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1.
Structure ; 32(5): 523-535.e5, 2024 May 02.
Article En | MEDLINE | ID: mdl-38401537

We leveraged variable-temperature 19F-NMR spectroscopy to compare the conformational equilibria of the human A2A adenosine receptor (A2AAR), a class A G protein-coupled receptor (GPCR), across a range of temperatures ranging from lower temperatures typically employed in 19F-NMR experiments to physiological temperature. A2AAR complexes with partial agonists and full agonists showed large increases in the population of a fully active conformation with increasing temperature. NMR data measured at physiological temperature were more in line with functional data. This was pronounced for complexes with partial agonists, where the population of active A2AAR was nearly undetectable at lower temperature but became evident at physiological temperature. Temperature-dependent behavior of complexes with either full or partial agonists exhibited a pronounced sensitivity to the specific membrane mimetic employed. Cellular signaling experiments correlated with the temperature-dependent conformational equilibria of A2AAR in lipid nanodiscs but not in some detergents, underscoring the importance of the membrane environment in studies of GPCR function.


Receptor, Adenosine A2A , Humans , Receptor, Adenosine A2A/metabolism , Receptor, Adenosine A2A/chemistry , Temperature , Protein Binding , Adenosine A2 Receptor Agonists/pharmacology , Adenosine A2 Receptor Agonists/chemistry , Adenosine A2 Receptor Agonists/metabolism , Nuclear Magnetic Resonance, Biomolecular , Models, Molecular , Protein Conformation , HEK293 Cells
2.
Int J Mol Sci ; 22(23)2021 Nov 29.
Article En | MEDLINE | ID: mdl-34884716

G-protein coupled receptors (GPCRs) are known for their low stability and large conformational changes upon transitions between multiple states. A widely used method for stabilizing these receptors is to make chimeric receptors by fusing soluble proteins (i.e., fusion partner proteins) into the intracellular loop 3 (ICL3) connecting the transmembrane helices 5 and 6 (TM5 and TM6). However, this fusion approach requires experimental trial and error to identify appropriate soluble proteins, residue positions, and linker lengths for making the fusion. Moreover, this approach has not provided state-targeting stabilization of GPCRs. Here, to rationally stabilize a class A GPCR, adenosine A2A receptor (A2AR) in a target state, we carried out the custom-made de novo design of α-helical fusion partner proteins, which can fix the conformation of TM5 and TM6 to that in an inactive state of A2AR through straight helical connections without any kinks or intervening loops. The chimeric A2AR fused with one of the designs (FiX1) exhibited increased thermal stability. Moreover, compared with the wild type, the binding affinity of the chimera against the agonist NECA was significantly decreased, whereas that against the inverse agonist ZM241385 was similar, indicating that the inactive state was selectively stabilized. Our strategy contributes to the rational state-targeting stabilization of GPCRs.


Adenosine A2 Receptor Agonists/metabolism , Proteins/metabolism , Receptor, Adenosine A2A/chemistry , Receptor, Adenosine A2A/metabolism , Recombinant Fusion Proteins/metabolism , Adenosine/metabolism , Adenosine A2 Receptor Agonists/chemistry , Humans , Ligands , Models, Molecular , Molecular Dynamics Simulation , Protein Conformation, alpha-Helical , Proteins/chemistry , Recombinant Fusion Proteins/chemistry
3.
Molecules ; 26(23)2021 Dec 04.
Article En | MEDLINE | ID: mdl-34885946

In this work, we evaluated the conformational effect promoted by the isosteric exchange of sulfur by selenium in the heteroaromatic ring of new N-acylhydrazone (NAH) derivatives (3-8, 13, 14), analogues of the cardioactive compounds LASSBio-294 (1) and LASSBio-785 (2). NMR spectra analysis demonstrated a chemical shift variation of the iminic Csp2 of NAH S/Se-isosters, suggesting a stronger intramolecular chalcogen interaction for Se-derivatives. To investigate the pharmacological profile of these compounds at the adenosine A2A receptor (A2AR), we performed a previously validated functional binding assay. As expected for bioisosteres, the isosteric-S/Se replacement affected neither the affinity nor the intrinsic efficacy of our NAH derivatives (1-8). However, the N-methylated compounds (2, 6-8) presented a weak partial agonist profile at A2AR, contrary to the non-methylated counterparts (1, 3-5), which appeared as weak inverse agonists. Additionally, retroisosterism between aromatic rings of NAH on S/Se-isosters mimicked the effect of the N-methylation on intrinsic efficacy at A2AR, while meta-substitution in the phenyl ring of the acyl moiety did not. This study showed that the conformational effect of NAH-N-methylation and aromatic rings retroisosterism changed the intrinsic efficacy on A2AR, indicating the S/Se-chalcogen effect to drive the conformational behavior of this series of NAH.


