Monday, December 23, 2024
No menu items!
HomeNatureDesign of customized coronavirus receptors

Design of customized coronavirus receptors

  • Millet, J. K., Jaimes, J. A. & Whittaker, G. R. Molecular diversity of coronavirus host cell entry receptors. FEMS Microbiol. Rev. 45, fuaa057 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, F. Receptor recognition mechanisms of coronaviruses: a decade of structural studies. J. Virol. 89, 1954–1964 (2015).

    Article 
    PubMed 

    Google Scholar
     

  • Guo, H. et al. Isolation of ACE2-dependent and -independent sarbecoviruses from Chinese horseshoe bats. J. Virol. 97, e0039523 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Cui, J., Li, F. & Shi, Z.-L. Origin and evolution of pathogenic coronaviruses. Nat. Rev. Microbiol. 17, 181–192 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Walls, A. C. et al. Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer. Nature 531, 114–117 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Walls, A. C. et al. Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion. Proc. Natl Acad. Sci. USA 114, 11157–11162 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Walls, A. C. et al. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 181, 281–292.e6 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Peng, G. et al. Crystal structure of mouse coronavirus receptor-binding domain complexed with its murine receptor. Proc. Natl Acad. Sci. USA 108, 10696–10701 (2011).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yan, R. et al. Structural basis for the different states of the spike protein of SARS-CoV-2 in complex with ACE2. Cell Res. 31, 717–719 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hoffmann, M. et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181, 271–280.e8 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Saunders, N. et al. TMPRSS2 is a functional receptor for human coronavirus HKU1. Nature 624, 207–214 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McCallum, M. et al. Human coronavirus HKU1 recognition of the TMPRSS2 host receptor. Cell 187, 4231–4245.e13 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xiong, Q. et al. Close relatives of MERS-CoV in bats use ACE2 as their functional receptors. Nature 612, 748–757 (2022).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Hofmann, H. et al. Human coronavirus NL63 employs the severe acute respiratory syndrome coronavirus receptor for cellular entry. Proc. Natl Acad. Sci. USA 102, 7988–7993 (2005).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Starr, T. N. et al. ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. Nature 603, 913–918 (2022).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Lee, J. et al. Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus. Cell Host Microbe 31, 1961–1973.e11 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lim, S., Zhang, M. & Chang, T. L. ACE2-independent alternative receptors for SARS-CoV-2. Viruses 14, 2535 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Baggen, J. et al. TMEM106B is a receptor mediating ACE2-independent SARS-CoV-2 cell entry. Cell 186, 3427–3442.e22 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Verheije, M. H. et al. Redirecting coronavirus to a nonnative receptor through a virus-encoded targeting adapter. J. Virol. 80, 1250–1260 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wan, Y. et al. Molecular mechanism for antibody-dependent enhancement of coronavirus entry. J. Virol. 94, e02015–19 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Maemura, T. et al. Antibody-dependent enhancement of SARS-CoV-2 infection is mediated by the IgG receptors FcγRIIA and FcγRIIIA but does not contribute to aberrant cytokine production by macrophages. mBio 12, e0198721 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Kibria, M. G. et al. Antibody-mediated SARS-CoV-2 entry in cultured cells. EMBO Rep. 24, e57724 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Junqueira, C. et al. FcγR-mediated SARS-CoV-2 infection of monocytes activates inflammation. Nature 606, 576–584 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cao, L. et al. De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Science 370, 426–431 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hoffmann, M. A. G. et al. ESCRT recruitment to SARS-CoV-2 spike induces virus-like particles that improve mRNA vaccines. Cell 186, 2380–2391.e9 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ying, T., Feng, Y., Wang, Y., Chen, W. & Dimitrov, D. S. Monomeric IgG1 Fc molecules displaying unique Fc receptor interactions that are exploitable to treat inflammation-mediated diseases. MAbs 6, 1201–1210 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xiang, Y. et al. Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2. Science 370, 1479–1484 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pinto, D. et al. Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature 583, 290–295 (2020).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Scheid, J. F. et al. B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV. Cell 184, 3205–3221.e24 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tortorici, M. A. et al. Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms. Science 370, 950–957 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cui, Z. et al. Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cell 185, 860–871.e13 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McCallum, M. et al. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell 184, 2332–2347.e16 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sun, X. et al. Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2. Nat Microbiol 7, 1063–1074 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pinto, D. et al. Broad betacoronavirus neutralization by a stem helix-specific human antibody. Science 373, 1109–1116 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sauer, M. M. et al. Structural basis for broad coronavirus neutralization. Nat. Struct. Mol. Biol. 28, 478–486 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Low, J. S. et al. ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies. Science 377, 735–742 (2022).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Piccoli, L. et al. Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology. Cell 183, 1024–1042.e21 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Walls, A. C. et al. Unexpected receptor functional mimicry elucidates activation of coronavirus fusion. Cell 176, 1026–1039.e15 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhang, S. et al. Loss of spike N370 glycosylation as an important evolutionary event for the enhanced infectivity of SARS-CoV-2. Cell Res. 32, 315–318 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ou, X. et al. Host susceptibility and structural and immunological insight of S proteins of two SARS-CoV-2 closely related bat coronaviruses. Cell Discov. 9, 78 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chi, X. et al. Comprehensive structural analysis reveals broad-spectrum neutralizing antibodies against SARS-CoV-2 Omicron variants. Cell Discov. 9, 37 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Cao, Y. et al. BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature 608, 593–602 (2022).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Chi, X. et al. A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2. Science 369, 650–655 (2020).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, D. et al. In vitro and in vivo functions of SARS-CoV-2 infection-enhancing and neutralizing antibodies. Cell 184, 4203–4219.e32 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Beaudoin-Bussières, G. et al. A Fc-enhanced NTD-binding non-neutralizing antibody delays virus spread and synergizes with a nAb to protect mice from lethal SARS-CoV-2 infection. Cell Rep. 38, 110368 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Barnes, C. O. et al. Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies. Cell 182, 828–842.e16 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Benton, D. J. et al. Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion. Nature 588, 327–330 (2020).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Starr, T. N. et al. SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape. Nature 597, 97–102 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Hunt, A. C. et al. Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice. Sci. Transl. Med. 14, eabn1252 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hsieh, C.-L. et al. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 369, 1501–1505 (2020).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • McCallum, M. et al. Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants. Science 374, 1621–1626 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • McCallum, M. et al. SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. Science 373, 648–654 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Shang, J. et al. Structure of mouse coronavirus spike protein complexed with receptor reveals mechanism for viral entry. PLoS Pathog. 16, e1008392 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, H. et al. TMPRSS2 and glycan receptors synergistically facilitate coronavirus entry. Cell 187, 4261–4271.e17 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pronker, M. F. et al. Sialoglycan binding triggers spike opening in a human coronavirus. Nature 624, 201–206 (2023).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Xu, J. et al. Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Nature 595, 278–282 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Xia, S. et al. Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion. Cell Res. 30, 343–355 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xia, S. et al. Structural and functional basis for pan-CoV fusion inhibitors against SARS-CoV-2 and its variants with preclinical evaluation. Signal Transduct. Target. Ther. 6, 288 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xia, S. et al. A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike. Sci. Adv. 5, eaav4580 (2019).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Menachery, V. D. et al. Trypsin treatment unlocks barrier for zoonotic bat coronavirus infection. J. Virol. 94, e01774–19 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Catanzaro, NJ. et al. ACE2 from Pipistrellus abramus bats is a receptor for HKU5 coronaviruses. Preprint at bioRxiv https://doi.org/10.1101/2024.03.13.584892 (2024).

