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1.
PLoS One ; 19(6): e0298254, 2024.
Article in English | MEDLINE | ID: mdl-38843201

ABSTRACT

BACKGROUND: In randomized controlled trials, Nirmatrelvir/ritonavir (NMV/r) and Molnupiravir (MPV) reduced the risk of severe/fatal COVID-19 disease. Real-world data are limited, particularly studies directly comparing the two agents. METHODS: Using the VA National COVID-19 database, we identified previously uninfected, non-hospitalized individuals with COVID-19 with ≥1 risk factor for disease progression who were prescribed either NMV/r or MPV within 3 days of a positive test. We used inverse probability of treatment weights (IPTW) to account for providers' preferences for a specific treatment. Absolute risk difference (ARD) with 95% confidence intervals were determined for those treated with NMV/r vs. MPV. The primary outcome was hospitalization or death within 30 days of treatment prescription using the IPTW approach. Analyses were repeated using propensity-score matched groups. RESULTS: Between January 1 and November 30, 2022, 9,180 individuals were eligible for inclusion (6,592 prescribed NMV/r; 2,454 prescribed MPV). The ARD for hospitalization/death for NMV/r vs MPV was -0.25 (95% CI -0.79 to 0.28). There was no statistically significant difference in ARD among strata by age, race, comorbidities, or symptoms at baseline. Kaplan-Meier curves did not demonstrate a difference between the two groups (p-value = 0.6). Analysis of the propensity-score matched cohort yielded similar results (ARD for NMV/r vs. MPV -0.9, 95% CI -2.02 to 0.23). Additional analyses showed no difference for development of severe/critical/fatal disease by treatment group. CONCLUSION: We found no significant difference in short term risk of hospitalization or death among at-risk individuals with COVID-19 treated with either NMV/r or MPV.


Subject(s)
Antiviral Agents , COVID-19 Drug Treatment , COVID-19 , Cytidine , Disease Progression , Hospitalization , Hydroxylamines , Leucine , Ritonavir , SARS-CoV-2 , Humans , Male , Female , Ritonavir/therapeutic use , Middle Aged , Hydroxylamines/therapeutic use , Cytidine/analogs & derivatives , Cytidine/therapeutic use , COVID-19/mortality , COVID-19/epidemiology , Antiviral Agents/therapeutic use , Leucine/analogs & derivatives , Leucine/therapeutic use , Aged , SARS-CoV-2/isolation & purification , Proline/analogs & derivatives , Proline/therapeutic use , Indoles/therapeutic use , Adult , Pandemics , Risk Factors , Coronavirus Infections/drug therapy , Coronavirus Infections/mortality , Pneumonia, Viral/drug therapy , Pneumonia, Viral/mortality , Pneumonia, Viral/virology , Betacoronavirus , Lactams , Nitriles
2.
Proc Natl Acad Sci U S A ; 121(24): e2400378121, 2024 Jun 11.
Article in English | MEDLINE | ID: mdl-38830096

ABSTRACT

Epitranscriptomic RNA modifications have emerged as important regulators of the fate and function of viral RNAs. One prominent modification, the cytidine methylation 5-methylcytidine (m5C), is found on the RNA of HIV-1, where m5C enhances the translation of HIV-1 RNA. However, whether m5C functionally enhances the RNA of other pathogenic viruses remains elusive. Here, we surveyed a panel of commonly found RNA modifications on the RNA of hepatitis B virus (HBV) and found that HBV RNA is enriched with m5C as well as ten other modifications, at stoichiometries much higher than host messenger RNA (mRNA). Intriguingly, m5C is mostly found on the epsilon hairpin, an RNA element required for viral RNA encapsidation and reverse transcription, with these m5C mainly deposited by the cellular methyltransferase NSUN2. Loss of m5C from HBV RNA due to NSUN2 depletion resulted in a partial decrease in viral core protein (HBc) production, accompanied by a near-complete loss of the reverse transcribed viral DNA. Similarly, mutations introduced to remove the methylated cytidines resulted in a loss of HBc production and reverse transcription. Furthermore, pharmacological disruption of m5C deposition led to a significant decrease in HBV replication. Thus, our data indicate m5C methylations as a critical mediator of the epsilon elements' function in HBV virion production and reverse transcription, suggesting the therapeutic potential of targeting the m5C methyltransfer process on HBV epsilon as an antiviral strategy.


Subject(s)
Cytidine , Hepatitis B virus , RNA, Viral , Reverse Transcription , Hepatitis B virus/genetics , Hepatitis B virus/metabolism , Hepatitis B virus/physiology , RNA, Viral/genetics , RNA, Viral/metabolism , Cytidine/analogs & derivatives , Cytidine/metabolism , Cytidine/genetics , Humans , Reverse Transcription/genetics , Methylation , Virus Replication/genetics , Epigenesis, Genetic , Virion/metabolism , Virion/genetics , Transcriptome
3.
Brief Bioinform ; 25(3)2024 Mar 27.
Article in English | MEDLINE | ID: mdl-38701415

