Corpus overview


Overview

MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (36)

NSP5 (1)

ProteinN (1)


Filter

Genes
Diseases
SARS-CoV-2 Proteins
    displaying 1 - 10 records in total 36
    records per page




    DNA-Directed Patterning for Versatile Validation and Characterization of a Lipid-Based Nanoparticle Model of SARS-CoV-2

    Authors: Molly Kozminsky; Thomas Carey; Lydia L. Sohn

    doi:10.26434/chemrxiv.14208455.v1 Date: 2021-03-16 Source: ChemRxiv

    Lipid-based nanoparticles have risen to the forefront of the COVID-19 pandemic MESHD—from encapsulation of vaccine components to modeling the virus, itself. Their rapid development in the face of the volatile nature of the pandemic requires high-throughput, highly flexible methods for characterization. DNA-directed patterning is a versatile method to immobilize and segregate lipid-based nanoparticles for subsequent analysis. DNA-directed patterning selectively conjugates oligonucleotides onto a glass substrate and then hybridizes them to complementary oligonucleotides tagged to the liposomes, thereby patterning them with great control and precision. The power of this method is demonstrated by characterizing a novel recapitulative lipid-based nanoparticle model of SARS-CoV-2 —S-liposomes— which present the SARS-CoV-2 spike PROTEIN ( S) protein PROTEIN on their surfaces. Patterning of a mixture of S-liposomes and liposomes that display the tetraspanin CD63 HGNC into discrete regions of a substrate is used to show that ACE2 HGNC specifically binds to S-liposomes. Importantly, DNA-directed patterning of S-liposomes is used to verify the performance of a commercially available neutralizing antibody against the S protein PROTEIN S protein HGNC. Ultimately, the introduction of S-liposomes to ACE2 HGNC-expressing cells demonstrates the biological relevance of DNA-directed patterning. Overall, DNA-directed patterning enables a wide variety of custom assays for the characterization of any lipid-based nanoparticle.

    SARS-CoV-2 comprehensive receptor profiling: mechanistic insight to drive new therapeutic strategies

    Authors: Sarah MV Brockbank; Raquel Faba-Rodriguez; Lyn Rosenbrier Ribeiro; Catherine Geh; Helen Thomas; Jenni Delight; Lucy Coverley; W Mark Abbott; Jo Soden; Jim Freeth

    doi:10.1101/2021.03.11.434937 Date: 2021-03-11 Source: bioRxiv

    Here we describe a hypothesis free approach to screen for interactions of SARS-CoV-2 spike MESHD SARS-CoV-2 spike PROTEIN ( S) protein PROTEIN with human cell surface receptors. We used a library screening approach to detect binding interactions across one of the largest known panels of membrane-bound and soluble receptors, comprising 5845 targets, expressed recombinantly in human cells. We were able confirm and replicate SARS-CoV-2 binding to ACE2 HGNC and other putative coreceptors such as CD209 HGNC and CLEC4M HGNC. More significantly, we identified interactions with a number of novel SARS-CoV-2 S binding proteins. Three of these novel receptors, NID1 HGNC, CNTN1 HGNC and APOA4 HGNC were specific to SARS-CoV-2, and not SARS-COV MESHD, with APOA4 HGNC binding the S-protein HGNC S-protein PROTEIN with equal affinity as ACE2 HGNC. With this knowledge we may further understand the disease pathogenesis of COVID-19 MESHD patients and how infection by SARS-CoV-2 may lead to differences in pathology in specific organs or indeed the virulence observed in different ethnicities. Importantly we illustrate a methodology which can be used for rapid, unbiassed identification of cell surface receptors, to support drug screening and drug repurposing approaches for this and future pandemics.

    Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations

    Authors: Mohamed Hendy; Samuel Kaufman; Mauricio Ponga

    doi:10.1101/2021.03.04.433970 Date: 2021-03-05 Source: bioRxiv

    The COVID19 MESHD pandemic, caused by SARS-CoV-2, has infected more than 100 million people worldwide. Due to the rapid spreading of SARS-CoV-2 and its impact, it is paramount to find effective treatments against it. Human neutralizing antibodies are an effective method to fight viral infection MESHD. However, the recent discovery of new strains that substantially change the S-protein HGNC S-protein PROTEIN sequence has raised concern about vaccines and antibodies' effectiveness. Here, we investigated the binding mechanisms between the S-protein HGNC S-protein PROTEIN and several antibodies. Multiple mutations were included to understand the strategies for antibody escape in new variants. We found that the combination of mutations K417N and E484K produced higher binding energy to ACE2 HGNC than the wild type, suggesting higher efficiency to enter host cells. The mutations' effect depends on the antibody class. While Class I enhances the binding avidity in the presence of N501Y mutation, class II antibodies showed a sharp decline in the binding affinity. Our simulations suggest that Class I antibodies will remain effective against the new strains. In contrast, Class II antibodies will have less affinity to the S-protein HGNC S-protein PROTEIN, potentially affecting these antibodies' efficiency.

