Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A<Subscript>2A</Subscript> adenosine receptor orthosteric binding site using a molecular docking approach? Insights from <Emphasis Type="Italic">Dockbench</Emphasis>

The allosteric modulation of G protein-coupled receptors (GPCRs) by sodium ions has received considerable attention as crystal structures of several receptors, in their inactive conformation, show a Na⁺ ion bound to specific residues which, in the human A_2A adenosine receptor (hA_2A AR), are Ser91^3.39, Trp246^6.48, Asn280^7.45, and Asn284^7.49. A cluster of water molecules completes the coordination of the sodium ion in the putative allosteric site. It is absolutely consolidated that the progress made in the field of GPCRs structural determination has increased the adoption of docking-driven approaches for the identification or the optimization of novel potent and selective ligands. Despite the extensive use of docking protocols in virtual screening approaches, to date, almost any of these studies have been carried out without taking into account the presence of the sodium cation and its first solvation shell in the putative allosteric binding site. In this study, we have focused our attention on determining how the presence of sodium ion binding and additionally its first hydration sphere, in hA_2AAR could influence the ligand positioning accuracy during molecular docking simulations for most of the available resting and activated hA_2A AR crystal structures, using DockBench as a comparative benchmarking tool and implementing a new correlation coefficient (EM). This work provides indications on the evidence that the posing performance (accuracy and/or precision) of the docking protocols in reproducing the crystallographic poses of different hA_2A AR antagonists is generally increased in the presence of the sodium cation and its first solvation shell, in agreement with experimental observations. Consequently, the inclusion of sodium ion and its first solvation shell should be considered in order to facilitate the selection of new potential ligands in all molecular docking-based virtual screening protocols that aim to find novel GPCRs antagonists and inverse agonists.     

Binding mode similarity measures for ranking of docking poses: a case study on the adenosine A<Subscript>2A</Subscript> receptor

We report an investigation designed to explore alternative approaches for ranking of docking poses in the search for antagonists of the adenosine A_2A receptor, an attractive target for structure-based virtual screening. Calculation of 3D similarity of docking poses to crystallographic ligand(s) as well as similarity of receptor–ligand interaction patterns was consistently superior to conventional scoring functions for prioritizing antagonists over decoys. Moreover, the use of crystallographic antagonists and agonists, a core fragment of an antagonist, and a model of an agonist placed into the binding site of an antagonist-bound form of the receptor resulted in a significant early enrichment of antagonists in compound rankings. Taken together, these findings showed that the use of binding modes of agonists and/or antagonists, even if they were only approximate, for similarity assessment of docking poses or comparison of interaction patterns increased the odds of identifying new active compounds over conventional scoring.     

Comparison of three GPCR structural templates for modeling of the P2Y<Subscript>12</Subscript> nucleotide receptor

The P2Y₁₂ receptor (P2Y₁₂R) is an ADP-activated G protein-coupled receptor (GPCR) that is an important target for antithrombotic drugs. Three homology models of P2Y₁₂R were compared, based on different GPCR structural templates: bovine rhodopsin (bRHO), human A_2A adenosine receptor (A_2AAR), and human C-X-C chemokine receptor type 4 (CXCR4). By criteria of sequence analysis (25.6% identity in transmembrane region), deviation from helicity in the second transmembrane helix (TM2), docked poses of ligands highlighting the role of key residues, accessibility of a conserved disulfide bridge that is reactive toward irreversibly-binding antagonists, and the presence of a shared disulfide bridge between the third extracellular loop (EL3) and the N-terminus, the CXCR4-based model appeared to be the most consistent with known characteristics of P2Y₁₂R. The docked poses of agonist 2MeSADP and charged anthraquinone antagonist PSB-0739 in the binding pocket of P2Y₁₂R-CXC agree with previously published site-directed mutagenesis studies of Arg256 and Lys280. A sulfonate at position 2 of the anthraquinone core created a strong interaction with the Lys174(EL2) side chain. The docking poses of the irreversibly-binding, active metabolite (existing as two diastereoisomers in vivo) of the clinically utilized antagonist Clopidogrel were compared. The free thiol group of the 4S diastereoisomer, but not the 4R isomer, was found in close proximity (~4.7 Å) to the sulfur atom of a disulfide bridge involving Cys175, suggesting greater activity in covalent binding. Therefore, ligand docking to the CXCR4-based model of the P2Y₁₂R predicted poses of both reversibly and irreversibly-binding small molecules, consistent with observed pharmacology and mutagenesis studies.     