ABSTRACT

N4-acetylcytidine (ac4C) is a modification found in ribonucleic acid (RNA) related to diseases. Expensive and labor-intensive methods hindered the exploration of ac4C mechanisms and the development of specific anti-ac4C drugs. Therefore, an advanced prediction model for ac4C in RNA is urgently needed. Despite the construction of various prediction models, several limitations exist: (1) insufficient resolution at base level for ac4C sites; (2) lack of information on species other than Homo sapiens; (3) lack of information on RNA other than mRNA; and (4) lack of interpretation for each prediction. In light of these limitations, we have reconstructed the previous benchmark dataset and introduced a new dataset including balanced RNA sequences from multiple species and RNA types, while also providing base-level resolution for ac4C sites. Additionally, we have proposed a novel transformer-based architecture and pipeline for predicting ac4C sites, allowing for highly accurate predictions, visually interpretable results and no restrictions on the length of input RNA sequences. Statistically, our work has improved the accuracy of predicting specific ac4C sites in multiple species from less than 40% to around 85%, achieving a high AUC > 0.9. These results significantly surpass the performance of all existing models.


Subject(s)
Cytidine , Cytidine/analogs & derivatives , RNA , Cytidine/genetics , RNA/genetics , RNA/chemistry , Humans , Computational Biology/methods , Animals , Software , Algorithms
4.
Iran J Med Sci ; 49(5): 275-285, 2024 May.
Article in English | MEDLINE | ID: mdl-38751873

ABSTRACT

Background: The RNA-dependent RNA polymerase (RdRp) inhibitors, molnupiravir and VV116, have the potential to maximize clinical benefits in the oral treatment of COVID-19. Subjects who consume these drugs may experience an increased incidence of adverse events. This study aimed to evaluate the safety profile of molnupiravir and VV116. Methods: A comprehensive search of scientific and medical databases, such as PubMed Central/Medline, Embase, Web of Science, and Cochrane Library, was conducted to find relevant articles in English from January 2020 to June 2023. Any kind of adverse events reported in the study were pooled and analyzed in the drug group versus the control group. Estimates of risk effects were summarized through the random effects model using Review Manager version 5.2, and sensitivity analysis was performed by Stata 17.0 software. Results: Fifteen studies involving 32,796 subjects were included. Eleven studies were placebo-controlled, and four were Paxlovid-controlled. Twelve studies reported adverse events for molnupiravir, and three studies described adverse events for VV116. The total odds ratio (OR) for adverse events in the RdRp inhibitor versus the placebo-controlled group was 1.01 (95% CI=0.84-1.22; I2=26%), P=0.88. The total OR for adverse events in the RdRp inhibitor versus the Paxlovid-controlled group was 0.32 (95% CI=0.16-0.65; I2=87%), P=0.002. Individual drug subgroup analysis in the placebo-controlled study showed that compared with the placebo group, a total OR for adverse events was 0.97 (95% CI, 0.85-1.10; I2=0%) in the molnupiravir group and 3.77 (95% CI=0.08-175.77; I2=85%) in the VV116 group. Conclusion: The RdRp inhibitors molnupiravir and VV116 are safe for oral treatment of COVID-19. Further evidence is necessary that RdRp inhibitors have a higher safety profile than Paxlovid.


Subject(s)
Antiviral Agents , COVID-19 Drug Treatment , Cytidine , Hydroxylamines , RNA-Dependent RNA Polymerase , Humans , Hydroxylamines/therapeutic use , Hydroxylamines/pharmacology , Cytidine/analogs & derivatives , Cytidine/therapeutic use , Cytidine/pharmacology , Antiviral Agents/therapeutic use , Antiviral Agents/adverse effects , Antiviral Agents/pharmacology , Administration, Oral , RNA-Dependent RNA Polymerase/antagonists & inhibitors , SARS-CoV-2 , Adenosine/analogs & derivatives
5.
Commun Biol ; 7(1): 587, 2024 May 16.
Article in English | MEDLINE | ID: mdl-38755254

ABSTRACT

DNA methylation is an important epigenetic mechanism involved in the anti-tumor immune response, and DNA methyltransferase inhibitors (DNMTi) have achieved impressive therapeutic outcomes in patients with certain cancer types. However, it is unclear how inhibition of DNA methylation bridges the innate and adaptive immune responses to inhibit tumor growth. Here, we report that DNMTi zebularine reconstructs tumor immunogenicity, in turn promote dendritic cell maturation, antigen-presenting cell activity, tumor cell phagocytosis by APCs, and efficient T cell priming. Further in vivo and in vitro analyses reveal that zebularine stimulates cGAS-STING-NF-κB/IFNß signaling to enhance tumor cell immunogenicity and upregulate antigen processing and presentation machinery (AgPPM), which promotes effective CD4+ and CD8+ T cell-mediated killing of tumor cells. These findings support the use of combination regimens that include DNMTi and immunotherapy for cancer treatment.