Hydrazones/chemistry , Receptor, Adenosine A2A/metabolism , Selenium/chemistry , Sulfur/chemistry , Thiophenes/chemistry , Adenosine A2 Receptor Agonists/chemistry , Adenosine A2 Receptor Agonists/pharmacology , Animals , Humans , Hydrazones/pharmacology , Male , Models, Molecular , Rats, Wistar , Selenium/pharmacology , Sulfur/pharmacology , Thiophenes/pharmacology
4.
J Med Chem ; 64(22): 16573-16597, 2021 11 25.
Article En | MEDLINE | ID: mdl-34783558

Adenosine is an immunosuppressive factor in the tumor microenvironment mainly through activation of the A2A adenosine receptor (A2AR), which is a mechanism hijacked by tumors to escape immune surveillance. Small-molecule A2AR antagonists are being evaluated in clinical trials as immunotherapeutic agents, but their efficacy is limited as standalone therapies. To enhance the antitumor effects of A2AR antagonists, dual-acting compounds incorporating A2AR antagonism and histone deacetylase (HDAC) inhibitory actions were designed and synthesized, based on co-crystal structures of A2AR. Compound 24e (IHCH-3064) exhibited potent binding to A2AR (Ki = 2.2 nM) and selective inhibition of HDAC1 (IC50 = 80.2 nM), with good antiproliferative activity against tumor cell lines in vitro. Intraperitoneal administration of 24e (60 mg/kg, bid) inhibited mouse MC38 tumor growth with a tumor growth inhibition rate of 95.3%. These results showed that dual-acting compounds targeting A2AR and HDAC are potentially immunotherapeutic agents that are worth further exploring.


Adenosine A2 Receptor Agonists/pharmacology , Antineoplastic Agents/pharmacology , Drug Design , Histone Deacetylase Inhibitors/pharmacology , Immunosuppressive Agents/pharmacology , Receptor, Adenosine A2A/metabolism , Adenosine A2 Receptor Agonists/chemistry , Animals , Antineoplastic Agents/chemistry , Histone Deacetylase Inhibitors/chemistry , Humans , Immunosuppression Therapy , Immunosuppressive Agents/chemistry , Mice , Proof of Concept Study , Structure-Activity Relationship
5.
PLoS Comput Biol ; 17(11): e1009152, 2021 11.
Article En | MEDLINE | ID: mdl-34818333

Transmembranal G Protein-Coupled Receptors (GPCRs) transduce extracellular chemical signals to the cell, via conformational change from a resting (inactive) to an active (canonically bound to a G-protein) conformation. Receptor activation is normally modulated by extracellular ligand binding, but mutations in the receptor can also shift this equilibrium by stabilizing different conformational states. In this work, we built structure-energetic relationships of receptor activation based on original thermodynamic cycles that represent the conformational equilibrium of the prototypical A2A adenosine receptor (AR). These cycles were solved with efficient free energy perturbation (FEP) protocols, allowing to distinguish the pharmacological profile of different series of A2AAR agonists with different efficacies. The modulatory effects of point mutations on the basal activity of the receptor or on ligand efficacies could also be detected. This methodology can guide GPCR ligand design with tailored pharmacological properties, or allow the identification of mutations that modulate receptor activation with potential clinical implications.


Receptor, Adenosine A2A/chemistry , Adenosine A2 Receptor Agonists/chemistry , Adenosine A2 Receptor Agonists/pharmacology , Adenosine A2 Receptor Antagonists/chemistry , Adenosine A2 Receptor Antagonists/pharmacology , Amino Acid Substitution , Computational Biology , Humans , Ligands , Models, Molecular , Molecular Dynamics Simulation , Point Mutation , Protein Conformation/drug effects , Receptor, Adenosine A2A/genetics , Receptor, Adenosine A2A/metabolism , Thermodynamics
6.
ACS Chem Biol ; 16(6): 991-1002, 2021 06 18.
Article En | MEDLINE | ID: mdl-34048655

