Adenosine Binding Sites Research Articles

The challenge of developing adenosine A2A antagonists for Parkinson disease: Istradefylline, preladenant, and tozadenant

Laboratory and clinical experience have pointed to the value of targeting motor pathways emerging from the striatum to treat problems arising in advanced Parkinson's disease (PD). These pathways are selectively populated with a subtype of adenosine binding sites (A2A receptors) that offer a target for improving PD symptomatology. Several compounds were developed that possess high selectivity and potency for blocking this receptor. Three of these compounds – istradefylline, preladenant, and tozadenant – were chosen for clinical development programs that culminated in Phase 3 multicenter randomized clinical trials. Each of these drugs exert virtually no off-target neurochemical effects. Clinical trials with these drugs focused upon reducing OFF time when administered adjunctly to levodopa and other antiparkinsonian medications. Despite promising Phase 2 data, preladenant did not show efficacy when tested in a randomized placebo-controlled Phase 3 clinical trial. Reports of hematological toxicity necessitated ceasing an ongoing Phase 3 investigation of tozadenant. Following a challenging approval process, based on the results of randomized clinical trials carried out in the U.S. and Japan, istradefylline received approval in these countries for treatment of OFF episodes.

Identification of dual site inhibitors of tankyrase through virtual screening of protein-ligand interaction fingerprint (PLIF)–derived pharmacophore models, molecular dynamics, and ADMET studies

Tankyrases are the group of poly (ADP-ribosyl) polymerases (PARPs) which are the attractive targets in various therapeutic areas such as cancer, antiviral, diabetes, and hormonal imbalance. The selective nature of tankyrase 1 and 2 inhibitors has created solid base to get dual site binders as they bind to induced adenosine binding site and nicotinamide binding site resulting in dual site inhibition. The present work describes the cheminformatics approach to find potential lead molecules as tankyrases dual site inhibitors through pharmacophore model by utilizing protein-ligand interaction fingerprints (PLIF) approach. The constructed pharmacophore model was used in virtually screening of ZINC and Interbioscreen database. Top ten hit molecules of virtual screening were subjected to molecular docking in order gain insights of key interactions at the adenosine and nicotinamide binding sites. The top hits were subjected to molecular dynamics simulation studies to gain deeper insights into probable mechanism of inhibition and stability of the complex. The top hit ZINC12973507 showed all the features required in key interactions at the active site of tankyrases and this hit molecule can be further explored as a potential drug candidate for dual site inhibition of tankyrases.

A2A and A2B adenosine receptors: The extracellular loop 2 determines high (A2A) or low affinity (A2B) for adenosine

A2A and A2B adenosine receptors (ARs) are closely related G protein-coupled receptor subtypes, which represent important (potential) drug targets. Despite their almost identical binding sites for adenosine, A2AARs are activated by low (nanomolar) adenosine concentrations, while A2BARs require micromolar concentrations. In the present study, we exchanged the extracellular loop 2 (ECL2) of the human A2AAR for that of the A2BAR. The resulting chimeric A2A(ECL2-A2B)AR was investigated in radioligand binding and cAMP accumulation assays in comparison to the wildtype A2AAR. While the ribose-modified adenosine analog N-ethylcarboxamidoadenosine (NECA) and its 2-substituted derivative CGS-21680 did not exhibit significant changes, adenosine showed dramatically reduced potency and affinity for the A2A(ECL2-A2B)AR mutant displaying similarly low potency as for the wt A2BAR. Supervised molecular dynamics simulation studies predicted a meta-binding site with high affinity for adenosine, but not for NECA, which may contribute to the observed effects.

Structural basis for inhibition of mycobacterial and human adenosine kinase by 7-substituted 7-(Het)aryl-7-deazaadenine ribonucleosides.

