Cryo-EM structures of adenosine receptor A3AR bound to selective agonists

Steric influence of 4'-position substituents and C2-Hexynyl group on A3AR antagonism in truncated 4'-Thioadenosine derivatives

A3 adenosine receptor (A3AR) has attracted significant interest due to its therapeutic potential in inflammation, neurodegenerative disorders, and cancer. This study investigates the structure-activity relationships (SAR) of truncated 4'-thioadenosine derivatives with modifications at the 4'- and C2-positions. Alkyl substituents of varying sizes (methyl, ethyl, isopropyl) were introduced at the 4'-position to evaluate steric effects, while C2-propynyl and hexynyl groups were incorporated to explore binding enhancement. The 4'-ethyl derivatives exhibit potent A3AR antagonistic effects, compared to the 4'-methyl series which exhibits partial agonist activity. C2-hexynyl substitution significantly enhanced binding affinity and antagonistic properties. In contrast, 4'-isopropyl derivatives lacked measurable binding, highlighting steric constraints at 4'-position. Docking studies revealed that none of the compounds formed interactions with Thr94, a residue critical for agonistic activity. This lack of interaction likely explains their observed antagonistic behavior, with the 4'-alkyl and C2-hexynyl substitutions appearing to play a significant role in this effect. This work underscores the role of steric bulk at the 4'-position and hydrophobic modifications at the C2-position in modulating A3AR activity, providing valuable insights for designing selective A3AR antagonists.

Research progress of CD73-adenosine signaling regulating hepatocellular carcinoma through tumor microenvironment

Adenosine signaling pathway is a kind of signal regulation hub widely existing in human body, which is involved in a series of physiological processes such as energy supply of body cells. CD73 is a highly concerned signaling protein in purine adenosine pathway, and its role in tumor development and prognosis has been paid more and more attention in recent years, especially in hepatocellular carcinoma (HCC). In this paper, the specific mechanism by which CD73-adenosine signaling regulates tumor microenvironment (TME) of liver cancer tumors was analyzed in detail, highlighting the importance of this pathway as a therapeutic target to combat tumor immunosuppression and enhance the anti-tumor immune response to prevent and treat hepatocellular carcinoma (HCC). In addition, a variety of current targeted therapeutic strategies for adenosine metabolic pathways are summarized, including the development of new drugs in the stage of preclinical research and clinical trials, and the mechanism of action, implementation possibility, and clinical effects of these therapies are discussed. By summarizing the latest scientific research results, in this review, we attempt to paint a panorama of the mechanism of adenosine action in tumor immunotherapy, with the aim to provide a solid theoretical basis and practical guidance for subsequent research and clinical application, ultimately promoting the development of more accurate and efficient tumor immunotherapy.

Structure-Activity Relationship Analysis of 2-Aryl-8-alkynyl Adenine and Nucleoside Scaffolds as A3 Adenosine Receptor Ligands

Numerous adenosine receptor (AR) ligands have been synthesized over many years, but the development of 2,8-disubstituted nucleoside derivatives was limited due to the lack of efficient synthetic methods. Leveraging Pd catalyst-controlled regioselective coupling, we embarked on structure-activity relationship (SAR) analyses at the C8 position. Our SAR studies revealed that an aliphatic alkyne chain of specific length, such as 1-hexyne, at the C8 position is ideally suited for hA2AAR interaction. A computational docking study revealed that the π-π interaction between His953.37 and C8-aromatic alkyne could induce an active conformation of hA3AR. Notably, compound 7b demonstrated exceptional potency and selectivity at hA3AR (K i,hA3 = 3.0 ± 0.5 nM), acting as the first 2,8-disubstituted nucleoside A3AR partial agonist. It underscores the strategic importance of C8 position modifications in modulating AR activity and function, paving the way for novel therapeutic agents targeting AR-mediated diseases.