X‐Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X‐ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand‐FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X‐ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno‐oncology.     

A2A Adenosine Receptor Antagonists: Are Triazolotriazine and Purine Scaffolds Interchangeable?

The A_2A adenosine receptor (A_2AAR) is one of the four subtypes activated by nucleoside adenosine, and the molecules able to selectively counteract its action are attractive tools for neurodegenerative disorders. In order to find novel A_2AAR ligands, two series of compounds based on purine and triazolotriazine scaffolds were synthesized and tested at ARs. Compound 13 was also tested in an in vitro model of neuroinflammation. Some compounds were found to possess high affinity for A_2AAR, and it was observed that compound 13 exerted anti-inflammatory properties in microglial cells. Molecular modeling studies results were in good agreement with the binding affinity data and underlined that triazolotriazine and purine scaffolds are interchangeable only when 5- and 2-positions of the triazolotriazine moiety (corresponding to the purine 2- and 8-positions) are substituted.     

Methodological approaches for the study of GABA<Subscript>A</Subscript> receptor pharmacology and functional responses

Inhibitory GABA_A receptor ion channels are the target for a wide range of clinically-used therapeutic agents. The complex structural diversity of these ligand-gated channels, revealed by molecular cloning studies, together with increasing requirements for higher-throughput functional assays in drug discovery, has led to the development of a wide range of techniques to examine GABA_A receptor pharmacology and function. In the current article we review some of the methodologies which have contributed to the expansion of knowledge in this field. The techniques include: molecular approaches, immunoprecipitation, and immunopurification to study receptor assembly, structure, and functional expression; in situ hybridization, immunocytochemistry, and autoradiography to examine receptor distribution in native tissues; radioligand binding, site-directed mutagenesis, and electrophysiology to examine pharmacology and allosteric modulation; and patch clamp, ion flux, microphysiometry, and a variety of novel fluorescence-based technologies to examine ion-channel function. The use of gene targetting approaches in transgenic mice has also provided important insights into the role of specific GABA_A receptor subtypes in vivo. The continuing evolution of novel technologies and assay approaches with appropriate sensitivity and resolution to measure subtle modulation of GABA_A ion channels will facilitate ongoing investigation of the physiological functions of these important inhibitory receptors.     

Cancer-Associated Mutations of the Adenosine A2A Receptor Have Diverse Influences on Ligand Binding and Receptor Functions

The adenosine A_2A receptor (A_2AAR) is a class A G-protein-coupled receptor (GPCR). It is an immune checkpoint in the tumor micro-environment and has become an emerging target for cancer treatment. In this study, we aimed to explore the effects of cancer-patient-derived A_2AAR mutations on ligand binding and receptor functions. The wild-type A_2AAR and 15 mutants identified by Genomic Data Commons (GDC) in human cancers were expressed in HEK293T cells. Firstly, we found that the binding affinity for agonist NECA was decreased in six mutants but increased for the V275A mutant. Mutations A165V and A265V decreased the binding affinity for antagonist ZM241385. Secondly, we found that the potency of NECA (EC₅₀) in an impedance-based cell-morphology assay was mostly correlated with the binding affinity for the different mutants. Moreover, S132L and H278N were found to shift the A_2AAR towards the inactive state. Importantly, we found that ZM241385 could not inhibit the activation of V275A and P285L stimulated by NECA. Taken together, the cancer-associated mutations of A_2AAR modulated ligand binding and receptor functions. This study provides fundamental insights into the structure–activity relationship of the A_2AAR and provides insights for A_2AAR-related personalized treatment in cancer.     