Subject(s)
Antigen Presentation , Cytidine , Membrane Proteins , Nucleotidyltransferases , Signal Transduction , Nucleotidyltransferases/metabolism , Nucleotidyltransferases/genetics , Animals , Membrane Proteins/metabolism , Membrane Proteins/genetics , Cytidine/analogs & derivatives , Cytidine/pharmacology , Antigen Presentation/drug effects , Mice , Signal Transduction/drug effects , Mice, Inbred C57BL , Cell Line, Tumor , Neoplasms/immunology , Neoplasms/drug therapy , Neoplasms/metabolism , Humans , Dendritic Cells/immunology , Dendritic Cells/drug effects , Dendritic Cells/metabolism , Female
6.
Int Immunopharmacol ; 135: 112317, 2024 Jun 30.
Article in English | MEDLINE | ID: mdl-38796965

ABSTRACT

Colorectal cancer (CRC) is a significant global health challenge, with increasing rates of incidence and mortality. Despite advancements in immunotherapy, resistance, particularly due to T cell exhaustion, remains a major hurdle. This study explores the role of YWHAH, mediated by N4-acetylcytidine (ac4C) modification, in CRC progression and its impact on CD8+ T cell exhaustion. Analysis of five paired CRC patient tissue samples using acetylated RNA immunoprecipitation and sequencing (acRIP-seq)identified ac4C-modified mRNAs. Functional assays, including cell culture, transfection, qRT-PCR, and immune assays, investigated the influence of YWHAH expression on CRC advancement. Bioinformatics analysis of TCGA data assessed the correlation between YWHAH and immune responses, as well as checkpoint inhibitors. Flow cytometry and Immunohistochemistry validated these findings, complemented by a co-culture experiment involving CD8+ T cells and CRC cell lines (LOVO and HCT116). acRIP-seq revealed YWHAH as a potential driver of CRC progression, exhibiting ac4C modification-mediated stability and upregulation. High YWHAH levels correlated with adverse outcomes and immune evasion in CRC patients, showing strong associations with immune checkpoint proteins and modest correlations with CD8+ T cell infiltration. Co-culture experiments demonstrated YWHAH-induced CD8+ T cell exhaustion, characterized by decreased proliferation and increased exhaustion markers. NAT10-mediated ac4C modification enhanced YWHAH stability in CRC. The involvement of YWHAH in CD8 + T cell exhaustion suggests its potential as a therapeutic target and prognostic marker in CRC immunotherapy, highlighting the intricate interplay between epitranscriptomic modifications, the tumor microenvironment, and immune responses in CRC progression.


Subject(s)
CD8-Positive T-Lymphocytes , Colorectal Neoplasms , Humans , Colorectal Neoplasms/immunology , Colorectal Neoplasms/pathology , CD8-Positive T-Lymphocytes/immunology , 14-3-3 Proteins/metabolism , 14-3-3 Proteins/genetics , Cell Line, Tumor , Cytidine/analogs & derivatives , Cytidine/pharmacology , Gene Expression Regulation, Neoplastic , Immune Checkpoint Inhibitors/therapeutic use , Immune Checkpoint Inhibitors/pharmacology , T-Cell Exhaustion
7.
J Med Virol ; 96(5): e29642, 2024 May.
Article in English | MEDLINE | ID: mdl-38708812

ABSTRACT

Molnupiravir, an oral direct-acting antiviral effective in vitro against SARS-CoV-2, has been largely employed during the COVID-19 pandemic, since December 2021. After marketing and widespread usage, a progressive increase in SARS-CoV-2 lineages characterized by a higher transition/transversion ratio, a characteristic signature of molnupiravir action, appeared in the Global Initiative on Sharing All Influenza Data (GISAID) and International Nucleotide Sequence Database Collaboration (INSDC) databases. Here, we assessed the drug effects by SARS-CoV-2 whole-genome sequencing on 38 molnupiravir-treated persistently positive COVID-19 outpatients tested before and after treatment. Seventeen tixagevimab/cilgavimab-treated outpatients served as controls. Mutational analyses confirmed that SARS-CoV-2 exhibits an increased transition/transversion ratio seven days after initiation of molnupiravir. Moreover we observed an increased G->A ratio compared to controls, which was not related to apolipoprotein B mRNAediting enzyme, catalytic polypeptide-like (APOBEC) activity. In addition, we demonstrated for the first time an increased diversity and complexity of the viral quasispecies.


Subject(s)
Antiviral Agents , COVID-19 Drug Treatment , Cytidine/analogs & derivatives , Genome, Viral , Hydroxylamines , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , SARS-CoV-2/drug effects , Antiviral Agents/therapeutic use , Antiviral Agents/pharmacology , Hydroxylamines/pharmacology , Hydroxylamines/therapeutic use , Male , Female , Case-Control Studies , Middle Aged , Cytidine/therapeutic use , Cytidine/pharmacology , Aged , Adult , Whole Genome Sequencing , Genetic Variation , Uridine/pharmacology , COVID-19/virology , Mutation
8.
BMC Nephrol ; 25(1): 124, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38589827

