Crystal structure of the adenosine A2A receptor bound to an antagonist reveals a potential allosteric pocket

Leveraging binding pose metadynamics to optimise target fishing predictions for three diverse ligands and their true targets

Computational target fishing plays an important role in target identification, particularly in drug discovery campaigns utilizing phenotypic screening. Numerous approaches exist to predict potential targets for a given ligand, but true targets may be inconsistently ranked. More advanced simulation methods may provide benefit in such cases by reranking these initial predictions. We evaluated the ability of binding pose metadynamics to improve the predicted rankings for three diverse ligands and their six true targets. Initial predictions using pharmacophore mapping showed no true targets ranked in the top 50 and two targets each ranked within the 50-100, 100-150, and 250-300 ranges respectively. Following binding pose metadynamics, ranking of true targets improved for four out of the six targets and included the highest ranked predictions overall, while rankings deteriorated for two targets. The revised rankings predicted two true targets ranked within the top 50, and one target each within the 50-100, 100-150, 150-200, and 200-250 ranges respectively. The findings of this study demonstrate that binding pose metadynamics may be of benefit in refining initial predictions from structure-based target fishing algorithms, thereby improving the efficiency of the target identification process in drug discovery efforts.

G Protein-Coupled Receptor-Ligand Pose and Functional Class Prediction

G protein-coupled receptor (GPCR) transmembrane protein family members play essential roles in physiology. Numerous pharmaceuticals target GPCRs, and many drug discovery programs utilize virtual screening (VS) against GPCR targets. Improvements in the accuracy of predicting new molecules that bind to and either activate or inhibit GPCR function would accelerate such drug discovery programs. This work addresses two significant research questions. First, do ligand interaction fingerprints provide a substantial advantage over automated methods of binding site selection for classical docking? Second, can the functional status of prospective screening candidates be predicted from ligand interaction fingerprints using a random forest classifier? Ligand interaction fingerprints were found to offer modest advantages in sampling accurate poses, but no substantial advantage in the final set of top-ranked poses after scoring, and, thus, were not used in the generation of the ligand-receptor complexes used to train and test the random forest classifier. A binary classifier which treated agonists, antagonists, and inverse agonists as active and all other ligands as inactive proved highly effective in ligand function prediction in an external test set of GPR31 and TAAR2 candidate ligands with a hit rate of 82.6% actual actives within the set of predicted actives.

Structural insight into the dual-antagonistic mechanism of AB928 on adenosine A2 receptors

The adenosine subfamily G protein-coupled receptors A2AR and A2BR have been identified as promising cancer immunotherapy candidates. One of the A2AR/A2BR dual antagonists, AB928, has progressed to a phase II clinical trial to treat rectal cancer. However, the precise mechanism underlying its dual-antagonistic properties remains elusive. Herein, we report crystal structures of the A2AR complexed with AB928 and a selective A2AR antagonist 2-118. The structures revealed a common binding mode on A2AR, wherein the ligands established extensive interactions with residues from the orthosteric and secondary pockets. In contrast, the cAMP assay and A2AR and A2BR molecular dynamics simulations indicated that the ligands adopted distinct binding modes on A2BR. Detailed analysis of their chemical structures suggested that AB928 readily adapted to the A2BR pocket, while 2-118 did not due to intrinsic differences. This disparity potentially accounted for the difference in inhibitory efficacy between A2BR and A2AR. This study serves as a valuable structural template for the future development of selective or dual inhibitors targeting A2AR/A2BR for cancer therapy.

Crystal structure reveals the binding mode and selectivity of a photoswitchable ligand for the adenosine A2A receptor

Rational synthetic expansion of photoresponsive ligands is important for photopharmacological studies. Adenosine A2A receptor (A2AR) is stimulated by adenosine and related in Parkinson's disease and other diseases. Here, we report the crystal structure of the A2AR in complex with the novel photoresponsive ligand photoNECA (blue) at 3.34 Å resolution. PhotoNECA (blue) was designed for this structural study and the cell-based assay showed a photoresponsive and receptor selective characteristics of photoNECA (blue) for A2AR. The crystal structure explains the binding mode, photoresponsive mechanism and receptor selectivity of photoNECA (blue). Our study would promote not only the rational design of photoresponsive ligands but also dynamic structural studies of A2AR.

Computational Workflow for Refining AlphaFold Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive Human Adenosine A3 Receptor

A structure-based drug design pipeline that considers both thermodynamic and kinetic binding data of ligands against a receptor will enable the computational design of improved drug molecules. For unresolved GPCR-ligand complexes, a workflow that can apply both thermodynamic and kinetic binding data in combination with alpha-fold (AF)-derived or other homology models and experimentally resolved binding modes of relevant ligands in GPCR-homologs needs to be tested. Here, as test case, we studied a congeneric set of ligands that bind to a structurally unresolved G protein-coupled receptor (GPCR), the inactive human adenosine A3 receptor (hA3R). We tested three available homology models from which two have been generated from experimental structures of hA1R or hA2AR and one model was a multistate alphafold 2 (AF2)-derived model. We applied alchemical calculations with thermodynamic integration coupled with molecular dynamics (TI/MD) simulations to calculate the experimental relative binding free energies and residence time (τ)-random accelerated MD (τ-RAMD) simulations to calculate the relative residence times (RTs) for antagonists. While the TI/MD calculations produced, for the three homology models, good Pearson correlation coefficients, correspondingly, r = 0.74, 0.62, and 0.67 and mean unsigned error (mue) values of 0.94, 1.31, and 0.81 kcal mol-1, the τ-RAMD method showed r = 0.92 and 0.52 for the first two models but failed to produce accurate results for the multistate AF2-derived model. With subsequent optimization of the AF2-derived model by reorientation of the side chain of R1735.34 located in the extracellular loop 2 (EL2) that blocked ligand's unbinding, the computational model showed r = 0.84 for kinetic data and improved performance for thermodynamic data (r = 0.81, mue = 0.56 kcal mol-1). Overall, after refining the multistate AF2 model with physics-based tools, we were able to show a strong correlation between predicted and experimental ligand relative residence times and affinities, achieving a level of accuracy comparable to an experimental structure. The computational workflow used can be applied to other receptors, helping to rank candidate drugs in a congeneric series and enabling the prioritization of leads with stronger binding affinities and longer residence times.

