as a Dopamine D1A Receptor Antagonist and D2L and D4 Receptor Agonist

Alterations in the expression and/or activity of brain G-protein-coupled receptors (GPCRs) such as dopamine D₁R, D_2LR, D₃R, and D₄R, vasopressin V_1AR, and serotonin 5-HT_1AR are noted in various neurodegenerative diseases (NDDs). Since studies have indicated that flavonoids can target brain GPCRs and provide neuroprotection via inhibition of monoamine oxidases (hMAOs), our study explored the functional role of kurarinone, an abundant lavandulated flavonoid in Sophora flavescens, on dopamine receptor subtypes, V_1AR, 5-HT_1AR, and hMAOs. Radioligand binding assays revealed considerable binding of kurarinone on D₁R, D_2LR, and D₄R. Functional GPCR assays unfolded the compound's antagonist behavior on D₁R (IC₅₀ 42.1 ± 0.35 μM) and agonist effect on D_2LR and D₄R (EC₅₀ 22.4 ± 3.46 and 71.3 ± 4.94 μM, respectively). Kurarinone was found to inhibit hMAO isoenzymes in a modest and nonspecific manner. Molecular docking displayed low binding energies during the intermolecular interactions of kurarinone with the key residues of the deep orthosteric binding pocket and the extracellular loops of D₁R, D_2LR, and D₄R, validating substantial binding affinities to these prime targets. With appreciable D_2LR and D₄R agonism and D₁R antagonism, kurarinone might be a potential compound that can alleviate clinical symptoms of Parkinson's disease and other NDDs.

A comprehensive in silico investigation into the nsSNPs of Drd2 gene predicts significant functional consequences in dopamine signaling and pharmacotherapy

DRD2 is a neuronal cell surface protein involved in brain development and function. Variations in the Drd2 gene have clinical significance since DRD2 is a pharmacotherapeutic target for treating psychiatric disorders like ADHD and schizophrenia. Despite numerous studies on the disease association of single nucleotide polymorphisms (SNPs) in the intronic regions, investigation into the coding regions is surprisingly limited. In this study, we aimed at identifying potential functionally and pharmaco-therapeutically deleterious non-synonymous SNPs of Drd2. A wide array of bioinformatics tools was used to evaluate the impact of nsSNPs on protein structure and functionality. Out of 260 nsSNPs retrieved from the dbSNP database, initially 9 were predicted as deleterious by 15 tools. Upon further assessment of their domain association, conservation profile, homology models and inter-atomic interaction, the mutant F389V was considered as the most impactful. In-depth analysis of F389V through Molecular Docking and Dynamics Simulation revealed a decline in affinity for its native agonist dopamine and an increase in affinity for the antipsychotic drug risperidone. Remarkable alterations in binding interactions and stability of the protein-ligand complex in simulated physiological conditions were also noted. These findings will improve our understanding of the consequence of nsSNPs in disease-susceptibility and therapeutic efficacy.

Aza-Flavanone Diminishes Parkinsonism in the Drosophila melanogaster Parkin Mutant

Parkinson's disease is a chronic and progressive neurodegenerative disease, induced by slow and progressive death of the dopaminergic (DA) neurons from the midbrain region called substantia nigra (SNc) leading to difficulty in locomotion. At present, very few potential therapeutic drugs are available for treatment, necessitating an urgent need for development. In the current study, the parkin transgenic Drosophila melanogaster model that induces selective loss in dopaminergic neurons and impairment of locomotory functions has been used to see the effect of the aza-flavanone molecule. D. melanogaster serves as an amazing in vivo model making valuable contribution in the development of promising treatment strategies. Our in-silico study showed spontaneous binding of this molecule to the D2 receptor making it a potential dopamine agonist. PARKIN protein is well conserved, and it has been reported that Drosophila PARKIN is 42% identical to human PARKIN. Interestingly, this molecule enhances the motor coordination and survivability rate of the transgenic flies along with an increase in expression of the master regulator of Dopamine synthesis, that is, tyrosine hydroxylase (TH), in the substantia nigra region of the fly brain. Moreover, it plays a significant effect on mitochondrial health and biogenesis via modulation of a conserved mitochondrial protein PHB2. Therefore, this molecule could lead to the development of an effective therapeutic approach for the treatment of PD.

Interactions of a boron-containing levodopa derivative on D2 dopamine receptor and its effects in a Parkinson disease model

Levodopa is a cornerstone in Parkinson's disease treatment. Beneficial effects are mainly by binding on D₂ receptors. Docking simulations of a set of compounds including well-known D₂-ligands and a pool of Boron-Containing Compounds (BCC), particularly boroxazolidones with a tri/tetra-coordinated boron atom, were performed on the D₂ Dopamine receptor (D2DR). Theoretical results yielded higher affinity of the compound DPBX, a Dopaboroxazolidone, than levodopa on D2DR. Essential interactions with residues in the third and sixth transmembrane domains of the D2DR appear to be crucial to induce and stabilize interactions in the active receptor state. Results from a motor performance evaluation of a murine model of Parkinson's disease agree with theoretical results, as DPBX showed similar efficacy to that of levodopa for diminishing MPTP-induced parkinsonism. This beneficial effect was disrupted with prior Risperidone (D2DR antagonist) administration, supporting the role of D2DR in the biological effect of DPBX. In addition, DPBX limited neuronal loss in substantia nigra in a similar manner to that of levodopa administration.

