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International Journal of Molecular... Jun 2022The biocompatibility of carrier nanomaterials in blood is largely hampered by their activating or inhibiting role on the clotting system, which in many cases prevents...
The biocompatibility of carrier nanomaterials in blood is largely hampered by their activating or inhibiting role on the clotting system, which in many cases prevents safe intravascular application. Here, we characterized an aqueous colloidal ethyl hydroxyethyl cellulose (EHEC) solution and tested its effect on ex vivo clot formation, platelet aggregation, and activation by thromboelastometry, aggregometry, and flow cytometry. We compared the impact of EHEC solution on platelet aggregation with biocompatible materials used in transfusion medicine (the plasma expanders gelatin polysuccinate and hydroxyethyl starch). We demonstrate that the EHEC solution, in contrast to commercial products exhibiting Newtonian flow behavior, resembles the shear-thinning behavior of human blood. Similar to established nanomaterials that are considered biocompatible when added to blood, the EHEC exposure of resting platelets in platelet-rich plasma does not enhance tissue thromboplastin- or ellagic acid-induced blood clotting, or platelet aggregation or activation, as measured by integrin αβ activation and P-selectin exposure. Furthermore, the addition of EHEC solution to adenosine diphosphate (ADP)-stimulated platelet-rich plasma does not affect the platelet aggregation induced by this agonist. Overall, our results suggest that EHEC may be suitable as a biocompatible carrier material in blood circulation and for applications in flow-dependent diagnostics.
Topics: Adenosine Diphosphate; Blood Platelets; Cellulose; Humans; Platelet Aggregation; Platelet Function Tests; Polymers
PubMed: 35742876
DOI: 10.3390/ijms23126432 -
ChemPlusChem Jan 2021The design and synthesis of molecular receptors for the selective binding of nucleoside phosphate anions (e. g. ATP, ADP, GTP, GDP, UDP) in aqueous media at... (Review)
Review
The design and synthesis of molecular receptors for the selective binding of nucleoside phosphate anions (e. g. ATP, ADP, GTP, GDP, UDP) in aqueous media at physiological pH is a valuable research endeavour, which could lead to new sensing tools for biomedical and drug discovery research. However, this target is very challenging due to similarities in anion size, structure and charge. This Minireview provides an account of the development of receptors capable of discriminating between ATP and ADP, and their utilisation in biological sensing applications. Particular focus is given to the application of receptors for the determination of ATP or ADP concentrations in biological media, tracking ATP levels (or the ATP/ADP ratio) in cells using fluorescence microscopy, or real-time monitoring of enzyme reactions involving ATP and ADP in vitro.
Topics: Adenosine Diphosphate; Adenosine Triphosphate; Animals; Biosensing Techniques; Humans; Molecular Probes
PubMed: 33058508
DOI: 10.1002/cplu.202000567 -
Journal of Molecular Cell Biology Mar 2022
Topics: Adenosine Diphosphate; Arginine; Caspases; Pyroptosis; Shigella
PubMed: 34888685
DOI: 10.1093/jmcb/mjab077 -
Organic Letters Jul 2023Adenosine diphosphate (ADP) ribosylation is an important post-translational modification (PTM) that plays a role in a wide variety of cellular processes. To study the...
Adenosine diphosphate (ADP) ribosylation is an important post-translational modification (PTM) that plays a role in a wide variety of cellular processes. To study the enzymes responsible for the establishment, recognition, and removal of this PTM, stable analogues are invaluable tools. We describe the design and synthesis of a 4-thioribosyl APRr peptide that has been assembled by solid phase synthesis. The key 4-thioribosyl serine building block was obtained in a stereoselective glycosylation reaction using an alkynylbenzoate 4-thioribosyl donor.
Topics: Adenosine Diphosphate Ribose; ADP-Ribosylation; Protein Processing, Post-Translational; Peptides; Glycosylation; Adenosine Diphosphate
PubMed: 37338412
DOI: 10.1021/acs.orglett.3c01554 -
Methods (San Diego, Calif.) Jul 2022Protein adenosine diphosphate-ribosylation (ADPr) is caused by the covalent binding of one or more ADP-ribose moieties to a target protein and regulates the biological...
Protein adenosine diphosphate-ribosylation (ADPr) is caused by the covalent binding of one or more ADP-ribose moieties to a target protein and regulates the biological functions of the target protein. To fully understand the regulatory mechanism of ADP-ribosylation, the essential step is the identification of the ADPr sites from the proteome. As the experimental approaches are costly and time-consuming, it is necessary to develop a computational tool to predict ADPr sites. Recently, serine has been found to be the major residue type for ADP-ribosylation but no predictor is available. In this study, we collected thousands of experimentally validated human ADPr sites on serine residue and constructed several different machine-learning classifiers. We found that the hybrid model, dubbed DeepSADPr, which integrated the one-dimensional convolutional neural network (CNN) with the One-Hot encoding approach and the word-embedding approach, compared favourably to other models in terms of both ten-fold cross-validation and independent test. Its AUC values reached 0.935 for ten-fold cross-validation. Its values of sensitivity, accuracy and Matthews's correlation coefficient reached 0.933, 0.867 and 0.740, respectively, with the fixed specificity value of 0.80. Overall, DeepSADPr is the first classifier for predicting Serine ADPr sites, which is available at http://www.bioinfogo.org/DeepSADPr.