"Eritadenine as a regulator of anxiety Disorders: An experimental and docking Approach"

Uncertainty persists regarding the specific chemical causal factors and their corresponding behavioral effects in anxiety disorders. Commonly employed first-line treatments for anxiety target G protein-coupled receptors (GPCRs), including inhibitors of monoaminergic systems. Alternatively, emerging natural bioactive strategies offer potential for mitigating adverse effects. Recent investigations have implicated adenosine in anxiety-triggering mechanisms, while eritadenine, an adenosine analog derived from Shiitake mushroom, has displayed promising attributes. This study explores eritadenine's potential as a bioactive substance for anxiety disorders in mice, employing behavioral tests, pentobarbital-sleep induction, and molecular docking. Behavioral test results reveal a pronounced anxiolytic and sedative-hypnotic pharmacological effect of eritadenine. Our findings suggest that eritadenine may modulate locomotor functions mediated by adenosine receptors, with a stronger affinity for binding to A2AAR over A1AR, thus eliciting these effects.

Molecular Biophysics of Class A G Protein Coupled Receptors-Lipids Interactome at a Glance-Highlights from the A2A Adenosine Receptor

G protein-coupled receptors (GPCRs) are embedded in phospholipid membrane bilayers with cholesterol representing 34% of the total lipid content in mammalian plasma membranes. Membrane lipids interact with GPCRs structures and modulate their function and drug-stimulated signaling through conformational selection. It has been shown that anionic phospholipids form strong interactions between positively charged residues in the G protein and the TM5-TM6-TM 7 cytoplasmic interface of class A GPCRs stabilizing the signaling GPCR-G complex. Cholesterol with a high content in plasma membranes can be identified in more specific sites in the transmembrane region of GPCRs, such as the Cholesterol Consensus Motif (CCM) and Cholesterol Recognition Amino Acid Consensus (CRAC) motifs and other receptor dependent and receptor state dependent sites. Experimental biophysical methods, atomistic (AA) MD simulations and coarse-grained (CG) molecular dynamics simulations have been applied to investigate these interactions. We emphasized here the impact of phosphatidyl inositol-4,5-bisphosphate (PtdIns(4,5)P₂ or PIP₂), a minor phospholipid component and of cholesterol on the function-related conformational equilibria of the human A_2A adenosine receptor (A_2AR), a representative receptor in class A GPCR. Several GPCRs of class A interacted with PIP₂ and cholesterol and in many cases the mechanism of the modulation of their function remains unknown. This review provides a helpful comprehensive overview for biophysics that enter the field of GPCRs-lipid systems.

Crystal structure of adenosine A2A receptor in complex with clinical candidate Etrumadenant reveals unprecedented antagonist interaction

The G_s protein-coupled adenosine A_2A receptor (A_2AAR) represents an emerging drug target for cancer immunotherapy. The clinical candidate Etrumadenant was developed as an A_2AAR antagonist with ancillary blockade of the A_2BAR subtype. It constitutes a unique chemotype featuring a poly-substituted 2-amino-4-phenyl-6-triazolylpyrimidine core structure. Herein, we report two crystal structures of the A_2AAR in complex with Etrumadenant, obtained with differently thermostabilized A_2AAR constructs. This led to the discovery of an unprecedented interaction, a hydrogen bond of T88^3.36 with the cyano group of Etrumadenant. T88^3.36 is mutated in most A_2AAR constructs used for crystallization, which has prevented the discovery of its interactions. In-vitro characterization of Etrumadenant indicated low selectivity versus the A₁AR subtype, which can be rationalized by the structural data. These results will facilitate the future design of AR antagonists with desired selectivity. Moreover, they highlight the advantages of the employed A_2AAR crystallization construct that is devoid of ligand binding site mutations.

Screening of Membrane Protein Production by Comparison of Transient Expression in Insect and Mammalian Cells

Membrane proteins are difficult biomolecules to express and purify. In this paper, we compare the small-scale production of six selected eukaryotic integral membrane proteins in insect and mammalian cell expression systems using different techniques for gene delivery. The target proteins were C terminally fused to the green fluorescent marker protein GFP to enable sensitive monitoring. We show that the choice of expression systems makes a considerable difference to the yield and quality of the six selected membrane proteins. Virus-free transient gene expression (TGE) in insect High Five cells combined with solubilization in dodecylmaltoside plus cholesteryl hemisuccinate generated the most homogeneous samples for all six targets. Further, the affinity purification of the solubilized proteins using the Twin-Strep^® tag improved protein quality in terms of yield and homogeneity compared to His-tag purification. TGE in High Five insect cells offers a fast and economically attractive alternative to the established methods that require either baculovirus construction and the infection of the insect cells or relatively expensive transient gene expression in mammalian cells for the production of integral membrane proteins.

Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A2A and A1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations

We used coarse-grained molecular dynamics (CG MD) simulations to study protein-cholesterol interactions for different activation states of the A_2A adenosine receptor (A_2AR) and the A₁ adenosine receptor (A₁R) and predict new cholesterol binding sites indicating amino acid residues with a high residence time in three biologically relevant membranes. Compared to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-cholesterol and POPC-phosphatidylinositol-bisphosphate (PIP₂)-cholesterol, the plasma mimetic membrane best described the cholesterol binding sites previously detected for the inactive state of A_2AR and revealed the binding sites with long-lasting amino acid residues. We observed that using the plasma mimetic membrane and plotting residues with cholesterol residence time ≥2 μs, our CG MD simulations captured most obviously the cholesterol-protein interactions. For the inactive A_2AR, we identified one more binding site in which cholesterol is bound to residues with a long residence time compared to the previously detected, for the active A₁R, three binding sites, and for the inactive A₁R, two binding sites. We calculated that for the active states, cholesterol binds to residues with a much longer residence time compared to the inactive state for both A_2AR and A₁R. The stability of the identified binding sites to A₁R or A_2AR with CG MD simulations was additionally investigated with potential of mean force calculations using umbrella sampling. We observed that the binding sites with residues to which cholesterol has a long residence time in A_2AR have shallow binding free energy minima compared to the related binding sites in A₁R, suggesting a stronger binding for cholesterol to A₁R. The differences in binding sites in which cholesterol is stabilized and interacts with residues with a long residence time between active and inactive states of A₁R and A_2AR can be important for differences in functional activity and orthosteric agonist or antagonist affinity and can be used for the design of allosteric modulators, which can bind through lipid pathways. We observed a stronger binding for cholesterol to A₁R (i.e., generally higher association rates) compared to A_2AR, which remains to be demonstrated. For the active states, cholesterol binds to residues with much longer residence times compared to the inactive state for both A_2AR and A₁R. Taken together, binding sites of active A₁R may be considered as promising allosteric targets.