    Intermolecular Interaction Analyses on SARS-CoV-2 Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 HGNC Receptor-Blocking Antibody/peptide Using Fragment Molecular Orbital Calculation

    Authors: Kazuki Watanabe; Chiduru Watanabe; Teruki Honma; Yu-Shi Tian; Yusuke Kawashima; Norihito Kawashita; Tatsuya Takagi; Kaori Fukuzawa

    doi:10.26434/chemrxiv.14135138.v1 Date: 2021-03-02 Source: ChemRxiv

    The spike glycoprotein PROTEIN ( S-protein PROTEIN S-protein HGNC) mediates SARS-CoV-2 entry via intermolecular interaction with human angiotensin-converting enzyme 2 HGNC ( hACE2 HGNC). The receptor-binding domain (RBD) of the S-protein HGNC S-protein PROTEIN has been considered critical for this interaction and acts as the target of numerous neutralizing antibodies and antiviral peptides. This study used the fragment molecular orbital (FMO) method to analyze the interactions between RBD and antibodies/peptides and extracted crucial residues that can be used to epitopes. The interactions evaluated as inter-fragment interaction energy (IFIE) values between the RBD and 12 antibodies/peptides showed a fairly good correlation with the experimental activity pIC50 (R2 = 0.540). Nine residues (T415, K417, Y421, F456, A475, F486, N487, N501, and Y505) were confirmed as crucial. Pair interaction energy decomposition analyses (PIEDA) showed that hydrogen bonds, electrostatic interactions, and π-orbital interactions are important. Our results provide essential information for understanding SARS-CoV-2-antibodies/peptide binding and may play roles in future antibody/antiviral drug design.

    In-Vitro Fluorescence Microscopy Studies Show Retention of Spike-Protein PROTEIN (SARS-Cov-2) on Cell Membrane in the Presence of Amodiaquin Dihydrochloride Dihydrate Drug

    Authors: Partha Pratim Mondal; Subhra Mandal; Tien Huynh; Jessica A. Chichester; Reynette Estelien; Julio Sanmiguel; Kristofer T. Michalson; Cheikh Diop; Dawid Maciorowski; Wenbin Qi; Elissa Hudspeth; Allison Cucalon; Cecilia D. Dyer; M. Betina Pampena; James J. Knox; Regina C. LaRocque; Richelle C. Charles; Dan Li; Maya Kim; Abigail Sheridan; Nadia Storm; Rebecca I. Johnson; Jared Feldman; Blake M. Hauser; Aisling Ryan; Dione T. Kobayashi; Ruchi Chauhan; Marion McGlynn; Edward T. Ryan; Aaron G. Schmidt; Brian Price; Anna Honko; Anthony Griffiths; Sam Yaghmour; Robert Hodge; Michael R. Betts; Mason W. Freeman; James M. Wilson; Luk H. Vandenberghe

    doi:10.1101/2021.01.05.424956 Date: 2021-01-05 Source: bioRxiv

    The ability of S-glycoprotein PROTEIN ( S-protein PROTEIN S-protein HGNC) in SARS-Cov-2 to bind to the host cell receptor protein (angiotensinconverting enzyme 2 HGNC ( ACE2 HGNC)) leading to its entry in cellular system determines its contagious index and global spread. Three available drugs (Riboflavin, Amodiaquin dihydrochloride dihydrate ( ADD MESHD) and Remidesivir) were investigated to understand the kinetics of S-protein HGNC S-protein PROTEIN and its entry inside a cellular environment. Optical microscopy and fluorescence-based assays on 293T cells (transfected with ACE2 HGNC plasmid) were used as the preamble for assessing the behaviour of S-protein PROTEIN S-protein HGNC in the presence of these drugs for the first 12 hours post S-protein PROTEIN S-protein HGNC - ACE2 HGNC binding. Preliminary results suggest relatively long retention of S-protein PROTEIN S-protein HGNC on the cell membrane in the presence of ADD drug. Evident from the %-overlap and colocalization of S-protein HGNC S-protein PROTEIN with endosome studies, a large fraction of S-protein HGNC S-protein PROTEIN entering the cell escape endosomal degradation process, suggesting S-protein HGNC S-protein PROTEIN takes non-endocytic mediated entry in the presence of ADD MESHD, whereas in the presence of Riboflavin, S-protein HGNC S-protein PROTEIN carry out normal endocytic pathway, comparable to control (no drug) group. Therefore, present study indicates ADD potentially affects S-protein HGNC S-protein PROTEIN's entry mechanism (endocytic pathway) in addition to its reported target action mechanism. Hence, ADD substantially interfere with S-protein PROTEIN S-protein HGNC cellular entrance mechanism. However, further detailed studies at molecular scale will clarify our understanding of exact intermediate molecular processes. The present study (based on limited data) reveal ADD MESHD could be potential candidate to manage Covid-19 MESHD functions through yet unknown molecular mechanism.