Allosteric ligands provide new opportunities to modulate G protein-coupled receptor (GPCR) function and present therapeutic benefits over orthosteric molecules. Negative allosteric modulators (NAMs) can inhibit the activation of a receptor and downstream signal transduction. Screening NAMs for a GPCR target is particularly challenging because of the difficulty in distinguishing NAMs from antagonists bound to the orthosteric site as they both show inhibitory effects in receptor signaling assays. Here we report an affinity mass spectrometry (MS)-based approach tailored to screening potential NAMs of a GPCR target especially from fragment libraries. Compared to regular surface plasmon resonance or NMR-based methods for fragment screening, our approach features a reduction of the protein and compound consumption by 2-4 orders of magnitude and an increase in the data acquisition speed by 2-3 orders of magnitude. Our affinity MS-based fragment screening led to the identification of a new NAM of the adenosine A2A receptor (A2AAR) bearing an unprecedented azetidine moiety predicted to occupy the allosteric sodium binding site. Molecular dynamics simulations, ligand structure-activity relationship (SAR) studies, and in-solution NMR analyses further revealed the unique binding mode and antagonistic property of this compound that differs considerably from HMA (5-(N,N-hexamethylene)amiloride), a well-characterized NAM of A2AAR. Taken together, our work would facilitate fragment-based screening of allosteric modulators, as well as guide the design of novel NAMs acting at the sodium ion pocket of class A GPCRs.


Adenosine A2 Receptor Agonists/pharmacology , Adenosine A2 Receptor Antagonists/pharmacology , Allosteric Regulation/drug effects , Receptor, Adenosine A2A/metabolism , Sodium/metabolism , Adenosine A2 Receptor Agonists/chemistry , Adenosine A2 Receptor Antagonists/chemistry , Allosteric Site/drug effects , Binding Sites/drug effects , Drug Discovery , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Receptor, Adenosine A2A/chemistry
7.
Structure ; 29(2): 170-176.e3, 2021 02 04.
Article En | MEDLINE | ID: mdl-33238145

In drug design, G protein-coupled receptor (GPCR) partial agonists enable one to fine-tune receptor output between basal and maximal signaling levels. Here, we add to the structural basis for rationalizing and monitoring partial agonism. NMR spectroscopy of partial agonist complexes of the A2A adenosine receptor (A2AAR) revealed conformations of the P-I-F activation motif that are distinctly different from full agonist complexes. At the intracellular surface, different conformations of helix VI observed for partial and full agonist complexes manifest a correlation between the efficacy-related structural rearrangement of this activation motif and intracellular signaling to partner proteins. While comparisons of A2AAR in complexes with partial and full agonists with different methods showed close similarity of the global folds, this NMR study now reveals subtle but distinct local structural differences related to partial agonism.


Drug Partial Agonism , Receptor, Adenosine A2A/chemistry , Adenosine A2 Receptor Agonists/chemistry , Adenosine A2 Receptor Agonists/pharmacology , Aminopyridines/chemistry , Aminopyridines/pharmacology , Binding Sites , Cell Line , Humans , Imidazoles/chemistry , Imidazoles/pharmacology , Molecular Dynamics Simulation , Protein Binding , Purines/chemistry , Purines/pharmacology , Pyrazoles/chemistry , Pyrazoles/pharmacology , Receptor, Adenosine A2A/metabolism
8.
PLoS Comput Biol ; 16(4): e1007818, 2020 04.
Article En | MEDLINE | ID: mdl-32298258

The activation process of G protein-coupled receptors (GPCRs) has been extensively studied, both experimentally and computationally. In particular, Molecular Dynamics (MD) simulations have proven useful in exploring GPCR conformational space. The typical behaviour of class A GPCRs, when subjected to unbiased MD simulations from their crystallized inactive state, is to fluctuate between inactive and intermediate(s) conformations, even with bound agonist. Fully active conformation(s) are rarely stabilized unless a G protein is also bound. Despite several crystal structures of the adenosine A2a receptor (A2aR) having been resolved in complex with co-crystallized agonists and Gs protein, its agonist-mediated activation process is still not completely understood. In order to thoroughly examine the conformational landscape of A2aR activation, we performed unbiased microsecond-length MD simulations in quadruplicate, starting from the inactive conformation either in apo or with bound agonists: endogenous adenosine or synthetic NECA, embedded in two homogeneous phospholipid membranes: 1,2-dioleoyl-sn-glycerol-3-phosphoglycerol (DOPG) or 1,2-dioleoyl-sn-glycerol-3-phosphocholine (DOPC). In DOPC with bound adenosine or NECA, we observe transition to an intermediate receptor conformation consistent with the known adenosine-bound crystal state. In apo state in DOPG, two different intermediate conformations are obtained. One is similar to that observed with bound adenosine in DOPC, while the other is closer to the active state but not yet fully active. Exclusively, in DOPG with bound adenosine or NECA, we reproducibly identify receptor conformations with fully active features, which are able to dock Gs protein. These different receptor conformations can be attributed to the action/absence of agonist and phospholipid-mediated allosteric effects on the intracellular side of the receptor.


