Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (1768)

ProteinN (161)

NSP5 (61)

ProteinS1 (51)

ComplexRdRp (48)


SARS-CoV-2 Proteins
    displaying 1 - 10 records in total 1768
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    Evaluation of Peppermint Leaf Flavonoids as SARS-CoV-2 Spike PROTEIN Receptor-Binding Domain Attachment Inhibitors to the Human ACE2 HGNC Receptor: A Molecular Docking Study

    Authors: Marcelo Lopes Pereira Júnior; Luiz Antônio Ribeiro Júnior

    id:2102.12651v1 Date: 2021-02-25 Source: arXiv

    One of the strategies in combating COVID-19 MESHD consists of virtual screening for possible inhibitors for the attachment of SARS-CoV-2 Spike PROTEIN receptor-binding domain (RBD) to the human ACE2 HGNC receptor. Here, we performed a molecular docking study to propose potential candidates to prevent the RBD/ ACE2 HGNC attachment. These candidates are sixteen different flavonoids present in the peppermint leaf. Results showed that Luteolin 7-O-neohesperidoside is the peppermint flavonoid with a higher binding affinity regarding the RBD/ ACE2 HGNC complex (about -9.18 Kcal/mol). On the other hand, Sakuranetin was the one with the lowest affinity (about -6.38 Kcal/mol). Binding affinities of the other peppermint flavonoids ranged from -6.44 Kcal/mol up to -9.05 Kcal/mol. The biding site surface analysis showed pocket-like regions on the RBD/ ACE2 HGNC complex that yield several interactions (mostly hydrogen bonds) between the flavonoid and the amino acid residues of the proteins. This study can open channels for the understanding of the roles of flavonoids against COVID-19 MESHD infection.

    A Novel SARS-CoV-2 Variant of Concern, B.1.526, Identified in New York

    Authors: Medini K Annavajhala; Hiroshi Mohri; Jason E Zucker; Zizhang Sheng; Pengfei Wang; Angela Gomez-Simmonds; David D Ho; Anne-Catrin Uhlemann

    doi:10.1101/2021.02.23.21252259 Date: 2021-02-25 Source: medRxiv

    Recent months have seen surges of SARS-CoV-2 infection MESHD across the globe along with considerable viral evolution. Extensive mutations in the spike protein PROTEIN of variants B.1.1.7, B1.351, and P.1 HGNC have raised concerns that the efficacy of current vaccines and therapeutic monoclonal antibodies could be threatened. In vitro studies have shown that one mutation, E484K, plays a crucial role in the loss of neutralizing activity of some monoclonal antibodies as well as most convalescent and vaccinee sera against variant B.1.351. In fact, two vaccine trials have recently reported lower protective efficacy in South Africa, where B.1.351 is dominant. To survey for these novel variants in our patient population in New York City, PCR assays were designed to identify viruses with two signature mutations, E484K and N501Y. We observed a steady increase in the detection rate from late December to mid-February MESHD, with an alarming rise to 12.3% in the past two weeks. Whole genome sequencing further demonstrated that most of our E484K isolates (n=49/65) fell within a single lineage: NextStrain clade 20C or Pangolin lineage B.1.526. Patients with this novel variant came from diverse neighborhoods in the metropolitan area, and they were on average older and more frequently hospitalized. Phylogenetic analyses of sequences in the database further reveal that this B.1.526 variant is scattered in the Northeast of US, and its unique set of spike mutations may also pose an antigenic challenge for current interventions.

    Visualization of SARS-CoV-2 Infection MESHD Scenes by 'Zero-Shot' Enhancements of Electron Microscopy Images

    Authors: Jakob Drefs; Sebastian Salwig; Jörg Lücke

    doi:10.1101/2021.02.25.432265 Date: 2021-02-25 Source: bioRxiv

    Electron microscopy (EM) recordings of infected tissues serve to diagnose a disease, and they can contribute to our understanding of infection processes. Consequently, a large number of EM images of the interaction of SARS-CoV-2 viruses with cells have been made available by numerous labs. However, due to EM recording techniques at high resolution, images of infection scenes are very noisy and they appear two dimensional ('flat'). Current research consequently aims (A) at methods that can remove noise, and (B) at techniques that allow for recovering a 3D impression of the virus or its parts. Here we discuss a novel method which can recover a spatial impression of a whole infection scene at high resolution. In contrast to previous approaches which aim at the reconstruction of single spike proteins PROTEIN or a single virus, the here used method can be applied to a single noisy EM image of an infection scene. As one example image, we show a high resolution image of SARS-CoV-2 viruses in Vero cell cultures (Fig. 1). The method we use is based on probabilistic machine learning algorithms which can operate in a 'zero-shot' setting, i.e., in a setting when just one noisy image (and no large and clean image corpus) is available. The probabilistic method we apply can estimate non-noisy images by inferring first order statistics (pixel means) across image patches using a previously learned probabilistic image representation. Estimating higher order statistics and appropriately chosen probabilistic models then allow for the generation of images that enhance details and give a spatial impression of a full nanoscopic scene.

