# bib

id: cord-342312-rnq1hfsj
author: Liu, Bingfeng
title: Recovered COVID-19 patients with recurrent viral RNA exhibit lower levels of anti-RBD antibodies
date: 2020-09-16
extension: .txt
mime: text/plain
words: 1138
sentence: 32
flesch: 44
cache: cache/cord-342312-rnq1hfsj.txt
txt: txt/cord-342312-rnq1hfsj.txt
summary:
  Because of the lack of clinical characteristics and the unknown significance of RP patients, it is critical to provide comprehensive serological profiling to guide the management of recovered COVID-19 patients after discharge. The results showed that RP patients induced significantly lower levels of anti-RBD IgG than PRN patients (p = 0.013) (Fig. 1c) .


id: cord-332185-a96r1k7a
author: Zhang, Shuyuan
date: 2020-09-22
extension: .txt
mime: text/plain
words: 1234
sentence: 39
flesch: 44
cache: cache/cord-332185-a96r1k7a.txt
txt: txt/cord-332185-a96r1k7a.txt
title:
  Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution

summary:
  The overall structures of homotrimeric RaTG13 and PCoV_GX spikes resemble the 107 previously reported pre-fusion structures of coronavirus spikes (Fig. 1A ). key: cord-332185-a96r1k7a authors: Zhang, Shuyuan; Qiao, Shuyuan; Yu, Jinfang; Zeng, Jianwei; Shan, Sisi; Lan, Jun; Tian, Long; Zhang, Linqi; Wang, Xinquan title: Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution date: 2020-09-22 journal: bioRxiv DOI: 10.1101/2020.09.21.307439 sha: doc_id: 332185 cord_uid: a96r1k7a In recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species transmission and infection.


id: cord-328578-9qzo18v3
author: Wang, Yunfei
title: SARS‐CoV‐2 S1 is superior to the RBD as a COVID‐19 subunit vaccine antigen
date: 2020-07-21
extension: .txt
mime: text/plain
words: 2019
sentence: 63
flesch: 39
cache: cache/cord-328578-9qzo18v3.txt
txt: txt/cord-328578-9qzo18v3.txt
summary:
  Ninety-six-well plates were coated with 2 μg/ml HEK293K cell-expressed recombinant SARS-CoV-2 S1 or RBD proteins overnight at 4 °C. key: cord-328578-9qzo18v3 authors: Wang, Yunfei; Wang, Lichun; Cao, Han; Liu, Cunbao title: SARS‐CoV‐2 S1 is superior to the RBD as a COVID‐19 subunit vaccine antigen date: 2020-07-21 journal: J Med Virol DOI: 10.1002/jmv.26320 sha: doc_id: 328578 cord_uid: 9qzo18v3 Since its emergence in December 2019, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has developed into a global pandemic within a matter of months.


id: cord-352934-ypls4zau
author: Wan, Jinkai
title: Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection
date: 2020-07-03
extension: .txt
mime: text/plain
words: 2411
sentence: 69
flesch: 40
cache: cache/cord-352934-ypls4zau.txt
txt: txt/cord-352934-ypls4zau.txt
summary:
  key: cord-352934-ypls4zau authors: Wan, Jinkai; Xing, Shenghui; Ding, Longfei; Wang, Yongheng; Gu, Chenjian; Wu, Yanling; Rong, Bowen; Li, Cheng; Wang, Siqing; Chen, Kun; He, Chenxi; Zhu, Dandan; Yuan, Songhua; Qiu, Chengli; Zhao, Chen; Nie, Lei; Gao, Zhangzhao; Jiao, Jingyu; Zhang, Xiaoyan; Wang, Xiangxi; Ying, Tianlei; Wang, Haibin; Xie, Youhua; Lu, Yanan; Xu, Jianqing; Lan, Fei title: Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection date: 2020-07-03 journal: Cell Rep DOI: 10.1016/j.celrep.2020.107918 sha: doc_id: 352934 cord_uid: ypls4zau Summary COVID-19 has become a worldwide threat to humans, and neutralizing antibodies have therapeutic potential. And we further confirmed that 553-13 and To identify neutralizing antibodies, we first employed pseudoviral infection assays 170 using HEK293T-ACE2 cells.


id: cord-332134-88wfcc3y
author: Li, Tingting
title: A potent synthetic nanobody targets RBD and protects mice from SARS-CoV-2 infection
date: 2020-09-24
extension: .txt
mime: text/plain
words: 2070
sentence: 73
flesch: 43
cache: cache/cord-332134-88wfcc3y.txt
txt: txt/cord-332134-88wfcc3y.txt
summary:
  Taken together, SR4 169 and MR17, and probably MR3, neutralize SARS-CoV-2 by competitively blocking the For biparatopic fusion, we first identified two sybodies, namely LR1 and LR5 (Fig. 208 3A, 3B), that could bind RBD in addition to MR3 using the BLI assay. The results showed that MR3 could block ACE2 (Fig. 2G) , and SR4 167 and MR17 (Fig. 2H, 2I) , suggesting it also binds to at least part of the RBM, although 168 the possibility of allosteric inhibition remains to be investigated.


id: cord-328189-jpkxjn6e
author: Brielle, Esther S.
title: The SARS-CoV-2 exerts a distinctive strategy for interacting with the ACE2 human receptor
date: 2020-03-12
extension: .txt
mime: text/plain
words: 2988
sentence: 113
flesch: 44
cache: cache/cord-328189-jpkxjn6e.txt
txt: txt/cord-328189-jpkxjn6e.txt
summary:
  Similar to the SARS-2002 virus, the COVID-19 virus enters the host cell by RBD binding to the host cell ACE2 receptor (7, 11, 12) . MERS RBD structure was taken from the complex with the neutralizing antibody CDC2-C2 (PDB 6C6Z, resolution 2.1Å) and structurally aligned onto SARS-2002 RBD in complex with ACE2 receptor.


id: cord-300784-4jeaqqn9
author: Ma, Huan
date: 2020-04-22
extension: .txt
mime: text/plain
words: 3496
sentence: 131
flesch: 46
cache: cache/cord-300784-4jeaqqn9.txt
txt: txt/cord-300784-4jeaqqn9.txt
title:
  COVID-19 diagnosis and study of serum SARS-CoV-2 specific IgA, IgM and IgG by a quantitative and sensitive immunoassay

summary:
  RBD-specific IgA, IgM, and IgG detection kits showed sensitivities of 98.6%, 96.8%, and 96.8%, and specificities of 98.1%, 92.3%, and 99.8%, respectively. RBD-specific IgA, 70 IgM, and IgG detection kits showed sensitivities of 98· 6%, 96· 8%, and 96· 8%, and specificities of 98· 1%, 71 92· 3%, and 99· 8%, respectively.


id: cord-326282-uxn64olw
author: Lu, Maolin
title: Real-time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles
date: 2020-09-13
extension: .txt
mime: text/plain
words: 3272
sentence: 118
flesch: 43
cache: cache/cord-326282-uxn64olw.txt
txt: txt/cord-326282-uxn64olw.txt
summary:
  5 The strength of the presented smFRET approach is revealed by the capacity to examine the dynamic properties of the S protein in real time, including: 1) the distinct conformational states that it spontaneously transits under physiological conditions; 2) the impact of sequence alterations on S protein dynamics; and 3) the responses of the S protein to cognate hACE2 receptor and antibody recognition. key: cord-326282-uxn64olw authors: Lu, Maolin; Uchil, Pradeep D.; Li, Wenwei; Zheng, Desheng; Terry, Daniel S.; Gorman, Jason; Shi, Wei; Zhang, Baoshan; Zhou, Tongqing; Ding, Shilei; Gasser, Romain; Prévost, Jérémie; Beaudoin-Bussières, Guillaume; Anand, Sai Priya; Laumaea, Annemarie; Grover, Jonathan R.; Liu, Lihong; Ho, David D.; Mascola, John R.; Finzi, Andrés; Kwong, Peter D.; Blanchard, Scott C.; Mothes, Walther title: Real-time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles date: 2020-09-13 journal: bioRxiv DOI: 10.1101/2020.09.10.286948 sha: doc_id: 326282 cord_uid: uxn64olw SARS-CoV-2 spike (S) mediates entry into cells and is critical for vaccine development against COVID-19.


id: cord-342557-a7q8vp8m
author: Chowdhury, Surid Mohammad
title: Antiviral Peptides as Promising Therapeutics against SARS-CoV-2
date: 2020-10-23
extension: .txt
mime: text/plain
words: 3576
sentence: 171
flesch: 48
cache: cache/cord-342557-a7q8vp8m.txt
txt: txt/cord-342557-a7q8vp8m.txt
summary:
  Binding free energies of AH-RBD, S2P25-RBD, S2P26-RBD, S2P28-RBD, and S2P30-RBD complexes were calculated, for which AH showed an average binding energy of −11.13 ± 0.03 kcal/ mol which was the highest compared to other peptides ( Figure 4a ). Sequence, length, inhibition efficiency, binding affinity, stepwise MLR analysis, interaction residues, and distribution of noncovalent interactions (PDF) Coronaviridae Study Group of the International Committee on Taxonomy of Viruses.


id: cord-323514-jaom3p6s
author: He, Yuxian
date: 2006-05-26
extension: .txt
mime: text/plain
words: 4016
sentence: 145
flesch: 43
cache: cache/cord-323514-jaom3p6s.txt
txt: txt/cord-323514-jaom3p6s.txt
title:
  A single amino acid substitution (R441A) in the receptor-binding domain of SARS coronavirus spike protein disrupts the antigenic structure and binding activity

summary:
  key: cord-323514-jaom3p6s authors: He, Yuxian; Li, Jingjing; Jiang, Shibo title: A single amino acid substitution (R441A) in the receptor-binding domain of SARS coronavirus spike protein disrupts the antigenic structure and binding activity date: 2006-05-26 journal: Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2006.03.139 sha: doc_id: 323514 cord_uid: jaom3p6s angiotensin-converting enzyme 2 The SARS-CoV S glycoprotein: expression and functional characterization Coronavirus spike proteins in viral entry and pathogenesis Molecular modelling of S1 and S2 subunits of SARS coronavirus spike glycoprotein Cellular entry of the SARS coronavirus SARS-associated coronavirus Coronavirus spike proteins in viral entry and pathogenesis Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus A model of the ACE2 structure and function as a SARS-CoV receptor Expression cloning of functional receptor used by SARS coronavirus Amino acids 270 to 510 of the severe acute respiratory syndrome coronavirus spike protein are required for interaction with receptor A 193-amino acid fragment of the SARS coronavirus S protein efficiently binds angiotensin-converting enzyme 2 Structure of SARS coronavirus spike receptor-binding domain complexed with receptor Structural characterization of the fusion-active complex of severe acute respiratory syndrome (SARS) coronavirus Interaction between heptad repeat 1 and 2 regions in spike protein of SARS-associated coronavirus: implications for virus fusogenic mechanism and identification of fusion inhibitors Structural characterization of the SARS-coronavirus spike S fusion protein core Severe acute respiratory syndrome vaccine development: experiences of vaccination against avian infectious bronchitis coronavirus Coronavirus immunogens Contributions of the structural proteins of severe acute respiratory syndrome coronavirus to protective immunity Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Mucosal immunisation of African green monkeys (Cercopithecus aethiops) with an attenuated parainfluenza virus expressing the SARS coronavirus spike protein for the prevention of SARS A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice Recombinant modified vaccinia virus ankara expressing the spike glycoprotein of severe acute respiratory syndrome coronavirus induces protective neutralizing antibodies primarily targeting the receptor binding region Inactivated SARS-CoV vaccine elicits high titers of spike protein-specific antibodies that block receptor binding and virus entry Identification of a critical neutralization determinant of severe acute respiratory syndrome (SARS)-associated coronavirus: importance for designing SARS vaccines Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine Receptor-binding domain of SARS coronavirus spike protein contains multiple conformational-dependant epitopes that induce highly potent neutralizing antibodies


id: cord-309898-sju15hev
author: Hu, Yiwen
date: 2020-11-02
extension: .txt
mime: text/plain
words: 4297
sentence: 144
flesch: 39
cache: cache/cord-309898-sju15hev.txt
txt: txt/cord-309898-sju15hev.txt
title:
  Comparative analysis of nanomechanical features of coronavirus spike proteins and correlation with lethality and infection rate

summary:
  key: cord-309898-sju15hev authors: Hu, Yiwen; Buehler, Markus J. title: Comparative analysis of nanomechanical features of coronavirus spike proteins and correlation with lethality and infection rate date: 2020-11-02 journal: Matter DOI: 10.1016/j.matt.2020.10.032 sha: doc_id: 309898 cord_uid: sju15hev The novel coronavirus disease, COVID-19, has spread rapidly around the world. Here, we provide a novel way in understanding coronavirus spike proteins, connecting their nanomechanical features – specifically its vibrational spectrum and quantitative measures of mobility – with virus lethality and infection rate.


id: cord-355728-wivk0bm0
author: Schoof, Michael
date: 2020-08-17
extension: .txt
mime: text/plain
words: 3664
sentence: 199
flesch: 60
cache: cache/cord-355728-wivk0bm0.txt
txt: txt/cord-355728-wivk0bm0.txt
title:
  An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation

summary:
  Cryogenic electron microscopy (cryo-EM) revealed that one exceptionally stable nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains (RBDs) locked into their inaccessible down-state, incapable of binding ACE2. A prototypical example of this class is nanobody Nb6, which 129 binds to Spike* and to RBD alone with a KD of 210 nM and 41 nM, respectively ( Fig.


id: cord-333465-cha7ndv5
author: Horspool, A. M.
date: 2020-08-31
extension: .txt
mime: text/plain
words: 4312
sentence: 207
flesch: 46
cache: cache/cord-333465-cha7ndv5.txt
txt: txt/cord-333465-cha7ndv5.txt
title:
  Interplay of antibody and cytokine production reveals CXCL-13 as a potential novel biomarker of lethal SARS-CoV-2 infection

summary:
  We demonstrated increasing antibody production to 421 multiple SARS-CoV-2 antigens over the first ten days of infection using a rapid-ELISA 422 assay. Patient mortality, sex, blood type, and age were all associated with differences in antibody production to SARS-CoV-2 antigens which may help explain variation in immunity between these populations.


id: cord-287205-k64svq6n
author: Pollet, Jeroen
date: 2020-11-05
extension: .txt
mime: text/plain
words: 4302
sentence: 144
flesch: 42
cache: cache/cord-287205-k64svq6n.txt
txt: txt/cord-287205-k64svq6n.txt
title:
  SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice

summary:
  This demonstrates that bound RBD proteins are structurally and possibly functionally 308 active and that after adsorption the protein does not undergo any significant conformational changes 309 that could result in the loss of possible key epitopes around the receptor-binding motif (RBM). Currently, there are several types of COVID-19 vaccine candidates in 444 advanced clinical trials 6,40-45 .


id: cord-340960-abanr641
author: Brigger, D.
date: 2020-09-30
extension: .txt
mime: text/plain
words: 4488
sentence: 192
flesch: 42
cache: cache/cord-340960-abanr641.txt
txt: txt/cord-340960-abanr641.txt
title:
  Accuracy of serological testing for SARS‐CoV‐2 antibodies: first results of a large mixed‐method evaluation study

summary:
  The manuscript was prepared according to the Standards for Reporting Diagnostic accuracy studies (STARD) guideline 32 . Few patients with anti-viral antibodies have been identified in the first 5 days following symptom onset but the positive rate rapidly increases thereafter 16, 17 .


id: cord-356264-q0yqnlyl
author: Armijos-Jaramillo, Vinicio
date: 2020-03-23
extension: .txt
mime: text/plain
words: 4990
sentence: 178
flesch: 45
cache: cache/cord-356264-q0yqnlyl.txt
txt: txt/cord-356264-q0yqnlyl.txt
title:
  SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability

summary:
  To resolve these ambiguities in positive selection sites we calculate putative selection sites with CODEML (using Bayes Empirical Bayes from M2 and M8 models) and FUBAR with different datasets reflecting the addition of novel sequences to online repositories (broad, closer, closer without MN996532 and MT084071 and closer without MT084071) and we obtain different results. This result does not disregard the presence of positive selection sites in SARS-CoV-2, nonetheless, it shows the limitation of the methods to identify with precision specific sites under positive selection in a precise taxon of a phylogenetic tree.


id: cord-339724-roj8ksvc
author: Lan, Jiaming
date: 2014-11-18
extension: .txt
mime: text/plain
words: 5043
sentence: 205
flesch: 45
cache: cache/cord-339724-roj8ksvc.txt
txt: txt/cord-339724-roj8ksvc.txt
title:
  Tailoring Subunit Vaccine Immunity with Adjuvant Combinations and Delivery Routes Using the Middle East Respiratory Coronavirus (MERS-CoV) Receptor-Binding Domain as an Antigen

summary:
  On the other hand, Th2 antibody responses can be induced by the Alum, as indicated by increased IgG1 relative to IgG2a The induction of a robust humoral, including potent neutralizing antibodies, and cellular immune response is likely essential for immediate and sustained protective immunity in a MERS-CoV vaccine design.


id: cord-344180-v8xs5ej8
author: Vadlamani, Bhaskar S.
title: Functionalized TiO(2) Nanotube-Based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2
date: 2020-10-17
extension: .txt
mime: text/plain
words: 5156
sentence: 208
flesch: 46
cache: cache/cord-344180-v8xs5ej8.txt
txt: txt/cord-344180-v8xs5ej8.txt
summary:
  Coronavirus Disease 2019 (COVID-19): Situation Report-69 The species Severe acute respiratory syndrome-related coronavirus: Classifying 2019-nCoV and naming it SARS-CoV-2 Cluster of SARS among Medical Students Exposed to Single Patient Identification of Severe Acute Respiratory Syndrome in Canada The SARS-CoV-2 outbreak: What we know The socio-economic implications of the coronavirus pandemic (COVID-19): A review Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia Positive RT-PCR Test Results in Patients Recovered From COVID-19 A SARS-CoV-2 surrogate virus neutralization test based on antibody-mediated blockage of ACE2-spike protein-protein interaction Diagnostic performance of seven rapid IgG/IgM antibody tests and the Euroimmun IgA/IgG ELISA in COVID-19 patients Coronavirus infections and immune responses Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19 Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: Implication for development of RBD protein as a viral attachment inhibitor and vaccine Satchi-Fainaro, R. Immune-mediated approaches against COVID-19 Identification of SARS-CoV RBD-targeting monoclonal antibodies with cross-reactive or neutralizing activity against SARS-CoV-2 Electrochemical biosensors for pathogen detection An electrochemical immunosensor for the corona virus associated with the Middle East respiratory syndrome using an array of gold nanoparticle-modified carbon electrodes A colorimetric and electrochemical immunosensor for point-of-care detection of enterovirus 71 Electrochemical detection of in fl uenza virus H9N2 based on both immunomagnetic extraction and gold catalysis using an immobilization-free screen printed carbon microelectrode An impedance immunosensor based on low-cost microelectrodes and speci fi c monoclonal antibodies for rapid detection of avian in fl uenza virus H5N1 in chicken swabs Amperometry electrochemical studies indicated that the sensor could detect the protein in the concentration range 14 to 1400 nM. The relationship between sensor response and protein concentration was found to be linear with the limit of detection as low as~0.7 nM levels.


