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Molecules (Basel, Switzerland) May 2024Azido-modified nucleosides have been extensively explored as substrates for click chemistry and the metabolic labeling of DNA and RNA. These compounds are also of... (Review)
Review
Azido-modified nucleosides have been extensively explored as substrates for click chemistry and the metabolic labeling of DNA and RNA. These compounds are also of interest as precursors for further synthetic elaboration and as therapeutic agents. This review discusses the chemistry of azidonucleosides related to the generation of nitrogen-centered radicals (NCRs) from the azido groups that are selectively inserted into the nucleoside frame along with the subsequent chemistry and biological implications of NCRs. For instance, the critical role of the sulfinylimine radical generated during inhibition of ribonucleotide reductases by 2'-azido-2'-deoxy pyrimidine nucleotides as well as the NCRs generated from azidonucleosides by radiation-produced (prehydrated and aqueous) electrons are discussed. Regio and stereoselectivity of incorporation of an azido group ("radical arm") into the frame of nucleoside and selective generation of NCRs under reductive conditions, which often produce the same radical species that are observed upon ionization events due to radiation and/or other oxidative conditions that are emphasized. NCRs generated from nucleoside-modified precursors other than azidonucleosides are also discussed but only with the direct relation to the same/similar NCRs derived from azidonucleosides.
Topics: Nucleosides; Azides; Nitrogen; Free Radicals; Click Chemistry
PubMed: 38792171
DOI: 10.3390/molecules29102310 -
Molecules (Basel, Switzerland) May 2024DNA is constantly damaged by various external and internal factors. In particular, oxidative damage occurs in a steady state, and 8-oxo-2'-deoxyguanosine (oxodG) is...
DNA is constantly damaged by various external and internal factors. In particular, oxidative damage occurs in a steady state, and 8-oxo-2'-deoxyguanosine (oxodG) is known as the main oxidative damage. OxodG is a strong genotoxic nucleoside and is thought to be involved in the pathogenesis of cancer and neurological diseases. However, a breakthrough method to detect the position of oxodG in DNA has not yet been developed. Therefore, we attempted to develop a novel method to detect oxodG in DNA using artificial nucleosides. Recently, we have succeeded in the recognition of oxodG in DNA by a single nucleotide elongation reaction using nucleoside derivatives based on a purine skeleton with a 1,3-diazaphenoxazine unit. In this study, we developed a new nucleoside derivative with a pyrimidine skeleton in order to further improve the recognition ability and enzymatic reaction efficiency. We, therefore, designed and synthesized 2'-deoxycytidine-1,3-diazaphenoxazine (Cdap) and its triphosphate derivatives. The results showed that it was incorporated into the primer strand relative to the dG template because of its cytidine skeleton, but it was more effective at the complementary position of the oxodG template. These results indicate that the new nucleoside derivative can be considered as one of the new candidates for the detection of oxodG in DNA.
Topics: 8-Hydroxy-2'-Deoxyguanosine; DNA; Deoxycytidine; Oxazines; Deoxyguanosine; DNA Damage; Nucleotides; Polyphosphates
PubMed: 38792131
DOI: 10.3390/molecules29102270 -
Science Advances May 2024The replication accuracy of DNA polymerase gamma (Pol γ) is essential for mitochondrial genome integrity. Mutation of human Pol γ arginine-853 has been linked to...
The replication accuracy of DNA polymerase gamma (Pol γ) is essential for mitochondrial genome integrity. Mutation of human Pol γ arginine-853 has been linked to neurological diseases. Although not a catalytic residue, Pol γ arginine-853 mutants are void of polymerase activity. To identify the structural basis for the disease, we determined a crystal structure of the Pol γ mutant ternary complex with correct incoming nucleotide 2'-deoxycytidine 5'-triphosphate (dCTP). Opposite to the wild type that undergoes open-to-closed conformational changes when bound to a correct nucleotide that is essential for forming a catalytically competent active site, the mutant complex failed to undergo the conformational change, and the dCTP did not base pair with its Watson-Crick complementary templating residue. Our studies revealed that arginine-853 coordinates an interaction network that aligns the 3'-end of primer and dCTP with the catalytic residues. Disruption of the network precludes the formation of Watson-Crick base pairing and closing of the active site, resulting in an inactive polymerase.