Functional Selectivity of Dopamine D1 Receptor Signaling: Retrospect and Prospect

Research progress on dopamine D₁ receptors indicates that signaling no longer is limited to G protein-dependent cyclic adenosine monophosphate phosphorylation but also includes G protein-independent β-arrestin-related mitogen-activated protein kinase activation, regulation of ion channels, phospholipase C activation, and possibly more. This review summarizes recent studies revealing the complexity of D₁ signaling and its clinical implications, and suggests functional selectivity as a promising strategy for drug discovery to magnify the merit of D₁ signaling. Functional selectivity/biased receptor signaling has become a major research front because of its potential to improve therapeutics through precise targeting. Retrospective pharmacological review indicated that many D₁ ligands have some degree of mild functional selectivity, and novel compounds with extreme bias at D₁ signaling were reported recently. Behavioral and neurophysiological studies inspired new methods to investigate functional selectivity and gave insight into the biased signaling of several drugs. Results from recent clinical trials also supported D₁ functional selectivity signaling as a promising strategy for discovery and development of better therapeutics.

Main interactions of dopamine and risperidone with the dopamine D2 receptor

Psychosis is one of the psychiatric disorders that is controlled by dopaminergic drugs such as antipsychotics that have affinity for the dopamine D2 receptor (DRD2). In this investigation we perform quantum chemical calculations of two molecules [dopamine and risperidone] within a large cavity of DRD2 that represents the binding site of the receptor. Dopamine is an endogenous neurotransmitter and risperidone is a second-generation antipsychotic. Non-covalent interactions of dopamine and risperidone with DRD2 are analyzed using the Quantum Theory of Atoms in Molecules (QTAIM) and the Non-Covalent Interaction index (NCI). The QTAIM results show that these molecules strongly interact with the receptor. There are 22 non-covalent interactions for dopamine and 54 for risperidone. The electron density evaluated at each critical binding point is small in both systems but it is higher for dopamine than for risperidone, indicating that the interactions of DRD2 with the first are stronger than with the second molecule. However, the binding energy is higher for risperidone (-72.6 kcal mol-1) than for dopamine (-22.8 kcal mol-1). Thus, the strength of the binding energy is due to the number of contacts rather than the strength of the interactions themselves. This could be related to the ability of risperidone to block DRD2 and may explain the efficacy of this drug for controlling the symptoms of schizophrenia, but likewise its secondary effects.

Docking Screens of Noncovalent Interaction Motifs of the Human Subtype-D2 Receptor-75 Schizophrenia Antipsychotic Complexes with Physicochemical Appraisal of Antipsychotics

Chemoinformatics appraisal and molecular docking were employed to investigate 225 complexes of 75 schizophrenia antipsychotics with the dopamine receptor subtypes D2R, D3R, and D4R. Considering the effective noncovalent interactions in the subtype-D2 receptor selectivity of antipsychotics, this study evaluated the possible physicochemical properties of ligands underlying the design of safer and more effective antipsychotics. The pan-assay interference compounds (PAINs) include about 25% of typical antipsychotics and 5% of atypicals. Popular antipsychotics like haloperidol, clozapine, risperidone, and aripiprazole are not PAINs. They have stronger interactions with D2R and D4R, but their interactions with D3R are slightly weaker, which is similar to the behavior of dopamine. In contrast to typical antipsychotics, atypical antipsychotics exhibit more noncovalent interactions with D4R than with D2R. These results suggest that selectivity to D2R and D4R comes from the synergy between hydrophobic and hydrogen-bonding interactions through their concomitant occurrence in the form of a hydrogen-bonding site adorned with hydrophobic contacts in antipsychotic-receptor complexes. All the antipsychotics had more synergic interactions with D2R and D4R in comparison with D3R. The atypical antipsychotics made a good distinction between the subtype D2 receptors with high selectivity to D4R. Among the popular antipsychotics, haloperidol, clozapine, and risperidone have hydrophobic-hydrogen-bonding synergy with D4R, while aripiprazole profits with D2R. The most important residue participating in the synergic interactions was threonine for D2R and cysteine for D4R. This work could be useful in informing and guiding future drug discovery and development studies aimed at receptor-specific antipsychotics.

Purple Sweet Potatoes from East Java of Indonesia Revealed the Macronutrient, Anthocyanin Compound and Antidepressant Activity Candidate

Introduction:

The development of new antidepressant is crucial to overcome the remission rate limitation. Anthocyanin on purple sweet potatoes (PSP) from East Java cultivar previously demonstrated a behavioural effect. However, the certain mechanism and the nutritional compound need further exploration.

Aim:

This study aimed to characterize macronutrient content, amino acids, anthocyanin, and revealed the potential of PSP from East Java-Indonesia as antidepressant agent through D2-dopamine receptor (D2DR).