id: cord-327654-9g8zcxaa
author: Chi, Xiaojing
date: 2020-09-10
extension: .txt
mime: text/plain
words: 5017
sentence: 225
flesch: 46
cache: cache/cord-327654-9g8zcxaa.txt
txt: txt/cord-327654-9g8zcxaa.txt
title:
  Humanized single domain antibodies neutralize SARS-CoV-2 by targeting the spike receptor binding domain

summary:
  For antibody neutralization assay, Vero cells were seeded in 96-well plates at 1 day prior to infection. Humanized sdAbs obtained in this study are about 125 amino acids with a single VHH domain in average molecular weight less than 15KDa (Fig. 1a) .


id: cord-343185-lbmbp9ca
author: Hansen, C. B.
title: SARS-CoV-2 antibody responses determine disease severity in COVID-19 infected individuals
date: 2020-07-29
extension: .txt
mime: text/plain
words: 5360
sentence: 215
flesch: 42
cache: cache/cord-343185-lbmbp9ca.txt
txt: txt/cord-343185-lbmbp9ca.txt
summary:
  In a recent phase 1 trial, antibody responses against a vaccine candidate (S-2P antigen) and the RBD were assessed, finding similar Ig responses in pattern and magnitude between both antigens (17) . In conclusion, we have established robust, flexible and specific ELISA-based platforms for detection SARS-CoV-2 antibodies and presented novel insight into the link between antibody responses and COVID-19 disease severity. .


id: cord-303868-aes92l6s
author: Steffen, Tara L.
date: 2020-08-22
extension: .txt
mime: text/plain
words: 6106
sentence: 197
flesch: 36
cache: cache/cord-303868-aes92l6s.txt
txt: txt/cord-303868-aes92l6s.txt
title:
  The receptor binding domain of SARS-CoV-2 spike is the key target of neutralizing antibody in human polyclonal sera

summary:
  To measure the functional effect of S1, S2, and RBD antibody depletion on virus specific neutralization we evaluated post-depletion neutralization activity by FRNT (Supplemental figure 3 ). This data has been further represented as % binding neutralizing antibodies based on the pre depletion FRNT50 values (Supplemental Figure 3D) .


id: cord-309182-t9ywnshj
author: Premkumar, Lakshmanane
date: 2020-06-11
extension: .txt
mime: text/plain
words: 6077
sentence: 229
flesch: 44
cache: cache/cord-309182-t9ywnshj.txt
txt: txt/cord-309182-t9ywnshj.txt
title:
  The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients

summary:
  We observed a strong correlation between levels of RBD binding antibodies and SARS-CoV-2 neutralizing antibodies in patients. While further studies are needed to fully evaluate RBD antibodies as correlate of protective immunity, the results to date indicate that RBD antibodies are a promising correlate of protection in the early convalescent phase.


id: cord-340472-9ijlj4so
author: Li, Wenhui
title: Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2
date: 2005-03-24
extension: .txt
mime: text/plain
words: 6650
sentence: 237
flesch: 47
cache: cache/cord-340472-9ijlj4so.txt
txt: txt/cord-340472-9ijlj4so.txt
summary:
  (B) HEK293T cells were transfected with plasmids encoding human ACE2, rat ACE2, or human ACE2 variants in which residues corresponding to those of rat ACE2 were introduced at the indicated position. (C) HEK293T cells transfected with plasmid encoding human ACE2, human ACE2 variants bearing the indicated palm-civet residues, palm-civet ACE2, or the palm-civet ACE2 variant D354G were metabolically labeled and lysed.


id: cord-333264-jdvb8px4
author: Hanke, Leo
title: An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction
date: 2020-09-04
extension: .txt
mime: text/plain
words: 6405
sentence: 267
flesch: 44
cache: cache/cord-333264-jdvb8px4.txt
txt: txt/cord-333264-jdvb8px4.txt
summary:
  The NP-VHH1:RBD data were only baseline-corrected, since dilution effects were not evident. Local fits to individual sensorgrams applying the standard 1:1 binding model appeared reasonable for the association phases at lower to intermediate RBD concentrations, as well as for all dissociation curves when fits were allowed to stay above zero (gray lines Fig.


id: cord-295482-qffg6r91
author: Wong, Alan H. M.
title: Receptor-binding loops in alphacoronavirus adaptation and evolution
date: 2017-11-23
extension: .txt
mime: text/plain
words: 6621
sentence: 244
flesch: 42
cache: cache/cord-295482-qffg6r91.txt
txt: txt/cord-295482-qffg6r91.txt
summary:
  The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding Pre-fusion structure of a human coronavirus spike protein Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains Contributions of the structural proteins of severe acute respiratory syndrome coronavirus to protective immunity Identification of human neutralizing antibodies against MERS-CoV and their role in virus adaptive evolution Effects of human anti-spike protein receptor binding domain antibodies on severe acute respiratory syndrome coronavirus neutralization escape and fitness The Evolution and Emergence of RNA Viruses Host-specific parvovirus evolution in nature is recapitulated by in vitro adaptation to different carnivore species Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission Human coronavirus 229E encodes a single ORF4 protein between the spike and the envelope genes Clinical isolates of human coronavirus 229E bypass the endosome for cell entry The role of mutational robustness in RNA virus evolution HIV pathogenesis: dynamics and genetics of viral populations and infected cells Analysis of human coronavirus 229E spike and nucleoprotein genes demonstrates genetic drift between chronologically distinct strains The behaviour of recent isolates of human respiratory coronavirus in vitro and in volunteers: evidence of heterogeneity among 229E-related strains Differences in neutralizing antigenicity between laboratory and clinical isolates of HCoV-229E isolated in Japan in 2004-2008 depend on the S1 region sequence of the spike protein The X-ray crystal structure of human aminopeptidase N reveals a novel dimer and the basis for peptide processing Structural bases of coronavirus attachment to host aminopeptidase N and its inhibition by neutralizing antibodies Mutational analysis of aminopeptidase N, a receptor for several group 1 coronaviruses, identifies key determinants of viral host range Allosteric inhibition of aminopeptidase N functions related to tumor growth and virus infection Human coronavirus 229E: receptor binding domain and neutralization by soluble receptor at 37 degrees C Broadly neutralizing antiviral antibodies As such, adaptation in a new species, changes in tissue tropism, and differences in receptor expression levels can all lead to changes in receptor binding affinity 29, 31, 48 .


id: cord-314676-ndke9agh
author: Gollapalli, Pavan
date: 2020-11-04
extension: .txt
mime: text/plain
words: 7133
sentence: 239
flesch: 42
cache: cache/cord-314676-ndke9agh.txt
txt: txt/cord-314676-ndke9agh.txt
title:
  Pathway enrichment analysis of virus-host interactome and prioritization of novel compounds targeting the spike glycoprotein receptor binding domain–human angiotensin-converting enzyme 2 interface to combat SARS-CoV-2

summary:
  Binding interactions of the S54 and the S55 ligand at the interface of the spike glycoprotein RBD-hACE2 complex after 300 ns MD simulations. For all amino acid residues except Ser375, RMSF is the lowest for the S55 ligand, followed by S54 ligand and the reference ligand, which corresponds to their decreasing binding affinities.


id: cord-336150-l8w7xk0b
author: Rathore, Jitendra Singh
title: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a newly emerged pathogen: an overview
date: 2020-08-25
extension: .txt
mime: text/plain
words: 7378
sentence: 290
flesch: 47
cache: cache/cord-336150-l8w7xk0b.txt
txt: txt/cord-336150-l8w7xk0b.txt
summary:
  Not so fast Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody Chloroquine is a potent inhibitor of SARS coronavirus infection and spread Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus Nitazoxanide has demonstrated potent in vitro activity against SARS CoV-2, with an EC 50 at 48 h of 2.12 Î¼M in Vero E6 cells .


id: cord-306438-db2rqz4d
author: Kalathiya, Umesh
date: 2020-05-14
extension: .txt
mime: text/plain
words: 6937
sentence: 312
flesch: 47
cache: cache/cord-306438-db2rqz4d.txt
txt: txt/cord-306438-db2rqz4d.txt
title:
  Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site

summary:
  Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular dynamics (MD) simulation. Interpretations from MD simulations suggest that the monomer form of spike protein is in constant motion showing transitions between an “up” and “down” state.


id: cord-343107-oj1re34k
author: Zhou, Haixia
date: 2019-07-11
extension: .txt
mime: text/plain
words: 8683
sentence: 317
flesch: 45
cache: cache/cord-343107-oj1re34k.txt
txt: txt/cord-343107-oj1re34k.txt
title:
  Structural definition of a neutralization epitope on the N-terminal domain of MERS-CoV spike glycoprotein

summary:
  It indicated that the combination of 7D10 with MERS-27 exhibited neither synergy nor antagonism. Mechanism of 7D10 neutralization. Here, we showed that 7D10 neutralization is not solely dependent on DPP4-binding competition, and its inhibition of the S trimer conformational transition after cell attachment also plays a significant role in the neutralization.


id: cord-333703-1ku3jc9s
author: Kraus, Aurora
date: 2020-11-08
extension: .txt
mime: text/plain
words: 8459
sentence: 260
flesch: 39
cache: cache/cord-333703-1ku3jc9s.txt
txt: txt/cord-333703-1ku3jc9s.txt
title:
  A zebrafish model for COVID-19 recapitulates olfactory and cardiovascular pathophysiologies caused by SARS-CoV-2

summary:
  521 Interestingly, we did not observe any changes in ace2 expression after 3h immersion with SARS-522 CoV-2 S RBD protein. 300 There are copious amounts of immune cells in the teleost olfactory organ ( Intranasal delivery of SARS-CoV-2 S RBD induces inflammatory responses and 318 widespread loss of olfactory receptor expression in adult zebrafish olfactory organ 319 320 The cellular landscape of the zebrafish olfactory epithelium was affected by SARS-CoV-2 S 321 RBD treatment and time ( Figure 4A -D).


id: cord-355807-q3bngari
author: Yepes-Pérez, Andres F.
date: 2020-10-29
extension: .txt
mime: text/plain
words: 8856
sentence: 295
flesch: 37
cache: cache/cord-355807-q3bngari.txt
txt: txt/cord-355807-q3bngari.txt
title:
  Uncaria tomentosa (cat’s claw): a promising herbal medicine against SARS-CoV-2/ACE-2 junction and SARS-CoV-2 spike protein based on molecular modeling

summary:
  Thus, crucial binding ligand interactions with LYS417, ARG403, TYR453, GLN493, ASN501, TYR505, SER494, TYR449, TYR495 PHE497 and GLY496 were maintained after 50-ns MD simulation into the binding pocket of SARS-CoV-2 RBD. Therefore, to demonstrate the ability of constituents of U. tomentosa to block binding of the SARS-CoV-2 spike protein to human ACE-2 receptor, we performed molecular docking studies around aforementioned critical amino acids, meaning this docking runs were carried out inside ACE-2 binding surface of RBD.


id: cord-341396-0tn06al2
author: Ni, Ling
title: Detection of SARS-CoV-2-specific humoral and cellular immunity in COVID-19 convalescent individuals
date: 2020-05-03
extension: .txt
mime: text/plain
words: 2112
sentence: 88
flesch: 56
cache: cache/cord-341396-0tn06al2.txt
txt: txt/cord-341396-0tn06al2.txt
summary:
  Main protease-specific T cells were detected in patient #1, 2 and 5, 2 while patients # 1, 2, 4, 5, 6, 7 and 8 showed S-RBD-specific T cells. Here, we collected blood from COVID-19 patients who have recently become virus-free and therefore were discharged, and detected SARS-CoV-2-specific humoral and cellular immunity in 8 newly discharged patients.


id: cord-321918-9jwma2y6
author: Xiu, Siyu
title: Inhibitors of SARS-CoV-2 Entry: Current and Future Opportunities
date: 2020-06-15
extension: .txt
mime: text/plain
words: 10551
sentence: 391
flesch: 42
cache: cache/cord-321918-9jwma2y6.txt
txt: txt/cord-321918-9jwma2y6.txt
summary:
  Hypertension A novel angiotensin-converting enzyme−related carboxypeptidase (ACE2) converts angiotensin I to angiotensin 1−9 Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target Screening and identification of linear B-cell epitopes and entry-blocking peptide of severe acute respiratory syndrome (SARS)-associated coronavirus using synthetic overlapping peptide library A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2 Using peptidomimetics and constrained peptides as valuable tools for inhibiting protein−protein interactions Novel peptide inhibitors of angiotensin-converting enzyme 2 Structure-based discovery of a novel angiotensin-converting enzyme 2 inhibitor Chloroquine is a potent inhibitor of SARS coronavirus infection and spread Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in Vitro Breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies Therapy and pharmacological properties of hydroxychloroquine and chloroquine in treatment of systemic lupus erythematosus, rheumatoid arthritis and related diseases In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Chronic hydroxychloroquine use associated with qt prolongation and refractory ventricular arrhythmia Conduction disorder and qt prolongation secondary to long-term treatment with chloroquine Chloroquine and hydroxychloroquine retinopathy-related risk factors in a turkish cohort Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) TACE antagonists blocking ACE2 shedding caused by the spike protein of SARS-CoV are candidate antiviral compounds ACE2 X-ray structures reveal a large hingebending motion important for inhibitor binding and catalysis Szczubialka, K. Novel polymeric inhibitors of HCoV-NL63 HTCC: broad range inhibitor of coronavirus entry Angiotensin-converting enzyme 2 protects from severe acute lung failure The discovery of angiotensin-converting enzyme 2 and its role in acute lung injury in mice Cell-based antiviral screening against coronaviruses: developing virus-specific and broad-spectrum inhibitors Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides Structures and polymorphic interactions of two heptad-repeat regions of the SARS virus S2 protein Inhibition of human coronavirus NL63 infection at early stages of the replication cycle Fusion core structure of the severe acute respiratory syndrome coronavirus (SARS-CoV): in search of potent SARS-CoV entry inhibitors Protective effect of intranasal regimens containing peptidic middle east respiratory syndrome coronavirus fusion inhibitor against mers-cov infection A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike Fusion mechanism of 2019-nCoV and fusion inhibitors targeting HR1 domain in spike protein Inhibition of SARS-CoV-2 infection (previously 2019-nCoV) by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion Identification of a novel inhibitor against Middle East respiratory syndrome coronavirus Peptide-based membrane fusion inhibitors targeting hcov-229e spike protein HR1 and HR2 domains SARS-CoV-2) based on SARS-CoV immunological studies Fully human monoclonal antibody directed to proteolytic cleavage site in severe acute respiratory syndrome (SARS) Situation Reports; World Health Organization COVID-19) Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Clathrin-dependent entry of severe acute respiratory syndrome coronavirus into target cells expressing ACE2 with the cytoplasmic tail deleted SARS coronavirus entry into host cells through a novel clathrin-and caveolae-independent endocytic pathway Ebola virus and severe acute respiratory syndrome coronavirus display late cell entry kinetics: evidence that transport to NPC1+ endolysosomes is a rate-defining step Coronavirus cell entry occurs through the endo-/ lysosomal pathway in a proteolysis-dependent manner Middle East respiratory syndrome coronavirus infection mediated by the transmembrane serine protease TMPRSS2 SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade Structure of the hemagglutinin precursor cleavage site, a determinant of influenza pathogenicity and the origin of the labile conformation Characterization of a highly conserved domain within the severe acute respiratory syndrome coronavirus spike protein S2 domain with characteristics of a viral fusion peptide Genetic analysis of the SARS-coronavirus spike glycoprotein functional domains involved in cell-surface expression and cell-to-cell fusion Identification and characterization of the putative fusion peptide of the severe acute respiratory syndrome-associated coronavirus spike protein Drug targets for corona virus: a systematic review Mouse hepatitis virus type 2 enters cells through a clathrin-mediated endocytic pathway independent of eps15 A decade after SARS: strategies for controlling emerging coronaviruses Severe Acute Respiratory Syndrome Coronavirus 2 Isolate Wuhan-Hu-1 A new coronavirus associated with human respiratory disease in China Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2 Learning from the past: possible urgent prevention and treatment options for severe acute respiratory infections caused by 2019-nCoV Pathology and pathogenesis of severe acute respiratory syndrome Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: an in silico analysis Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2 Structure of SARS coronavirus spike receptor-binding domain complexed with receptor Design and biological activities of novel inhibitory peptides for SARS-CoV spike protein and angiotensin-converting enzyme 2 interaction Identification of critical determinants on ACE2 for SARS-CoV entry and development of a potent entry inhibitor Faccin-Galhardi, L. C. Antibody therapy for the control of viral diseases: an update Monoclonal antibodies for prophylaxis and therapy of infectious diseases.


id: cord-260406-qvc2fb0c
author: Chen, Long
date: 2020-10-26
extension: .txt
mime: text/plain
words: 2334
sentence: 96
flesch: 47
cache: cache/cord-260406-qvc2fb0c.txt
txt: txt/cord-260406-qvc2fb0c.txt
title:
  Severe Acute Respiratory Syndrome Coronavirus‐2 Spike Protein Nanogel as a Pro‐Antigen Strategy with Enhanced Protective Immune Responses

summary:
  [18] In addition, the change in surface charge may play an important role in lymph node uptake. [12] A critical reason for the low immunogenicity of S-RBD lies in its poor targeting ability to lymph nodes, which is crucial for antigen uptake and processing by dendritic cells (DCs) and macrophages.


id: cord-321854-cy8vyb6j
author: Ripperger, Tyler J.
date: 2020-10-14
extension: .txt
mime: text/plain
words: 3297
sentence: 109
flesch: 38
cache: cache/cord-321854-cy8vyb6j.txt
txt: txt/cord-321854-cy8vyb6j.txt
title:
  Orthogonal SARS-CoV-2 Serological Assays Enable Surveillance of Low Prevalence Communities and Reveal Durable Humoral Immunity.

summary:
  It remains possible that antibody titers will wane substantially at later times. 556 Correlation r values between antibody titers and neutralizing titers were determined using a 558 Pearson correlation.


id: cord-353748-y1a52z8e
author: Bhattacharya, Rajarshi
date: 2021-01-02
extension: .txt
mime: text/plain
words: 3332
sentence: 126
flesch: 51
cache: cache/cord-353748-y1a52z8e.txt
txt: txt/cord-353748-y1a52z8e.txt
title:
  A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2

summary:
  Nisin H differs from nisin F by 7 residues, F1I, M6L, T18G, Y21 M, H27 N, I30V and K31H. Nisin Q is different from nisin H due to the presence of isoleucine, leucine, valine, glycine, leucine, asparagine, valine and histidine at positions 1, 6, 15, 18, 21, 27, 30 and 31, respectively. In multiple sequence alignment (Fig. 1) of amino acid residues of eight nisin variants (nisin A, Z, Q, H, P, U, U2 and F), nisin Z shared 82.35% amino acid sequence similarity with nisin H, whereas nisin P, U, U2, Q and F shared only 70.97%, 67.74%,67.74%, 76.47% and 79.41%, respectively with nisin H (Table S2) .