Adenosine kinase (ADK) from Mycobacterium tuberculosis (Mtb) was selected as a target for design of antimycobacterial nucleosides. Screening of 7-(het)aryl-7-deazaadenine ribonucleosides with Mtb and human (h) ADKs and testing with wild-type and drug-resistant Mtb strains identified specific inhibitors of Mtb ADK with micromolar antimycobacterial activity and low cytotoxicity. X-ray structures of complexes of Mtb and hADKs with 7-ethynyl-7-deazaadenosine showed differences in inhibitor interactions in the adenosine binding sites. 1D (1)H STD NMR experiments revealed that these inhibitors are readily accommodated into the ATP and adenosine binding sites of Mtb ADK, whereas they bind preferentially into the adenosine site of hADK. Occupation of the Mtb ADK ATP site with inhibitors and formation of catalytically less competent semiopen conformation of MtbADK after inhibitor binding in the adenosine site explain the lack of phosphorylation of 7-substituted-7-deazaadenosines. Semiempirical quantum mechanical analysis confirmed different affinity of nucleosides for the Mtb ADK adenosine and ATP sites.

Adenosine stimulates human sperm motility via A2 receptors.

The effects of adenosine and its analogues on human sperm motility were studied using a transmembrane migration method. Specific binding sites for adenosine in human sperm were also investigated. Adenosine and 5'-N-ethylcarboxamidoadenosine (NECA) stimulated human sperm motility with similar efficacies and the maximal amplitudes of motility increases were both about 70%. 3,7-Dimethyl-1-propargylxanthine (DMPX), a potent A2 antagonist, competitively antagonized NECA-induced motility stimulation. Successively higher concentrations of DMPX shifted the dose-response curve of NECA to the right in a nearly parallel fashion. Dipyridamole, an inhibitor of adenosine uptake, does not reduce the ability of adenosine to stimulate human sperm motility. In radioligand-binding studies, adenosine A1 selective analogues, cyclopentyl-1,3-dipropylxanthine and 1-methyl-2-phenylethyl adenosine, have little competitive effect on [3H]NECA binding in human sperm membrane. These results provide evidence that adenosine enhances human sperm motility via adenosine A2 receptors on the surface of sperm membranes.

The biphasic effects of centrally and peripherally administered caffeine on ethanol-induced motor incoordination in mice.

The possible biphasic effect of caffeine on acute ethanol-induced motor incoordination by rotorod evaluation was investigated in mice. Caffeine in various doses was administered intracerebroventricularly (i.c.v.) to mice implanted with permanent indwelling stainless steel guide cannulae and intraperitoneally (i.p.) to non-cannulated animals. A motor incoordinating test dose of ethanol, 2 g kg-1, was given i.p. in both cases. Caffeine less than 25 micrograms administered i.c.v., dose-dependently attenuated while 75 micrograms i.c.v. potentiated ethanol (i.p.)-induced motor incoordination. Similarly, caffeine less than 20 mg kg-1 given i.p., dose-dependently attenuated while 62.5 mg kg-1 potentiated ethanol (i.p.)-induced motor incoordination. The data obtained demonstrated that caffeine given either i.c.v. or i.p. exerted biphasic effects on ethanol-induced motor incoordination. The data also suggested that caffeine antagonized ethanol-induced motor micrograms i.c.v.; less than 20 mg kg-1 i.p.) caffeine is well known to display high affinity for adenosine binding sites. Therefore, the present investigation lends further support to our earlier suggestion that adenosine may be involved in the motor impairing effect of ethanol.

Structural Insights into the Architecture and Allostery of Full-Length AMP-Activated Protein Kinase

AMP-activated protein kinase (AMPK) is a heterotrimeric complex composed of α catalytic subunit, β scaffolding subunit, and γ regulatory subunit with critical roles in maintaining cellular energy homeostasis. However, the molecular architecture of the intact complex and the allostery associated with the adenosine binding-induced regulation of kinase activity remain unclear. Here, we determine the three-dimensional reconstruction and subunit organization of the full-length rat AMPK (α1β1γ1) through single-particle electron-microscopy. By comparing the structures of AMPK in ATP- and AMP-bound states, we are able to visualize the sequential conformational changes underlying kinase activation that transmits from the adenosine binding sites in the γ subunit to the kinase domain of the α subunit. These results not only make substantial revision to the current model of AMPK assembly, but also highlight a central role of the linker sequence of the α subunit in mediating the allostery of AMPK.