Irreversible Antagonists for the Adenosine A2B Receptor

Blockade of the adenosine A_2B receptor (A_2BAR) represents a potential novel strategy for the immunotherapy of cancer. In the present study, we designed, synthesized, and characterized irreversible A_2BAR antagonists based on an 8-p-sulfophenylxanthine scaffold. Irreversible binding was confirmed in radioligand binding and bioluminescence resonance energy transfer(BRET)-based Gα₁₅ protein activation assays by performing ligand wash-out and kinetic experiments. p-(1-Propylxanthin-8-yl)benzene sulfonyl fluoride (6a, PSB-21500) was the most potent and selective irreversible A_2BAR antagonist of the present series with an apparent K_i value of 10.6 nM at the human A_2BAR and >38-fold selectivity versus the other AR subtypes. The corresponding 3-cyclopropyl-substituted xanthine derivative 6c (PSB-21502) was similarly potent, but was non-selective versus A₁- and A_2AARs. Attachment of a reactive sulfonyl fluoride group to an elongated xanthine 8-substituent (12, K_i 7.37 nM) resulted in a potent, selective, reversibly binding antagonist. Based on previous docking studies, the lysine residue K269^7.32 was proposed to react with the covalent antagonists. However, the mutant K269L behaved similarly to the wildtype A_2BAR, indicating that 6a and related irreversible A_2BAR antagonists do not interact with K269^7.32. The new irreversible A_2BAR antagonists will be useful tools and have the potential to be further developed as therapeutic drugs.     

Development of Bicyclo[3.1.0]hexane-Based A3 Receptor Ligands: Closing the Gaps in the Structure–Affinity Relationships

The adenosine A₃ receptor is a promising target for treating and diagnosing inflammation and cancer. In this paper, a series of bicyclo[3.1.0]hexane-based nucleosides was synthesized and evaluated for their P1 receptor affinities in radioligand binding studies. The study focused on modifications at 1-, 2-, and 6-positions of the purine ring and variations of the 5′-position at the bicyclo[3.1.0]hexane moiety, closing existing gaps in the structure–affinity relationships. The most potent derivative 30 displayed moderate A₃AR affinity (Ki of 0.38 μM) and high A₃R selectivity. A subset of compounds varied at 5′-position was further evaluated in functional P2Y₁R assays, displaying no off-target activity.     

Side chain flexibility and the pore dimensions in the GABA<Subscript>A</Subscript> receptor

Permeation of ions through open channels and their accessibility to pore-targeting drugs depend on the pore cross-sectional dimensions, which are known only for static X-ray and cryo-EM structures. Here, we have built homology models of the closed, open and desensitized α₁β₂γ₂ GABA_A receptor (GABA_AR). The models are based, respectively, on the X-ray structure of α₃ glycine receptor (α₃ GlyR), cryo-EM structure of α₁ GlyR and X-ray structure of β₃ GABA_AR. We employed Monte Carlo energy minimizations to explore how the pore lumen may increase due to repulsions of flexible side chains from a variable-diameter electroneutral atom (an expanding sphere) pulled through the pore. The expanding sphere computations predicted that the pore diameter averaged along the permeation pathway is larger by approximately 3 Å than that computed for the models with fixed sidechains. Our models predict three major pore constrictions located at the levels of ?2′, 9′ and 20′ residues. Residues around the ?2′ and 9′ rings are known to form the desensitization and activation gates of GABA_AR. Our computations predict that the 20′ ring may also serve as GABA_AR gate whose physiological role is unclear. The side chain flexibility of residues ?2′, 9′ and 20′ and hence the dimensions of the constrictions depend on the GABA_AR functional state.     