Systematic analyses of the sequence conservation and ligand interaction patterns of purinergic P1 and P2Y receptors provide a structural basis for receptor selectivity

Purinergic receptors are membrane proteins that regulate numerous cellular functions by catalyzing reactions involving purine nucleotides or nucleosides. Among the three receptor families, i.e., P1, P2X, and P2Y, the P1 and P2Y receptors share common structural features of class A GPCR. Comprehensive sequence and structural analysis revealed that the P1 and P2Y receptors belong to two distinct groups. They exhibit different ligand-binding site features that can distinguish between specific activators. These specific amino acid residues in the binding cavity may be involved in the selectivity and unique pharmacological behavior of each subtype. In this study, we conducted a structure-based analysis of purinergic P1 and P2Y receptors to identify their evolutionary signature and obtain structural insights into ligand recognition and selectivity. The structural features of the P1 and P2Y receptor classes were compared based on sequence conservation and ligand interaction patterns. Orthologous protein sequences were collected for the P1 and P2Y receptors, and sequence conservation was calculated based on Shannon entropy to identify highly conserved residues. To analyze the ligand interaction patterns, we performed docking studies on the P1 and P2Y receptors using known ligand information extracted from the ChEMBL database. We analyzed how the conserved residues are related to ligand-binding sites and how the key interacting residues differ between P1 and P2Y receptors, or between agonists and antagonists. We extracted new similarities and differences between the receptor subtypes, and the results can be used for designing new ligands by predicting hotspot residues that are important for functional selectivity.

Dual A1/A3 Adenosine Receptor Antagonists: Binding Kinetics and Structure-Activity Relationship Studies Using Mutagenesis and Alchemical Binding Free Energy Calculations

Drugs targeting adenosine receptors (AR) can provide treatment for diseases. We report the identification of 7-(phenylamino)-pyrazolo[3,4-c]pyridines L2-L10, A15, and A17 as low-micromolar to low-nanomolar A₁R/A₃R dual antagonists, with 3-phenyl-5-cyano-7-(trimethoxyphenylamino)-pyrazolo[3,4-c]pyridine (A17) displaying the highest affinity at both receptors with a long residence time of binding, as determined using a NanoBRET-based assay. Two binding orientations of A17 produce stable complexes inside the orthosteric binding area of A₁R in molecular dynamics (MD) simulations, and we selected the most plausible orientation based on the agreement with alanine mutagenesis supported by affinity experiments. Interestingly, for drug design purposes, the mutation of L250^6.51 to alanine increased the binding affinity of A17 at A₁R. We explored the structure-activity relationships against A₁R using alchemical binding free energy calculations with the thermodynamic integration coupled with the MD simulation (TI/MD) method, applied on the whole G-protein-coupled receptor-membrane system, which showed a good agreement (r = 0.73) between calculated and experimental relative binding free energies.

GPCR Agonist-to-Antagonist Conversion: Enabling the Design of Nucleoside Functional Switches for the A2A Adenosine Receptor

Modulators of the G protein-coupled A_2A adenosine receptor (A_2AAR) have been considered promising agents to treat Parkinson’s disease, inflammation, cancer, and central nervous system disorders. Herein, we demonstrate that a thiophene modification at the C8 position in the common adenine scaffold converted an A_2AAR agonist into an antagonist. We synthesized and characterized a novel A_2AAR antagonist, 2 (LJ-4517), with K_i = 18.3 nM. X-ray crystallographic structures of 2 in complex with two thermostabilized A_2AAR constructs were solved at 2.05 and 2.80 Å resolutions. In contrast to A_2AAR agonists, which simultaneously interact with both Ser277^7.42 and His278^7.43, 2 only transiently contacts His278^7.43, which can be direct or water-mediated. The n-hexynyl group of 2 extends into an A_2AAR exosite. Structural analysis revealed that the introduced thiophene modification restricted receptor conformational rearrangements required for subsequent activation. This approach can expand the repertoire of adenosine receptor antagonists that can be designed based on available agonist scaffolds.

Comparative studies of AlphaFold, RoseTTAFold and Modeller: a case study involving the use of G-protein-coupled receptors

Neural network (NN)-based protein modeling methods have improved significantly in recent years. Although the overall accuracy of the two non-homology-based modeling methods, AlphaFold and RoseTTAFold, is outstanding, their performance for specific protein families has remained unexamined. G-protein-coupled receptor (GPCR) proteins are particularly interesting since they are involved in numerous pathways. This work directly compares the performance of these novel deep learning-based protein modeling methods for GPCRs with the most widely used template-based software—Modeller. We collected the experimentally determined structures of 73 GPCRs from the Protein Data Bank. The official AlphaFold repository and RoseTTAFold web service were used with default settings to predict five structures of each protein sequence. The predicted models were then aligned with the experimentally solved structures and evaluated by the root-mean-square deviation (RMSD) metric. If only looking at each program’s top-scored structure, Modeller had the smallest average modeling RMSD of 2.17 Å, which is better than AlphaFold’s 5.53 Å and RoseTTAFold’s 6.28 Å, probably since Modeller already included many known structures as templates. However, the NN-based methods (AlphaFold and RoseTTAFold) outperformed Modeller in 21 and 15 out of the 73 cases with the top-scored model, respectively, where no good templates were available for Modeller. The larger RMSD values generated by the NN-based methods were primarily due to the differences in loop prediction compared to the crystal structures.

Development of an Allostery Responsive Chromatographic Method for Screening Potential Allosteric Modulator of Beta2-adrenoceptor from a Natural Product-Derived DNA-Encoded Chemical Library

Allosteric ligands are promising drugs owing to their remote regulations of the orthosteric ligand signaling pathway. There are few allosteric ligands due to the lack of handy and efficacious method for the screening. Herein, we developed an affinity chromatographic method for allosteric ligand screening by immobilizing purified beta2 adrenoceptor (β₂-AR) onto macroporous silica gel by a two-point tethering method. The method relies on the occupation of the orthosteric site by an antagonist and the chelation of N-terminal His-tag of the receptor and Ni²⁺ coated on the gel. The immobilized β₂-AR demonstrated the greatest allosteric responsive feature when Cmpd-15 (0.25 μM) was included in the mobile phase. Under the same conditions, the association constants of three agonists (salbutamol, terbutaline, and tulobuterol) reduced to 47%, 19%, and 27% compared with the data without the inclusion of Cmpd-15 in the mobile phase. APF was screened as a potential allosteric modulator of β₂-AR by applying the immobilized receptor in a natural product-derived DNA-encoded chemical library (DEL). Relying on these results, we reasoned that the current method has potential in screening allosteric ligands of the receptor. We expect that it is applicable for the discovery of new allosteric binding sites of a target protein and screening allosteric modulators of the other receptors from complex samples.