Neurotransmitter Receptor Imbalances in Motor Cortex and Basal Ganglia in Hepatic Encephalopathy

Hepatic encephalopathy (HE) in chronic liver disease is characterized by neuropsychiatric and motor disturbances and associated with a net increase of inhibitory neurotransmission. Though many studies, mostly carried out in animal models, have linked dysfunctions of single neurotransmitter systems with the pathogenesis of HE, reports concerning neurotransmitter receptor alterations are controversial. Little is known about the situation in humans. We carried out a multireceptor assessment of HE-associated changes in neurotransmitter receptor densities and affinities in human post-mortem brain samples. Dissociation constants and densities of different binding sites for glutamate, GABA, acetylcholine, norepinephrine, serotonin, dopamine and adenosine were determined by in vitro binding assays and quantitative receptor autoradiography in the motor cortex and putamen of HE and control brains. HE cases do not build a homogeneous group, but differ concerning direction and intensity of binding site density divergences from control values. The acetylcholine M2 binding site dissociation constant was significantly higher in HE brains. Nicotinic acetylcholine and adenosine type 1 and 2A densities were significantly down-regulated in the putamen of HE brains. Our data suggest that neurotransmitter alterations are probably not the primary key factor responsible for the neuropsychiatric and motor disturbances associated with HE.

Streamless aggregation of Dictyostelium in the presence of isopropylidenadenosin

Starving cells of Dictyostelium discoideum undergo a developmental cycle were cAMP is autocatalytically produced and relayed from cell to cell, resulting in the propagation of excitation waves over a spatially extended population. Later on the homogeneous cell layer transforms into a pattern of cell streams directed perpendicular to the cAMP waves. Here we chemically influence aggregation competent cells by isopropylidenadenosin (IPA), an adenosine derivative. It can be assumed, that IPA acts via specific adenosine binding sites localized in the cellular membrane. We find, however, that pattern formation and cellular aggregation under the influence of IPA differ considerably compared to experiments with adenosine. In particular, our observations point towards an inhibitory effect on adenylate cyclase (ACA), the key enzyme in the autocatalytic production process of cAMP inside the cell. Our results suggest the existence of a direct coupling (via intracellular affection) or indirect coupling (via inhibition of cAMP binding) of the specific adenosine receptors to the regulatory circuit that controls cyclic intra- and extracellular cAMP concentration.

Adenosine does not bind to the growth hormone secretagogue receptor type-1a (GHS-R1a)

Ghrelin regulates GH secretion and energy homeostasis through the GH secretagogue receptor type-1a (GHS-R1a). This G-protein coupled receptor shows the peculiarity to transduce information provided not just by ghrelin as well as by adenosine through a supposed binding site different from the characterized ghrelin-binding pocket. Indeed, adenosine triggers intracellular calcium rise through a distinct signaling pathway to the one described for ghrelin, although it fails to stimulate GH secretion. Despite multiple active conformations of GHS-R1a, suggested as an explanation for a ligand-dependent activation of the downstream signaling, the concept of adenosine as agonist for GHS-R1a has been re-evaluated. The results revealed that calcium rise of both ghrelin and adenosine appears to be mediated by receptors that did not show the same sensitivity to protein kinase C (PKC) activity in GHS-R1a-transfected HEK 293 cells (HEK-GHS-R1a cells). The binding analyses showed the same number of adenosine-binding sites in both HEK 293 (B(max) = 2.01 +/- 0.15 fmol/cell) and HEK-GHS-R1a cells (B(max) = 1.90 +/- 0.11 fmol/cell). This binding was unaltered by different GHS-R1a antagonists. Western blot analysis showed a similar endogenous expression of endogenous adenosine receptor type-2b and -3 in both cell lines. The K(d) values for adenosine were 1.78 microM in HEK 293 cells and 6.30 microM in HEK-GHS-R1a cells, pointing to a modification of agonist affinity induced by overexpression of the GHS-R1a. Additionally, adenosine failed to induce the GHS-R1a endocytosis, although it attenuates the ghrelin-induced GHS-R1a endocytosis. In conclusion, adenosine is not an agonist of the GHS-R1a and its action is mediated by the endogenous adenosine receptor type-2b and -3, which is able to partially use the intracellular signaling machinery of HEK-GHS-R1a cells.

