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BMJ Case Reports Feb 2024A man in his 50s presented in an emergency with breathlessness and chest discomfort. On evaluation, he was diagnosed with coronary artery disease, with more than 80%...
A man in his 50s presented in an emergency with breathlessness and chest discomfort. On evaluation, he was diagnosed with coronary artery disease, with more than 80% narrowing of the right coronary and left circumflex arteries. The patient underwent percutaneous coronary intervention and was started on dual antiplatelet (DAPT) therapy. After starting DAPT, the patient developed gross haematuria with a drop in haematocrit. Further evaluation revealed a left renal mass with urinary bladder clots. Because of the risk of stent thrombosis on stopping DAPT, radical nephrectomy was deferred, and the patient underwent left renal artery angioembolisation and bladder clot evacuation. On the follow-up, the patient was stable with a gradual decrease in renal mass size, and after a year, the patient underwent definitive surgery. The patient is doing well in 4 years of follow-up with no metastasis.
Topics: Humans; Male; Carcinoma, Renal Cell; Coronary Artery Disease; Dinucleoside Phosphates; Drug Therapy, Combination; Drug-Eluting Stents; Hemorrhage; Kidney Neoplasms; Myocardial Infarction; Platelet Aggregation Inhibitors; Thrombosis; Middle Aged
PubMed: 38423578
DOI: 10.1136/bcr-2023-257750 -
International Journal of Molecular... Dec 2023To improve the chemical regulation on the activity of cyclic dinucleotides (CDNs), we here designed a reduction-responsive dithioethanol (DTE)-based dCDN prodrug...
To improve the chemical regulation on the activity of cyclic dinucleotides (CDNs), we here designed a reduction-responsive dithioethanol (DTE)-based dCDN prodrug (DTE-dCDN). Prodrug improved the cell permeability with the intracellular levels peaking in 2 h in THP-1 cells. Under the reductive substance such as GSH or DTT, prodrug could be quickly decomposed in 30 min to release the parent dCDN. In THP1-Lucia cells, prodrug also retained a high bioactivity with the EC of 0.96 μM, which was 51-, 43-, and 3-fold more than the 2',3'-cGAMP (EC = 48.6 μM), the parent compound 3',3'-c-di-dAMP (EC = 41.3 μM), and ADU-S100 (EC = 2.9 μM). The high bioactivity of prodrug was validated to be highly correlated with the activation of the STING signaling pathway. Furthermore, prodrug could also improve the transcriptional expression levels of , , and in THP-1 cells. These results will be helpful to the development of chemically controllable CDN prodrugs with a high cellular permeability and potency.
Topics: Deoxyribose; Alarmins; Dinucleoside Phosphates; Permeability; Prodrugs
PubMed: 38203256
DOI: 10.3390/ijms25010086 -
Journal of Biomolecular Structure &... 2024Mycobacterium tuberculosis RecA (MtRecA), a protein involved in DNA repair, homologous recombination and SOS pathway, contributes to the development of multidrug...
Mycobacterium tuberculosis RecA (MtRecA), a protein involved in DNA repair, homologous recombination and SOS pathway, contributes to the development of multidrug resistance. ATP binding-site in RecA has been a drug target to disable RecA dependent DNA repair. For the first time, experiments have shown the existence and binding of c-di-AMP to a novel allosteric site in the C-terminal-Domain (CTD) of RecA (MsRecA), a close homolog of MtRecA. In addition, it was observed that the c-di-AMP was not binding to Escherichia coli RecA (EcRecA). This article analyses the possible interactions of the three RecA homologs with the various c-di-AMP conformations to gain insights into the structural basis of the natural preference of c-di-AMP to MsRecA and not to EcRecA, using the structural biology tools. The comparative analysis, based on amino acid composition, homology, motifs, residue types, docking, molecular dynamics simulations and binding free energy calculations, indeed, conclusively indicates strong binding of c-di-AMP to MsRecA. Having very similar results as MsRecA, it is highly plausible for c-di-AMP to strongly bind MtRecA as well. These insights from the in-silico studies adds a new therapeutic approach against TB through design and development of novel allosteric inhibitors for the first time against MtRecA.Communicated by Ramaswamy H. Sarma.