    Bioactive Agents Contained in Different Nasal Sprays May Defeat SARS-Cov-2: A Repurposing and In-Silico Approach

    Authors: Mohammad Faheem Khan; Waseem Ahmad Ansari; Tanveer Ahamad; Mohsin Ali Khan; Zaw Ali Khan; Aqib Sarfraz; Mohd Aamish Khan

    doi:10.21203/rs.3.rs-135981/v1 Date: 2020-12-25 Source: ResearchSquare

    Recently, Coronavirus Disease 2019 MESHD ( COVID-19 MESHD), caused by fast-spreading and highly contagious severe acute respiratory syndrome coronavirus-2 MESHD (SARS-CoV-2), has been declared as a pandemic disease of the 21st century by the World Health Organization (WHO). SARS-CoV-2 enters into the human respiratory system by binding of the viral surface spike glycoprotein PROTEIN ( S-protein PROTEIN S-protein HGNC) to angiotensin-converting enzyme2 HGNC ( ACE2 HGNC) receptor that is found in the nasal passage and oral cavity of a human. Both spike protein PROTEIN and the ACE2 HGNC receptor have been identified as promising therapeutic targets to develop anti-SARS-CoV-2 drugs. Although in the last few months, various studies have identified some promising molecules against both the receptors including human ACE2 HGNC and SARS-CoV-2 spike PROTEIN protein, still there is no vaccine or therapeutic drugs as of today. The repurposing of FDA-approved drugs may provide a rapid and potential treatment to combat COVID-19 MESHD by using high throughput virtual screening approach. In the present study, we have used the repurposing approach for bioactive agents of the nasal spray against human ACE2 HGNC and SARS-CoV-2 spike PROTEIN protein to identify the anti- COVID-19 MESHD agents with the help of molecular docking study. To this, we screened the sixteen bioactive agents of the nasal spray by analyzing their binding free energy and binding mode through molecular docking study. As a result, bioactive agents such as ciclesonide, levocabastine, and triamcinolone acetonide were found as highly active ligands with potent binding affinities against both the targets human ACE2 HGNC and SARS-CoV-2 spike PROTEIN proteins. Thus, these bioactive agents may effectively assist to control the COVID-19 MESHD by inhibiting the human ACE2 HGNC receptor as well as spike protein PROTEIN of SARS-CoV-2.

    SARS-CoV-2 Spike PROTEIN SARS-CoV-2 Spike MESHD Protein Impairs Endothelial Function via Downregulation of ACE2

    Authors: Cara R. Schiavon; Ming He; Hui Shen; Yichi Zhang; Yoshitake Cho; Leonardo Andrade; Gerry S. Shadel; Mark Hepokoski; Jin Zhang; Jason X.-J. Yuan; Atul Malhotra; Uri Manor; John Y-J. Shyy; Daniel Batlle; Thomas J Hope; Yang Shen; Yuan Luo; Young Chae; Hui Zhang; Suchitra Swaminathan; Glenn C. Randall; Alexis R Demonbreun; Michael G Ison; Deyu Fang; Huiping Liu; Nicholas C. Morano; Gregory J. Krause; Joseph M. Sweeney; Kelsie Cowman; Stephanie Allen; Jayabhargav Annam; Ariella Applebaum; Daniel Barboto; Ahmed Khokhar; Brianna J. Lally; Audrey Lee; Max Lee; Avinash Malaviya; Reise Sample; Xiuyi A. Yang; Yang Li; Rafael Ruiz; Raja Thota; Jason Barnhill; Doctor Y. Goldstein; Joan Uehlinger; Scott J. Garforth; Steven C. Almo; Jonathan R. Lai; Morayma Reyes Gil; Amy S. Fox; Kartik Chandran; Tao Wang; Johanna P. Daily; Liise-anne Pirofski