    Antiviral Resistance against Viral Mutation: Praxis and Policy for SARS CoV-2

    Authors: Robert Clark Penner

    doi:10.1101/2021.02.25.432861 Date: 2021-02-25 Source: bioRxiv

    New tools developed by Moderna, BioNTech/Pfizer and Oxford/Astrazeneca provide universal solutions to previously problematic aspects of drug or vaccine delivery, uptake and toxicity MESHD, portending new tools across the medical sciences. A novel method is presented based on estimating protein backbone free energy via geometry to predict effective antiviral targets, antigens and vaccine cargoes that are resistant to viral mutation. This method, partly described in earlier work of the author, is reviewed and reformulated here in light of the profusion of recent structural data on the SARS CoV-2 spike PROTEIN glycoprotein and its latest mutations. Scientific and regulatory challenges to nucleic acid therapeutic and vaccine development and deployment are also discussed.

    Pyroptosis of syncytia formed by fusion of SARS-CoV-2 Spike PROTEIN SARS-CoV-2 Spike MESHD and ACE2 HGNC expressing cells

    Authors: Huabin Ma; Zhoujie Zhu; Huaipeng Lin; Shanshan Wang; Peipei Zhang; Yanguo Li; Long Li; Jinling Wang; Yufen Zhao; Jiahuai Han

    doi:10.1101/2021.02.25.432853 Date: 2021-02-25 Source: bioRxiv

    SARS-Cov-2 infected cells fused with the ACE2 HGNC-positive neighboring cells forming syncytia. However, the effect of syncytia in disease development is largely unknown. We established an in vitro cell-cell fusion system and used it to mimic the fusion of SARS-CoV-2 infected MESHD cells with ACE2 HGNC-expressing cells to form syncytia. We found that Caspase-9 HGNC was activated after syncytia formation, and Caspase-3/7 was activated downstream of Caspase-9 HGNC, but it triggered GSDME-dependent pyroptosis rather than apoptosis. What is more, single cell RNA-sequencing data showed that both ACE2 HGNC and GSDME were expression in alveolar type MESHD 2 cells in human lung. We propose that pyroptosis is the fate of syncytia formed by SARS-CoV-2 infected host MESHD cells and ACE2 HGNC-positive cells, which indicated that lytic death of syncytia MESHD may contribute to the excessive inflammatory responses in severe COVID-19 MESHD patients.

    Quantifying Antibodies Directed against the SARS-CoV-2 Spike PROTEIN Protein S1 PROTEIN Subunit

    Authors: Anna Schaffner; Lorenz Risch; Stefanie Aeschbacher; Corina Risch; Myriam C. Weber; Sarah L. Thiel; Katharina Jüngert; Michael Pichler; Kirsten Grossmann; Nadia Wohlwend; Thomas Lung; Dorothea Hillmann; Susanna Bigler; Thomas Bodmer; Mauro Imperiali; Harald Renz; Philipp Kohler; Pietro Vernazza; Christian R. Kahlert; Raphael Twerenbold; Matthias Paprotny; David Conen; Martin Risch

    doi:10.21203/ Date: 2021-02-25 Source: ResearchSquare

    With the COVID-19 pandemic MESHD causing a global health crisis, accurate diagnosis is critical. Diagnosing acute disease MESHD relies on RT-PCR tests measuring the presence of SARS-CoV-2 in the sampled material but in patients with suspected COVID-19 MESHD with a negative RT-PCR result, measuring anti-viral antibodies can help clinicians identify infected individuals. Antibody testing can also determine if someone was previously infected and help to measure the prevalence of the virus in a community. A new study characterizes an assay measuring total antibodies – combined IgA, IgM, and IgG isotypes – against SARS-CoV-2. The assay, ECLIA, specifically measures antibodies against the S1 subunit of the viral spike, which carries the virus’s receptor binding domain. Researchers in Liechtenstein evaluated ECLIA in a population with 125 cases of confirmed SARS-CoV-2 infection MESHD and 1159 individuals without evidence of COVID-19 MESHD. The results showed a test sensitivity of 97.6%, while the specificity was 99.8%. Antibody levels were highest in hospitalized patients and lower in symptomatic patients outside the hospital and those with asymptomatic infection. Following COVID-19 MESHD, smokers developed lower antibody titers than non-smokers, whereas patients without fever MESHD had lower antibody titers than patients with fever MESHD. Following COVID-19 MESHD, smokers developed lower antibody titers than non-smokers, whereas patients without fever MESHD had lower antibody titers than patients with fever MESHD suggesting that the assay may be able to test the association between clinical characteristics and antibody levels and help identify individuals with potential cross-reactivity to SARS-CoV-2.