Design, synthesis, and biological evaluation of 5'-deoxy (N)-methanocarbanucleoside derivatives as A3 adenosine receptor ligands

Based on the potent and selective antagonism exhibited by truncated North (N)-methanocarba adenosine analogs, we synthesized a series of 5'-deoxy (N)-methanocarba nucleosides to explore their structure-activity relationships (SAR). The stereoselective synthesis of the North cyclopropyl-fused alcohol was achieved from d-ribose using ring-closing metathesis, oxidative rearrangement, and cyclopropanation as key steps. Mitsunobu reactions were employed to condense nucleobases with glycosyl donors, followed by N6 functionalization with various amines. Despite their innovative design, all synthesized analogs exhibited lower binding affinity compared to the 4'-thio series and fully truncated (N)-methanocarba adenosine. Docking studies revealed that the 4'-methyl group of the rigid North conformational sugar introduces steric clashes, which likely contribute to the reduced affinity. These findings underscore the critical role of sugar conformation and steric effects in receptor interactions, providing valuable insights for the development of potent and selective A3AR ligands.

Design, Synthesis and Biological Evaluation of N6-Substituted-C2-Alkynyl-4'-Thionucleoside and 4'-Trucatedthionucleoside Derivatives as Novel A3 Adenosine Receptor Ligands

Adenosine receptors (ARs) play crucial roles in various physiological processes, making them significant targets for therapeutic intervention. This study focuses on the design, synthesis, and evaluation of N6-substituted-C2-alkynyl-4'-thioadenosine and truncated 4'-thioadenosine derivatives as selective ligands for the human A3 adenosine receptor (hA3 AR). Binding affinity assays demonstrated that modifications at the C2-alkyne and N6-amine positions significantly influenced receptor selectivity and potency. Compound 3b showed high affinity for hA3 AR (Ki = 1.8 nM) with excellent subtype selectivity and acted as an agonist. In contrast, truncated derivative 6b was an antagonist, while 6s, which shares the same sugar structure as 6b, functioned as a partial agonist, highlighting the roles of sugar and base moieties in ligand function. Molecular docking studies provided further insight into distinct binding modes, demonstrating the impact of minor structural variations on ligand-receptor binding dynamics. These findings contribute to the development of potent and selective A3 AR modulators by emphasizing the importance of fine structural adjustments in ligand design.

E. B. Hershberg Award: Taming Inflammation by Tuning Purinergic Signaling

The author presents his personal story from early contributions in purinergic receptor research to present-day structure-guided medicinal chemistry. Modulating purinergic signaling (encompassing pyrimidine nucleotides as well) and other nucleoside targets with small molecules is fruitful for identifying new directions for therapeutic intervention. Purinergic signaling encompasses four adenosine receptors, eight P2Y receptors that respond to various extracellular nucleotides, and trimeric P2X receptors that respond mainly to ATP. Each organ and tissue in the body expresses some combination of this family of cell-surface receptors, along with the enzymes and transporters that form, degrade, and process the native nucleoside and nucleotide agonists. The purinergic signaling system responds to physiological stress to an organ, for example by increasing the energy supply or decreasing the energy demand. The receptors are widespread on immune cells, such that P2Y and P2X receptor activation boosts the immune response when and where it is needed, for example to repel infection. In contrast, the adenosine receptors, which are activated later in the process─as stress-elevated ATP is hydrolyzed locally to adenosine by ectonucleotidases─tend to put the brakes on inflammation and can be used to correct an imbalance in pro- versus anti-inflammatory signals, such as in chronic pain. Hypoxia activates the immunosuppressive extracellular adenosine-A2A adenosine receptor axis, as originally formulated by Sitkovsky, which suppresses the immune response in the tumor microenvironment to make a cancer more aggressive. Conversely, the anti-inflammatory effects of adenosine receptor agonists have numerous therapeutic applications. Modulators of P2Y receptors, which respond to extracellular nucleotides, also show promise for treating chronic pain, metabolic disorders, and inflammation. Thus, control of this signaling system can be harnessed for treating a wide range of conditions, from cancer and neurodegeneration to autoimmune inflammatory diseases to ischemia of the brain or heart. The author's receiving the American Chemical Society's top award for medicinal chemistry in 2023 provides an opportunity to summarize these developments from their origins in empirical probing of receptor-ligand structure-activity relationship (SAR) to the current structure-based approaches, including conformational control of selectivity toward purinergic signaling. The work on each target receptor began either before or soon after it was cloned, and the initial focus was an academic exercise to use organic chemistry to develop a SAR for each target. The Jacobson lab has introduced chemical probes for 17 of the purinergic receptors as well as for associated regulators. Furthermore, surprisingly, some of the conformationally constrained nucleoside analogues can be designed to inhibit non-purinergic targets selectively, such as opioid and serotonin receptors and monoamine transporters. Only later did therapeutic applications of these pharmacological probes become apparent. Thus, the medicinal chemistry has largely enabled biological research on purinergic signaling by making definitive tool compounds available. Five compounds from the Jacobson laboratory (four adenosine derivatives) are currently in clinical trials for various chronic (autoimmune inflammatory and liver conditions) and acute (stroke, traumatic brain injury) conditions.

