Evolution of the SARS-CoV-2 spike protein in the human host

Abstract Variants of SARS-CoV-2 have emerged which contain multiple substitutions in the surface spike glycoprotein that have been associated with increased transmission and resistance to neutralising antibodies and antisera. We have examined the structure and receptor binding properties of spike proteins from the B.1.1.7 (UK) and B.1.351 (SA) variants to better understand the evolution of the virus in humans. Both variants’ spikes have the same mutation, N501Y, in their receptor-binding domains that confers tighter ACE2 binding and this substitution relies on a common earlier substitution (D614G) to achieve the tighter binding. Each variant spike has also acquired a key change in structure that impacts virus pathogenesis. Unlike other SARS-CoV-2 spikes, the spike from the UK variant is stable against detrimerisation on binding ACE2. This feature primarily arises from the acquisition of a substitution at the S1-S2 furin site that allows for near-complete cleavage. In the SA variant spike, the presence of a new substitution, K417N, again on the background of the D614G substitution, enables the spike trimer to adopt fully open conformations that are required for receptor binding. Both types of structural change likely contribute to the increased effectiveness of these viruses for infecting human cells.

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Structure and binding properties of Pangolin-CoV spike glycoprotein inform the evolution of SARS-CoV-2

Nature Communications ◽

10.1038/s41467-021-21006-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Antoni G. Wrobel ◽

Donald J. Benton ◽

Pengqi Xu ◽

Lesley J. Calder ◽

Annabel Borg ◽

...

Keyword(s):

Receptor Binding ◽

Binding Domain ◽

Spike Protein ◽

Receptor Binding Domain ◽

Spike Glycoprotein ◽

Binding Properties ◽

Origin And Evolution ◽

Closed Conformation ◽

Bat Coronavirus

AbstractCoronaviruses of bats and pangolins have been implicated in the origin and evolution of the pandemic SARS-CoV-2. We show that spikes from Guangdong Pangolin-CoVs, closely related to SARS-CoV-2, bind strongly to human and pangolin ACE2 receptors. We also report the cryo-EM structure of a Pangolin-CoV spike protein and show it adopts a fully-closed conformation and that, aside from the Receptor-Binding Domain, it resembles the spike of a bat coronavirus RaTG13 more than that of SARS-CoV-2.

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SARS-CoV-2 B.1.617 emergence and sensitivity to vaccine-elicited antibodies

10.1101/2021.05.08.443253 ◽

2021 ◽

Author(s):

Isabella Ferreira ◽

Rawlings Datir ◽

Guido Papa ◽

Steven Kemp ◽

Bo Meng ◽

...

Keyword(s):

Receptor Binding ◽

Growth Rates ◽

Cleavage Site ◽

Syncytium Formation ◽

Binding Domain ◽

Spike Protein ◽

Receptor Binding Domain ◽

Additive Effects ◽

Neutralising Antibodies ◽

Indian State

The B.1.617 variant emerged in the Indian state of Maharashtra in late 2020 and has spread throughout India and to at least 40 countries. There have been fears that two key mutations seen in the receptor binding domain L452R and E484Q would have additive effects on evasion of neutralising antibodies. Here we delineate the phylogenetics of B.1.617 and spike mutation frequencies, in the context of others bearing L452R. The defining mutations in B.1.617.1 spike are L452R and E484Q in the RBD that interacts with ACE2 and is the target of neutralising antibodies. All B.1.617 viruses have the P681R mutation in the polybasic cleavage site region in spike. We report that B.1.617.1 spike bearing L452R, E484Q and P681R mediates entry into cells with slightly reduced efficiency compared to Wuhan-1. This spike confers modestly reduced sensitivity to BNT162b2 mRNA vaccine-elicited antibodies that is similar in magnitude to the loss of sensitivity conferred by L452R or E484Q alone. Furthermore we show that the P681R mutation significantly augments syncytium formation upon the B.1.617.1 spike protein, potentially contributing to increased pathogenesis observed in hamsters and infection growth rates observed in humans.