Methods:

This study was characterized the macronutrient content using proximate analysis. The amino acids were analysed using Ultra-Performance Liquid Chromatography (UPLC) and High-Performance Liquid Chromatography (HPLC). Anthocyanin was identified using Ultra High-Performance Liquid Chromatography (UHPLC). Molecular docking was conducted to predict the interaction between anthocyanins and D2 dopamine receptor.

Results:

We were found the predominance of water on proximate analysis. Alanine was demonstrated as the highest content of amino acid. Cyanidin, cyanidin-3-O-glucoside and peonidin-3-O-glucoside were identified as major anthocyanin content. Molecular docking was showed that cyanidin bound to similar binding site with dopamine on D2DR with stronger interaction than cyanidin-3-glucoside.

Conclusion:

Current study was indicated that cyanidin as major anthocyanin from purple sweet potatoes has potential health beneficial as antidepressant potential candidate.

Preferential Coupling of Dopamine D2S and D2L Receptor Isoforms with Gi1 and Gi2 Proteins-In Silico Study

The dopamine D₂ receptor belongs to rhodopsin-like G protein-coupled receptors (GPCRs) and it is an important molecular target for the treatment of many disorders, including schizophrenia and Parkinson's disease. Here, computational methods were used to construct the full models of the dopamine D₂ receptor short (D_2S) and long (D_2L) isoforms (differing with 29 amino acids insertion in the third intracellular loop, ICL3) and to study their coupling with G_i1 and G_i2 proteins. It was found that the D_2L isoform preferentially couples with the G_i2 protein and D_2S isoform with the G_i1 protein, which is in accordance with experimental data. Our findings give mechanistic insight into the interplay between isoforms of dopamine D₂ receptors and G_i proteins subtypes, which is important to understand signaling by these receptors and their mediation by pharmaceuticals, in particular psychotic and antipsychotic agents.

A quantum chemical approach representing a new perspective concerning agonist and antagonist drugs in the context of schizophrenia and Parkinson's disease

Schizophrenia and Parkinson's disease can be controlled with dopamine antagonists and agonists. In order to improve the understanding of the reaction mechanism of these drugs, in this investigation we present a quantum chemical study of 20 antagonists and 10 agonists. Electron donor acceptor capacity and global hardness are analyzed using Density Functional Theory calculations. Following this theoretical approach, we provide new insights into the intrinsic response of these chemical species. In summary, antagonists generally prove to be better electron acceptors and worse electron donors than dopamine, whereas agonists present an electron donor-acceptor capacity similar to that of dopamine. The chemical hardness is a descriptor that captures the resistance of a chemical compound to change its number of electrons. Within this model, harder molecules are less polarizable and more stable systems. Our results show that the global hardness is similar for dopamine and agonists whilst antagonists present smaller values. Following the Hard and Soft Acid and Bases principle, it is possible to conclude that dopamine and agonists are hard bases while antagonists are soft acids, and this can be related to their activity. From the electronic point of view, we have evolved a new perspective for the classification of agonist and antagonist, which may help to analyze future results of chemical interactions triggered by these drugs.

Novel Diels-Alder Type Adducts from Morus alba Root Bark Targeting Human Monoamine Oxidase and Dopaminergic Receptors for the Management of Neurodegenerative Diseases

In this study, we delineate the human monoamine oxidase (hMAO) inhibitory potential of natural Diels–Alder type adducts, mulberrofuran G (1), kuwanon G (2), and albanol B (3), from Morus alba root bark to characterize their role in Parkinson’s disease (PD) and depression, focusing on their ability to modulate dopaminergic receptors (D₁R, D_2LR, D₃R, and D₄R). In hMAO-A inhibition, 1–3 showed mild effects (50% inhibitory concentration (IC₅₀): 54‒114 μM). However, 1 displayed moderate inhibition of the hMAO-B isozyme (IC₅₀: 18.14 ± 1.06 μM) followed by mild inhibition by 2 (IC₅₀: 57.71 ± 2.12 μM) and 3 (IC₅₀: 90.59 ± 1.72 μM). Our kinetic study characterized the inhibition mode, and the in silico docking predicted that the moderate inhibitor 1 would have the lowest binding energy. Similarly, cell-based G protein-coupled receptors (GPCR) functional assays in vector-transfected cells expressing dopamine (DA) receptors characterized 1–3 as D₁R/D_2LR antagonists and D₃R/D₄R agonists. The half-maximum effective concentration (EC₅₀) of 1–3 on DA D₃R/D₄R was 15.13/17.19, 20.18/21.05, and 12.63/‒ µM, respectively. Similarly, 1–3 inhibited 50% of the DA response on D₁R/D_2LR by 6.13/2.41, 16.48/31.22, and 7.16/18.42 µM, respectively. A computational study revealed low binding energy for the test ligands. Interactions with residues Asp110, Val111, Tyr365, and Phe345 at the D₃R receptor and Asp115 and His414 at the D₄R receptor explain the high agonist effect. Likewise, Asp187 at D₁R and Asp114 at D_2LR play a crucial role in the antagonist effects of the ligand binding. Our overall results depict 1–3 from M. alba root bark as good inhibitors of hMAO and potent modulators of DA function as D₁R/D_2LR antagonists and D₃R/D₄R agonists. These active constituents in M. alba deserve in-depth study for their potential to manage neurodegenerative disorders (NDs), particularly PD and psychosis.