Topics: Binding Sites; Mycobacterium smegmatis; Mycobacterium tuberculosis; Allosteric Site; Rec A Recombinases; Bacterial Proteins; Dinucleoside Phosphates
PubMed: 38093709
DOI: 10.1080/07391102.2023.2227709 -
International Journal of Molecular... Nov 2023Dinucleoside polyphosphates (NpNs) are considered novel signalling molecules involved in the induction of plant defence mechanisms. However, NpN signal recognition and...
Dinucleoside polyphosphates (NpNs) are considered novel signalling molecules involved in the induction of plant defence mechanisms. However, NpN signal recognition and transduction are still enigmatic. Therefore, the aim of our research was the identification of the NpN receptor and signal transduction pathways evoked by these nucleotides. Earlier, we proved that purine and pyrimidine NpNs differentially affect the phenylpropanoid pathway in suspension-cultured cells. Here, we report, for the first time, that both diadenosine tetraphosphate (ApA) and dicytidine tetraphosphate (CpC)-induced stomatal closure in . Moreover, we showed that plasma membrane purinoreceptor P2K1/DORN1 (does not respond to nucleotide 1) is essential for ApA-induced stomata movements but not for CpC. Wild-type Col-0 and the knockout mutant were used. Examination of the leaf epidermis mutant provided evidence that P2K1/DORN1 is a part of the signal transduction pathway in stomatal closure evoked by extracellular ApA but not by CpC. Reactive oxygen species (ROS) are involved in signal transduction caused by ApA and CpC, leading to stomatal closure. ApA induced and CpC suppressed the transcriptional response in wild-type plants. Moreover, in leaves, the effect of ApA on gene expression was impaired. The interaction between P2K1/DORN1 and ApA leads to changes in the transcription of signalling hubs in signal transduction pathways.
Topics: Arabidopsis; Dinucleoside Phosphates; Signal Transduction; Cell Membrane; Receptors, Purinergic
PubMed: 38069010
DOI: 10.3390/ijms242316688 -
Electrophoresis Apr 2024Cyclic dinucleotides (CDNs) are important second messengers in bacteria and eukaryotes. Detailed characterization of their physicochemical properties is a prerequisite...
Cyclic dinucleotides (CDNs) are important second messengers in bacteria and eukaryotes. Detailed characterization of their physicochemical properties is a prerequisite for understanding their biological functions. Herein, we examine acid-base and electromigration properties of selected CDNs employing capillary electrophoresis (CE), density functional theory (DFT), and nuclear magnetic resonance (NMR) spectroscopy to provide benchmark pK values, as well as to unambiguously determine the protonation sites. Acidity constants (pK) of the NH moieties of adenine and guanine bases and actual and limiting ionic mobilities of CDNs were determined by nonlinear regression analysis of the pH dependence of their effective electrophoretic mobilities measured by CE in aqueous background electrolytes in a wide pH range (0.98-11.48), at constant temperature (25°C), and constant ionic strength (25 mM). The thermodynamic pK values were found to be in the range 3.31-4.56 for adenine and 2.28-3.61 for guanine bases, whereas the pK of enol group of guanine base was in the range 10.21-10.40. Except for systematic shifts of ∼2 pK, the pK values calculated by the DFT-D3//COSMO-RS composite protocol that included large-scale conformational sampling and "cross-morphing" were in a relatively good agreement with the pKs determined by CE and predict N1 atom of adenine and N7 atom of guanine as the protonation sites. The protonation of the N1 atom of adenine and N7 atom of guanine in acidic background electrolytes (BGEs) and the dissociation of the enol group of guanine in alkaline BGEs was confirmed also by NMR spectroscopy.
Topics: Electrophoresis, Capillary; Hydrogen-Ion Concentration; Protons; Magnetic Resonance Spectroscopy; Dinucleoside Phosphates; Thermodynamics; Density Functional Theory
PubMed: 38059733
DOI: 10.1002/elps.202300232 -
Angewandte Chemie (International Ed. in... Feb 2024The recent expansion of the field of RNA chemical modifications has changed our understanding of post-transcriptional gene regulation. Apart from internal nucleobase...