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SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability

10.1101/2020.03.21.001933 ◽

2020 ◽

Cited By ~ 4

Author(s):

Vinicio Armijos-Jaramillo ◽

Justin Yeager ◽

Claire Muslin ◽

Yunierkis Perez-Castillo

Keyword(s):

Receptor Binding ◽

Evolutionary Dynamics ◽

Hot Spot ◽

Critical Role ◽

Human Cells ◽

Binding Domain ◽

Host Cells ◽

Spike Protein ◽

Receptor Binding Domain ◽

Salt Bridges

AbstractThe emergence of SARS-CoV-2 has resulted in more than 200,000 infections and nearly 9,000 deaths globally so far. This novel virus is thought to have originated from an animal reservoir, and acquired the ability to infect human cells using the SARS-CoV cell receptor hACE2. In the wake of a global pandemic it is essential to improve our understanding of the evolutionary dynamics surrounding the origin and spread of a novel infectious disease. One way theory predicts selection pressures should shape viral evolution is to enhance binding with host cells. We first assessed evolutionary dynamics in select betacoronavirus spike protein genes to predict where these genomic regions are under directional or purifying selection between divergent viral lineages at various scales of relatedness. 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. Next, to gain further insights into factors associated with coronaviruses recognition of the human host receptor, we performed modeling studies of five different coronaviruses and their potential binding to hACE2. Modeling results indicate that interfering with the salt bridges at hot spot 353 could be an effective strategy for inhibiting binding, and hence for the prevention of coronavirus infections. We also propose that a glycine residue at the receptor binding domain of the spike glycoprotein can have a critical role in permitting bat variants of the coronaviruses to infect human cells.

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Multimerization- and glycosylation-dependent receptor binding of SARS-CoV-2 spike proteins

10.1101/2020.09.04.282558 ◽

2020 ◽

Author(s):

Kim M. Bouwman ◽

Ilhan Tomris ◽

Hannah L. Turner ◽

Roosmarijn van der Woude ◽

Gerlof P. Bosman ◽

...

Keyword(s):

Binding Affinity ◽

Cell Lines ◽

Receptor Binding ◽

Expression Profiles ◽

Spike Protein ◽

Binding Studies ◽

Binding Properties ◽

Experimental Animals ◽

High Mannose ◽

Mutant Cells

Receptor binding studies using recombinant SARS-CoV proteins have been hampered due to challenges in approaches creating spike protein or domains thereof, that recapitulate receptor binding properties of native viruses. We hypothesized that trimeric RBD proteins would be suitable candidates to study receptor binding properties of SARS-CoV-1 and -2. Here we created monomeric and trimeric fluorescent RBD proteins, derived from adherent HEK293T, as well as in GnTI mutant cells, to analyze the effect of complex vs high mannose glycosylation on receptor binding. The results demonstrate that trimeric fully glycosylated proteins are superior in receptor binding compared to monomeric and immaturely glycosylated variants. Although differences in binding to commonly used cell lines were minimal between the different RBD preparations, substantial differences were observed when respiratory tissues of experimental animals were stained. The RBD trimers demonstrated distinct ACE2 expression profiles in bronchiolar ducts and confirmed the higher binding affinity of SARS-CoV-2 over SARS-CoV-1. Our results show that fully glycosylated trimeric RBD proteins are attractive to analyze receptor binding and explore ACE2 expression profiles in tissues.

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Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7

10.1101/2021.01.25.428137 ◽

2021 ◽

Cited By ~ 11

Author(s):

Pengfei Wang ◽

Manoj S. Nair ◽

Lihong Liu ◽

Sho Iketani ◽

Yang Luo ◽

...

Keyword(s):

Receptor Binding ◽

Protective Efficacy ◽

Spike Protein ◽

Binding Motif ◽

Receptor Binding Domain ◽

Effective Interventions ◽

Recent Emergence ◽

New Challenges ◽

The Uk ◽

Antibody Resistance

The COVID-19 pandemic has ravaged the globe, and its causative agent, SARS-CoV-2, continues to rage. Prospects of ending this pandemic rest on the development of effective interventions. Single and combination monoclonal antibody (mAb) therapeutics have received emergency use authorization1–3, with more in the pipeline4–7. Furthermore, multiple vaccine constructs have shown promise8, including two with ~95% protective efficacy against COVID-199,10. However, these interventions were directed toward the initial SARS-CoV-2 that emerged in 2019. The recent emergence of new SARS-CoV-2 variants B.1.1.7 in the UK11 and B.1.351 in South Africa12 is of concern because of their purported ease of transmission and extensive mutations in the spike protein. We now report that B.1.1.7 is refractory to neutralization by most mAbs to the N-terminal domain (NTD) of spike and relatively resistant to a few mAbs to the receptor-binding domain (RBD). It is not more resistant to convalescent plasma or vaccinee sera. Findings on B.1.351 are more worrisome in that this variant is not only refractory to neutralization by most NTD mAbs but also by multiple individual mAbs to the receptor-binding motif on RBD, largely due to an E484K mutation. Moreover, B.1.351 is markedly more resistant to neutralization by convalescent plasma (9.4 fold) and vaccinee sera (10.3-12.4 fold). B.1.351 and emergent variants13,14 with similar spike mutations present new challenges for mAb therapy and threaten the protective efficacy of current vaccines.