Organoruthenium Antagonists of Human A3 Adenosine Receptors

Human A₃ adenosine receptor (hA₃AR) is a membrane‐bound G protein‐coupled receptor implicated in a number of severe pathological conditions, including cancer, in which it acts as a potential therapeutic target. To derive structure–activity relationships on pyrazolo–triazolo–pyrimidine (PTP)‐based A₃AR antagonists, we developed a new class of organometallic inhibitors through replacement of the triazolo moiety with an organoruthenium fragment. The objective was to introduce by design structural diversity into the PTP scaffold in order to tune their binding efficacy toward the target receptor. These novel organoruthenium antagonists displayed good aquatic stability and moderate binding affinity toward the hA₃ receptor in the low micromolar range. The assembly of these complexes through a template‐driven approach with selective ligand replacement at the metal center to control their steric and receptor‐binding properties is discussed.     

X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X-ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand-FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X-ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno-oncology.     

Development of new chromatographic tools based on A2A adenosine receptor subtype for ligand characterization and screening by FAC-MS

A liquid chromatographic stationary phase containing immobilized membranes from cells expressing A_2A adenosine receptor (A_2AAR) is firstly described. Cellular membranes from CHO cells stably transfected with human A_2AAR vector (A_2A(+)) and from the same cell line transfected with the corresponding empty vector (A_2A(?)) were entrapped on immobilized artificial membrane (IAM) support and packed into 6.6 mm I.D. glass columns to create A_2A(+)-IAM and A_2A(?)-IAM stationary phases. Frontal chromatography experiments on both A_2A(+)-IAM and A_2A(?)-IAM columns demonstrated the presence of a low specific interaction with the receptor. However, immobilized A_2A retained its ability to specifically bind known ligands as demonstrated by the agreement of the calculated K _d values with two different chromatographic protocols in comparison to previously reported data. In order to maximize the specific interaction, the same cellular membranes were immobilized on the inner surface of a silica capillary (40 cm?×?100 μm I.D.) by non-covalent interactions using the avidin–biotin coupling system to create two open tubular columns A_2A(+)-OT and A_2A(?)-OT. The open tubular system was characterized by ranking experiments for affinity studies in mixture useful for the selection of new potential candidates.

Ligand-, structure- and pharmacophore-based molecular fingerprints: a case study on adenosine A1, A2A, A2B, and A3 receptor antagonists

FLAP fingerprints are applied in the ligand-, structure- and pharmacophore-based mode in a case study on antagonists of all four adenosine receptor (AR) subtypes. Structurally diverse antagonist collections with respect to the different ARs were constructed by including binding data to human species only. FLAP models well discriminate ??active?? (=highly potent) from ??inactive?? (=weakly potent) AR antagonists, as indicated by enrichment curves, numbers of false positives, and AUC values. For all FLAP modes, model predictivity slightly decreases as follows: A_2BR?>?A_2AR?>?A₃R?>?A₁R antagonists. General performance of FLAP modes in this study is: ligand-?>?structure-?>?pharmacophore- based mode. We also compared the FLAP performance with other common ligand- and structure-based fingerprints. Concerning the ligand-based mode, FLAP model performance is superior to ECFP4 and ROCS for all AR subtypes. Although focusing on the early first part of the A_2A, A_2B and A₃ enrichment curves, ECFP4 and ROCS still retain a satisfactory retrieval of actives. FLAP is also superior when comparing the structure-based mode with PLANTS and GOLD. In this study we applied for the first time the novel FLAPPharm tool for pharmacophore generation. Pharmacophore hypotheses, generated with this tool, convincingly match with formerly published data. Finally, we could demonstrate the capability of FLAP models to uncover selectivity aspects although single AR subtype models were not trained for this purpose.     