    Increased transmission of SARS-CoV-2 lineage B.1.1.7 (VOC 2020212/01) is not accounted for by a replicative advantage in primary airway cells or antibody escape

    Authors: Jonathan C Brown; Daniel H. Goldhill; Jie Zhou; Thomas P Peacock; Rebecca Frise; Niluka Goonawardane; Laury Baillon; Ruthiran Kugathasan; Andreia Pinto; Paul F McKay; Jack Hassard; Maya Moshe; Aran Singanayagam; Thomas Burgoyne; - PHE Virology Consortium; Wendy S Barclay

    doi:10.1101/2021.02.24.432576 Date: 2021-02-24 Source: bioRxiv

    Lineage B.1.1.7 (Variant of Concern 202012/01) is a new SARS-CoV-2 variant which was first sequenced in the UK in September 2020 before becoming the majority strain in the UK and spreading worldwide. The rapid spread of the B.1.1.7 variant results from increased transmissibility but the virological characteristics which underpin this advantage over other circulating strains remain unknown. Here, we demonstrate that there is no difference in viral replication between B.1.1.7 and other contemporaneous SARS-CoV-2 strains in primary human airway epithelial (HAE) cells. However, B.1.1.7 replication is disadvantaged in Vero cells potentially due to increased furin-mediated cleavage of its spike protein PROTEIN as a result of a P681H mutation directly adjacent to the S1/S2 cleavage site. In addition, we show that B.1.1.7 does not escape neutralisation by convalescent or post-vaccination sera. Thus, increased transmission of B.1.1.7 is not caused by increased replication, as measured on HAE cells, or escape from serological immunity.

    SARS-COV-2 Spike Glycoprotein PROTEIN as Inhibitory Target for Insilico Screening of Natural Compounds

    Authors: Damilola Alex Omoboyowa; Balogun Toheeb A; Onyeka S. Chukwudozie; Victor N. Nweze; Oluwatosin A. Saibu; Alausa Abdulahi

    doi:10.21203/ Date: 2021-02-23 Source: ResearchSquare

    Coronavirius disease MESHD 2019 ( Covid-19 MESHD) pandemic caused by SARS-Cov-2 has raised global health concern without approved drug for management of this lie threatening disease. The aim of this study was to predict the inhibitory potential of quercetin-3-o-rutinoside against SARS-Cov-2 spike glycoprotein PROTEIN. Targeting the SARS-Cov-2 spike protein PROTEIN from angiotensin converting enzyme 2 complex (pdb: 6lzg) is gaining importance. In this study, in silico computational relationship between plant-derived natural drug and spike glycoprotein PROTEIN was predicted. The results were evaluated based on glide (Schrodinger) dock score. Among the five (5) screened compounds, quercetin-3-o-rutinoside has the best docking score (-9.296) with the target. Molecular dynamic ( MD MESHD) simulation study was performed for 1000ps to confirm the stability behavior of the spike protein PROTEIN and quercetin-3-o-rutinoside complex. The MD simulation study validated the stability of quercetin-3-o-rutinoside in the spike protein PROTEIN binding pocket as potent inhibitor.

    Evolving Infection Paradox of SARS-CoV-2: Fitness Costs Virulence?

    Authors: A. S. M. Rubayet Ul Alam; Ovinu Kibria Islam; Md. Shazid Hasan; Mir Raihanul Islam; Shafi Mahmud; Hassan M. AlEmran; Iqbal K Jahid; Keith A. Crandall; M. Anwar Hossain

