Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 137 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 5057 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 54 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 133 RBD 108 SARS 43 ACE2 27 Fig 19 MERS 15 figure 10 CoV-2 7 protein 6 COVID-19 5 ELISA 4 antibody 3 site 3 d614 3 cell 3 Spike 3 DPP4 2 rbd 2 patient 2 Supplementary 2 RNA 2 East 2 APN 1 zebrafish 1 virus 1 ty1 1 strain 1 spike 1 selection 1 receptor 1 rbd(s 1 plasma 1 ns1 1 international 1 cr3022 1 covid-19 1 alum 1 ab8 1 VSV 1 VHH 1 TNT 1 THP-1 1 TGEV 1 TBS 1 Supplemental 1 Sb#68 1 Sb#15 1 SR31 1 S55 1 S54 1 S377 Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 5238 protein 3999 antibody 3642 cell 2467 receptor 2374 spike 2187 virus 1894 coronavirus 1821 % 1736 infection 1697 domain 1526 structure 1497 residue 1373 interaction 1371 vaccine 1312 figure 1227 binding 1221 response 1200 study 1148 patient 1076 site 941 analysis 934 assay 924 mouse 869 neutralization 865 mutation 782 sequence 781 model 773 epitope 767 region 749 entry 747 host 745 affinity 721 fusion 704 datum 701 complex 695 result 673 c 672 surface 660 acid 653 antigen 651 s 649 syndrome 637 sample 630 time 624 level 622 day 608 expression 608 cov 602 titer 600 disease Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 7489 SARS 5910 RBD 4918 CoV-2 3094 ACE2 2421 S 2195 CoV 1670 MERS 1526 al 1459 . 1407 Fig 1160 et 790 COVID-19 762 S1 539 S2 514 Fc 487 ELISA 396 sera 365 IgG 356 Figure 349 C 338 RNA 330 Coronavirus 316 Spike 300 Table 296 East 293 Middle 273 PBS 254 IgM 241 T 238 N 225 EM 218 MD 214 NTD 210 IgA 204 China 199 M 198 Supplementary 196 pH 196 RBM 196 PCR 192 mAbs 192 DPP4 191 K 184 Protein 183 PDB 181 Structure 170 A 160 B 155 Nbs 155 CoV-1 Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 2384 we 1040 it 288 they 181 i 131 them 50 us 32 he 24 you 20 itself 13 one 7 themselves 6 rrbd-15 6 qag-2 6 iga1 3 s230 3 igg1 3 hace2 3 ab8 2 s 2 l452 2 iga2 1 ≥100 1 y505a 1 y453f 1 w.-h. 1 u 1 she 1 relion3.1 1 rasp-1 1 protein−protein 1 pro507 1 leu443 1 imagej 1 hrid 1 c526 1 b4galt7 1 asn501 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 19182 be 3445 bind 3038 use 2650 have 1818 show 1573 neutralize 932 base 674 include 650 perform 647 indicate 627 contain 624 express 577 compare 572 block 566 follow 562 identify 558 determine 554 induce 551 find 548 suggest 548 do 483 target 472 observe 471 reveal 464 provide 434 incubate 426 report 409 detect 403 obtain 401 develop 393 mediate 386 describe 385 add 380 generate 380 associate 368 increase 359 purify 358 measure 353 demonstrate 352 test 352 analyze 348 result 345 make 342 form 341 reduce 336 produce 327 inhibit 325 collect 315 confirm 309 cause Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 2043 - 1906 human 1511 viral 1463 high 1364 not 1140 also 921 specific 876 respiratory 768 other 759 anti 723 more 680 severe 666 well 639 structural 638 different 603 immune 584 low 524 further 521 acute 516 respectively 511 then 508 single 474 molecular 469 most 465 however 460 only 456 novel 453 recombinant 453 highly 440 such 429 non 427 monoclonal 417 first 416 similar 416 potent 395 positive 393 clinical 387 potential 376 as 371 convalescent 371 available 328 same 327 previously 326 therapeutic 325 large 323 therefore 318 several 316 small 315 conformational 314 negative Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 175 most 134 high 94 least 82 good 57 Most 47 low 26 large 15 steep 13 great 11 strong 8 short 8 early 7 close 6 late 5 small 3 long 3 RBD+MF59 3 -8 2 topmost 2 simple 2 rASP-1 2 near 2 fast 2 bad 2 W553 2 Ad5hDPP4 1 ~98 1 ~15 1 weak 1 tt 1 quick 1 nAb 1 leftmost 1 hDPP4 1 farth 1 easy 1 clear 1 cheap 1 ccl20 1 big 1 backr 1 VHH-72 1 T49V 1 NS1 1 MOST 1 K986P 1 D539N 1 B100 1 -removal 1 -E Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 294 most 79 least 9 well 2 highest 2 8his 1 worst 1 v617ngly 1 lowest 1 furthest 1 early 1 -j Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 129 doi.org 7 orcid.org 6 www.who.int 6 github.com 5 www.ebi.ac.uk 5 creativecommons.org 4 www.rcsb.org 4 ccg.epfl.ch 3 www.ncbi.nlm.nih.gov 3 www.nature.com 3 www.gisaid.org 3 coronavirus.jhu.edu 3 biorender.com 2 zinc.docking.org 2 www.softberry.com 2 www.megasoftware.net 2 www.mdpi.com 2 www.isrctn.com 2 www.bioinformatics.org 2 web.cbio.uct.ac.za 2 pymol.org 2 pubs.acs.org 2 orcid 2 npg.nature.com 2 joaorodrigues.github.io 2 isaric4c.net 2 creat 1 zinc15.docking.org 1 wwwbiorxivorg 1 www.who 1 www.scottcblanchardlab.com 1 www.rcsb 1 www.pymol.org 1 www.jalview.org 1 www.ja 1 www.imgt.org 1 www.graphpad.com 1 www.fludb.org 1 www.fda.gov 1 www.ensembl.org 1 www.emro.who.int 1 www.dcvmn.org 1 www.cogconsortium.uk 1 www.chemcomp.com 1 www.cgl.ucsf.edu 1 www.cbs 1 www.bioinformatics.babraham.ac.uk 1 www.beiresources.org 1 www 1 virological.org Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 15 http://doi.org/10.1101/2020.08.24.20180877 15 http://doi.org/10.1101/2020.07.27.20162321 14 http://doi.org/10.1101/2020.08.18.20177303 11 http://doi.org/10.1101/2020.10.15.20213512 10 http://doi.org/10.1101/2020.09.07.20190173 9 http://doi.org/10.1101 8 http://doi.org/10.1101/2020.07.15.20154443 7 http://doi.org/10.1101/2020.04.17.20064907 6 http://doi.org/10.1101/2020.06.05.136861 5 http://doi.org/10 5 http://creativecommons.org/ 4 http://doi.org/10.1101/2020.05.17.20104869 3 http://www.nature.com/reprintsPublisher's 3 http://www.ebi.ac.uk/ 3 http://doi.org/10.1101/2020.06.21.20132944 3 http://doi.org/10.1038/s41598-020-74761-y 3 http://ccg.epfl.ch/cgi-bin/pwmtools 2 http://zinc.docking.org/substances/subsets/fda/ 2 http://www.who.int/emergencies/mers-cov/en/ 2 http://www.softberry.com 2 http://www.ncbi.nlm.nih.gov/gene 2 http://www.megasoftware.net 2 http://www.isrctn.com/ISRCTN66726260 2 http://www.gisaid.org 2 http://www.bioinformatics.org 2 http://web.cbio.uct.ac.za/~brejnev 2 http://pymol.org/ 2 http://orcid 2 http://npg.nature.com/ 2 http://joaorodrigues.github.io/ace2-animal-models/ 2 http://github.com/MurrellGroup/Ty1 2 http://doi.org/10.1038/s41467-020-18174-5 2 http://creat 2 http://biorender.com/ 1 http://zinc15.docking.org 1 http://wwwbiorxivorg/content/101101/20200612148726v1 1 http://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ 1 http://www.who.int/emergencies/ 1 http://www.who.int/emer 1 http://www.who.int/blueprint/priority-diseases/en/ 1 http://www.who 1 http://www.scottcblanchardlab.com/software 1 http://www.rcsb.org/structure/6LZG 1 http://www.rcsb.org/pdb/ 1 http://www.rcsb.org/pdb 1 http://www.rcsb.org 1 http://www.rcsb 1 http://www.pymol.org 1 http://www.ncbi.nlm.nih.gov/igblast/ 1 http://www.mdpi.com/2077-0383/9/10/3188/s1 Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 2 consortiumcontact@cogconsortium.uk 1 wangyc@nifdc.org.cn 1 tomzhao@u.northwestern.edu 1 tmandelclausen@health.ucsd.edu 1 research@f1000.com 1 qincf@bmi.ac.cn 1 priyamvada.acharya@duke.edu 1 prem@med.unc.edu 1 n-patankar@northwestern.edu 1 mit666666@pitt.edu 1 mbuehler@mit.edu 1 gaof@im.ac.cn 1 deeptab@arizona.edu 1 chendong@tsinghua.edu.cn 1 anzhenchenfang@163.com Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 177 receptor binding domain 35 receptor binding domains 30 cells were then 26 cov-2 neutralizing antibodies 16 receptor binding motif 15 receptor binding site 12 antibodies block covid-19 12 antibody blocking sars 12 study are available 11 cov neutralizing antibodies 9 study did not 8 residues are critical 7 cov-2 neutralizing antibody 7 protein contains multiple 7 spikes are resistant 6 cells expressing human 6 protein are more 6 protein induces highly 6 protein is highly 5 ace2 expressing hek293 5 antibodies targeting multiple 5 antibodies targeting sars 5 cells expressing ace2 5 cells expressing angiotensin 5 rbd is not 5 rbd was also 5 receptor binding region 4 ace2 is also 4 antibodies neutralize sars 4 cells expressing s 4 cells were co 4 cells were subsequently 4 coronavirus indicating person 4 cov neutralizing antibody 4 cov uses dipeptidyl 4 cov-2 is essential 4 cov-2 is highly 4 domain is responsible 4 patients did not 4 protein is also 4 protein is responsible 4 proteins are highly 4 rbd binding titer 3 ace2 blocking antibodies 3 ace2 does not 3 ace2 is likely 3 ace2 is widely 3 ace2 reveals undiscovered 3 antibodies targeting different 3 cells were further Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 antibodies is not very 1 ace2 are not cross 1 antibodies are not typically 1 antibodies were not able 1 antibody had no effect 1 cells showed no signal 1 cells were not susceptible 1 cov-2 is not due 1 domain is not part 1 domain is not well 1 domain was not part 1 infection are not yet 1 infections are not yet 1 interaction are not well 1 interaction is not available 1 interactions are not promising 1 patients did not yet 1 patients had no effect 1 patients show no detectable 1 protein are no more 1 protein was not due 1 rbd is not able 1 rbd is not as 1 rbd is not complete 1 rbd is not large 1 rbd was not sufficient 1 response was not significantly 1 responses were not adversely 1 s has not yet 1 structure is not yet 1 structure revealed no noticeable 1 structures are no longer 1 study indicated not only 1 study showed no mutations 1 study was not most 1 vaccine does not yet 1 vaccines are not well 1 vaccines are not yet 1 virus is not capable 1 virus showed no change A rudimentary bibliography -------------------------- id = cord-280939-d478p8u6 author = Abe, Kento T. title = A simple protein-based surrogate neutralization assay for SARS-CoV-2 date = 2020-10-02 keywords = ACE2; ELISA; RBD; SARS; Supplemental summary = Here, we present a safe and efficient protein-based assay for the detection of serum and plasma antibodies that block the interaction of the SARS-CoV-2 spike protein receptor binding domain (RBD) with its receptor, angiotensin-converting enzyme 2 (ACE2). Here, we present a safe and efficient protein-based assay for the detection of serum and plasma antibodies that block the interaction of the SARS-CoV-2 spike protein receptor binding domain (RBD) with its receptor, angiotensin-converting enzyme 2 (ACE2). SARS-CoV-2 ELISAs are performed by immobilizing a recombinantly produced viral antigen (such as the spike trimer or RBD) ( Figure 1B and Supplemental Figures 1 and 2; supplemental material available online with this article; https://doi.org/10.1172/jci.insight.142362DS1) (see Methods) onto multiwell plastic plates that are then incubated with diluted patient serum or plasma samples. doi = 10.1172/jci.insight.142362 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 keywords = ACE2; RBD; SARS; figure; protein summary = Based on the structural complementarity and steric impediments between the S protein and human ACE2 (hACE2) protein membranes, we mapped the glycosylation sites of both models [21] [22] [23] [24] and performed molecular dynamics simulations (MDS) by 250 ns to stabilize the glycosylated SARS-CoV2 spike (S) and hACE2 complex (suppl. Given the possibility that occupancy at glycosylated residues or S-RBD binding sites by estrogens could modify the affinity of the SARS-CoV2 virus and alter entry into the cell thereby reducing infectivity, we sought to further examine these interactions using a range of complementary experimental approaches (see Table S1 ). In an effort to explore the potential protective effects of female sex hormones against SARS-CoV-2 infection, we examined the impact of estradiol (17β-diol) and a dietary-derived phytoestrogen (S-equol) on hACE2 structure and protein expression by a combination of in silico modeling, in vitro, and in vivo analysis. doi = 10.1101/2020.07.29.227249 id = cord-356264-q0yqnlyl author = Armijos-Jaramillo, Vinicio title = SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date = 2020-03-23 keywords = RBD; SARS; selection; site summary = With this analysis, we determine a region inside the receptor-binding domain with putative sites under positive selection interspersed among highly conserved sites, which are implicated in structural stability of the viral spike protein and its union with human receptor hACE2. We employ a multidisciplinary approach to look for evidence of diversifying selection on the S-protein gene, and model the interactions between human ACE2 (hACE2) and the RBD of selected coronavirus strains, which ultimately afforded us novel insights detailing virus and host cell interactions. All these experiments were performed again using the S-protein genes of a shorter list of accessions and more distantly related (broad dataset) to SARS-COV-2 (AY304488, AY395003, DQ412043, FJ882957, KY417144, MG772933, MG772934, MN908947, NC_004718) to test the reproducibility of the predicted branches and sites under positive selection. Modeling results suggest that interference with the hot spot 353 could be and effective strategy for inhibiting the recognition of the RBD of the SARS-COV-2 spike protein by its human host receptor ACE2 and hence prevent infections. doi = 10.1101/2020.03.21.001933 id = cord-323324-h2a25xym author = Armijos‐Jaramillo, Vinicio title = SARS‐CoV‐2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date = 2020-05-07 keywords = ACE2; RBD; SARS summary = doi = 10.1111/eva.12980 id = cord-319855-78xmxymu author = BR, Bharath 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 date = 2020-07-01 keywords = ACE2; RBD; SARS summary = doi = 10.12688/f1000research.24143.1 id = cord-262043-66qle52a author = Basit, Abdul title = Truncated human angiotensin converting enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent date = 2020-05-20 keywords = ACE2; RBD; SARS; protein summary = Spike (S) glycoprotein is the structural protein of SARS-CoV-2 located on the envelope surface, involve in interaction with angiotensin converting enzyme 2 (ACE2), a cell surface receptor, followed by entry into the host cell. The protein-protein docking and molecular dynamic simulation showed that tACE2 has higher binding affinity for RBD and form more stabilized complex with RBD than the intact ACE2. We designed a truncated version (tACE2) of ACE2 receptor covering the binding residues and performed protein-protein docking and molecular dynamic simulations to analyze its binding affinity for RBD and complex stability. 