Topics: Base Pairing; Catalytic Domain; Humans; DNA Polymerase gamma; Models, Molecular; Mutation; Deoxycytosine Nucleotides; Crystallography, X-Ray; Protein Binding
PubMed: 38787958
DOI: 10.1126/sciadv.adl3214 -
Scientific Reports May 2024The treatment of HCV and its sequelae are used to be predominantly based on Interferon (IFN). However, this was associated with significant adverse events as a result of... (Comparative Study)
Comparative Study
The treatment of HCV and its sequelae are used to be predominantly based on Interferon (IFN). However, this was associated with significant adverse events as a result of its immunostimulant capabilities. Since their introduction, the directly acting antiviral drugs (DAAs), have become the standard of care to treat of HCV and its complications including mixed cryoglobulinemic vasculitis (MCV). In spite of achieving sustained viral response (SVR), there appeared many reports describing unwelcome complications such as hepatocellular and hematological malignancies as well as relapses. Prolonged inflammation induced by a multitude of factors, can lead to DNA damage and affects BAFF and APRIL, which serve as markers of B-cell proliferation. We compared, head-to-head, three antiviral protocols for HCV-MCV treatment As regards the treatment response and relapse, levels of BAFF and APRIL among pegylated interferon α-based and free regimens (Sofosbuvir + Ribavirin; SOF-RIBA, Sofosbuvir + Daclatasvir; SOF-DACLA). Regarding clinical response HCV-MCV and SVR; no significant differences could be identified among the 3 different treatment protocols, and this was also independent form using IFN. We found no significant differences between IFN-based and free regimens DNA damage, markers of DNA repair, or levels of BAFF and APRIL. However, individualized drug-to-drug comparisons showed many differences. Those who were treated with IFN-based protocol showed decreased levels of DNA damage, while the other two IFN-free groups showed increased DNA damage, being the worst in SOF-DACLA group. There were increased levels of BAFF through follow-up periods in the 3 protocols being the best in SOF-DACLA group (decreased at 24 weeks). In SOF-RIBA, CGs relapsed significantly during the follow-up period. None of our patients who were treated with IFN-based protocol had significant clinico-laboratory relapse. Those who received IFN-free DAAs showed a statistically significant relapse of constitutional manifestations. Our findings suggest that IFN-based protocols are effective in treating HCV-MCV similar to IFN-free protocols. They showed lower levels of DNA damage and repair. We believe that our findings may offer an explanation for the process of lymphoproliferation, occurrence of malignancies, and relapses by shedding light on such possible mechanisms.
Topics: Humans; Cryoglobulinemia; Antiviral Agents; Male; Vasculitis; Middle Aged; Female; Aged; Hepacivirus; Ribavirin; Sofosbuvir; Imidazoles; Valine; Pyrrolidines; B-Cell Activating Factor; Interferon-alpha; Drug Therapy, Combination; Hepatitis C; Treatment Outcome; Hepatitis C, Chronic; Carbamates
PubMed: 38782988
DOI: 10.1038/s41598-024-60490-z -
Trials May 2024The SARS CoV-2 pandemic has resulted in more than 1.1 million deaths in the USA alone. Therapeutic options for critically ill patients with COVID-19 are limited. Prior...
SCARLET (Supplemental Citicoline Administration to Reduce Lung injury Efficacy Trial): study protocol for a single-site, double-blinded, placebo-controlled, and randomized Phase 1/2 trial of i.v. citicoline (CDP-choline) in hospitalized SARS CoV-2-infected patients with hypoxemic acute respiratory...
BACKGROUND
The SARS CoV-2 pandemic has resulted in more than 1.1 million deaths in the USA alone. Therapeutic options for critically ill patients with COVID-19 are limited. Prior studies showed that post-infection treatment of influenza A virus-infected mice with the liponucleotide CDP-choline, which is an essential precursor for de novo phosphatidylcholine synthesis, improved gas exchange and reduced pulmonary inflammation without altering viral replication. In unpublished studies, we found that treatment of SARS CoV-2-infected K18-hACE2-transgenic mice with CDP-choline prevented development of hypoxemia. We hypothesize that administration of citicoline (the pharmaceutical form of CDP-choline) will be safe in hospitalized SARS CoV-2-infected patients with hypoxemic acute respiratory failure (HARF) and that we will obtain preliminary evidence of clinical benefit to support a larger Phase 3 trial using one or more citicoline doses.
