scholarly journals Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM

2020 ◽  
Vol 7 (1) ◽  
pp. eabe5575
Author(s):  
Cong Xu ◽  
Yanxing Wang ◽  
Caixuan Liu ◽  
Chao Zhang ◽  
Wenyu Han ◽  
...  
Keyword(s):  
Global Health ◽  
Receptor Binding ◽  
Viral Entry ◽  
Conformational Dynamics ◽  
Conformational Transitions ◽  
Fusion Peptide ◽  
Host Cells ◽  
Receptor Binding Domain ◽  
Specific Recognition ◽  
Viral Determinants

The recent outbreaks of SARS-CoV-2 pose a global health emergency. The SARS-CoV-2 trimeric spike (S) glycoprotein interacts with the human ACE2 receptor to mediate viral entry into host cells. We report the cryo-EM structures of a tightly closed SARS-CoV-2 S trimer with packed fusion peptide and an ACE2-bound S trimer at 2.7- and 3.8-Å resolution, respectively. Accompanying ACE2 binding to the up receptor-binding domain (RBD), the associated ACE2-RBD exhibits continuous swing motions. Notably, the SARS-CoV-2 S trimer appears much more sensitive to the ACE2 receptor than the SARS-CoV S trimer regarding receptor-triggered transformation from the closed prefusion state to the fusion-prone open state, potentially contributing to the superior infectivity of SARS-CoV-2. We defined the RBD T470-T478 loop and Y505 as viral determinants for specific recognition of SARS-CoV-2 RBD by ACE2. Our findings depict the mechanism of ACE2-induced S trimer conformational transitions from the ground prefusion state toward the postfusion state, facilitating development of anti–SARS-CoV-2 vaccines and therapeutics.

scholarly journals Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM

2020 ◽  
Author(s):  
Cong Xu ◽  
Yanxing Wang ◽  
Caixuan Liu ◽  
Chao Zhang ◽  
Wenyu Han ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Receptor Binding ◽  
Viral Entry ◽  
Conformational Dynamics ◽  
Conformational Transitions ◽  
Fusion Peptide ◽  
Host Cells ◽  
Structural Basis ◽  
Receptor Binding Domain ◽  
Viral Determinants

AbstractThe recent outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid international spread pose a global health emergency. The trimeric spike (S) glycoprotein interacts with its receptor human ACE2 to mediate viral entry into host-cells. Here we present cryo-EM structures of an uncharacterized tightly closed SARS-CoV-2 S-trimer and the ACE2-bound-S-trimer at 2.7-Å and 3.8-Å-resolution, respectively. The tightly closed S-trimer with inactivated fusion peptide may represent the ground prefusion state. ACE2 binding to the up receptor-binding domain (RBD) within S-trimer triggers continuous swing-motions of ACE2-RBD, resulting in conformational dynamics of S1 subunits. Noteworthy, SARS-CoV-2 S-trimer appears much more sensitive to ACE2-receptor than SARS-CoV S-trimer in terms of receptor-triggered transformation from the closed prefusion state to the fusion-prone open state, potentially contributing to the superior infectivity of SARS-CoV-2. We defined the RBD T470-T478 loop and residue Y505 as viral determinants for specific recognition of SARS-CoV-2 RBD by ACE2, and provided structural basis of the spike D614G-mutation induced enhanced infectivity. Our findings offer a thorough picture on the mechanism of ACE2-induced conformational transitions of S-trimer from ground prefusion state towards postfusion state, thereby providing important information for development of vaccines and therapeutics aimed to block receptor binding.

scholarly journals A Fungal Defensin Targets the SARS−CoV−2 Spike Receptor−Binding Domain

2021 ◽  
Vol 7 (7) ◽  
pp. 553
Author(s):  
Bin Gao ◽  
Shunyi Zhu
Keyword(s):  
Receptor Binding ◽  
Viral Entry ◽  
Single Point ◽  
Binding Domain ◽  
Host Cells ◽  
Single Point Mutation ◽  
Binding Motif ◽  
Microsporum Canis ◽  
Receptor Binding Domain ◽  
Fungal Defensin