  • Qing, E. et al. Inter-domain communication in SARS-CoV-2 spike proteins controls protease-triggered cell entry. Cell Rep. 39, 110786 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Takano, T., Kawakami, C., Yamada, S., Satoh, R. & Hohdatsu, T. Antibody-dependent enhancement occurs upon re-infection with the identical serotype virus in feline infectious peritonitis virus infection. J. Vet. Med. Sci. 70, 1315–1321 (2008).

    Article 
    PubMed 

    Google Scholar
     

  • Loo, L. et al. Fibroblast-expressed LRRC15 is a receptor for SARS-CoV-2 spike and controls antiviral and antifibrotic transcriptional programs. PLoS Biol. 21, e3001967 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schwegmann-Weßels, C. et al. Comparison of vesicular stomatitis virus pseudotyped with the S proteins from a porcine and a human coronavirus. J. Gen. Virol. 90, 1724–1729 (2009).

    Article 
    PubMed 

    Google Scholar
     

  • Du, Y. et al. A broadly neutralizing humanized ACE2-targeting antibody against SARS-CoV-2 variants. Nat. Commun. 12, 5000 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Whitt, M. A. Generation of VSV pseudotypes using recombinant ΔG-VSV for studies on virus entry, identification of entry inhibitors, and immune responses to vaccines. J. Virol. Methods 169, 365–374 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nie, J. et al. Quantification of SARS-CoV-2 neutralizing antibody by a pseudotyped virus-based assay. Nat. Protoc. 15, 3699–3715 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Reed, L. J. & Muench, H. A simple method of estimating fifty per cent endpoints. Am. J. Epidemiol. 27, 493–497 (1938).

    Article 

    Google Scholar
     

  • Lempp, F. A. et al. Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies. Nature 598, 342–347 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Bowen, J. E. et al. SARS-CoV-2 spike conformation determines plasma neutralizing activity elicited by a wide panel of human vaccines. Sci. Immunol. 7, eadf1421 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Russo, C. J. & Passmore, L. A. Electron microscopy: ultrastable gold substrates for electron cryomicroscopy. Science 346, 1377–1380 (2014).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Suloway, C. et al. Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151, 41–60 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tegunov, D. & Cramer, P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat. Methods 16, 1146–1152 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Methods 17, 1214–1221 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zivanov, J., Nakane, T. & Scheres, S. H. W. A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis. IUCrJ 6, 5–17 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zivanov, J., Nakane, T. & Scheres, S. H. W. Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in −3.1. IUCrJ 7, 253–267 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, S. et al. High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy 135, 24–35 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pettersen, E. F. et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, R. Y.-R. et al. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife 5, e17219 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Frenz, B. et al. Automatically fixing errors in glycoprotein structures with Rosetta. Structure 27, 134–139.e3 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D 74, 519–530 (2018).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Barad, B. A. et al. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nat. Methods 12, 943–946 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Agirre, J. et al. Privateer: software for the conformational validation of carbohydrate structures. Nat. Struct. Mol. Biol. 22, 833–834 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, W. et al. Bats are natural reservoirs of SARS-like coronaviruses. Science 310, 676–679 (2005).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Hu, B. et al. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog. 13, e1006698 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ge, X.-Y. et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503, 535–538 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ju, X. et al. A novel cell culture system modeling the SARS-CoV-2 life cycle. PLoS Pathog. 17, e1009439 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Guo, H. et al. ACE2-independent bat sarbecovirus entry and replication in human and bat cells. mBio 13, e0256622 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • RELATED ARTICLES

    Most Popular

    Recent Comments