The recent expansion of the field of RNA chemical modifications has changed our understanding of post-transcriptional gene regulation. Apart from internal nucleobase modifications, 7-methylguanosine was long thought to be the only eukaryotic RNA cap. However, the discovery of non-canonical RNA caps in eukaryotes revealed a new niche of previously undetected RNA chemical modifications. We are the first to report the existence of a new non-canonical RNA cap, diadenosine tetraphosphate (Ap A), in human and rat cell lines. Ap A is the most abundant dinucleoside polyphosphate in eukaryotic cells and can be incorporated into RNA by RNA polymerases as a non-canonical initiating nucleotide (NCIN). Using liquid chromatography-mass spectrometry (LC-MS), we show that the amount of capped Ap A-RNA is independent of the cellular concentration of Ap A. A decapping enzyme screen identifies two enzymes cleaving Ap A-RNA,NUDT2 and DXO, both of which also cleave other substrate RNAs in vitro. We further assess the translatability and immunogenicity of Ap A-RNA and show that although it is not translated, Ap A-RNA is recognized as self by the cell and does not elicit an immune response, making it a natural component of the transcriptome. Our findings open a previously unexplored area of eukaryotic RNA regulation.
Topics: Rats; Animals; Humans; Dinucleoside Phosphates; RNA Caps; Mammals; Nudix Hydrolases; Phosphoric Monoester Hydrolases
PubMed: 37934413
DOI: 10.1002/anie.202314951 -
Molecular Microbiology Dec 2023Cyclic dimeric adenosine monophosphate (c-di-AMP) has been well studied in bacteria, including those of the genus Streptococcus, since the first recognition of this... (Review)
Review
Cyclic dimeric adenosine monophosphate (c-di-AMP) has been well studied in bacteria, including those of the genus Streptococcus, since the first recognition of this dinucleotide in 2008. Streptococci possess a sole diadenylate cyclase, CdaA, and distinct c-di-AMP phosphodiesterases. Interestingly, cdaA is required for viability of some streptococcal species but not all when streptococci are grown in standard laboratory media. Bacteria of this genus also have distinct c-di-AMP effector proteins, diverse c-di-AMP-signaling pathways, and subsequent biological outcomes. In streptococci, c-di-AMP may influence bacterial growth, morphology, biofilm formation, competence program, drug resistance, and bacterial pathogenesis. c-di-AMP secreted by streptococci has also been shown to interact with the mammalian host and induces immune responses including type I interferon production. In this review, we summarize the reported c-di-AMP networks in seven species of the genus Streptococcus, which cause diverse clinical manifestations, and propose future perspectives to investigate the signaling molecule in these streptococcal pathogens.
Topics: Animals; Bacterial Proteins; Second Messenger Systems; Dinucleoside Phosphates; Cyclic AMP; Bacteria; Streptococcus; Mammals
PubMed: 37898560
DOI: 10.1111/mmi.15187 -
Bioorganic Chemistry Dec 2023Xeno nucleic acids (XNA) are an increasingly important class of hypermodified nucleic acids with great potential in bioorganic chemistry and synthetic biology. Glycol... (Review)
Review
Xeno nucleic acids (XNA) are an increasingly important class of hypermodified nucleic acids with great potential in bioorganic chemistry and synthetic biology. Glycol nucleic acid (GNA) is constructed from a three-carbon 1,2-propanediol (propylene glycol) backbone attached to a nucleobase entity, representing the simplest known XNA. This review is intended to present GNA nucleosides from a synthetic chemistry perspective-a perspective that serves as a starting point for biological studies. Therefore this account focuses on synthetic methods for GNA nucleoside synthesis, as well as their postsynthetic chemical transformations. The properties and biological activity of GNA constituents are also highlighted. A literature survey shows four major approaches toward GNA nucleoside scaffold synthesis. These approaches pertain to glycidol ring-opening, Mitsunobu, S2, and dihydroxylation reactions. The general arsenal of reactions used in GNA chemistry is versatile and encompasses the Sonogashira reaction, Michael addition, silyl-Hilbert-Johnson reaction, halogenation, alkylation, cyclization, Rh-catalyzed N-allylation, Sharpless catalytic dihydroxylation, and Yb(OTf)-catalyzed etherification. Additionally, various phosphorylation reactions have enabled the synthesis of diverse types of GNA nucleotides, dinucleoside phosphates, phosphordiamidites, and oligos. Furthermore, recent advances in GNA chemistry have resulted in the synthesis of previously unknown redox-active (ferrocenyl) and luminescent (pyrenyl and phenanthrenyl) GNA nucleosides, which are also covered in this review.