Adenosine A2 Receptor Agonists , Phospholipids , Receptor, Adenosine A2A , Adenosine/chemistry , Adenosine/metabolism , Adenosine A2 Receptor Agonists/chemistry , Adenosine A2 Receptor Agonists/metabolism , Binding Sites , Humans , Molecular Dynamics Simulation , Phosphatidylcholines , Phosphatidylglycerols , Phospholipids/chemistry , Phospholipids/metabolism , Protein Conformation , Receptor, Adenosine A2A/chemistry , Receptor, Adenosine A2A/metabolism
9.
Sci Adv ; 6(12): eaay8544, 2020 03.
Article En | MEDLINE | ID: mdl-32206717

The lipid composition of the plasma membrane is a key parameter in controlling signal transduction through G protein-coupled receptors (GPCRs). Adenosine A2A receptor (A2AAR) is located in the lipid bilayers of cells, containing acyl chains derived from docosahexaenoic acid (DHA). For the NMR studies, we prepared A2AAR in lipid bilayers of nanodiscs, containing DHA chains and other acyl chains. The DHA chains in nanodiscs enhanced the activation of G proteins by A2AAR. Our NMR studies revealed that the DHA chains redistribute the multiple conformations of A2AAR toward those preferable for G protein binding. In these conformations, the rotational angle of transmembrane helix 6 is similar to that in the A2AAR-G protein complex, suggesting that the population shift of the equilibrium causes the enhanced activation of G protein by A2AAR. These findings provide insights into the control of neurotransmissions by A2AAR and the effects of lipids on various GPCR functions.


Adenosine A2 Receptor Agonists/chemistry , Adenosine A2 Receptor Agonists/pharmacology , Docosahexaenoic Acids/chemistry , Docosahexaenoic Acids/pharmacology , Magnetic Resonance Spectroscopy , Receptor, Adenosine A2A/chemistry , Receptor, Adenosine A2A/metabolism , Cell Membrane/metabolism , Docosahexaenoic Acids/analogs & derivatives , Lipid Bilayers , Models, Molecular , Molecular Conformation , Protein Binding , Recombinant Proteins , Signal Transduction , Solvents , Structure-Activity Relationship
10.
Biochem Pharmacol ; 174: 113827, 2020 04.
Article En | MEDLINE | ID: mdl-31987853

Adenosine analogues have high affinity and selectivity for adenosine receptors (AR), and exhibit anti-platelet activity. Plasma proteins play an important role in the regulation of platelet function and may influence the action of anti-platelet compounds. Little is known about the interactions of AR agonists with plasma proteins. This study investigates the interplay between AR agonists and plasma proteins and the consequences of those interactions. Surface plasmon resonance was employed together with molecular docking study to determine the binding kinetics of four selected ARagonists (PSB0777, Cl-Ado, MRE0094, UK432097) to several carrier proteins and to clarify the nature of these interactions. The influence of a whole plasma and of some plasma components on the effectiveness of ARagonists in the inhibition of platelet function was assessed by flow cytometry (platelet activation) and ELISA (platelet adhesion). Plasma proteins remarkably diminished the effectiveness of ARagonists in inhibiting platelet activation and adhesion in vitro. ARagonists were found to strongly bind to human serum albumin (HSA) and the protein components of lipoproteins - apolipoproteins; HSA was essential for the binding of water-soluble PSB0777, whereas apolipoproteins were needed for interactions with poorly-water soluble compounds such as UK432097 and MRE0094. In addition, HSA was shown to significantly reduce the effectiveness of PSB0777 in inhibiting ADP-induced platelet activation. In conclusion, HSA and lipoproteins are important carriers for ARagonists, which can affect pharmacodynamics of ARagonists used as platelet inhibitors.