ABSTRACT

BACKGROUND: Kidney transplant recipients (KTRs) are at risk of severe coronavirus disease 2019 (COVID-19), and even now that Omicron subvariants have become dominant, cases of severe disease are certain to occur. The aims of this retrospective study were to evaluate the efficacy of antiviral treatment for COVID-19 and to identify risk factors for severe disease in KTRs during Omicron subvariant-dominant periods. METHODS: A total of 65 KTRs diagnosed with COVID-19 who received antiviral treatment between July 2022 and September 2023 were analyzed. Mild cases received oral molnupiravir (MP) as outpatient therapy, while moderate or worse cases received intravenous remdesivir (RDV) as inpatient therapy. In principle, mycophenolate mofetil was withdrawn and switched to everolimus. We investigated the efficacy of antiviral treatment and compared the clinical parameters of mild/moderate and severe/critical cases to identify risk factors for severe COVID-19. RESULTS: Among 65 cases, 49 were mild, 6 were moderate, 9 were severe, and 1 was of critical severity. MP was administered to 57 cases; 49 (86%) improved and 8 (14%) progressed. RDV was administered to 16 cases; 14 (87%) improved and 2 (13%) progressed. Seventeen (26%) cases required hospitalization, and none died. Comparisons of the severe/critical group (n = 10) with the mild/moderate group (n = 55) demonstrated that the severe/critical group had a significantly higher median age (64 vs. 53 years, respectively; p = 0.0252), prevalence of diabetes (70% vs. 22%, respectively; p = 0.0047) and overweight/obesity (40% vs. 11%, respectively; p = 0.0393), as well as a significantly longer median time from symptom onset to initial antiviral therapy (3 days vs. 1 day, respectively; p = 0.0026). Multivariate analysis showed that a longer time from symptom onset to initial antiviral treatment was an independent risk factor for severe COVID-19 (p = 0.0196, odds ratio 1.625, 95% confidence interval 1.081-2.441). CONCLUSION: These findings suggest that a longer time from symptom onset to initial antiviral treatment is associated with a higher risk of severe COVID-19 in KTRs. Initiating antiviral treatment as early as possible is crucial for preventing severe outcomes; this represents a valuable insight into COVID-19 management in KTRs.


Subject(s)
COVID-19 , Cytidine/analogs & derivatives , Hydroxylamines , Kidney Transplantation , Humans , Retrospective Studies , Treatment Outcome , Risk Factors , Antiviral Agents/therapeutic use , Transplant Recipients
9.
Clin Transl Sci ; 17(2): e13732, 2024 02.
Article in English | MEDLINE | ID: mdl-38593352

ABSTRACT

Molnupiravir is an oral prodrug of the broadly active, antiviral ribonucleoside analog N-hydroxycytidine (NHC). The primary circulating metabolite NHC is taken up into cells and phosphorylated to NHC-triphosphate (NHC-TP). NHC-TP serves as a competitive substrate for viral RNA-dependent RNA polymerase (RdRp), which results in an accumulation of errors in the viral genome, rendering virus replication incompetent. Molnupiravir has demonstrated activity against SARS-CoV-2 both clinically and preclinically and has a high barrier to development of viral resistance. Little to no molnupiravir is observed in plasma due to rapid hydrolysis to NHC. Maximum concentrations of NHC are reached at 1.5 h following administration in a fasted state. The effective half-life of NHC is 3.3 h, reflecting minimal accumulation in the plasma following twice-daily (Q12H) dosing. The terminal half-life of NHC is 20.6 h. NHC-TP exhibits a flatter profile with a lower peak-to-trough ratio compared with NHC, which supports Q12H dosing. Renal and hepatic pathways are not major routes of elimination, as NHC is primarily cleared by metabolism to uridine and cytidine, which then mix with the endogenous nucleotide pools. In a phase III study of nonhospitalized patients with COVID-19 (MOVe-OUT), 5 days of treatment with 800 mg molnupiravir Q12H significantly reduced the incidence of hospitalization or death compared with placebo. Patients treated with molnupiravir also had a greater reduction in SARS-CoV-2 viral load and improved clinical outcomes, compared with those receiving placebo. The clinical effectiveness of molnupiravir has been further demonstrated in several real-world evidence studies. Molnupiravir is currently authorized or approved in more than 25 countries.


Subject(s)
Cytidine/analogs & derivatives , Ribonucleosides , Translational Science, Biomedical , Humans , Cytidine/pharmacology , Hydroxylamines , SARS-CoV-2
10.
Mol Cell ; 84(8): 1611-1625.e3, 2024 Apr 18.
Article in English | MEDLINE | ID: mdl-38640896

ABSTRACT

We recently reported the distribution of N4-acetylcytidine (ac4C) in HeLa mRNA at base resolution through chemical reduction and the induction of C:T mismatches in sequencing (RedaC:T-seq). Our results contradicted an earlier report from Schwartz and colleagues utilizing a similar method termed ac4C-seq. Here, we revisit both datasets and reaffirm our findings. Through RedaC:T-seq reanalysis, we establish a low basal error rate at unmodified nucleotides that is not skewed to any specific mismatch type and a prominent increase in C:T substitutions as the dominant mismatch type in both treated wild-type replicates, with a high degree of reproducibility across replicates. In contrast, through ac4C-seq reanalysis, we uncover significant data quality issues including insufficient depth, with one wild-type replicate yielding 2.7 million reads, inconsistencies in reduction efficiencies between replicates, and an overall increase in mismatches involving thymine that could obscure ac4C detection. These analyses bolster the detection of ac4C in HeLa mRNA through RedaC:T-seq.