Structure-Kinetic Profiling of Haloperidol Analogues at the Human Dopamine D2 Receptor

Haloperidol is a typical antipsychotic drug (APD) associated with an increased risk of extrapyramidal side effects (EPSs) and hyperprolactinemia relative to atypical APDs such as clozapine. Both drugs are dopamine D₂ receptor (D₂R) antagonists, with contrasting kinetic profiles. Haloperidol displays fast association/slow dissociation at the D₂R, whereas clozapine exhibits relatively slow association/fast dissociation. Recently, we have provided evidence that slow dissociation from the D₂R predicts hyperprolactinemia, whereas fast association predicts EPS. Unfortunately, clozapine can cause severe side effects independent of its D₂R action. Our results suggest an optimal kinetic profile for D₂R antagonist APDs that avoids EPS. To begin exploring this hypothesis, we conducted a structure-kinetic relationship study of haloperidol and revealed that subtle structural modifications dramatically change binding kinetic rate constants, affording compounds with a clozapine-like kinetic profile. Thus, optimization of these kinetic parameters may allow development of novel APDs based on the haloperidol scaffold with improved side-effect profiles.

Identification of functional divergence sites in dopamine receptors of vertebrates

Dopamine is one of the major neurotransmitters in the brain and body, and regulates a wide variety of functions via its binding with dopamine receptors. Abnormalities in dopamine receptors have also been found to be related to various neurological disorders. For such reason, dopamine receptors are among the key components to understanding the molecular mechanisms of many diseases, they are also the potential drug targets for the treatment of many diseases. Till now, five different dopamine receptors (D1-D5) have been identified in mammals, which are assumed to be evolved from a common ancestor after multiple gene duplication events and functional divergence. Thus, identifying the specific features of each dopamine receptor, will not only provide clues for understanding the functional differences between the receptors, but also help us to design drugs specific for a certain subtype of receptor. In this study, we investigated the functional divergence in dopamine receptors in representative vertebrate species by analyzing their molecular evolution features. Our results showed that the coefficients for type I functional divergence (θ_I) were significantly greater than 0 for all the pairwise comparisons between the five dopamine receptors, suggesting that type I functional divergence, i.e., altered functional constraints or different evolutionary rates, may have taken place at some amino acids in the receptors. We further identified 84 potential type I functional divergence peptide sites for the pairwise comparisons between the D1-like and D2-like are identified in total. When these sites were mapped to the 3D structure of dopamine receptors, most of them were included in ICL3, M6 and M7 domains. Especially, sixteen of these sites may be the major sites associated with the changes of properties between D1-like and D2-like receptors. These sites provide molecular basis for further studies such as dopamine receptor function exploration and subtype specific drug design and screening.

Metabolites of Vinca Alkaloid Vinblastine: Tubulin Binding and Activation of Nausea-Associated Receptors

Vinblastine (VLB) is an antimitotic drug that binds to the vinca site of tubulin. The molecule possesses a high molecular weight and a complex chemical structure with many possibilities of metabolization. Despite advances in drug discovery research in reducing drug toxicity, the cause and mechanism of VLB-induced adverse drug reactions (ADRs) remains poorly understood. VLB is metabolized to at least 35 known metabolites, which have been identified and collected in this present work. This study also explores how VLB metabolites affect nausea-associated receptors such as muscarinic, dopaminergic, and histaminic. The metabolites have stronger binding interactions than acetylcholine (ACh) for muscarinic M₁, M₄, and M₅ receptors and demonstrate similar binding profiles to that of the natural substrate, ACh. The affinities of VLB metabolites to dopaminergic and histaminic receptors, their absorption, distribution, metabolism, excretion, toxicity properties, and the superiority of VLB to ACh for binding to M₅R, indicate their potential to trigger activation of nausea-associated receptors during chemotherapy with VLB. It has been shown that metabolite 20-hydroxy-VLB (metabolite 10) demonstrates a stronger binding affinity to the vinca site of tubulin than VLB; however, they have similar modes of action. VLB and metabolite 10 have similar gastric solubility (FaSSGF), intestinal solubility (FeSSIF), and log P values. Metabolite 10 has a more acceptable pharmacokinetic profile than VLB, a better gastric and intestinal solubility. Furthermore, metabolite 10 was found to be less bound to plasma proteins than VLB. These are desired and essential features for effective drug bioavailability. Metabolite 10 is not a substrate of CYP2D6 and thus is less likely to cause drug-drug interactions and ADRs compared to its parent drug. The hydroxyl group added upon metabolism of VLB suggests that it can also be a reasonable starting compound for designing the next generation of antimitotic drugs to overcome P-glycoprotein-mediated multidrug resistance, which is often observed with vinca alkaloids.

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

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.