Coronavirus Disease 2019 (COVID−19) elicited by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS−CoV−2) is calling for novel targeted drugs. Since the viral entry into host cells depends on specific interactions between the receptor−binding domain (RBD) of the viral Spike protein and the membrane−bound monocarboxypeptidase angiotensin converting enzyme 2 (ACE2), the development of high affinity RBD binders to compete with human ACE2 represents a promising strategy for the design of therapeutics to prevent viral entry. Here, we report the discovery of such a binder and its improvement via a combination of computational and experimental approaches. The binder micasin, a known fungal defensin from the dermatophytic fungus Microsporum canis with antibacterial activity, can dock to the crevice formed by the receptor−binding motif (RBM) of RBD via an extensive shape complementarity interface (855.9 Å2 in area) with numerous hydrophobic and hydrogen−bonding interactions. Using microscale thermophoresis (MST) technique, we confirmed that micasin and its C−terminal γ−core derivative with multiple predicted interacting residues exhibited a low micromolar affinity to RBD. Expanding the interface area of micasin through a single point mutation to 970.5 Å2 accompanying an enhanced hydrogen bond network significantly improved its binding affinity by six−fold. Our work highlights the naturally occurring fungal defensins as an emerging resource that may be suitable for the development into antiviral agents for COVID−19.

scholarly journals SARS-CoV-2 receptor binding domain fusion protein efficiently neutralizes virus infection

2021 ◽  
Vol 17 (12) ◽  
pp. e1010175
Author(s):  
Abigael Eva Chaouat ◽  
Hagit Achdout ◽  
Inbal Kol ◽  
Orit Berhani ◽  
Gil Roi ◽  
...  
Keyword(s):  
Virus Infection ◽  
Enzymatic Activity ◽  
Receptor Binding ◽  
Viral Entry ◽  
Surface Expression ◽  
Binding Domain ◽  
Host Cells ◽  
Receptor Binding Domain ◽  
High Virus

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic. Currently, as dangerous mutations emerge, there is an increased demand for specific treatments for SARS-CoV-2 infected patients. The spike glycoprotein on the virus membrane binds to the angiotensin converting enzyme 2) ACE2 (receptor on host cells through its receptor binding domain (RBD) to mediate virus entry. Thus, blocking this interaction may inhibit viral entry and consequently stop infection. Here, we generated fusion proteins composed of the extracellular portions of ACE2 and RBD fused to the Fc portion of human IgG1 (ACE2-Ig and RBD-Ig, respectively). We demonstrate that ACE2-Ig is enzymatically active and that it can be recognized by the SARS-CoV-2 RBD, independently of its enzymatic activity. We further show that RBD-Ig efficiently inhibits in-vivo SARS-CoV-2 infection better than ACE2-Ig. Mechanistically, we show that anti-spike antibody generation, ACE2 enzymatic activity, and ACE2 surface expression were not affected by RBD-Ig. Finally, we show that RBD-Ig is more efficient than ACE2-Ig at neutralizing high virus titers. We thus propose that RBD-Ig physically blocks virus infection by binding to ACE2 and that RBD-Ig should be used for the treatment of SARS-CoV-2-infected patients.

scholarly journals A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2

2012 ◽  
Vol 94 (3) ◽  
pp. 288-296 ◽  
Author(s):  
Anna-Winona Struck ◽  
Marco Axmann ◽  
Susanne Pfefferle ◽  
Christian Drosten ◽  
Bernd Meyer
Keyword(s):  
Receptor Binding ◽  
Viral Entry ◽  
Binding Domain ◽  
Host Cells ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Corona Virus ◽  
Protein Blocks ◽  
Human Receptor

scholarly journals Allosteric Cross-Talk Among SARS-CoV-2 Spike’s Receptor-Binding Domain Mutations Triggers an Effective Hijacking of Human Cell Receptor

2021 ◽  
Author(s):  
Angelo Spinello ◽  
Andrea Saltalamacchia ◽  
Jure Borišek ◽  
Alessandra Magistrato
Keyword(s):  
Receptor Binding ◽  
Viral Entry ◽  
Cell Receptor ◽  
Binding Domain ◽  
Host Cells ◽  
Evolutionary Strategies ◽  
Receptor Binding Domain ◽  
Angiotensin Converting Enzyme 2 ◽  
Societal Challenge ◽  
Dynamics Simulations

