Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS1 (28)

ProteinS (17)

NSP5 (2)

NSP3 (2)

ComplexRdRp (2)


SARS-CoV-2 Proteins
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    Immunolocalization studies of vimentin HGNC and ACE2 HGNC on the surface of cells exposed to SARS-CoV-2 Spike MESHD SARS-CoV-2 Spike PROTEIN proteins

    Authors: Vasiliki Lalioti; Silvia González-Sanz; Irene Lois-Bermejo; Patricia González-Jiménez; Álvaro Viedma-Poyatos; Andrea Merino; María A Pajares; Dolores Pérez-Sala

    doi:10.1101/2021.05.04.442648 Date: 2021-05-04 Source: bioRxiv

    The Spike protein PROTEIN from SARS-CoV-2 mediates docking of the virus onto cells and contributes to viral invasion. Several cellular receptors are involved in SARS-CoV-2 Spike PROTEIN SARS-CoV-2 Spike MESHD docking at the cell surface, including ACE2 HGNC and neuropilin. The intermediate filament protein vimentin HGNC has been reported to be present at the surface of certain cells and act as a co-receptor for several viruses; furthermore, its potential involvement in interactions with Spike proteins PROTEIN has been proposed. Here we have explored the binding of Spike protein PROTEIN constructs to several cell types using low-temperature immunofluorescence approaches in live cells, to minimize internalization. Incubation of cells with tagged Spike S MESHD or Spike S1 subunit PROTEIN led to discrete dotted patterns at the cell surface, which showed scarce colocalization with a lipid raft marker, but consistent coincidence with ACE2 HGNC. Under our conditions, vimentin HGNC immunoreactivity appeared as spots or patches unevenly distributed at the surface of diverse cell types. Remarkably, several observations including potential antibody internalization and adherence to cells of vimentin HGNC-positive structures present in the extracellular medium exposed the complexity of vimentin HGNC cell surface immunoreactivity, which requires careful assessment. Notably, overall colocalization of Spike and vimentin HGNC signals markedly varied with the cell type and the immunodetection sequence. In turn, vimentin HGNC-positive spots moderately colocalized with ACE2 HGNC; however, a particular enrichment was detected at elongated structures positive for acetylated tubulin, consistent with primary cilia, which also showed Spike binding. Thus, these results suggest that vimentin HGNC- ACE2 HGNC interaction could occur at selective locations near the cell surface, including ciliated structures, which can act as platforms for SARS-CoV-2 docking.

    Convergent antibody responses to the SARS-CoV-2 spike PROTEIN protein in convalescent and vaccinated individuals

    Authors: Elaine C. Chen; Pavlo Gilchuk; Seth J. Zost; Naveenchandra Suryadevara; Emma S. Winkler; Carly R. Cabel; Elad Binshtein; Rachel E. Sutton; Jessica L. Rodriguez; Samuel Day; Luke Myers; Andrew Trivette; Jazmean K. Williams; Edgar Davidson; Shuaizhi Li; Benjamin J. Doranz; Samuel K. Campos; Robert H. Carnahan; Curtis A. Thorne; Michael S. Diamond; James E. Crowe Jr.

    doi:10.1101/2021.05.02.442326 Date: 2021-05-03 Source: bioRxiv

    Unrelated individuals can produce genetically similar clones of antibodies, known as public clonotypes, which have been seen in responses to different infectious diseases MESHD as well as healthy individuals. Here we identify 37 public clonotypes in memory B cells from convalescent survivors of SARS-CoV-2 infection MESHD or in plasmablasts from an individual after vaccination with mRNA-encoded spike protein PROTEIN. We identified 29 public clonotypes, including clones recognizing the receptor-binding domain (RBD) in the spike protein S1 PROTEIN subunit (including a neutralizing, ACE2 HGNC-blocking clone that protects in vivo), and others recognizing non-RBD epitopes that bound the heptad repeat 1 region of the S2 domain. Germline-revertant forms of some public clonotypes bound efficiently to spike protein PROTEIN, suggesting these common germline-encoded antibodies are preconfigured for avid recognition. Identification of large numbers of public clonotypes provides insight into the molecular basis of efficacy of SARS-CoV-2 vaccines and sheds light on the immune pressures driving the selection of common viral escape mutants.