Subject(s)
Cytidine/analogs & derivatives , Nucleotides , Humans , Reproducibility of Results , RNA, Messenger/genetics
11.
Proc Natl Acad Sci U S A ; 121(17): e2320713121, 2024 Apr 23.
Article in English | MEDLINE | ID: mdl-38621119

ABSTRACT

As the SARS-CoV-2 virus continues to spread and mutate, it remains important to focus not only on preventing spread through vaccination but also on treating infection with direct-acting antivirals (DAA). The approval of Paxlovid, a SARS-CoV-2 main protease (Mpro) DAA, has been significant for treatment of patients. A limitation of this DAA, however, is that the antiviral component, nirmatrelvir, is rapidly metabolized and requires inclusion of a CYP450 3A4 metabolic inhibitor, ritonavir, to boost levels of the active drug. Serious drug-drug interactions can occur with Paxlovid for patients who are also taking other medications metabolized by CYP4503A4, particularly transplant or otherwise immunocompromised patients who are most at risk for SARS-CoV-2 infection and the development of severe symptoms. Developing an alternative antiviral with improved pharmacological properties is critical for treatment of these patients. By using a computational and structure-guided approach, we were able to optimize a 100 to 250 µM screening hit to a potent nanomolar inhibitor and lead compound, Mpro61. In this study, we further evaluate Mpro61 as a lead compound, starting with examination of its mode of binding to SARS-CoV-2 Mpro. In vitro pharmacological profiling established a lack of off-target effects, particularly CYP450 3A4 inhibition, as well as potential for synergy with the currently approved alternate antiviral, molnupiravir. Development and subsequent testing of a capsule formulation for oral dosing of Mpro61 in B6-K18-hACE2 mice demonstrated favorable pharmacological properties, efficacy, and synergy with molnupiravir, and complete recovery from subsequent challenge by SARS-CoV-2, establishing Mpro61 as a promising potential preclinical candidate.


Subject(s)
Antiviral Agents , Cytidine/analogs & derivatives , Hepatitis C, Chronic , Hydroxylamines , Lactams , Leucine , Nitriles , Proline , Ritonavir , Humans , Animals , Mice , Antiviral Agents/pharmacology , Clinical Protocols , Drug Combinations
12.
Immun Inflamm Dis ; 12(4): e1262, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38652021

ABSTRACT

BACKGROUND AND AIM: This systematic review and meta-analysis aimed to compare the effectiveness and safety of molnupiravir and sotrovimab in the treatment of patients with coronavirus disease 2019 (COVID-19). METHODS: Cochrane Library, Web of Science, PubMed, medRxiv, and Google Scholar were systematically searched to identify relevant evidence up to December 2023. The risk of bias was assessed using the risk of bias in nonrandomized studies of interventions tool. Data were analyzed using Comprehensive Meta-Analysis (CMA). RESULTS: Our search identified and included 13 studies involving 16166 patients. The meta-analysis revealed a significant difference between the molnupiravir and sotrovimab groups in terms of the mortality rate (odds ratio [OR] = 2.07, 95% confidence interval [CI]: 1.16, 3.70). However, no significant difference was observed between the two groups in terms of hospitalization rate (OR = 0.71, 95% CI: 0.47, 1.06), death or hospitalization rate (OR = 1.51, 95% CI: 0.81, 2.83), and intensive care unit admission (OR = 0.59, 95% CI: 0.07, 4.84). In terms of safety, molnupiravir was associated with a higher incidence of adverse events (OR = 1.67, 95% CI: 1.21, 2.30). CONCLUSION: The current findings indicate that sotrovimab may be more effective than molnupiravir in reducing the mortality rate in COVID-19 patients. However, no statistical difference was observed between the two treatments for other effectiveness outcomes. The certainty of evidence for these findings was rated as low or moderate. Further research is required to provide a better comparison of these interventions in treating COVID-19 patients.


Subject(s)
Antibodies, Monoclonal, Humanized , Antibodies, Neutralizing , Antiviral Agents , COVID-19 Drug Treatment , Cytidine , Cytidine/analogs & derivatives , Hydroxylamines , SARS-CoV-2 , Humans , Hydroxylamines/therapeutic use , Cytidine/therapeutic use , Antiviral Agents/therapeutic use , Antiviral Agents/adverse effects , SARS-CoV-2/drug effects , Antibodies, Monoclonal, Humanized/therapeutic use , Antibodies, Monoclonal, Humanized/adverse effects , COVID-19/mortality , COVID-19/virology , Treatment Outcome , Hospitalization/statistics & numerical data
13.
Anal Chem ; 96(18): 6870-6874, 2024 May 07.
Article in English | MEDLINE | ID: mdl-38648202

ABSTRACT

Accurate detection of endogenous miRNA modifications, such as N6-methyladenosine (m6A), 7-methylguanosine (m7G), and 5-methylcytidine (m5C), poses significant challenges, resulting in considerable uncertainty regarding their presence in mature miRNAs. In this study, we demonstrate for the first time that liquid chromatography coupled with a tandem mass spectrometry (LC-MS/MS) nucleoside analysis method is a practical tool for quantitatively analyzing human miRNA modifications. The newly designed liquid-solid two-step hybridization (LSTH) strategy enhances specificity for miRNA purification, while LC-MS/MS offers robust capability in recognizing modifications and sufficient sensitivity with detection limits ranging from attomoles to low femtomoles. Therefore, it provides a more reliable approach compared to existing techniques for revealing modifications in endogenous miRNAs. With this approach, we characterized m6A, m7G, and m5C modifications in miR-21-5p, Let-7a/e-5p, and miR-10a-5p isolated from cultured cells and observed unexpectedly low abundance (<1% at each site) of these modifications.


