Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (2072)

ProteinN (185)

NSP5 (63)

ProteinS1 (55)

ComplexRdRp (52)


SARS-CoV-2 Proteins
    displaying 2041 - 2050 records in total 2072
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    Increasing Host Cellular Receptor--Angiotensin-Converting Enzyme 2 ( ACE2 HGNC) Expression by Coronavirus may Facilitate 2019-nCoV Infection MESHD

    Authors: Pei-Hui Wang

    doi:10.1101/2020.02.24.963348 Date: 2020-02-27 Source: bioRxiv

    The ongoing outbreak of a new coronavirus (2019-nCoV) causes an epidemic of acute respiratory syndrome MESHD in humans. 2019-nCoV rapidly spread to national regions and multiple other countries, thus, pose a serious threat to public health. Recent studies show that spike (S) proteins PROTEIN of 2019-nCoV and SARS-CoV MESHD may use the same host cell receptor called angiotensin-converting enzyme 2 ( ACE2 HGNC) for entering into host cells. The affinity between ACE2 HGNC and 2019-nCoV S is much higher than ACE2 HGNC binding to SARS-CoV S protein MESHD S protein PROTEIN, explaining that why 2019-nCoV seems to be more readily transmitted from the human to human. Here, we reported that ACE2 HGNC can be significantly upregulated after infection of various viruses including SARS-CoV MESHD and MERS-CoV. Basing on findings here, we propose that coronavirus infection MESHD can positively induce its cellular entry receptor to accelerate their replication and spread, thus drugs targeting ACE2 HGNC expression may be prepared for the future emerging infectious diseases MESHD caused by this cluster of viruses.

    Epitope-based peptide vaccines predicted against novel coronavirus disease caused by SARS-CoV-2

    Authors: Lin Li; Ting Sun; YuFei He; Wendong Li; Yubo Fan; Jing Zhang

    doi:10.1101/2020.02.25.965434 Date: 2020-02-27 Source: bioRxiv

    The outbreak of the 2019 novel coronavirus (SARS-CoV-2) has infected thousands of people with a large number of deaths across 26 countries. The sudden appearance of the virus leads to the limited existing therapies for SARS-CoV-2. Therefore, vaccines and antiviral medicines are in desperate need. This study took immune-informatics approaches to identify B- and T-cell epitopes for surface glycoprotein (S PROTEIN) of SARS-CoV-2, followed by estimating their antigenicity and interactions with the human leukocyte antigen (HLA) alleles. We identified four B cell epitopes, two MHC class-I and nine MHC class-II binding T-cell epitopes, which showed highly antigenic features. Allergenicity, toxicity MESHD and physiochemical properties analysis confirmed the specificity and selectivity of epitopes. The stability and safety of epitopes were confirmed by digestion analysis. No mutations were observed in all the selected B- and T-cell epitopes across all isolates from different locations worldwide. Epitopes were thus identified and some of them can be potential candidates for vaccine development.

    COVID-19 MESHD Spike-host cell receptor GRP78 HGNC binding site prediction

    Authors: Ibrahim Ibrahim; Doaa Abdelmalek; Mohamed Elshahat; Abdo Elfiky

    doi:10.21203/rs.2.24599/v1 Date: 2020-02-24 Source: ResearchSquare

    Coronaviruses have been circulating between animals and humans repeatedly. A novel human coronavirus, named COVID-19 MESHD, has recently emerged in Hubei Province, China. Within the first two months, more than 2200 deaths have been confirmed, and there have been more than 79,000 hospitalized patients, mainly in China. Understanding the virus mode of host cell recognition may help to fight the disease and save lives. The spike protein PROTEIN of coronaviruses is the main driving force for host cell recognition. In this study, the COVID-19 MESHD corona viral spike binding site to the cell-surface receptor (Glucose Regulated Protein 78 (GRP78)) is predicted using combined molecular modeling docking and structural bioinformatics. The cyclic peptide Pep42 (CTVALPGGYVRVC) was reported earlier to be the docking platform of GRP78 in cancer MESHD cells. The COVID-19 MESHD spike protein PROTEIN is modeled using its counterpart, the SARS spike. Sequence and structural alignments show that four regions, in addition to its cyclic nature (the S-S bond), have sequence and physicochemical similarities to the cyclic Pep42. Protein-protein docking was performed to test the four regions of the spike that fit tightly in the GRP78 Substrate Binding Domain β (SBDβ). The docking pose revealed the involvement of the SBDβ of GRP78 and the receptor-binding domain of the coronavirus spike protein PROTEIN in recognition of the host cell receptor. We reveal that the binding is more favorable between regions III (C391-C525) and IV (C480-C488) of the spike protein PROTEIN model and GRP78. Region IV is the main driving force for GRP78 binding with the predicted binding affinity of -9.8 kcal/mol. These nine residues (region IV) of the spike can be used to develop therapeutics specific against COVID-19 MESHD.