    Perturbation of ACE2 HGNC structural ensembles by SARS-CoV-2 spike PROTEIN protein binding

    Authors: Arzu Uyar; Alex Dickson

    doi:10.1101/2021.03.02.433608 Date: 2021-03-02 Source: bioRxiv

    The human ACE2 HGNC enzyme serves as a critical first recognition point of coronaviruses, including SARS-CoV-2. In particular, the extracellular domain of ACE2 HGNC interacts directly with the S1 tailspike protein of the SARS-CoV-2 virion through a broad protein-protein interface. Although this interaction has been characterized by X-ray crystallography and Cryo-EM, these structures do not reveal significant differences in ACE2 HGNC structure upon S1 protein PROTEIN binding. In this work, using several all-atom molecular dynamics simulations, we show persistent differences in ACE2 HGNC structure upon binding. These differences are determined with the Linear Discriminant Analysis (LDA) machine learning method and validated using independent training and testing datasets, including long trajectories generated by D. E. Shaw Research on the Anton 2 supercomputer. In addition, long trajectories for 78 potent ACE2 HGNC-binding compounds, also generated by D. E. Shaw Research, were projected onto the LDA classification vector in order to determine whether the ligand-bound ACE2 HGNC structures were compatible with S1 protein PROTEIN binding. This allows us to predict which compounds are "apo-like" vs "complex-like", as well as to pinpoint long-range ligand-induced allosteric changes of ACE2 HGNC structure.

    In vitro screening of herbal medicinal products for their supportive curing potential in the context of SARS-CoV-2

    Authors: Hoai Tran; Philipp Peterburs; Jan Seibel; Dimitri Abramov-Sommariva; Evelyn Lamy

    doi:10.1101/2021.03.01.433344 Date: 2021-03-01 Source: bioRxiv

    Background: Herbal medicinal products have a long-standing history of use in the therapy of common respiratory infections MESHD. In the COVID-19 pandemic MESHD, they may have the potential for symptom relief in non-severe or moderate disease cases. Here we describe the results derived by in vitro screening of five herbal medicinal products with regard to their potential to i) interfere with the binding of the human Angiotensin-converting enzyme 2 HGNC ( ACE2 HGNC) receptor with the SARS-CoV-2 Spike MESHD SARS-CoV-2 Spike PROTEIN S1 protein PROTEIN, ii) modulate the release of the human defensin HBD1 and cathelicidin LL-37 HGNC from human A549 lung cells upon Spike S1 protein PROTEIN stimulation and iii) modulate the release of IFN-{gamma HGNC} from activated human peripheral blood mononuclear cells (PBMC). The investigated extracts were: Sinupret extract (SINx), Bronchipret thyme-ivy (BRO TE), Bronchipret thyme-primrose (BRO TP), Imupret (IMU), and Tonsipret (TOP). Methods: The inhibitory effect of the herbal medicinal products on the binding interaction of Spike S1 protein PROTEIN and the human ACE2 receptor was measured by ELISA. The effects on intracellular IFN-{gamma HGNC} expression in stimulated human PBMCs were measured by flow cytometry. Regulation on HBD1 HGNC and LL-37 HGNC expression and secretion was assessed in 25d long-term cultured human lung A549 epithelial cells by RT-PCR and ELISA. Results: IMU and BRO TE concentration-dependently inhibited the interaction between spike protein PROTEIN and the ACE2 HGNC Receptor. However, this effect was only observed in the cell-free assay at a concentration range which was later on determined as cytotoxic to human PBMC. SINx, TOP and BRO TP significantly upregulated the intracellular expression of antiviral IFN{gamma HGNC} from stimulated PBMC. Co-treatment of A549 cells with IMU or BRO TP together with SARS-CoV-2 spike MESHD SARS-CoV-2 spike PROTEIN protein significantly upregulated mRNA expression (IMU) and release (IMU and BRO TP) of HBD1 HGNC and LL-37 HGNC (BRO TP). Conclusions: The in vitro screening results provide first evidence for an immune activating potential of some of the tested herbal medicinal extracts in the context of SARS-CoV-2. Whether these could be helpful in prevention of SARS-CoV-2 invasion MESHD or supportive in recovery from SARS-CoV-2 infection MESHD needs deeper understanding of the observations.