Subject(s)
Adenosine/analogs & derivatives , Cytidine/analogs & derivatives , Guanosine/analogs & derivatives , MicroRNAs , Tandem Mass Spectrometry , MicroRNAs/analysis , Tandem Mass Spectrometry/methods , Humans , Chromatography, Liquid/methods , Adenosine/analysis , Nucleic Acid Hybridization , Guanosine/analysis , Liquid Chromatography-Mass Spectrometry
14.
Int J Infect Dis ; 143: 107021, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38561040

ABSTRACT

OBJECTIVES: Evaluate and compare the efficacy and safety of molnupiravir and favipiravir in outpatients with mild to moderate COVID-19 and at risk of severe COVID-19. METHODS: In an open-label, parallel-group, multicenter trial in Thailand, participants with moderate COVID-19 and at least one factor associated with severe COVID-19 were randomly assigned 1:1 to receive oral molnupiravir or oral favipiravir (standard of care). Phone calls for remote symptom assessment were made on Days 6, 15, and 29. Participants with worsening symptoms were instructed to return to the hospital. The primary endpoint was pulmonary involvement by Day 29, as evidenced by ≥2 of the following: dyspnea, oxygen saturation <92% or imaging. RESULTS: Nine hundred seventy-seven participants (487 molnupiravir, 490 favipiravir) were enrolled from 8 July 2022 to 19 January 2023. 98% had received ≥1 dose of COVID-19 vaccine and 83% ≥3 doses. By Day 29, pulmonary involvement occurred in 0% (0/483) in molnupiravir arm versus 1% (5/482) in favipiravir arm (-1.0%; Newcombe 95.2% CI: -2.4% to -0.0%; P = 0.021); all-cause death in 0% (0/483) and <1% (1/482); COVID-19 related hospitalization in <1% (1/483) and 1% (3/482); treatment-related adverse event in 1% (5/483) and 1% (4/486); and serious adverse event in 1% (4/483) and 1% (4/486). CONCLUSIONS: Favipiravir and molnupiravir had a similar efficacy and safety profile. Whether either of the two reduced the risk of complications during the omicron era in this population with a low risk of pulmonary involvement and a high vaccine coverage remains unclear. There were no differences in any of the safety endpoints. THAI CLINICAL TRIALS REGISTRY ID: TCTR20230111009.


Subject(s)
Amides , Antiviral Agents , COVID-19 Drug Treatment , Cytidine/analogs & derivatives , Pyrazines , SARS-CoV-2 , Humans , Amides/therapeutic use , Male , Pyrazines/therapeutic use , Pyrazines/adverse effects , Pyrazines/administration & dosage , Female , Thailand , Antiviral Agents/therapeutic use , Antiviral Agents/adverse effects , Antiviral Agents/administration & dosage , Middle Aged , Adult , Cytidine/therapeutic use , Cytidine/adverse effects , Cytidine/administration & dosage , Hydroxylamines/therapeutic use , Hydroxylamines/adverse effects , Hydroxylamines/administration & dosage , Aged , Treatment Outcome , COVID-19 , Outpatients
15.
Bioorg Chem ; 147: 107379, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38643567

ABSTRACT

Coronaviruses are a group of enveloped viruses with non-segmented, single-stranded, and positive-sense RNA genomes. It belongs to the 'Coronaviridae family', responsible for various diseases, including the common cold, SARS, and MERS. The COVID-19 pandemic, which began in March 2020, has affected 209 countries, infected over a million people, and claimed over 50,000 lives. Significant efforts have been made by repurposing several approved drugs including antiviral, to combat the COVID-19 pandemic. Molnupiravir is found to be the first orally acting efficacious drug to treat COVID-19 cases. It was approved for medical use in the UK in November 2021 and other countries, including USFDA, which granted approval an emergency use authorization (EUA) for treating adults with mild to moderate COVID-19 patients. Considering the importance of molnupiravir, the present review deals with its various synthetic strategies, pharmacokinetics, bio-efficacy, toxicity, and safety profiles. The comprehensive information along with critical analysis will be very handy for a wide range of audience including medicinal chemists in the arena of antiviral drug discovery especially anti-viral drugs against any variant of COVID-19.


Subject(s)
Antiviral Agents , COVID-19 Drug Treatment , COVID-19 , Cytidine , Hydroxylamines , SARS-CoV-2 , Humans , Antiviral Agents/pharmacology , Antiviral Agents/chemistry , Antiviral Agents/therapeutic use , Antiviral Agents/chemical synthesis , Hydroxylamines/therapeutic use , Hydroxylamines/chemistry , Hydroxylamines/pharmacology , COVID-19/virology , SARS-CoV-2/drug effects , Cytidine/analogs & derivatives , Cytidine/therapeutic use , Cytidine/pharmacology , Cytidine/chemistry , Cytidine/chemical synthesis , Uridine/pharmacology , Uridine/analogs & derivatives , Uridine/chemical synthesis , Uridine/chemistry , Uridine/therapeutic use , Pandemics , Betacoronavirus/drug effects , Coronavirus Infections/drug therapy , Pneumonia, Viral/drug therapy
16.
Virus Res ; 345: 199371, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38621598