    doi:10.1101/2020.12.04.409144 Date: 2020-12-04 Source: bioRxiv

    Coronavirus disease 2019 MESHD ( COVID-19 MESHD) includes the cardiovascular complications in addition to respiratory disease MESHD. SARS-CoV-2 infection MESHD impairs endothelial function and induces vascular inflammation MESHD, leading to endotheliitis. SARS-CoV-2 infection MESHD relies on the binding of Spike glycoprotein PROTEIN ( S protein PROTEIN S protein HGNC) to angiotensin converting enzyme 2 HGNC ( ACE2 HGNC) in the host cells. We show here that S protein HGNC S protein PROTEIN alone can damage vascular endothelial cells (ECs) in vitro and in vivo, manifested by impaired mitochondrial function, decreased ACE2 HGNC expression and eNOS activity, and increased glycolysis. The underlying mechanism involves S protein PROTEIN S protein HGNC downregulation of AMPK HGNC and upregulation of MDM2 HGNC, causing ACE2 HGNC destabilization. Thus, the S protein PROTEIN S protein HGNC-exerted vascular endothelial damage via ACE2 HGNC downregulation overrides the decreased virus infectivity.

    The N-glycosylation sites and Glycan-binding ability of S-protein HGNC S-protein PROTEIN in SARS-CoV-2 Coronavirus

    Authors: Wentian Chen; Ziye Hui; Xiameng Ren; Yijie Luo; Jian Shu; Hanjie Yu; Zheng Li

    doi:10.1101/2020.12.01.406025 Date: 2020-12-01 Source: bioRxiv

    The emerging acute respiratory disease MESHD, COVID-19 MESHD, caused by SARS-CoV-2 Coronavirus (SARS2 CoV) has spread fastly all over the word. As a member of RNA viruses, the glycosylation of envelope glycoprotein plays the crucial role in protein folding, evasing host immune system, invading host cell membrane, even affecting host preference. Therefore, detail glyco-related researches have been adopted in the Spike protein (S PROTEIN S-protein HGNC) of SARS2 CoV from the bioinformatic perspective. Phylogenic analysis of S-protein HGNC S-protein PROTEIN sequences revealed the evolutionary relationship of N-glycosylation sites in different CoVs. Structural comparation of S-proteins PROTEIN indicated their similarity and distributions of N-glycosylation sites. Further potential sialic acid or galactose affinity domains have been described in the S-protein HGNC S-protein PROTEIN by docking analysis. Molecular dynamic simulation for the glycosylated complexus of S-protein HGNC S-protein PROTEIN- ACE2 HGNC implied that the complicate viral binding of receptor-binding domain may be influenced by peripheric N-glycans from own and adjacent monoers. These works will contribute to investigate the N-glycosylation in S-protein HGNC S-protein PROTEIN and explain the highly contagious of COVID-19 MESHD.

    Long-Term Persistence of Spike Antibody and Predictive Modeling of Antibody Dynamics Following Infection with SARS-CoV-2

    Authors: Louis Grandjean; Anja Saso; Arturo Torres Ortiz; Tanya Lam; James Hatcher; Rosie Thistlethwaite; Mark Harris; Timothy Best; Marina Johnson; Helen Wagstaffe; Elizabeth Ralph; Annabelle Mai; Caroline Colijn; Judith Breuer; Matthew Buckland; Kimberly Gilmour; David Goldblatt; - The Co-Stars Study Team