Adenosine A2 Receptor Agonists/pharmacology , Adenosine/pharmacology , Blood Platelets/drug effects , Blood Platelets/metabolism , Platelet Activation/drug effects , Platelet Aggregation Inhibitors/pharmacology , Adenosine/analogs & derivatives , Adenosine/chemistry , Adenosine A2 Receptor Agonists/chemistry , Adult , Female , Furans/chemistry , Furans/pharmacology , Humans , Male , Molecular Docking Simulation/methods , Platelet Activation/physiology , Platelet Aggregation/drug effects , Platelet Aggregation/physiology , Protein Binding/drug effects , Protein Binding/physiology , Receptors, Purinergic P1/metabolism , Young Adult
11.
Sci Rep ; 9(1): 14199, 2019 10 02.
Article En | MEDLINE | ID: mdl-31578448

G-protein coupled receptors (GPCRs) play a pivotal role in transmitting signals at the cellular level. Structural insights can be exploited to support GPCR structure-based drug discovery endeavours. Despite advances in GPCR crystallography, active state structures are scarce. Molecular dynamics (MD) simulations have been used to explore the conformational landscape of GPCRs. Efforts have been made to retrieve active state conformations starting from inactive structures, however to date this has not been possible without using an energy bias. Here, we reconstruct the activation pathways of the apo adenosine receptor (A2A), starting from an inactive conformation, by applying adaptive sampling MD combined with a goal-oriented scoring function. The reconstructed pathways reconcile well with experiments and help deepen our understanding of A2A regulatory mechanisms. Exploration of the apo conformational landscape of A2A reveals the existence of ligand-competent states, active intermediates and state-dependent cholesterol hotspots of relevance for drug discovery. To the best of our knowledge this is the first time an activation process has been elucidated for a GPCR starting from an inactive structure only, using a non-biased MD approach, opening avenues for the study of ligand binding to elusive yet pharmacologically relevant GPCR states.


Adenosine A2 Receptor Agonists/chemistry , Cholesterol/chemistry , Protein Conformation , Receptor, Adenosine A2A/ultrastructure , Cholesterol/genetics , Drug Discovery , Humans , Ligands , Molecular Dynamics Simulation , Receptor, Adenosine A2A/chemistry , Receptor, Adenosine A2A/genetics , Receptors, G-Protein-Coupled/agonists , Receptors, G-Protein-Coupled/chemistry , Receptors, G-Protein-Coupled/genetics
12.
Pharmacol Biochem Behav ; 181: 110-116, 2019 06.
Article En | MEDLINE | ID: mdl-31054946

Repetitive behaviors are diagnostic for autism spectrum disorder (ASD) and commonly observed in other neurodevelopmental disorders. Currently, there are no effective pharmacological treatments for repetitive behavior in these clinical conditions. This is due to the lack of information about the specific neural circuitry that mediates the development and expression of repetitive behavior. Our previous work in mouse models has linked repetitive behavior to decreased activation of the subthalamic nucleus, a brain region in the indirect and hyperdirect pathways in the basal ganglia circuitry. The present experiments were designed to further test our hypothesis that pharmacological activation of the indirect pathway would reduce repetitive behavior. We used a combination of adenosine A1 and A2A receptor agonists that have been shown to alter the firing frequency of dorsal striatal neurons within the indirect pathway of the basal ganglia. This drug combination markedly and selectively reduced repetitive behavior in both male and female C58 mice over a six-hour period, an effect that required both A1 and A2A agonists as neither alone reduced repetitive behavior. The adenosine A1 and A2A receptor agonist combination also significantly increased the number of Fos transcripts and Fos positive cells in dorsal striatum. Fos induction was found in both direct and indirect pathway neurons suggesting that the drug combination restored the balance of activation across these complementary basal ganglia pathways. The adenosine A1 and A2A receptor agonist combination also maintained its effectiveness in reducing repetitive behavior over a 7-day period. These findings point to novel potential therapeutic targets for development of drug therapies for repetitive behavior in clinical disorders.


Adenosine A1 Receptor Agonists/therapeutic use , Adenosine A2 Receptor Agonists/therapeutic use , Adenosine/analogs & derivatives , Compulsive Behavior/drug therapy , Phenethylamines/therapeutic use , Stereotyped Behavior/drug effects , Adenosine/administration & dosage , Adenosine/chemistry , Adenosine/therapeutic use , Adenosine A1 Receptor Agonists/administration & dosage , Adenosine A1 Receptor Agonists/chemistry , Adenosine A2 Receptor Agonists/administration & dosage , Adenosine A2 Receptor Agonists/chemistry , Analysis of Variance , Animals , Autism Spectrum Disorder/drug therapy , Autism Spectrum Disorder/metabolism , Behavior, Animal/drug effects , Corpus Striatum/cytology , Drug Therapy, Combination , Female , Male , Mice , Mice, Inbred C57BL , Models, Animal , Neurons/metabolism , Peanut Oil/chemistry , Peanut Oil/pharmacology , Phenethylamines/administration & dosage , Phenethylamines/chemistry , Phenotype , Proto-Oncogene Proteins c-fos/metabolism
13.
Chem Biol Drug Des ; 94(2): 1568-1573, 2019 08.
Article En | MEDLINE | ID: mdl-30985956