METHODS
We will conduct a single-site, double-blinded, placebo-controlled, and randomized Phase 1/2 dose-ranging and safety study of Somazina® citicoline solution for injection in consented adults of any sex, gender, age, or ethnicity hospitalized for SARS CoV-2-associated HARF. The trial is named "SCARLET" (Supplemental Citicoline Administration to Reduce Lung injury Efficacy Trial). We hypothesize that SCARLET will show that i.v. citicoline is safe at one or more of three doses (0.5, 2.5, or 5 mg/kg, every 12 h for 5 days) in hospitalized SARS CoV-2-infected patients with HARF (20 per dose) and provide preliminary evidence that i.v. citicoline improves pulmonary outcomes in this population. The primary efficacy outcome will be the SO:FO ratio on study day 3. Exploratory outcomes include Sequential Organ Failure Assessment (SOFA) scores, dead space ventilation index, and lung compliance. Citicoline effects on a panel of COVID-relevant lung and blood biomarkers will also be determined.
DISCUSSION
Citicoline has many characteristics that would be advantageous to any candidate COVID-19 therapeutic, including safety, low-cost, favorable chemical characteristics, and potentially pathogen-agnostic efficacy. Successful demonstration that citicoline is beneficial in severely ill patients with SARS CoV-2-induced HARF could transform management of severely ill COVID patients.
TRIAL REGISTRATION
The trial was registered at www.
CLINICALTRIALS
gov on 5/31/2023 (NCT05881135).
TRIAL STATUS
Currently enrolling.
Topics: Humans; Cytidine Diphosphate Choline; Double-Blind Method; SARS-CoV-2; COVID-19; Randomized Controlled Trials as Topic; COVID-19 Drug Treatment; Clinical Trials, Phase II as Topic; Pneumonia, Viral; Treatment Outcome; Hypoxia; Male; Pandemics; Coronavirus Infections; Hospitalization; Female; Betacoronavirus; Clinical Trials, Phase I as Topic; Respiratory Insufficiency; Administration, Intravenous; Adult
PubMed: 38760804
DOI: 10.1186/s13063-024-08155-0 -
PloS One 2024More than 58 million individuals worldwide are inflicted with chronic HCV. The disease carries a high risk of end stage liver disease, i.e., cirrhosis and hepatocellular...
More than 58 million individuals worldwide are inflicted with chronic HCV. The disease carries a high risk of end stage liver disease, i.e., cirrhosis and hepatocellular carcinoma. Although direct-acting antiviral agents (DAAs) have revolutionized therapy, the emergence of drug-resistant strains has become a growing concern. Conventional cellular models, Huh7 and its derivatives were very permissive to only HCVcc (JFH-1), but not HCV clinical isolates. The lack of suitable host cells had hindered comprehensive research on patient-derived HCV. Here, we established a novel hepatocyte model for HCV culture to host clinically pan-genotype HCV strains. The immortalized hepatocyte-like cell line (imHC) derived from human mesenchymal stem cell carries HCV receptors and essential host factors. The imHC outperformed Huh7 as a host for HCV (JFH-1) and sustained the entire HCV life cycle of pan-genotypic clinical isolates. We analyzed the alteration of host markers (i.e., hepatic markers, cellular innate immune response, and cell apoptosis) in response to HCV infection. The imHC model uncovered the underlying mechanisms governing the action of IFN-α and the activation of sofosbuvir. The insights from HCV-cell culture model hold promise for understanding disease pathogenesis and novel anti-HCV development.
Topics: Humans; Hepatocytes; Hepacivirus; Antiviral Agents; Sofosbuvir; Cell Line; Virus Replication; Interferon-alpha; Hepatitis C; Apoptosis; Mesenchymal Stem Cells
PubMed: 38739590
DOI: 10.1371/journal.pone.0303265 -
International Journal of Molecular... Apr 2024Numerous studies suggest the involvement of adenosine-5'-triphosphate (ATP) and similar nucleotides in the pathophysiology of asthma. Androgens, such as testosterone...