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) . doi = 10.1080/07391102.2020.1768150 id = cord-353748-y1a52z8e author = Bhattacharya, Rajarshi title = A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 date = 2021-01-02 keywords = RBD; SARS summary = title: A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 Nisin, a food-grade antimicrobial peptide produced by lactic acid bacteria has been examined for its probable interaction with the human ACE2 (hACE2) receptor, the site where spike protein of SARS-CoV-2 binds. Among the eight nisin variants examined, nisin H, nisin Z, nisin U and nisin A showed a significant binding affinity towards hACE2, higher than that of the RBD (receptor binding domain) of the SARS-CoV-2 spike protein. The present study attempts to investigate the ability of food-grade nisin A and its natural variants to block the interaction between hACE2 and the spike protein of SARS-CoV-2, a key step of COVID-19 disease initiation. The binding affinity of docked structures of all eight variants of nisin in complex with hACE2 was calculated as ΔG derived from analysis with Prodigy for each complex in comparison with the RBD of spike protein of SARS-CoV-2. doi = 10.1016/j.virol.2020.10.002 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 keywords = RBD; SARS summary = doi = 10.1101/2020.09.04.282558 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 keywords = ACE2; RBD summary = We compare the interaction between the human ACE2 receptor and the SARS-CoV-2 spike protein with that of other pathogenic coronaviruses using molecular dynamics simulations. Herein, we analyze the binding of several CoV RBDs to ACE2 with molecular dynamics (MD) simulations and compare the stability, relative interaction strength, and dynamics of the interaction between the viral spike protein and the human ACE2 receptor. While the sequence identity between the RBDs of COVID-19 and SARS-2002 is 73% (Table 1) , we observe a significantly higher residue substitution rate at the interaction interface with the ACE2 receptor. Our MD simulation analysis reveals that the SARS-des has a substantially lower interaction scores with ACE2 (median of -2199.2, Fig. S2) , as expected for an optimized human ACE2-binding RBD design. We relied on the crystal structure of the spike protein receptor-binding domain from a SARS coronavirus designed human strain complexed with the human receptor ACE2 (PDB 3SCI, resolution 2.9Å) as a template for comparative modeling. doi = 10.1101/2020.03.10.986398 id = cord-340960-abanr641 author = Brigger, D. title = Accuracy of serological testing for SARS‐CoV‐2 antibodies: first results of a large mixed‐method evaluation study date = 2020-09-30 keywords = ELISA; RBD; SARS summary = In a mixed‐design evaluation study, we compared the diagnostic accuracy of serological immunoassays that are based on various SARS‐CoV‐2 proteins and assessed the neutralizing activity of antibodies in patient sera. A total of 54 randomly selected sera from individuals who were tested positive in either of the three ELISA immunoassays as well as 6 negative controls were assessed in a live SARS-CoV-2 neutralization assay (all collected in April 2020). Recombinantly expressed RBD has been used to establish an in-house ELISA for the detection of IgM and IgG anti-SARS-CoV-2 antibodies in human serum samples (supplementary Fig. 1a,b) . A total of 54 randomly selected sera from individuals who were tested positive in either of the three ELISA immunoassays as well as 6 negative controls were assessed in a live SARS-CoV-2 neutralization assay using ACE2-expressing Vero-E6 cells (34 inpatient samples, and 26 samples of medical personnel). doi = 10.1111/all.14608 id = cord-299783-8ti6r0eh author = Bruni, M. title = Persistence of anti-SARS-CoV-2 antibodies in non-hospitalized COVID-19 convalescent health care workers date = 2020-08-01 keywords = RBD; SARS; Spike summary = doi = 10.1101/2020.07.30.20164368 id = cord-318018-ybdkp398 author = Bruni, Margherita title = Persistence of Anti-SARS-CoV-2 Antibodies in Non-Hospitalized COVID-19 Convalescent Health Care Workers date = 2020-10-01 keywords = COVID-19; RBD; SARS; Spike summary = Sera from healthcare workers affected by non-severe COVID-19 were longitudinally collected over four weeks, and compared to sera from patients hospitalized in Intensive Care Units (ICU) and SARS-CoV-2-negative subjects for the presence of IgM, IgG and IgA antibodies as well as soluble pro-inflammatory mediators in the sera. Our data show that humoral immune responses against SARS-CoV-2 correlated with disease severity in terms of both antibody titers, persistence over time and serum levels of pro-inflammatory cytokines. Here we show that humoral immune responses against SARS-CoV-2 correlated with disease severity in terms of both antibody titers, persistence over time and serum levels of pro-inflammatory mediators. Moreover, we showed that the vast majority of COVID-19 mildly symptomatic patients analyzed in the study halved their anti-RBD antibody titers after 4 weeks from viral negativization, thus confirming the short lifespan of humoral immune responses against SARS-CoV-2. doi = 10.3390/jcm9103188 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 keywords = ACE2; RBD; SARS; figure summary = Deep mutagenesis of the isolated receptor-binding domain (RBD) by yeast surface display 44 has easily identified mutations in S that retain high expression and ACE2 affinity, yet are no longer bound 45 by monoclonal antibodies and confer resistance (19) . An alternative protein-based antiviral to monoclonal antibodies is to use soluble ACE2 (sACE2) as a 56 decoy to compete for receptor-binding sites on the viral spike (6, (22) (23) (24) (25) of diverse SARS-associated betacoronaviruses that use ACE2 for entry. The sequence 162 diversity observed among natural betacoronaviruses, which display high diversity at the ACE2 binding 163 site, is therefore replicated in the deep mutational scan, which predicts the SARS-CoV-2 spike tolerates 164 substantial genetic diversity at the receptor-binding site for function. From this accessible sequence 165 diversity SARS-CoV-2 might feasibly mutate to acquire resistance to monoclonal antibodies or 166 engineered decoy receptors targeting the ACE2-binding site. doi = 10.1101/2020.10.18.344622 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 keywords = ACE2; BFE; RBD; SARS; antibody summary = By integrating genetics, biophysics, deep learning, and algebraic topology, we deduce that some of the mutations such as M153I, S254F, and S255F may weaken the binding of S protein and antibodies, and potentially disrupt the efficacy and reliability of antibody therapies and vaccines in the development. The vaccination mechanism is to stimulate the primary immune response of the human body, which will activate T cells and B cells to generate the antibodies and long-lived memory cells that prevent infectious diseases, which is one of the most effective and economical means for combating with COVID-19 at this stage. Notably, understanding how mutations have changed the SARS-CoV-2 structure, function, infectivity, activity, and virulence is of great importance for coming up with life-saving strategies in virus control, containment, prevention, and medication, especially in the antibodies and vaccines development. Next, we study the BFE changes ∆∆G induced by 39 mutations on the SARS-CoV-2 S protein RBD for the antibody Fab 2-4 (PDB: 6XEY) in Figure 6 . doi = nan id = cord-260406-qvc2fb0c author = Chen, Long title = Severe Acute Respiratory Syndrome Coronavirus‐2 Spike Protein Nanogel as a Pro‐Antigen Strategy with Enhanced Protective Immune Responses date = 2020-10-26 keywords = RBD summary = doi = 10.1002/smll.202004237 id = cord-252919-647zcjgu author = Chen, Yun title = Structure analysis of the receptor binding of 2019-nCoV date = 2020-02-17 keywords = ACE2; RBD; SARS summary = We performed a structural analysis of the receptor binding domain (RBD) of spike glycoprotein responsible for entry of coronaviruses into host cells. Structural analysis suggests that ACE2 from these animals can potentially bind RBD of 2019-nCoV, making them all possible natural hosts for the virus. In this study, we analyzed the structure of spike glycoprotein RBD of 2019-nCoV and identified a unique feature that potentially allows a high affinity binding to ACE2 in human cells. There are 16 amino acid residues in SARS-CoV RBD that are directly in contact with ACE2, of which 8 are conserved in 2019-nCoV (see Fig. 1B ). Among the 16 amino acid residues in RBD of SARS that are in contact with ACE2, 14, 14, 7, and 8 are shared by SARSv, civet, bat, and 2019-nCoV, respectively (Fig. 1B) . Our study suggests unique structural features of the spike glycoprotein RBD of 2019-nCoV that confers potentially higher affinity binding for its receptor than found with SARS-CoV. doi = 10.1016/j.bbrc.2020.02.071 id = cord-327654-9g8zcxaa author = Chi, Xiaojing title = Humanized single domain antibodies neutralize SARS-CoV-2 by targeting the spike receptor binding domain date = 2020-09-10 keywords = CoV-2; Fig; RBD; SARS summary = doi = 10.1038/s41467-020-18387-8 id = cord-342557-a7q8vp8m author = Chowdhury, Surid Mohammad title = Antiviral Peptides as Promising Therapeutics against SARS-CoV-2 date = 2020-10-23 keywords = RBD; SARS; figure summary = [Image: see text] Over 50 peptides, which were known to inhibit SARS-CoV-1, were computationally screened against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. Peptides that showed higher S protein-binding affinity compared to the α-helix (AH) of the ACE2 peptidase were further analyzed with molecular dynamics (MD) simulation and the structure− activity relationship (SAR) in order to achieve a high-affinity binder for the S protein. 30 Initially, stepwise multiple linear regression (MLR) was performed considering these properties as variables to predict the calculated binding affinity of the test peptides with the RBD of the SARS CoV-2 spike protein. All 51 peptides were docked to the RBD of the SARS CoV-2 spike protein using PatchDock. Various residues including Glu484, Tyr449, and Tyr505 present in the ACE2 binding site of the RBD were involved in noncovalent interaction with the antiviral peptides ( Figure 1a) . doi = 10.1021/acs.jpcb.0c05621 id = cord-256156-mywhe6w9 author = Clausen, Thomas Mandel title = SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2 date = 2020-09-14 keywords = ACE2; Fig; RBD; SARS; cell; protein summary = We show that SARS-CoV-2 spike protein interacts with both cellular heparan sulfate and angiotensin converting enzyme 2 (ACE2) through its Receptor Binding Domain (RBD). Unfractionated heparin, non-anticoagulant heparin, heparin lyases, and lung heparan sulfate potently block spike protein binding and/or infection by pseudotyped virus and authentic SARS-CoV-2 virus. In this report, we show that the ectodomain of the SARS-CoV-2 spike (S) protein interacts with cell surface HS through the Receptor Binding Domain (RBD) in the S1 subunit. Adjacent to the ACE2 binding site and exposed in the RBD lies a group of positively-charged amino acid residues that represents a potential site that could interact with heparin or heparan sulfate ( Fig. 1A and Suppl. The SARS-CoV-2 spike protein depends on cellular heparan sulfate for cell binding. Heparin inhibits cellular invasion by SARS-CoV-2: structural dependence of the interaction of the surface protein (spike) S1 receptor binding domain with heparin doi = 10.1016/j.cell.2020.09.033 id = cord-331786-wgt7kg6f author = Diego-Martin, Borja title = Pilot production of SARS-CoV-2 related proteins in plants: a proof of concept for rapid repurposing of indoors farms into biomanufacturing facilities date = 2020-10-13 keywords = Fig; RBD; SARS; antibody summary = For this purpose, we tested our ability to produce, in the framework of an academic lab and in a matter of weeks, milligram amounts of six different recombinant monoclonal antibodies against SARS-CoV-2 in Nicotiana benthamiana. In parallel, we also produced the recombinant SARS-CoV-2 N protein and its Receptor Binding Domain (RBD) in planta and used them to test the binding specificity of the recombinant mAbs. Finally, for two of the antibodies we assayed a simple scale-up production protocol based on the extraction of apoplastic fluid. Finally, we performed sandwich ELISA tests of sybody17 and nanobody72 ( Fig 5E and Fig 5F, respectively) using the total and concentrated apoplastic fluid as detection reagent against serial dilutions of crude plant extracts from RBD-producing plants, showing that this simple antibody preparation can be directly employed in detection procedures without the need of additional purification steps. doi = 10.1101/2020.10.13.331306 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 keywords = RBD; SARS; VHH summary = doi = 10.1038/s41598-020-74761-y id = cord-285900-3rr0j5tk author = Du, Lanying title = Introduction of neutralizing immunogenicity index to the rational design of MERS coronavirus subunit vaccines date = 2016-11-22 keywords = Fig; MERS; NII; RBD summary = doi = 10.1038/ncomms13473 id = cord-328003-yovp8squ author = Duan, Liangwei title = The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens date = 2020-10-07 keywords = ACE2; CoV-2; RBD; SARS; protein summary = Here, we provide a comprehensive overview of the wealth of research related to the SARS-CoV-2 S glycoprotein biosynthesis, structure, function, and antigenicity, aiming to provide useful insights into the design and development of the S protein-based vaccines as well as therapeutics to prevent or treat the ongoing global spread of SARS-CoV-2/COVID-19. Prefusion structures of human coronavirus HKU1 (HCoV-HKU1) and mouse hepatitis virus S protein ectodomains without two consecutive proline mutations reveal only fully closed conformation (37, 42) , similar to that observed for a full-length, wild-type prefusion form of the SARS-CoV-2 S glycoprotein (41) . Therefore, SARS-CoV-2 evades immune surveillance also through conformational masking, which is well-documented for HIV-1 (43, 44) ; while at the same time, the S protein could transiently sample the functional state to engage ACE2, consistent with the notion that the fusion glycoprotein of highly pathogenic viruses have evolved to perform its functions while evading host neutralizing antibody responses. doi = 10.3389/fimmu.2020.576622 id = cord-310636-y7n22ykt author = Garcia-Beltran, W. F. title = COVID-19 neutralizing antibodies predict disease severity and survival date = 2020-10-20 keywords = SARS; covid-19; figure; international; rbd summary = doi = 10.1101/2020.10.15.20213512 id = cord-267001-csgmc155 author = George, Parakkal Jovvian title = The Potency of an Anti-MERS Coronavirus Subunit Vaccine Depends on a Unique Combinatorial Adjuvant Formulation date = 2020-05-27 keywords = MERS; RBD; alum; figure summary = Moreover, immunization with rASP-1 co-administered with the alum-adjuvanted RBD vaccine in separate sites resulted in an enhanced frequency of TfH and GC B cells within the draining lymph nodes, both of which were positively associated with the titers of the neutralizing antibody response related to anti-MERS-CoV protective immunity. When the total IgG response to the MERS-RBD antigen was studied using the MERS-CoV S1 protein as the target protein, we found that although the RBD-specific total IgG antibody titers were ~8 times higher in mice that were vaccinated by co-administrating rASP-1 and the alum-adjuvanted RBD vaccine in separate sites (G6-142,525 end point titer), they were not significantly different from those elicited by immunization with RBD + rASP-1 + alum administered in a single inoculum (G5-18,149 end point titer), or with the alum-adjuvanted RBD vaccine (G4-53,104 end point titer; Figure S1A ). doi = 10.3390/vaccines8020251 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 keywords = ACE2; RBD; SARS summary = Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier coronavirus SARS-COV in 2002 via extensive molecular dynamics (MD) simulations. 7 Based on the sequence similarity between RBD of nCOV-2019 and SARS-COV and also the tight binding between RBD of nCOV-2019 and ACE2, it is most probable that nCOV-2019 uses this receptor on human cells to gain entry into the body. The focus of this article is to elucidate the differences between the interface of SARS-COV and nCOV-2019 with ACE2 to understand with atomic resolution the interaction mechanism and hotspot residues at the RBD/ACE2 interface using long-timescale molecular dynamics (MD) simulation. The binding energetics between ACE2 and the RBD of SARS-COV, nCOV-2019 and all its mutant complexes were investigated by the MMPBSA method. Computational Simulations Reveal the Binding Dynamics between Human ACE2 and the Receptor Binding Domain of SARS-CoV-2 Spike Protein doi = 10.1101/2020.06.27.175448 id = cord-346670-34wfy52f author = Gobeil, Sophie M-C. title = D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction date = 2020-10-12 keywords = RBD; SARS; d614 summary = Most structures of the SARS-CoV-2 S ectodomain currently available include two mutations, one to disrupt the furin cleavage site (RRAR to GSAS = S-GSAS), and a double proline mutation (PP) of residues 986-987, designed to prevent conformational change to the post-fusion state (Wrapp et al., 2020) . While the SARS-CoV-2 S ectodomain construct that includes mutations of residues K986 and V987, between the HR1 and CH subdomains (S2 domain), to prolines (PP) (named S-GSAS/PP in this study) (Figure 1 ) is widely used in the field, the origin of this PP construct was based upon the stabilization of the pre-fusion conformation of other coronavirus spikes (Pallesen et al., 2017; Walls et al., 2020; Wrapp et al., 2020) . Similar to observations made with the S-GSAS/D614G S ectodomain structure, the RBD up/down motion in the furin-cleaved G614 S ectodomain was associated with a movement in the SD1 domain and in the region of the RBD-to-NTD linker that joined the SD1 b sheet ( Figure 7C, S8B) . doi = 10.1101/2020.10.11.335299 id = cord-314676-ndke9agh author = Gollapalli, Pavan 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 date = 2020-11-04 keywords = ACE2; RBD; S54; S55; SARS summary = doi = 10.1080/07391102.2020.1841681 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 keywords = SARS; rbd(s; virus summary = doi = 10.1002/cbic.202000618 id = cord-348455-vcxalkeo author = Graham, N. R. 