id: cord-323967-2mo915u1
author: Miersch, Shane
date: 2020-11-01
extension: .txt
mime: text/plain
words: 3237
sentence: 77
flesch: 34
cache: cache/cord-323967-2mo915u1.txt
txt: txt/cord-323967-2mo915u1.txt
title:
  Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations

summary:
  95 To estimate affinities, ELISAs were performed with serial dilutions of IgG protein binding 96 to biotinylated S protein trimer captured with immobilized streptavidin, and these assays showed 97 that three IgGs bound with EC50 values in the sub-nanomolar range (Fig. 1B,C and Table 1 ). Screening of 384 clones for 90 binding to CoV-2 RBD, revealed 348 Fab-phage clones that bound to the RBD but not to 91 streptavidin.


id: cord-329392-fufattj8
author: den Hartog, Gerco
date: 2020-08-08
extension: .txt
mime: text/plain
words: 4345
sentence: 169
flesch: 36
cache: cache/cord-329392-fufattj8.txt
txt: txt/cord-329392-fufattj8.txt
title:
  SARS-CoV-2–Specific Antibody Detection for Seroepidemiology: A Multiplex Analysis Approach Accounting for Accurate Seroprevalence

summary:
  Many countries now aim to assess the protective status of the general population for COVID-19 using antibody assays. For the ROC analyses antibody concentrations of cross-sectional Pienter3 participants (n = 224), ILI patients with coronavirus (n = 74), or other viral infection (n = 110) were used as the negative control group and PCR-confirmed COVID-19 samples (n = 115) with various clinical severities were used in the positive group.


id: cord-351760-698voi9y
author: Han, Hui-Ju
date: 2018-11-30
extension: .txt
mime: text/plain
words: 4167
sentence: 168
flesch: 45
cache: cache/cord-351760-698voi9y.txt
txt: txt/cord-351760-698voi9y.txt
title:
  Neutralizing Monoclonal Antibodies as Promising Therapeutics against Middle East Respiratory Syndrome Coronavirus Infection

summary:
  Development of therapeutic neutralizing mAbs targeting those critically conserved residues might be important for combating MERS-CoV. Moreover, a study found a mouse-derived neutralizing mAb, 5F9, which bound to a possible linear epitope in the NTD of the MERS-CoV S1 subunit, exhibited efficient neutralizing activity against pseudovirus and live MERS-CoV in cell entry tests. There are no approved vaccines or therapies for MERS until now.


id: cord-327711-welf0eb1
author: Zhou, Daming
title: Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient
date: 2020-06-13
extension: .txt
mime: text/plain
words: 4867
sentence: 156
flesch: 45
cache: cache/cord-327711-welf0eb1.txt
txt: txt/cord-327711-welf0eb1.txt
summary:
  Surface plasmon resonance (SPR) measurements for EY6A Fab showed high affinity binding to immobilised SARS-CoV-2 RBD (KD = 2 nM, although the value for immobilised EY6A IgG was somewhat higher) as derived from the kinetic data (Methods, Extended Data Fig. 1 , Extended Data Table 1 ). EY6A Fab binds tightly (KD of 2 nM) the receptor binding domain (RBD) of the viral Spike glycoprotein and a 2.6Å crystal structure of an RBD/EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site.


id: cord-335316-x2t5h5gu
author: Madariaga, M. L. L.
date: 2020-06-23
extension: .txt
mime: text/plain
words: 4330
sentence: 174
flesch: 40
cache: cache/cord-335316-x2t5h5gu.txt
txt: txt/cord-335316-x2t5h5gu.txt
title:
  Clinical predictors of donor antibody titer and correlation with recipient antibody response in a COVID-19 convalescent plasma clinical trial

summary:
  The aim of this study was to establish a translational convalescent plasma program to investigate the relationship between clinical and serological parameters in convalescent plasma donors and define the antibody response of convalescent plasma recipients. Despite variability in donor titer, 80% of convalescent plasma recipients showed significant increase in antibody levels post-transfusion.


id: cord-319571-fspmgg4s
author: Sehailia, Moussa
date: 2020-07-22
extension: .txt
mime: text/plain
words: 4899
sentence: 141
flesch: 35
cache: cache/cord-319571-fspmgg4s.txt
txt: txt/cord-319571-fspmgg4s.txt
title:
  Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19

summary:
  At the cellular level, direct and indirect mechanisms of CQ and HCQ are believed to inhibit immune activation by reducing Toll-like receptor signaling and cytokine production and, in T cells, reducing CD154 expression (Schrezenmeier & D€ orner, 2020) ; however, the absence of binding assay studies between the SProtein and hACE2 protein in the presence of HCQ opens the door to two main possibilities (Vincent et al., 2005) : the first possibility revolves around HCQ prevention of terminal glycosylation of hACE2 protein which consequently impacts the final attachment between the SProtein and hACE2 protein, whereas the second possibility revolves around HCQ interaction with the receptor binding domain (RBD) of SProtein, thus preventing its docking on hACE2 receptor. Figure 8 indicates a good protein-ligand stability for all three complexes, with HCQ protein complex showing the lowest RMSD value (0.22 Å) followed by artenimol-protein complex (0.24 Å) and artemisinin-protein complex (0.26 Å).


id: cord-338538-uea9kwge
author: Shehata, Mahmoud M.
title: Bacterial Outer Membrane Vesicles (OMVs)-Based Dual Vaccine for Influenza A H1N1 Virus and MERS-CoV
date: 2019-05-28
extension: .txt
mime: text/plain
words: 6299
sentence: 231
flesch: 41
cache: cache/cord-338538-uea9kwge.txt
txt: txt/cord-338538-uea9kwge.txt
summary:
  Therefore, OMVs vaccines may be used without extra adjuvant to increase the immunogenicity and produce antiviral innate immune responses against various influenza virus infections via activation of macrophages [42] [43] Therefore, OMVs vaccines may be used without extra adjuvant to increase the immunogenicity and produce antiviral innate immune responses against various influenza virus infections via activation of macrophages [42] [43]


id: cord-318444-sgm24q1i
author: Walter, Justin D.
title: Sybodies targeting the SARS-CoV-2 receptor-binding domain
date: 2020-05-16
extension: .txt
mime: text/plain
words: 5915
sentence: 235
flesch: 38
cache: cache/cord-318444-sgm24q1i.txt
txt: txt/cord-318444-sgm24q1i.txt
summary:
  Concave ADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCX-VXVGXXYXGQGTQVTVS Phylogene c tree of RBD sybodies. Additionally, we identified a pair of anti-RBD sybodies that can simultaneously bind to the RBD.


id: cord-353161-mtq6yh25
author: Rodrigues, João PGLM
title: Insights on cross-species transmission of SARS-CoV-2 from structural modeling
date: 2020-06-05
extension: .txt
mime: text/plain
words: 6174
sentence: 280
flesch: 51
cache: cache/cord-353161-mtq6yh25.txt
txt: txt/cord-353161-mtq6yh25.txt
summary:
  SARS-CoV-2 neg species lack important polar and charged ACE2 residues On further inspection, we find that SARS-CoV-2 neg models rank worse due to a substantial decrease in electrostatic energy (Figure 3 ), indicating loss of polar interface contacts, namely hydrogen bonds and saltbridges ( Figure 4) . HADDOCK score of individual ACE2 interface residues.


id: cord-285900-3rr0j5tk
author: Du, Lanying
date: 2016-11-22
extension: .txt
mime: text/plain
words: 6483
sentence: 233
flesch: 41
cache: cache/cord-285900-3rr0j5tk.txt
txt: txt/cord-285900-3rr0j5tk.txt
title:
  Introduction of neutralizing immunogenicity index to the rational design of MERS coronavirus subunit vaccines

summary:
  Whether an outcome of viral evolution or vaccine design, these immunodominant non-neutralizing epitopes on viral RBDs can outcompete other epitopes in triggering host immune responses, so that the resulting immune responses target these non-neutralizing epitopes while neglecting neutralizing epitopes on viral RBDs (refs 7-10) . Thus, masking an epitope on the RBD core structure with a high negative NII refocuses the host immune response on neutralizing epitopes on the RBM, leading to enhanced neutralizing immunogenicity of the RBD vaccine.


id: cord-329011-spiuqngp
author: Huang, Yuan
date: 2020-08-03
extension: .txt
mime: text/plain
words: 6074
sentence: 236
flesch: 45
cache: cache/cord-329011-spiuqngp.txt
txt: txt/cord-329011-spiuqngp.txt
title:
  Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19

summary:
  In addition, the SARS-CoV-2 S CTD binding interface has more residues that directly interact with the receptor ACE2 than does SARS-RBD (21 versus 17), and a larger surface area is buried with SARS-CoV-2 S CTD in complex with ACE2 than with SARS S RBD. The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex Site-specific glycan analysis of the SARS-CoV-2 spike Fusion mechanism of 2019-nCoV and fusion inhibitors targeting HR1 domain in spike protein Coronavirus membrane fusion mechanism offers a potential target for antiviral development Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein TMPRSS2 activates the human coronavirus 229E for cathepsin-independent host cell entry and is expressed in viral target cells in the respiratory epithelium SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor Cleavage of spike protein of SARS coronavirus by protease factor Xa is associated with viral infectivity Structural and functional basis of SARS-CoV-2 entry by using human ACE2 Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike Physiological and molecular triggers for SARS-CoV membrane fusion and entry into host cells Heptad repeat sequences are located adjacent to hydrophobic regions in several types of virus fusion glycoproteins Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus Peptide-based membrane fusion inhibitors targeting HCoV-229E spike protein HR1 and HR2 domains Bat-to-human: spike features determining 'host jump' of coronaviruses SARS-CoV, MERS-CoV, and beyond Interaction between heptad repeat 1 and 2 regions in spike protein of SARS-associated coronavirus: implications for virus fusogenic mechanism and identification of fusion inhibitors


id: cord-332855-u0amf1oh
author: Parsons, Lisa M.
date: 2019-03-22
extension: .txt
mime: text/plain
words: 7009
sentence: 318
flesch: 54
cache: cache/cord-332855-u0amf1oh.txt
txt: txt/cord-332855-u0amf1oh.txt
title:
  Glycosylation of the viral attachment protein of avian coronavirus is essential for host cell and receptor binding

summary:
  Glycosylation sites in the spike protein are highly conserved across viral genotypes, suggesting an important role for this modification in the virus life cycle. glycomics analysis revealed that glycosylation sites have specific proportions of N-glycan subtypes.


id: cord-346670-34wfy52f
author: Gobeil, Sophie M-C.
date: 2020-10-12
extension: .txt
mime: text/plain
words: 7110
sentence: 220
flesch: 45
cache: cache/cord-346670-34wfy52f.txt
txt: txt/cord-346670-34wfy52f.txt
title:
  D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction

summary:
  The D614G mutation alters S protein conformational dynamics. We observed an increased proportion of the 3-RBD-down S compared to the uncleaved D614G S ectodomain, thus reporting a change in the RBD conformational dynamics upon furin cleavage.


id: cord-333089-ufyzqgqk
author: Aguilar-Pineda, Jorge Alberto
title: Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry
date: 2020-07-29
extension: .txt
mime: text/plain
words: 6978
sentence: 274
flesch: 45
cache: cache/cord-333089-ufyzqgqk.txt
txt: txt/cord-333089-ufyzqgqk.txt
summary:
  Our findings that estrogens interfere with S protein and ACE2 interactions in silico that is associated with reduced S protein uptake in an in vitro model of SARS-CoV-2 infectivity in cultured human endothelial cells are consistent with prior studies demonstrating that estrogens have antiviral properties against HIV, Ebola and hepatitis viruses 33 . We then examined the ability of estrogen molecules to interfere with S protein uptake into pulmonary epithelial cells using an in vivo model of SARS-CoV2 infectivity.


id: cord-347587-auook38y
author: Zhao, Guangyu
date: 2018-08-29
extension: .txt
mime: text/plain
words: 6620
sentence: 250
flesch: 49
cache: cache/cord-347587-auook38y.txt
txt: txt/cord-347587-auook38y.txt
title:
  A Novel Nanobody Targeting Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Receptor-Binding Domain Has Potent Cross-Neutralizing Activity and Protective Efficacy against MERS-CoV

summary:
  The binding between Nbs and MERS-CoV S1 or RBD protein was detected using a BiacoreS200 instrument (GE Healthcare) as previously described (29) . MERS-CoV S1 or RBD protein, as well as the RBDs with or without D539A mutation to hDPP4 receptor, a two-tailed Student t test was used.


id: cord-352527-eeyqh9nc
author: Zhou, Yusen
title: Advances in MERS-CoV Vaccines and Therapeutics Based on the Receptor-Binding Domain
date: 2019-01-14
extension: .txt
mime: text/plain
words: 5878
sentence: 206
flesch: 37
cache: cache/cord-352527-eeyqh9nc.txt
txt: txt/cord-352527-eeyqh9nc.txt
summary:
  An epidemiological outbreak study Outbreak of Middle East respiratory syndrome at tertiary care hospital Transmission of Middle East respiratory syndrome coronavirus infections in healthcare settings Hospital-associated Middle East respiratory syndrome coronavirus infections Hospital-associated Middle East respiratory syndrome coronavirus infections Family cluster of Middle East respiratory syndrome coronavirus infections Healthcare-associated infections: The hallmark of Middle East respiratory syndrome coronavirus with review of the literature Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: A report of nosocomial transmission Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection Human intestinal tract serves as an alternative infection route for Middle East respiratory syndrome coronavirus Persistence of antibodies against Middle East respiratory syndrome coronavirus Presence of Middle East respiratory syndrome coronavirus antibodies in Saudi Arabia: A nationwide, cross-sectional, serological study Feasibility of using convalescent plasma immunotherapy for MERS-CoV infection, Saudi Arabia Feasibility, safety, clinical, and laboratory effects of convalescent plasma therapy for patients with Middle East respiratory syndrome coronavirus infection: A study protocol Challenges of convalescent plasma infusion therapy in Middle East respiratory coronavirus infection: A single centre experience Safety and tolerability of a novel, polyclonal human anti-MERS coronavirus antibody produced from transchromosomic cattle: A phase 1 randomised, double-blind, single-dose-escalation study Prospects for a MERS-CoV spike vaccine Current advancements and potential strategies in the development of MERS-CoV vaccines Is the discovery of the novel human betacoronavirus 2c EMC/2012 (HCoV-EMC) the beginning of another SARS-like pandemic? CoV spike protein: A key target for antivirals Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans Engineering a replication-competent, propagation-defective Middle East respiratory syndrome coronavirus as a vaccine candidate Reverse genetics with a full-length infectious cDNA of the Middle East Report of two cases & review of the literature MERS-CoV infection in a pregnant woman in Korea Middle East respiratory syndrome coronavirus in pediatrics: A report of seven cases from Saudi Arabia Middle East respiratory syndrome coronavirus infection during pregnancy: A Report of 5 cases from Saudi Arabia An outbreak of Middle East respiratory syndrome coronavirus infection in South Korea Probable transmission chains of Middle East respiratory syndrome coronavirus and the multiple generations of secondary infection in South Korea Further evidence for bats as the evolutionary source of Middle East respiratory syndrome coronavirus Bat origins of MERS-CoV supported by bat coronavirus HKU4 usage of human receptor CD26 Receptor usage and cell entry of bat coronavirus HKU4 provide insight into bat-to-human transmission of MERS coronavirus Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis) Discovery of novel bat coronaviruses in south China that use the same receptor as Middle East respiratory syndrome coronavirus Rapid detection of MERS coronavirus-like viruses in bats: Pote1ntial for tracking MERS coronavirus transmission and animal origin Receptor usage of a novel bat lineage C Betacoronavirus reveals evolution of Middle East respiratory syndrome-related coronavirus spike proteins for human dipeptidyl peptidase 4 binding MERS-CoV spillover at the camel-human interface Prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels in Abu Dhabi Emirate Middle East respiratory syndrome coronavirus in dromedary camels: An outbreak investigation High prevalence of MERS-CoV infection in camel workers in Saudi Arabia The prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) antibodies in dromedary camels in Israel Serologic evidence for MERS-CoV infection in dromedary camels Sero-prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) specific antibodies in dromedary camels in Tabuk, Saudi Arabia Dromedary camels in northern Mali have high seropositivity to MERS-CoV Cross-sectional surveillance of Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels and other mammals in Egypt Serological evidence of MERS-CoV antibodies in dromedary camels (Camelus dromedaries) in Laikipia county Reported direct and indirect contact with dromedary camels among laboratory-confirmed MERS-CoV cases Middle East respiratory syndrome coronavirus: Risk factors and determinants of primary, household, and nosocomial transmission Unusual presentation of Middle East respiratory syndrome coronavirus leading to a large outbreak in Riyadh during 2017 Outbreaks of Middle East respiratory syndrome in two hospitals initiated by a single patient in Daejeon MERS-CoV outbreak following a single patient exposure in an emergency room in South Korea:


id: cord-280939-d478p8u6
author: Abe, Kento T.
title: A simple protein-based surrogate neutralization assay for SARS-CoV-2
date: 2020-10-02
extension: .txt
mime: text/plain
words: 7601
sentence: 277
flesch: 46
cache: cache/cord-280939-d478p8u6.txt
txt: txt/cord-280939-d478p8u6.txt
summary:
  Coronavirus Spike Protein and Tropism Changes Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor Neutralizing Antibodies against SARS-CoV-2 and Other Human Coronaviruses Broadly neutralizing antiviral antibodies Deployment of convalescent plasma for the prevention and treatment of COVID-19 Two Detailed Plaque Assay Protocols for the Quantification of Infectious SARS-CoV-2 Protocol and Reagents for Pseudotyping Lentiviral Particles with SARS-CoV-2 Spike Protein for Neutralization Assays Pseudotype Neutralization Assays: From Laboratory Bench to Data Analysis A serological assay to detect SARS-CoV-2 seroconversion in humans Evidence for sustained mucosal and systemic antibody responses to SARS-CoV-2 antigens in COVID-19 patients Dynamics of neutralizing antibody titers in the months after SARS-CoV-2 infection Longitudinal evaluation and decline of antibody responses in SARS-CoV-2 infection Neutralizing and binding antibody kinetics of COVID-19 patients during hospital and convalescent phases SARS-CoV-2 infection induces robust, neutralizing antibody responses that are stable for at least 3 months A SARS-CoV-2 surrogate virus neutralization test based on antibody-mediated blockage of ACE2-spike protein-protein interaction Convergent antibody responses to SARS-CoV-2 in convalescent individuals Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2 A human monoclonal antibody blocking SARS-CoV-2 infection A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2. While ELISA-based assays to detect and quantitate antibodies to SARS-CoV-2 in patient samples have been developed, the detection of neutralizing antibodies typically requires more demanding cell-based viral assays.


id: cord-328003-yovp8squ
author: Duan, Liangwei
date: 2020-10-07
extension: .txt
mime: text/plain
words: 7368
sentence: 176
flesch: 23
cache: cache/cord-328003-yovp8squ.txt
txt: txt/cord-328003-yovp8squ.txt
title:
  The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens

summary:
  The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. Accordingly, there has been mounting interest in exploring the potential of immunogenic glycan moieties as vaccine candidates against multiple viruses, including SARS-CoV-2 (75, 76) .


id: cord-354868-pqn59ojj
author: Yao, Hebang
title: A high-affinity RBD-targeting nanobody improves fusion partner’s potency against SARS-CoV-2
date: 2020-09-25
extension: .txt
mime: text/plain
words: 3260
sentence: 141
flesch: 49
cache: cache/cord-354868-pqn59ojj.txt
txt: txt/cord-354868-pqn59ojj.txt
summary:
  To screen RBD binders by size exclusion chromatography (SEC) using unpurified sybodies, RBD was fluorescently labelled as follows. Crystallographic studies reveal that SR31 binds to RBD at a conserved and ‘greasy’ site distal to RBM.