Topics: Nucleic Acids; Nucleosides; Glycols; Nucleotides; Propylene Glycol
PubMed: 37871392
DOI: 10.1016/j.bioorg.2023.106921 -
The Journal of General Virology Oct 2023Poxviruses (family ) have long dsDNA genomes and infect a wide range of hosts, including insects, birds, reptiles and mammals. These viruses have substantial incidence,...
Poxviruses (family ) have long dsDNA genomes and infect a wide range of hosts, including insects, birds, reptiles and mammals. These viruses have substantial incidence, prevalence and disease burden in humans and in other animals. Nucleotide and dinucleotide composition, mostly CpG and TpA, have been largely studied in viral genomes because of their evolutionary and functional implications. We analysed here the nucleotide and dinucleotide composition, as well as codon usage bias, of a set of representative poxvirus genomes, with a very diverse host spectrum. After correcting for overall nucleotide composition, entomopoxviruses displayed low overall GC content, no enrichment in TpA and large variation in CpG enrichment, while chordopoxviruses showed large variation in nucleotide composition, no obvious depletion in CpG and a weak trend for TpA depletion in GC-rich genomes. Overall, intergenome variation in dinucleotide composition in poxviruses is largely accounted for by variation in overall genomic GC levels. Nonetheless, using vaccinia virus as a model, we found that genes expressed at the earliest times in infection are more CpG-depleted than genes expressed at later stages. This observation has parallels in betahepesviruses (also large dsDNA viruses) and suggests an antiviral role for the innate immune system (e.g. via the zinc-finger antiviral protein ZAP) in the early phases of poxvirus infection. We also analysed codon usage bias in poxviruses and we observed that it is mostly determined by genomic GC content, and that stratification after host taxonomy does not contribute to explaining codon usage bias diversity. By analysis of within-species diversity, we show that genomic GC content is the result of mutational biases. Poxvirus genomes that encode a DNA ligase are significantly AT-richer than those that do not, suggesting that DNA repair systems shape mutation biases. Our data shed light on the evolution of poxviruses and inform strategies for their genetic manipulation for therapeutic purposes.
Topics: Animals; Humans; Poxviridae; Nucleotides; Codon; Evolution, Molecular; Mammals; Dinucleoside Phosphates; Antiviral Agents
PubMed: 37792576
DOI: 10.1099/jgv.0.001897 -
Current Protocols Sep 2023Cyclic diadenosine monophosphate (c-di-AMP) is a bacterial cyclic dinucleotide (CDN) comprising two adenosine monophosphates covalently linked by two...
Cyclic diadenosine monophosphate (c-di-AMP) is a bacterial cyclic dinucleotide (CDN) comprising two adenosine monophosphates covalently linked by two 3',5'-phosphodiester bonds. c-di-AMP works as a second messenger, regulating many biological processes in bacteria such as cell wall homeostasis, DNA integrity, and sporulation via specific protein and/or RNA receptors. Moreover, c-di-AMP can function as an immunomodulatory agent in eukaryote cells via the stimulator of interferon genes (STING) signaling pathway. This protocol describes the chemical synthesis of two c-di-AMP analogs with a sulfur atom at the 4'-position of the furanose ring instead of an oxygen atom: c-di-4'-thioAMP (1) and cAMP-4'-thioAMP (2). Analogs 1 and 2 have resistance to phosphodiesterase-mediated degradation and are therefore useful for understanding the diverse biological phenomena regulated by c-di-AMP. In this protocol, two 4'-thioadenosine monomers are initially prepared via a Pummerer-like reaction assisted by hypervalent iodine. The CDN skeleton is then constructed through two key reactions based on phosphoramidite chemistry: dimerization of two appropriately protected nucleoside monomers to produce a linear dinucleotide, followed by macrocyclization of the resulting linear dinucleotide to form the CDN skeleton. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Preparation of 4'-thioadenosine monomers 13 and 14 Basic Protocol 2: Preparation of c-di-4'-thioAMP (1) and cAMP-4'-thioAMP (2).
Topics: Dinucleoside Phosphates; Thionucleosides; Homeostasis; Cyclic AMP
PubMed: 37725690
DOI: 10.1002/cpz1.892