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. date = 2020-07-22 keywords = RBD; SARS summary = 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. date: 2020-07-22 The receptor-binding domain of the CoV spike (RBD-S) protein is important in host cell recognition and infection and antibodies targeting this domain are often neutralizing. We first piloted our antigen preps for the RBD-S IgG screening assay using serum 81 samples from a PCR-confirmed severe COVID-19 patient (defined as admission to the Intensive 82 Care Unit, ICU) who was admitted to the hospital 10 days following symptom onset and based 83 on an early report suggesting that SARS-CoV-2 could trigger antibody responses in this 84 timeframe (24). Anti-S titers in patients with a negative RBD-S test were 138 generally low and in RBD-positive samples, followed the same trends as RBD-reactivity, 139 providing further confirmation of robust serological responses to SARS-CoV-2 during acute 140 COVID-19. doi = 10.1101/2020.07.15.20154443 id = cord-351760-698voi9y author = Han, Hui-Ju title = Neutralizing Monoclonal Antibodies as Promising Therapeutics against Middle East Respiratory Syndrome Coronavirus Infection date = 2018-11-30 keywords = DPP4; MERS; RBD summary = The receptor-binding domain (RBD) in the spike protein of MERS-CoV is a major target, and mouse, camel, or human-derived neutralizing mAbs targeting RBD have been developed. In vivo study demonstrated that prophylaxis with m336 reduced virus titers in the lung of rabbits infected with MERS-CoV [15] , and m336 also provided transgenic mice expressing human DPP4 with full prophylactic and therapeutic protection from MERS-CoV [16] . A Conformation-Dependent Neutralizing Monoclonal Antibody Specifically Targeting Receptor-Binding Domain in Middle East Respiratory Syndrome Coronavirus Spike Protein Prophylaxis with a Middle East Respiratory Syndrome Coronavirus (MERS-CoV)-Specific Human Monoclonal Antibody Protects Rabbits From MERS-CoV Infection Passive Transfer of a Germline-like Neutralizing Human Monoclonal Antibody Protects Transgenic Mice Against Lethal Middle East Respiratory Syndrome Coronavirus Infection Human Neutralizing Monoclonal Antibody Inhibition of Middle East Respiratory Syndrome Coronavirus Replication in the Common Marmoset 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 doi = 10.3390/v10120680 id = cord-319590-f9qcabcx author = Han, Yanxiao title = Computational Design of ACE2-Based Peptide Inhibitors of SARS-CoV-2 date = 2020-04-14 keywords = RBD; SARS summary = doi = 10.1021/acsnano.0c02857 id = cord-333264-jdvb8px4 author = Hanke, Leo title = An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction date = 2020-09-04 keywords = ACE2; Fig; RBD; SARS; cell; ty1 summary = Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. The S ectodomain was purified from filtered supernatant on Streptactin XT resin (IBA Lifesciences), followed by size-exclusion chromatography on a Superdex 200 in 5 mM Tris pH 8, 200 mM NaCl. The RBD domain (RVQ-VNF) of SARS-CoV-2 was cloned upstream of an enterokinase cleavage site and a human IgG1 Fc. This plasmid was used to transiently transfect FreeStyle 293F cells using the FreeStyle MAX reagent. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 doi = 10.1038/s41467-020-18174-5 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 keywords = ELISA; July; RBD; SARS summary = Here we have developed novel flexible ELISA-based assays for specific detection of SARS-CoV-2 antibodies against the receptor-binding domain (RBD): An antigen sandwich-ELISA relevant for large population screening and three isotype-specific assays for in-depth diagnostics. Detection of IgM, IgA and IgG antibodies against SARS-CoV-2 protein N was evaluated by analyzing 136 positive samples and 174 negative controls and ROC curve analyses were assessed to estimate the assay performance . To provide a better insight into antibody seroconversion during SARS-CoV-2 infection and reactivity against different locations on protein S and protein N, we conducted IgM, IgA and IgG detection in 90 positive samples against 14 protein fragments and short peptides located on the protein S and protein N structures, full-length RBD, protein S and protein N (Figure 2A ). We have developed an ELISA-based platform for detection SARS-CoV-2 antibodies comprising an indirect RBD S-ELISA for pan Ig detection and direct ELISAs for in-depth analyses of the IgM, IgA and IgG isotype responses towards RBD and protein N. doi = 10.1101/2020.07.27.20162321 id = cord-323514-jaom3p6s author = He, Yuxian 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 keywords = R441A; RBD; SARS summary = Abstract The spike (S) protein of severe acute respiratory syndrome coronavirus (SARS-CoV) has two major functions: interacting with the receptor to mediate virus entry and inducing protective immunity. Coincidently, the receptor-binding domain (RBD, residues 318–510) of SAR-CoV S protein is a major antigenic site to induce neutralizing antibodies. We also demonstrated that the RBD-Fc bearing R441A mutation could not bind to soluble and cell-associated angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV and failed to block S protein-mediated pseudovirus entry, indicating that this point mutation also disrupted the receptor-binding motif (RBM) in the RBD. In this study, we used the RBD-Fc as a model to study how a single residue mutation in the RBD can abolish the major function of full-length S protein, since this molecule can efficiently bind to the receptor ACE2 and contains multiple conformation-dependent epitopes (Conf I-VI) capable of inducing highly potent neutralizing antibodies [29] . doi = 10.1016/j.bbrc.2006.03.139 id = cord-296657-mymndjvd author = Higuchi, Yusuke title = High affinity modified ACE2 receptors prevent SARS-CoV-2 infection date = 2020-09-16 keywords = ACE2; RBD; SARS summary = The extracellular domain of modified ACE2 fused to the Fc region of the human immunoglobulin IgG1 had stable structure and neutralized SARS-CoV-2 pseudotyped lentivirus and authentic virus with more than 100-fold lower concentration than wild-type. Engineering ACE2 decoy receptors with directed evolution is a promising approach to develop a SARS-CoV-2 neutralizing drug that has affinity comparable to monoclonal antibodies yet displaying resistance to escape mutations of virus. Three cycles of screening resulted in an identification of mutant ACE2 clones with more than 100-fold higher binding affinity to the RBD and lower half-maximal inhibitory concentration (IC50) for SARS-CoV-2 pseudotyped lentivirus as well as authentic virus. We engineered ACE2 to bind the RBD of the SARS-CoV-2 spike protein with the combination of surface display of mutagenized library and fluorescence-activated cell sorting (FACS) to perform the evolution in 293T human cells. doi = 10.1101/2020.09.16.299891 id = cord-281793-tj4m01s4 author = Ho, Mitchell title = Perspectives on the development of neutralizing antibodies against SARS-CoV-2 date = 2020-05-20 keywords = ACE2; RBD; SARS summary = Crossreactive antibodies (e.g., 47D11, S309, and VHH-72) that bind highly conserved epitopes on the RBDs of SARS-CoV and SARS-CoV-2 could have broad neutralization activities against viral infection. The receptor binding domain (RBD) of the SARS-CoV-2 S protein contains several novel residues that might be introduced through recombination with the pangolin coronavirus, indicating a possible critical step in the evolution of the ability of SARS-CoV-2 to infect humans [10] . isolated a human monoclonal antibody (named "rRBD-15") that inhibits the interaction of the RBD of SARS-CoV-2 and the ACE2 and neutralizes the pseudovirus infection [5] . The structure complex of 47D11 and the RBD (or the S1/S protein) would reveal a novel conserved site on the RBD for broad-neutralizing antibodies against SARSr-CoVs. In addition to 47D11, another human antibody (S309) isolated from memory B cells of a SARS survivor infected in 2003 neutralizes SARS-CoV-2 [18] . doi = 10.1093/abt/tbaa009 id = cord-333465-cha7ndv5 author = Horspool, A. M. title = Interplay of antibody and cytokine production reveals CXCL-13 as a potential novel biomarker of lethal SARS-CoV-2 infection date = 2020-08-31 keywords = August; RBD; SARS summary = 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. We evaluated anti-193 SARS-CoV-2 antibody production to 3 antigens (RBD, N, and S1) in 82 in-patients 194 Table 1 ) by developing a novel rapid-ELISA technique. Our survey of SARS-CoV-2 positive patients demonstrated that antibody (IgG) 198 production to RBD, N, and S1 proteins developed over the first 10 to 20 days post-199 symptom onset (Figure 1a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. To accurately assess 223 differences in antibody production independently of disease outcome, we quantified anti-224 SARS-CoV-2 IgG production in patients who survived infection grouped by biological sex, 225 . . https://doi.org/10.1101/2020.08.24.20180877 doi: medRxiv preprint significantly increased in patients that did not survive SARS-CoV-2 infection compared to 272 those that did (Figure 4d ). doi = 10.1101/2020.08.24.20180877 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 keywords = RBD; SARS summary = Our group is developing a two-pronged approach to advance recombinant protein-based vaccines to prevent COVID-19 caused by SARS-CoV-2 and other coronavirus infections. One vaccine is based on a yeast-derived (Pichia pastoris) recombinant protein comprised of the receptor-binding domain (RBD) of the SARS-CoV formulated on alum and referred to as the CoV RBD219-N1 Vaccine. In addition to their low cost and suitability for use in public immunization programs in lowand middle-income countries, we pursued RBD recombinant protein-based vaccines as a technology to maximize safety relative to other platforms, such as virus vectors that have previously been found to induce immune enhancement. Optimization of the Production Process and Characterization of the Yeast-Expressed SARS-CoV Recombinant Receptor-Binding Domain (RBD219-N1), a SARS Vaccine Candidate Potential for developing a SARS-CoV receptor-binding domain (RBD) recombinant protein as a heterologous human vaccine against coronavirus infectious disease (COVID)-19 Yeast-Expressed SARS-CoV Recombinant Receptor-Binding Domain (RBD219-N1) Formulated with Alum Induces Protective Immunity and Reduces Immune Enhancement doi = 10.1371/journal.pntd.0008548 id = cord-309898-sju15hev author = Hu, Yiwen title = Comparative analysis of nanomechanical features of coronavirus spike proteins and correlation with lethality and infection rate date = 2020-11-02 keywords = MERS; RBD; SARS summary = doi = 10.1016/j.matt.2020.10.032 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 keywords = RBD; SARS summary = A subset of anti-spike (10 of 32) and over half of anti-nucleocapsid (19 of 35) antibodies cross-reacted with other betacoronaviruses tested and harboured extensive somatic mutations, indicative of an expansion of memory B cells upon SARS-CoV-2 infection. The MAbs with 161 strong anti-RBD binding have a relatively long heavy chain CDR3 length (50% 162 binding concentration <0.5 µg/ml versus >0.5 µg/ml, p=0.03, two-tailed Mann-163 Whitney test; Supplemental Figure 3 The 32 anti-spike glycoprotein MAbs were systematically examined by plaque 173 reduction neutralisation (PRNT) assay for neutralisation of wild type SARS-CoV-2 174 virus (see methods; summarised in Table 1 ). Potent neutralising antibodies to the RBD of SARS-CoV-2 spike glycoprotein were 188 identified and we thus analyse the blockade of the ACE2-RBD interaction by anti-189 RBD antibodies in two assays ( Figure 3 , Table 1 The structure of VHH72-Fc bound to RBD is known (17) and its footprint on the 198 RBD does not overlap that of ACE2, so inhibition is thought to occur by steric 199 hindrance. doi = 10.1101/2020.08.28.267526 id = cord-329011-spiuqngp author = Huang, Yuan title = Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19 date = 2020-08-03 keywords = ACE2; CoV-2; RBD; SARS summary = The spike (S) protein of SARS-CoV-2, which plays a key role in the receptor recognition and cell membrane fusion process, is composed of two subunits, S1 and S2. A large number of glycosylated S proteins cover the surface of SARS-CoV-2 and bind to the host cell receptor angiotensinconverting enzyme 2 (ACE2), mediating viral cell entry [8] . The SARS-CoV-2 S protein is highly conserved among all human coronaviruses (HCoVs) and is involved in receptor recognition, viral attachment, and entry into host cells. Structure of the S1 subunit The binding of virus particles to cell receptors on the surface of the host cell is the initiation of virus infection; therefore, receptor recognition is an important determinant of viral entry and a drug design target. Therefore, the development of antibodies targeting this functional motif may cross-bind and neutralize these two viruses and related CoVs. Antiviral peptides prevent SARS-CoV-2 membrane fusion and can potentially be used for the prevention and treatment of infection. doi = 10.1038/s41401-020-0485-4 id = cord-256572-sqz8yc7b author = Huo, Jiandong title = Neutralization of SARS-CoV-2 by destruction of the prefusion Spike date = 2020-05-06 keywords = ACE2; RBD; SARS; cr3022 summary = The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric Spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2 (ACE2), initiating conformational changes that drive membrane fusion. We find that monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and report the crystal structure at 2.4 Å of the Fab/RBD complex. Potent nanomolar affinity neutralising human monoclonal antibodies against the SARS-CoV RBD have been identified that attach at the ACE2 receptor binding site (including M396, CR3014 and 80R (Ter Meulen et al., 2006; Sui et al., 2004; Zhu et al., 2007) ). We determined the crystal structure of the SARS-CoV-2 RBD-CR3022 Fab complex (see Methods and Table S3 ) to investigate the relationship between the binding epitopes of ACE2 and CR3022. Full interpretation of the detailed interactions between CR3022 and the RBD was enabled by the second crystal form which diffracted to high resolution, 2.4 Å, and the structure of which was refined to give an R-work/R-free of 0.213/0.239 and good stereochemistry (Methods, Table S3, Figure S5 ). doi = 10.1101/2020.05.05.079202 id = cord-338517-1mxcssjj author = Ishay, Yuval title = Antibody response to SARS‐Co‐V‐2, diagnostic and therapeutic implications date = 2020-08-26 keywords = COVID-19; RBD; SARS; antibody; patient summary = The phage display method, allowing rapid and wide display of proteins directly correlated to their associated genes, can detect NAbs against SARS-CoV from both naïve and immune antibody libraries, capable of blocking the binding of S1 domain, thereby showing virus neutralization and prophylaxis capability either in vitro or in the animal models (31, 33, 36) . Another method, possibly allowing the production and utilization of existing NAbs, may include the use of Epstein-Barr virus (EBV) transformation of human B cells to improve the isolation of NAbs from the memory B cells harvested from the SARS-CoV infected patients (11) . Experimental and clinical data on the use of convalescent plasma products and humanized monoclonal antibodies for H5N1 influenza infection have also shown positive outcomes, and this treatment was proposed as a mean for overcoming anti-viral drug resistance (62, 79, 80) . In a study involving 20 patients with severe pandemic influenza A (H1N1) 2009 virus infection, administration of convalescent plasma reduced respiratory tract viral load, serum cytokine response, and mortality (81) . doi = 10.1002/hep4.1600 id = cord-301347-22lt6h40 author = Jarvis, Matthew C. title = Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus date = 2016-01-01 keywords = PEDV; RBD; strain summary = Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. Despite excising a large portion of the genome prior to analysis, the Bayesian trees illustrate two distinct entries of PEDV into the US and characterize the evolution of PEDV compared to other CoVs. Modeling of the pAPN RBD region has revealed that Asian strains have increasing diversity compared to previously developed vaccines, and the variability in both the American and Asian strains needs to be considered for future vaccine development. Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene doi = 10.1016/j.prevetmed.2015.10.020 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 keywords = COVID-19; RBD; RNA; SARS summary = With increasing structural data of key proteins in both SARS-CoV-2 and the host, such as the spike glycoprotein (S), the main protease (M pro ), RNA-dependent RNA polymerase (RdRp), and human angiotensin-converting enzyme 2 (hACE2), the structure-based design of new drugs has emerged as the most promising antiviral strategy. Several structure-based drug discovery studies have investigated the interaction of inhibitors in the substrate-binding pockets of SARS-CoV-2 M pro ( Figure 3C ) (Dai et al., 2020; Jin et al., 2020; Zhang et al., 2020b) . Because most inhibitors occupy the substrate binding pocket of SARS-CoV-2 FIGURE 4 | CryoEM structure of RdRp in complex with cofactors (nsp7 and nsp8), RNA template, and remdesivir. In addition, we provided structural insights into the mechanism of action of well-characterized drugs targeting the interaction between hACE2 and the spike protein of SARS-CoV-2 for viral entry, as well as M pro and RdRp for viral replication. doi = 10.3389/fmicb.2020.01723 id = cord-285758-c18arb6s author = Jiang, Shibo title = SARS Vaccine Development date = 2005-07-17 keywords = RBD; SARS summary = The spike (S) protein of SARS-CoV is the major inducer of neutralizing antibodies, and the receptor-binding domain (RBD) in the S1 subunit of S protein contains multiple conformational neutralizing epitopes. (30) reported that mucosal immunization of African green monkeys with an attenuated parainfluenza virus expressing S protein resulted in production of neutralizing antibodies and protected animals from infection by challenge with SARS-CoV. These findings suggest that RBD contains the major neutralizing epitopes in the S protein and is an ideal SARS vaccine candidate because RBD contains the receptor-binding site, which is critical for virus attachment to the target cell for infection (15, (17) (18) (19) . 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) 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 doi = 10.3201/eid1107.050219 id = cord-292578-co5essuw author = Johnson, Marina title = Evaluation of a novel multiplexed assay for determining IgG levels and functional activity to SARS-CoV-2 date = 2020-08-02 keywords = RBD; SARS summary = doi = 10.1016/j.jcv.2020.104572 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 keywords = RBD; SARS; figure summary = doi = 10.1101/2020.05.17.20104869 id = cord-306438-db2rqz4d author = Kalathiya, Umesh title = Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site date = 2020-05-14 keywords = ACE2; RBD; SARS; figure; spike summary = doi = 10.3390/jcm9051473 id = cord-015235-lv8mll28 author = Kim, Hyun title = Functional analysis of the receptor binding domain of SARS coronavirus S1 region and its monoclonal antibody date = 2014-04-16 keywords = ACE2; Fig; RBD; SARS summary = The receptor-binding domain (RBD) positioned in S1 can specifically bind to angiotensin-converting enzyme 2 (ACE2) on target cells, and ACE2 regulates the balance between vasoconstrictors and vasodilators within the heart and kidneys. Infection of SARS-CoV is initiated by binding of the S protein to the angiotensin-converting enzyme 2 (ACE2) functional receptor expressed on target cells (Li et al. Our cellular enzyme-linked immunosorbent assay (ELISA) and competitive binding assay using a polyclonal ACE2 antibody indicated that our prepared recombinant RBD fusion protein binds to various tissues as well as NIH3T3 and HEK293 cells through ACE2. After washing with PBS, the RBD fusion protein was incubated for 1 h at room temperature to bind with the ACE2 molecules on the cell membranes. Next, we examined whether RBD binding was blocked by the ACE2 antibody in a Western blot using mouse tissue cell lysates with a pair of membranes. doi = 10.1007/s13258-014-0186-9 id = cord-276833-haci44cy author = Kim, Ju 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 keywords = HBD; RBD; THP-1 summary = We analyzed the mechanisms by which HBD 2 primes innate antiviral immunity and polarized activation of macrophage-like THP-1 cells using the receptor-binding domain (RBD) of Middle East respiratory syndrome coronavirus (MERS-CoV) spike protein (S RBD) as a model antigen. We previously reported that HBD 2 promotes an antiviral innate immune response in macrophage-like THP-1 cells and elicits an enhanced Ag-specific and virus-neutralizing antibody (Ab) response in vivo using the receptor binding domain (RBD) of MERS-CoV spike protein (S RBD) as a model Ag (Kim et al., 2018) . In this study, we investigated the mechanism by which HBD 2 enhances the type I IFN immune response in THP-1 cells by modulating Nod2 signaling pathways using HBD 2-conjugated S RBD of MERS-CoV. HBD 2-conjugated Ag stimulates the Nod2 signaling procedure, which leads to type I IFN production in macrophage-like THP-1 cells MERS-CoV infection inhibits the production of IFN-α/β and the host antiviral immune response . doi = 10.1016/j.imbio.2019.05.004 id = cord-280941-ds6x0yym author = Kim, Young-Seok title = Chaperna-Mediated Assembly of Ferritin-Based Middle East Respiratory Syndrome-Coronavirus Nanoparticles date = 2018-05-17 keywords = MERS; RBD; RNA; figure summary = The receptor-binding domain (RBD) of Middle East respiratory syndrome-coronavirus (MERS-CoV) was fused with the RNA-interaction domain (RID) and bacterioferritin, and expressed in Escherichia coli in a soluble form. The concentration of the ion Fe(2+), salt, and fusion linker also contributed to the assembly in vitro, and the stability of the NPs. The kinetic "pace-keeping" role of chaperna in the super molecular assembly of antigen monomers holds promise for the development and delivery of NPs and virus-like particles as recombinant vaccines and for serological detection of viral infections. Taken together, the results confirmed the immunologically relevant conformation of the MERS-CoV RBD displayed on the hybrid ferritin particles, and the crucial role of RNA in controlling the kinetic pathway for the assembly of viral antigen monomers into stable NPs. To evaluate the immunogenicity of ferritin-based NPs, BALB/c mice (n = 5) were immunized with RBD, RBD-FR, and RBD-[SSG]-FR NPs antigens. doi = 10.3389/fimmu.2018.01093 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 keywords = RBD; SARS summary = The viral spike glycoprotein (S) utilizes angiotensin-converting enzyme 2 (ACE2) as a host protein receptor and mediates fusion of the viral and host membranes, making S essential to viral entry into host cells and host species tropism. Subsequent studies of the highly pathogenic human coronavirus S proteins of SARS-64 CoV 15,22 and MERS-CoV 17,22 showed that these viral S1 RBD do indeed sample an ''up'' 65 conformation where the receptor-binding site is accessible. 70 To examine the hypothesized conformational transitions induced by proteolysis and 71 receptor binding, we used single-particle cryo-EM to determine structures of S in uncleaved, 72 S1/S2 cleaved and ACE2-bound states. Three-dimensional classification of the S1 RBD 73 positions and corresponding atomic protein models revealed that neither ACE2-binding nor 74 trypsin cleavage at the S1/S2 boundary induced substantial conformational changes in the CoV may use a distinct mechanism of FP2 membrane insertion. Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein 381 reveal a prerequisite conformational state for receptor binding doi = 10.1101/292672 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 keywords = Fig; RBD; SARS summary = The data demonstrate high prevalence of spike-and RBD-specific IgM and IgA, similar to that of IgG1, in plasma/serum from COVID-19 patients and their significant contributions to virusneutralizing activities. In Fig. 3 , comparing levels of total Ig with the different Ig isotypes showed a highly significant correlation with IgG1 for both Abs specific for spike and RBD indicating that IgG1 is the major isotype induced by SARS-CoV-2 infection. To ask directly to what extent Abs of different isotypes mediate neutralization, we evaluated the neutralization activities of IgM, IgG, and IgA fractions purified from plasma from five COVID-19-convalescent individuals (RP#1-5). Several SARS-CoV-2 vaccine candidates tested in animal models and humans were shown to induce IgG responses against spike and RBD as well as virus neutralizing activities, but in many of these studies, the induction of other Ig isotypes was not evaluated 46-49 . doi = 10.1101/2020.08.18.20177303 id = cord-333703-1ku3jc9s author = Kraus, Aurora title = A zebrafish model for COVID-19 recapitulates olfactory and cardiovascular pathophysiologies caused by SARS-CoV-2 date = 2020-11-08 keywords = ACE2; COVID-19; CoV-2; RBD; SARS; figure; zebrafish summary = Exposure of larvae to SARS-CoV-2 Spike (S) receptor binding domain (RBD) recombinant protein was sufficient to elevate larval heart rate and treatment with captopril, an ACE inhibitor, reverted this effect. In mice and humans, ace2 expression is detected in 121 sustentacular cells, olfactory stem cells known as horizontal and globose basal cells in the 122 olfactory epithelium, and vascular cells (pericytes) in the olfactory bulb (Brann et al., 2020 The present study reports for the first time that zebrafish larvae exposed to SARS-CoV-2 appear 134 to mount innate immune responses that resemble cytokine responses of mild COVID-19 patients. 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 doi = 10.1101/2020.11.06.368191 id = cord-339724-roj8ksvc author = Lan, Jiaming 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 date = 2014-11-18 keywords = A+C; I+C; MERS; RBD summary = 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 Interestingly, robust RBD-specific antibody and T-cell responses were induced in mice immunized with the rRBD protein in combination with IFA and CpG ODN, but low level of neutralizing antibodies were elicited. In this study, different adjuvants combination regimens including alum, IFA, CpG and poly(I:C) were compared in an effort to promote balance between Th1 and Th2 immune response to bystander rRBD antigen spanning residues 367-606 of MERS-CoV S in a murine model to develop an effective vaccine against MERS-CoV infection. The results indicated that rRBD protein combined with any adjuvant, including alum, IFA, CpG or poly(I:C), could induce a RBD-specific IgG antibody response in the majority of mice after the second immunisation. doi = 10.1371/journal.pone.0112602 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 keywords = RBD; SARS; d614 summary = doi = 10.1016/j.cell.2020.07.012 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 keywords = Fig; RBD; SARS summary = doi = 10.1101/2020.06.09.143438 id = cord-300847-ycuiso0g author = Li, Wei title = Rapid selection of a human monoclonal antibody that potently neutralizes SARS-CoV-2 in two animal models date = 2020-06-02 keywords = Fig; RBD; SARS summary = We identified panels of fully human monoclonal antibodies (mAbs) from eight large phage-displayed Fab, scFv and VH libraries by panning against the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. By using phage display we have previously identified a number of potent fully human mAbs (m396, m336, m102.4) against emerging viruses including severe acute respiratory syndrome coronavirus (SARS-CoV) (4) , Middle East respiratory syndrome coronavirus (MERS-CoV) (5) and henipaviruses (6, 7) , respectively, which are also highly effective in animal models of infection (8) (9) (10) (11) ; one of them was administered on a compassionate basis to humans exposed to henipaviruses and successfully evaluated in a clinical trial (12) . 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. doi = 10.1101/2020.05.13.093088 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 keywords = -fc; ACE2; RBD; SARS; ab8; figure summary = It potently neutralized mouse adapted SARS-CoV-2 in wild type mice at a dose as low as 2 mg/kg and exhibited high prophylactic and therapeutic efficacy in a hamster model of SARS-CoV-2 infection, possibly enhanced by its relatively small size. To identify potent neutralizing V H s against SARS-CoV-2, we panned our large (10 11 clones) and diverse phage-displayed human V H antibody library against recombinant RBD. One of those V H s, ab8, in an Fc (human IgG1, crystallizable fragment) fusion format, showed potent neutralization activity and specificity against SARS-CoV-2 both in vitro and in two animal models. They also suggest that the double mutations Q498T/P499Y on RBD did not influence V H -Fc ab8 binding and contribute to the validation of the mouse adapted SARS-CoV-2 model for evaluation of neutralizing antibody efficacy. In conclusion, we identified a fully human antibody V H domain that shows strong competition with ACE2 for binding to RBD and potent neutralization of SARS-CoV-2 in vitro and in two animal models. doi = 10.1016/j.cell.2020.09.007 id = cord-340472-9ijlj4so author = Li, Wenhui title = Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2 date = 2005-03-24 keywords = ACE2; RBD; SARS summary = Figure 3B -D shows three views of the crystal structure of human ACE2, in which residues that convert rat ACE2 to an efficient SARS-CoV receptor are shown in red, and additional residues whose alteration interferes with S1-Ig association are shown in yellow. (C) Murine leukemia viruses (MLV) expressing green fluorescent protein (GFP), lacking its endogenous envelope glycoprotein (MLV-GFP), and pseudotyped with the S protein of SARS-CoV (TOR2 isolate) were incubated with HEK293T cells transfected with plasmids encoding the indicated human or rat ACE2 variants. We have shown that entry is the primary barrier to SARS-CoV infection of murine Surface plasmon resonance experiments in which the indicated RBD-Ig TOR2 variants shown in Figure 6B bound to immobilized anti-human antibody were assayed for association with soluble human ACE2. S-protein alterations at residues 479 and 487 are important for high-affinity association with human ACE2, and for efficient infection of cells expressing this receptor. doi = 10.1038/sj.emboj.7600640 id = cord-253438-k8iqv1jb author = Li, Yujun title = SARS-CoV-2 and Three Related Coronaviruses Utilize Multiple ACE2 Orthologs and Are Potently Blocked by an Improved ACE2-Ig date = 2020-10-27 keywords = ACE2; Fig; RBD; SARS summary = We found that ACE2 orthologs of a wide range of domestic and wild mammals, including camels, cattle, horses, goats, sheep, cats, rabbits, and pangolins, were able to support cell entry of SARS-CoV-2, suggesting that these species might be able to harbor and spread this virus. In this study, we found that ACE2 orthologs of a wide range of domestic and wild animals can support cell entry of SARS-CoV-2 and three related coronaviruses, providing insights into identifying animal hosts of these viruses. The RBD of Bat-CoV RaTG13 then showed a binding profile significantly different and narrower than the other three RBDs. Note that human ACE2 and ACE2 orthologs of some domestic animals, including camels, cattle, horses, goats, sheep, cats, and rabbits, support efficient binding to all the four tested RBDs, suggesting that these ACE2 orthologs might be generally functional for supporting cell entry of the four tested viruses. doi = 10.1128/jvi.01283-20 id = cord-281536-8y7yxcp4 author = Lim, Hocheol 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 date = 2020-10-08 keywords = FMO; RBD; SARS summary = doi = 10.1038/s41598-020-73820-8 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 keywords = RBD summary = To evaluate the effect of specific antibodies on RP status, we compared the levels of anti-SARS-CoV-2 IgG to the S, RBD, HR1-HR2, N, and M proteins in these patients during their convalescent period ( Fig. 1c; Fig. S3 ). The P value was calculated using a two-tailed Mann-Whitney U test the level of IgM to the RBD protein among these recovered patients also correlated with the S, HR1-HR2, and N proteins (r = 0.67, p < 0.0001; r = 0.56, p < 0.0001; and r = 0.60, p < 0.0001, respectively) (Fig. S6b) . In addition, a positive correlation was also observed between age and IgG level to the RBD, S, HR1-HR2, and N proteins (r = 0.38, P = 0.0077; r = 0.40, P = 0.0055; r = 0.45, P = 0.0017; and r = 0.44, P = 0.0021, respectively; Fig. S7 ), indicating the important role of age in the generation of specific binding antibodies. The online version of this article (https://doi.org/10.1038/s41423-020-00528-0) contains supplementary material.Competing