Exploring C2 and N6 Substituent Effects on Truncated 4'-Thioadenosine Derivatives as Dual A2A and A3 Adenosine Receptor Ligands

Based on high binding affinity of truncated 2-hexynyl-4'-thioadenosine (3 a) at both A2A adenosine receptor (AR) and A3 AR, we explored structure-activity relationship (SAR) of the C2-substitution by altering chain length of the 2-hexynyl moiety, thereby evaluating the hydrophobic pocket size. A series of truncated N6-substituted 4'-thioadenosine derivatives with C2-alkynyl substitution were successfully synthesized from D-mannose, using a palladium-catalyzed Sonogashira coupling reaction as the key step, whose structures were confirmed by the X-ray crystal structure of 4 h. As the size of the alkynyl group at the C2-position increased, the binding affinity improved; however, when the substituted group was larger than hexynyl, the binding affinity decreased. The introduction of a bulky hydrophobic group such as 3-halobenzyl group at the free N6-amino group decreased the binding affinity at hA2AAR. These results confirm our previous findings that a free amino group at N6-position and longer hydrophobic chain at C2-position are essential for hA2A AR binding affinity. The introduction of a bulky hydrophobic group at free N6-amino group maintained the binding affinity at hA3 AR. The binding mode of truncated 2-substituted-4'-thioadenosine derivatives to hA2A and hA3 AR were predicted by a molecular docking study.

Ligand and Residue Free Energy Perturbations Solve the Dual Binding Mode Proposal for an A2BAR Partial Agonist

Adenosine receptors, particularly A2BAR, are gaining attention for their role in pathological conditions such as cancer immunotherapy, prompting the exploration for promising therapeutic applications. Despite numerous selective A2BAR antagonists, the lack of selective full agonists makes the partial agonist BAY60-6583 one of the most interesting activators of this receptor. Recent cryo-EM structures have univocally revealed the binding mode of nonselective ribosidic agonists such as adenosine and its derivative NECA to A2BAR; however, two independent structures with BAY60-6583 show alternative binding orientations, raising the question of which is the physiologically relevant binding mode. In situations such as this, computational simulations that accurately predict shifts in binding free energy can complement experimental structures. Our study combines QligFEP and QresFEP protocols to directly compare the binding affinity of BAY60-6583 between alternative binding modes as well as providing a direct comparison of in silico mutagenesis studies on each pose with experimental mutational effects. Both methods converge on the experimentally determined binding mode that better explains both the existing SAR and mutagenesis data for this ligand. Our results allow the elucidation of the experimental binding orientation that should be considered as a basis for designing partial agonist derivatives with improved affinity and selectivity and underscore the value of free energy perturbation methods in aiding structure-based drug design.

Modulating vertebrate physiology by genomic fine-tuning of GPCR functions

G protein-coupled receptors (GPCRs) play a crucial role as membrane receptors, facilitating the communication of eukaryotic species with their environment and regulating cellular and organ interactions. Consequently, GPCRs hold immense potential in contributing to adaptation to ecological niches and responding to environmental shifts. Comparative analyses of vertebrate genomes reveal patterns of GPCR gene loss, expansion, and signatures of selection. Integrating these genomic data with insights from functional analyses of gene variants enables the interpretation of genotype-phenotype correlations. This review underscores the involvement of GPCRs in adaptive processes, presenting numerous examples of how alterations in GPCR functionality influence vertebrate physiology or, conversely, how environmental changes impact GPCR functions. The findings demonstrate that modifications in GPCR function contribute to adapting to aquatic, arid, and nocturnal habitats, influencing camouflage strategies, and specializing in particular dietary preferences. Furthermore, the adaptability of GPCR functions provides an effective mechanism in facilitating past, recent, or ongoing adaptations in animal domestication and human evolution and should be considered in therapeutic strategies and drug development.

