Aptamer-based assembly systems for SARS-CoV-2 detection and therapeutics

Chemical Society Reviews, Год журнала: 2024, Номер 53(13), С. 6830 - 6859

Опубликована: Янв. 1, 2024

This review presents the recent progress on aptamers that have been explored for SARS-CoV-2 detection and therapeutics, wherein construction principles characteristics of aptamer-based assembly systems are systematically summarized.

Язык: Английский

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Molecular characterization of SARS-CoV-2 nucleocapsid protein

Frontiers in Cellular and Infection Microbiology, Год журнала: 2024, Номер 14

Опубликована: Май 23, 2024

Corona Virus Disease 2019 (COVID-19) is a highly prevalent and potent infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Until now, the world still endeavoring to develop new ways diagnose treat COVID-19. At present, clinical prevention treatment of COVID-19 mainly targets spike protein on surface SRAS-CoV-2. However, with continuous emergence SARS-CoV-2 Variants concern (VOC), targeting therapy shows high degree limitation. The Nucleocapsid Protein (N protein) conserved in virus evolution involved key process viral infection assembly. It most expressed structural after humans has immunogenicity. Therefore, N as factor replication basic research application great potential value. This article reviews progress structure biological function protein, diagnosis drug order promote researchers’ further understanding lay theoretical foundation for possible outbreak sudden diseases future.

Язык: Английский

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AnnCovDB: a manually curated annotation database for mutations in SARS-CoV-2 spike protein

Database, Год журнала: 2025, Номер 2025

Опубликована: Янв. 1, 2025

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been circulating and adapting within the human population for >4 years. A large number of mutations have occurred in viral genome, resulting significant variants known as concern (VOCs) interest (VOIs). The spike (S) protein harbors many characteristic VOCs VOIs, efforts made to explore functional effects S protein, which can cause or contribute infection, transmission, immune evasion, pathogenicity, illness severity. However, knowledge understanding are dispersed throughout various publications, there is a lack well-structured database annotation that based on manual curation. AnnCovDB provides manually curated annotations SARS-CoV-2. Mutations carried by at least 8000 GISAID were chosen, then utilized query keywords search PubMed database. searched publications revealed 2093 entities 205 single 93 multiple curated. These organized into multilevel hierarchical categories user convenience. For example, one entity N501Y mutation was ‘Infectious cycle➔Attachment➔ACE2 binding affinity➔Increase’. be used specific browse through function entities. Database URL: https://AnnCovDB.app.bio-it.tech/

Язык: Английский

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Elucidating the molecular docking and binding dynamics of aptamers with spike proteins across SARS-CoV-2 variants of concern

Frontiers in Microbiology, Год журнала: 2025, Номер 16

Опубликована: Фев. 14, 2025

DNA aptamers with high binding affinity against SARS-CoV-2 spike proteins have been selected and analyzed. To better understand the affinities between (S-proteins) of relevant variants concerns (VOCs), in silico vitro characterization are excellent approaches to implement. Here, we identified generated aptamer sequences targeting S-protein VOCs through systematic evolution ligands by exponential enrichment (SELEX). In , prediction was conducted, followed a step-by-step workflow for secondary tertiary structures determination, modeling, molecular docking target S-protein. The strategy limited only providing predictions possible outcomes based on scores, ranking complemented analysis using direct enzyme-linked oligonucleotides assay (ELONA), which showed dissociation constants ( K d ) within 32 nM–193 nM range across three significant VOCs. These highly specific (Alpha Apt, Delta Omicron Apt) can be further studied as potential candidates both diagnostic therapeutic applications.

Язык: Английский

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JN.1 variants circulating in Italy from October 2023 to April 2024: genetic diversity and immune recognition

BMC Infectious Diseases, Год журнала: 2025, Номер 25(1)

Опубликована: Фев. 28, 2025

The continuous emergence of SARS-CoV-2 variants and subvariants poses significant public health challenges. latest designated subvariant JN.1, with all its descendants, shows more than 30 mutations in the spike gene. JN.1 has raised concerns due to genomic diversity potential enhance transmissibility immune evasion. This study aims analyse molecular characteristics JN.1-related lineages (JN.1*) identified Italy from October 2023 April 2024 evaluate neutralization activity against a subsample sera individuals vaccinated XBB.1.5 mRNA. gene 794 JN.1* strain was evaluated phylogenetic analysis conducted compare distance XBB.1.5. Moreover, serum assays were performed on 19 healthcare workers (HCWs) monovalent mRNA booster assess neutralizing capacity JN.1. Sequence displayed high variability between investigation confirmed substantial differentiation regions 29 shared mutations, which 17 located within RBD region. Pre-booster observed 42% HCWs sera, increasing significantly post-booster, showing three months after vaccination. A correlation found anti-trimeric Spike IgG levels titers highlights Italy. Results vaccine suggested enhanced

Язык: Английский

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Correlation between D614G-mutated SARS-CoV-2 and CD4+/CD8+ T cells expression in Egyptian COVID-19 patients

The Journal of Basic and Applied Zoology, Год журнала: 2025, Номер 86(1)