Rat brain guanosine binding site: Biological studies and pseudo-Receptor construction

Rat brain guanosine binding sites were studied by (i) a pharmacological approach to confirm the hypothesis of the existence of specific G-coupled receptors for guanosine ( 1) and, for the first time, delineate a structure–activity relationship for a series of guanosine derivatives; (ii) a molecular modelling approach to design a pseudo-receptor construction. GTP and its non-hydrolysable analogue Gpp[NH]p decreased [ 3H]-guanosine binding to rat brain membranes. Gpp[NH]p 30 and 100 μM induced a dose-dependent decrease in [ 3H]-guanosine affinity and PTX pretreatment of rat brain membranes caused a 50% reduction in binding. In slices from rat brain cortex, guanosine induced a dose-dependent increase in intracellular cAMP. This increase is specific for guanosine, since neither the pretreatment with adenosine deaminase nor the A 1 and A 2 adenosine receptor antagonists were able to modify the guanosine-induced cAMP accumulation. The structure–activity relationship showed that the potency order of the best substances able to displace 50 nM [ 3H]-guanosine was guanosine ( 1)=6-thioguanosine ( 3)>8-bromoguanosine ( 4)>inosine ( 10)>7-methylguanosine ( 6)=3′-deoxyguanosine ( 9)>2′-deoxyguanosine ( 8)=guanine ( 11)=6-thioguanine ( 12)>> N 2-methylguanosine ( 5). The competition studies confirmed that [ 3H]-guanosine site was distinct from the well characterized ATP and adenosine binding sites. The present results are rationalized in terms of a putative pseudo-receptor construct which includes all the relevant physicochemical interaction between guanosine analogues and their putative binding sites. This construct will be useful for the in silico screening of compound libraries in search for new potent and structurally diverse pharmacological tools.

Diagnostic chemical shift markers for loop conformation and substrate and cofactor binding in dihydrofolate reductase complexes.

Heteronuclear NMR methods have been used to probe the conformation of four complexes of Escherichia coli dihydrofolate reductase (DHFR) in solution. (1)H(N), (15)N, and (13)C(alpha) resonance assignments have been made for the ternary complex with folate and oxidized NADP(+) cofactor and the ternary complex with folate and a reduced cofactor analog, 5,6-dihydroNADPH. The backbone chemical shifts have been compared with those of the binary complex of DHFR with the substrate analog folate and the binary complex with NADPH (the holoenzyme). Analysis of (1)H(N) and (15)N chemical shifts has led to the identification of marker resonances that report on the active site conformation of the enzyme. Other backbone amide resonances report on the presence of ligands in the pterin binding pocket and in the adenosine and nicotinamide-ribose binding sites of the NADPH cofactor. The chemical shift data indicate that the enzyme populates two dominant structural states in solution, with the active site loops in either the closed or occluded conformations defined by X-ray crystallography; there is no evidence that the open conformation observed in some X-ray structures of E. coli DHFR are populated in solution.

Adenosine binding sites at S-adenosylhomocysteine hydrolase are controlled by the NAD +/NADH ratio of the enzyme

S-Adenosylhomocysteine hydrolase (AdoHcy hydrolase) catalyzes the reversible hydrolysis of S-adenosylhomocysteine (AdoHcy) to adenosine (Ado) and homocysteine. On the basis of the kinetics of Ado binding to AdoHcy hydrolase we have shown that AdoHcy hydrolase binds Ado with different affinities [Kidney Blood Press. Res. 19 (1996) 100]. Since AdoHcy hydrolase in its totally reduced form binds Ado with high affinity we determined in the present study the Ado binding characteristics of purified AdoHcy hydrolase from bovine kidney (native form) and of reconstituted forms with defined NAD +/NADH ratios. AdoHcy hydrolase in its native form and at a ratio of 50% NAD + and 50% NADH exhibits two binding sites for Ado with a K D 1 of 9.2±0.6 nmol/L and a K D 2 of 1.4±0.1 μmol/L, respectively. Binding of Ado to AdoHcy hydrolase in its NADH form and in its NAD + form exhibits only one binding site with high affinity 48.3±2.7 nmol/L for the NADH form and with a low affinity of 4.9±0.3 μmol/L for the NAD + form. To identify these two Ado binding sites, AdoHcy hydrolase was covalently modified with [2- 3 H ]-8-azido-Ado. After irradiation of the native AdoHcy hydrolase two different photolabeled peptides were isolated and identified as Asp 307-Val 325 and Tyr 379-Thr 410. When the reconstituted AdoHcy hydrolase in its NADH and in its NAD + form was irradiated with [2- 3 H ]-8-azido-Ado only one peptide was identified as Asn 312-Lys 318 from the NADH form and as Asp 391-Ala 396 from the NAD + form. Based on the crystallographic data, the labeled peptide Asp 391-Ala 396 (low affinity binding site), appears to belong to the catalytic domain of AdoHcy hydrolase, whereas the labeled peptide, identified as Asn 312-Lys 318 (high affinity binding site), is located in the NAD domain. In conclusion, our data show that AdoHcy hydrolase has two different Ado binding sites which are dependent upon the enzyme-bound NAD +/NADH ratios.