id: cord-332948-h297ukuu
author: Olotu, Fisayo A.
date: 2020-10-16
extension: .txt
mime: text/plain
words: 5186
sentence: 203
flesch: 42
cache: cache/cord-332948-h297ukuu.txt
txt: txt/cord-332948-h297ukuu.txt
title:
  Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain.

summary:
  Assessment of Binding Site Prediction Methods and a Protocol for Validation of Predicted Binding Sites Identifying and characterizing binding sites and assessing druggability Fpocket: An open source platform for ligand pocket detection PrankWeb: a web server for ligand binding site prediction and visualization New method for fast and accurate binding-site identification and analysis Therapeutic target-site variability in α 1-antitrypsin characterized at high J o u r n a l P r e The N protein makes up the nucleocapsid and other viral genome-related processes 21 while the M protein is the most abundant of the four, playing major roles in maintaining viral structural integrity as well as coordinating other structural proteins.


id: cord-331786-wgt7kg6f
author: Diego-Martin, Borja
date: 2020-10-13
extension: .txt
mime: text/plain
words: 7052
sentence: 243
flesch: 38
cache: cache/cord-331786-wgt7kg6f.txt
txt: txt/cord-331786-wgt7kg6f.txt
title:
  Pilot production of SARS-CoV-2 related proteins in plants: a proof of concept for rapid repurposing of indoors farms into biomanufacturing facilities

summary:
  We carried out a final agroinfiltration for recombinant antibody production using a total of 112 plants, equivalent to approximately 2.5 kilograms of fresh plant material. For antibody production we used wild-type and RNAi ΔXT/FT glycoengineered N. benthamiana plant lines, the latter lacking plantspecific Xylose and Fucose glycosylation (Strasser et al., 2008) .


id: cord-338517-1mxcssjj
author: Ishay, Yuval
title: Antibody response to SARS‐Co‐V‐2, diagnostic and therapeutic implications
date: 2020-08-26
extension: .txt
mime: text/plain
words: 7408
sentence: 244
flesch: 29
cache: cache/cord-338517-1mxcssjj.txt
txt: txt/cord-338517-1mxcssjj.txt
summary:
  Prior to and concurrently with the isolation of specific antibodies, SARS-CoV S1-specific serum from convalescent SARS patients or from animals was proposed to cross-neutralize the SARS-CoV-2 infection by reducing S proteinmediated SARS-CoV-2 entry (30) . Convalescent plasma or immunoglobulins were effective in SARS patients whose condition continued to deteriorate.


id: cord-348455-vcxalkeo
author: Graham, N. R.
date: 2020-07-22
extension: .txt
mime: text/plain
words: 4114
sentence: 184
flesch: 54
cache: cache/cord-348455-vcxalkeo.txt
txt: txt/cord-348455-vcxalkeo.txt
title:
  Kinetics and Isotype Assessment of Antibodies Targeting the Spike Protein Receptor Binding Domain of SARS-CoV-2 In COVID-19 Patients as a function of Age and Biological Sex.

summary:
  Furthermore, we found a very strong correlation 126 between RBD and spike IgG ( Figure In the patient-specific RBD IgG data ( Figure S2A ) we found several patterns: initial 134 seroconversion (e.g. patients 0003, and 0017), rapid increases (e.g. patients 0005, 0006, 0009, 135 0011, 0020, occurring between days 10-20), and plateaued responses (e.g. patients 0012 and 136 0021, occurring mainly after day 20). We also assessed protective anti-spike RBD responses 173 as a function of level of hospital care and disease severity and found that duration of ICU-level 174 care was associated with higher responses, possibly due to an extended period of SARS-CoV-2 175 replication during severe disease.


id: cord-315437-h6xjudm0
author: Nyon, Mun Peak
title: Engineering a stable CHO cell line for the expression of a MERS-coronavirus vaccine antigen
date: 2018-03-27
extension: .txt
mime: text/plain
words: 6656
sentence: 229
flesch: 42
cache: cache/cord-315437-h6xjudm0.txt
txt: txt/cord-315437-h6xjudm0.txt
summary:
  While these mAbs bound strongly to the non-denatured (no DTT) S377-588-Fc proteins expressed in both adCHO and HEK293T, they had significantly reduced affinity to RBD proteins treated with DTT, a reducing agent cleaving disulfide bonds of RBDs and thus disrupting a protein's native conformation (Fig. 4e) . Middle East respiratory syndrome coronavirus The middle east respiratory syndrome coronavirus -a continuing risk to global health security Vaccine development against prioritized epidemic infectious diseases Inovio Reports New Positive Clinical Data on Vaccine Advances in the Fight Against Emerging Infectious Diseases Innate immune signaling by, and genetic adjuvants for DNA vaccination The future of human DNA vaccines Receptor recognition mechanisms of coronaviruses: a decade of structural studies Middle East respiratory syndrome: current status and future prospects for vaccine development Vaccines for the prevention against the threat of MERS-CoV Yeast-expressed recombinant protein of the receptor-binding domain in SARS-CoV spike protein with deglycosylated forms as a SARS vaccine candidate Roadmap to developing a recombinant coronavirus S protein receptor-binding domain vaccine for severe acute respiratory syndrome Receptor-binding domain-based subunit vaccines against MERS-CoV Searching for an ideal vaccine candidate among different MERS coronavirus receptor-binding fragments-the importance of immunofocusing in subunit vaccine design Identification of an ideal adjuvant for receptor-binding domain-based subunit vaccines against Middle East respiratory syndrome coronavirus Recombinant receptorbinding domains of multiple Middle East Respiratory Syndrome Coronaviruses (MERS-CoVs) induce cross-neutralizing antibodies against divergent human and camel MERS-CoVs and antibody escape mutants Receptor-binding domain of MERS-CoV with optimal immunogen dosage and immunization interval protects human transgenic mice from MERS-CoV infection A truncated receptor-binding domain of MERS-CoV spike protein potently inhibits MERS-CoV infection and induces strong neutralizing antibody responses: implication for developing therapeutics and vaccines Characteristics of early-and lateonset rapid eye movement sleep behavior disorder in China: a case-control study Generation of a transgenic mouse model of Middle East respiratory syndrome coronavirus infection and disease Characterization and demonstration of the value of a lethal mouse model of Middle East respiratory syndrome coronavirus infection and disease Evaluation of stable and highly productive gene amplified CHO cell line based on the location of amplified genes A recombinant receptorbinding domain of MERS-CoV in trimeric form protects human dipeptidyl peptidase 4 (hDPP4) transgenic mice from MERS-CoV infection Junctional and allelespecific residues are critical for MERS-CoV neutralization by an exceptionally potent germline-like antibody Exceptionally potent neutralization of Middle East respiratory syndrome coronavirus by human monoclonal antibodies A conformation-dependent neutralizing monoclonal antibody specifically targeting receptor-binding domain in Middle East respiratory syndrome coronavirus spike protein Immunization with inactivated Middle East Respiratory Syndrome coronavirus vaccine leads to lung immunopathology on challenge with live virus Optimized signal peptides for the development of high expressing CHO cell lines MERS-CoV spike protein: a key target for antivirals Evaluation of transfection methods for transient gene expression in Chinese hamster ovary cells Gene expression in Mammalian cells and its applications Designing CD4 immunoadhesins for AIDS therapy Ebola virus glycoprotein Fc fusion protein confers protection against lethal challenge in vaccinated mice A neonatal Fc receptortargeted mucosal vaccine strategy effectively induces HIV-1 antigen-specific immunity to genital infection Adjuvant-free immunization with hemagglutinin-Fc fusion proteins as an approach to influenza vaccines APC targeting enhances immunogenicity of a novel multistage Fc-fusion tuberculosis vaccine in mice Fc-fusion proteins: new developments and future perspectives Stabilisation of the Fc fragment of human IgG1 by engineered intradomain disulfide bonds A plea to reduce or replace fetal bovine serum in cell culture media Advances in Mammalian cell line development technologies for recombinant protein production Identification of a receptorbinding domain in the S protein of the novel human coronavirus Middle East respiratory syndrome coronavirus as an essential target for vaccine development Novel vectors for the expression of antibody molecules using variable regions generated by polymerase chain reaction This study was supported through the US-Malaysian Vaccine Development Program, funded by the University of Malaya, and grants from the NIH (R01AI098775-03S1 and R21AI128311).


id: cord-323324-h2a25xym
author: Armijos‐Jaramillo, Vinicio
date: 2020-05-07
extension: .txt
mime: text/plain
words: 3353
sentence: 123
flesch: 45
cache: cache/cord-323324-h2a25xym.txt
txt: txt/cord-323324-h2a25xym.txt
title:
  SARS‐CoV‐2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability

summary:
  Homology models were constructed using this structure as template for the RBDs of SARS-CoV-2 (SARS2, GeneBank ID MN908947), the Bat SARS-like coronavirus isolate Rm1 (Rm1, GeneBank ID DQ412043), and the Bat SARS-like coronavirus isolate Rs4231 (Rs4231, GeneBank ID KY417146). The predicted RBD-hACE2 complexes for SARS2, SARS, and SARS2-MUT are depicted in Figure 3 .


id: cord-339093-mwxkvwaz
author: Li, Wei
title: High potency of a bivalent human VH domain in SARS-CoV-2 animal models
date: 2020-09-04
extension: .txt
mime: text/plain
words: 11471
sentence: 458
flesch: 51
cache: cache/cord-339093-mwxkvwaz.txt
txt: txt/cord-339093-mwxkvwaz.txt
summary:
  V H ab8 antibody was identified by panning of the phage library. Single antibody domains (sAbd), e.g., camelid V H H (15 kDa) exhibit strong antigen binding and high stability (Harmsen and De Haard, 2007) .


id: cord-265697-bbvlowyo
author: Sang, Eric R.
date: 2020-08-31
extension: .txt
mime: text/plain
words: 7326
sentence: 235
flesch: 37
cache: cache/cord-265697-bbvlowyo.txt
txt: txt/cord-265697-bbvlowyo.txt
title:
  Integrate structural analysis, isoform diversity, and interferon-inductive propensity of ACE2 to predict SARS-CoV2 susceptibility in vertebrates

summary:
  Our current results demonstrate several previously unstudied immunogenetic properties of animal ACE2 genes and imply some domestic animals, including dogs, pigs and cattle/goats, may obtain some immunogenetic diversity to confront SARS-CoV2 infection and face a less Figure 6 . Data show that animal ACE2 gene promoters are evolutionally different in containing IFN-or virus-stimulated response elements (ISRE, PRDI, IFRs, and/or STAT1/3 factors) and cis-elements responsive to proinflammatory mediators.


id: cord-296187-nnv2e7gr
author: Mulgaonkar, Nirmitee
title: Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19
date: 2020-08-18
extension: .txt
mime: text/plain
words: 4966
sentence: 219
flesch: 50
cache: cache/cord-296187-nnv2e7gr.txt
txt: txt/cord-296187-nnv2e7gr.txt
summary:
  key: cord-296187-nnv2e7gr authors: Mulgaonkar, Nirmitee; Wang, Haoqi; Mallawarachchi, Samavath; Fernando, Sandun; Martina, Byron; Ruzek, Daniel title: Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19 date: 2020-08-18 journal: bioRxiv DOI: 10.1101/2020.06.18.158196 sha: doc_id: 296187 cord_uid: nnv2e7gr The rapid geographic expansion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the infectious agent of Coronavirus Disease 2019 (COVID-19) pandemic, poses an immediate need for potent drugs. VSV-G particles cells do not carry spike proteins and thus, no significant entry inhibition occurred, suggesting that entry inhibition is likely mediated through the spike protein.


id: cord-292578-co5essuw
author: Johnson, Marina
date: 2020-08-02
extension: .txt
mime: text/plain
words: 2114
sentence: 74
flesch: 41
cache: cache/cord-292578-co5essuw.txt
txt: txt/cord-292578-co5essuw.txt
title:
  Evaluation of a novel multiplexed assay for determining IgG levels and functional activity to SARS-CoV-2

summary:
  Samples were screened for IgG to SARS-CoV-2 N protein using a commercially available kit (Epitope Diagnostics Inc, San Diego, USA) as previously described (8) . An advantage of this assay is its ability to measure antibody induced inhibition of ACE-2 receptor-spike interaction thought to be the major mechanism by which SARS viruses, including SARS-CoV-2 attach to host cell surfaces (11, 12) .


id: cord-335118-oa9jfots
author: Taka, E.
title: Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor
date: 2020-09-21
extension: .txt
mime: text/plain
words: 5314
sentence: 206
flesch: 50
cache: cache/cord-335118-oa9jfots.txt
txt: txt/cord-335118-oa9jfots.txt
summary:
  In SMD simulations of SARS-CoV-2, Cα atoms of ACE2 residues S19-S43, T78-P84, Q325-N330, G352-I358, and P389-R393 were kept fixed, whereas Cα atoms of RBD residues K417-I418, G446-F456, Y473-A475, and N487-Y505 were steered (Fig. 3A) . CR1 releasing last when SARS-CoV-2 RBD was pulled away from ACE2 PD.


id: cord-344871-486sk4wc
author: Wu, Jianping
date: 2016-09-16
extension: .txt
mime: text/plain
words: 7121
sentence: 275
flesch: 53
cache: cache/cord-344871-486sk4wc.txt
txt: txt/cord-344871-486sk4wc.txt
title:
  Biochemical and structural characterization of the interface mediating interaction between the influenza A virus non-structural protein-1 and a monoclonal antibody

summary:
  A virus A monoclonal antibody binds to threonine 49 in the non-structural 1 protein of influenza A virus and interferes with its ability to modulate viral replication Roles of the phosphorylation of specific serines and threonines in the NS1 protein of human influenza A viruses Monoclonal antibodies targeting the HR2 domain and the region immediately upstream of the HR2 of the S protein neutralize in vitro infection of severe acute respiratory syndrome coronavirus HADDOCK: a protein-protein docking approach based on biochemical or biophysical information Conserved surface features form the double-stranded RNA binding site of non-structural protein 1 (NS1) from influenza A and B viruses Structural basis for dsRNA recognition by NS1 protein of influenza A virus Assay Optimization and Screening of RNA-Protein Interactions by AlphaScreen The multifunctional NS1 protein of influenza A virus strains that circulate in humans differ in the ability of their NS1 proteins to block the activation of IRF3 and interferon-beta transcription Virulence of H5N1 avian influenza virus enhanced by a 15-nucleotide deletion in the viral nonstructural gene RNA binding by the novel helical domain of the influenza virus NS1 protein requires its dimer structure and a small number of specific basic amino acids Binding of influenza A virus NS1 protein to dsRNA in vitro The influenza virus NS1 protein is a poly(A)-binding protein that inhibits nuclear export of mRNAs containing poly(A)


id: cord-305742-wf6qxplf
author: Gomez, Santiago A.
title: Binding of SARS–CoV–2 to cell receptors: a tale of molecular evolution
date: 2020-09-28
extension: .txt
mime: text/plain
words: 3460
sentence: 144
flesch: 48
cache: cache/cord-305742-wf6qxplf.txt
txt: txt/cord-305742-wf6qxplf.txt
summary:
  Accordingly, aiming at understanding the fundamental forces driving the attachment of RBD(S) to host cells, virus· · · cell bonding interactions were dissected following these steps: 1. cell bonding interactions than reoptimizing the isolated pairs), and (a) Computed accurate interaction energies using highly correlated domain based local pair-natural orbital coupled-cluster (DLPNO-CCSD(T)/aug-cc-pVDZ) single point energy calculations [41, 42] on the dimers and in the monomers.


id: cord-319590-f9qcabcx
author: Han, Yanxiao
title: Computational Design of ACE2-Based Peptide Inhibitors of SARS-CoV-2
date: 2020-04-14
extension: .txt
mime: text/plain
words: 2773
sentence: 120
flesch: 51
cache: cache/cord-319590-f9qcabcx.txt
txt: txt/cord-319590-f9qcabcx.txt
summary:
  In summary, using classical molecular dynamics simulations, we have shown that peptide inhibitors extracted from ACE2 provide highly promising trails for SARS-CoV-2 blocking. 10 In the early attempts of SARS-CoV blocking, short peptide inhibitors were studied and amino acid mutations were implemented to the S protein of SARS-CoV. 12, 13


id: cord-291790-z5rwznmv
author: Li, Qianqian
title: The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity
date: 2020-07-17
extension: .txt
mime: text/plain
words: 4910
sentence: 210
flesch: 56
cache: cache/cord-291790-z5rwznmv.txt
txt: txt/cord-291790-z5rwznmv.txt
summary:
  122 As expected, the two types of pseudotyped viruses are different in the infection efficiency in the 123 26 cell lines ( Figure 2) . The last column was employed as the 476 cells control without pseudotyped virus.


id: cord-300847-ycuiso0g
author: Li, Wei
date: 2020-06-02
extension: .txt
mime: text/plain
words: 2815
sentence: 103
flesch: 44
cache: cache/cord-300847-ycuiso0g.txt
txt: txt/cord-300847-ycuiso0g.txt
title:
  Rapid selection of a human monoclonal antibody that potently neutralizes SARS-CoV-2 in two animal models

summary:
  After washing, bound hACE2-Fc was detected by using HRP conjugated streptavidin After washing, bound CR3022 was detected by using HRP conjugated anti human Fc antibody. Thus, to generate high affinity and safe mAbs we used eight very large (size ~ 10 11 clones each) naive human antibody libraries in Fab, scFv or VH format using PBMCs from 490 individuals total obtained before the SARS-CoV-2 outbreak.


id: cord-326337-s0fp5z1q
author: Chan, Kui K.
title: An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants
date: 2020-10-19
extension: .txt
mime: text/plain
words: 4597
sentence: 141
flesch: 40
cache: cache/cord-326337-s0fp5z1q.txt
txt: txt/cord-326337-s0fp5z1q.txt
summary:
  Saturation mutagenesis of the receptor-binding domain followed by in vitro selection, with wild type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild type receptor. 216 Soluble ACE2 2 .v2.4 has three mutations from wild type ACE2: T27Y buried within the RBD 233 interface, and L79T and N330Y at the interface periphery ( Figure 5A) .


id: cord-296319-fwn97wds
author: Juno, J. A.
title: Immunogenic profile of SARS-CoV-2 spike in individuals recovered from COVID-19
date: 2020-05-21
extension: .txt
mime: text/plain
words: 5339
sentence: 247
flesch: 51
cache: cache/cord-296319-fwn97wds.txt
txt: txt/cord-296319-fwn97wds.txt
summary:
  The very low frequencies of spike -RBD + B cells likely 154 constitute a mix of background staining and B cells that recognise RBD epitopes 155 occluded in recombinant S or intact virus. + B cells cells were identified using gating strategy shown in Figure S5 .


id: cord-309411-2dfiwo65
author: Paris, Kristina A.
title: Loss of pH switch unique to SARS-CoV2 supports unfamiliar virus pathology
date: 2020-06-23
extension: .txt
mime: text/plain
words: 4736
sentence: 186
flesch: 51
cache: cache/cord-309411-2dfiwo65.txt
txt: txt/cord-309411-2dfiwo65.txt
summary:
  To answer this question, we need to consider that viral particles in the respiratory system are under small external strains from, e.g., shear flow in the respiratory airways, when engaging cell surface receptors. On the other hand, if only a small number of cell surface receptors are available, then receptor diffusion will be the limiting step to accrue the critical number of receptors needed for endocytosis, and longer RBD/ACE2 dwelling times will be required.