    Targeting CoV-2 Spike RBD and ACE-2 HGNC Interaction with Flavonoids of Anatolian Propolis by in silico and in vitro Studies in terms of possible COVID-19 MESHD therapeutics

    Authors: Halil Ibrahim Guler; Fulya Ay Sal; Zehra Can; Yakup Kara; Oktay Yildiz; Ali Osman Belduz; Sabriye Canakci; Sevgi Kolayli

    doi:10.1101/2021.02.22.432207 Date: 2021-02-22 Source: bioRxiv

    Propolis is a multi-functional bee product with a rich in polyphenols. In this study, the inhibition effect of Anatolian propolis against SARS coronavirus-2 (SARS CoV-2) was investigated as in vitro and in silico. Raw and commercial of propolis samples were used in the study and it was found that both of were rich in caffeic acid, p-coumaric acid, ferulic acid, t-cinnamic acid, hesperetin, chrysin, pinocembrin and caffeic acid phenethyl ester ( CAPE HGNC) by HPLC-UV analysis. The ethanolic propolis extracts (EPE) were used in the screening ELISA test against the spike S1 protein PROTEIN (SARS Cov-2): ACE-2 HGNC inhibition KIT HGNC for in vitro study. Binding energy constants of these polyphenols to the CoV-2 Spike S1 RBD and ACE-2 HGNC proteinwere calculated separately as molecular docking study using AutoDock 4.2 molecular docking software. In addition, pharmacokinetics and drug-likeness properties of these eight polyphenols were calculated according to the SwissADME tool. Binding energy constant of pinocembrin was found the highest for both receptors, followed by chrysin, CAPE HGNC and hesperetin. In silico ADME behavior of the eight polyphenol was found potential ability to work effectively as novel drugs. The findings of both studies showed that propolis has a high inhibitory potential against Covid-19 MESHD virus.However, further studies are needed.

    A novel antibody against the furin HGNC cleavage site of SARS-CoV-2 spike PROTEIN protein: effects on proteolytic cleavage and ACE2 HGNC binding

    Authors: Michael G Spelios; Jeanne M Capanelli; Adam W Li

    doi:10.1101/2021.02.09.430451 Date: 2021-02-09 Source: bioRxiv

    SARS-CoV-2 harbors a unique S1/S2 furin HGNC cleavage site within its spike protein PROTEIN, which can be cleaved by furin HGNC and other proprotein convertases. Proteolytic activation of SARS-CoV-2 spike PROTEIN protein at the S1 PROTEIN/S2 boundary facilitates interaction with host ACE2 HGNC receptor for cell entry. To address this, high titer antibody was generated against the SARS-CoV-2-specific furin HGNC motif. Using a series of innovative ELISA-based assays, this furin HGNC site blocking antibody displayed high sensitivity and specificity for the S1/S2 furin HGNC cleavage site, and demonstrated effective blockage of both enzyme-mediated cleavage and spike- ACE2 HGNC interaction. The results suggest that immunological blocking of the furin HGNC cleavage site may afford a suitable approach to stem proteolytic activation of SARS-CoV-2 spike PROTEIN protein and curtail viral infectivity.

    New-Onset IgG Autoantibodies in Hospitalized Patients with COVID-19 MESHD

    Authors: Sarah Esther Chang; Allan Feng; Wenzhao Meng; Sokratis Apostolidis; Elisabeth Mack; Maja Artandi; Linda Barman; Kate Bennett; Saborni Chakraborty; Iris Chang; Peggie Cheung; Sharon Chinthrajah; Shaurya Dhingra; Evan Do; Amanda Finck; Andrew Gaano; Reinhard Gessner; Heather M. Giannini; Joyce Gonzalez; Sarah Greib; Margrit Guendisch; Alex Ren Hsu; Alex Kuo; Monali Manohar; Rong Mao; Indira Neeli; Andreas Neubauer; Oluwatosin Oniyide; Abigail Elizabeth Powell; Rajan Puri; Harald Renz; Jeffrey M. Schapiro; Payton Anders Weidenbacher; Rich Wittman; Neera Ahuja; Ho-Ryun Chung; Prasanna Jagannathan; Judith James; Peter S. Kim; Nuala J. Meyer; Kari Christine Nadeau; Marko Radic; William H. Robinson; Upinder Singh; Taia T. Wang; E. John Wherry; Chrysanthi Skevaki; Eline T. Luning Prak; Paul J Utz