Discovery of a High Affinity Adenosine A1/A3 Receptor Antagonist with a Novel 7-Amino-pyrazolo[3,4-d]pyridazine Scaffold

Here we describe the design and synthesis of pyrazolo[3,4-d]pyridazines as adenosine receptor (AR) ligands. We demonstrate that the introduction of a 3-phenyl group, together with a 7-benzylamino and 1-methyl group at the pyrazolopyridazine scaffold, generated the antagonist compound 10b, which displayed 21 nM affinity and a residence time of ∼60 min, for the human A₁R, 55 nM affinity and a residence time of ∼73 min, for the human A₃R and 1.7 μΜ affinity for the human A_2BR while not being toxic. Strikingly, the 2-methyl analog of 10b, 15b, had no significant affinity. Docking calculations and molecular dynamics simulations of the ligands inside the orthosteric binding area suggested that the 2-methyl group in 15b hinders the formation of hydrogen bonding interactions with N^6.55 which are considered critical for the stabilization inside the orthosteric binding cavity. We, therefore, demonstrate that 10a is a novel scaffold for the development of high affinity AR ligands. From the mutagenesis experiments the biggest effect was observed for the Y271^7.46A mutation which caused an ∼10-fold reduction in the binding affinity of 10b.

Purinergic receptors modulators: An emerging pharmacological tool for disease management

Purinergic signaling is mediated through extracellular nucleotides (adenosine 5'-triphosphate, uridine-5'-triphosphate, adenosine diphosphate, uridine-5'-diphosphate, and adenosine) that serve as signaling molecules. In the early 1990s, purines and pyrimidine receptors were cloned and characterized drawing the attention of scientists toward this aspect of cellular signaling. This signaling pathway is comprised of four subtypes of adenosine receptors (P1), eight subtypes of G-coupled protein receptors (P2YRs), and seven subtypes of ligand-gated ionotropic receptors (P2XRs). In current studies, the pathophysiology and therapeutic potentials of these receptors have been focused on. Various ligands, modulating the functions of purinergic receptors, are in current clinical practices for the treatment of various neurodegenerative disorders and cardiovascular diseases. Moreover, several purinergic receptors ligands are in advanced phases of clinical trials as a remedy for depression, epilepsy, autism, osteoporosis, atherosclerosis, myocardial infarction, diabetes, irritable bowel syndrome, and cancers. In the present study, agonists and antagonists of purinergic receptors have been summarized that may serve as pharmacological tools for drug design and development.

Regionally selective cardiovascular responses to adenosine A2A and A2B receptor activation

Adenosine is a local mediator that regulates changes in the cardiovascular system via activation of four G protein-coupled receptors (A₁ , A_2A , A_2B , A₃ ). Here, we have investigated the effect of A_2A and A_2B -selective agonists on vasodilatation in three distinct vascular beds of the rat cardiovascular system. NanoBRET ligand binding studies were used to confirm receptor selectivity. The regional hemodynamic effects of adenosine A_2A and A_2B selective agonists were investigated in conscious rats. Male Sprague-Dawley rats (350-450 g) were chronically implanted with pulsed Doppler flow probes on the renal artery, mesenteric artery, and the descending abdominal aorta. Cardiovascular responses were measured following intravenous infusion (3 min for each dose) of the A_2A -selective agonist CGS 21680 (0.1, 0.3, 1 µg kg^-1 min^-1 ) or the A_2B -selective agonist BAY 60-6583 (4,13.3, 40 µg kg^-1 min^-1 ) following predosing with the A_2A -selective antagonist SCH 58261 (0.1 or 1 mg kg^-1 min^-1 ), the A_2B /A_2A antagonist PSB 1115 (10 mg kg^-1 min^-1 ) or vehicle. The A_2A -selective agonist CGS 21680 produced a striking increase in heart rate (HR) and hindquarters vascular conductance (VC) that was accompanied by a significant decrease in mean arterial pressure (MAP) in conscious rats. In marked contrast, the A_2B -selective agonist BAY 60-6583 significantly increased HR and VC in the renal and mesenteric vascular beds, but not in the hindquarters. Taken together, these data indicate that A_2A and A_2B receptors are regionally selective in their regulation of vascular tone. These results suggest that the development of A_2B receptor agonists to induce vasodilatation in the kidney may provide a good therapeutic approach for the treatment of acute kidney injury.

International Union of Basic and Clinical Pharmacology. CXII: Adenosine Receptors: A Further Update

Our previous International Union of Basic and Clinical Pharmacology report on the nomenclature and classification of adenosine receptors (2011) contained a number of emerging developments with respect to this G protein-coupled receptor subfamily, including protein structure, protein oligomerization, protein diversity, and allosteric modulation by small molecules. Since then, a wealth of new data and results has been added, allowing us to explore novel concepts such as target binding kinetics and biased signaling of adenosine receptors, to examine a multitude of receptor structures and novel ligands, to gauge new pharmacology, and to evaluate clinical trials with adenosine receptor ligands. This review should therefore be considered a further update of our previous reports from 2001 and 2011. SIGNIFICANCE STATEMENT: Adenosine receptors (ARs) are of continuing interest for future treatment of chronic and acute disease conditions, including inflammatory diseases, neurodegenerative afflictions, and cancer. The design of AR agonists ("biased" or not) and antagonists is largely structure based now, thanks to the tremendous progress in AR structural biology. The A2A- and A2BAR appear to modulate the immune response in tumor biology. Many clinical trials for this indication are ongoing, whereas an A2AAR antagonist (istradefylline) has been approved as an anti-Parkinson agent.

Molecular Simulations and Drug Discovery of Adenosine Receptors

G protein-coupled receptors (GPCRs) represent the largest family of human membrane proteins. Four subtypes of adenosine receptors (ARs), the A1AR, A2AAR, A2BAR and A3AR, each with a unique pharmacological profile and distribution within the tissues in the human body, mediate many physiological functions and serve as critical drug targets for treating numerous human diseases including cancer, neuropathic pain, cardiac ischemia, stroke and diabetes. The A1AR and A3AR preferentially couple to the Gi/o proteins, while the A2AAR and A2BAR prefer coupling to the Gs proteins. Adenosine receptors were the first subclass of GPCRs that had experimental structures determined in complex with distinct G proteins. Here, we will review recent studies in molecular simulations and computer-aided drug discovery of the adenosine receptors and also highlight their future research opportunities.