id: cord-284102-rovyvv45
author: Wagner, Teresa R.
title: NeutrobodyPlex - Nanobodies to monitor a SARS-CoV-2 neutralizing immune response
date: 2020-09-28
extension: .txt
mime: text/plain
words: 2921
sentence: 92
flesch: 36
cache: cache/cord-284102-rovyvv45.txt
txt: txt/cord-284102-rovyvv45.txt
summary:
  From this, we can assume that 227 our RBD Nbs covering large parts of the RBD:ACE2 interface might be suitable to monitor the 228 emergence and presence of neutralizing antibodies in patients. In contrast, NM1228 169 (Nb-Set1) as well as NM1230 (Nb-Set2) contacted the RBD at amino acid residues overlapping 170 with the RBD:ACE2 binding interface, whereas NM1230 additionally covers parts of the spike-171 like loop region on one edge of the ACE2 interface at the top front/ lower left side (Front View, 172 which did not contact any amino acid residues involved in the RBD:ACE2 interface but rather 179 binds to the opposite site (Front View, Figure 5 ).


id: cord-285758-c18arb6s
author: Jiang, Shibo
title: SARS Vaccine Development
date: 2005-07-17
extension: .txt
mime: text/plain
words: 2308
sentence: 74
flesch: 30
cache: cache/cord-285758-c18arb6s.txt
txt: txt/cord-285758-c18arb6s.txt
summary:
  CD209L (L-SIGN) is a receptor for severe acute respiratory syndrome coronavirus Interaction between the heptad repeat 1 and 2 regions in spike protein of SARSassociated coronavirus: implication for virus fusogenic mechanism and identification of fusion inhibitors Structural characterization of the SARS-coronavirus spike S fusion protein core Crystal structure of SARS-CoV spike protein fusion core A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice Identification of two neutralizing regions on the severe acute respiratory syndrome coronavirus spike glycoprotein produced from the mammalian expression system Amino acids 1055 to 1192 in the S2 region of severe acute respiratory syndrome coronavirus s protein induce neutralizing antibodies: implications for the development of vaccines and antiviral agents B-cell responses in patients who have recovered from severe acute respiratory syndrome target a dominant site in the S2 domain of the surface spike glycoprotein Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Mucosal immunisation of African green monkeys (Cercopithecus aethiops) with an attenuated parainfluenza virus expressing the SARS coronavirus spike protein for the prevention of SARS Identification of immunodominant sites on the spike protein of severe acute respiratory syndrome (SARS) coronavirus: implication for developing SARS diagnostics and vaccines Identification of antigenic sites mediating antibody-dependent enhancement of feline infectious peritonitis virus infectivity Enhancement of human immunodeficiency virus type-1 (HIV-1) infection by antisera to peptides from the envelope glycoproteins gp120/gp41 Immunization with modified vaccinia virus Ankara-based recombinant vaccine against severe acute respiratory syndrome is associated with enhanced hepatitis in ferrets Identification of a critical neutralization determinant of severe acute respiratory syndrome (SARS)-associated coronavirus: importance for designing SARS vaccines Recombinant modified vaccinia virus Ankara expressing the spike glycoprotein of severe acute respiratory syndrome coronavirus induces protective neutralizing antibodies primarily targeting the receptor binding region Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine Receptor-binding domain of SARS coronavirus spike protein contains multiple conformationdependent epitopes that induce highly potent neutralizing antibodies Molecular and biological characterization of human monoclonal antibodies binding to the spike and nucleocapsid proteins of severe acute respiratory syndrome coronavirus Severe acute respiratory syndrome Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China Molecular epidemiology of the novel coronavirus that causes severe acute respiratory syndrome Evasion of antibody neutralization in emerging severe acute respiratory syndrome coronaviruses Effectiveness of precautions against droplets and contact in prevention of nosocomial transmission of severe acute respiratory syndrome (SARS) Immunogenicity of SARS inactivated vaccine in BALB/c mice Inactivated SARS-CoV vaccine elicits high titers of spike protein-specific antibodies that block receptor binding and virus entry Epitope mapping and biological function analysis of antibodies produced by immunization of mice with an inactivated Chinese isolate of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) Intranasal immunization with inactivated SARS-CoV (SARS-associated coronavirus) induced local and serum antibodies in mice Caution urged on SARS vaccines Glycan arrays lead to the discovery of autoimmunogenic activity of SARS-CoV SARS-associated coronavirus Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus A model of the ACE2 structure and function as a SARS-CoV receptor A 193-amino-acid fragment of the SARS coronavirus S protein efficiently binds angiotensin-converting enzyme 2 The SARS-CoV S glycoprotein: expression and functional characterization The secret life of ACE2 as a receptor for the SARS virus pH-dependent entry of severe acute respiratory syndrome coronavirus is mediated by the spike glycoprotein and enhanced by dendritic cell transfer through DC-SIGN


id: cord-262145-i29e3fge
author: Huang, Kuan-Ying A.
title: Breadth and function of antibody response to acute SARS-CoV-2 infection in humans
date: 2020-10-19
extension: .txt
mime: text/plain
words: 2974
sentence: 82
flesch: 40
cache: cache/cord-262145-i29e3fge.txt
txt: txt/cord-262145-i29e3fge.txt
summary:
  Data are presented as mean ± 823 standard error of the mean ACE2-blocking activity of anti-RBD antibody compared to ACE2-Fc (see methods): +, partial; ++ Abbreviations: IFA, immunofluorescence; RBD, receptor-binding domain; PRNT, plaque reduction 835 neutralisation assay The presence of pre-existing immune memory to betacoronavirus that cross-react with 322 SARS-CoV-2 is supported by the accumulation of somatic mutations in the genes 323 encoding cross-reactive antibodies isolated from COVID-19 patients (Figures 2c and 324 2d, Supplemental Tables 2 and 3 ).


id: cord-301347-22lt6h40
author: Jarvis, Matthew C.
date: 2016-01-01
extension: .txt
mime: text/plain
words: 4265
sentence: 149
flesch: 43
cache: cache/cord-301347-22lt6h40.txt
txt: txt/cord-301347-22lt6h40.txt
title:
  Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus

summary:
  The major clade of US PEDV strains was supported by high posterior probability (100%) and appears to have diverged further into two highly supported sublineages (99% and 100% posterior probability). The estimated tMRCA of the minor clade of US PEDV strains is July 2009-2011, and the estimated tMRCA of the major clade of US PEDV strains is September 2010-August 2012.


id: cord-285039-9piio754
author: Zhou, Haixia
date: 2019-09-14
extension: .txt
mime: text/plain
words: 1941
sentence: 107
flesch: 56
cache: cache/cord-285039-9piio754.txt
txt: txt/cord-285039-9piio754.txt
title:
  Crystallization and Structural Determination of the Receptor-Binding Domain of MERS-CoV Spike Glycoprotein

summary:
  The purification method is the same as that of RBD protein. For details on the principles and methodology of protein crystallography, please refer to the range of other excellent textbooks.


id: cord-308310-wtmjt3hf
author: Zha, Lisha
date: 2020-05-14
extension: .txt
mime: text/plain
words: 2022
sentence: 81
flesch: 48
cache: cache/cord-308310-wtmjt3hf.txt
txt: txt/cord-308310-wtmjt3hf.txt
title:
  Development of a COVID-19 vaccine based on the receptor binding domain displayed on virus-like particles

summary:
  Unreacted SMPH and RBD proteins were removed using Amicon-Ultra 0.5, 100K (Merck-Millipore, Burlington, Mass). The coupling reactions were performed with 0.3x molar excess of RBD, 0.3x RBD, or equal molar amount of RBD regarding the CuMVTT (shaking at 23°C for 3 hours at 1200 rpm on DSG Titertek; Flow Laboratories, Irvine, United Kingdom).


id: cord-260412-yjr83ef6
author: Hotez, Peter J.
title: Developing a low-cost and accessible COVID-19 vaccine for global health
date: 2020-07-29
extension: .txt
mime: text/plain
words: 2343
sentence: 92
flesch: 38
cache: cache/cord-260412-yjr83ef6.txt
txt: txt/cord-260412-yjr83ef6.txt
summary:
  For instance, Texas Children's Center for Vaccine Development (CVD) at Baylor College of Medicine, in collaboration with its nonprofit product development partners-Seattle-based PATH and Infectious Disease Research Institute (IDRI)-have been spearheading a coronavirus vaccine program focusing on recombinant subunit protein vaccines produced in a globally available microbial fermentation platform, and optimized to maximize yield following expression and protein purification [7, 8] . Regarding the former, against SARS CoV homologous virus challenge the vaccine formulated on alum exhibits high levels of protective immunity and with evidence of minimal or no immune enhancement [10] .


id: cord-268144-maa8c4a4
author: Zhang, Yuan
date: 2007-02-17
extension: .txt
mime: text/plain
words: 2565
sentence: 64
flesch: 24
cache: cache/cord-268144-maa8c4a4.txt
txt: txt/cord-268144-maa8c4a4.txt
title:
  Computational characterization and design of SARS coronavirus receptor recognition and antibody neutralization

summary:
  In silico prediction based on homology modelling and energy calculations A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury Angiotensin-converting enzyme 2 in lung diseases Angiotensin-converting enzyme 2: a functional receptor for SARS coronavirus Pathogenesis of severe acute respiratory syndrome Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus Structure of SARS coronavirus spike receptor-binding domain complexed with receptor Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2 Conformational states of the severe acute respiratory syndrome coronavirus spike protein ectodomain Surface ultrastructure of SARS coronavirus revealed by atomic force microscopy Retroviruses pseudotyped with the severe acute respiratory syndrome coronavirus spike protein efficiently infect cells expressing angiotensin-converting enzyme 2 Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody The FoldX web server: an online force field 10 Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association Evaluation of human monoclonal antibody 80R for immunoprophylaxis of severe acute respiratory syndrome by an animal study, epitope mapping, and analysis of spike variants ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis ACE2: from vasopeptidase to SARS virus receptor A 193-amino acid fragment of the SARS coronavirus S protein efficiently binds angiotensinconverting enzyme 2 Immunological responses against SARS-coronavirus infection in humans Severe acute respiratory syndrome coronavirus entry into host cells: opportunities for therapeutic intervention Immunogenicity of a receptor-binding domain of SARS coronavirus spike protein in mice: Implications for a subunit vaccine A study on antigenicity and receptor-binding ability of fragment 450-650 of the spike protein of SARS coronavirus The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling Structural insights into SARS coronavirus proteins Architecture of the SARS coronavirus prefusion spike The protein data bank The SARS coronavirus S glycoprotein receptor binding domain: fine mapping and functional characterization Potential antivirals and antiviral strategies against SARS coronavirus infections Severe acute respiratory syndrome coronavirus pathogenesis, disease and vaccines: an update Receptorbinding domain of SARS-CoV spike protein induces long-term protective immunity in an animal model The SH3-fold family: experimental evidence and prediction of variations in the folding pathways Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling Identification of critical active-site residues in angiotensin-converting enzyme-2 (ACE2) by site-directed mutagenesis Membrane-associated zinc peptidase families: comparing ACE and ACE2 Identification of critical determinants on ACE2 for SARS-CoV entry and development of a potent entry inhibitor Vaccine design for severe acute respiratory syndrome coronavirus Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Identification of a critical neutralization determinant of severe acute respiratory syndrome (SARS)-associated coronavirus: importance for designing SARS vaccines Identification and characterization of novel neutralizing epitopes in the receptor-binding domain of SARS-CoV spike protein: revealing the critical antigenic determinants in inactivated SARS-CoV vaccine Antigenic and immunogenic characterization of recombinant baculovirus-expressed severe acute respiratory syndrome coronavirus spike protein: implication for vaccine design A single amino acid substitution (R441A) in the receptor-binding domain of SARS coronavirus spike protein disrupts the antigenic structure and binding activity Crossneutralization of human and palm civet severe acute respiratory syndrome coronaviruses by antibodies targeting the receptor-binding domain of spike protein Design and biological activities of novel inhibitory peptides for SARS-CoV spike protein and angiotensin-converting enzyme 2 interaction Cellular entry of the SARS coronavirus Structure-based discovery of a novel angiotensin-converting enzyme 2 inhibitor Structural basis of neutralization by a human anti-severe acute respiratory syndrome spike protein antibody, 80R Angiotensinconverting enzyme 2 protects from severe acute lung failure SARS vaccine development Identification of novel small-molecule inhibitors of severe acute respiratory syndromeassociated coronavirus by chemical genetics


id: cord-288761-fyvr0tc1
author: Santiago, César
title: Allosteric inhibition of aminopeptidase N functions related to tumor growth and virus infection
date: 2017-04-10
extension: .txt
mime: text/plain
words: 5878
sentence: 231
flesch: 50
cache: cache/cord-288761-fyvr0tc1.txt
txt: txt/cord-288761-fyvr0tc1.txt
summary:
  In addition, drugs that bind the active site inhibited both coronavirus binding to cell surface APN and infection; the drugs probably hindered APN transition to the virus-specific open form. APN proteins secreted to culture supernatants were purified by affinity chromatography with anti-HA 12AC5 mAb (Roche), followed by size exclusion chromatography in HEPES-saline buffer (20 mM HEPES, 150 mM NaCl) pH 7.5.


id: cord-300707-k9uk14b3
author: Bouwman, Kim M.
title: Multimerization- and glycosylation-dependent receptor binding of SARS-CoV-2 spike proteins
date: 2020-09-04
extension: .txt
mime: text/plain
words: 2332
sentence: 70
flesch: 39
cache: cache/cord-300707-k9uk14b3.txt
txt: txt/cord-300707-k9uk14b3.txt
summary:
  120 To illustrate the expression yields of SARS spike proteins or domains thereof 121 we measured the fluorescence in the cell culture supernatant (Fig 1C) . afford additional means for fluorescent-based experiments [13] , and thus are 101 attractive to be fused to RBD proteins.


id: cord-312560-onfabcfv
author: Klingler, J.
title: Role of IgM and IgA Antibodies to the Neutralization of SARS-CoV-2
date: 2020-08-21
extension: .txt
mime: text/plain
words: 5884
sentence: 240
flesch: 48
cache: cache/cord-312560-onfabcfv.txt
txt: txt/cord-312560-onfabcfv.txt
summary:
  Summary of relative Ig isotype levels and neutralization titers. Using a pseudovirus assay 45 , we also measured neutralizing activities in plasma and serum samples and in Ig isotype fractions to determine the neutralizing capacity of IgM, IgA, and IgG.


id: cord-252919-647zcjgu
author: Chen, Yun
title: Structure analysis of the receptor binding of 2019-nCoV
date: 2020-02-17
extension: .txt
mime: text/plain
words: 3480
sentence: 158
flesch: 55
cache: cache/cord-252919-647zcjgu.txt
txt: txt/cord-252919-647zcjgu.txt
summary:
  3 aligns parts of ACE2 sequences that contain all the interaction sites in contact with SARS-CoV RBD according to the published co-crystal structure [6] . Amino acid residues in the RBD/ ACE2 binding interface plays a crucial role in determining the binding affinity.


id: cord-297747-kifqgskc
author: Lupala, Cecylia S.
date: 2020-03-27
extension: .txt
mime: text/plain
words: 4596
sentence: 153
flesch: 48
cache: cache/cord-297747-kifqgskc.txt
txt: txt/cord-297747-kifqgskc.txt
title:
  Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein

summary:
  For ACE2 residues near the binding interface (within 4.0 Å of the RBD), the RMSD is smaller than 0.43 Å compared to the SARS-RBD/ACE2 complex. The residues near the CoV2-RBD/ACE2 interface (defined as the combined set of ACE2 residues within 4.0 Å of RBD and the RBD residues within 4.0 Å of the ACE2) exhibited a difference of 0.43 Å RMSD, which is comparable to the difference between the two independently reported crystal models (an RMSD of 0.25 Å for the same comparison).


id: cord-256572-sqz8yc7b
author: Huo, Jiandong
title: Neutralization of SARS-CoV-2 by destruction of the prefusion Spike
date: 2020-05-06
extension: .txt
mime: text/plain
words: 5392
sentence: 192
flesch: 48
cache: cache/cord-256572-sqz8yc7b.txt
txt: txt/cord-256572-sqz8yc7b.txt
summary:
  Whilst this work was being prepared for publication a paper reporting that CR3022 does not neutralise SARS-CoV-2 and describing the structure of the complex with the RBD at 3.1 Å resolution was published (Yuan et al., 2020) . (Yuan et al., 2020) .


id: cord-318018-ybdkp398
author: Bruni, Margherita
date: 2020-10-01
extension: .txt
mime: text/plain
words: 5489
sentence: 179
flesch: 37
cache: cache/cord-318018-ybdkp398.txt
txt: txt/cord-318018-ybdkp398.txt
title:
  Persistence of Anti-SARS-CoV-2 Antibodies in Non-Hospitalized COVID-19 Convalescent Health Care Workers

summary:
  The presence of few false positives among the COVID-negative population tested with the viral nucleocapsid protein as compared to the RBD might be a consequence of a mistakenly detection of anti-N antibodies previously raised against common cold coronaviruses which cross-react with the SARS-CoV-2 nucleocapsid [23] . On the contrary, even in the early convalescent phase, those cytokines were undetectable in the sera of non-hospitalized COVID-19 patients (Figure 2A) .


id: cord-263481-w5ytp1q7
author: Lokman, Syed Mohammad
date: 2020-06-02
extension: .txt
mime: text/plain
words: 3021
sentence: 101
flesch: 42
cache: cache/cord-263481-w5ytp1q7.txt
txt: txt/cord-263481-w5ytp1q7.txt
title:
  Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach

summary:
  The spatial distribution of S protein sequences having different variation over time reveals that most of the variants (17 out of 240 S glycoprotein sequences) were reported from the US J o u r n a l P r e -p r o o f Journal Pre-proof followed by 3 out of 2 sequences (including Y145 deletion) and 2 out of 50 sequences from India and China, respectively (Fig. 5) . Based on the phylogenetic studies, the SARS-CoV-2 is categorized as a member of the genus Betacoronavirus, the same lineage that includes SARS coronavirus (SARS-CoV)


id: cord-299783-8ti6r0eh
author: Bruni, M.
date: 2020-08-01
extension: .txt
mime: text/plain
words: 3287
sentence: 122
flesch: 38
cache: cache/cord-299783-8ti6r0eh.txt
txt: txt/cord-299783-8ti6r0eh.txt
title:
  Persistence of anti-SARS-CoV-2 antibodies in non-hospitalized COVID-19 convalescent health care workers

summary:
  In order to measure the presence and evolution of antibody responses against different viral proteins, we set up and validated an in-house direct ELISA assay based on three distinct SARS-CoV-2 viral antigens, i.e. eukaryotically-expressed RBD and Spike and bacterially-expressed Nucleocapsid protein. Noteworthy, in non-severe COVID-19 infections, antibody titers against RBD and Spike, but not against the N protein, as well as pro-inflammatory cytokines decreased within a month after viral clearance.