    doi:10.1101/2020.11.20.20235697 Date: 2020-11-23 Source: medRxiv

    Background: Antibodies to Severe Acute Respiratory Syndrome Coronavirus-2 MESHD (SARS-CoV-2) have been shown to neutralize the virus in-vitro. Similarly, animal challenge models suggest that neutralizing antibodies isolated from SARS-CoV-2 infected MESHD individuals prevent against disease upon re-exposure to the virus. Understanding the nature and duration of the antibody response following SARS-CoV-2 infection MESHD is therefore critically important. Methods: Between April and October 2020 we undertook a prospective cohort study of 3555 healthcare workers in order to elucidate the duration and dynamics of antibody responses following infection with SARS-CoV-2. After a formal performance evaluation against 169 PCR confirmed cases and negative controls, the Meso-Scale Discovery assay was used to quantify in parallel, antibody titers to the SARS-CoV-2 nucleoprotein (N PROTEIN), spike (S) protein PROTEIN and the receptor-binding-domain (RBD) of the S-protein HGNC S-protein PROTEIN. All seropositive participants were followed up monthly for a maximum of 7 months; those participants that were symptomatic, with known dates of symptom-onset, seropositive by the MSD assay and who provided 2 or more monthly samples were included in the analysis. Survival analysis was used to determine the proportion of sero-reversion (switching from positive to negative) from the raw data. In order to predict long-term antibody dynamics, two hierarchical longitudinal Gamma models were implemented to provide predictions for the lower bound (continuous antibody decay to zero, 'Gamma-decay') and upper bound (decay-to-plateau due to long lived plasma cells, 'Gamma-plateau') long-term antibody titers. Results: A total of 1163 samples were provided from 349 of 3555 recruited participants who were symptomatic, seropositive by the MSD assay, and were followed up with 2 or more monthly samples. At 200 days post symptom onset, 99% of participants had detectable S-antibody whereas only 75% of participants had detectable N-antibody. Even under our most pessimistic assumption of persistent negative exponential decay, the S-antibody was predicted to remain detectable in 95% of participants until 465 days [95% CI 370-575] after symptom onset. Under the Gamma-plateau model, the entire posterior distribution of S-antibody titers at plateau remained above the threshold for detection indefinitely. Surrogate neutralization assays demonstrated a strong positive correlation between antibody titers to the S-protein PROTEIN S-protein HGNC and blocking of the ACE-2 HGNC receptor in-vitro [R2=0.72, p<0.001]. By contrast, the N-antibody waned rapidly with a half-life of 60 days [95% CI 52-68]. Discussion: This study has demonstrated persistence of the spike antibody in 99% of participants at 200 days following SARS-CoV-2 symptoms MESHD and rapid decay of the nucleoprotein PROTEIN antibody. Diagnostic tests or studies that rely on the N-antibody as a measure of seroprevalence must be interpreted with caution. Our lowest bound prediction for duration of the spike antibody was 465 days and our upper bound predicted spike antibody to remain indefinitely in line with the long-term seropositivity reported for SARS-CoV infection MESHD. The long-term persistence of the S-antibody, together with the strong positive correlation between the S-antibody and viral surrogate neutralization in-vitro, has important implications for the duration of functional immunity following SARS-CoV-2 infection MESHD.

    A new proposed mechanism of some known drugs targeting the SARS-CoV-2 spike PROTEIN glycoprotein using molecular docking

    Authors: Tarek Moussa; Nevien Sabry

    doi:10.21203/rs.3.rs-105677/v1 Date: 2020-11-10 Source: ResearchSquare

    COVID-19 MESHD is caused by the novel enveloped beta-coronavirus with a genomic RNA closely related to severe acute respiratory syndrome-corona virus MESHD ( SARS-CoV MESHD) and is named coronavirus 2 (SARS-CoV-2). The receptor binding domain (RBD) of the S-protein PROTEIN S-protein HGNC interacts with the human ACE-2 HGNC receptor that enables the initiation of viral entry. Hence, blocking the S-protein PROTEIN S-protein HGNC interactions by means of synthetic compounds mark the pivotal step for targeting SARS-CoV-2. Most of the six compounds were observed to fit nicely with specific noncovalent interactions, including H bonds, electrostatic, Van der Waals and hydrophobic bonds (pi and sigma bonds). Oseltamivir was found to be the most strongly interacting with the RBD, exhibiting high values of full fitness MESHD and low free energy of binding. it formed multiple noncovalent bonds in the region of the active site. Hydroxychloroquine also demonstrated high binding affinity in the solvent accessbility state and fit nicely into the active pocket of the S-protein PROTEIN S-protein HGNC. The results revealed that these compounds could be potent inhibitors of S-protein PROTEIN S-protein HGNC that could, to some extent, block its interaction with ACE-2 HGNC. It is obvious from the 3D structure of SARS-CoV-2 spike PROTEIN protein was changed with the interaction of different drugs, which led to the unsuitability to bind ACE2 HGNC receptor. Hence, laboratory studies elucidating the action of these compounds on SARS-CoV-2 are warranted for clinical assessments. Chloroquine, hydroxychloroquine and oseltamivir interacted well with the receptor binding domain of S-protein PROTEIN S-protein HGNC via noncovalent interactions and recommended as excellent candidates for COVID-19 MESHD

The ZB MED preprint Viewer preVIEW includes all COVID-19 related preprints from medRxiv and bioRxiv, from ChemRxiv, from ResearchSquare, from arXiv and from Preprints.org and is updated on a daily basis (7am CET/CEST).
The web page can also be accessed via API.

Sources


Annotations

All
None
MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


Export subcorpus as...

This service is developed in the project nfdi4health task force covid-19 which is a part of nfdi4health.

nfdi4health is one of the funded consortia of the National Research Data Infrastructure programme of the DFG.