A series of novel 7-amino-5-oxo-2-substituted-aryl/hetero-aryl-5,8-dihydro[1,2,4]triazolo[1,5-a]pyridine-6-carbonitriles (4a-4t) was synthesized, characterized and evaluated for their binding affinity and selectivity towards hA1 , hA2A , hA2B and hA3 adenosine receptors (ARs). Compound 4a with a phenyl ring at 2-position of the triazolo moiety of the scaffold showed high affinity and selectivity for hA1 AR (Ki hA1  = 0.076 µM, hA2A  = 25.6 µM and hA3  > 100 µM). Introduction of various electron donating and withdrawing groups at different positions of the phenyl ring resulted in drastic reduction in affinity and selectivity towards all the ARs, except compound 4b with a 4-hydroxyphenyl group at 2-position. Interestingly, the replacement of the phenyl ring with a smaller heterocyclic thiophene ring (π excessive system) resulted in further improvement of affinity for hA1 AR of compound 4t (Ki hA1  = 0.051 µM, hA2A  = 9.01 µM and hA3  > 13.9 µM) while retaining the significant selectivity against all other AR subtypes similar to compound 4a. The encouraging results for compounds 4a and 4t indicate that substitution at 2-position of the scaffold with π-excessive systems other than thiophene may lead to even more potent and selective hA1 AR antagonists.


Adenosine A2 Receptor Agonists , Adenosine A3 Receptor Agonists , Molecular Docking Simulation , Pyridines , Receptor, Adenosine A2A/chemistry , Receptor, Adenosine A3/chemistry , Adenosine A2 Receptor Agonists/chemical synthesis , Adenosine A2 Receptor Agonists/chemistry , Adenosine A3 Receptor Agonists/chemical synthesis , Adenosine A3 Receptor Agonists/chemistry , Animals , CHO Cells , Cricetulus , Humans , Pyridines/chemical synthesis , Pyridines/chemistry , Structure-Activity Relationship
14.
Curr Pharm Des ; 25(7): 774-782, 2019.
Article En | MEDLINE | ID: mdl-30848185

A2A receptor belongs to the family of GPCRs, which are the most abundant membrane protein family. Studies in the last few decades have shown the therapeutic applications of A2A receptor in various diseases. In the present mini-review, we have discussed the recent progress in the in-silico studies of the A2A receptor. Herein, we described the different structures of A2A receptor, the discovery of new agonists and antagonists using virtualscreening/ docking, pharmacophore modeling, and QSAR based pharmacophore modeling. We have also discussed various molecular dynamics (MD) simulations studies of A2A receptor in complex with ligands.


Adenosine A2 Receptor Agonists/chemistry , Adenosine A2 Receptor Antagonists/chemistry , Computer-Aided Design , Drug Design , Ligands , Molecular Dynamics Simulation , Quantitative Structure-Activity Relationship , Receptor, Adenosine A2A
15.
Structure ; 27(4): 703-712.e3, 2019 04 02.
Article En | MEDLINE | ID: mdl-30713025

Agonist binding in the extracellular region of the G protein-coupled adenosine A2A receptor increases its affinity to the G proteins in the intracellular region, and vice versa. The structural basis for this effect is not evident from the crystal structures of A2AR in various conformational states since it stems from the receptor dynamics. Using atomistic molecular dynamics simulations on four different conformational states of the adenosine A2A receptor, we observed that the agonists show decreased ligand mobility, lower entropy of the extracellular loops in the active-intermediate state compared with the inactive state. In contrast, the entropy of the intracellular region increases to prime the receptor for coupling the G protein. Coupling of the G protein to A2AR shrinks the agonist binding site, making tighter receptor agonist contacts with an increase in the strength of allosteric communication compared with the active-intermediate state. These insights provide a strong basis for structure-based ligand design studies.