Identification of anti-Parkinson's Disease Lead Compounds from Aspergillus ochraceus Targeting Adenosin Receptors A2A

Two novel alkaloids compounds together with fifteen know metabolites were identified from Aspergillus ochraceus. The stereochemistry features of the new molecules were determined via HRESIMS, NMR, ECD, and XRD analyses. Amongst these, compounds two compounds exhibited potential efficacy as anti-Parkinson's disease with the EC₅₀ values of 2.30 and 2.45 μM , respectively. ADMET prediction showed that these compounds owned favorable drug-like characteristics and safe toxicity scores towards CNS drugs. Virtual screening analyses manifested that the compounds exhibited not only robust and reliable interactions to adenosine receptors A_2A, but also higher binding selectivity to A_2A receptors than to A₁ and A₃ receptors. Molecular dynamics simulation demonstrated the reliability of molecular docking results and the stability of the complexes obtained with the novel compounds and A_2A receptors in natural environments. It is the first time that anti-PD lead compounds have been identified from Aspergillus ochraceus and targeting adenosine A_2A receptors.     

Thermal decomposition paths in A<Subscript>2</Subscript>CuCl<Subscript>4</Subscript> complexes: anilinium and its derivatives

The thermal decomposition paths of anilinium, 4-chloro anilinium tetrachlorocopper(II) complexes are compared to their benzilinium derivative. All these complexes crystallize in the layered structure, typical for a A₂MX₄ family, are studied in literature for their magnetic, semiconducting properties. TG analyses of (anilinium)₂CuCl₄ (A) and (4-chloro anilinium)₂CuCl₄ (B) loses one molecule of organic ammonium hydrochloride along with one molecule of amine, to form (H)CuCl₃, which subsequently completely decomposes to Cu above 500 °C. On the other hand, (benzilinium)₂CuCl₄ (C) loses two molecules of hydrochloride along with chlorine molecule first then two molecules of benzyl amine with formation of Cu above 300 °C. DSC studies on C have shown reversible endothermic phase transition at 130.95 °C (−1.98 J g⁻¹) while heating and exothermic phase transition at 117.07 °C (0.93 J g⁻¹) while cooling. Thus, the observed changes in the decomposition pathway can be correlated to the order–disorder phase transition occurred in the compound C.     

Theoretical studies on the interaction of partial agonists with the 5-HT<Subscript>2A</Subscript> receptor

A series of 51 5-HT_2A partial agonistic arylethylamines (primary or benzylamines) from different structural classes (indoles, methoxybenzenes, quinazolinediones) was investigated by fragment regression analysis (FRA), docking and 3D-QSAR approaches. The data, pEC₅₀ values and intrinsic activities (E_max) on rat arteries, show high variability of pEC₅₀ from 4 to 10 and of E_max from 15 to 70%. FRA indicates which substructures affect potency or intrinsic activity. The high contribution of halogens in para position of phenethylamines to pEC₅₀ points to a specific hydrophobic pocket. Other results suggest the significance of hydrogen bonds of the aryl moiety for activation and the contrary effect of benzyl groups on affinity (increasing) and intrinsic activity (decreasing). Results from fragment regression and data on all available mutants were considered to derive a common binding site at the rat 5-HT_2A receptor. After generation and MD simulations of a receptor model based on the β₂-adrenoceptor structure, typical derivatives were docked, leading to the suggestion of common interactions, e.g., with serines in TM3 and TM5 and with a cluster of aromatic amino acids in TM5 and TM6. The whole series was aligned by docking and minimization of the complexes. The pEC₅₀ values correlate well with Sybyl docking energies and hydrophobicity of the aryl moieties. With this alignment, CoMFA and CoMSIA approaches based on a training set of 36 and a test set of 15 compounds were performed. The correlation of pEC₅₀ with steric, electrostatic, hydrophobic and H-bond acceptor fields resulted in sufficient fit (q ²: 0.75–0.8, r ²: 0.92–0.95) and predictive power (r _pred²: 0.85–0.88). The important interaction regions largely reflect the patterns provided by the putative binding site. In particular, the fit of the aryl moieties and benzyl substituents to two hydrophobic pockets is evident.     