Ciliotherapy: Remote Control of Primary Cilia Movement and Function by Magnetic Nanoparticles

Patients with polycystic kidney disease (PKD) are characterized with uncontrolled hypertension. Hypertension in PKD is a ciliopathy, an abnormal function and/or structure of primary cilia. Primary cilia are cellular organelles with chemo and mechanosensory roles. In the present studies, we designed a cilia-targeted (CT) delivery system to deliver fenoldopam specifically to the primary cilia. We devised the iron oxide nanoparticle (NP)-based technology for ciliotherapy. Live imaging confirmed that the CT-Fe₂O₃-NPs specifically targeted primary cilia in cultured cells in vitro and vascular endothelia in vivo. Importantly, the CT-Fe₂O₃-NPs enabled the remote control of the movement and function of a cilium with an external magnetic field, making the nonmotile cilium exhibit passive movement. The ciliopathic hearts displayed hypertrophy with compromised functions in left ventricle pressure, stroke volume, ejection fraction, and overall cardiac output because of prolonged hypertension. The CT-Fe₂O₃-NPs significantly improved cardiac function in the ciliopathic hypertensive models, in which the hearts also exhibited arrhythmia, which was corrected with the CT-Fe₂O₃-NPs. Intraciliary and cytosolic Ca²⁺ were increased when cilia were induced with fluid flow or magnetic field, and this served as a cilia-dependent mechanism of the CT-Fe₂O₃-NPs. Fenoldopam-alone caused an immediate decrease in blood pressure, followed by reflex tachycardia. Pharmacological delivery profiles confirmed that the CT-Fe₂O₃-NPs were a superior delivery system for targeting cilia more specifically, efficiently, and effectively than fenoldopam-alone. The CT-Fe₂O₃-NPs altered the mechanical properties of nonmotile cilia, and these nano-biomaterials had enormous clinical potential for ciliotherapy. Our studies further indicated that ciliotherapy provides a possibility toward personalized medicine in ciliopathy patients.

Multifunctional arylsulfonamide derivatives with 5-HT6/5-HT7 receptor antagonistic activity: a structural study

Nowadays, a search for antagonists co-acting on serotonin receptor subtypes 6 and 7 (5-HT₆R and 5-HT₇R, respectively) is of great interest due to the increasing number of patients suffering from dementia and related behavioural and psychological symptoms. The X-ray crystal structures of four promising multifunctional ligands in the hydrochloride forms were determined, namely 4-(6-fluoro-1,2-benzoxazol-3-yl)-1-[3-(3-methylbenzenesulfonamido)propyl]piperidin-1-ium chloride, C₂₂H₂₇FN₃O₃S⁺·Cl^-, (I), 4-(6-fluoro-1,2-benzoxazol-3-yl)-1-[4-(5-fluoro-3-methylbenzo[b]thiophene-2-sulfonamido)butyl]piperidin-1-ium chloride, C₂₅H₂₈F₂N₃O₃S₂⁺·Cl^-, (II), 4-(6-fluoro-1,2-benzoxazol-3-yl)-1-[4-(6-fluorobenzo[b]thiophene-2-sulfonamido)butyl]piperidin-1-ium chloride, C₂₄H₂₆ClFN₃O₃S₂⁺·Cl^-, (III), and 4-(6-fluoro-1,2-benzoxazol-3-yl)-1-[3-(3-chloro-4-fluorobenzenesulfonamido)propyl]piperidin-1-ium chloride, C₂₁H₂₂ClF₂N₃O₃S₂⁺·Cl^-, (IV). Two pharmacologically important functional groups, i.e. arylsulfonamide and piperidinyl-fluorobenzisoxazole, are linked by three- and four-membered aliphatic chains. These compounds crystallize as hydrochloride salts in monoclinic space groups, i.e. C2/c for (I), P2₁/c for (II) and (III), and P2₁/n for (IV). In the asymmetric unit, a charge-assisted hydrogen bond is observed between the cation located at the piperidine N atom and the chloride anion. The protonated piperidine N atom is critical to the pharmacological activity for the compounds, allowing for a strong interaction with monoaminergic receptors in the central nervous system. The sulfonyl group plays the role of a hydrogen-bond acceptor in the pharmacophore model and is involved in several C-H...O interactions. Two aromatic fragments of the presented structures are involved in C-H...π contacts, which were studied by Hirshfeld structure analysis. The distances between the mentioned functional groups are in agreement with pharmacophore models given in the literature. The studied interactions observed in the crystal structure indicate the main forces responsible for ligand-receptor recognition and binding.

Computer-aided Drug Design Applied to Parkinson Targets

Background

Parkinson’s disease (PD) is a progressive neurodegenerative disorder characterized by debilitating motor deficits, as well as autonomic problems, cognitive declines, changes in affect and sleep disturbances. Although the scientific community has performed great efforts in the study of PD, and from the most diverse points of view, the disease remains incurable. The exact mechanism underlying its progression is unclear, but oxidative stress, mitochondrial dysfunction and inflammation are thought to play major roles in the etiology.

Objective

Current pharmacological therapies for the treatment of Parkinson’s disease are mostly inadequate, and new therapeutic agents are much needed.