Minute-timescale free-energy calculations reveal a pseudo-active state in the adenosine A2A receptor activation mechanism

G protein-coupled receptors (GPCRs) are membrane proteins targeted by over one-third of marketed drugs. Understanding their activation mechanism is essential for precise regulation of drug pharmacological response. In this work, we elucidate the conformational landscape of the adenosine A2A receptor (A2AR) activation mechanism in its basal apo form and under different ligand-bound conditions through minute-timescale free-energy calculations. We identified a pseudo-active state (pAs) of the A2AR apo form, stabilized by specific "microswitch" residues, including a salt bridge established between the conserved residues R5.66 and E6.30. The pAs enables A2AR to couple with Gs protein upon rearrangement of the intracellular end of transmembrane helix 6, providing unprecedented structural insights into receptor function and signaling dynamics. Our simulation protocol is versatile and can be adapted to study the activation of any GPCRs, potentially making it a valuable tool for drug design and "biased signaling" studies.

The role of the endocannabinoid system in the pathogenesis and treatment of epilepsy

Epilepsy is a group of chronic neurological brain disorders characterized by recurrent spontaneous unprovoked seizures, which are accompanied by significant neurobiological, cognitive, and psychosocial impairments. With a global prevalence of approximately 0.5-1 % of the population, epilepsy remains a serious public health concern. Despite the development and widespread use of over 20 anticonvulsant drugs, around 30 % of patients continue to experience drug-resistant seizures, leading to a substantial reduction in quality of life and increased mortality risk. Given the limited efficacy of current treatments, exploring new therapeutic approaches is critically important. In recent years, Gi-protein-coupled receptors, particularly cannabinoid receptors CB1 and CB2, have garnered increasing attention as promising targets for the treatment seizures and prevention of epilepsy. Emerging evidence suggests a significant role of the cannabinoid system in modulating neuronal activity and protecting against hyperexcitability, underscoring the importance of further research in this area. This review provides up-to-date insights into the pathogenesis and treatment of epilepsy, with a special focus on the role of the cannabinoid system, highlighting the need for continued investigation to develop more effective therapeutic strategies.

Stereochemical influence of 4'-methyl substitutions on truncated 4'-thioadenosine derivatives: Impact on A3 adenosine receptor binding and antagonism

Herein, we investigated the stereochemical effects of 4'-methyl substitution on A3 adenosine receptor (A3AR) ligands by synthesizing and evaluating a series of truncated 4'-thioadenosine derivatives featuring 4'-α-methyl, 4'-β-methyl, and 4',4'-dimethyl substitutions. We successfully synthesized these derivatives, using the stereoselective addition of an organometallic reagent, KSAc-mediated sulfur cyclization, and Vorbrüggen condensation. Binding assays demonstrated that the 4'-β-methyl substitution conferred the highest affinity for A3AR, with compound 1 h exhibiting a Ki = 3.5 nM, followed by the 4',4'-dimethyl and 4'-α-methyl substitutions. Notably, despite the absence of the 5'-OH group, compound 1 h unexpectedly displayed partial agonism. Computational docking studies indicated that compound 1 h, the β-methyl derivative, adopted a South conformation and maintained strong interactions within the receptor, including a critical interaction with Thr94, a residue known to be notable for agonistic effects. Conversely, compound 2 h, the α-methyl derivative, also adopted a South conformation but resulted in a flattened structure that hindered interactions with Thr94 and Asn250. The dimethyl derivative 3 h exhibited steric clashes with Thr94, contributing to a reduction in binding affinity. However, the docking results for 3 h indicated a North conformation, suggesting that the change in sugar conformation due to the additional 4'-methyl group altered the angle between the α-methyl group and the sugar plane, enabling binding despite the increased steric bulk. These findings suggest that not only do the substituents and their stereochemistry influence receptor-ligand interactions, but the conformation and the resulting spatial orientation of the substituents also play a crucial role in modulating receptor-ligand interaction. This stereochemical insight offers a valuable framework for the design of new, selective, and potent A3AR ligands, potentially facilitating the development of novel therapeutics for A3AR-related diseases such as glaucoma, inflammation, and cancer.

Identification of Hub Genes and Immune Infiltration in Coronary Artery Disease: A Risk Prediction Model

Purpose

Our study aimed to establish a prediction model for coronary artery disease (CAD) that integrates immune infiltration and a gene expression signature.