Synthesis and biological evaluation of <Superscript>99m</Superscript>Tc-HEDTA/HYNIC-MPP4 complex for 5-HT<Subscript>1A</Subscript> receptor imaging

5-HT_1A receptor is associated with a variety of pathophysiology of neuropsychiatric disorders. Accordingly, we have synthesized a new 5-HT_1A receptor ligand (HYNIC-MPP4) and labeled it with ^99mTc using N-(2-hydroxyethyl)ethylenediaminetriacetic acid (HEDTA) as coligand. ^99mTc-HEDTA/HYNIC-MPP4 was prepared under pH 6 at room temperature. Biodistribution of 99mTc-HEDTA/HYNIC-MPP4 in normal mice showed that this complex had moderate brain uptake (0.60% ID·g⁻¹ at 2 min p.i.) and good retention. The hippocampus had the highest radioactivity uptake at 2 min p.i. (1.84% ID⋆g⁻¹). The ratio of Hipp/CB was 3.1 at 2 min p.i. and increased to 4.4 at 60 min p.i. After blocking with 8-hydroxy-2-(dipropylamino) tetralin, the uptake of hippocampus was decreased significantly from 1.84% ID·g⁻¹ to 0.53% ID·g⁻¹ at 2 min p.i., while the cerebellum had no significant decrease. This ^99mTc complex could be a potent agent for 5-HT_1A receptor imaging. Supported by the National Natural Science Foundation of China (Grant No. 20401004) and the Analysis and Test fund of Beijing Normal University     

Ligand design by targeting a binding site water

Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood. We investigated how altered interactions with a water network can influence ligand binding to a receptor. A series of ligands of the A_2A adenosine receptor, which either interacted with or displaced an ordered binding site water, were studied experimentally and by molecular dynamics simulations. An analog of the endogenous ligand that was unable to hydrogen bond to the ordered water lost affinity and this activity cliff was captured by molecular dynamics simulations. Two compounds designed to displace the ordered water from the binding site were then synthesized and evaluated experimentally, leading to the discovery of an A_2A agonist with nanomolar activity. Calculation of the thermodynamic profiles resulting from introducing substituents that interacted with or displaced the ordered water showed that the gain of binding affinity was enthalpy driven. Detailed analysis of the energetics and binding site hydration networks revealed that the enthalpy change was governed by contributions that are commonly neglected in structure-based drug optimization. In particular, simulations suggested that displacement of water from a binding site to the bulk solvent can lead to large energy contributions. Our findings provide insights into the molecular driving forces of protein–ligand binding and strategies for rational drug design.

Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood.     

Design,Synthesis and Biological Evaluation of 1,3,5-Triazine Derivatives Targeting hA1 and hA3 Adenosine Receptor

Adenosine mediates various physiological activities in the body. Adenosine receptors (ARs) are widely expressed in tumors and the tumor microenvironment (TME), and they induce tumor proliferation and suppress immune cell function. There are four types of human adenosine receptor (hARs): hA₁, hA_2A, hA_2B, and hA₃. Both hA₁ and hA₃ AR play an important role in tumor proliferation. We designed and synthesized novel 1,3,5-triazine derivatives through amination and Suzuki coupling, and evaluated them for binding affinities to each hAR subtype. Compounds 9a and 11b showed good binding affinity to both hA₁ and hA₃ AR, while 9c showed the highest binding affinity to hA₁ AR. In this study, we discovered that 9c inhibits cell viability, leading to cell death in lung cancer cell lines. Flow cytometry analysis revealed that 9c caused an increase in intracellular reactive oxygen species (ROS) and a depolarization of the mitochondrial membrane potential. The binding mode of 1,3,5-triazine derivatives to hA₁ and hA₃ AR were predicted by a molecular docking study.