Topics: ADP-Ribosylation; Adenosine Diphosphate Ribose; Humans; Protein Processing, Post-Translational; Proteome; Serine
PubMed: 34560250
DOI: 10.1016/j.ymeth.2021.09.008 -
Molecules (Basel, Switzerland) Jun 2022Coumarin was first discovered in Tonka bean and then widely in other plants. Coumarin has an anticoagulant effect, and its derivative, warfarin, is a vitamin K analogue...
Coumarin was first discovered in Tonka bean and then widely in other plants. Coumarin has an anticoagulant effect, and its derivative, warfarin, is a vitamin K analogue that inhibits the synthesis of clotting factors and is more widely used in the clinical treatment of endovascular embolism. At present, many artificial chemical synthesis methods can be used to modify the structure of coumarin to develop many effective drugs with low toxicity. In this study, we investigated the effects of six coumarin derivatives on the platelet aggregation induced by adenosine diphosphate (ADP). We found that the six coumarin derivatives inhibited the active form of GPIIb/IIIa on platelets and hence inhibit platelet aggregation. We found that 7-hydroxy-3-phenyl 4H-chromen-4-one (7-hydroxyflavone) had the most severe effect. In addition, we further analyzed the downstream signal transduction of the ADP receptor, including the release of calcium ions and the regulation of cAMP, which were inhibited by the six coumarin derivatives selected in this study. These results suggest that coumarin derivatives inhibit coagulation by inhibiting the synthesis of coagulation factors and they may also inhibit platelet aggregation.
Topics: Adenosine Diphosphate; Blood Platelets; Coumarins; Platelet Activation; Platelet Aggregation; Platelet Aggregation Inhibitors; Platelet Glycoprotein GPIIb-IIIa Complex
PubMed: 35807298
DOI: 10.3390/molecules27134054 -
International Journal of Molecular... May 2022Maintaining a robust, stable source of energy for doing chemical and physical work is essential to all living organisms. In eukaryotes, metabolic energy (ATP) production... (Review)
Review
Maintaining a robust, stable source of energy for doing chemical and physical work is essential to all living organisms. In eukaryotes, metabolic energy (ATP) production and consumption occurs in two separate compartments, the mitochondrial matrix and the cytosol. As a result, understanding eukaryotic metabolism requires knowledge of energy metabolism in each compartment and how metabolism in the two compartments is coordinated. Central to energy metabolism is the adenylate energy state ([ATP]/[ADP][Pi]). ATP is synthesized by oxidative phosphorylation (mitochondrial matrix) and glycolysis (cytosol) and each compartment provides the energy to do physical work and to drive energetically unfavorable chemical syntheses. The energy state in the cytoplasmic compartment has been established by analysis of near equilibrium metabolic reactions localized in that compartment. In the present paper, analysis is presented for energy-dependent reactions localized in the mitochondrial matrix using data obtained from both isolated mitochondria and intact tissues. It is concluded that the energy state ([ATP]/[ADP][Pi]) in the mitochondrial matrix, calculated from the free (unbound) concentrations, is not different from the energy state in the cytoplasm. Corollaries are: (1) ADP in both the cytosol and matrix is selectively bound and the free concentrations are much lower than the total measured concentrations; and (2) under physiological conditions, the adenylate energy states in the mitochondrial matrix and cytoplasm are not substantially different.
Topics: Adenosine Diphosphate; Adenosine Monophosphate; Adenosine Triphosphate; Cytosol; Energy Metabolism; Eukaryota
PubMed: 35628359
DOI: 10.3390/ijms23105550 -
Biochemical Pharmacology Oct 2021P2Y receptors (P2YRs) are a δ group of rhodopsin-like G protein-coupled receptors (GPCRs) with many essential functions in physiology and pathology, such as platelet... (Review)
Review
P2Y receptors (P2YRs) are a δ group of rhodopsin-like G protein-coupled receptors (GPCRs) with many essential functions in physiology and pathology, such as platelet aggregation, immune responses, neuroprotective effects, inflammation, and cellular proliferation. Thus, they are among the most researched therapeutic targets used for the clinical treatment of diseases (e.g., the antithrombotic drug clopidogrel and the dry eye treatment drug diquafosol). GPCRs transmit signals as dimers to increase the diversity of signalling pathways and pharmacological activities. Many studies have frequently confirmed dimerization between P2YRs and other GPCRs due to their functions in cardiovascular and cerebrovascular processes in vivo and in vitro. Recently, some P2YR dimers that dynamically balance physiological functions in the body were shown to be involved in effective signal transduction and exert pathological responses. In this review, we summarize the types, pharmacological changes, and active regulators of P2YR-related dimerization, and delineate new functions and pharmacological activities of P2YR-related dimers, which may be a novel direction to improve the effectiveness of medications.