Adenosine receptor antagonists: Recent advances and therapeutic perspective

Adenosine is an endogenous purine-based nucleoside expressed nearly in all body tissues. It regulates various body functions by activating four G-protein coupled receptors, A₁, A_2A, A_2B, and A₃. These receptors are widely acknowledged as drug targets for treating different neurological, metabolic, and inflammatory diseases. Although numerous adenosine receptor inhibitors have been developed worldwide, achieving target selectivity is still a big hurdle in drug development. However, the identification of specific radioligands-based affinity assay, fluorescent ligands, and MS-based ligand assay have contributed to the development of selective and potent adenosine ligands. In recent years various small heterocyclic-based molecules have shown some promising results. Istradefylline has been approved for treating Parkinson's in Japan, while preladenant, tozadenant, CVT-6883, MRS-1523, and many more are under different phases of clinical development. The present review is focused on the quest to develop potent and selective adenosine inhibitors from 2013 to early 2021 by various research groups. The review also highlights their biological activity, selectivity, structure-activity relationship, molecular docking, and mechanistic studies. A special emphsesis on drug designing strategies has been also given the manuscript. The comprehensive compilation of research work carried out in the field will provide inevitable scope for designing and developing novel adenosine inhibitors with improved selectivity and efficacy.

Homo-oligomerization of the human adenosine A2A receptor is driven by the intrinsically disordered C-terminus

G protein-coupled receptors (GPCRs) have long been shown to exist as oligomers with functional properties distinct from those of the monomeric counterparts, but the driving factors of oligomerization remain relatively unexplored. Herein, we focus on the human adenosine A2A receptor (A2AR), a model GPCR that forms oligomers both in vitro and in vivo. Combining experimental and computational approaches, we discover that the intrinsically disordered C-terminus of A2AR drives receptor homo-oligomerization. The formation of A2AR oligomers declines progressively with the shortening of the C-terminus. Multiple interaction types are responsible for A2AR oligomerization, including disulfide linkages, hydrogen bonds, electrostatic interactions, and hydrophobic interactions. These interactions are enhanced by depletion interactions, giving rise to a tunable network of bonds that allow A2AR oligomers to adopt multiple interfaces. This study uncovers the disordered C-terminus as a prominent driving factor for the oligomerization of a GPCR, offering important insight into the effect of C-terminus modification on receptor oligomerization of A2AR and other GPCRs reconstituted in vitro for biophysical studies.

Purinergic GPCR transmembrane residues involved in ligand recognition and dimerization

We compare the GPCR-ligand interactions and highlight important residues for recognition in purinergic receptors-from both X-ray crystallographic and cryo-EM structures. These include A1 and A2A adenosine receptors, and P2Y1 and P2Y12 receptors that respond to ADP and other nucleotides. These receptors are important drug discovery targets for immune, metabolic and nervous system disorders. In most cases, orthosteric ligands are represented, except for one allosteric P2Y1 antagonist. This review catalogs the residues and regions that engage in contacts with ligands or with other GPCR protomers in dimeric forms. Residues that are in proximity to bound ligands within purinergic GPCR families are correlated. There is extensive conservation of recognition motifs between adenosine receptors, but the P2Y1 and P2Y12 receptors are each structurally distinct in their ligand recognition. Identifying common interaction features for ligand recognition within a receptor class that has multiple structures available can aid in the drug discovery process.

Molecular Dynamics Simulations for the Determination of the Characteristic Structural Differences between Inactive and Active States of Wild Type and Mutants of the Orexin2 Receptor

The orexin2 receptor (OX2R), which is classified as a class A G protein-coupled receptor (GPCR), is the target of our study. We performed over 20 several-microsecond-scale molecular dynamics simulations of the wild type and mutants of OX2R to extract the characteristics of the structural changes taking place in the active state. We introduced mutations that exhibited the stable inactive state and the constitutively active state in class A GPCRs. In these simulations, significant characteristic structural changes were observed in the V309^6.40Y mutant, which corresponded to a constitutively active mutant. These conformational changes include the outward movement of the transmembrane helix 6 (TM6) and the inward movement of TM7, which are common structural changes in the activation of GPCRs. In addition, we extracted a suitable index for the quantitative evaluation of the active and inactive states of GPCRs, namely, the inter-atomic distance of Cα atoms between x(3.46) and Y(7.53). The structures of the inactive and active states solved by X-ray crystallography and cryo-electron microscopy can be classified using the inter-atomic distance. Furthermore, we clarified that the inward movement of TM7 requires the swapping of M305^6.36 on TM6 and L367^7.56 on TM7. Finally, we discussed the structural advantages of TM7 inward movement for GPCR activation.

Binding Characterization of Agonists and Antagonists by MCCS: A Case Study from Adenosine A2A Receptor

Characterizing the structural basis of ligand recognition of adenosine A_2A receptor (AA_2AR) will facilitate its rational design and development of small molecules with high affinity and selectivity, as well as optimal therapeutic effects for pain, cancers, drug abuse disorders, etc. In the present work, we applied our reported algorithm, molecular complex characterizing system (MCCS), to characterize the binding features of AA_2AR based on its reported 3D structures of protein-ligand complexes. First, we compared the binding score to the reported experimental binding affinities of each compound. Then, we calculated an output example of residue energy contribution using MCCS and compared the results with data obtained from MM/GBSA. The consistency in results indicated that MCCS is a powerful, fast, and accurate method. Sequentially, using a receptor-ligand data set of 57 crystallized structures of AA_2ARs, we characterized the binding features of the binding pockets in AA_2AR, summarized the key residues that distinguish antagonist from agonist, produced heatmaps of residue energy contribution for clustering various statuses of AA_2ARs, explored the selectivity between AA_2AR and AA_1AR, etc. All the information provided new insights into the protein features of AA_2AR and will facilitate its rational drug design.

Pathways and Mechanism of Caffeine Binding to Human Adenosine A2A Receptor

Caffeine (CFF) is a common antagonist to the four subtypes of adenosine G-protein-coupled receptors (GPCRs), which are critical drug targets for treating heart failure, cancer, and neurological diseases. However, the pathways and mechanism of CFF binding to the target receptors remain unclear. In this study, we have performed all-atom-enhanced sampling simulations using a robust Gaussian-accelerated molecular dynamics (GaMD) method to elucidate the binding mechanism of CFF to human adenosine A_2A receptor (A_2AAR). Multiple 500–1,000 ns GaMD simulations captured both binding and dissociation of CFF in the A_2AAR. The GaMD-predicted binding poses of CFF were highly consistent with the x-ray crystal conformations with a characteristic hydrogen bond formed between CFF and residue N6.55 in the receptor. In addition, a low-energy intermediate binding conformation was revealed for CFF at the receptor extracellular mouth between ECL2 and TM1. While the ligand-binding pathways of the A_2AAR were found similar to those of other class A GPCRs identified from previous studies, the ECL2 with high sequence divergence serves as an attractive target site for designing allosteric modulators as selective drugs of the A_2AAR.