interests: The authors declare no competing interests. doi = 10.1038/s41423-020-00528-0 id = cord-258902-h0wrs01h author = Liu, Xianglei title = Enhanced Elicitation of Potent Neutralizing Antibodies by the SARS-CoV-2 Spike Receptor Binding Domain Fc Fusion Protein in Mice date = 2020-09-22 keywords = 293T; RBD; SARS summary = title: Enhanced Elicitation of Potent Neutralizing Antibodies by the SARS-CoV-2 Spike Receptor Binding Domain Fc Fusion Protein in Mice The cell-cell fusion assay results correlated well with the virus neutralization potency and could be used for high-throughput screening of large panels of anti-SARS-CoV-2 antibodies and vaccines without the requirement of live virus infection in BSL3 containment. Based on its highly homology to SARS-CoV, SARS-CoV-2 RBD is corroborated to contain immune dominant epitopes capable of eliciting antibodies that can neutralize viral infection and block viral entry by competing hACE2 Pseudovirus neutralization assay was then performed by incubation of SARS-CoV-2 pseudovirus with serially diluted mice serum for 1h at 37 °C, followed by addition of the mixture into pre-seeded 293T-ACE2 cells. On day 0 (pre-immunization), day 13 and day 27, mouse sera were collected and analyzed for RBD binding, pseudovirus and live virus neutralization, and cell-cell fusion inhibition. doi = 10.1016/j.vaccine.2020.09.058 id = cord-263481-w5ytp1q7 author = Lokman, Syed Mohammad title = Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach date = 2020-06-02 keywords = CoV-2; RBD; SARS summary = MERS-CoV uses dipeptidyl peptidase-4 (DPP4) as entry receptor [11] whereas SARS-CoV and SARS-CoV-2 utilize ACE-2 (angiotensin converting enzyme-2) [12] , abundantly available in lung alveolar epithelial cells and enterocytes, suggesting S glycoprotein as a potential drug target to halt the entry of SARS-with remarkable properties like glutamine-rich 42 aa long exclusive molecular signature (DSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIE) in position 983-1024 of polyprotein 1ab (pp1ab) [16] , diversified receptor-binding domain (RBD), unique furin cleavage site (PRRAR↓SV) at S1/S2 boundary in S glycoprotein which could play roles in viral pathogenesis, diagnosis and treatment [17] . There is growing evidence that spike protein, a 1273 amino acid long glycoprotein having multiple domains, possibly plays a major role in SARS-CoV-2 pathogenesis. In this study, we have analyzed 320 genomic sequences of SARS-CoV-2 to identify mutations between the available genomes followed by the amino acid variations in the glycoprotein S to foresee their impact on the viral entry to host cell from structural biology viewpoint. doi = 10.1016/j.meegid.2020.104389 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 keywords = CD26; MERS; RBD; SARS summary = Here we delineate the molecular basis of this specific interaction by presenting the first crystal structures of both the free receptor binding domain (RBD) of the MERS-CoV spike protein and its complex with CD26. Here we delineate the molecular basis of this specific interaction by presenting the first crystal structures of both the free receptor binding domain (RBD) of the MERS-CoV spike protein and its complex with CD26. Sequence alignment indicates, among betacoronaviruses, a possible structural conservation for the region homologous to the MERS-CoV RBD core, but a high variation in the external receptor binding motif region for virus-specific pathogenesis such as receptor recognition. Sequence alignment indicates, among betacoronaviruses, a possible structural conservation for the region homologous to the MERS-CoV RBD core, but a high variation in the external receptor binding motif region for virus-specific pathogenesis such as receptor recognition. doi = 10.1038/nature12328 id = cord-326282-uxn64olw author = Lu, Maolin title = Real-time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles date = 2020-09-13 keywords = RBD; SARS summary = doi = 10.1101/2020.09.10.286948 id = cord-297747-kifqgskc author = Lupala, Cecylia S. title = Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein date = 2020-03-27 keywords = ACE2; RBD; SARS summary = Using homology modeling and molecular dynamics (MD) simulation methods, we report here the detailed structure of the ACE2 in complex with the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. The simulation data further revealed critical residues at the complex interface and provided more details about the interactions between the SARS-CoV-2 RBD and human ACE2. When this study was started, neither the crystal structure of the SARS-CoV-2 spike protein nor the RBD segment were determined, so the homology modeling approach was applied to construct the model of the SARS-CoV-2 spike RBD in complex with the human ACE2 binding domain (denoted as CoV2-RBD/ACE2 in the following). Although the crystal structure and the predicted model of the CoV2-RBD/ACE2 complex provide important information about the binding interactions at the molecular interfaces, MD simulations can extend the knowledge to a dynamics regime in a fully solvated environment. doi = 10.1101/2020.03.24.005561 id = cord-300784-4jeaqqn9 author = Ma, Huan title = COVID-19 diagnosis and study of serum SARS-CoV-2 specific IgA, IgM and IgG by a quantitative and sensitive immunoassay date = 2020-04-22 keywords = RBD; SARS summary = doi = 10.1101/2020.04.17.20064907 id = cord-335316-x2t5h5gu author = Madariaga, M. L. L. title = Clinical predictors of donor antibody titer and correlation with recipient antibody response in a COVID-19 convalescent plasma clinical trial date = 2020-06-23 keywords = COVID-19; antibody; plasma; rbd summary = This was a prospective open label clinical study to assess the feasibility, safety and immunological impact of delivering anti-SARS-CoV-2 convalescent plasma to hospitalized patients aged 18 years or older with severe or life-threatening COVID-19 disease within 21 days from the onset of their illness. Univariate regression analysis for antibody titer (anti-RBD and anti-spike) was conducted against age, sex, body mass index (BMI), previous pregnancy, previous blood donation, blood type, symptoms (fever, cough, sore throat, dyspnea, abdominal pain, aguesia, anosmia, fatigue, myalgia, headache), co-morbidities (respiratory, cardiovascular, renal, diabetes, autoimmune disease, cancer, liver disease), smoking history, travel in the past 3 months to the United States, Asia or Europe, symptom duration, interval from symptoms resolution to plasma donation, and hospitalization. To determine predictors of anti-RBD and anti-spike antibody titer, we performed best subset multivariable analysis including age, sex, blood type, history of previous blood donation, fever, cough, fatigue, myalgia, symptom duration, hospitalization and travel in the United States within the past 3 months. doi = 10.1101/2020.06.21.20132944 id = cord-323967-2mo915u1 author = Miersch, Shane title = Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations date = 2020-11-01 keywords = Fig; RBD; SARS summary = doi = 10.1101/2020.10.31.362848 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 keywords = ACE2; RBD; SARS; VSV summary = doi = 10.1101/2020.06.18.158196 id = cord-291420-40xsypzt author = Nelson-Sathi, Shijulal title = Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction date = 2020-10-01 keywords = RBD; SARS summary = title: Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction Formation of a stable binding interface between the Spike (S) protein Receptor Binding Domain (RBD) of SARS-CoV-2 and Angiotensin-Converting Enzyme 2 (ACE2) of host actuates viral entry. In silico structure modelling of interfaces induced by mutations on residues which directly engage ACE2 or lie in the near vicinity revealed molecular rearrangements and binding energies unique to each RBD mutant. The structural analysis of the mutated spike glycoprotein of SARS-CoV-2 RBD domain was done to assess the impact of interface amino acid residue mutations on binding affinity towards the human ACE2 (hACE2) receptor. Comparative analysis of structures showed key differences in all three binding clusters of SARS-CoV-2 RBD wild type and mutant interfaces with human or mouse ACE2 (Figure 2C, 2D and Table S1 ). doi = 10.1101/2020.05.02.071811 id = cord-260334-xo8ruswo author = New, R.R.C. title = Antibody-mediated protection against MERS-CoV in the murine model() date = 2019-07-09 keywords = MERS; MF59; RBD summary = Murine antisera with neutralising activity for the coronavirus causative of Middle East respiratory syndrome (MERS) were induced by immunisation of Balb/c mice with the receptor binding domain (RBD) of the viral Spike protein. To test the neutralising capacity of these antisera in vivo, susceptibility to MERS-CoV was induced in naive recipient Balb/c mice by the administration of an adenovirus vector expressing the human DPP4 receptor (Ad5-hDPP4) for MERS-CoV, prior to the passive transfer of the RBD-specific murine antisera to the transduced mice. The data gained indicate that this dual-route vaccination with novel formulations of the RBD-Fc, induced systemic and mucosal anti-viral immunity with demonstrated in vitro and in vivo neutralisation capacity for clinical strains of MERS-CoV. We have used this transduced mouse model to test the capacity of the antiserum derived from the dual route immunisation to neutralise MERS-CoV in vivo, by passive transfer prior to challenge with the EMC2012 strain and we have demonstrated a significant reduction in viral load in lung tissue in transduced mice. doi = 10.1016/j.vaccine.2019.05.074 id = cord-268894-amfv3z2y author = Nguyen-Contant, Phuong title = S protein-reactive IgG and memory B cell production after human SARS-CoV-2 infection includes broad reactivity to the S2 subunit date = 2020-07-21 keywords = RBD; SARS summary = doi = 10.1101/2020.07.20.213298 id = cord-292883-7hvq9qaj author = Nguyen-Contant, Phuong title = S Protein-Reactive IgG and Memory B Cell Production after Human SARS-CoV-2 Infection Includes Broad Reactivity to the S2 Subunit date = 2020-09-25 keywords = RBD; SARS summary = doi = 10.1128/mbio.01991-20 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 keywords = RBD; SARS summary = In this study, we collected blood from COVID-19 patients who have recently become 5 virus-free and therefore were discharged, and analyzed their SARS-CoV-2-specific antibody 6 and T cell responses. NP-and S-RBD-specific 9 IgM and IgG antibodies were both detected in the sera of newly discharged patients, 10 compared with healthy donor groups. Anti-SARS-CoV-2 IgG antibodies were also more 11 obviously observed than IgM in the follow-up patients (#9-14), when compared with healthy 12 donors ( Figure 1B ). As shown in Figure 3C , compared with healthy donors, 25 the numbers of IFN-γ-secreting NP-specific T cells in patients #1, 2, 4, 5 and 8 were much 26 higher than other patients, suggesting that they had developed SARS-CoV-2-specific T cell responses. More interestingly, when combining all 14 patients in our analysis, there 9 was a significant correlation between the neutralizing antibody titers and the numbers of NPIn this study, we characterized SARS-CoV-2-specific humoral and cellular immunity in 2 recovered patients. doi = 10.1016/j.immuni.2020.04.023 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 keywords = 588-fc; MERS; RBD; S377 summary = doi = 10.1016/j.vaccine.2018.02.065 id = cord-320238-qbjrlog1 author = Okba, Nisreen M. A. title = Particulate multivalent presentation of the receptor binding domain induces protective immune responses against MERS-CoV date = 2020-05-29 keywords = MERS; RBD; figure summary = doi = 10.1080/22221751.2020.1760735 id = cord-332948-h297ukuu author = Olotu, Fisayo A. 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. date = 2020-10-16 keywords = CoV-2; RBD; SARS; protein; site summary = authors: Olotu, Fisayo A.; Omolabi, Kehinde F.; Soliman, Mahmoud E.S. 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. 30 Identification of other functional (allosteric) sites on the prefusion S protein could present another dynamic and effective approach of preventing SARS-CoV-2 infectivity relative to its interaction with the host cell ACE2 and proteases. 53 Relatively, this study was implemented to (i) identify potential druggable sites across the S1 and S2 domains of the SARS-CoV-2 S protein other than the RBD-hACE2 interface (ii) perform high-throughput (virtual) screening of ~1500 FDA approved drugs against the most druggable site(s) (iii) investigate the binding dynamics and interaction mechanisms of the compounds and their consequential effects on the S-protein RBD-ACE2 complex. We believe this systematic study will be able to provide structural and molecular insights into possible allosteric sites on SARS-CoV-2 S protein suitable for selective targeting and structureComputational methodologies doi = 10.1016/j.imu.2020.100451 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 keywords = ACE2; Fig; RBD; SARS summary = doi = 10.1101/2020.06.16.155457 id = cord-332855-u0amf1oh author = Parsons, Lisa M. title = Glycosylation of the viral attachment protein of avian coronavirus is essential for host cell and receptor binding date = 2019-03-22 keywords = Fig; M41; RBD; site summary = In silico docking experiments with the recently published cryo-EM structure of the M41 IBV spike protein and our glycosylation results revealed a potential ligand receptor site that is ringed by four glycosylation sites that dramatically impact ligand binding. However, the Beaudette strain is a cell culture-adapted strain, is nonvirulent in chickens (15) , and does not bind chicken tissues known to be important for infectivity (11) , making it difficult to extrapolate these results to clinically relevant IBVs. To characterize and assess the role that glycosylation plays when interacting with host tissues through the RBD of pathogenic IBV strain M41, we used a combination of molecular and analytical techniques, including histochemistry, ELISA, circular dichroism (CD), MS, and docking analyses as listed in Table 1 . Six of the 10 glycosylation sites in the RBD domain of IBV M41 were essential for binding to chicken trachea tissue and an ELISA-presented sialylated oligosaccharide ligand. doi = 10.1074/jbc.ra119.007532 id = cord-287205-k64svq6n author = Pollet, Jeroen 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 date = 2020-11-05 keywords = Alhydrogel; RBD; RBD219-N1C1; SARS summary = doi = 10.1101/2020.11.04.367359 id = cord-309182-t9ywnshj author = Premkumar, Lakshmanane title = The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients date = 2020-06-11 keywords = Fig; RBD; SARS summary = doi = 10.1126/sciimmunol.abc8413 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 keywords = ACE2; RBD; SARS summary = A deep mutational scan of ACE2 expressed on human cells identified mutations that increase S affinity and guided the engineering of a potent and broad soluble receptor decoy. • The experimental mutational landscape of ACE2 for binding the RBD of SARS-CoV-2 provides a blueprint for engineering high affinity decoy receptors. Following FACS selection of the human culture to enrich a cell population with high binding activity for SARS-CoV-2 protein S, RNA transcripts were isolated and Illumina sequenced. The deep mutational scan of ACE2 revealed that mutations can indeed be found to enhance binding toward SARS-CoV-2 RBD (Figure 2) , suitable for engineering high affinity soluble decoy receptors [15] . A soluble ACE2 variant that combines three mutations, called sACE2 2 .v2.4, was found to be highly expressed, is a stable monodisperse dimer, binds SARS-CoV-2 S with picomolar affinity and potently neutralizes infection of a susceptible cell line by authentic virus. doi = 10.1080/14789450.2020.1833721 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 keywords = ACE2; CoV-2; MERS; RBD; SARS summary = The essential surface glycoprotein of SARS-CoV-2 known as spike (S) protein, essential for host cell receptor binding, showed only 72% similarity with SARS-CoV at the nucleotide level. Comparative genome analysis of RaTG13, a virus from a Rhinolophusaffinis (i.e. horseshoe) bat sampled from Yunnan province in China in 2013, with SARS-CoV-2, showed that SARS-CoV-2 has 96% similarity at the nucleotide sequence level . Later, it was found that the disease was caused by a virus designated as a novel human coronavirus, MERS-CoV, phylogenetic