ABSTRACTThe rapid and relentless emergence of novel highly transmissible SARS-CoV-2 variants, possibly decreasing vaccine efficacy, currently represents a formidable medical and societal challenge. These variants frequently hold mutations on the Spike protein’s Receptor-Binding Domain (RBD), which, binding to the Angiotensin-Converting Enzyme 2 (ACE2) receptor, mediates viral entry into the host cells.Here, all-atom Molecular Dynamics simulations and Dynamical Network Theory of the wild-type and mutant RBD/ACE2 adducts disclose that while the N501Y mutation (UK variant) enhances the Spike’s binding affinity towards ACE2, the N501Y, E484K and K417N mutations (South African variant) aptly adapt to increase SARS-CoV-2 propagation via a two-pronged strategy: (i) effectively grasping ACE2 through an allosteric signaling between pivotal RBD structural elements; and (ii) impairing the binding of antibodies elicited by infected/vaccinated patients. This information, unlocking the molecular terms and evolutionary strategies underlying the increased virulence of emerging SARS-CoV-2 variants, set the basis for developing the next-generation anti-COVID-19 therapeutics.TOC GRAPHICS

scholarly journals Proteolytic Transformation and Stimulation of SARSCov-2 Spike Protein with Human ACE-2 Receptor

2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Sohail S ◽  
◽  
Rana H ◽  
Awan DS ◽  
Sohail F ◽  
...  
Keyword(s):  
Amino Acid ◽  
Receptor Binding ◽  
Viral Entry ◽  
Attachment Site ◽  
Binding Domain ◽  
Host Cells ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Major Pathway ◽  
Important Relationship

Severe acute respiratory syndrome coronavirus has a great role in causing respiratory illness in humans and has the most important relationship of its spike proteins with host ACE-2 receptors. After entry into the human body, the viral S protein receptor-binding domain binds to human ACE-2 receptor. Two modes explained in this paper of an ACE-2 shedding. The shedding induces the process of viral entry to host cells by binding SARS-CoV-2 proteins. The residues of arginine and lysine in the ACE-2 receptor from 652 to 659 amino acid cleavage by ADAM17 but in TMPRSS2 the residues can be seen on amino acid from 697 to 716. Corona virus genome shows some structural proteins that are responsible for the cellular entry and facilitate the attachment of a virus to the host cell. Virus recognizes the attachment site and binds with it and enter into the cell. Spike protein is split from the cleavage site along its two subunits S1 and S2 then during this process. S2 subunit release RBD (Receptor- Binding Domain) of S1 mediated to the ACE-2. The RBD of S1 consists of 200 amino acid domains. The unknown protein B6ATI which is a neutral amino acid transporter located in ileum is the basic cause for formation of ACE-2 homodimer. In this way S1 domain provides site for another S2 domain. This leads to concealing of the ACE-2 ectodomain cleavage-sites, shedding. It prevents endocytosis of the receptor blocking a major pathway in the viral entry.

scholarly journals Interaction of human ACE2 to membrane-bound SARS-CoV-1 and SARS-CoV-2 S glycoproteins

2020 ◽  
Author(s):  
Sai Priya Anand ◽  
Yaozong Chen ◽  
Jérémie Prévost ◽  
Romain Gasser ◽  
Guillaume Beaudoin-Bussières ◽  
...  
Keyword(s):  
Angiotensin Converting Enzyme ◽  
Receptor Binding ◽  
Viral Entry ◽  
Conformational Transitions ◽  
Binding Domain ◽  
Receptor Binding Domain ◽  
Converting Enzyme ◽  
Spike Glycoprotein ◽  
Angiotensin Converting Enzyme 2 ◽  
Membrane Bound