id: cord-321166-nvphu1fm
author: Thomson, Emma C.
date: 2020-11-05
extension: .txt
mime: text/plain
words: 9836
sentence: 347
flesch: 46
cache: cache/cord-321166-nvphu1fm.txt
txt: txt/cord-321166-nvphu1fm.txt
title:
  The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity

summary:
  7.4% of the tested sera showed a greater than 2-fold reduction in binding to N439K RBD as compared to WT RBD (Figures 5A-B and S3) . The sera from the six individuals known to have recovered from infection with SARS-CoV-2 N439K virus showed no change in binding levels to WT RBD as compared to N439K RBD (Figures 5A-B and S3) .


id: cord-263090-29n9tsk9
author: Roy, Susmita
title: Dynamical asymmetry exposes 2019-nCoV prefusion spike
date: 2020-04-21
extension: .txt
mime: text/plain
words: 4634
sentence: 188
flesch: 47
cache: cache/cord-263090-29n9tsk9.txt
txt: txt/cord-263090-29n9tsk9.txt
summary:
  An investigation for small globular proteins SWISS-MODEL: homology modelling of protein structures and complexes The human coronavirus HCoV-229E S-protein structure and receptor binding SMOG 2: A Versatile Software Package for Generating Structure-Based Models The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function. An investigation for small globular proteins SWISS-MODEL: homology modelling of protein structures and complexes The human coronavirus HCoV-229E S-protein structure and receptor binding SMOG 2: A Versatile Software Package for Generating Structure-Based Models The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.


id: cord-274480-aywdmj6o
author: Song, Wenfei
title: Identification of residues on human receptor DPP4 critical for MERS-CoV binding and entry
date: 2014-10-21
extension: .txt
mime: text/plain
words: 2820
sentence: 104
flesch: 49
cache: cache/cord-274480-aywdmj6o.txt
txt: txt/cord-274480-aywdmj6o.txt
summary:
  RBD D539 has salt-bridge interaction with hDPP4 residue K267 (B). However, the surrounding hydrophilic surface consists of RBD residues D510, E513 and Y540, and DPP4 residues H298, R317 and Q344.


id: cord-296657-mymndjvd
author: Higuchi, Yusuke
title: High affinity modified ACE2 receptors prevent SARS-CoV-2 infection
date: 2020-09-16
extension: .txt
mime: text/plain
words: 3531
sentence: 130
flesch: 42
cache: cache/cord-296657-mymndjvd.txt
txt: txt/cord-296657-mymndjvd.txt
summary:
  key: cord-296657-mymndjvd authors: Higuchi, Yusuke; Suzuki, Tatsuya; Arimori, Takao; Ikemura, Nariko; Kirita, Yuhei; Ohgitani, Eriko; Mazda, Osam; Motooka, Daisuke; Nakamura, Shota; Matsuura, Yoshiharu; Matoba, Satoaki; Okamoto, Toru; Takagi, Junichi; Hoshino, Atsushi title: High affinity modified ACE2 receptors prevent SARS-CoV-2 infection date: 2020-09-16 journal: bioRxiv DOI: 10.1101/2020.09.16.299891 sha: doc_id: 296657 cord_uid: mymndjvd The SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme 2 (ACE2) receptor via receptor binding domain (RBD) to enter into the cell. High affinity modified ACE2 fused with Fc is the promising strategy to neutralize SARS-CoV-2.


id: cord-281536-8y7yxcp4
author: Lim, Hocheol
date: 2020-10-08
extension: .txt
mime: text/plain
words: 3534
sentence: 126
flesch: 47
cache: cache/cord-281536-8y7yxcp4.txt
txt: txt/cord-281536-8y7yxcp4.txt
title:
  Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital method

summary:
  In this work, to find common hot spot amino acids on the interfaces between the RBD domain and hACE2 of the three complexes, RBD-SARS-CoV-2/hACE2 (twelve experimental structural data), RBD-SARS-CoV-1/ hACE2 (four experimental structural data), and RBD-HCoV-NL63/hACE2 (one experimental structural data), we performed FMO-DFTB3/D/PCM calculations. In order to find common hot spot amino acids in RBD-SARS-CoV-1 against hACE2 and SARS-CoV-1 antibodies, we illustrated the FMO results with a 3D-SPIEs-based map.


id: cord-267001-csgmc155
author: George, Parakkal Jovvian
date: 2020-05-27
extension: .txt
mime: text/plain
words: 7747
sentence: 243
flesch: 42
cache: cache/cord-267001-csgmc155.txt
txt: txt/cord-267001-csgmc155.txt
title:
  The Potency of an Anti-MERS Coronavirus Subunit Vaccine Depends on a Unique Combinatorial Adjuvant Formulation

summary:
  Importantly, we found a significant and positive correlation between the neutralizing antibody titers in sera of mice vaccinated with rASP-1 and the alum adjuvanted RBD vaccine separately and the fold increase in the frequency of TfH and GC B cells recruited in the draining LN ( Figures 4C and 5D) . Our findings not only indicate that this unique combinatorial adjuvanted RBD vaccine regimen improved the immunogenicity of RBD, but also point to the importance of utilizing combinatorial adjuvants for the induction of synergistic protective immune responses.


id: cord-263042-qdmunb9l
author: Zhao, Yongkun
date: 2016-11-24
extension: .txt
mime: text/plain
words: 3379
sentence: 120
flesch: 44
cache: cache/cord-263042-qdmunb9l.txt
txt: txt/cord-263042-qdmunb9l.txt
title:
  Passive immunotherapy for Middle East Respiratory Syndrome coronavirus infection with equine immunoglobulin or immunoglobulin fragments in a mouse model

summary:
  Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study Hospital outbreak of Middle East respiratory syndrome coronavirus Prophylactic and postexposure efficacy of a potent human monoclonal antibody against MERS coronavirus Transmission of MERS-coronavirus in household contacts Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection Identification of a receptor-binding domain in the S protein of the novel human coronavirus Middle East respiratory syndrome coronavirus as an essential target for vaccine development Immunological profile of antivenoms: preclinical analysis of the efficacy of a polyspecific antivenom through antivenomics and neutralization assays Towards improving clinical management of Middle East respiratory syndrome coronavirus infection Identification of a critical neutralization determinant of severe acute respiratory syndrome (SARS)-associated coronavirus: importance for designing SARS vaccines A humanized neutralizing antibody against MERS-CoV targeting the receptor-binding domain of the spike protein Passive immunotherapy for influenza A H5N1 virus infection with equine hyperimmune globulin F(ab')2 in mice Human polyclonal immunoglobulin G from transchromosomic bovines inhibits MERS-CoV in vivo The effectiveness of convalescent plasma and hyperimmune immunoglobulin for the treatment of severe acute respiratory infections of viral etiology: a systematic review and exploratory meta-analysis The receptor binding domain of the new Middle East respiratory syndrome coronavirus maps to a 231-residue region in the spike protein that efficiently elicits neutralizing antibodies Severe acute respiratory syndrome Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia MERS-CoV virus-like particles produced in insect cells induce specific humoural and cellular imminity in rhesus macaques Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Rapid generation of a mouse model for Middle East respiratory syndrome Passive immunotherapy with dromedary immune serum in an experimental animal model for Middle East respiratory syndrome coronavirus infection Treatment with hyperimmune equine immunoglobulin or immunoglobulin fragments completely protects rodents from Ebola virus infection Inhibition of infection caused by severe acute respiratory syndrome-associated coronavirus by equine neutralizing antibody in aged mice Middle East respiratory syndrome Ad5-hDPP4 transduced BALB/c mice (6wks, female) were injected intraperitoneally with 200 mL horse serum However, neutralizing antibody titers in MERS patients are generally low and the limited number of MERS survivors makes this approach impractical (Drosten et al., 2013) .


id: cord-310230-9wfb43gt
author: Ghorbani, Mahdi
title: Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations
date: 2020-06-27
extension: .txt
mime: text/plain
words: 3482
sentence: 126
flesch: 45
cache: cache/cord-310230-9wfb43gt.txt
txt: txt/cord-310230-9wfb43gt.txt
summary:
  Fine Mapping and Functional Characterization Development and Characterization of a Severe Acute Respiratory Syndrome-Associated Coronavirus-Neutralizing Human Monoclonal Antibody That Provides Effective Immunoprophylaxis in Mice Neutralizing Human Monoclonal Antibodies to Severe Acute Respiratory Syndrome Coronavirus: Target, Mechanism of Action, and Therapeutic Potential Human Monoclonal Antibody Combination against SARS Coronavirus: Synergy and Coverage of Escape Mutants Vaccine Efficacy in Senescent Mice Challenged with Recombinant SARS-CoV Bearing Epidemic and Zoonotic Spike Variants Structural Basis for Potent Cross-Neutralizing Human Monoclonal Antibody Protection against Lethal Human and Zoonotic Severe Acute Respiratory Syndrome Coronavirus Challenge Escape from Human Monoclonal Antibody Neutralization Affects In Vitro and In Vivo Fitness of Severe Acute Respiratory Syndrome Coronavirus Disease and Diplomacy: GISAID's Innovative Contribution to Global Health Structural Basis for Receptor Recognition by the Novel Coronavirus from Wuhan MCSM-PPI2: predicting the effects of mutations on protein The SARS Coronavirus S Glycoprotein Receptor Binding Domain: Residues K479 and S487 in SARS-Civet are in close proximity with these hotspots and mutations at these residues caused SARS to bind ACE2 with significantly higher affinity than SARS-Civet and played a major role in civet-to-human and human-to-human transmission of SARS coronavirus in 2002.


id: cord-310636-y7n22ykt
author: Garcia-Beltran, W. F.
title: COVID-19 neutralizing antibodies predict disease severity and survival
date: 2020-10-20
extension: .txt
mime: text/plain
words: 10932
sentence: 366
flesch: 37
cache: cache/cord-310636-y7n22ykt.txt
txt: txt/cord-310636-y7n22ykt.txt
summary:
  Here we found that severely ill COVID-19 patients had the highest levels of anti-RBD antibodies, which other studies have similarly described (Shrock et al. , 2020) . Remarkably, we find that anti-RBD antibody levels, neutralization titer, and neutralization potency index predicted disease severity and survival, yet lacked cross-neutralizing activity to pre-emergent WIV1-CoV. Taken together, our results highlight the impact of an effective humoral immune response on COVID-19, as quantified by a neutralization potency index, and describe the A cross-sectional cohort of 113 COVID-19 cases confirmed by SARS-CoV-2 nasopharyngeal PCR was studied and followed for at least 3 months.


id: cord-276833-haci44cy
author: Kim, Ju
date: 2019-05-18
extension: .txt
mime: text/plain
words: 5440
sentence: 187
flesch: 38
cache: cache/cord-276833-haci44cy.txt
txt: txt/cord-276833-haci44cy.txt
title:
  Human β-defensin 2 is involved in CCR2-mediated Nod2 signal transduction, leading to activation of the innate immune response in macrophages

summary:
  key: cord-276833-haci44cy authors: Kim, Ju; Yang, Ye Lin; Jang, Yong-Suk title: Human β-defensin 2 is involved in CCR2-mediated Nod2 signal transduction, leading to activation of the innate immune response in macrophages date: 2019-05-18 journal: Immunobiology DOI: 10.1016/j.imbio.2019.05.004 sha: doc_id: 276833 cord_uid: haci44cy Beta-defensins contribute to host innate defense against various pathogens, including viruses, although the details of their roles in innate immune cells are unclear. These findings suggest that further studies on modulation of the balance between pro-and anti-inflammatory cytokines and network among innate immune cells, such as M1/M2 macrophage polarization, would facilitate the development of novel therapeutic approaches for immunological disorders.


id: cord-319855-78xmxymu
author: BR, Bharath
date: 2020-07-01
extension: .txt
mime: text/plain
words: 4806
sentence: 201
flesch: 49
cache: cache/cord-319855-78xmxymu.txt
txt: txt/cord-319855-78xmxymu.txt
title:
  In silico screening of known small molecules to bind ACE2 specific RBD on Spike glycoprotein of SARS-CoV-2 for repurposing against COVID-19

summary:
  Meanwhile, the subsequent neighbours were Pangolin MP789 and SARS-CoV. As depicted in Figure 4 , the alignment between the S-protein of SARS-CoV-2 and that of Bat coronavirus RaTG13 was closer than with the S-protein of SARS-CoV.


id: cord-292883-7hvq9qaj
author: Nguyen-Contant, Phuong
date: 2020-09-25
extension: .txt
mime: text/plain
words: 5385
sentence: 184
flesch: 43
cache: cache/cord-292883-7hvq9qaj.txt
txt: txt/cord-292883-7hvq9qaj.txt
title:
  S Protein-Reactive IgG and Memory B Cell Production after Human SARS-CoV-2 Infection Includes Broad Reactivity to the S2 Subunit

summary:
  In particular, we were interested in the presence of SARS-CoV-2-reactive MBCs in unexposed subjects that could confer some protection against SARS-CoV-2 and in formation of MBCs by SARS-CoV-2 infection to provide durable protection against reinfection. Abs that target the S2 subunit have been shown to have virus-neutralizing activity, raising the possibility that the presence of preexisting anti-S2 IgG confers some protection against SARS-CoV-2 (25) .


id: cord-276493-hoaxv5e0
author: Jeong, Gi Uk
title: Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review
date: 2020-07-14
extension: .txt
mime: text/plain
words: 5702
sentence: 198
flesch: 43
cache: cache/cord-276493-hoaxv5e0.txt
txt: txt/cord-276493-hoaxv5e0.txt
summary:
  (Dai et al., 2020; Jin et al., 2020; Zhang et al., 2020b) . (Dai et al., 2020; Jin et al., 2020; Zhang et al., 2020b) .


id: cord-290290-wyx9ib7s
author: Sinegubova, Maria V.
date: 2020-11-05
extension: .txt
mime: text/plain
words: 6012
sentence: 231
flesch: 43
cache: cache/cord-290290-wyx9ib7s.txt
txt: txt/cord-290290-wyx9ib7s.txt
title:
  High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector

summary:
  We developed a simple purification scheme that consistently yielded up to 30 mg of RBD protein per liter of the simple shake flask cell culture. This All cell populations, secreting RBD proteins, were analyzed by the quantitative PCR and it was found, that increased productivity of populations, adapted to higher concentrations of MTX corresponds to higher copy numbers of target gene (Fig 3C) .


id: cord-320238-qbjrlog1
author: Okba, Nisreen M. A.
date: 2020-05-29
extension: .txt
mime: text/plain
words: 6205
sentence: 240
flesch: 43
cache: cache/cord-320238-qbjrlog1.txt
txt: txt/cord-320238-qbjrlog1.txt
title:
  Particulate multivalent presentation of the receptor binding domain induces protective immune responses against MERS-CoV

summary:
  Furthermore, using a SypTag/SpyCatcher system and LS particles, we tested whether immune focusing with/ without multivalent presentation of the viral RBD can lead to enhanced protection against a MERS-CoV challenge in rabbits. Using this approach, we found no significant increase in anti-scaffold antibody responses compared to the homologous prime-boost scheme ( Figure 4C ).


id: cord-291420-40xsypzt
author: Nelson-Sathi, Shijulal
date: 2020-10-01
extension: .txt
mime: text/plain
words: 2283
sentence: 89
flesch: 44
cache: cache/cord-291420-40xsypzt.txt
txt: txt/cord-291420-40xsypzt.txt
title:
  Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction

summary:
  In addition, RBD mutations identified in this study can serve as a molecular directory for experimental biologists to perform functional validation experiments. For the Maximum-likelihood phylogeny reconstruction, we have used the SARS-CoV-2 genomes containing RBD mutations, and 10 genomes were sampled as representatives for each known subtype with Wuhan RefSeq strain as root.


id: cord-315415-3aotsb2g
author: Dong, Jianbo
title: Development of humanized tri-specific nanobodies with potent neutralization for SARS-CoV-2
date: 2020-10-20
extension: .txt
mime: text/plain
words: 7214
sentence: 291
flesch: 49
cache: cache/cord-315415-3aotsb2g.txt
txt: txt/cord-315415-3aotsb2g.txt
summary:
  In this study we used computer-aided design to construct multi-specific VHH antibodies fused to human IgG1 Fc domains based on the epitope predictions for leading VHHs. Our selected VHH binders in tri-specific antibodies possibly cover both of these regions (Fig. 5 ).


id: cord-254735-8reu45yz
author: Reguera, Juan
date: 2012-08-02
extension: .txt
mime: text/plain
words: 8111
sentence: 336
flesch: 54
cache: cache/cord-254735-8reu45yz.txt
txt: txt/cord-254735-8reu45yz.txt
title:
  Structural Bases of Coronavirus Attachment to Host Aminopeptidase N and Its Inhibition by Neutralizing Antibodies

summary:
  To confirm the contribution of the PRCV or TGEV RBD bbarrel tip in pAPN receptor recognition, we analyzed binding of wild type and mutant TGEV RBD proteins to cell surfaceexpressed pAPN ( Figure 4A ). pAPN protein was run through a Superdex 200 16/60 column (GE Healthcare) with HEPESsaline buffer pH 7.5.


id: cord-183197-dxmto1tu
author: Zhao, Tom Y.
title: Tetracycline as an inhibitor to the coronavirus SARS-CoV-2
date: 2020-08-13
extension: .txt
mime: text/plain
words: 1589
sentence: 47
flesch: 27
cache: cache/cord-183197-dxmto1tu.txt
txt: txt/cord-183197-dxmto1tu.txt
summary:
  Tetracyline appears to bind preferably to polar or slightly lipophilic RBD residues, which comprise the majority of amino acids that form persistent hydrogen bonds with ACE2 8;9 . RBD 7.58 Chloroquine-RBD 5.59 Doxycycline-RBD 5.16 Tetracycline-RBD 2.98 Table 2 : The binding efficiency 13 (magnitude of binding energy normalized by contact interface area) of the spike protein RBD as well as the Tetracycline-RBD, Doxycycline-RBD and Chloroquine-RBD complexes to the human cell receptor ACE2.


id: cord-273893-3nd6ptrg
author: Lu, Guangwen
title: Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26
date: 2013-07-07
extension: .txt
mime: text/plain
words: 4682
sentence: 197
flesch: 50
cache: cache/cord-273893-3nd6ptrg.txt
txt: txt/cord-273893-3nd6ptrg.txt
summary:
  By a pairwise comparison, we unexpectedly found that all those CD26 residues identified in the virus-receptor interface are also involved in ADA binding, indicating a competition between ADA and the virus for CD26 receptor. The complex structure was solved by molecular replacement module of Phaser 33 , with the solved RBD structure and previously reported CD26 structure (PDB code, 2BGR) as the search models.


id: cord-262043-66qle52a
author: Basit, Abdul
date: 2020-05-20
extension: .txt
mime: text/plain
words: 4883
sentence: 168
flesch: 43
cache: cache/cord-262043-66qle52a.txt
txt: txt/cord-262043-66qle52a.txt
title:
  Truncated human angiotensin converting enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent

summary:
  Another recent study has reported a 23 amino acid based peptide, a homologue of ACE2 binding interface, which successfully bind with S protein with low nanomolar affinity . Based on the HADDOCK score and the docking RMSD value, the docked complexes of ACE2 and tACE2 with RBD were analyzed for binding affinity DG (kcal mol À1 ) and stability using protein binding energy prediction (PRODIGY) server (Xue et al., 2016) .