    doi:10.1101/2021.02.21.21252137 Date: 2021-02-23 Source: medRxiv

    Background: SARS-CoV-2 is continuously spreading worldwide at an unprecedented scale and evolved into seven clades according to GISAID where four (G, GH, GR and GV) are globally prevalent in 2020. These major predominant clades of SARS-CoV-2 are continuously increasing COVID-19 MESHD cases worldwide; however, after an early rise in 2020, the death-case ratio has been decreasing to a plateau. G clade viruses contain four co-occurring mutations in their genome (C241T+C3037T+C14408T: RdRp PROTEIN.P323L+A23403G:spike.D614G). GR, GH, and GV strains are defined by the presence of these four mutations in addition to the clade-featured mutation in GGG28881-28883AAC:N. RG203-204KR, G25563T: ORF3a PROTEIN.Q57H, and C22227T:spike.A222V+C28932T-N.A220V+G29645T, respectively. The research works are broadly focused on the spike protein PROTEIN mutations that have direct roles in receptor binding, antigenicity, thus viral transmission and replication fitness. However, mutations in other proteins might also have effects on viral pathogenicity and transmissibility. How the clade-featured mutations are linked with viral evolution in this pandemic through gearing their fitness MESHD and virulence is the main question of this study. Methodology: We thus proposed a hypothetical model, combining a statistical and structural bioinformatics approach, endeavors to explain this infection paradox by describing the epistatic effects of the clade-featured co-occurring mutations on viral fitness MESHD and virulence. Results and Discussion: The G and GR/GV clade strains represent a significant positive and negative association, respectively, with the death-case ratio (incidence rate ratio or IRR = 1.03, p <0.001 and IRR= 0.99/0.97, p < 0.001), whereas GH clade strains showed no association with the Docking analysis showed the higher infectiousness of a spike mutant through more favorable binding of G614 with the elastase-2 HGNC. RdRp PROTEIN mutation p.P323L significantly increased genome-wide mutations (p<0.0001) since more expandable RdRp PROTEIN (mutant)- NSP8 PROTEIN interaction may accelerate replication. Superior RNA stability and structural variation at NSP3 HGNC NSP3 PROTEIN:C241T might impact upon protein or RNA interactions. Another silent 5'UTR:C241T mutation might affect translational efficiency and viral packaging. These G-featured co-occurring mutations might increase the viral load, alter immune responses in host and hence can modulate intra-host genomic plasticity. An additional viroporin ORF3a PROTEIN:p.Q57H mutation, forming GH-clade, prevents ion permeability by cysteine (C81)-histidine (H57) inter-transmembrane-domain interaction mediated tighter constriction of the channel pore and possibly reduces viral release and immune response. GR strains, four G clade mutations and N:p.RG203-204KR, would have stabilized RNA interaction by more flexible and hypo-phosphorylated SR-rich region. GV strains seemingly gained the evolutionary advantage of superspreading event through confounder factors; nevertheless, N:p.A220V might affect RNA binding. Conclusion: These hypotheses need further retrospective and prospective studies to understand detailed molecular and evolutionary events featuring the fitness MESHD and virulence of SARS-CoV-2.

    Structural and functional characterization of SARS-CoV-2 RBD domains produced in mammalian cells

    Authors: Christoph Gstoettner; Tao Zhang; Anja Resemann; Sophia Ruben; Stuart Pengelley; Detlev Suckau; Tim Welsink; Manfred Wuhrer; Elena Dominguez-Vega

    doi:10.1101/2021.02.23.432424 Date: 2021-02-23 Source: bioRxiv

    As the SARS-CoV-2 pandemic is still ongoing and dramatically influences our life, the need for recombinant proteins for diagnostics, vaccine development, and research is very high. The spike (S) protein PROTEIN, and particularly its receptor binding domain (RBD), mediates the interaction with the ACE2 HGNC receptor on host cells and may be modulated by its structural features. Therefore, well characterized recombinant RBDs are essential. We have performed an in-depth structural and functional characterization of RBDs expressed in Chinese hamster ovary ( CHO MESHD) and human embryonic kidney MESHD (HEK293) cells. To structurally characterize the native RBDs (comprising N- and O-glycans and additional posttranslational modifications) a multilevel mass spectrometric approach was employed. Released glycan and glycopeptide analysis were integrated with intact mass analysis, glycan-enzymatic dissection and top-down sequencing for comprehensive annotation of RBD proteoforms. The data showed distinct glycosylation for CHO MESHD- and HEK293-RBD with the latter exhibiting antenna fucosylation, higher level of sialylation and a combination of core 1 and core 2 type O-glycans. Additionally, from both putative O-glycosylation sites, we could confirm that O-glycosylation was exclusively present at T323, which was previously unknown. For both RBDs, the binding to SARS-CoV-2 antibodies of positive patients and affinity to ACE2 receptor was addressed showing comparable results. This work not only offers insights into RBD structural and functional features but also provides a workflow for characterization of new RBDs and batch-to-batch comparison.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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