    Cryo-EM structures of HKU2 and SADS-CoV spike glycoproteins PROTEIN and insights into coronavirus evolution

    Authors: Jinfang Yu; Shuyuan Qiao; Runyu Guo; Xinquan Wang

    doi:10.1101/2020.02.23.961912 Date: 2020-02-24 Source: bioRxiv

    A new porcine coronavirus SADS-CoV MESHD was recently identified from suckling piglets with severe diarrhea MESHD in southern China and its genome sequence is most identical (~95% identity) to that of bat -coronavirus HKU2. It again indicates bats are the natural reservoir of many coronaviruses that have great potential for cross-species transmission to animals and humans by recombination and/or mutation. Here we report the cryo-EM structures of HKU2 and SADS-CoV spike MESHD spike glycoprotein PROTEIN trimers at 2.38 [A] and 2.83 [A] resolution, respectively. HKU2 and SADS-CoV spikes MESHD exhibit very high structural similarity, with subtle differences mainly distributed in the NTD and CTD of the S1 subunit responsible for cell attachment and receptor binding. We systematically analyzed and compared the NTD, CTD, SD1 and SD2 domains of the S1 subunit and the S2 subunit of HKU2 spike with those of -, {beta}-, {gamma}-, and {delta}-coronavirus spikes. The results show that the NTD MESHD and CTD of HKU2/SADS-CoV are probably the most ancestral in the evolution of spike. Although the S2 subunit mediating membrane fusion is highly conserved, the connecting region after fusion peptide in HKU2/SADS-CoV S2 subunit also adopts a conformation distinct from other coronaviruses. These results structurally demonstrate a close evolutionary relationship between HKU2 /SADS-CoV and {beta}-coronavirus spikes and provide new insights into the evolution and cross-species transmission of coronaviruses.

    Potential T-cell and B-cell Epitopes of 2019-nCoV

    Authors: Ethan Fast; Russ B Altman; Binbin Chen

    doi:10.1101/2020.02.19.955484 Date: 2020-02-21 Source: bioRxiv

    As of early March, 2019-nCoV has infected more than one hundred thousand people and claimed thousands of lives. 2019-nCoV is a novel form of coronavirus that causes COVID-19 MESHD and has high similarity with SARS-CoV MESHD. No approved vaccine yet exists for any form of coronavirus. Here we use computational tools from structural biology and machine learning to identify 2019-nCoV T-cell and B-cell epitopes based on viral protein antigen presentation and antibody binding properties. These epitopes can be used to develop more effective vaccines and identify neutralizing antibodies. We identified 405 viral peptides with good antigen presentation scores for both human MHC-I and MHC-II alleles, and two potential neutralizing B-cell epitopes near the 2019-nCoV spike protein PROTEIN receptor binding domain (440-460 and 494-506). Analyzing mutation profiles of 68 viral genomes from four continents, we identified 96 coding-change mutations. These mutations are more likely to occur in regions with good MHC-I presentation scores (p=0.02). No mutations are present near the spike protein PROTEIN receptor binding domain. Based on these findings, the spike protein PROTEIN is likely immunogenic and a potential vaccine candidate. We validated our computational pipeline with SARS-CoV MESHD experimental data. Significance StatementThe novel coronavirus 2019-nCoV has affected more than 100 countries and continues to spread. There is an immediate need for effective vaccines that contain antigens which trigger responses from human T-cells and B-cells (known as epitopes). Here we identify potential T-cell epitopes through an analysis of human antigen presentation, as well as B-cell epitopes through an analysis of protein structure. We identify a list of top candidates, including an epitope located on 2019-nCoV spike protein PROTEIN that potentially triggers both T-cell and B-cell responses. Analyzing 68 samples, we observe that viral mutations are more likely to happen in regions with strong antigen presentation, a potential form of immune evasion. Our computational pipeline is validated with experimental data from SARS-CoV.

    A Multiscale and Comparative Model for Receptor Binding of 2019 Novel Coronavirus and the Implication of its Life Cycle in Host Cells