id: cord-259185-qg4jwbes
author: Vadlamani, B. S.
title: Functionalized TiO2 nanotube-based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2
date: 2020-09-09
extension: .txt
mime: text/plain
words: 3993
sentence: 180
flesch: 45
cache: cache/cord-259185-qg4jwbes.txt
txt: txt/cord-259185-qg4jwbes.txt
summary:
  Causing an Outbreak of Pneumonia Positive RT-PCR Test Results in Patients Recovered From COVID-19 A SARS-CoV-2 surrogate virus neutralization test ( sVNT ) based on antibody-mediated blockage of ACE2-spike ( RBD ) protein-protein interaction Diagnostic performance of seven rapid IgG / IgM antibody tests and the Euroimmun IgA / IgG ELISA in COVID-19 patients Coronavirus infections and immune responses Structural and functional properties of SARS-CoV-2 spike protein : potential antivirus drug development for COVID-19 Characterization of the receptorbinding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine. Amperometry electrochemical studies indicated that the sensor could detect the protein in the concentration range 14 nM to 1400 nM. The relationship between sensor response and protein concentration was found to be linear with the limit of detection as low as ~0.7 nM levels.


id: cord-311035-s3tkbh9r
author: Procko, Erik
title: Deep mutagenesis in the study of COVID-19: a technical overview for the proteomics community
date: 2020-10-21
extension: .txt
mime: text/plain
words: 4039
sentence: 144
flesch: 36
cache: cache/cord-311035-s3tkbh9r.txt
txt: txt/cord-311035-s3tkbh9r.txt
summary:
  The enrichment ratios calculated for each variant in the sorted ACE2 library provide a mutational landscape that defines the relative phenotypes of thousands of ACE2 mutations for binding to SARS-CoV-2 S In this way, information was collected on how ACE2 mutations impact expression and RBD binding from a single FACS experiment.


id: cord-280941-ds6x0yym
author: Kim, Young-Seok
date: 2018-05-17
extension: .txt
mime: text/plain
words: 9430
sentence: 361
flesch: 44
cache: cache/cord-280941-ds6x0yym.txt
txt: txt/cord-280941-ds6x0yym.txt
title:
  Chaperna-Mediated Assembly of Ferritin-Based Middle East Respiratory Syndrome-Coronavirus Nanoparticles

summary:
  Six-week-old female BALB/c mice were immunized with 20 µg/ mouse of the RBD-FR, RBD-[SSG]-FR, or RBD protein generated as described above, or with commercially available MERS-CoV RBD protein (MERS-RBD-005P; eEnzyme) as antigen in BSL-2 facility in YLARC. [RBD-[SSG]-FR, RBD-FR, RBD, and FR (negative control)]-immunized mouse serum inhibited binding of RBD protein to hDPP4 receptor (45, 46) .


id: cord-314574-3e6u4aza
author: Tian, Xiaolong
date: 2020-02-17
extension: .txt
mime: text/plain
words: 1873
sentence: 69
flesch: 46
cache: cache/cord-314574-3e6u4aza.txt
txt: txt/cord-314574-3e6u4aza.txt
title:
  Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody

summary:
  Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan A pneumonia outbreak associated with a new coronavirus of probable bat origin Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies Human monoclonal antibody as prophylaxis for SARS coronavirus infection in ferrets. In previous studies, a number of potent monoclonal antibodies against SARS coronavirus (SARS-CoV) have been identified [3] [4] [5] [6] [7] .


id: cord-297072-f5lmstyn
author: Struck, Anna-Winona
date: 2012-01-16
extension: .txt
mime: text/plain
words: 5112
sentence: 199
flesch: 53
cache: cache/cord-297072-f5lmstyn.txt
txt: txt/cord-297072-f5lmstyn.txt
title:
  A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2

summary:
  Residues of the spike protein (S) Amino acid sequence well as the association and dissociation rates of ligands interacting with protein receptors. A concentration dependent SPR affinity plot was performed with 110 fmol of receptor protein immobilized.


id: cord-263167-es806qhz
author: Rogers, Thomas F.
date: 2020-06-15
extension: .txt
mime: text/plain
words: 4521
sentence: 183
flesch: 46
cache: cache/cord-263167-es806qhz.txt
txt: txt/cord-263167-es806qhz.txt
title:
  Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model

summary:
  In contrast, there are fewer RBD binding antibodies but a larger proportion of these neutralize SARS-CoV-2 pseudovirus. Overall, the data highlight epitope RBD-A as the preferred target for eliciting neutralizing antibodies and that corresponding increases in affinity of mAbs to RBD-A will likely result in corresponding increases in neutralization potency.


id: cord-273891-7w334xgt
author: Kirchdoerfer, Robert N.
title: Receptor binding and proteolysis do not induce large conformational changes in the SARS-CoV spike
date: 2018-03-31
extension: .txt
mime: text/plain
words: 3321
sentence: 104
flesch: 42
cache: cache/cord-273891-7w334xgt.txt
txt: txt/cord-273891-7w334xgt.txt
summary:
  We were 136 further able to identify S1 RBD conformations at the non-ACE2 occupied RBD positions to 137 represent each population of S1 RBD conformations among ACE2-bound S. 138 As hypothesized by previous structural work 15-17,22 , the S1 RBD recognizes ACE2 with 139 an 'up' S1 RBD conformation. Fine sorting of S1 RBD positions of the trypsin-224 cleaved S reveals a very similar distribution of 'up' S1 RBD conformations available for receptor 225 binding as in the uncleaved samples, although we additionally observe a small proportion of S1 226 RBD in the all-'down' conformation (Fig. 5c) .


id: cord-258902-h0wrs01h
author: Liu, Xianglei
date: 2020-09-22
extension: .txt
mime: text/plain
words: 5032
sentence: 187
flesch: 44
cache: cache/cord-258902-h0wrs01h.txt
txt: txt/cord-258902-h0wrs01h.txt
title:
  Enhanced Elicitation of Potent Neutralizing Antibodies by the SARS-CoV-2 Spike Receptor Binding Domain Fc Fusion Protein in Mice

summary:
  The impact of his tag on the detection of RBD binding titer is marginal ( Figure. S2C) . Four groups of 8-10 week old female BALB/c mice (n=5) were immunized twice (day 0 and day 14) subcutaneously with RBD proteins (10 μg/mouse) with or without adjuvant MF59.


id: cord-278869-7zr1118b
author: Ravichandran, Supriya
title: Antibody repertoire induced by SARS-CoV-2 spike protein immunogens
date: 2020-05-13
extension: .txt
mime: text/plain
words: 2386
sentence: 80
flesch: 39
cache: cache/cord-278869-7zr1118b.txt
txt: txt/cord-278869-7zr1118b.txt
summary:
  Immunity Antigenic fingerprinting of H5N1 avian influenza 405 using convalescent sera and monoclonal antibodies reveals potential vaccine and diagnostic 406 targets Vaccines with MF59 Adjuvant Expand the 409 Antibody Repertoire to Target Protective Sites of Pandemic Avian H5N1 Influenza Virus Human antibody 412 repertoire after VSV-Ebola vaccination identifies novel targets and virus-neutralizing IgM 413 antibodies Antigenic Fingerprinting following Primary RSV Infection in Young Children Identifies Novel Antigenic Sites and Reveals Unlinked 416 Evolution of Human Antibody Repertoires to Fusion and Attachment Glycoproteins AS03-adjuvanted H5N1 vaccine promotes antibody diversity 420 and affinity maturation, NAI titers, cross-clade H5N1 neutralization, but not H1N1 cross-subtype 421 neutralization MF59 adjuvant enhances diversity and affinity of antibody-mediated 424 immune response to pandemic influenza vaccines High-Affinity 427 H7 Head and Stalk Domain-Specific Antibody Responses to an Inactivated Influenza H7N7 Vaccine After Priming With Live Attenuated Influenza Vaccine Longitudinal Human Antibody Repertoire against Complete Viral Proteome from Ebola Virus Survivor Reveals Protective Sites for Vaccine Design intravenous immunoglobulin for adults with influenza A or B infection (FLU-IVIG): a double-blind, 437 randomised, placebo-controlled trial Antigenic Fingerprinting of Respiratory Syncytial Virus (RSV)-A-Infected 440 Hematopoietic Cell Transplant Recipients Reveals Importance of Mucosal Anti-RSV G Antibodies 441 in Control of RSV Infection in Humans The 443 COVID-19 vaccine development landscape Characterization of the receptor-445 binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as 446 a viral attachment inhibitor and vaccine A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2 H5 N-terminal beta sheet promotes oligomerization of H7-HA1 that induces better 452 antibody affinity maturation and enhanced protection against H7N7 and H7N9 viruses compared 453 to inactivated influenza vaccine 456 Differential human antibody repertoires following Zika infection and the implications for 457 serodiagnostics and disease outcome 2020) with a single receptor-binding domain (RBD) in the up conformation, wherever available using UCSF Chimera software. Although S2 contains the fusion peptide, it does not appear to be as immunogenic, 186 compared with S1 or RBD, in generating binding antibodies to the intact spike (S1+S2) 187 ectodomain, as observed in both IgG ELISA and SPR.


id: cord-275185-9br8lwma
author: Zeng, Hao
date: 2020-10-06
extension: .txt
mime: text/plain
words: 6621
sentence: 261
flesch: 46
cache: cache/cord-275185-9br8lwma.txt
txt: txt/cord-275185-9br8lwma.txt
title:
  The efficacy assessment of convalescent plasma therapy for COVID-19 patients: a multi-center case series

summary:
  Herein, we performed a retrospective observational study involving eight critical or severe patients with COVID-19 from four designated hospitals in the southwest region of China, aiming to explore the potential efficacy and safety of CP therapy, and to provide more evidence for the quality control of donated plasma and reasonable clinical application of CP transfusion. As the patients have been treated by antiviral drugs and oxygen support before CP therapy, the body temperature, heart rate, and systolic pressure were normal even prior to CP transfusion, and kept unchanged within 5 days after CP transfusion as indicated in Table 4 .


id: cord-281793-tj4m01s4
author: Ho, Mitchell
title: Perspectives on the development of neutralizing antibodies against SARS-CoV-2
date: 2020-05-20
extension: .txt
mime: text/plain
words: 3756
sentence: 151
flesch: 45
cache: cache/cord-281793-tj4m01s4.txt
txt: txt/cord-281793-tj4m01s4.txt
summary:
  Future therapeutic applications could include cocktail therapy by combining Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study The race is on for antibodies that stop the new coronavirus Antibody therapies for the treatment of COVID-19 Isolation of a human monoclonal antibody specific for the receptor binding domain of SARS-CoV-2 using a competitive phage biopanning strategy Induction of neutralizing antibodies by human papillomavirus vaccine generated in mammalian cells Construction and next-generation sequencing analysis of a large phage-displayed VNAR single-domain antibody library from six naive nurse sharks Renin-angiotensin-aldosterone system inhibitors in patients with Covid-19 Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decadelong structural studies of SARS coronavirus The proximal origin of SARS-CoV-2 Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV Human neutralizing antibodies elicited by SARS-CoV-2 infection A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV A human monoclonal antibody blocking SARS-CoV-2 infection Structural and functional analysis of a potent sarbecovirus neutralizing antibody Structural basis for potent neutralization of Betacoronaviruses by single-domain Camelid antibodies Crystal structure of a shark single-domain antibody V region in complex with lysozyme A cold-blooded view of adaptive immunity Ancient species offers contemporary therapeutics: an update on shark VNAR single domain antibody sequences, phage libraries and potential clinical applications General strategy to humanize a Camelid single-domain antibody and identification of a universal humanized nanobody scaffold Phylogenetic network analysis of SARS-CoV-2 genomes Patient-derived mutations impact pathogenicity of SARS-CoV-2 Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 A potent neutralizing human antibody reveals the N-terminal domain of the Spike protein of SARS-CoV-2 as a site of vulnerability Monoclonal antibodies targeting the HR2 domain and the region immediately upstream of the HR2 of the S protein neutralize in vitro infection of severe acute respiratory syndrome coronavirus Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion Therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in Wuhan Neutralization of SARS-CoV-2 spike pseudotyped virus by recombinant ACE2-Ig Inhibition of SARS pseudovirus cell entry by lactoferrin binding to heparan sulfate proteoglycans Glypicans as cancer therapeutic targets Isolation of antibodies to Heparan Sulfate on Glypicans by phage display Human monoclonal antibody targeting the heparan sulfate chains of Glypican-3 inhibits HGF-mediated migration and motility of hepatocellular carcinoma cells Epitope mapping by a Wnt-blocking antibody: evidence of the Wnt binding domain in heparan sulfate Infectious entry and neutralization of pathogenic JC polyomaviruses Human monoclonal antibody combination against SARS coronavirus: synergy and coverage of escape mutants Towards a solution to MERS: protective human monoclonal antibodies targeting different domains and functions of the MERS-coronavirus spike glycoprotein antibodies (including multiple single domain antibodies) that target different epitopes via different mechanisms. The group used a competitive screening strategy to isolate human antibodies from a phage display library.


id: cord-268894-amfv3z2y
author: Nguyen-Contant, Phuong
date: 2020-07-21
extension: .txt
mime: text/plain
words: 4676
sentence: 160
flesch: 45
cache: cache/cord-268894-amfv3z2y.txt
txt: txt/cord-268894-amfv3z2y.txt
title:
  S protein-reactive IgG and memory B cell production after human SARS-CoV-2 infection includes broad reactivity to the S2 subunit

summary:
  Our key findings are as follows: (i) the presence of IgG 223 reactive to the S2 subunit of SARS-CoV-2 in most unexposed subjects, likely reflecting cross-224 reactivity to HCoVs, (ii) markedly increased levels of IgG against the SARS-CoV-2 S and N 225 proteins, including reactivity to the RBD and S2 subunit of S, in convalescent subjects, (iii) 226 increased IgG binding to the S protein of the OC43 HCoV, but not 229E HCoV, in convalescent 227 subjects, reflecting greater cross-reactivity between S2 subunits of betacoronaviruses, (iv) strong 228 formation of IgG MBCs reactive with the RBD and S2 subunit of the SARS-CoV-2 S protein in 229 convalescent subjects, and (v) formation of IgG MBCs reactive with the S protein of OC43, but 230 not 229E, in convalescent subjects, consistent with S2 subunit cross-reactivity between 231 Approximately one-third of our cohort of non-SARS-CoV-2-exposed subjects had low 233 levels of IgG against the SARS-CoV-2 S and N proteins. (D) Comparison of serum 533 IgG concentrations (upper panels) and IgG MBC numbers CoV-2 S (left-hand side) and N (right-hand side) proteins.


id: cord-260334-xo8ruswo
author: New, R.R.C.
title: Antibody-mediated protection against MERS-CoV in the murine model()
date: 2019-07-09
extension: .txt
mime: text/plain
words: 5762
sentence: 193
flesch: 43
cache: cache/cord-260334-xo8ruswo.txt
txt: txt/cord-260334-xo8ruswo.txt
summary:
  Hospital outbreak of Middle East respiratory syndrome coronavirus Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans MERS-CoV origin and animal reservoir Novel betacoronavirus in dromedaries of the Middle East Middle East respiratory syndrome coronavirus (MERS-CoV): animal to human interaction Spiking the MERS-coronavirus receptor Crystal structure of the receptor-binding domain from newly emerged middle east respiratory syndrome coronavirus Structure of MERS-CoV spike receptor-binding domain complexed with human receptor DPP4 A truncated receptor-binding domain of MERS-CoV spike protein potently inhibits MERS-CoV infection and induces strong neutralizing antibody responses: implication for developing therapeutics and vaccines Receptor-binding domain of MERS-CoV with optimal immunogen dosage and immunization interval protects human transduced mice from MERS-CoV infection Evaluation of candidate vaccine approaches for MERS-CoV Introduction of neutralising immunogenncity index to the rational design of MERS coronavirus sub-unit vaccines Recombinant receptor binding domain protein induces partial protective immunity in rhesus macaques against Middle East respiratory syndrome coronavirus challenge MERS-CoV spike protein: targets for vaccines and therapeutics Toward developing a preventive MERS-CoV vaccine-report from a workshop organized by the Saudi Arabia ministry of health and the international vaccine institute Protein coated microcrystals formulated with model antigens and modified with calcium phosphate exhibit enhanced phagocytosis and immunogenicity A new oil-based antigen delivery formulation for both oral and parenteral vaccination Reverse micelle-encapsulated recombinant baculovirus as an oral vaccine against H5N1 infection in mice Dual route vaccination for plague with emergency use applications Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans Severe respiratory illness caused by a novel coronavirus Rapid generation of a mouse model for Middle East respiratory syndrome Real-time reverse transcription-PCR assay panel for middle east respiratory syndrome coronavirus Cutting edge: Mincle is essential for recognition and adjuvanticity of the mycobacterial cord factor and its synthetic analog trehalose-dibehenate Subsequent challenge of the recipient transduced mice by the intra-nasal route with a clinical isolate of the MERS-CoV resulted in a significantly reduced viral load in their lungs, compared with transduced mice receiving a negative control antibody.


id: cord-015235-lv8mll28
author: Kim, Hyun
date: 2014-04-16
extension: .txt
mime: text/plain
words: 5877
sentence: 240
flesch: 53
cache: cache/cord-015235-lv8mll28.txt
txt: txt/cord-015235-lv8mll28.txt
title:
  Functional analysis of the receptor binding domain of SARS coronavirus S1 region and its monoclonal antibody

summary:
  The same amounts of RBD protein and ACE2 antibody were simultaneously incubated with the cells for 30 min and detected with the RBD antibody ( Fig. 4b; column 3). There are many reports of SARS S or RBD protein binding to ACE2 on host cell membrane proteins using an antibody against SARS-CoV and by other methods.


id: cord-253438-k8iqv1jb
author: Li, Yujun
date: 2020-10-27
extension: .txt
mime: text/plain
words: 5444
sentence: 199
flesch: 50
cache: cache/cord-253438-k8iqv1jb.txt
txt: txt/cord-253438-k8iqv1jb.txt
title:
  SARS-CoV-2 and Three Related Coronaviruses Utilize Multiple ACE2 Orthologs and Are Potently Blocked by an Improved ACE2-Ig

summary:
  The numbering is based on human ACE2 protein, and the residues different from the corresponding ones in human ACE2 are highlighted in blue. Recombinant RBD and soluble ACE2 proteins have been shown to potently block SARS-CoV entry (26, 27) .


id: cord-102920-z5q3wo7v
author: Sang, Eric R.
date: 2020-06-28
extension: .txt
mime: text/plain
words: 6466
sentence: 253
flesch: 39
cache: cache/cord-102920-z5q3wo7v.txt
txt: txt/cord-102920-z5q3wo7v.txt
title:
  Integrate Structural Analysis, Isoform Diversity, and Interferon-Inductive Propensity of ACE2 to Refine SARS-CoV2 Susceptibility Prediction in Vertebrates

summary:
  Our current results demonstrate several previously unstudied immunogenetic properties of animal ACE2 genes and imply some domestic animals, including dogs, pigs and cattle/goats, may obtain some immunogenetic diversity to confront SARS-CoV2 infection and face less COVID-19 risk than may have been previously thought. Data show that animal ACE2 gene promoters are evolutionally different in containing IFN-or virus-stimulated response elements (ISRE, PRDI, IFRs, and/or STAT1/3 factors) and cis-elements responsive to pro-inflammatory mediators.