Опубликована: Март 8, 2025

Abstract Background Rapid pulmonary replication of SARS-CoV-2 can potentially trigger a strong immune response. In people with coronavirus disease 2019 (COVID-19) symptoms, cytokine storm syndrome often leads to acute respiratory distress and failure, which are key causes mortality. Viral infections activate both the innate adaptive systems, cellular response particularly role T lymphocytes being crucial for actual antiviral defense beside COVID-19. Among variants SARS-CoV-2, D614G mutation in spike protein has become furthermost widespread strain globally during pandemic. This is linked increased infectivity transmissibility been identified as most frequent reported Egypt. Results The rate CD8+ cells was significantly ( P < 0.001) ICU-admitted patients compared healthy mild while frequency CD4+ decreased ICU relative other groups. CD4+/CD8+ ratio demonstrated 100% sensitivity specificity predicting severity. cell responses subsequent infection D614G-mutated strain, showing an increase from day 6 17 post-infection. Additionally, specific HLA-A alleles, including HLA-A24:02 HLA-A02:01, were associated evaluation peptides. Conclusion may serve valuable prognostic marker severity COVID-19 patients. Monitoring levels could help identify symptoms who at threat requiring admission. Furthermore, Egyptian

Язык: Английский

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Short-Read and Long-Read Whole Genome Sequencing for SARS-CoV-2 Variants Identification

Viruses, Год журнала: 2025, Номер 17(4), С. 584 - 584

Опубликована: Апрель 18, 2025

Genomic surveillance of SARS-CoV-2 is crucial for detecting emerging variants and informing public health responses. Various sequencing technologies are used whole genome SARS-CoV-2. This cross-platform benchmark study applied established bioinformatics tools to assess improve the performance Illumina NovaSeq, Oxford Nanopore Technologies MinION, Pacific Biosciences Sequel II platforms in identifying lineage assignment. NovaSeq produced highest number reads bases, depth coverage, completeness consensus genomes, stable mapping coverage across open reading frames genome, consistent assignments. The long-read had lower yields, depth, limiting qualified sequences assignment variant identification. However, implementing proper quality controls on sequence data overcame these limitations achieved assignments all three platforms. advancements library preparation technology likely enhance expand effectively addressing current analysis. By merging unique advantages both short- methods, we can significantly genomic provide insights into strategies other RNA viruses, pending further validation. may lead precise tracking viral evolution support policy decisions.

Язык: Английский

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Host Cell Proteases Involved in Human Respiratory Viral Infections and Their Inhibitors: A Review

Viruses, Год журнала: 2024, Номер 16(6), С. 984 - 984

Опубликована: Июнь 19, 2024

Viral tropism is most commonly linked to receptor use, but host cell protease use can be a notable factor in susceptibility infection. Here we review the of proteases by human viruses, focusing on those with primarily respiratory tropism, particularly SARS-CoV-2. We first describe various classes present tract, as well elsewhere body, and incorporate targeting these therapeutic drugs for humans. Host are also systemic spread viruses play important roles outside tract; therefore, address how affect across spectrum infections that occur humans, intending understand extrapulmonary

Язык: Английский

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Mutation Trajectory of Omicron SARS-CoV-2 Virus, Measured by Principal Component Analysis

COVID, Год журнала: 2024, Номер 4(4), С. 571 - 581

Опубликована: Апрель 22, 2024

Since 2019, the SARS-CoV-2 virus has caused a global pandemic, resulting in widespread infections and ongoing mutations. Analyzing these mutations is essential for predicting future impacts. Unlike influenza mutations, displayed distinct selective patterns that were concentrated spike protein small ORFs. In contrast to gradual accumulation seen lead abrupt emergence of new variants subsequent outbreaks. This phenomenon may be attributed their targeted cellular substances; unlike virus, which mutated evade acquired immunity, appeared mutate target individuals who have not been previously infected. The Omicron variant, emerged late 2021, demonstrates significant set it apart from previous variants. rapid mutation rate now reached level comparable 30 years variation. most recent JN.1, exhibits discernible trajectory change

Язык: Английский

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Arylamines QSAR-Based Design and Molecular Dynamics of New Phenylthiophene and Benzimidazole Derivatives with Affinity for the C111, Y268, and H73 Sites of SARS-CoV-2 PLpro Enzyme

Pharmaceuticals, Год журнала: 2024, Номер 17(5), С. 606 - 606

Опубликована: Май 9, 2024

A non-structural SARS-CoV-2 protein, PLpro, is involved in post-translational modifications cells, allowing the evasion of antiviral immune response mechanisms. In this study, potential PLpro inhibitory drugs were designed using QSAR, molecular docking, and dynamics. combined QSAR equation with physicochemical Free-Wilson descriptors was formulated. The r2, q2, r2test values 0.833, 0.770, 0.721, respectively. From equation, it found that presence an aromatic ring a basic nitrogen atom crucial for obtaining good activity. Then, series structures binding sites C111, Y268, H73 created. best compounds to exhibit pIC50 9.124 docking scoring -14 kcal/mol. stability cavities confirmed by dynamics studies. high number stable contacts interactions over time exhibited aryl-thiophenes Pred14 Pred15, making them candidates.

Язык: Английский

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