Methods

613 differentially expressed genes (DEGs) and 12 hub genes were screened via the GSE113079 dataset. The pathway enrichment analysis indicated that these genes (613 DEGs and 12 hub genes) were closely associated with the inflammatory and immune responses. Based on the differentially expressed miRNA (DEmiRNA)-DEG regulatory network and immune cell infiltration, the Lasso algorithm constructed a CAD risk prediction model containing the risk score and immune score. Then, ROC-AUC and polymerase chain reaction (PCR) were performed for validation.

Results

Six hub genes (PTGER1, PIK3R1, ADRA2A, CORT, CXCL12, and S1PR5) had a high distinguishing capability (AUC > 0.90). In addition, the miRNAs targeting 12 hub genes were predicted and intersected with the DEmiRNAs, and the DEmiRNA-DEG regulatory network was then constructed. Two LASSO models and a novel CAD risk prediction model were constructed through LASSO regression analysis, and they both accurately obtained the risk of CAD. The CAD risk prediction model shows good performance (AUC = 0.988). We also constructed a valid nomogram, and PCR results verified three downregulation hub genes and one upregulation gene in the CAD risk model.

Conclusion

We demonstrated the molecular mechanism of the hub genes in CAD and provided a valuable tool for predicting the risk of CAD.

Structural insights into the agonist selectivity of the adenosine A3 receptor

Adenosine receptors play pivotal roles in physiological processes. Adenosine A3 receptor (A3R), the most recently identified adenosine receptor, is expressed in various tissues, exhibiting important roles in neuron, heart, and immune cells, and is often overexpressed in tumors, highlighting the therapeutic potential of A3R-selective agents. Recently, we identified RNA-derived N6-methyladenosine (m6A) as an endogenous agonist for A3R, suggesting the relationship between RNA-derived modified adenosine and A3R. Despite extensive studies on the other adenosine receptors, the selectivity mechanism of A3R, especially for A3R-selective agonists such as m6A and namodenoson, remained elusive. Here, we identify tRNA-derived N6-isopentenyl adenosine (i6A) as an A3R-selective ligand via screening of modified nucleosides against the adenosine receptors. Like m6A, i6A is found in the human body and may be an endogenous A3R ligand. Our cryo-EM analyses elucidate the A3R-Gi complexes bound to adenosine, 5'-N-ethylcarboxamidoadenosine (NECA), m6A, i6A, and namodenoson at overall resolutions of 3.27 Å (adenosine), 2.86 Å (NECA), 3.19 Å (m6A), 3.28 Å (i6A), and 3.20 Å (namodenoson), suggesting the selectivity and activation mechanism of A3R. We further conduct structure-guided engineering of m6A-insensitive A3R, which may aid future research targeting m6A and A3R, providing a molecular basis for future drug discovery.

Structure-Activity Relationship of Truncated 4'-Selenonucleosides: A3 Adenosine Receptor Activity and Binding Selectivity

This study explored the impact of structural modifications on truncated 4'-selenonucleosides as ligands for the A3 adenosine receptor (AR). We synthesized and evaluated a series of these compounds for their binding affinities, functional activities, and structural interactions by using computational modeling. The SAR study revealed that all compounds exhibited selective and notable hA3AR binding, among which 6l (K i = 5.2 nM) and 6m (K i = 5.7 nM) were found as the best binding compounds. The representative N 6-cyclopropyl compound 6m was found to be a partial agonist, contrasting with the antagonist profiles of truncated 4'-oxo and 4'-thionucleosides. Computational docking highlighted 6m's unique interaction with Thr94 at the A3AR binding site. This research not only advances our understanding of A3AR ligand interactions but also highlights the potential of truncated 4'-selenonucleosides as effective A3AR modulators.