    Authors: Zhaoqian Su; Yinghao Wu

    doi:10.1101/2020.02.20.958272 Date: 2020-02-21 Source: bioRxiv

    The respiratory syndrome MESHD caused by a new type of coronavirus has been emerging from China and caused more than 1000 death globally since December 2019. This new virus, called 2019 novel coronavirus (2019-nCoV) uses the same receptor called Angiotensinconverting enzyme 2 ( ACE2 HGNC) to attack humans as the coronavirus that caused the severe acute respiratory syndrome MESHD (SARS) seventeen years ago. Both viruses recognize ACE2 HGNC through the spike proteins (S PROTEIN S-protein HGNC) on their surfaces. It was found that the S-protein PROTEIN S-protein HGNC from the SARS coronavirus ( SARS-CoV MESHD) bind stronger to ACE2 HGNC than 2019-nCoV. However, function of a bio-system is often under kinetic, rather than thermodynamic, control. To address this issue, we constructed a structural model for complex formed between ACE2 HGNC and the S-protein PROTEIN S-protein HGNC from 2019-nCoV, so that the rate of their association can be estimated and compared with the binding of S-protein HGNC S-protein PROTEIN from SARS-CoV MESHD by a multiscale simulation method. Our simulation results suggest that the association of new virus to the receptor is slower than SARS, which is consistent with the experimental data obtained very recently. We further integrated this difference of association rate between virus and receptor into a mathematical model which describes the life cycle of virus in host cells and its interplay with the innate immune system. Interestingly, we found that the slower association between virus and receptor can result in longer incubation period, while still maintaining a relatively higher level of viral concentration in human body. Our computational study therefore provides, from the molecular level, one possible explanation that the new disease by far spread much faster than SARS.

    Molecular mechanism of evolution and human infection with the novel coronavirus (2019-nCoV)

    Authors: Jiahua He; Huanyu Tao; Yumeng Yan; Sheng-You Huang; Yi Xiao

    doi:10.1101/2020.02.17.952903 Date: 2020-02-21 Source: bioRxiv

    Since December, 2019, an outbreak of pneumonia MESHD caused by the new coronavirus (2019-nCoV) has hit the city of Wuhan in the Hubei Province. With the continuous development of the epidemic, it has become a national public health crisis and calls for urgent antiviral treatments or vaccines. The spike protein PROTEIN on the coronavirus envelope is critical for host cell infection MESHD and virus vitality. Previous studies showed that 2019-nCoV is highly homologous to human SARS-CoV MESHD and attaches host cells though the binding of the spike receptor binding domain (RBD) domain to the angiotensin-converting enzyme II ( ACE2 HGNC). However, the molecular mechanisms of 2019-nCoV binding to human ACE2 HGNC and evolution of 2019-nCoV remain unclear. In this study, we have extensively studied the RBD- ACE2 HGNC complex, spike protein PROTEIN, and free RBD systems of 2019-nCoV and SARS-CoV MESHD using protein-protein docking and molecular dynamics (MD) simulations. It was shown that the RBD- ACE2 HGNC binding free energy for 2019-nCoV is significantly lower than that for SARS-CoV MESHD, which is consistent with the fact that 2019-nCoV is much more infectious than SARS-CoV MESHD. In addition, the spike protein PROTEIN of 2019-nCoV shows a significantly lower free energy than that of SARS-CoV MESHD, suggesting that 2019-nCoV is more stable and able to survive a higher temperature than SARS-CoV MESHD. This may also provide insights into the evolution of 2019-nCoV because SARS-like coronaviruses are thought to have originated in bats that are known to have a higher body-temperature than humans. It was also revealed that the RBD of 2019-nCoV is much more flexible especially near the binding site and thus will have a higher entropy penalty upon binding ACE2 HGNC, compared to the RBD of SARS-CoV MESHD. That means that 2019-nCoV will be much more temperature-sensitive in terms of human infection than SARS-CoV MESHD. With the rising temperature, 2019-nCoV is expected to decrease its infection ability much faster than SARS-CoV MESHD, and get controlled more easily. The present findings are expected to be helpful for the disease prevention and control as well as drug and vaccine development of 2019-nCoV.

    Functional pangenome analysis provides insights into the origin, function and pathways to therapy of SARS-CoV-2 coronavirus

    Authors: Intikhab Alam; Allan K Kamau; Maxat Kulmanov; Stefan T Arold; Arnab T Pain; Takashi Gojobori; Carlos M. Duarte