Discovery of novel dual adenosine A1/A2A receptor antagonists using deep learning, pharmacophore modeling and molecular docking

Adenosine receptors (ARs) have been demonstrated to be potential therapeutic targets against Parkinson's disease (PD). In the present study, we describe a multistage virtual screening approach that identifies dual adenosine A1 and A2A receptor antagonists using deep learning, pharmacophore models, and molecular docking methods. Nineteen hits from the ChemDiv library containing 1,178,506 compounds were selected and further tested by in vitro assays (cAMP functional assay and radioligand binding assay); of these hits, two compounds (C8 and C9) with 1,2,4-triazole scaffolds possessing the most potent binding affinity and antagonistic activity for A1/A2A ARs at the nanomolar level (pKi of 7.16-7.49 and pIC50 of 6.31-6.78) were identified. Further molecular dynamics (MD) simulations suggested similarly strong binding interactions of the complexes between the A1/A2A ARs and two compounds (C8 and C9). Notably, the 1,2,4-triazole derivatives (compounds C8 and C9) were identified as the most potent dual A1/A2A AR antagonists in our study and could serve as a basis for further development. The effective multistage screening approach developed in this study can be utilized to identify potent ligands for other drug targets.

Characterization of binding kinetics of A2AR to Gαs protein by surface plasmon resonance

Because of their surface localization, G protein-coupled receptors (GPCRs) are often pharmaceutical targets as they respond to a variety of extracellular stimuli (e.g., light, hormones, small molecules) that may activate or inhibit a downstream signaling response. The adenosine A_2A receptor (A_2AR) is a well-characterized GPCR that is expressed widely throughout the human body, with over 10 crystal structures determined. Truncation of the A_2AR C-terminus is necessary for crystallization as this portion of the receptor is long and unstructured; however, previous work suggests shortening of the A_2AR C-terminus from 412 to 316 amino acids (A_2AΔ316R) ablates downstream signaling, as measured by cAMP production, to below that of constitutive full-length A_2AR levels. As cAMP production is downstream of the first activation event-coupling of G protein to its receptor-investigating that first step in activation is important in understanding how the truncation effects native GPCR function. Here, using purified receptor and Gα_s proteins, we characterize the association of A_2AR and A_2AΔ316R to Gα_s with and without GDP or GTPγs using surface plasmon resonance (SPR). Gα_s affinity for A_2AR was greatest for apo-Gα_s, moderately affected in the presence of GDP and nearly completely ablated by the addition of GTPγs. Truncation of the A_2AR C-terminus (A_2AΔ316R) decreased the affinity of the unliganded receptor for Gα_s by ∼20%, suggesting small changes to binding can greatly impact downstream signaling.

The Specificity of Downstream Signaling for A1 and A2AR Does Not Depend on the C-Terminus, Despite the Importance of This Domain in Downstream Signaling Strength

Recent efforts to determine the high-resolution crystal structures for the adenosine receptors (A₁R and A_2AR) have utilized modifications to the native receptors in order to facilitate receptor crystallization and structure determination. One common modification is a truncation of the unstructured C-terminus, which has been utilized for all the adenosine receptor crystal structures obtained to date. Ligand binding for this truncated receptor has been shown to be similar to full-length receptor for A_2AR. However, the C-terminus has been identified as a location for protein-protein interactions that may be critical for the physiological function of these important drug targets. We show that variants with A_2AR C-terminal truncations lacked cAMP-linked signaling compared to the full-length receptor constructs transfected into mammalian cells (HEK-293). In addition, we show that in a humanized yeast system, the absence of the full-length C-terminus affected downstream signaling using a yeast MAPK response-based fluorescence assay, though full-length receptors showed native-like G-protein coupling. To further study the G protein coupling, we used this humanized yeast platform to explore coupling to human-yeast G-protein chimeras in a cellular context. Although the C-terminus was essential for Gα protein-associated signaling, chimeras of A₁R with a C-terminus of A_2AR coupled to the A₁R-specific Gα (i.e., Gαi1 versus Gαs). This surprising result suggests that the C-terminus is important in the signaling strength, but not specificity, of the Gα protein interaction. This result has further implications in drug discovery, both in enabling the experimental use of chimeras for ligand design, and in the cautious interpretation of structure-based drug design using truncated receptors.

Covalent allosteric modulation: An emerging strategy for GPCRs drug discovery

Designing covalent allosteric modulators brings new opportunities to the field of drug discovery towards G-protein-coupled receptors (GPCRs). Targeting an allosteric binding pocket can allow a modulator to have protein subtype selectivity and low drug resistance. Utilizing covalent warheads further enables the modulator to increase the binding potency and extend the duration of action. This review starts with GPCR allosteric modulation to discuss the structural biology of allosteric binding pockets, the different types of allosteric modulators, as well as the advantages of employing allosteric modulation. This is followed by a discussion on covalent modulators to clarify how covalent ligands can benefit the receptor modulation and to illustrate moieties that can commonly be used as covalent warheads. Finally, case studies are presented on designing class A, B, and C GPCR covalent allosteric modulators to demonstrate successful stories on combining allosteric modulation and covalent binding. Limitations and future perspectives are also covered.

Discovery of novel 1,3,5-triazine as adenosine A2A receptor antagonist for benefit in Parkinson's disease

Parkinson's disease (PD) is a chronic neuro-degenerative ailment characterized by impairment in various motor and nonmotor functions of the body. In the past few years, adenosine A₂ A receptor (A₂ AR) antagonists have attracted much attention due to significant relief in PD. Therefore, in the current study, we intend to disclose the development of novel 1,3,5-triazines as A₂ AR antagonist. The radioligand binding and selectivity of analogs were tested in HEK293 (human embryonic kidney) and the cells were transfected with pcDNA 3.1(+) containing full-length human A₂ AR cDNA and pcDNA 3.1(+) containing full-length human A₁ R cDNA, where they exhibit selective affinity for A₂ AR. Molecular docking analysis was also conducted to rationalize the probable mode of action, binding affinity, and orientation of the most potent molecule (7c) at the active site of A₂ AR. It has been shown that compound 7c form numerous nonbonded interactions in the active site of A₂ AR by interacting with Ala59, Ala63, Ile80, Val84 Glu169, Phe168, Met270, and Ile274. The study revealed 1,3,5-triazines as a novel class of A₂ AR antagonists.