Numerous studies suggest the involvement of adenosine-5'-triphosphate (ATP) and similar nucleotides in the pathophysiology of asthma. Androgens, such as testosterone (TES), are proposed to alleviate asthma symptoms in young men. ATP and uridine-5'-triphosphate (UTP) relax the airway smooth muscle (ASM) via purinergic P2Y and P2Y receptors and K channel opening. We previously demonstrated that TES increased the expression of voltage-dependent K (K) channels in ASM. This study investigates how TES may potentiate ASM relaxation induced by ATP and UTP. Tracheal tissues treated with or without TES (control group) from young male guinea pigs were used. In organ baths, tracheas exposed to TES (40 nM for 48 h) showed enhanced ATP- and UTP-evoked relaxation. Tetraethylammonium, a K channel blocker, annulled this effect. Patch-clamp experiments in tracheal myocytes showed that TES also increased ATP- and UTP-induced K currents, and this effect was abolished with flutamide (an androgen receptor antagonist). K channels were involved in this phenomenon, which was demonstrated by inhibition with 4-aminopyridine. RB2 (an antagonist of almost all P2Y receptors except for P2Y), as well as N-ethylmaleimide and SQ 22,536 (inhibitors of G proteins and adenylyl cyclase, respectively), attenuated the enhancement of the K currents induced by TES. Immunofluorescence and immunohistochemistry studies revealed that TES did not modify the expression of P2Y receptors or COX-1 and COX-2, while we have demonstrated that this androgen augmented the expression of K1.2 and K1.5 channels in ASM. Thus, TES leads to the upregulation of P2Y signaling and K channels in guinea pig ASM, enhancing ATP and UTP relaxation responses, which likely limits the severity of bronchospasm in young males.
Topics: Animals; Uridine Triphosphate; Guinea Pigs; Muscle Relaxation; Male; Adenosine Triphosphate; Trachea; Testosterone; Adenylyl Cyclases; Muscle, Smooth; Potassium Channels, Voltage-Gated; Signal Transduction; Receptors, Purinergic P2
PubMed: 38731872
DOI: 10.3390/ijms25094652 -
Saudi Journal of Kidney Diseases and... Nov 2023Patients with end-stage renal disease (ESRD) are at an increased risk of hepatitis C virus (HCV) infection. This study evaluated the prevalence of HCV infection in...
Prevalence of Hepatitis C Virus Infection and Efficacy of Sofosbuvir-Velpatasvir and Sofosbuvir-Daclatasvir Treatment Regimens in End-stage Renal Disease Patients on Maintenance Hemodialysis.
Patients with end-stage renal disease (ESRD) are at an increased risk of hepatitis C virus (HCV) infection. This study evaluated the prevalence of HCV infection in patients with ESRD on maintenance hemodialysis (MHD) and studied the effectiveness of sofosbuvir-velpatasvir and sofosbuvir-daclatasvir regimens in these patients. This study included patients with ESRD on MHD between January 2019 and December 2021 who were screened for HCV serology status. HCV-positive patients received sofosbuvir-velpatasvir or sofosbuvir-daclatasvir. Efficacy was assessed by the sustained virological response (SVR), and safety assessments included monitoring adverse events and laboratory parameters. Out of 1330 patients, 188 patients (14.1%) were positive for anti-HCV, with Genotype 1 being the most common genotype. Of these, 106 patients were included. The majority were males (61.3%), and the mean age was 48.4 years. Hypertension (45.3%) was the most common cause of renal failure, followed by diabetes (31.1%). Most patients (63.2%) were positive for HCV in the first 2 years of their dialysis treatment. Out of 106 patients, only 54 had received blood transfusions. Ninety-four (88.7%) patients received sofosbuvir-velpatasvir, whereas 12 (11.3%) received sofosbuvir-daclatasvir. SVR at 12 and 24 weeks after stopping treatment was seen in all (100%) patients. Asthenia and fatigue were the most common adverse events (11.2%). No patients reported on-treatment virologic failure or discontinuation of treatment because of adverse events. The prevalence of HCV infection in this population was 14.1%, and treatment of HCV infection using sofosbuvir-velpatasvir or sofosbuvir-daclatasvir regimens was well tolerated and effective.
Topics: Humans; Male; Female; Middle Aged; Sofosbuvir; Imidazoles; Renal Dialysis; Kidney Failure, Chronic; Carbamates; Valine; Pyrrolidines; Antiviral Agents; Heterocyclic Compounds, 4 or More Rings; Drug Combinations; Adult; Prevalence; Treatment Outcome; Hepatitis C; Aged; Hepacivirus; Sustained Virologic Response; Saudi Arabia; Hepatitis C, Chronic
PubMed: 38725207
DOI: 10.4103/sjkdt.sjkdt_19_23 -
Nucleic Acids Research Jun 2024In recent years, several noncanonical RNA caps derived from cofactors and metabolites have been identified. Purine-containing RNA caps have been extensively studied,...