Purine and deazapurine nucleosides: synthetic approaches, molecular modelling and biological activity

A number of ligands for the adenosine binding sites has been obtained by using nucleoside convergent and divergent synthesis. Most of our nucleosides have been synthesized by coupling 2,6-dichloropurine ( 1), 2,6-dichloro-1-deazapurine ( 2), 2,6-dichloro-3-deazapurine ( 3) with ribose, 2- and 3-deoxyribose and 2,3-dideoxyribose derivatives. The use of these versatile synthons allowed the introduction of various substituents in 2- and/or 6-positions. The glycosylation site and the anomeric configuration of the obtained nucleosides were assigned on the basis of spectroscopic studies and confirmed by molecular models. A series of potent adenosine receptor ligands has been obtained by using divergent approaches, mostly starting from guanosine. Substitutions in 2, 6, 8, and 5′ position of adenosine molecule led to ligands selective for the different adenosine receptor subtypes. Furthermore, we investigated the molecular bases of the different behavior of 2- and 8-alkynyl adenosines, by means of NMR experiments and molecular modeling studies. With docking experiments, we demonstrated that the two class of molecules should have different binding modes that explain their different degree of affinity and the shift of their activity from agonistic (2-substituted derivatives) to antagonistic (8-substituted derivatives).

The ratio of the cofactor NAD +/NADH of S-adenosylhomocysteine hydrolase controls the adenosine binding sites.

The ratio of the cofactor NAD +/NADH of S-adenosylhomocysteine hydrolase controls the adenosine binding sites.

Pharmacology of a unique adenosine binding site in rat brain using a selective ligand.

1. In order to further characterize the adenosine binding sites that we previously purified and termed P3 purinergic receptor-like protein (P3LP), a reliable binding assay method was developed using [3H]-5'-N-ethylcarboxamidoadenosine (NECA) as a radioligand and the newly developed high-affinity selective ligand 9-(6,7-dideoxy-beta-D-allo-hept-5-ynofuranosyl) adenine (HAK2701) as a selective displacer. 2. Using this assay method, it was found that rat brain membranes possess high- and low-affinity [3H]-NECA binding sites. The high-affinity binding site showed KD and Bmax values of 19.7+/-2.5 nmol/L and 0.192+/-0.05 pmol/mg protein, respectively, and the KD value for the low-affinity binding site was 4260+/-330 nmol/L. The KD value for the high-affinity site agreed well with that of the [3H]-NECA binding site determined with the partially purified P3LP preparation described previously. 3. The distribution of P3LP in rat tissues was determined using the [3H]-NECA binding method described above. The highest level of P3LP was in the cerebellum followed by the olfactory bulb and the spinal cord. 4. The order of the affinity for various purinergic or related compounds to P3LP in rat brain preparations was also determined by the [3H]-NECA binding method to be HAK2701 > NECA = adenosine 5'-O-(2-thiodiphosphate) > cAMP = beta,gamma-methyleneadenosine 5'-triphosphate > diadenosine tetraphosphate > alpha,beta-methyleneadenosine 5'-triphosphate > 5'-deoxy-5'-methylthioadenosine > N6-cyclopentyladenosine. 5. These studies reveal that the [3H]-NECA binding assay in combination with HAK2701 is successful in the characterization of P3LP, especially the membrane-bound form.