Adenosine A2 Receptor Agonists/chemistry , Adenosine-5'-(N-ethylcarboxamide)/chemistry , Adenosine/chemistry , GTP-Binding Proteins/chemistry , Receptor, Adenosine A2A/chemistry , Adenosine/metabolism , Adenosine A2 Receptor Agonists/metabolism , Adenosine-5'-(N-ethylcarboxamide)/metabolism , Allosteric Regulation , Allosteric Site , Catalytic Domain , GTP-Binding Proteins/genetics , GTP-Binding Proteins/metabolism , Humans , Ligands , Models, Molecular , Molecular Dynamics Simulation , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protein Stability , Receptor, Adenosine A2A/genetics , Receptor, Adenosine A2A/metabolism , Thermodynamics
16.
PLoS One ; 14(1): e0204378, 2019.
Article En | MEDLINE | ID: mdl-30605479

Safety pharmacology screening against a wide range of unintended vital targets using in vitro assays is crucial to understand off-target interactions with drug candidates. With the increasing demand for in vitro assays, ligand- and structure-based virtual screening approaches have been evaluated for potential utilization in safety profiling. Although ligand based approaches have been actively applied in retrospective analysis or prospectively within well-defined chemical space during the early discovery stage (i.e., HTS screening and lead optimization), virtual screening is rarely implemented in later stage of drug discovery (i.e., safety). Here we present a case study to evaluate ligand-based 3D QSAR models built based on in vitro antagonistic activity data against adenosine receptor 2A (A2A). The resulting models, obtained from 268 chemically diverse compounds, were used to test a set of 1,897 chemically distinct drugs, simulating the real-world challenge of safety screening when presented with novel chemistry and a limited training set. Due to the unique requirements of safety screening versus discovery screening, the limitations of 3D QSAR methods (i.e., chemotypes, dependence on large training set, and prone to false positives) are less critical than early discovery screen. We demonstrated that 3D QSAR modeling can be effectively applied in safety assessment prior to in vitro assays, even with chemotypes that are drastically different from training compounds. It is also worth noting that our model is able to adequately make the mechanistic distinction between agonists and antagonists, which is important to inform subsequent in vivo studies. Overall, we present an in-depth analysis of the appropriate utilization and interpretation of pharmacophore-based 3D QSAR models for safety screening.


Adenosine A2 Receptor Antagonists/chemistry , Drug Discovery/methods , High-Throughput Screening Assays/methods , Receptor, Adenosine A2A/chemistry , Small Molecule Libraries/chemistry , Adenosine A2 Receptor Agonists/chemistry , Adenosine A2 Receptor Agonists/pharmacology , Feasibility Studies , Models, Molecular , Quantitative Structure-Activity Relationship , Receptor, Adenosine A2A/metabolism , Small Molecule Libraries/adverse effects
17.
J Comput Aided Mol Des ; 32(12): 1337-1346, 2018 12.
Article En | MEDLINE | ID: mdl-30361971

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 A2A adenosine receptor (hA2A AR), are Ser913.39, Trp2466.48, Asn2807.45, and Asn2847.49. 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 hA2AAR could influence the ligand positioning accuracy during molecular docking simulations for most of the available resting and activated hA2A 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 hA2A 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.


Adenosine A2 Receptor Agonists/chemistry , Adenosine A2 Receptor Antagonists/chemistry , Molecular Docking Simulation/methods , Receptor, Adenosine A2A/metabolism , Sodium/chemistry , Allosteric Site , Cations, Monovalent/chemistry , Databases, Protein , Drug Inverse Agonism , Humans , Ligands , Protein Binding , Protein Conformation
18.
Mol Inform ; 37(8): e1800009, 2018 08.
Article En | MEDLINE | ID: mdl-29673107

One of the most largely accepted concepts in the G protein-coupled receptors (GPCRs) field is that the ligand, either agonist or antagonist, recognizes its receptor with a stoichiometry of 1 : 1. Recent experimental evidence, reporting ternary complexes formed by GPCR:orthosteric: allosteric ligands, has complicated the ligand-receptor 1 : 1 binding scenario. Molecular modeling simulations have been used to retrieve insights on the whole ligand-receptor recognition process, beyond information on the final bound state provided by experimental techniques. The simulation of adenosine binding pathways towards the A2A adenosine receptor highlighted the presence of alternative binding sites (meta-binding sites) beside the canonical orthosteric one, mainly in proximity to the extracellular vestibule. In light of all these considerations, we investigated the possibility that a second molecule of adenosine engages its receptor when this is already in the holo form, generating a ternary complex with a stoichiometry of 2 : 1. Unexpectedly, supervised molecular dynamics (SuMD) simulations showed that the A2A adenosine receptor could bind the second molecule of adenosine in one of the possible meta-binding sites as well as into its orthosteric site. The formation of this ternary complex, which favored the formation of the intracellular "ionic lock" between R102 (3.50) and E228 (6.30), could putatively be framed in the context of a negative allosteric regulation.