Methods

In this review, recent advances in computer-aided drug design for the rational design of new compounds against Parkinson disease; using methods such as Quantitative Structure-Activity Relationships (QSAR), molecular docking, molecular dynamics and pharmacophore modeling are discussed.

Results

In this review, four targets were selected: the enzyme monoamine oxidase, dopamine agonists, acetylcholine receptors, and adenosine receptors.

Conclusion

Computer aided-drug design enables the creation of theoretical models that can be used in a large database to virtually screen for and identify novel candidate molecules.

Evolution of dopamine receptors: phylogenetic evidence suggests a later origin of the DRD2l and DRD4rs dopamine receptor gene lineages

Dopamine receptors are integral membrane proteins whose endogenous ligand is dopamine. They play a fundamental role in the central nervous system and dysfunction of dopaminergic neurotransmission is responsible for the generation of a variety of neuropsychiatric disorders. From an evolutionary standpoint, phylogenetic relationships among the DRD₁ class of dopamine receptors are still a matter of debate as in the literature different tree topologies have been proposed. In contrast, phylogenetic relationships among the DRD₂ group of receptors are well understood. Understanding the time of origin of the different dopamine receptors is also an issue that needs further study, especially for the genes that have restricted phyletic distributions (e.g., DRD_2l and DRD_4rs). Thus, the goal of this study was to investigate the evolution of dopamine receptors, with emphasis on shedding light on the phylogenetic relationships among the D₁ class of dopamine receptors and the time of origin of the DRD_2l and DRD_4rs gene lineages. Our results recovered the monophyly of the two groups of dopamine receptors. Within the DRD₁ group the monophyly of each paralog was recovered with strong support, and phylogenetic relationships among them were well resolved. Within the DRD₁ class of dopamine receptors we recovered the sister group relationship between the DRD_1C and DRD_1E, and this clade was recovered sister to a cyclostome sequence. The DRD₁ clade was recovered sister to the aforementioned clade, and the group containing DRD₅ receptors was sister to all other DRD₁ paralogs. In agreement with the literature, among the DRD₂ class of receptors, DRD₂ was recovered sister to DRD₃, whereas DRD₄ was sister to the DRD₂/DRD₃ clade. According to our phylogenetic tree, the DRD_2l and DRD_4rs gene lineages would have originated in the ancestor of gnathostomes between 615 and 473 mya. Conservation of sequences required for dopaminergic neurotransmission and small changes in regulatory regions suggest a functional refinement of the dopaminergic pathways along evolution.

Profiling G protein-coupled receptors of Fasciola hepatica identifies orphan rhodopsins unique to phylum Platyhelminthes

G protein-coupled receptors (GPCRs) are established drug targets. Despite their considerable appeal as targets for next-generation anthelmintics, poor understanding of their diversity and function in parasitic helminths has thwarted progress towards GPCR-targeted anti-parasite drugs. This study facilitates GPCR research in the liver fluke, Fasciola hepatica, by generating the first profile of GPCRs from the F. hepatica genome. Our dataset describes 147 high confidence GPCRs, representing the largest cohort of GPCRs, and the largest set of in silico ligand-receptor predictions, yet reported in any parasitic helminth. All GPCRs fall within the established GRAFS nomenclature; comprising three glutamate, 135 rhodopsin, two adhesion, five frizzled, one smoothened, and one secretin GPCR. Stringent annotation pipelines identified 18 highly diverged rhodopsins in F. hepatica that maintained core rhodopsin signatures, but lacked significant similarity with non-flatworm sequences, providing a new sub-group of potential flukicide targets. These facilitated identification of a larger cohort of 76 related sequences from available flatworm genomes, representing new members of existing groups (PROF1/Srfb, Rho-L, Rho-R, Srfa, Srfc) of flatworm-specific rhodopsins. These receptors imply flatworm specific GPCR functions, and/or co-evolution with unique flatworm ligands, and could facilitate the development of exquisitely selective anthelmintics. Ligand binding domain sequence conservation relative to deorphanised rhodopsins enabled high confidence ligand-receptor matching of seventeen receptors activated by acetylcholine, neuropeptide F/Y, octopamine or serotonin. RNA-Seq analyses showed expression of 101 GPCRs across various developmental stages, with the majority expressed most highly in the pathogenic intra-mammalian juvenile parasites. These data identify a broad complement of GPCRs in F. hepatica, including rhodopsins likely to have key functions in neuromuscular control and sensory perception, as well as frizzled and adhesion/secretin families implicated, in other species, in growth, development and reproduction. This catalogue of liver fluke GPCRs provides a platform for new avenues into our understanding of flatworm biology and anthelmintic discovery.

Cell imaging of dopamine receptor using agonist labeling iridium(iii) complex

A long-lived complex 13 could selectively bind to dopamine receptors (D1R/D2R) and monitor their internalization in living cells.