id: cord-261877-4y37676n
author: Xu, Cong
date: 2020-06-30
extension: .txt
mime: text/plain
words: 8815
sentence: 274
flesch: 45
cache: cache/cord-261877-4y37676n.txt
txt: txt/cord-261877-4y37676n.txt
title:
  Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM

summary:
  Unlike the observations made with SARS-CoV and MERS-CoV S trimers, we did not detect S trimer with two RBD domains up with bound ACE2 (Kirchdoerfer et al., 2018; Pallesen et al., 2017) . Our data suggested there is one RBD in the up conformation and is trapped with ACE2 in the S-ACE2 complex; ACE2 can greatly shift the conformational landscape of S trimer, and trigger continuous swing motions of ACE2-RBD in the context of the S trimer resulting in conformational dynamics in S1 subunits.


id: cord-308428-zw26usmh
author: Walter, Justin D.
title: Highly potent bispecific sybodies neutralize SARS-CoV-2
date: 2020-11-10
extension: .txt
mime: text/plain
words: 10557
sentence: 429
flesch: 48
cache: cache/cord-308428-zw26usmh.txt
txt: txt/cord-308428-zw26usmh.txt
summary:
  Although the global resolution of the spike protein in complex with both sybodies is around 3 Å, the local resolution of the RBDs with bound sybodies was only in the range of 6-7 Å, presumably due to conformational flexibility (Fig. S6) . Loop 0.180 Phylogene c tree of RBD sybodies.


id: cord-281005-6gi18vka
author: Singh, Praveen Kumar
date: 2020-09-01
extension: .txt
mime: text/plain
words: 3164
sentence: 130
flesch: 48
cache: cache/cord-281005-6gi18vka.txt
txt: txt/cord-281005-6gi18vka.txt
title:
  Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development

summary:
  4, 5 In the present study, we found that although multiple genetic variants were identified in the same country, yet there were some unique mutations found in a particular country, which suggests that diversity of S protein mutations might have significant role in the pathogenicity of this virus in countries with high or low mortality rates, as proposed by others also. Conclusion S protein is the major target for vaccine development, but several mutations were predicted in the antigenic epitopes of S protein across all genomes available globally.


id: cord-274280-x5s4l0pp
author: Yang, Jinsung
title: Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor
date: 2020-09-11
extension: .txt
mime: text/plain
words: 7353
sentence: 295
flesch: 50
cache: cache/cord-274280-x5s4l0pp.txt
txt: txt/cord-274280-x5s4l0pp.txt
summary:
  Here, we analyze the biophysical properties of the SARS-CoV-2 S-glycoprotein binding, on model surfaces and on living cells, to ACE2 receptors using force-distance (FD) curve-based atomic force microscopy (FD-curve-based AFM) (Fig. 1c) . As SARS-CoV-2 binding to ACE2 receptors is thought to play a key role in the first binding step at the cellular membrane 3 Fig.


id: cord-253447-4w6caxwu
author: Zeng, Xin
date: 2020-04-20
extension: .txt
mime: text/plain
words: 2892
sentence: 127
flesch: 50
cache: cache/cord-253447-4w6caxwu.txt
txt: txt/cord-253447-4w6caxwu.txt
title:
  Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy

summary:
  The wells were washed and blocked with 1% PVA, and then the mixture of antibody library (10 10 pfu per well) and free RBD-His protein (100ng per well) was added. A specific binder of target protein was added during the binding step for the selection of blocking antibodies.


id: cord-024319-isbqs7hg
author: Zeng, Xin
date: 2020-04-30
extension: .txt
mime: text/plain
words: 3061
sentence: 133
flesch: 50
cache: cache/cord-024319-isbqs7hg.txt
txt: txt/cord-024319-isbqs7hg.txt
title:
  Isolation of a human monoclonal antibody specific for the receptor binding domain of SARS-CoV-2 using a competitive phage biopanning strategy

summary:
  Sera from SARS-CoV S-immunized mice, not rabbits or SARS recovered patients, showed modest neutralization activity against SARS-CoV-2 [6, 11] , while sera from COVID-19 recovered patients had no effect on SARS pseudovirus [11] . The wells were washed and blocked with 1% PVA, and then the mixture of antibody library (1×10 10 pfu per well) and free RBD-His protein (100ng per well) was added.


id: cord-256156-mywhe6w9
author: Clausen, Thomas Mandel
title: SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2
date: 2020-09-14
extension: .txt
mime: text/plain
words: 8996
sentence: 344
flesch: 49
cache: cache/cord-256156-mywhe6w9.txt
txt: txt/cord-256156-mywhe6w9.txt
summary:
  To explore if HS, ACE2 and spike interact at the cell surface, we investigated the impact of ACE2 expression on S protein cell binding. Bound protein was washed with buffer and eluted with 0.2 M imidazole in washing buffer.


id: cord-103940-a2cqw8kg
author: Shi, Yuejun
date: 2020-06-09
extension: .txt
mime: text/plain
words: 3221
sentence: 122
flesch: 52
cache: cache/cord-103940-a2cqw8kg.txt
txt: txt/cord-103940-a2cqw8kg.txt
title:
  Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins

summary:
  Mice sera of HCoV-229E S trimer (orange) and HCoV-229E Since the S1 protein is expressed in a monomeric form, RBD is not restricted by 257 We compared the structures of S trimers and RBDs among alpha-coronaviruses 258 (Figs. 1B and 6A) .


id: cord-133453-23rfdkuw
author: Chen, Jiahui
title: Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies
date: 2020-10-13
extension: .txt
mime: text/plain
words: 8197
sentence: 411
flesch: 51
cache: cache/cord-133453-23rfdkuw.txt
txt: txt/cord-133453-23rfdkuw.txt
summary:
  From these studies, we infer that some of S protein mutations may disrupt the binding of antibodies and S protein, which will further affect the efficacy and reliability of vaccines. To investigate the influences of existing S protein mutations on the binding free energy (BFE) of S protein and antibodies, we consider 133 mutations occurred on the S protein RBD which are relevant to the binding of SARS-CoV-2 S protein and antibodies as well as ACE2.


# ent

id: cord-318444-sgm24q1i
sid: 205
eid: 2
type: ORG
entity:
  grftisrdnakntvylqmnslkpedtavyycrvfvgwhyfgqgtqvtvs sb#2 qvqlvesggglvqaggslrlscatsgfpvyqanmhwyrqapgkerewvaaiqsygdgthyadsvk grftisrdnakntvylqmnslkpedtavyycravyvgmhyfgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 205
eid: 3
type: ORG
entity:
  sb#3 qvqlvesggglvqaggslrlscaasgfpvnyktmwwyrqapgkerewvaaiwsyghtthyadsvk grftisrdnakntvylqmnslkpedtavyycvvwvghnyegqgtqvtvs sb#4 qvqlvesggglvqaggslrlscaasgfpvyaqnmhwyrqapgkerewvaaiyshgywtlyadsvk grftisrdnakntvylqmnslkpedtavyycevqvgawytgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 205
eid: 4
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvfsghmhwyrqapgkerewvaailsngdsthyadsvk grftisrdnakntvylqmnslkpedtavyycrvhvgahyfgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 205
eid: 5
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpveqgrmywyrqapgkerewvaaiishgtvtvyadsvk grftisrdnakntvylqmnslkpedtavyycyvyvgaqywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 205
eid: 6
type: ORG
entity:
  qvqlvesggglvqaggslrlscaasgfpvlftymhwyrqapgkerewvaaiwssgnstwyadsvk grftisrdnakntvylqmnslkpedtavyycfvkvgnwyagqgtqvtvs sb#8


id: cord-318444-sgm24q1i
sid: 205
eid: 7
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvnagnmhwyrqapgkerewvaaiqsygrttyyadsvk grftisrdnakntvylqmnslkpedtavyycrvfvgmhyfgqgtqvtvs sb#9 qvqlvesggglvqaggslrlscaasgfpvssstmtwyrqapgkerewvaainsygwethyadsvk grftisrdnakntvylqmnslkpedtavyycyvyvggsyigqgtqvtvs sb#10 qvqlvesggglvqaggslrlscaasgfpvqshymrwyrqapgkerewvaaiestghhtayadsvk grftisrdnakntvylqmnslkpedtavyyctvyvgyeyhgqgtqvtvs sb#11 qvqlvesggglvqaggslrlscaasgfpvetenmhwyrqapgkerewvaaiyshgmwtayadsvk grftisrdntkntvylqmnslkpedtavyycevevgkwyfgqgtqvtvs sb#12 qvqlvesggglvqaggslrlscaasgfpvkasrmywyrqapgkerewvaaiqsfgevtwyadsvk


id: cord-318444-sgm24q1i
sid: 205
eid: 8
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvqaremewyrqapgkerewvaaikstgtytayaysvk grftisrdnakntvylqmnslkpedtavyycyvyvgssyigqgtqvtvs


id: cord-318444-sgm24q1i
sid: 205
eid: 9
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvknfemewyrkapgkerewvaaiqsggvetyyadsvk grftisrdnakntvylqmnslkpedtavyycfvyvgrsyigqgtqvtvs sb#16 qvqlvesggglvqaggslrlscaasgfpvayktmwwyrqapgkerewvaaiesygikwtryadsv kgrftisrdnakntvylqmnslkpedtavyycivwvgaqyhgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 205
eid: 10
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvagrnmwwyrqapgkerewvaaiyssgtyteyadsvk grftisrdnakntvylqmnslkpedtavyychvwvgslykgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 205
eid: 11
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvkharmwwyrqapgkerewvaaidshgdttwyadsvk grftisrdnakntvylqmnslkpedtavyycyvyvgasywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 205
eid: 12
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvnshemtwyrqapgkerewvaaiqstgtvteyadsvk grftisrdnakntvylqmnslkpedtavyycyvyvgssylgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 205
eid: 13
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpveqremewyrqapgkerewvaaidsngnytfyadsvk grftisrdnakntvylqmnslkpedtavyycyvyvgksyigqgtqvtvs


id: cord-318444-sgm24q1i
sid: 205
eid: 14
type: PERSON
entity:
  grftisrdnakntvylqmnslkpedtavyycfvgvgthyagqgtqvtvs sb#23 qvqlvesggglvqaggslrlscaasgfpvyaaemewyrqapgkerewvaaissqgtityyadsvk grftisrdnakntvylqmnslkpedtavyycfvyvgksyigqgtqvsvs sb#25 qvqlvesggglvqaggslrlscaasgfpvhawemawyrqapgkerewvaairsfgssthyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdfgthhyaydywgqgtqvtvs sb#26 qvqlvesggglvqaggslrlscaasgfpvntwwmhwyrqapgkerewvaaitswgfrtyyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdkgmavqwydywgqgtqvtvs sb#27 qvqlvesggglvqaggslrlscaasgfpvyntwmewyrqapgkerewvaaitshgyktyyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdegdmftaydywgqgtqvtvs sb#28 qvqlvesggglvqaggslrlscaasgfpvyhstmfwyrqapgkerewvaaiyssgqhtyyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdsgqwrqeydywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 206
eid: 1
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvehemawyrqapgkerewvaairsmgrktlyadsvkg rftisrdnakntvylqmnslkpedtavyycnvkdfgytwheydywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 206
eid: 2
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvtmawmwwyrqapgkerewvaairsegvrtyyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdygqahayydywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 206
eid: 3
type: LOC
entity:
  qvqlvesggglvqaggslrlscaasgfpvnshfmewyrqapgkerewvaaiqhssgfhtyyadsv kgrftisrdnakntvylqmnslkpedtavyycnvkdtgttedydywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 206
eid: 4
type: PERSON
entity:
  qvqldesggglvqaggslrlscaasgfpvyhawmewyrqapgkerewvaaitssgrhtyyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdagrvynsydywgqgtqvtvs sb#33 qvqlvesggglvqaggslrlscaasgfpvahawmewyrqapgkerewvaaitsygyktyyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdtgtyrfyydywgqgtqvtvs sb#34


id: cord-318444-sgm24q1i
sid: 206
eid: 5
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvwnqtmvwyrqapgkerewvaaiwsmghtyyadsvkg rftisrdnakntvylqmnslkpedtavyycnvkdagvynryydywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 206
eid: 6
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvehywmewyrqapgkerewvaaitsfgyrtyyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdwgfashaydywgqgiqvtvs


id: cord-318444-sgm24q1i
sid: 206
eid: 7
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpeiawemawyrqapgkerewvaairsfgertlyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdfgwqhqeydywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 206
eid: 8
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvyhaymewyrqapgkerewvaaiysngehtyyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdsgsfnqaydywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 206
eid: 9
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvewshmhwyrqapgkerewvaaivskggytlyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdygvhfkrydywgqgtqvtvi


id: cord-318444-sgm24q1i
sid: 207
eid: 1
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvfhvwmewyrqapgkerewvaaidsagwhtyyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdagnttsaydywgqgtqvtvs sb#40


id: cord-318444-sgm24q1i
sid: 207
eid: 2
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvyynwmewyrqapgkerewvaaihsngdetfyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdidaeayaydywgqgtqvtvs sb#41


id: cord-318444-sgm24q1i
sid: 207
eid: 3
type: ORG
entity:
  qvqlvesggglvqaggslrlscaasgfpvyhvwmewyrqapgkerewvaaitssgshtyyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdsgqwrvqydywgqgtqvtvs sb#42 qvqlvesggglvqaggslrlscaasgfpvywhhmhwyrqapgkerewvaaiiswgwyttyadsvk


id: cord-318444-sgm24q1i
sid: 207
eid: 4
type: ORG
entity:
  grftisrdnakntvylqmnslkpedtavyycnvkdhgaqnqmydywgqgtqvtvs sb#45 qvqlvesggglvqaggslrlscaasgfpvyrdrmawyrqapgkerewvaaiysagqqtryadsvk grftisrdnakntvylqmnslkpedtavyycnvkdvghhyeyydywgqgtqvtvs sb#46 qvqlvesggglvqaggslrlscaasgfpvdngymhwyrqapgkerewvaaidsygwhtiyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdkgqmraaydywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 207
eid: 5
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvswhsmywyrqapgkerewvaaifsegdwtyyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdygssyykydywgqgtqvtvs sb#48


id: cord-318444-sgm24q1i
sid: 207
eid: 6
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvsqsvmawyrqapgkerewvaaiyskgqythyadsvk grftisrdnakntvylqmnslkpedtavyycnvkdagssywdydywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 207
eid: 7
type: PERSON
entity:
  qvqlvesgggsvqaggslrlscaasgyidkivylgwfrqapgkeregvaalytlsghtyyadsvk grftvsldnakntvylqmnslkpedtalyycaaateghahalyrlhyywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 207
eid: 8
type: PERSON
entity:
  qvqlvesggglvqaggslrlscaasgfpvyqgemhwyrqapgkerewvaairstgvqtwyadsvk grftisrdnakntvylqmnslkpedtavyycrvwvgthyfgqgtqvtvs sb#52


id: cord-318444-sgm24q1i
sid: 207
eid: 9
type: PERSON
entity:
  qvqlvesgggsvqaggslrlscaasgniqriyylgwfrqapgkeregvaalmtytghtyyadsvk grftvsldnakntvylqmnslkpedtalyycaaayvgaenplpysmygywgqgtqvtvs sb#53 qvqlvesgggsvqaggslrlscaasgqishikylgwfrqapgkeregvaalitrwgqtyyadsvk grftvsldnakntvylqmnslkpedtalyycaaadygasdplwfihylywgqgtqvtvs sb#55 qvqlvesgggsvqaggslrlscaasgkiwtikylgwfrqapgkeregvaalmtrwgytyyadsvk grftvsldnakntvylqmnslkpedtalyycaaanygsnfplaeedywywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 207
eid: 11
type: ORG
entity:
  grftvsldnakntvylqmnslkpedtalyycaaayyfgddiplwweaysywgqgtqvtvs sb#58 qvqlvesgggsvqaggslrlscaasgnistieylgwfrqapgkeregvaalytwhgqtyyadsvk grftvsldnakntvylqmnslkpedtalyycaaarwgrhmplsateysywgqgtqvtvs sb#59 qvqlvesgggsvqaggslrlscaasgniesiyylgwfrqapgkeregvaalwtgdgetyyadsvk grftvsldnakntvylqmnslkpedtalyycaaaawgnsaplttyryyywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 207
eid: 12
type: ORG
entity:
  sb#61 qvqlvesgggsvqaggslrlscaasgfiygitylgwfrqapgkeregvaalvtwngqtyyadsvk grftvsldnakntvylqmnslkpedtalyycaaadwgydwplwdewywywgqgtqvtvs sb#62


id: cord-318444-sgm24q1i
sid: 207
eid: 13
type: PERSON
entity:
  qvqlvesgggsvqaggslrlscaasgtiadikylgwfrqapgkeregvaalmtrwgstyyadsvk grftvsldnakntvylqmnslkpedtalyycaaanyganyplysqqysywgqgtqvtvs sb#63


id: cord-318444-sgm24q1i
sid: 207
eid: 15
type: PERSON
entity:
  qvqlvesgggsvqaggslrlscaasgeiesifylgwfrqapgkeregvaalytyvgqtyyadsvk grftvsldnakntvylqmnslkpedtalyycaaasygaahplsimryyywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 207
eid: 16
type: PERSON
entity:
  qvqlvesgggsvqaggslrlscaasgtiahikylgwfrqapgkeregvaalmtkwgqtyyadsvk grftvsldnakntvylqmnslkpedtalyycaaasyganfplkasdysywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 207
eid: 17
type: PERSON
entity:
  qvqlvesgggsvqaggslrlscaasgsiqaitylgwfrqapgkeregvaalvtwngqtyyadsvk grftvsldnakntvylqmnslkpedtalyycaaadwgydwplwdewywywgqgtqvtvs sb#67 qvqlvesgggsvqaggslrlscaasgsissitylgwfrqapgkeregvaalvtysgntyyadsvk grftvsldnakntvylqmnslkpedtalyycaaatwghswplyndeywywgqgsqvtvs sb#68


id: cord-318444-sgm24q1i
sid: 207
eid: 18
type: PERSON
entity:
  qvqlvesgggsvqaggslrlscaasgsissitylgwfrqapgkeregvaalitvnghtyyadsvk grftvsldnakntvylqmnslkpedtalyycaaaawgyawplhqddywywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 207
eid: 19
type: PERSON
entity:
  qvqlvesgggsvqaggslrlscaasgsissitylgwfrqapgkeregvaalntfngttyyadsvk grftvsldnakntvylqmnslkpedtalyycaaatwgyswpliaeynwywgqgtqvtvs


id: cord-318444-sgm24q1i
sid: 207
eid: 20
type: PERSON
entity:
  qvqlvesgggsvqaggslrlscaasgsissitylgwfrqapgkeregvaalktqagftyyadsvk grftvsldnakntvylqmnslkpedtalyycaaanwgyswplyeaddwywgqgtqvtvs


id: cord-333264-jdvb8px4
sid: 193
eid: 1
type: ORG
entity:
  qvqlvetggglvqpggslrlscaasgftfss vymnwvrqapgkgpewvsrispnsgnigytdsvkgrftisrdnakn tlylqmnnlkpedtalyycaiglnlssssvrgqgtqvtvss ngs