    doi:10.1101/2021.01.27.21250559 Date: 2021-01-29 Source: medRxiv

    Coronavirus Disease 2019 MESHD ( COVID-19 MESHD), caused by Severe Acute Respiratory Syndrome Coronavirus-2 MESHD (SARS-CoV-2), is associated with a wide range of clinical manifestations, including autoimmune features and autoantibody production. We developed three different protein arrays to measure hallmark IgG autoantibodies associated with Connective Tissue Diseases (CTDs), Anti-Cytokine Antibodies (ACA), and anti-viral antibody responses in 147 hospitalized COVID-19 MESHD patients in three different centers. Autoantibodies were identified in approximately 50% of patients, but in <15% of healthy controls. When present, autoantibodies largely targeted autoantigens associated with rare disorders such as myositis MESHD, systemic sclerosis MESHD and CTD overlap syndromes. Anti-nuclear antibodies (ANA) were observed in ~25% of patients. Patients with autoantibodies tended to demonstrate one or a few specificities whereas ACA were even more prevalent, and patients often had antibodies to multiple cytokines. Rare patients were identified with IgG antibodies against angiotensin converting enzyme-2 ( ACE-2 HGNC). A subset of autoantibodies and ACA developed de novo following SARS-CoV-2 infection MESHD while others were transient. Autoantibodies tracked with longitudinal development of IgG antibodies that recognized SARS-CoV-2 structural proteins such as S1 PROTEIN, S2, M, N and a subset of non-structural proteins, but not proteins from influenza, seasonal coronaviruses or other pathogenic viruses. COVID-19 MESHD patients with one or more autoantibodies tended to have higher levels of antibodies against SARS-CoV-2 Nonstructural Protein 1 ( NSP1 HGNC) and Methyltransferase (ME). We conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 MESHD patients and are positively correlated with immune responses to SARS-CoV-2 proteins MESHD.

    Hypoxia reduces cell attachment of SARS-CoV-2 spike PROTEIN protein by modulating the expression of ACE2 HGNC and heparan sulfate

    Authors: Endika Prieto-Fernandez; Leire Egia-Mendikute; Laura Vila-Vecilla; So Young Lee; Alexandre Bosch; Adrian Barreira-Manrique; Ana Garcia del Rio; Asier Antonana-Vildosola; Borja Jimenez-Lasheras; Asis Palazon; Emma Woodoff-Leith; Dushyant P Purohit; Gabriel E Hoffman; Schahram Akbarian; Mary Fowkes; John Crary; Guo-Cheng Yuan; Panos Roussos; Garth Huberty; Fyodor D. Urnov; Petros Giannikopoulos; Jennifer A. Doudna; Tiannan Guo

    doi:10.1101/2021.01.09.426021 Date: 2021-01-11 Source: bioRxiv

    A main clinical parameter of Covid-19 MESHD pathophysiology is hypoxia MESHD. Here we show that hypoxia decreases MESHD the attachment of the receptor binding domain (RBD) and the S1 subunit (S1) of the spike PROTEIN protein to epithelial cells. In Vero E6 cells, hypoxia MESHD reduces the protein levels of ACE2, which might in part explain the observed reduction of the infection MESHD rate. However, hypoxia MESHD also inhibits the binding of the spike to human lung epithelial cells lacking ACE2 HGNC expression, indicating that hypoxia MESHD modulates the expression of additional binding partners of SARS-CoV-2. We show that hypoxia MESHD also decreases the total cell surface levels of heparan sulfate, a known attachment receptor of SARS-CoV-2, by reducing the expression of syndecan-1 HGNC and syndecan3 HGNC, the main proteoglycans containing heparan sulfate. Our study indicates that hypoxia MESHD acts to prevent SARS-CoV-2 infection MESHD, suggesting that the hypoxia MESHD signaling pathway might offer therapeutic opportunities for the treatment of Covid-19 MESHD.