Purinergic Signaling: Impact of GPCR Structures on Rational Drug Design

The purinergic signaling system includes membrane-bound receptors for extracellular purines and pyrimidines, and enzymes/transporters that regulate receptor activation by endogenous agonists. Receptors include: adenosine (A1 , A2A , A2B, and A3 ) and P2Y (P2Y1 , P2Y2 , P2Y4 , P2Y6 , P2Y11 , P2Y12 , P2Y13 , and P2Y14 ) receptors (all GPCRs), as well as P2X receptors (ion channels). Receptor activation, especially accompanying physiological stress or damage, creates a temporal sequence of signaling to counteract this stress and either mobilize (P2Rs) or suppress (ARs) immune responses. Thus, modulation of this large signaling family has broad potential for treating chronic diseases. Experimentally determined structures represent each of the three receptor families. We focus on selective purinergic agonists (A1 , A3 ), antagonists (A3 , P2Y14 ), and allosteric modulators (P2Y1 , A3 ). Examples of applying structure-based design, including the rational modification of known ligands, are presented for antithrombotic P2Y1 R antagonists and anti-inflammatory P2Y14 R antagonists and A3 AR agonists. A3 AR agonists are a potential, nonaddictive treatment for chronic neuropathic pain.

Tumor Immunotherapy Using A2A Adenosine Receptor Antagonists

The A_2A adenosine receptor (A_2AAR) plays critical roles in human physiology and pathophysiology, which makes it an important drug target. Previous drug-discovery efforts targeting the A_2AAR have been focused on the use of A_2AAR antagonists for the treatment of Parkinson's disease. More recently, the A_2AAR has attracted additional attention for its roles in immuno-oncology, and a number of A_2AAR antagonists are currently used as lead compounds for antitumor drugs in both preclinical models and clinical trials. This review surveys recent advances in the development of A_2AAR antagonists for cancer immunotherapy. The therapeutic potential of representative A_2AAR antagonists is discussed based on both animal efficacy studies and clinical data.

Adenosine A2A Receptor Antagonists for Cancer Immunotherapy

Currently, the most promising therapeutic modality for cancer treatment is the blockade of immune checkpoint pathways, which has revolutionized cancer therapy in the past 15 years. Strategies targeting and modulating adenosine A_2A receptor (A_2AR), an emerging alternative immune checkpoint, have shown the potential to produce significant therapeutic effects. In this review, we describe the immunosuppressive activities of A_2AR and A_2BR in the tumor microenvironment (TME), followed by a summary and discussion of the structure-activity relationship (SAR) of the A_2AR (and dual A_2AR/A_2BR) antagonists that have been experimentally confirmed to exert oncoimmunological effects. This review also provides an update on the compounds under clinical evaluation and insights into the ligand binding modes of the receptor.

In Silico Drug Design for Purinergic GPCRs: Overview on Molecular Dynamics Applied to Adenosine and P2Y Receptors

Molecular modeling has contributed to drug discovery for purinergic GPCRs, including adenosine receptors (ARs) and P2Y receptors (P2YRs). Experimental structures and homology modeling have proven to be useful in understanding and predicting structure activity relationships (SAR) of agonists and antagonists. This review provides an excursus on molecular dynamics (MD) simulations applied to ARs and P2YRs. The binding modes of newly synthesized A1AR- and A3AR-selective nucleoside derivatives, potentially of use against depression and inflammation, respectively, have been predicted to recapitulate their SAR and the species dependence of A3AR affinity. P2Y12R and P2Y1R crystallographic structures, respectively, have provided a detailed understanding of the recognition of anti-inflammatory P2Y14R antagonists and a large group of allosteric and orthosteric antagonists of P2Y1R, an antithrombotic and neuroprotective target. MD of A2AAR (an anticancer and neuroprotective target), A3AR, and P2Y1R has identified microswitches that are putatively involved in receptor activation. The approach pathways of different ligands toward A2AAR and P2Y1R binding sites have also been explored. A1AR, A2AAR, and A3AR were utilizes to study allosteric phenomena, but locating the binding site of structurally diverse allosteric modulators, such as an A3AR enhancer LUF6000, is challenging. Ligand residence time, a predictor of in vivo efficacy, and the structural role of water were investigated through A2AAR MD simulations. Thus, new MD and other modeling algorithms have contributed to purinergic GPCR drug discovery.

Allosteric Antagonism of the A2A Adenosine Receptor by a Series of Bitopic Ligands

Allosteric antagonism by bitopic ligands, as reported for many receptors, is a distinct modulatory mechanism. Although several bitopic A_2A adenosine receptor (A_2AAR) ligand classes were reported as pharmacological tools, their receptor binding and functional antagonism patterns, i.e., allosteric or competitive, were not well characterized. Therefore, here we systematically characterized A_2AAR binding and functional antagonism of two distinct antagonist chemical classes. i.e., fluorescent conjugates of xanthine amine congener (XAC) and SCH442416. Bitopic ligands were potent, weak, competitive or allosteric, based on the combination of pharmacophore, linker and fluorophore. Among antagonists tested, XAC, XAC245, XAC488, SCH442416, MRS7352 showed K_i binding values consistent with K_B values from functional antagonism. Interestingly, MRS7396, XAC-X-BY630 (XAC630) and 5-(N,N-hexamethylene)amiloride (HMA) were 9–100 times weaker in displacing fluorescent MRS7416 binding than radioligand binding. XAC245, XAC630, MRS7396, MRS7416 and MRS7322 behaved as allosteric A_2AAR antagonists, whereas XAC488 and MRS7395 antagonized competitively. Schild analysis showed antagonism slopes of 0.42 and 0.47 for MRS7396 and XAC630, respectively. Allosteric antagonists HMA and MRS7396 were more potent in displacing [³H]ZM241385 binding than MRS7416 binding. Sodium site D52N mutation increased and decreased affinity of HMA and MRS7396, respectively, suggesting possible preference for different A_2AAR conformations. The allosteric binding properties of some bitopic ligands were rationalized and analyzed using the Hall two-state allosteric model. Thus, fluorophore tethering to an orthosteric ligand is not neutral pharmacologically and may confer unexpected properties to the conjugate.

Insights into adenosine A2A receptor activation through cooperative modulation of agonist and allosteric lipid interactions

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.

Computational insights into the molecular mechanisms of differentiated allosteric modulation at the mu opioid receptor by structurally similar bitopic modulators

Targeting the mu opioid receptor (MOR) by applying orthosteric ligands is the most frequently employed method to treat opioid use disorder (OUD). Unfortunately, most of MOR orthosteric ligands produce severe side effects, mainly due to their low selectivity over other opioid receptors. In contrast, some G protein-coupled receptor allosteric modulators have been reported to exhibit high subtype selectivity and can effectively modulate the potency and/or efficacy of orthosteric ligands. Recently, NAQ and its analog NCQ were identified as novel MOR bitopic modulators. Interestingly, NAQ and NCQ were similar in structure but exhibited different efficacy profiles to the MOR. NAQ exhibited an antagonism activity to the MOR while NCQ showed a partial agonism activity to the MOR. In the present study, molecular modeling methods were applied to explore the putative molecular mechanisms of their different functional profiles to the MOR. When NAQ binding with the inactive MOR, the 'address' portion of NAQ interacted with the MOR allosteric site but showed no significant allosteric modulation of the efficacy of the 'message' portion of NAQ. However, when NCQ binding with the inactive and active MOR, the 'address' portion of NCQ seemed to be able to positively modulate the efficacy of the 'message' portion of NCQ at varying levels. Evidentially, the substituents at the 1'- and 4'-positions of the isoquinoline ring of NCQ seemed to play a critical role in the modulatory function of the 'address' portion of NCQ. These findings will be invaluable to develop our next generation of MOR bitopic modulators with high affinity and subtype selectivity to potentially treat OUD.