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Structural Analysis of Receptor Binding Domain Mutations in SARS-CoV-2 Variants of Concern that Modulate ACE2 and Antibody Binding

10.1101/2021.08.25.457711 ◽

2021 ◽

Cited By ~ 1

Author(s):

Dhiraj Mannar ◽

James W Saville ◽

Xing Zhu ◽

Shanti S. Srivastava ◽

Alison M. Berezuk ◽

...

Keyword(s):

Structural Analysis ◽

South African ◽

Receptor Binding ◽

Antibody Binding ◽

Binding Domain ◽

Spike Protein ◽

Receptor Binding Domain ◽

Biochemical Assays ◽

The Uk ◽

Spike Proteins

SummaryThe recently emerged SARS-CoV-2 South African (B. 1.351) and Brazil/Japan (P.1) variants of concern (VoCs) include a key mutation (N501Y) found in the UK variant that enhances affinity of the spike protein for its receptor, ACE2. Additional mutations are found in these variants at residues 417 and 484 that appear to promote antibody evasion. In contrast, the Californian VoCs (B.1.427/429) lack the N501Y mutation, yet exhibit antibody evasion. We engineered spike proteins to express these RBD VoC mutations either in isolation, or in different combinations, and analyzed the effects using biochemical assays and cryo-EM structural analyses. Overall, our findings suggest that the emergence of new SARS-CoV-2 variant spikes can be rationalized as the result of mutations that confer either increased ACE2 affinity, increased antibody evasion, or both, providing a framework to dissect the molecular factors that drive VoC evolution.

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Investigation of interaction between close and open types of SARS-Cov-2 spike glycoprotein with synthesized and natural Compounds as inhibitor; Molecular Docking Study

10.21203/rs.3.rs-38089/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Masume Jomhori ◽

Hamid Mosaddeghi

Keyword(s):

Binding Site ◽

Receptor Binding ◽

Antiviral Drug ◽

Severe Infection ◽

Docking Study ◽

Spike Protein ◽

Spike Glycoprotein ◽

Molecular Docking Study ◽

Antiviral Compound ◽

Pubchem Database

Abstract Purpose Viral diseases are increasingly endangering universal public health because of a shortage of successful antiviral therapies. The novel pandemic 2019 n-Cov2 disease (COVID-19) is recently identified as viral disorder triggered by a new type of coronavirus. This type of coronavirus binds to the host human receptors through the Spike glycoprotein(S) Receptor Binding Domain (RBD). Two types of spike protein have been identified in open and closed states in which the open type causes severe infection. Thus, this receptor is a significant target for antiviral drug design.Methods Totally 111*2 natural and synthetic compounds were chosen from the PubChem database as ligands. To recognize the ability of direct contact between ligands and the binding site of 2019 n-Cov 2 -ACE2 protein, we have docked all compounds to the protein using AutoDock Vina. The FaF3-Drugs, Pan Assay Intrusion Compounds (PAINS), absorption, distribution, metabolism, excretion (ADME) and Lipinski's rules were used to evaluate the drug-like properties of the identified ligands. Antiviral compound prediction (AVC pred) also was used to assess antivirus properties.Results The results showed that seven ligands out of all had interactions with spike protein-angiotensin converting enzyme 2 binding site. We have found that six out of seven ligands show drug-like characteristics. We also found that the fluorophenyl and propane groups of ligands had the best interaction with the binding site of the protein.Conclusion Further, our results showed the ability of these ligands to prevent receptor binding of the spike protein SARS-CoV-2, so they would be considered as novel compounds of COVID-19 therapy drugs.