ABSTRACT

BACKGROUND: The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has lasted for three years. Coinfection with seasonal influenza may occur resulting in more severe diseases. The interaction between these two viruses for infection and the effect of antiviral treatment remains unclear. METHODS: A SARS-CoV-2 and influenza H1N1 coinfection model on Calu-3 cell line was established, upon which the simultaneous and sequential coinfection was evaluated by comparing the viral load. The efficacy of molnupiravir and baloxavir against individual virus and coinfection were also studied. RESULTS: The replication of SARS-CoV-2 was significantly interfered when the influenza virus was infected simultaneously or in advance (p < 0.05). On the contrary, the replication of the influenza virus was not affected by the SARS-CoV-2. Molnupiravir monotherapy had significant inhibitory effect on SARS-CoV-2 when the concentration reached to 6.25 µM but did not show any significant anti-influenza activity. Baloxavir was effective against influenza within the dosage range and showed significant effect of anti-SARS-CoV-2 at 16 µM. In the treatment of coinfection, molnupiravir had significant effect for SARS-CoV-2 from 6.25 µM to 100 µM and inhibited H1N1 at 100 µM (p < 0.05). The tested dosage range of baloxavir can inhibit H1N1 significantly (p < 0.05), while at the highest concentration of baloxavir did not further inhibit SARS-CoV-2, and the replication of SARS-CoV-2 significantly increased in lower concentrations. Combination treatment can effectively inhibit influenza H1N1 and SARS-CoV-2 replication during coinfection. Compared with molnupiravir or baloxavir monotherapy, combination therapy was more effective in less dosage to inhibit the replication of both viruses. CONCLUSIONS: In coinfection, the replication of SARS-CoV-2 would be interfered by influenza H1N1. Compared with molnupiravir or baloxavir monotherapy, treatment with a combination of molnupiravir and baloxavir should be considered for early treatment in patients with SARS-CoV-2 and influenza coinfection.


Subject(s)
Antiviral Agents , COVID-19 , Coinfection , Dibenzothiepins , Influenza A Virus, H1N1 Subtype , Influenza, Human , SARS-CoV-2 , Viral Load , Virus Replication , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Humans , SARS-CoV-2/drug effects , Influenza, Human/drug therapy , Influenza, Human/virology , Coinfection/drug therapy , Coinfection/virology , Virus Replication/drug effects , Dibenzothiepins/therapeutic use , Influenza A Virus, H1N1 Subtype/drug effects , COVID-19/virology , Viral Load/drug effects , Pyridones/pharmacology , Pyridones/therapeutic use , Cell Line , Morpholines/pharmacology , Morpholines/therapeutic use , Triazines/pharmacology , Triazines/therapeutic use , COVID-19 Drug Treatment , Hydroxylamines/pharmacology , Hydroxylamines/therapeutic use , Thiazoles/pharmacology , Thiazoles/therapeutic use , Cytidine/analogs & derivatives
17.
Mikrochim Acta ; 191(5): 270, 2024 04 17.
Article in English | MEDLINE | ID: mdl-38630200

ABSTRACT

A comparative analysis of molecularly imprinted polymers based on different synthesis techniques was performed for the recognition of molnupiravir (MOL). The polymerizations were performed with 3-thienyl boronic acid (3-TBA) as a functional monomer by electropolymerization (EP) and with guanine methacrylate (GuaM) as a functional monomer by photopolymerization (PP). Morphological and electrochemical characterizations of the developed sensors were investigated to verify the constructed sensors. Moreover, quantum chemical calculations were used to evaluate changes on the electrode surface at the molecular and electronic levels. The dynamic linear range of both designed sensors under optimized experimental conditions was found to be 7.5 × 10-12-2.5 × 10-10 M and 7.5 × 10-13-2.5 × 10-11 M for EP and PP, respectively. The effect of various interfering agents on MOL peak current was assessed for the selectivity of the study. In the presence of 100 times more interfering agents, the RSD and recovery values were determined. The RSD values of GuaM/MOL@MIP/GCE and poly(Py-co-3-PBA)/MOL@MIP/GCE sensors were found to be 1.99% and 1.72%, respectively. Furthermore, the recovery values of the MIP-based sensors were 98.18-102.69% and 98.05-103.72%, respectively. In addition, the relative selectivity coefficient (k') of the proposed sensor was evaluated, and it exhibited good selectivity for MOL with respect to the NIP sensor. The prepared sensor was successfully applied to determine MOL in commercial serum samples and capsule form. In conclusion, the developed sensors provided excellent reproducibility, repeatability, high sensitivity, and selectivity against the MOL molecule.


Subject(s)
Boronic Acids , Cytidine/analogs & derivatives , Hydroxylamines , Molecularly Imprinted Polymers , Reproducibility of Results , Electrodes , Guanine , Methacrylates
18.
Antiviral Res ; 225: 105840, 2024 May.
Article in English | MEDLINE | ID: mdl-38438015

ABSTRACT

Host targeting antiviral drugs (HTA) are directed against cellular mechanisms which can be exploited by viruses. These mechanisms are essential for viral replication, because missing functions cannot be compensated by the virus. However, this assumption needs experimental proof. Here we compared the HTA Zapnometinib (ZMN), with direct acting antivirals (DAA) (Remdesivir (RDV), Molnupiravir (MPV), Nirmatrelvir (NTV), Ritonavir (RTV), Paxlovid PAX)), in terms of their potency to induce reduced drug susceptibilities in SARS-CoV-2. During serial passage of δ-B1.617.2 adaptation to all DAAs occurred, while the inhibitory capacity of ZMN was not altered. Known single nucleotide polymorphisms (SNPs) responsible for partial resistances were found for RDV, NTV and PAX. Additionally, the high mutagenic potential of MPV was confirmed and decreased drug efficacies were found for the first time. Reduced DAA efficacy did not alter the inhibitory potential of ZMN. These results show that ZMN confers a high barrier towards the development of viral resistance and has the potential to act against partially DAA-insensitive viruses.