Tryptophan environment in adenosine deaminase: I. Enzyme modification with N-bromosuccinimide in the presence of adenosine and EHNA analogues

Adenosine deaminase from bovine cerebral hemisphere (white and gray matter) and spleen was treated with N-bromosuccinimide, a reagent known to oxidize selectively tryptophan residues in proteins. Spectrally observable tryptophan modification was accompanied by enzyme inactivation. Tsow graphics revealed that two Trps are essential for the activity of enzyme from both tissues. Enzyme inhibitors and substrate analogues, derivatives of erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA) and adenosine, were able to protect Trp against modification, and this effect correlated in general with the enzyme activity protection. In the presence of adenosine deaza analogues (the noninhibitor tubercidin among them) only two Trps were modified in the fully inactivated enzyme. In the presence of EHNA and its deaza analogues, full inactivation of the enzyme was accompanied by the modification of four Trps. The obtained data confirm the previous hypothesis about the presence on the enzyme of different binding sites for adenosine and EHNA derivatives that are responsible for the different effects on the enzyme conformation elicited by the corresponding derivatives. Moreover, these data allow us to suggest that Trp residues, still unidentified by X-ray analysis, are essential for the functioning of the enzyme.

Genetic, biochemical, and crystallographic characterization of Fhit-substrate complexes as the active signaling form of Fhit.

Alterations in the FHIT gene at 3p14.2 occur as early and frequent events in the development of several common human cancers. The ability of human Fhit-negative cells to form tumors in nude mice is suppressed by stable reexpression of Fhit protein. Fhit protein is a diadenosine P1,P3-triphosphate (ApppA) hydrolase whose fungal and animal homologs form a branch of the histidine triad (HIT) superfamily of nucleotide-binding proteins. Because the His-96 --> Asn substitution of Fhit, which retards ApppA hydrolase activity by seven orders of magnitude, did not block tumor-suppressor activity in vivo, we determined whether this mutation affected ApppA binding or particular steps in the ApppA catalytic cycle. Evidence is presented that His-96 --> Asn protein binds ApppA well and forms an enzyme-AMP intermediate extremely poorly, suggesting that Fhit-substrate complexes are the likely signaling form of the enzyme. The cocrystal structure of Fhit bound to Ado-p-CH2-p-ps-Ado (IB2), a nonhydrolyzable ApppA analog, was refined to 3.1 A, and the structure of His-96 --> Asn Fhit with IB2 was refined to 2.6 A, revealing that two ApppA molecules bind per Fhit dimer; identifying two additional adenosine-binding sites on the dimer surface; and illustrating that His-98 is positioned to donate a hydrogen bond to the scissile bridging oxygen of ApppA substrates. The form of Fhit bound to two ApppA substrates would present to the cell a dramatically phosphorylated surface, prominently displaying six phosphate groups and two adenosine moieties in place of a deep cavity lined with histidines, arginines, and glutamines.

Potent and Selective Ligands for Adenosine Binding Sites

A number of selective ligands for the different binding sites of adenosine have been synthesized and tested in several pharmacological models. The aim of these synthetic efforts is both to improve the knowledge of structure-activity relationships in the adenosine-related biological systems and to develop drugs from some of these molecules.

Identification of adenosine receptors in human spermatozoa.

1. The effects of adenosine receptor agonists and antagonists on human sperm motility have been studied. Specific binding sites for adenosine and its analogues on human sperm were also investigated. 2. Agonists stimulated human sperm motility in a dose-dependent manner with a potency order of 5'-N-ethylcarboxamidoadenosine (NECA, EC50 = 0.3 mumol/L) > 2-[p-(carboxyethyl)phenylethylamino]-5'-N- ethylcarboxamidoadenosine (CGS-21680, EC50 = 10 mumol/L) > adenosine (EC50 = 100 mumol/L). 3. NECA-stimulated motility was competitively inhibited by various adenosine receptor antagonists. The potency order was 3,7-dimethyl-1-propargylxanthine > 8-(p-sulfophenyl) theophylline > xanthine amino congener. 4. The radioligand [3H]-NECA bound to sperm membrane in a saturable manner with a Bmax of 21.3 pmol/mg protein and equilibrium Kd of 4 mumol/L. Adenosine agonists and antagonists competed for [3H]-NECA binding with the same rank order of potency as for the stimulation of human sperm motility. 5. GTP gamma s inhibited 63% of specific [3H]-NECA binding with IC50 value of 11 nmol/L. This suggests that the [3H]-NECA binding sites may be coupled to one or more G proteins. 6. These results indicate the presence of adenosine A2 receptors on human sperm which are responsible for adenosine-mediated enhancement of sperm motility.