    ACE2 HGNC peptide fragment interacts with several sites on the SARS-CoV-2 spike PROTEIN protein S1 PROTEIN

    Authors: Aleksei Kuznetsov; Piret Arukuusk; Heleri Härk; Erkki Juronen; Ülo Langel; Mart Ustav; Jaak Järv; Haixi Sun; Wei Zhang; Ziqian Xu; Beiwei Ye; Xiaoju Yuan; Pengyan Wang; Ning Zhang; Yuhuan Gong; Chengrong Bian; Zhaohai Wang; Linxiang Yu; Jin Yan; Fanping Meng; Changqing Bai; Xiaoshan Wang; Xiaopan Liu; Kai Gao; Liang Wu; Longqi F. Liu; Ying Gu; Yuhai J. Bi; Yi Shi; Shaogeng Zhang; Chen Zhu; Xun Xu; Guizhen Wu; George Gao; Naibo Yang; William Liu; Penghui Yang

    doi:10.1101/2020.12.29.424682 Date: 2020-12-29 Source: bioRxiv

    The influence of the peptide QAKTFLDKFNHEAEDLFYQ on the kinetics of the SARS-CoV-2 spike PROTEIN protein S1 PROTEIN binding to angiotensin-converting enzyme 2( ACE2 HGNC) was studied to model the interaction of the virus with its host cell. This peptide corresponds to the sequence 24-42 of the ACE2 HGNC 1 domain, which is the binding site for the S1 protein PROTEIN. The on-rate and off-rate of S1- ACE2 HGNC complex formation were measured in the presence of various peptide concentrations using Bio-Layer Interferometry (BLI). The formation of the S1- ACE2 HGNC complex was inhibited when the S1 protein PROTEIN was preincubated with the peptide, however, no significant inhibitory effect was observed in the absence of preincubation. Dissociation kinetics revealed that the peptide remained bound to the S1- ACE2 HGNC complex and stabilized this complex. Computational mapping of the S1 protein PROTEIN surface for peptide binding revealed two additional sites, located at some distance from the receptor binding domain (RBD) of S1. These additional binding sites affect the interaction between the peptide, the S1 protein PROTEIN, and ACE2 HGNC.

    A Recombinant Protein SARS-CoV-2 Candidate Vaccine Elicits High-titer Neutralizing Antibodies in Macaques.

    Authors: Gary Baisa; David Rancour; Keith Mansfield; Monika Burns; Lori Martin; Daise Cunha; Jessica Fischer; Frauke Muecksch; Theodora Hatziioannou; Paul D. Bieniasz; Fritz Schomburg; Kimberly Luke

    doi:10.21203/ Date: 2020-12-29 Source: ResearchSquare

    BackgroundVaccines that generate robust and long-lived protective immunity against SARS-CoV-2 infection MESHD are urgently required. MethodsWe assessed the potential of vaccine candidates based on the SARS-CoV-2 spike PROTEIN in cynomolgus macaques (M. fascicularis) by examining their ability to generate spike binding antibodies with neutralizing activity. Antigens were derived from two distinct regions of the spike S1 subunit PROTEIN, either the N-terminal domain or an extended C-terminal domain containing the receptor-binding domain and were fused to the human IgG1 Fc domain. Three groups of 2 animals each were immunized with either antigen, alone or in combination. The development of antibody responses was evaluated through 20 weeks post-immunization. ResultsA robust IgG response to the spike protein PROTEIN was detected as early as 2 weeks after immunization with either protein and maintained for over 20 weeks. Sera from animals immunized with antigens derived from the RBD were able to prevent binding of soluble spike proteins PROTEIN to the ACE2 HGNC receptor, shown by in vitro binding assays, while sera from animals immunized with the N-terminal domain alone lacked this activity. Crucially, sera from animals immunized with the extended receptor binding domain but not the N-terminal domain had potent neutralizing activity against SARS-CoV-2 pseudotyped virus, with titers in excess of 10,000, greatly exceeding that typically found in convalescent humans. Neutralizing activity persisted for more than 20 weeks. ConclusionsThese data support the utility of spike subunit-based antigens as a vaccine for use in humans.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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