Topics: Adenosine Diphosphate; Adenosine Triphosphate; Animals; Humans; Protein Multimerization; Purinergic P2Y Receptor Agonists; Purinergic P2Y Receptor Antagonists; Receptors, G-Protein-Coupled; Receptors, Purinergic P2Y
PubMed: 34274353
DOI: 10.1016/j.bcp.2021.114689 -
Nature Mar 2024To survive bacteriophage (phage) infections, bacteria developed numerous anti-phage defence systems. Some of them (for example, type III CRISPR-Cas, CBASS, Pycsar and...
To survive bacteriophage (phage) infections, bacteria developed numerous anti-phage defence systems. Some of them (for example, type III CRISPR-Cas, CBASS, Pycsar and Thoeris) consist of two modules: a sensor responsible for infection recognition and an effector that stops viral replication by destroying key cellular components. In the Thoeris system, a Toll/interleukin-1 receptor (TIR)-domain protein, ThsB, acts as a sensor that synthesizes an isomer of cyclic ADP ribose, 1''-3' glycocyclic ADP ribose (gcADPR), which is bound in the Smf/DprA-LOG (SLOG) domain of the ThsA effector and activates the silent information regulator 2 (SIR2)-domain-mediated hydrolysis of a key cell metabolite, NAD (refs. ). Although the structure of ThsA has been solved, the ThsA activation mechanism remained incompletely understood. Here we show that 1''-3' gcADPR, synthesized in vitro by the dimeric ThsB' protein, binds to the ThsA SLOG domain, thereby activating ThsA by triggering helical filament assembly of ThsA tetramers. The cryogenic electron microscopy (cryo-EM) structure of activated ThsA revealed that filament assembly stabilizes the active conformation of the ThsA SIR2 domain, enabling rapid NAD depletion. Furthermore, we demonstrate that filament formation enables a switch-like response of ThsA to the 1''-3' gcADPR signal.
Topics: Adenosine Diphosphate Ribose; Bacteria; Bacterial Proteins; Bacteriophages; Cryoelectron Microscopy; Hydrolysis; NAD; Protein Domains; Protein Multimerization; Protein Stability
PubMed: 38383786
DOI: 10.1038/s41586-024-07092-x -
British Journal of Pharmacology Sep 2019Parkinson's disease (PD) involves an initial loss of striatal dopamine terminals evolving into degeneration of dopamine neurons in substantia nigra (SN), which can be...
BACKGROUND AND PURPOSE
Parkinson's disease (PD) involves an initial loss of striatal dopamine terminals evolving into degeneration of dopamine neurons in substantia nigra (SN), which can be modelled by 6-hydroxydopamine (6-OHDA) administration. Adenosine A receptor blockade attenuates PD features in animal models, but the source of the adenosine causing A receptor over-activation is unknown. As ATP is a stress signal, we have tested if extracellular catabolism of adenine nucleotides into adenosine (through ecto-5'-nucleotidase or CD73) leads to A receptor over-activation in PD.
EXPERIMENTAL APPROACH
Effects of blocking CD73 with α,β-methylene ADP (AOPCP) were assayed in 6-OHDA-treated rats and dopamine-differentiated neuroblastoma SH-SY5Y cells.
KEY RESULTS
6-OHDA increased ATP release and extracellular conversion into adenosine through CD73 up-regulation in SH-SY5Y cells. Removing extracellular adenosine with adenosine deaminase, blocking CD73 with AOPCP, or blocking A receptors with SCH58261 were equi-effective in preventing 6-OHDA-induced damage in SH-SY5Y cells. In vivo striatal exposure to 6-OHDA increased ATP release and extracellular formation of adenosine from adenosine nucleotides and up-regulated CD73 and A receptors in striatal synaptosomes. Intracerebroventricular administration of AOPCP phenocopied effects of SCH58261, attenuating 6-OHDA-induced (a) increase of contralateral rotations after apomorphine, (b) reduction of dopamine content in striatum and SN, (c) loss of TH staining in striatum and SN, (d) motor dysfunction in the cylinder test, and (e) short-term memory impairment in the object recognition test.
CONCLUSION AND IMPLICATIONS
Our data indicate that increased ATP-derived adenosine formation is responsible for A receptor over-activation in PD, suggesting CD73 as a new target to manage PD.
Topics: 5'-Nucleotidase; Adenosine; Adenosine A2 Receptor Antagonists; Adenosine Diphosphate; Adenosine Triphosphate; Animals; Cell Line, Tumor; Humans; Male; Oxidopamine; Parkinsonian Disorders; Pyrimidines; Rats, Wistar; Receptor, Adenosine A2A; Triazoles
PubMed: 31220343
DOI: 10.1111/bph.14771