    doi:10.1101/2020.02.17.952895 Date: 2020-02-21 Source: bioRxiv

    The spread of the novel coronavirus (SARS-CoV-2) has triggered a global emergency, that demands urgent solutions for detection and therapy to prevent escalating health, social and economic impacts. The spike protein (S PROTEIN) of this virus enables binding to the human receptor ACE2 HGNC, and hence presents a prime target for vaccines preventing viral entry into host cells1. The S proteins PROTEIN from SARS-CoV-1 and SARS-CoV-2 MESHD are similar2, but structural differences in the receptor binding domain (RBD) preclude the use of SARS-CoV-1-specific neutralizing antibodies to inhibit SARS-CoV-23. Here we used comparative pangenomic analysis of all sequenced Betacoronaviruses to reveal that, among all core gene clusters present in these viruses, the envelope protein E PROTEIN shows a variant shared by SARS and SARS-Cov2 with two completely-conserved key functional features, an ion-channel and a PDZ-binding Motif (PBM). These features trigger a cytokine storm that activates the inflammasome, leading to increased edema MESHD in lungs causing the acute respiratory distress syndrome MESHD ( ARDS MESHD)4-6, the leading cause of death MESHD in SARS-CoV-1 and SARS-CoV-2 infection7 MESHD SARS-CoV-2 infection MESHD7,8. However, three drugs approved for human use may inhibit SARS-CoV-1 and SARS-CoV-2 Protein E PROTEIN, either acting upon the ion channel (Amantadine and Hexamethylene amiloride9,10) or the PBM (SB2035805), thereby potentially increasing the survival of the host, as already demonstrated for SARS-CoV-1in animal models. Hence, blocking the SARS protein E PROTEIN inhibits development of ARDS in vivo. Given that our results demonstrate that the protein E PROTEIN subcluster for the SARS clade is quasi-identical for the key functional regions of SARS-CoV-1 and SARS-CoV-2, we conclude that use of approved drugs shown to act as SARS E protein PROTEIN inhibitors can help prevent further casualties from COVID-2019 while vaccines and other preventive measures are being developed.

    Vulnerabilities in coronavirus glycan shields despite extensive glycosylation

    Authors: Yasunori Watanabe; Zachary T. Berndsen; Jayna Raghwani; Gemma E. Seabright; Joel D. Allen; Jason S McLellan; Ian A. Wilson; Thomas A. Bowden; Andrew B. Ward; Max Crispin

    doi:10.1101/2020.02.20.957472 Date: 2020-02-21 Source: bioRxiv

    Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome MESHD ( MERS MESHD) coronaviruses (CoVs) are zoonotic pathogens with high fatality rates and pandemic potential. Vaccine development has focussed on the principal target of the neutralizing humoral immune response, the spike ( S) glycoprotein PROTEIN, which mediates receptor recognition and membrane fusion. Coronavirus S proteins PROTEIN are extensively glycosylated viral fusion proteins, encoding around 69-87 N-linked glycosylation sites per trimeric spike. Using a multifaceted structural approach, we reveal a specific area of high glycan density on MERS MESHD S that results in the formation of under-processed oligomannose-type glycan clusters, which was absent on SARS and HKU1 CoVs. We provide a comparison of the global glycan density of coronavirus spikes with other viral proteins including HIV-1 envelope, Lassa virus glycoprotein complex, and influenza hemagglutinin, where glycosylation plays a known role in shielding immunogenic epitopes. Consistent with the ability of the antibody-mediated immune response to effectively target and neutralize coronaviruses, we demonstrate that the glycans of coronavirus spikes are not able to form an efficacious high-density global shield to thwart the humoral immune response. Overall, our data reveal how differential organisation of viral glycosylation across class I viral fusion proteins influence not only individual glycan compositions but also the immunological pressure across the viral protein surface.

    Structure, function and antigenicity of the SARS-CoV-2 spike PROTEIN glycoprotein

    Authors: Alexandra C Walls; Young-Jun Park; M. Alexandra Tortorici; Abigail Wall; Andrew T McGuire; David Veesler

    doi:10.1101/2020.02.19.956581 Date: 2020-02-20 Source: bioRxiv

    The recent emergence of a novel coronavirus associated with an ongoing outbreak of pneumonia MESHD (Covid-2019) resulted in infections of more than 72,000 people and claimed over 1,800 lives. Coronavirus spike ( S) glycoprotein PROTEIN trimers promote entry into cells and are the main target of the humoral immune response. We show here that SARS-CoV-2 S mediates entry in VeroE6 cells and in BHK cells transiently transfected with human ACE2 HGNC, establishing ACE2 HGNC as a functional receptor for this novel coronavirus. We further demonstrate that the receptor-binding domains of SARS-CoV-2 S and SARS-CoV S MESHD bind with similar affinities to human ACE2 HGNC, which correlates with the efficient spread of SARS-CoV-2 among humans. We found that the SARS-CoV-2 S glycoprotein PROTEIN harbors a furin cleavage site at the boundary between the S1/S2 subunits, which is processed during biogenesis and sets this virus apart from SARS-CoV MESHD and other SARS-related CoVs. We determined a cryo-electron microscopy structure of the SARS-CoV-2 S ectodomain trimer, demonstrating spontaneous opening of the receptor-binding domain, and providing a blueprint for the design of vaccines and inhibitors of viral entry. Finally, we demonstrate that SARS-CoV S MESHD murine polyclonal sera potently inhibited SARS-CoV-2 S-mediated entry into target cells, thereby indicating that cross-neutralizing antibodies targeting conserved S epitopes can be elicited upon vaccination.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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