Hit-to-Lead Optimization of Heterocyclic Carbonyloxycarboximidamides as Selective Antagonists at Human Adenosine A3 Receptor

Antagonism of the human adenosine A3 receptor (hA3R) has potential therapeutic application. Alchemical relative binding free energy calculations of K18 and K32 suggested that the combination of a 3-(2,6-dichlorophenyl)-isoxazolyl group with 2-pyridinyl at the ends of a carbonyloxycarboximidamide group should improve hA3R affinity. Of the 25 new analogues synthesized, 37 and 74 showed improved hA3R affinity compared to K18 (and K32). This was further improved through the addition of a bromine group to the 2-pyridinyl at the 5-position, generating compound 39. Alchemical relative binding free energy calculations, mutagenesis studies and MD simulations supported the compounds' binding pattern while suggesting that the bromine of 39 inserts deep into the hA3R orthosteric pocket, so highlighting the importance of rigidification of the carbonyloxycarboximidamide moiety. MD simulations highlighted the importance of rigidification of the carbonyloxycarboximidamide, while suggesting that the bromine of 39 inserts deep into the hA3R orthosteric pocket, which was supported through mutagenesis studies 39 also selectively antagonized endogenously expressed hA3R in nonsmall cell lung carcinoma cells, while pharmacokinetic studies indicated low toxicity enabling in vivo evaluation. We therefore suggest that 39 has potential for further development as a high-affinity hA3R antagonist.

Lipid Trolling to Optimize A3 Adenosine Receptor-Positive Allosteric Modulators (PAMs)

A3 adenosine receptor (A3AR) positive allosteric modulators (PAMs) (2,4-disubstituted-1H-imidazo[4,5-c]quinolin-4-amines) allosterically increase the Emax of A3AR agonists, but not potency, due to concurrent orthosteric antagonism. Following mutagenesis/homology modeling of the proposed lipid-exposed allosteric binding site on the cytosolic side, we functionalized the scaffold, including heteroatom substitutions and exocyclic phenylamine extensions, to increase allosteric binding. Strategically appended linear alkyl-alkynyl chains with terminal amino/guanidino groups improved allosteric effects at both human and mouse A3ARs. The chain length, functionality, and attachment position were varied to modulate A3AR PAM activity. For example, 26 (MRS8247, p-alkyne-linked 8 methylenes) and homologues increased agonist Cl-IB-MECA's Emax and potency ([35S]GTPγS binding). The putative mechanism involves a flexible, terminally cationic chain penetrating the lipid environment for stable electrostatic anchoring to cytosolic phospholipid head groups, suggesting "lipid trolling", supported by molecular dynamic simulation of the active-state model. Thus, we have improved A3AR PAM activity through rational design based on an extrahelical, lipidic binding site.

2-Substituted (N)-Methanocarba A3 Adenosine Receptor Agonists: In Silico, In Vitro, and In Vivo Characterization

2-Arylethynyl (N)-methanocarba adenosine 5'-methylamides are selective A3 adenosine receptor (AR) agonists containing a preestablished receptor-preferred pseudoribose conformation. Here, we compare analogues having bulky 2-substitution, either containing or lacking an ethynyl spacer between adenine and a cyclic group. 2-Aryl compounds 9-11, 13, 14, 19, 22, 23, 27, 29, 31, and 34, lacking a spacer, had human (h) A3AR K i values of 2-30 nM, and others displayed lower affinity. Mouse (m) A3AR affinity varied, with 2-arylethynyl having a higher affinity than 2-aryl analogues (7, 8 > 3c, 3d > 3b). However, 2-aryl-4'-truncated derivatives had greatly reduced hA3AR affinity, even containing affinity-enhancing N 6-dopamine-derived substituents. Molecular modeling, including molecular dynamics simulation, predicted stable poses in the canonical A3AR agonist binding site, but 2-aryl (ECL2 interactions) and 2-arylethynyl (TM2 interactions) substituents have different conformations and environments. In a hA3AR miniGαi recruitment assay, 31 (MRS8062) was (slightly) more potent compared to a β-arrestin2 recruitment assay, both in engineered HEK293T cells, and its maximal efficacy (E max) was much higher (165%) than reference agonist NECA's. Thus, in the 2-aryl series, A3AR affinity and selectivity were variable and generally reduced compared to the 2-arylethynyl series, with a greater dependence on the specific aryl group present. Selected compounds were studied in vivo in an ischemic model of peripheral artery disease (PAD). Rigidified 2-arylethynyl analogues 3a-3c were protective in this model of skeletal muscle ischemia-reperfusion injury/claudication, as previously shown only for moderately A3AR-selective ribosides or (N)-methanocarba derivatives. Thus, we have expanded the A3AR agonist SAR for (N)-methanocarba adenosines.