Subject(s)
COVID-19 , Cytidine/analogs & derivatives , Hepatitis C, Chronic , Hydroxylamines , Humans , Antiviral Agents , SARS-CoV-2 , Ritonavir
19.
Antiviral Res ; 225: 105858, 2024 May.
Article in English | MEDLINE | ID: mdl-38490342

ABSTRACT

Chikungunya virus (CHIKV) is a mosquito-borne virus transmitted by Aedes mosquitoes. While there are no antiviral therapies currently available to treat CHIKV infections, several licensed oral drugs have shown significant anti-CHIKV activity in cells and in mouse models. However, the efficacy in mosquitoes has not yet been assessed. Such cross-species antiviral activity could be favorable, since virus inhibition in the mosquito vector might prevent further transmission to vertebrate hosts. Here, we explored the antiviral effect of ß-d-N4-hydroxycytidine (NHC, EIDD-1931), the active metabolite of molnupiravir, on CHIKV replication in Aedes aegypti mosquitoes. Antiviral assays in mosquito cells and in ex vivo cultured mosquito guts showed that NHC had significant antiviral activity against CHIKV. Exposure to a clinically relevant concentration of NHC did not affect Ae. aegypti lifespan when delivered via a bloodmeal, but it slightly reduced the number of eggs developed in the ovaries. When mosquitoes were exposed to a blood meal containing both CHIKV and NHC, the compound did not significantly reduce virus infection and dissemination in the mosquitoes. This was confirmed by modelling and could be explained by pharmacokinetic analysis, which revealed that by 6 h post-blood-feeding, 90% of NHC had been cleared from the mosquito bodies. Our data show that NHC inhibited CHIKV replication in mosquito cells and gut tissue, but not in vivo when mosquitoes were provided with a CHIKV-infectious bloodmeal spiked with NHC. The pipeline presented in this study offers a suitable approach to identify anti-arboviral drugs that may impede replication in mosquitoes.


Subject(s)
Aedes , Chikungunya Fever , Chikungunya virus , Cytidine/analogs & derivatives , Animals , Mice , Chikungunya virus/physiology , Virus Replication , Antiviral Agents
20.
BMJ Open ; 14(3): e083342, 2024 Mar 15.
Article in English | MEDLINE | ID: mdl-38490659

ABSTRACT

OBJECTIVES: Although guidelines recommend antiviral therapy for outpatients with COVID-19 who are at high risk of progressing to severe conditions, such as older adults, many patients do not receive appropriate treatment. Little is known, however, about the physician factors associated with the prescription of guideline-recommended antiviral therapy for patients with COVID-19. DESIGN: A cross-sectional study. SETTING: Data including outpatient visits in primary care clinics in Japan from April to August 2023. PARTICIPANTS: We analysed 30 953 outpatients aged ≥65 years treated with COVID-19 (mean (SD) age, 75.0 (7.6) years; 17 652 women (57.0%)) in 1394 primary care clinics. OUTCOME MEASURES: The primary outcome was the prescription of guideline-recommended antivirals (ie, nirmatrelvir-ritonavir or molnupiravir), adjusted for patient characteristics, months of visits and regions. RESULTS: Antiviral prescriptions were concentrated among a small proportion of physicians; for example, the top 10% of physicians that had the largest number of nirmatrelvir-ritonavir prescriptions accounted for 92.4% of all nirmatrelvir-ritonavir prescriptions. After adjusting for potential confounders, physicians with higher patient volumes were more likely to prescribe guideline-recommended antivirals to their patients (adjusted OR (aOR) for high vs low volume, 1.76; 95% CI 1.31 to 2.38; adjusted p<0.001). We found no evidence that the likelihood of guideline-recommended antiviral prescription differed based on physicians' gender (aOR for women vs men, 1.24; 95% CI 0.88 to 1.74; adjusted p=0.48) or age (aOR for 45-59 vs <45 years, 1.16; 95% CI 0.87 to 1.54; adjusted p=0.48; aOR for ≥60 vs <45 years, 0.88; 95% CI 0.66 to 1.16; adjusted p=0.48). These patterns were similar when examining nirmatrelvir-ritonavir and molnupiravir separately. CONCLUSIONS: Our findings suggest that provider-level factors, such as the clinical experience of treating the patients with COVID-19, play an important role in the appropriate prescription of antiviral medications for COVID-19 in the primary care setting.


Subject(s)
COVID-19 , Cytidine/analogs & derivatives , Hydroxylamines , Lactams , Leucine , Nitriles , Proline , Male , Humans , Female , Aged , Japan/epidemiology , Cross-Sectional Studies , Ritonavir/therapeutic use , Antiviral Agents/therapeutic use
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