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SARS-CoV-2 Prion-Like Domains in Spike Proteins Enables Higher Affinity to ACE2

10.20944/preprints202003.0422.v1 ◽

2020 ◽

Author(s):

George Tetz ◽

Victor Tetz

Keyword(s):

Receptor Binding ◽

Cell Receptor ◽

Binding Domain ◽

Spike Protein ◽

Striking Difference ◽

Receptor Binding Domain ◽

Viral Receptor ◽

Functional Roles ◽

Binding Domains ◽

Spike Proteins

Currently, the world is struggling with the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Prion-like domains are critical for virulence and the development of therapeutic targets; however, the prion-like domains in the SARS-CoV-2 proteome have not been analyzed. In this in silico study, using the PLAAC algorithm, we identified the presence of prion-like domains in SARS-CoV-2 spike protein. Compared with other viruses, a striking difference was observed in the distribution of prion-like domains in the spike, since SARS-CoV-2 was the only coronavirus with a prion-like domain found in the receptor-binding domain of the S1 region of the spike protein. The presence and unique distribution of prion-like domains in the SARS-CoV-2 receptor-binding domains of spike proteins is particularly interesting, since although SARS-CoV-2 and SARS-CoV S share the same host cell receptor, angiotensin-converting enzyme 2 (ACE2), SARS-CoV-2 demonstrates a 10- to 20-fold higher affinity for ACE2. Finally, we identified prion-like domains in the α1 helix of the ACE2 receptor that interacts with the viral receptor-binding domain of SARS-CoV-2. Taken together, the present findings indicate that the identified PrDs in the SARS-CoV-2 receptor-binding domain (RBD) and ACE2 region that interacts with RBD have important functional roles in viral adhesion and entry.

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Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution

10.1101/2020.09.21.307439 ◽

2020 ◽

Author(s):

Shuyuan Zhang ◽

Shuyuan Qiao ◽

Jinfang Yu ◽

Jianwei Zeng ◽

Sisi Shan ◽

...

Keyword(s):

Receptor Binding ◽

Viral Protein ◽

Cell Entry ◽

Cellular Receptor ◽

Conformational Sampling ◽

Spike Glycoprotein ◽

Sequence Comparisons ◽

Inactive State ◽

Binding Domains ◽

Critical Residues

AbstractIn recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species transmission and infection. Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. All three receptor-binding domains (RBDs) of these two spike trimers are in the “down” conformation, indicating they are more prone to adopt this receptor-binding inactive state. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. Through structure and sequence comparisons, we identified critical residues in the RBD that underlie the different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes and propose that N-linked glycans serve as conformational control elements of the RBD. These results collectively indicate that strong RBD-ACE2 binding and efficient RBD conformational sampling are required for the evolution of SARS-CoV-2 to gain highly efficient infection.

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The neutralization potency of anti-SARS-CoV-2 therapeutic human monoclonal antibodies is retained against novel viral variants

10.1101/2021.04.01.438035 ◽

2021 ◽

Author(s):

Efi Makdasi ◽

Anat Zvi ◽

Ron Alcalay ◽

Tal Noy-Porat ◽

Eldar Peretz ◽

...

Keyword(s):

South Africa ◽

Monoclonal Antibodies ◽

Receptor Binding ◽

Clinical Use ◽

Receptor Binding Domain ◽

Spike Glycoprotein ◽

Human Monoclonal Antibodies ◽

Wide Range ◽

The Uk

SummaryA wide range of SARS-CoV-2 neutralizing monoclonal antibodies (mAbs) were reported to date, most of which target the spike glycoprotein and in particular its receptor binding domain (RBD) and N-terminal domain (NTD) of the S1 subunit. The therapeutic implementation of these antibodies has been recently challenged by the emerging SARS-CoV-2 variants, harboring an extensively-mutated spike versions. Consequently, the re-assessment of mAbs, previously reported to neutralize the original early-version of the virus, represents an assignment of high priority.With respect to the evolving mutations in the virus spike RBD, we evaluated the aptitude of four previously selected mAbs, targeting distinct epitopes, to bind RBD versions harboring individual mutations at positions 501, 477, 484, 439, 417 and 453. Mutations of these residues represent the prevailing worldwide distributed modifications of the RBD, previously reported to mediate escape from antibody neutralization. Additionally, the in vitro neutralization efficacies of the four RBD-specific mAbs, as well as two NTD-specific mAbs, were evaluated against two frequent SARS-CoV-2 variants of concern (VOCs): (i) the B.1.1.7 variant, emerged in the UK and (ii) the B.1.351 variant, emerged in South Africa. B.1.351, was previously suggested to escape many therapeutic mAbs, including those authorized for clinical use.The results of the present study, clearly indicate that in spite of mutation accumulation in the spike of the virus, some neutralizing mAbs preserve their potency to combat SARS-CoV-2 emerged variants. In particular, the previously reported highly potent MD65 mAb is shown to retain its ability to bind the prevalent novel viral mutations and to effectively neutralize the B.1.1.7 and B.1.351 variants of high clinical concern.

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