Adenosine A2 Receptor Agonists/pharmacology , Adenosine/pharmacology , Molecular Docking Simulation , Receptors, Adenosine A2/metabolism , Adenosine/chemistry , Adenosine A2 Receptor Agonists/chemistry , Dose-Response Relationship, Drug , Humans , Protein Binding , Receptors, Adenosine A2/chemistry , Supervised Machine Learning
19.
Eur J Med Chem ; 150: 127-139, 2018 Apr 25.
Article En | MEDLINE | ID: mdl-29525433

A new series of amino-3,5-dicyanopyridines (3-28) as analogues of the adenosine hA2B receptor agonist BAY60-6583 (compound 1) was synthesized. All the compounds that interact with the hA2B adenosine receptor display EC50 values in the range 9-350 nM behaving as partial agonists, with the only exception being the 2-{[4-(4-acetamidophenyl)-6-amino-3,5-dicyanopyridin-2-yl]thio}acetamide (8) which shows a full agonist profile. Moreover, the 2-[(1H-imidazol-2-yl)methylthio)]-6-amino-4-(4-cyclopropylmethoxy-phenyl)pyridine-3,5-dicarbonitrile (15) turns out to be 3-fold more active than 1 although less selective. This result can be considered a real breakthrough due to the currently limited number of non-adenosine hA2B AR agonists reported in literature. To simulate the binding mode of nucleoside and non-nucleoside agonists at the hA2B AR, molecular docking studies were performed at homology models of this AR subtype developed by using two crystal structures of agonist-bound A2A AR as templates. These investigations allowed us to represent a hypothetical binding mode of hA2B receptor agonists belonging to the amino-3,5-dicyanopyridine series and to rationalize the observed SAR.


Adenosine A2 Receptor Agonists/pharmacology , Receptor, Adenosine A2B/metabolism , Adenosine A2 Receptor Agonists/chemical synthesis , Adenosine A2 Receptor Agonists/chemistry , Aminopyridines , Dose-Response Relationship, Drug , Humans , Molecular Docking Simulation , Molecular Structure , Nitriles , Structure-Activity Relationship
20.
Curr Med Chem ; 25(30): 3597-3612, 2018.
Article En | MEDLINE | ID: mdl-29532748

BACKGROUND: Adenosine is an endogenous purine nucleoside, which mediates a variety of important biological processes and diseases, such as vasodilation, inflammation, cancer, wound healing, ischemia reperfusion injury, Parkinson disease, infectious diseases, and other CNS disorders. Particularly important are the A2A receptors that have been expressed in the lung, liver, heart, cardiovascular tissues, leukocytes, neutrophils, and endothelial cells. This review provides an update of the latest A2A receptor agonists developed in the period 2005-2017, their selectivity regarding other adenosine receptors and their potential therapeutic applications. METHODS: I have conducted an extensive search from the most common bibliographic databases for critically review the most recent works on the A2A receptor agonists and their therapeutic applications in inflammation, asthma and chronic obstructive pulmonary disease, myocardial perfusion imaging, sepsis, rheumatoid arthritis, and wound healing, among others. RESULTS: In the last decade, a great deal of effort has been devoted to develop adenosine receptor agonists and antagonists for treatment of a number of diseases. Thus, for A2A receptor agonists more than 130 papers and reviews have been found, many of them highlighting the usefulness of these compounds in the field. CONCLUSIONS: Although so far many of the A2A receptor agonists have failed in clinical trials due to their side effects, some of them have been approved for protection against cardiac ischemia-reperfusion injury and anemia. The recently reported crystal structure of the human A2A receptor in complex with the agonist UK-432097 is a fundamental keystone for the development of new and selective A2A ligands with new therapeutic applications.


Adenosine A2 Receptor Agonists/metabolism , Receptor, Adenosine A2A/metabolism , Adenosine A2 Receptor Agonists/chemistry , Adenosine A2 Receptor Agonists/therapeutic use , Arthritis, Rheumatoid/drug therapy , Arthritis, Rheumatoid/pathology , Asthma/drug therapy , Asthma/pathology , Humans , Inflammation/pathology , Inflammation/prevention & control , Myocardial Perfusion Imaging , Pulmonary Disease, Chronic Obstructive/drug therapy , Pulmonary Disease, Chronic Obstructive/pathology , Receptor, Adenosine A2A/chemistry , Sepsis/drug therapy , Sepsis/pathology , Structure-Activity Relationship
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