AbstractA novel severe acute respiratory (SARS)-like coronavirus (SARS-CoV-2) is responsible for the current global coronavirus disease 2019 (COVID-19) pandemic, infecting millions of people and causing hundreds of thousands of deaths. The viral entry of SARS-CoV-2 depends on an interaction between the receptor binding domain of its trimeric Spike glycoprotein and the human angiotensin converting enzyme 2 (ACE2) receptor. A better understanding of the Spike/ACE2 interaction is still required to design anti-SARS-CoV-2 therapeutics. Here, we investigated the degree of cooperativity of ACE2 within both the SARS-CoV-2 and the closely related SARS-CoV-1 membrane-bound S glycoproteins. We show that there exist differential inter-protomer conformational transitions between both Spike trimers. Interestingly, the SARS-CoV-2 spike exhibits a positive cooperativity for monomeric soluble ACE2 binding when compared to the SARS-CoV-1 spike, which might have more structural restrains. Our findings can be of importance in the development of therapeutics that block the Spike/ACE2 interaction.

scholarly journals Stereotypic neutralizing VH antibodies against SARS-CoV-2 spike protein receptor binding domain in COVID-19 patients and healthy individuals

2021 ◽  
pp. eabd6990
Author(s):  
Sang Il Kim ◽  
Jinsung Noh ◽  
Sujeong Kim ◽  
Younggeun Choi ◽  
Duck Kyun Yoo ◽  
...  
Keyword(s):  
B Cells ◽  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
De Novo ◽  
Binding Domain ◽  
Host Cells ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Healthy Individuals

Stereotypic antibody clonotypes exist in healthy individuals and may provide protective immunity against viral infections by neutralization. We observed that 13 out of 17 patients with COVID-19 had stereotypic variable heavy chain (VH) antibody clonotypes directed against the receptor-binding domain (RBD) of SARS-CoV-2 spike protein. These antibody clonotypes were comprised of immunoglobulin heavy variable (IGHV)3-53 or IGHV3-66 and immunoglobulin heavy joining (IGHJ)6 genes. These clonotypes included IgM, IgG3, IgG1, IgA1, IgG2, and IgA2 subtypes and had minimal somatic mutations, which suggested swift class switching after SARS-CoV-2 infection. The different immunoglobulin heavy variable chains were paired with diverse light chains resulting in binding to the RBD of SARS-CoV-2 spike protein. Human antibodies specific for the RBD can neutralize SARS-CoV-2 by inhibiting entry into host cells. We observed that one of these stereotypic neutralizing antibodies could inhibit viral replication in vitro using a clinical isolate of SARS-CoV-2. We also found that these VH clonotypes existed in six out of 10 healthy individuals, with IgM isotypes predominating. These findings suggest that stereotypic clonotypes can develop de novo from naïve B cells and not from memory B cells established from prior exposure to similar viruses. The expeditious and stereotypic expansion of these clonotypes may have occurred in patients infected with SARS-CoV-2 because they were already present.

scholarly journals Sialic acid-Dependent Binding and Viral Entry of SARS-CoV-2

2021 ◽  
Author(s):  
Linh Nguyen ◽  
Kelli McCord ◽  
Duong Bui ◽  
Kim Bouwman ◽  
Elena Kitova ◽  
...  
Keyword(s):  
Sialic Acid ◽  
Cell Surface ◽  
Heparan Sulfate ◽  
Receptor Binding ◽  
Viral Entry ◽  
Receptor Binding Domain ◽  
Artificial Membrane ◽  
Neuraminidase Treatment ◽  
S Protein ◽  
Knock Out

Abstract Emerging evidence suggests that host glycans influence infection by SARS-CoV-2. Here, we reveal that the receptor-binding domain (RBD) of the spike (S)-protein on SARS-CoV-2 recognizes oligosaccharides containing sialic acid (SA), with preference for the oligosaccharide of monosialylated gangliosides. Gangliosides embedded within an artificial membrane also bind the RBD. The monomeric affinities (Kd = 100-200 μM) of gangliosides for the RBD are similar to heparan sulfate, another negatively charged glycan ligand of the RBD proposed as a viral co-receptor. RBD binding and infection of SARS-CoV-2 pseudotyped lentivirus to ACE2-expressing cells is decreased upon depleting cell surface SA level using three approaches: sialyltransferase inhibition, genetic knock-out of SA biosynthesis, or neuraminidase treatment. These effects on RBD binding and pseudotyped viral entry are recapitulated with pharmacological or genetic disruption of glycolipid biosynthesis. Together, these results suggest that sialylated glycans, specifically glycolipids, facilitate viral entry of SARS-CoV-2.

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