data showed that it belonged to lineage C of the Betacoronavirusgenus and was highly similar to bat coronaviruses HKU4 (Tylonycterispachypus) and HKU5 (Pipistrelluspipistrellus; Lau et al. When cell lines over-expressed the transmembrane protein ''angiotensin-converting enzyme 2'' (ACE2) from humans, bats, pig or civet cats and were infected with SARS-CoV-2, results showed that they became hypersensitized to infection, thus indicating that ACE2 is a SARS-CoV-2 receptor . Recently, neutralizing monoclonal antibodies and nanobodies against the RBD domain of S protein showed protection against SARS-CoV and MERS-CoV (Du et al. doi = 10.1093/femspd/ftaa042 id = cord-278869-7zr1118b author = Ravichandran, Supriya title = Antibody repertoire induced by SARS-CoV-2 spike protein immunogens date = 2020-05-13 keywords = RBD; S1+S2 summary = To better understand antibody response induced by spike protein-based vaccines, we immunized rabbits with various SARS-CoV-2 spike protein antigens: S-ectodomain (S1+S2) (aa 16-1213), which lacks the cytoplasmic and transmembrane domains (CT-TM), the S1 domain (aa 16-685), the receptor-binding domain (RBD) (aa 319-541), and the S2 domain (aa 686-1213 as control). The spike ectodomain (S1+S2) generated antibodies that predominantly bound to S1+S2 108 6 (black bar), followed by the S1 protein (blue bar), and 3-fold lower antibody binding to the RBD 109 and the S2 domain (red and green bars, respectively) (Fig. 1D ). Antibody off-rate constants, which describe the fraction of antigen-antibody complexes 119 that decay per second, were determined directly from the serum sample interaction with SARS-120 CoV-2 spike ectodomain (S1+S2), S1, S2, and RBD using SPR in the dissociation phase only for 121 sensorgrams with Max RU in the range of 20-100 RU (Suppl. doi = 10.1101/2020.05.12.091918 id = cord-254735-8reu45yz author = Reguera, Juan title = Structural Bases of Coronavirus Attachment to Host Aminopeptidase N and Its Inhibition by Neutralizing Antibodies date = 2012-08-02 keywords = APN; PRCV; RBD; TGEV; figure summary = Here we describe the crystal structures of the receptor-binding domains (RBDs) of two closely related CoV strains, transmissible gastroenteritis virus (TGEV) and porcine respiratory CoV (PRCV), in complex with their receptor, porcine APN (pAPN), or with a neutralizing antibody. The report uncovers a unique virus-receptor recognition mode that engages a glycan N-linked to the pAPN ectodomain, revealing structural determinants of the receptor-binding specificity in CoVs. Neutralizing antibodies target viral residues used for binding to the APN receptor and entry into host cells, showing that efficient CoV neutralization requires immune responses focused toward key receptor binding motifs in the virus envelope. The RBD tip, shown here as the pAPN-binding edge of the domain (Figure 3) , is the main S protein determinant of antigenic site A, recognized by the most effective neutralizing antibodies of TGEV and related CoV infections [25, 26] . doi = 10.1371/journal.ppat.1002859 id = cord-321854-cy8vyb6j author = Ripperger, Tyler J. title = Orthogonal SARS-CoV-2 Serological Assays Enable Surveillance of Low Prevalence Communities and Reveal Durable Humoral Immunity. date = 2020-10-14 keywords = RBD; SARS; figure summary = doi = 10.1016/j.immuni.2020.10.004 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 keywords = ACE2; HADDOCK; RBD; SARS summary = We found that species known not to be susceptible to SARS-CoV-2 infection have non-conservative mutations in several ACE2 amino acid residues that disrupt key polar and charged contacts with the viral spike protein. Collectively, our results provide a structural framework that explains why certain animal species are not susceptible to SARS-CoV-2 infection, and also suggests potential mutations that can enhance binding to the viral RBD. Although it is well-known that docking scores do not quantitatively correlate with experimental binding affinities [19] , these scores suggest that SARS-CoV-2 neg species lack one or more key ACE2 residues that contribute significantly to the interaction with RBD. Models of SARS-CoV-2 neg species -chicken, duck, guinea pig, mouse, and rat -generally have higher (worse) HADDOCK scores than average (Figure 2 ), suggesting that these species'' non-susceptibility to infection could stem from deficient RBD binding to ACE2. doi = 10.1101/2020.06.05.136861 id = cord-263167-es806qhz author = Rogers, Thomas F. title = Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model date = 2020-06-15 keywords = ACE2; Fig; RBD; SARS summary = We showed that passive transfer of a nAb provides protection against disease in high-dose SARS-CoV-2 challenge in Syrian hamsters, as revealed by maintained weight and low lung viral titers in treated animals. Donor plasma were tested for binding to recombinant SARS-CoV-2 and SARS-CoV-1 S and receptor binding domain (RBD) proteins, for binding to cell surface expressed spikes and for neutralization in both live replicating virus and pseudovirus assays (Fig. 2, B to D, and fig. The bulk-transformed ligation products for both the heavy chain and light chain were transfected and tested for binding to RBD and S protein, and for neutralization in the SARS-CoV-2 pseudovirus assay using HeLa-ACE2 target cells ( fig. To investigate the relationship between in vitro neutralization and protection in vivo against SARS-CoV-2, we selected two mAbs for passive transfer/challenge experiments in a Syrian hamster animal model based on a summary of the nAb data (table S3 and fig. doi = 10.1126/science.abc7520 id = cord-263090-29n9tsk9 author = Roy, Susmita title = Dynamical asymmetry exposes 2019-nCoV prefusion spike date = 2020-04-21 keywords = Fig; RBD; SARS summary = In this study, a structural-topology based model Hamiltonian of C3 symmetric trimeric spike is developed to explore its complete conformational energy landscape using molecular dynamic simulations. B. Side and top views of the homo-trimeric structure of SARS-CoV-2 spike protein with one RBD of the S1 subunit head rotated in the up conformation. A number of Cryo-EM structures captured the ''up'' and ''down'' conformations of the RBD domain of spike proteins of other coronaviruses including SARS-CoV-2 where the S1 subunit undergoes a hinge-like conformational movement prerequisite for receptor binding (Fig. 2C) (7, 8, 10, 17) . Analysis of all the simulations yields the 2-D free energy landscape of the trimeric spike protein of SARS-CoV-2 ( Fig 3B) with its all possible conformations. This generates a homo-trimeric SARS-CoV-2 spike where this initial structure has important components in terms of intra and inter-chain contacts (interaction) leading to an ''S1-head-up'' and an ''S1-head-down'' conformation for each protomer. doi = 10.1101/2020.04.20.052290 id = cord-102920-z5q3wo7v author = Sang, Eric R. title = Integrate Structural Analysis, Isoform Diversity, and Interferon-Inductive Propensity of ACE2 to Refine SARS-CoV2 Susceptibility Prediction in Vertebrates date = 2020-06-28 keywords = ACE2; Fig; RBD; SARS summary = Previous reports using structural analysis of the viral spike protein (S) binding its cell receptor of angiotensin-converting enzyme 2 (ACE2), indicate a broad SARS-CoV2 susceptibility in wild and particularly domestic animals. In addition to showing a broad susceptibility potential across mammalian species based on structural analysis, our results also reveal that domestic animals including dogs, pigs, cattle and goats may evolve ACE2-related immunogenetic diversity to restrict SARS-CoV2 infections. Along with showing a broad susceptibility potential across mammalian species based on structural analysis [26] [27] [28] , our results further reveal that domestic animals including dogs, pigs, cattle and goats may evolve previously unexamined immunogenetic diversity to restrict SARS-CoV2 infections. In addition to structural analysis of simulated S-RBD-ACE2 interaction, we propose that several immunogenetic factors, including the evolution of S-binding-void ACE2 isoforms in some domestic animals, the species-specific IFN system, and epigenetic regulation of IFN-stimulated property of host ACE2 genes, contribute to the viral susceptibility and the development of COVID-19-like symptoms in certain animal species [15, 38, 39, 49] . doi = 10.1101/2020.06.27.174961 id = cord-265697-bbvlowyo author = Sang, Eric R. title = Integrate structural analysis, isoform diversity, and interferon-inductive propensity of ACE2 to predict SARS-CoV2 susceptibility in vertebrates date = 2020-08-31 keywords = ACE2; IFN; RBD; SARS summary = doi = 10.1016/j.heliyon.2020.e04818 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 keywords = APN; Fig; RBD summary = These structures identified three distinct APN conformations, based on active site accessibility, which we termed closed, intermediate and open forms (Fig. 1a) . The phenylalanine was located in the loop that connects α 26 and α 27 in the single domain IV ARM repeat of human and pig APN (Fig. 2a) ; it penetrated the active site groove in the closed conformation and locked the peptide, ready for hydrolysis. CoV binding to APN would lock the protein in its open conformation (Fig. 2b) , preventing the ectodomain movement probably necessary for peptide hydrolysis (Fig. 2a) . In flow cytometry, we determined the binding of an RBD-Fc fusion protein to cells that expressed pAPN or an active site mutant (pAPN-HH/AA), alone or with various drugs (Fig. 4a,b) . Disulfide bonds that lock the APN closed conformation or drugs that prevent opening of the ectodomain inhibited CoV protein binding and cell infection, whereas porcine CoV S proteins probably hinder APN transition to the closed form and peptide hydrolysis. doi = 10.1038/srep46045 id = cord-355728-wivk0bm0 author = Schoof, Michael title = An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation date = 2020-08-17 keywords = Fig; RBD; SARS; Spike summary = Here, we develop single-domain antibodies (nanobodies) that potently disrupt the interaction between the SARS-CoV-2 Spike and ACE2. 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. Class I nanobodies emerged with highly 144 variable activity in this assay with Nb6 and Nb11 as two of the most potent clones with IC50 145 values of 370 and 540 nM, respectively (Table 1) To define the binding sites of Nb6 and Nb11, we determined their cryogenic electron 156 microscopy (cryo-EM) structures bound to Spike* ( Fig. 2A state RBDs only contacts a single RBD (Fig. 2D) . 277 278 mNb6-tri displays further gains in potency in both pseudovirus and live SARS-CoV-2 infection 279 assays with IC50 values of 120 pM (5.0 ng/mL) and 54 pM (2.3 ng/mL), respectively (Fig. 4H-I, 280 Table 1). doi = 10.1101/2020.08.08.238469 id = cord-319571-fspmgg4s author = Sehailia, Moussa 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 date = 2020-07-22 keywords = HCQ; RBD; SARS summary = doi = 10.1080/07391102.2020.1796809 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 keywords = MERS; RBD; figure summary = Herein, we generated a bacterial outer membrane vesicles (OMVs)-based vaccine presenting the antigenic stable chimeric fusion protein of the H1-type haemagglutinin (HA) of the pandemic influenza A virus (H1N1) strain from 2009 (H1N1pdm09) and the receptor binding domain (RBD) of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) (OMVs-H1/RBD). In addition, the OMVs-H1/RBD vaccinated mice showed a significant increase of neutralizing antibodies against the MERS-CoV strain HKU-NRCE-270 at week 2 and reached the highest neutralizing titer 160 (7.3 log2) at week eight compared to the control group (p < 0.001) (Figures 2c and 3a) . Based on these observations we engineered the expression of antigenically-stable and immunogenic (OMVs)-based bivalent vaccine that elicits protective antibodies (Abs) following immunization to control infections with H1N1pdm09 and MERS-CoV. In summary, the results show that the generated (OMVs-H1/RBD)-based vaccine presenting the antigenic stable chimeric fusion protein of H1-type HA of the pandemic influenza A virus (H1N1) strain and RBD of MERS-CoV induces specific neutralizing antibodies against H1N1pdm09 and MERS-CoV leading to protection of immunized mice against both viruses. doi = 10.3390/vaccines7020046 id = cord-103940-a2cqw8kg author = Shi, Yuejun title = Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins date = 2020-06-09 keywords = RBD; SARS summary = Currently, structural studies have shown that Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) RBDs are in lying and standing state, respectively. In this study, 130 we selected SARS-CoV, SARS-CoV-2, and HCoV-229E as models, which adopt the 131 two RBD states, and evaluated and compared immune responses to the S trimers and 132 7 RBDs of these coronaviruses through immunological and bioinformatics approaches. 133 We also investigated the mechanism through which the HCoV-229E S trimer 134 produced effective nAbs. Finally, we provide possible vaccine strategies for alphaTo address this issue, we performed B-cell epitope predictions for the S trimers 152 and RBDs of alpha-CoV (HCoV-229E) and beta-CoVs (SARS-CoV and 153 SARS-CoV-2). Taken together, these results showed that the intact and stable S1 subunit of 240 HCoV-229E is a prerequisite for the production of effective nAbs. Furthermore, our experimental results show that RBD has a higher ability to bind 242 12 to the receptor hAPN (Fig. 4B) , which indicates that the characteristics of RBD itself 243 may lead to the generation of less neutralizing antibodies. doi = 10.1101/2020.06.09.141580 id = cord-290290-wyx9ib7s author = Sinegubova, Maria V. 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 date = 2020-11-05 keywords = CHO; CoV-2; RBD; SARS; cell; protein summary = doi = 10.1101/2020.11.04.368092 id = cord-281005-6gi18vka author = Singh, Praveen Kumar title = Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development date = 2020-09-01 keywords = RBD; SARS; protein summary = title: Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development Therefore, we aimed to predict the mutations in the spike protein (S) of the SARS-CoV-2 genomes available worldwide and analyze its impact on the antigenicity. A total of 1,604 spike proteins were extracted from 1,325 complete genome and 279 partial spike coding sequences of SARS-CoV-2 available in NCBI till May 1, 2020 and subjected to multiple sequence alignment to find the mutations corresponding to the reported single nucleotide polymorphisms (SNPs) in the genomic study. In this study, we aimed to predict the mutations in the spike protein (S) of SARS-CoV-2 genomes available in the database (whole genome sequences as well as partial coding sequences of spike protein) and analyze the effect of each mutation on the antigenicity of the predicted epitopes. doi = 10.1055/s-0040-1715790 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 keywords = DPP4; MERS; RBD summary = Middle East respiratory syndrome coronavirus (MERS-CoV) infects host cells through binding the receptor binding domain (RBD) on its spike glycoprotein to human receptor dipeptidyl peptidase 4 (hDPP4). Previously, we have generated a panel of MERS-CoV mutant RBD proteins at the residues D539, Y499, D510, E513, L506, W553 and V555 to characterize their impacts on binding activity to hDPP4 and the entry efficiency into target cells. To study the impacts of the substitutions of the critical residues on hDPP4 described above on the interaction between MERS-CoV RBD and hDDP4, we determined the binding efficiency between these two proteins by employing SPR technique. To further study the importance of the critical residues on hDPP4 on viral entry, we measured the entry efficiency of pseudovirus into COS7 cells expressing the wide-type and mutant forms of hDPP4. These results are consistent with our findings and suggest these residues play an important role in RBD binding and viral entry, and determining the tropism to MERS-CoV infection. doi = 10.1016/j.virol.2014.10.006 id = cord-303868-aes92l6s author = Steffen, Tara L. title = The receptor binding domain of SARS-CoV-2 spike is the key target of neutralizing antibody in human polyclonal sera date = 2020-08-22 keywords = RBD; SARS summary = doi = 10.1101/2020.08.21.261727 id = cord-297072-f5lmstyn author = Struck, Anna-Winona 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 date = 2012-01-16 keywords = ACE2; RBD; SARS summary = 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 Peptide (438)YKYRYL(443) is part of the receptor-binding domain (RBD) of the spike protein of SARS-CoV. The interaction of SARS-CoV with its receptor ACE2 is an attractive drug target as epitopes of the RBD on the spike protein may serve as leads for the design of effective entry inhibitors (Du et al., 2009) . This method allows the determination of the binding specificity, as Table 2 Synthetic peptide library of fourteen 6mer peptides comprising RBD-residues N435-E452 and A471-S500 of SARS-CoV spike protein. We found a hexapeptide in the receptor-binding domain (RBD) of the S protein of SARS-CoV that carries a significant portion of the binding affinity of the virus to the human cell. Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein doi = 10.1016/j.antiviral.2011.12.012 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 keywords = ACE2; RBD; SARS summary = By performing all-atom Molecular Dynamics (MD) simulations, we identified an extended network of salt bridges, hydrophobic and electrostatic interactions, and hydrogen bonding between the receptor-binding domain (RBD) of the S protein and ACE2. Initial studies have constructed a homology model of SARS-CoV-2 RBD in complex with ACE2, based on the SARS-CoV crystal structure (8, 14) and performed conventional MD (cMD) simulations totaling 10 ns (15, 16) and 100 ns (17, 18) in length to estimate binding free energies (15, 16) and interaction scores (18) . In this study, we performed a comprehensive set of all-atom MD simulations totaling 16.5 µs in length using the recently-solved structure of the RBD of the SARS-CoV-2 S protein in complex with the PD of ACE2 (7) . In 20 SMD simulations (each 15 ns, totaling 300 ns in length, table S1), the average work applied to unbind RBD from PD was 71.1 ± 12.7 kcal/mol (mean ± s.d.), demonstrating that the S protein binds stably to ACE2 (Fig. 3B) . doi = 10.1101/2020.09.21.305490 id = cord-321166-nvphu1fm author = Thomson, Emma C. title = The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity date = 2020-11-05 keywords = CoV-2; N439; RBD; RBM; SARS; d614; figure summary = doi = 10.1101/2020.11.04.355842 id = cord-314574-3e6u4aza author = Tian, Xiaolong title = Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody date = 2020-02-17 keywords = RBD; SARS summary = Considering the relatively high identity of receptor-binding domain (RBD) in 2019-nCoV and SARS-CoV, it is urgent to assess the cross-reactivity of anti-SARS CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV. Interestingly, some of the most potent SARS-CoV-specific neutralizing antibodies (e.g. m396, CR3014) that target the ACE2 binding site of SARS-CoV failed to bind 2019-nCoV spike protein, implying that the difference in the RBD of SARS-CoV and 2019-nCoV has a critical impact for the cross-reactivity of neutralizing antibodies, and that it is still necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD. Next, we expressed and purified several representative SARS-CoV-specific antibodies which have been reported to target RBD and possess potent neutralizing activities, including m396 [3] , CR3014 [4] , CR3022 [5] , as well as a MERS-CoV-specific human monoclonal antibody m336 developed by our laboratory [15] , and measured their binding ability to 2019-nCoV RBD by ELISA (Figure 1(e)) . doi = 10.1080/22221751.2020.1729069 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 keywords = RBD; SARS summary = In this work, we report the synthesis of a cheap yet highly sensitive cobalt-functionalized TiO2 nanotubes (Co-TNTs)-based electrochemical biosensor and its efficacy for rapid detection of spike glycoprotein of SARS-CoV-2 by examining S-RBD protein as the reference material. Our manuscript reports the synthesis of a cheap yet highly sensitive cobalt-functionalized TiO2 nanotubes (Co-TNTs)-based electrochemical biosensor for rapid detection of spike glycoprotein of SARS-CoV-2. . https://doi.org/10.1101/2020.09.07.20190173 doi: medRxiv preprint asymptomatic individuals are needed, which is feasible only after the development of a simple, portable and rapid point-of-use sensor for the detection of SARS-CoV-2. In the current work, we have determined the potential of Co-functionalized TiO2 nanotubes (Co-TNTs) for the electrochemical detection of S-RBD protein of SARS-CoV-2. Our data showed that cobalt functionalized TNTs could selectively detect the S-RBD protein of SARS-CoV-2 using the amperometry electrochemical technique in ~ 30 secs. doi = 10.1101/2020.09.07.20190173 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 keywords = RBD; SARS; TNT summary = In this work, we report the synthesis of a cheap, yet highly sensitive, cobalt-functionalized TiO(2) nanotubes (Co-TNTs)-based electrochemical sensor for rapid detection of SARS-CoV-2 through sensing the spike (receptor binding domain (RBD)) present on the surface of the virus. In the current work, we have determined the potential of Co-functionalized TiO2 nanotubes (Co-TNTs) for the electrochemical detection of S-RBD protein of SARS-CoV-2. In the current work, we have determined the potential of Co-functionalized TiO2 nanotubes (Co-TNTs) for the electrochemical detection of S-RBD protein of SARS-CoV-2. Our data shows that cobalt functionalized TNTs can selectively detect the S-RBD protein of SARS-CoV-2 using the amperometry electrochemical technique in ~30 s. Our data shows that cobalt functionalized TNTs can selectively detect the S-RBD protein of SARS-CoV-2 using the amperometry electrochemical technique in ~30 s. In this study, we developed a Co-metal functionalized TNT as a sensing material for electrochemical detection of SARS-CoV-2 infection through the detection of the receptor binding domain (RBD) of spike glycoprotein. doi = 10.3390/s20205871 id = cord-284102-rovyvv45 author = Wagner, Teresa R. title = NeutrobodyPlex - Nanobodies to monitor a SARS-CoV-2 neutralizing immune response date = 2020-09-28 keywords = ACE2; RBD; SARS summary = Here we identified 11 unique nanobodies (Nbs) with high binding affinities to the SARS-CoV-2 spike receptor domain (RBD). Considering that Nbs targeting diverse epitopes within the RBD:ACE2 interface are beneficial 201 in both reducing viral infectivity and preventing mutational escape, we next combined the most 202 potent inhibitory and neutralizing candidates derived from Nb-Set1 (NM1226, NM1228) and 203 We incubated our previously generated color-coded beads 232 comprising RBD, S1 domain or homotrimeric spike with serum samples from patients or non-233 infected individuals, in addition to dilution series of the combinations NM1226/ NM1230 or 234 NM1228/ NM1230 and used this to detect patient-derived IgGs bound to the respective 235 antigens. As a result, we modified our previously described multiplex immunoassay 303 (MULTICOV-AB, 20 ) and developed a novel diagnostic test called NeutrobodyPlex to monitor 304 the presence and the emergence of neutralizing antibodies in serum samples of SARS-CoV-2 305 infected individuals. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block 681 interaction with ACE2 doi = 10.1101/2020.09.22.308338 id = cord-308428-zw26usmh author = Walter, Justin D. title = Highly potent bispecific sybodies neutralize SARS-CoV-2 date = 2020-11-10 keywords = ACE2; Fig; RBD; S-2P; SARS; Sb#15; Sb#68 summary = Here, we report the generation of synthetic nanobodies, known as sybodies, against the receptor-binding domain (RBD) of SARS-CoV-2 spike protein. We identified a sybody pair (Sb#15 and Sb#68) that can bind simultaneously to the RBD, and block ACE2 binding, thereby neutralizing pseudotyped and live SARS-CoV-2 viruses. However, binders of the isolated RBD may not effectively engage the aforementioned pre-fusion conformation of the spike protein, which could account for the poor neutralization ability of recently described single-domain antibodies that were raised against the RBD of SARS-CoV-2 spike protein [29] . Since Sb#15 and Sb#68 can bind simultaneously to the RBD and the full-length spike protein, we mixed Sb#15 and Sb#68 together to investigate potential additive or synergistic neutralizing activity of these two independent sybodies. To gain structural insights into how Sb#15 and Sb#68 recognize the RBD, we performed single particle cryo-EM analysis of the spike protein in complex with the sybodies. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 doi = 10.1101/2020.11.10.376822 id = cord-318444-sgm24q1i author = Walter, Justin D. title = Sybodies targeting the SARS-CoV-2 receptor-binding domain date = 2020-05-16 keywords = ECD; ELISA; RBD; SARS; TBS summary = doi = 10.1101/2020.04.16.045419 id = cord-352934-ypls4zau author = Wan, Jinkai title = Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection date = 2020-07-03 keywords = RBD; SARS summary = title: Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection We screened sera samples from 11 patients recently recovered from COVID-19, and 119 found all individuals showed certain levels of serological responses, with #507 and 120 #501 being the weakest, to SARS-CoV-2 Spike RBD and S1 proteins ( Figure 1A ). We 121 also found that 10 sera, except for 507, showed neutralization abilities against 122 SARS-CoV-2 pseudoviral infection of HEK293T cells stably expressing human ACE2 123 ( Figure 1B ). In order to screen for SARS-CoV-2 spike antigen specific monoclonal antibodies, we 143 used two primary assays based on ELISA (enzyme linked immunosorbent assay) and 144 FCA (flow cytometry assay), respectively. Human monoclonal antibodies block the binding of SARS-CoV-2 spike protein to angiotensin 561 converting enzyme 2 receptor A potent neutralizing human antibody reveals the N-terminal domain of the 564 Spike protein of SARS-CoV-2 as a site of vulnerability Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific 612 human monoclonal antibody doi = 10.1016/j.celrep.2020.107918 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 keywords = RBD summary = When immunized in mice, the S1 domain induced much higher IgG and IgA antibody levels than the RBD and more efficiently neutralized SARS‐CoV‐2 when adjuvanted with alum. Article SARS-CoV-2 S1 induces higher IgG and IgA titers than RBD 2 weeks after the third intramuscular immunization (Figure 2A) , both S1-specific (S1-coated plate in Figure 2 ) and RBD-specific (RBD-coated plate in Figure 2 ) antibodies were analyzed. HEK293K cell-expressed recombinant S1 (S1 immunized) and E.coli-expressed norovirus shell domain-S1 fusion protein (S-S1 immunized) induced similar S1-specific IgG titers (64 000) and similar RBD-specific titers (8 000) ( Figure 2B ). HEK293K cell-expressed recombinant RBD (RBD immunized) and E.coli-expressed norovirus shell domain-RBD fusion proteins (S-RBD immunized) induced low levels of IgG1 and IgG2a titers specific to both S1 (S1 coated in Figure 3A&B ) and the RBD (RBD coated in Figure 3A&B ). doi = 10.1002/jmv.26320 id = cord-295482-qffg6r91 author = Wong, Alan H. M. title = Receptor-binding loops in alphacoronavirus adaptation and evolution date = 2017-11-23 keywords = Fig; HCoV-229E; RBD; Supplementary; receptor summary = Here we report the X-ray crystal structure of the receptor-binding domain (RBD) of the human coronavirus, HCoV-229E, in complex with the ectodomain of its receptor, aminopeptidase N (APN). Phylogenetic analysis shows that the natural HCoV-229E receptor-binding loop variation observed defines six RBD classes whose viruses have successively replaced each other in the human population over the past 50 years. The structure shows that receptor binding is mediated solely by three extended loops, a feature shared by HCoV-NL63 and the closely related porcine respiratory coronavirus, PRCoV. The six RBDs differ in their receptor-binding affinity and their ability to be bound by a neutralizing antibody (9.8E12) and taken together, our findings suggest that the HCoV-229E sequence variation observed arose through adaptation and selection. HCoV-229E infection in humans does not provide protection against different isolates 37 , and viruses that contain a new RBD class that cannot be bound by the existing repertoire of loop-binding neutralizing antibodies provide an explanation for this observation. doi = 10.1038/s41467-017-01706-x id = cord-344871-486sk4wc author = Wu, Jianping title = Biochemical and structural characterization of the interface mediating interaction between the influenza A virus non-structural protein-1 and a monoclonal antibody date = 2016-09-16 keywords = 2H6-Fab; ELISA; Fig; NS1(RBD; ns1 summary = We have previously shown that a non-structural protein 1 (NS1)-binding monoclonal antibody, termed as 2H6, can significantly reduce influenza A virus (IAV) replication when expressed intracellularly. As comparative ELISA in this and previous studies 29 showed that residues N48 and T49 in NS1(RBD) are important for the interaction with mAb 2H6, they were defined as active residues involved in the binding interaction to generate a series of models of the NS1(RBD) and 2H6-Fab complex. Overall, the predicted model from cluster 2 is consistent with our comparative ELISA data and suggests that residues N48 and T49 are important for the binding between NS1(RBD) and 2H6-Fab because their side-chains could make hydrogen bonds with residues in the VH-CDR2 of the Fab. In addition, R44 of NS1(RBD) was distal from the antibody-antigen interface, which is consistent with the results from comparative ELISA ( Figure S1 ) showing that substitution of R44 of NS1(RBD) with K did not affect its interaction with mAb 2H6. doi = 10.1038/srep33382 id = cord-321918-9jwma2y6 author = Xiu, Siyu title = Inhibitors of SARS-CoV-2 Entry: Current and Future Opportunities date = 2020-06-15 keywords = ACE2; CoV; CoV-2; MERS; RBD; SARS summary = The spike protein can be divided into two domains; S1 is responsible for angiotensin-converting enzyme II(ACE2) recognition, the recently identified host cell receptor, and S2 mediates membrane fusion (Figure 2 ). 98 99 On the basis of this approach, they identified two small molecules, TGG (12, Table 4 ) and luteolin (13) , that can bind avidly to the SARS-CoV S2 protein and inhibit viral entry of SARS-CoV into Vero E6 cells with IC 50 values of 4.5 and 10.6 μM, respectively. 113 A high-throughput screen (HTS) of a 1000-compound library that resulted in the identification of MDL28170 (17 , Table 4 ) by Bates et al., and in an antiviral activity assay, 17 specifically inhibited cathepsin L-mediated substrate cleavage and blocked SARS-CoV viral entry, with an IC 50 value of 2.5 nM and EC 50 value in the range of 100 nM. doi = 10.1021/acs.jmedchem.0c00502 id = cord-261877-4y37676n author = Xu, Cong title = Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM date = 2020-06-30 keywords = ACE2; Fig; RBD; SARS summary = Recent cryoelectron microscopy (cryo-EM) studies on the stabilized ectodomain of SARS-CoV-2 S protein revealed a closed state of S trimer with three RBD domains in "down" conformation (Walls et al., 2020) , as well as an open state with one RBD in the "up" conformation, corresponding to the receptor-accessible state (Walls et al., 2020; Wrapp et al., 2020) . To gain a thorough picture on how the receptor ACE2 binding induces conformational dynamics of the SARS-CoV-2 S trimer and triggers transition towards the postfusion state, we determine the cryo-EM structure of SARS-CoV-2 S trimer in complex with human ACE2 PD domain to 3.8 Å resolution (termed SARS-CoV-2 S-ACE2, Figs. Based on the data, we put forward a mechanism of ACE2 binding-induced conformational transitions of SARS-CoV-2 S trimer from the tightly closed ground prefusion state transforming towards the postfusion state (Fig. 6) . Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding doi = 10.1101/2020.06.30.177097 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 keywords = ACE2; Fig; RBD; SARS summary = doi = 10.1038/s41467-020-18319-6 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 keywords = RBD; SARS; SR31 summary = title: A high-affinity RBD-targeting nanobody improves fusion partner''s potency against SARS-CoV-2 Considerable research have been devoted to the development of neutralizing antibodies, including llama-derived single-chain nanobodies, to target the receptor-binding motif (RBM) and to block ACE2-RBD binding. A high-affinity RBD binder without neutralizing activity 85 Previously, we generated 99 sybodies from three highly diverse synthetic libraries by ribosome and phage display with in vitro selections against the SARS-CoV-2 RBD. Consistent with its inability to neutralize SARS-CoV-2 pseudovirus, SR31 did not affect RBD-ACE2 binding (Fig. 1C) . Most RBD-targeting neutralizing antibodies, including neutralizing nanobodies characterized so far (8, 13-15, 19, 20, 22-24, 26-28, 34, 35, 37) , engage the RBD at the receptor-binding motif (RBM) (Fig. 3A) , thus competing off ACE2 and preventing viral entry. Taken together, the structural data rationalize the high-affinity binding between SR31 and RBD, and its inability to neutralize SARS-CoV-2. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 doi = 10.1101/2020.09.24.312595 id = cord-355807-q3bngari author = Yepes-Pérez, Andres F. 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 date = 2020-10-29 keywords = ACE-2; Proanthocyanidin; RBD; SARS summary = Molecular modeling was carried out to evaluate the potential antiviral properties of the components of the medicinal herb Uncaria tomentosa (cat''s claw) focusing on the binding interface of the RBD–ACE-2 and the viral spike protein. tomentosa against focusing both on the binding interface of the RBD-ACE-2 and inside SARS-CoV-2 RBD spike protein, (2) simulations of ligand pathway of the best predicted compounds from step 1 to evaluate convenient entrance mechanism of the compounds to the binding site, (3) MD simulation to assess the stability of the best protein-ligand complexes from 1, (4) calculation of pharmacokinetics parameters for the most qualified compounds resulting from the previous parts of the docking protocol. Next, we used the cryo-EM structure of SARS-CoV-2 spike protein (PDB code: 6VYB) in their open state (Lipinski et al., 2012) to explore the potential inhibition of components of the cat''s claw, selecting ACE-2-binding pocket to this study. doi = 10.1080/07391102.2020.1837676 id = cord-275185-9br8lwma author = Zeng, Hao title = The efficacy assessment of convalescent plasma therapy for COVID-19 patients: a multi-center case series date = 2020-10-06 keywords = COVID-19; RBD; SARS; patient summary = Following CP transfusion, six out of eight patients showed improved oxygen support status; chest CT indicated varying degrees of absorption of pulmonary lesions in six patients within 8 days; the viral load was decreased to a negative level in five patients who had the previous viremia; other laboratory parameters also tended to improve, including increased lymphocyte counts, decreased C-reactive protein, procalcitonin, and indicators for liver function. 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. 23 Assessing the effects of neutralizing activity of CP on the patients'' clinical efficacy, we found that patients treated by CP with high NAT50 (>1:640) had more obvious improvement than patients receiving low NAT50 value (≤1:640) of CP, including shorter negative conservation time of viral RNA, and higher increment of IgG level after CP transfusion. doi = 10.1038/s41392-020-00329-x id = cord-024319-isbqs7hg author = Zeng, Xin title = Isolation of a human monoclonal antibody specific for the receptor binding domain of SARS-CoV-2 using a competitive phage biopanning strategy date = 2020-04-30 keywords = ACE2; RBD; SARS summary = title: Isolation of a human monoclonal antibody specific for the receptor binding domain of SARS-CoV-2 using a competitive phage biopanning strategy SARS-CoV-2 relies on its spike protein, in particular the receptor binding domain (RBD), to bind human cell receptor angiotensin-converting enzyme 2 (ACE2) for viral entry, and thus targeting RBD holds the promise for preventing SARS-CoV-2 infection. It was proved to competitively block the binding of RBD to ACE2 and potently inhibit SARS-CoV-2 pseudovirus infection with IC(50) values of 12 nM. Several high-affinity antibodies targeting SARS-CoV-2 RBD and blocking its binding to ACE2 were isolated, and the top 1 lead exhibited a neutralization activity of SARS-CoV-2 pseudotyped VSV infection. These antibodies all compete with ACE2 to bind SARS-CoV RBD, but their epitopes only have limited overlaps of the Two SARS-CoV-2 RBD-specific antibodies selected from different strategies showed different neutralization activities. doi = 10.1093/abt/tbaa008 id = cord-253447-4w6caxwu author = Zeng, Xin title = Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy date = 2020-04-20 keywords = ACE2; RBD; SARS summary = title: Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy SARS-CoV-2 relies on its spike protein, in particular the receptor binding domain (RBD), to bind human cell receptor angiotensin-converting enzyme 2 (ACE2) for viral entry, and thus targeting RBD holds the promise for preventing SARS-CoV-2 infection. In this work, a competitive biopanning strategy of a phage display antibody library was applied to screen blocking antibodies against RBD. It was proved to competitively block the binding of RBD to ACE2 protein, and potently inhibit SARS-CoV-2 pseudovirus infection of ACE2-overexpressing Hela cells with IC50 values of 12nM. Several high-affinity antibodies targeting SARS-CoV-2 RBD and blocking its binding to ACE2 were isolated, and the top 1 lead exhibited a neutralization activity of SARS-CoV-2 pseudotyped VSV infection. A high-affinity antibody against the target protein can be screened from a phage display antibody library using the standard biopanning process, but its binding epitopes are identified by some extra steps, such as epitope mapping and competitive ELISA. doi = 10.1101/2020.04.19.049643 id = cord-308310-wtmjt3hf author = Zha, Lisha title = Development of a COVID-19 vaccine based on the receptor binding domain displayed on virus-like particles date = 2020-05-14 keywords = RBD; SARS summary = Higly repetitive display of RBD on immunologically optimized virus-like particles derived from cucumber mosaic virus resulted in a vaccine candidate (RBD-CuMVTT) that induced high levels of specific antibodies in mice which were able to block binding of spike protein to ACE2 and potently neutralized the SARS-CoV-2 virus in vitro. Higly repetitive display of RBD on immunologically optimized virus-like particles derived from cucumber mosaic virus resulted in a vaccine candidate (RBD-CuMVTT) that induced high levels of specific antibodies in mice which were able to block binding of spike protein to ACE2 and potently neutralized the SARS-CoV-2 virus in vitro. The receptor binding domain (RBD) of the SARS spike protein binds to ACE2 and is an important target for neutralizing antibodies [5] [6] [7] . Hence, the RBD-CuMVTT vaccine candidate is able to induce high levels of SARS-CoV-2 neutralizing antibodies. Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine doi = 10.1101/2020.05.06.079830 id = cord-332185-a96r1k7a author = Zhang, Shuyuan title = Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution date = 2020-09-22 keywords = RBD; SARS summary = doi = 10.1101/2020.09.21.307439 id = cord-268144-maa8c4a4 author = Zhang, Yuan title = Computational characterization and design of SARS coronavirus receptor recognition and antibody neutralization date = 2007-02-17 keywords = RBD; SARS summary = The sequential determination of crystal structures of the SARS coronavirus spike receptor-binding domain (RBD) in complex with its cellular receptor or neutralizing antibody opened a door for the design and development of antiviral competitive inhibitors. As an envelope glycoprotein, the spike protein of severe acute respiratory syndrome coronavirus (SARS-CoV) plays a key role in the viral entry and neutralization (Bartlam et al., 2005; Denison, 2004; Lau and Peiris, 2005; Xu and Gao, 2004; Zhu, 2004) . 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 Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association doi = 10.1016/j.compbiolchem.2007.02.005 id = cord-347587-auook38y author = Zhao, Guangyu 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 date = 2018-08-29 keywords = Fig; MERS; Nbs; RBD summary = 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 In this study, we developed a novel neutralizing Nb (NbMS10) and its human-Fc-fused version (NbMS10-Fc), both of which target the MERS-CoV spike protein receptor-binding domain (RBD). Identification and characterization of MERS-CoV-RBD-specific Nbs. To construct the Nb (i.e., VHH) library, we immunized llama with recombinant MERS-CoV RBD (residues 377 to 588, EMC2012 strain) containing a C-terminal human IgG1 Fc tag (i.e., RBD-Fc) and isolated peripheral blood mononuclear cells (PBMCs) from the immunized llama. To examine of the role of the D539A mutation in DPP4 binding, we carried out an ELISA to detect the binding between DPP4 and The plates were coated with RBD-Fd protein (2 g/ml) and treated with or without DTT, followed by sequential incubation with serial dilutions of NbMS10 or NbMS10-Fc and goat anti-llama and HRP-conjugated anti-goat IgG antibodies. doi = 10.1128/jvi.00837-18 id = cord-183197-dxmto1tu author = Zhao, Tom Y. title = Tetracycline as an inhibitor to the coronavirus SARS-CoV-2 date = 2020-08-13 keywords = ACE2; RBD summary = Tetracycline appears to target viral residues that are usually involved in significant hydrogen bonding with ACE2; this inhibition of cellular infection complements the anti-inflammatory and cytokine suppressing capability of Tetracycline, and may further reduce the duration of ICU stays and mechanical ventilation induced by the coronavirus SARS-CoV-2. The amino acid residues of the RBD involved in hydrogen bonding with the Tetracycline molecule are Tyr 449, Asn 501, Gly 496, and Tyr 505 (Fig. 1) , which have been shown to be crucial for the SARS-CoV 2 RBD in binding to ACE2 for cellular access 8 . To verify this statement, steered molecular dynamics simulations were carried out to find the potential of mean force (PMF) along a singular dissociation pathway for the inhibited and uninhibited RBD-ACE2 complexes. The tetracycline class of antibiotics, including Tetracycline, Oxytetracycline, and Doxycycline may be helpful in the fight against the coronavirus SARS-CoV-2, due to its preferential association with the important residues in the viral receptor binding domain and the resulting strong inhibition of the RBD-ACE2 complex. doi = nan id = cord-263042-qdmunb9l author = Zhao, Yongkun title = Passive immunotherapy for Middle East Respiratory Syndrome coronavirus infection with equine immunoglobulin or immunoglobulin fragments in a mouse model date = 2016-11-24 keywords = East; MERS; RBD summary = Passive transfer of equine immune antibodies significantly reduced virus titers and accelerated virus clearance from the lungs of MERS-CoV infected mice. Our data show that horses immunized with MERS-CoV VLPs can serve as a primary source of protective F(ab'')(2) for potential use in the prophylactic or therapeutic treatment of exposed or infected patients. Several research groups have developed and produced anti-MERS patientderived or humanized monoclonal neutralizing antibodies in vitro that were able to protect MERS-CoV infected mice (Corti et al., 2015; Li et al., 2015; Zhao et al., 2014) . Prophylactic or therapeutic treatment of MERS-CoV infected mice with either IgG or F(ab'') 2 significantly decreased the virus load in their lungs. In both prophylactic and therapeutic settings, passive transfer of equine immune antibodies resulted in a 2e4 log reduction of virus titers in the lungs of MERS-CoV infected mice, and accelerated virus clearance in the serum treated group (Fig. 5A, B) . doi = 10.1016/j.antiviral.2016.11.016 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 keywords = Data; EY6A; Fig; RBD; SARS summary = Cryo-EM analyses of the pre-fusion Spike incubated with EY6A Fab reveal a complex of the intact trimer with three Fabs bound and two further multimeric forms comprising destabilized Spike attached to Fab. EY6A binds what is probably a major neutralising epitope, making it a candidate therapeutic for COVID-19. A neutralisation test for EY6A based on quantitative PCR detection of virus in the supernatant bathing infected Vero E6 cells after 5 days of culture, showed a ~1000-fold reduction in virus signal (Methods, Extended Data Fig. 3 ) indicating that it is highly neutralising. To elucidate the epitope of EY6A, we determined the crystal structures of the deglycosylated SARS-CoV-2 RBD in complex with EY6A Fab alone and in a ternary complex incorporating a nanobody (Nb) which has been shown to compete with ACE2 (for data on a closely related Nb see Huo 2020, submitted), as a crystallisation chaperone. doi = 10.1101/2020.06.12.148387 id = cord-285039-9piio754 author = Zhou, Haixia title = Crystallization and Structural Determination of the Receptor-Binding Domain of MERS-CoV Spike Glycoprotein date = 2019-09-14 keywords = MERS; RBD summary = Three-dimensional structures of the receptor-binding domain (RBD) of MERS-CoV spike glycoprotein bound to cellular receptor and monoclonal antibodies (mAbs) have been determined by X-ray crystallography, providing structural information about receptor recognition and neutralizing mechanisms of mAbs at the atomic level. The first three-dimensional structure of the MERS-CoV spike glycoprotein receptor-binding domain (RBD), providing the molecular basis of viral attachment to host cells, was determined in the complex with it cellular receptor dipeptidyl peptidase 4 (DPP4, also called CD26) by X-ray crystallography [1] . After obtaining the phases of these diffracted X-rays by heavy-atom derivative, anomalous scattering or molecular replacement methods, a protein crystallographer then calculates the density of electrons with the protein crystal and builds a structural model based on the density map. MER-CoV RBD can be expressed using the Bac-to-Bac baculovirus expression system (Fig. 1 ), collected and captured using NTA Sepharose (GE Healthcare) and then further purified by gel filtration chromatography using a Superdex 200 High Performance column (GE Healthcare). doi = 10.1007/978-1-0716-0211-9_4 id = cord-343107-oj1re34k author = Zhou, Haixia title = Structural definition of a neutralization epitope on the N-terminal domain of MERS-CoV spike glycoprotein date = 2019-07-11 keywords = DPP4; Fig; MERS; NTD; RBD; Supplementary summary = Most neutralizing antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV) target the receptor-binding domain (RBD) of the spike glycoprotein and block its binding to the cellular receptor dipeptidyl peptidase 4 (DPP4). Here we report the monoclonal antibody 7D10 that binds to the N-terminal domain (NTD) of the spike glycoprotein and inhibits the cell entry of MERS-CoV with high potency. The 7D10 antibody recognizes the NTD of MERS-CoV S glycoprotein and neutralizes the infectivity of pseudotyped and live virus with a potency comparable to those of the most active RBD-targeting antibodies. The NTD N222Q mutation also dramatically reduced the binding and neutralization by 7D10, but did not dramatically affect the cell infection of pseudotyped MERS-CoV ( Supplementary Fig. 11) . A conformation-dependent neutralizing monoclonal antibody specifically targeting receptor-binding domain in Middle East respiratory syndrome coronavirus spike protein A humanized neutralizing antibody against MERS-CoV targeting the receptor-binding domain of the spike protein doi = 10.1038/s41467-019-10897-4 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 keywords = East; MERS; Middle; RBD summary = A number of MERS vaccines have been developed based on viral RBD, including nanoparticles, virus-like particles (VLPs), and recombinant proteins, and their protective efficacy has been evaluated in animal models, including mice with adenovirus 5 (Ad5)-directed expression of human DPP4 (Ad5/hDPP4), hDPP4-transgenic (hDPP4-Tg) mice, and non-human primates (NHPs) [88] [89] [90] [91] [92] [93] [94] . 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 Recombinant receptor-binding 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 A conformation-dependent neutralizing monoclonal antibody specifically targeting receptor-binding domain in Middle East respiratory syndrome coronavirus spike protein 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 doi = 10.3390/v11010060 id = cord-329392-fufattj8 author = den Hartog, Gerco title = SARS-CoV-2–Specific Antibody Detection for Seroepidemiology: A Multiplex Analysis Approach Accounting for Accurate Seroprevalence date = 2020-08-08 keywords = RBD; SARS summary = doi = 10.1093/infdis/jiaa479