In recent years, several noncanonical RNA caps derived from cofactors and metabolites have been identified. Purine-containing RNA caps have been extensively studied, with multiple decapping enzymes identified and efficient capture and sequencing protocols developed for nicotinamide adenine dinucleotide (NAD)-RNA, which allowed for a stepwise elucidation of capping functions. Despite being identified as an abundant noncanonical RNA-cap, UDP-sugar-capped RNA remains poorly understood, which is partly due to its complex in vitro preparation. Here, we describe a scalable synthesis of sugar-capped uridine-guanosine dinucleotides from readily available protected building blocks and their enzymatic conversion into several cell wall precursor-capped dinucleotides. We employed these capped dinucleotides in T7 RNA polymerase-catalyzed in vitro transcription reactions to efficiently generate RNAs capped with uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), its N-azidoacetyl derivative UDP-GlcNAz, and various cell wall precursors. We furthermore identified four enzymes capable of processing UDP-GlcNAc-capped RNA in vitro: MurA, MurB and MurC from Escherichia coli can sequentially modify the sugar-cap structure and were used to introduce a bioorthogonal, clickable moiety, and the human Nudix hydrolase Nudt5 was shown to efficiently decap UDP-GlcNAc-RNA. Our findings underscore the importance of efficient synthetic methods for capped model RNAs. Additionally, we provide useful enzymatic tools that could be utilized in the development and application of UDP-GlcNAc capture and sequencing protocols. Such protocols are essential for deepening our understanding of the widespread yet enigmatic GlcNAc modification of RNA and its physiological significance.
Topics: Uridine Diphosphate N-Acetylglucosamine; RNA Caps; Endoribonucleases; DNA-Directed RNA Polymerases; Humans; Escherichia coli; Viral Proteins
PubMed: 38716860
DOI: 10.1093/nar/gkae353 -
Scientific Reports May 2024Access to Hepatis C treatment in Sub-Saharan Africa is a clinical, public health and ethical concern. The multi-country open-label trial TAC ANRS 12311 allowed assessing... (Clinical Trial)
Clinical Trial
Access to Hepatis C treatment in Sub-Saharan Africa is a clinical, public health and ethical concern. The multi-country open-label trial TAC ANRS 12311 allowed assessing the feasibility, safety, efficacy of a specific care model of HCV treatment and retreatment in patients with hepatitis C in Sub Saharan Africa. Between November 2015 and March 2017, with follow-up until mid 2019, treatment-naïve patients with HCV without decompensated cirrhosis or liver cancer were recruited to receive 12 week-treatment with either sofosbuvir + ribavirin (HCV genotype 2) or sofosbuvir + ledipasvir (genotype 1 or 4) and retreatment with sofosbuvir + velpatasvir + voxilaprevir in case of virological failure. The primary outcome was sustained virological response at 12 weeks after end of treatment (SVR12). Secondary outcomes included treatment adherence, safety and SVR12 in patients who were retreated due to non-response to first-line treatment. The model of care relied on both viral load assessment and educational sessions to increase patient awareness, adherence and health literacy. The study recruited 120 participants, 36 HIV-co-infected, and 14 cirrhotic. Only one patient discontinued treatment because of return to home country. Neither death nor severe adverse event occurred. SVR12 was reached in 107 patients (89%): (90%) in genotype 1 or 2, and 88% in GT-4. All retreated patients (n = 13) reached SVR12. HCV treatment is highly acceptable, safe and effective under this model of care. Implementation research is now needed to scale up point-of-care HCV testing and SVR assessment, along with community involvement in patient education, to achieve HCV elimination in Sub-Saharan Africa.
Topics: Adult; Female; Humans; Male; Middle Aged; Africa, Central; Africa, Western; Aminoisobutyric Acids; Antiviral Agents; Benzimidazoles; Benzopyrans; Carbamates; Cyclopropanes; Drug Therapy, Combination; Feasibility Studies; Fluorenes; Genotype; Hepacivirus; Hepatitis C; Hepatitis C, Chronic; Heterocyclic Compounds, 4 or More Rings; Lactams, Macrocyclic; Leucine; Proline; Quinoxalines; Ribavirin; Sofosbuvir; Sulfonamides; Sustained Virologic Response; Treatment Outcome
PubMed: 38702350
DOI: 10.1038/s41598-024-57013-1