Dopamine receptor expression is correlated with certain types of cancers, including lung, breast and colon cancers. In this study, we report luminescent iridium(iii) complexes (11–14) as intracellular dopamine receptor (D1R/D2R) cell imaging agents. Complexes 11 and 13, which are conjugated with a dopamine receptor agonist, showed superior cell imaging characteristics, high stability and low cytotoxicity (>100 μM) in A549 lung cancer cells. siRNA knockdown and dopamine competitive assays indicated that complexes 11 and 13 could selectively bind to dopamine receptors (D1R/D2R) in A549 cells. Fluorescence lifetime microscopy demonstrated that complex 13 has a longer luminescence lifetime at the wavelength of 560–650 nm than DAPI and other chromophores in biological fluids. The long luminescence lifetime of complex 13 not only provides an opportunity for efficient dopamine receptor tracking in biological media, but also enables the temporal separation of the probe signal from the intense background signal by fluorescence lifetime microscopy for efficient analysis. Complex 13 also shows high photostability, which could allow it to be employed for long-term cellular imaging. Furthermore, complex 13 could selectively track the internalization process of dopamine receptors (D1R/D2R) in living cells. To the best of our knowledge, complex 13 is the first metal-based compound that has been used to monitor intracellular dopamine receptors in living cells.

Mechanism of Off-Target Interactions and Toxicity of Tamoxifen and Its Metabolites

Tamoxifen is an estrogen modulator that acts to competitively inhibit the binding of endogenous estrogens. It is widely used for treatment of breast cancer; however, analogous with many antineoplastic agents, tamoxifen is associated with numerous adverse effects, most prominently nausea. We have identified several off-target receptors of tamoxifen and 22 of its metabolites that include histamine H1 and H3, and muscarinic M1, M4, and M5 subtypes, and dopamine D2 receptor. We have shown how they are associated with tamoxifen and its metabolites' toxicity through a comprehensive computational analysis of their interaction modes, which were also compared to that of the related endogenous substrates of each receptor. The results were further evaluated using available in vivo and in vitro data. The presented work provides foundational knowledge toward the determination of the precise mechanism of nausea induction, and in particular, interactions of tamoxifen and its metabolites with the receptors involved in that biomolecular pathway. This study can assist in predicting the potential undesired effects of the chemicals with common pharmacophores or similar fragments to that of tamoxifen and its metabolites and serve drug discovery research in developing more effective and tolerable tamoxifen analogues or chemotherapeutic agents.

Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions

A scoring protocol based on implicit membrane-based scoring functions and a new protocol for optimizing the positioning of proteins inside the membrane was evaluated for its capacity to discriminate native-like states from misfolded decoys. A decoy set previously established by the Baker lab (Proteins: Struct., Funct., Genet. 2006, 62, 1010-1025) was used along with a second set that was generated to cover higher resolution models. The Implicit Membrane Model 1 (IMM1), IMM1 model with CHARMM 36 parameters (IMM1-p36), generalized Born with simple switching (GBSW), and heterogeneous dielectric generalized Born versions 2 (HDGBv2) and 3 (HDGBv3) were tested along with the new HDGB van der Waals (HDGBvdW) model that adds implicit van der Waals contributions to the solvation free energy. For comparison, scores were also calculated with the distance-scaled finite ideal-gas reference (DFIRE) scoring function. Z-scores for native state discrimination, energy vs root-mean-square deviation (RMSD) correlations, and the ability to select the most native-like structures as top-scoring decoys were evaluated to assess the performance of the scoring functions. Ranking of the decoys in the Baker set that were relatively far from the native state was challenging and dominated largely by packing interactions that were captured best by DFIRE with less benefit of the implicit membrane-based models. Accounting for the membrane environment was much more important in the second decoy set where especially the HDGB-based scoring functions performed very well in ranking decoys and providing significant correlations between scores and RMSD, which shows promise for improving membrane protein structure prediction and refinement applications. The new membrane structure scoring protocol was implemented in the MEMScore web server ( http://feiglab.org/memscore ).

Dopamine-2 receptor extracellular N-terminus regulates receptor surface availability and is the target of human pathogenic antibodies from children with movement and psychiatric disorders

Anti-Dopamine-2 receptor (D2R) antibodies have been recently identified in a subgroup of children with autoimmune movement and psychiatric disorders, however the epitope(s) and mechanism of pathogenicity remain unknown. Here we report a major biological role for D2R extracellular N-terminus as a regulator of receptor surface availability, and as a major epitope targeted and impaired in brain autoimmunity. In transfected human cells, purified anti-D2R antibody from patients specifically and significantly reduced human D2R surface levels. Next, human D2R mutants modified in their extracellular domains were subcloned, and we analyzed the region bound by 35 anti-D2R antibody-positive patient sera using quantitative flow cytometry on live transfected cells. We found that N-glycosylation at amino acids N5 and/or N17 was critical for high surface expression in interaction with the last 15 residues of extracellular D2R N-terminus. No anti-D2R antibody-positive patient sera bound to the three extracellular loops, but all patient sera (35/35) targeted the extracellular N-terminus. Overall, patient antibody binding was dependent on two main regions encompassing amino acids 20 to 29, and 23 to 37. Residues 20 to 29 contributed to the majority of binding (77%, 27/35), among which 26% (7/27) sera bound to amino acids R20, P21, and F22, 37% (10/27) patients were dependent on residues at positions 26 and 29, that are different between humans and mice, and 30% (8/27) sera required R20, P21, F22, N23, D26, and A29. Seven patient sera bound to the region 23 to 37 independently of D26 and A29, but most sera exhibited N-glycosylation-independent epitope recognition at N23. Interestingly, no evident segregation of binding pattern according to patient clinical phenotype was observed. D2R N-terminus is a central epitope in autoimmune movement and psychiatric disorders and this knowledge could help the design of novel specific immune therapies tailored to improve patient outcome.

OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method

In the two transmembrane protein types, outer membrane proteins (OMPs) perform diverse important biochemical functions, including substrate transport and passive nutrient uptake and intake. Hence their 3D structures are expected to reveal these functions. Because experimental structures are scarce, predicted 3D structures are more adapted to OMP research instead, and the inter-barrel residue contact is becoming one of the most remarkable features, improving prediction accuracy by describing the structural information of OMPs. To predict OMP structures accurately, we explored an OMP inter-barrel residue contact prediction method: OMPcontact. Multiple OMP-specific features were integrated in the method, including residue evolutionary covariation, topology-based transmembrane segment relative residue position, OMP lipid layer accessibility, and residue evolution conservation. These features describe the properties of a residue pair in different respects: sequential, structural, evolutionary, and biochemical. Within a 3-residues slide window, a Support Vector Machine (SVM) could accurately determinate the inter-barrel contact residue pair using above features. A 5-fold cross-valuation process was applied in testing the OMPcontact performance against a non-redundant OMP set with 75 samples inside. The tests compared four evolutionary covariation methods and screen analyzed the adaptive ones for inter-barrel contact prediction. The results showed our method not only efficiently realized the prediction, but also scored the possibility for residue pairs reliably. This is expected to improve OMP tertiary structure prediction. Therefore, OMPcontact will be helpful in compiling a structural census of outer membrane protein.

Polypharmacology of dopamine receptor ligands

Most neurological diseases have a multifactorial nature and the number of molecular mechanisms discovered as underpinning these diseases is continuously evolving. The old concept of developing selective agents for a single target does not fit with the medical need of most neurological diseases. The development of designed multiple ligands holds great promises and appears as the next step in drug development for the treatment of these multifactorial diseases. Dopamine and its five receptor subtypes are intimately involved in numerous neurological disorders. Dopamine receptor ligands display a high degree of cross interactions with many other targets including G-protein coupled receptors, transporters, enzymes and ion channels. For brain disorders like Parkinsońs disease, schizophrenia and depression the dopaminergic system, being intertwined with many other signaling systems, plays a key role in pathogenesis and therapy. The concept of designed multiple ligands and polypharmacology, which perfectly meets the therapeutic needs for these brain disorders, is herein discussed as a general ligand-based concept while focusing on dopaminergic agents and receptor subtypes in particular.

Ligand Binding Pathways of Clozapine and Haloperidol in the Dopamine D2 and D3 Receptors

The binding of a small molecule ligand to its protein target is most often characterized by binding affinity and is typically viewed as an on/off switch. The more complex reality is that binding involves the ligand passing through a series of intermediate states between the solution phase and the fully bound pose. We have performed a set of 29 unbiased molecular dynamics simulations to model the binding pathways of the dopamine receptor antagonists clozapine and haloperidol binding to the D2 and D3 dopamine receptors. Through these simulations we have captured the binding pathways of clozapine and haloperidol from the extracellular vestibule to the orthosteric binding site and thereby, we also predict the bound pose of each ligand. These are the first long time scale simulations of haloperidol or clozapine binding to dopamine receptors. From these simulations, we have identified several important stages in the binding pathway, including the involvement of Tyr7.35 in a "handover" mechanism that transfers the ligand between the extracellular vestibule and Asp3.32. We have also performed interaction and cluster analyses to determine differences in binding pathways between the D2 and D3 receptors and identified metastable states that may be of use in drug design.

Structural signatures of DRD4 mutants revealed using molecular dynamics simulations: Implications for drug targeting

Human Dopamine Receptor D4 (DRD4) orchestrates several neurological functions and represents a target for many psychological disorders. Here, we examined two rare variants in DRD4; V194G and R237L, which elicit functional alterations leading to disruption of ligand binding and G protein coupling, respectively. Using atomistic molecular dynamics (MD) simulations, we provide in-depth analysis to reveal structural signatures of wild and mutant complexes with their bound agonist and antagonist ligands. We constructed intra-protein network graphs to discriminate the global conformational changes induced by mutations. The simulations also allowed us to elucidate the local side-chain dynamical variations in ligand-bound mutant receptors. The data suggest that the mutation in transmembrane V (V194G) drastically disrupts the organization of ligand binding site and causes disorder in the native helical arrangement. Interestingly, the R237L mutation leads to significant rewiring of side-chain contacts in the intracellular loop 3 (site of mutation) and also affects the distant transmembrane topology. Additionally, these mutations lead to compact ICL3 region compared to the wild type, indicating that the receptor would be inaccessible for G protein coupling. Our findings thus reveal unreported structural determinants of the mutated DRD4 receptor and provide a robust framework for design of effective novel drugs.