Neutrophil Signaling That Challenges Dogmata of G Protein-Coupled Receptor Regulated Functions

Activation as well as recruitment of neutrophils, the most abundant leukocyte in human blood, to sites of infection/inflammation largely rely on surface-exposed chemoattractant receptors. These receptors belong to the family of 7-transmembrane domain receptors also known as G protein-coupled receptors (GPCRs) due to the fact that part of the downstream signaling relies on an activation of heterotrimeric G proteins. The neutrophil GPCRs share significant sequence homologies but bind many structurally diverse activating (agonistic) and inhibiting (antagonistic) ligands, ranging from fatty acids to purines, peptides, and lipopeptides. Recent structural and functional studies of neutrophil receptors have generated important information on GPCR biology in general; this knowledge aids in the overall understanding of general pharmacological principles, governing regulation of neutrophil function and inflammatory processes, including novel leukocyte receptor activities related to ligand recognition, biased/functional selective signaling, allosteric modulation, desensitization mechanisms and reactivation, and communication (cross-talk) between GPCRs. This review summarizes the recent discoveries and pharmacological hallmarks with focus on neutrophil GPCRs. In addition, unmet challenges are dealt with, including recognition by the receptors of diverse ligands and how biased signaling mediates different biological effects.

Targeting Purinergic Signaling and Cell Therapy in Cardiovascular and Neurodegenerative Diseases

Extracellular purines exert several functions in physiological and pathophysiological mechanisms. ATP acts through P2 receptors as a neurotransmitter and neuromodulator and modulates heart contractility, while adenosine participates in neurotransmission, blood pressure, and many other mechanisms. Because of their capability to differentiate into mature cell types, they provide a unique therapeutic strategy for regenerating damaged tissue, such as in cardiovascular and neurodegenerative diseases. Purinergic signaling is pivotal for controlling stem cell differentiation and phenotype determination. Proliferation, differentiation, and apoptosis of stem cells of various origins are regulated by purinergic receptors. In this chapter, we selected neurodegenerative and cardiovascular diseases with clinical trials using cell therapy and purinergic receptor targeting. We discuss these approaches as therapeutic alternatives to neurodegenerative and cardiovascular diseases. For instance, promising results were demonstrated in the utilization of mesenchymal stem cells and bone marrow mononuclear cells in vascular regeneration. Regarding neurodegenerative diseases, in general, P2X7 and A_2A receptors mostly worsen the degenerative state. Stem cell-based therapy, mainly through mesenchymal and hematopoietic stem cells, showed promising results in improving symptoms caused by neurodegeneration. We propose that purinergic receptor activity regulation combined with stem cells could enhance proliferative and differentiation rates as well as cell engraftment.

Insights to the Binding of a Selective Adenosine A3 Receptor Antagonist Using Molecular Dynamic Simulations, MM-PBSA and MM-GBSA Free Energy Calculations, and Mutagenesis

Adenosine A₃ receptor (A₃R) is a promising drug target cancer and for a number of other conditions like inflammatory diseases, including asthma and rheumatoid arthritis, glaucoma, chronic obstructive pulmonary disease, and ischemic injury. Currently, there is no experimentally determined structure of A₃R. We explored the binding profile of O4-{[3-(2,6-dichlorophenyl)-5-methylisoxazol-4-yl]carbonyl}-2-methyl-1,3-thiazole-4-carbohydroximamide (K18), which is a new specific and competitive antagonist at the orthosteric binding site of A₃R. MD simulations and MM-GBSA calculations of the WT A₃R in complex with K18 combined with in vitro mutagenic studies show that the most plausible binding conformation for the dichlorophenyl group of K18 is oriented toward trans-membrane helices (TM) 5, 6 and reveal important residues for binding. Further, MM-GBSA calculations distinguish mutations that reduce or maintain or increase antagonistic activity. Our studies show that selectivity of K18 toward A₃R is defined not only by direct interactions with residues within the orthosteric binding area but also by remote residues playing a significant role. Although V169^5.30 is considered to be a selectivity filter for A₃R binders, when it was mutated to glutamic acid, K18 maintained antagonistic potency, in agreement with our previous results obtained for agonists binding profile investigation. Mutation of the direct interacting residue L90^3.32 in the low region and the remote L264^7.35 in the middle/upper region to alanine increases antagonistic potency, suggesting an empty space in the orthosteric area available for increasing antagonist potency. These results approve the computational model for the description of K18 binding at A₃R, which we previously performed for agonists binding to A₃R, and the design of more effective antagonists based on K18.

Toward G protein-coupled receptor structure-based drug design using X-ray lasers

Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β2-adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins.

Reconstruction of apo A2A receptor activation pathways reveal ligand-competent intermediates and state-dependent cholesterol hotspots

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.

Structural Characterization of Agonist Binding to an A3 Adenosine Receptor through Biomolecular Simulations and Mutagenesis Experiments

The adenosine A₃ receptor (A₃R) binds adenosine and is a drug target against cancer cell proliferation. Currently, there is no experimental structure of A₃R. Here, we have generated a molecular model of A₃R in complex with two agonists, the nonselective 1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-β-d-ribofuranuronamide (NECA) and the selective 1-deoxy-1-[6-[[(3-iodophenyl)methyl]amino]-9H-purin-9-yl]-N-methyl-β-d-ribofuranuronamide (IB-MECA). Molecular dynamics simulations of the wild-type A₃R in complex with both agonists, combined with in vitro mutagenic studies revealed important residues for binding. Further, molecular mechanics-generalized Born surface area calculations were able to distinguish mutations that reduce or negate agonistic activity from those that maintained or increased the activity. Our studies reveal that selectivity of IB-MECA toward A₃R requires not only direct interactions with residues within the orthosteric binding area but also with remote residues. Although V169^5.30 is considered to be a selectivity filter for A₃R binders, when it was mutated to glutamic acid or alanine, the activity of IB-MECA increased by making new van der Waals contacts with TM5. This result may have implications in the design of new A₃R agonists.