A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2

Neutralizing antibodies could potentially be used as antivirals against the coronavirus disease 2019 (COVID-19) pandemic. Here, we report isolation of four human-origin monoclonal antibodies from a convalescent patient, all of which display neutralization abilities. The antibodies B38 and H4 block binding between the spike glycoprotein receptor binding domain (RBD) of the virus and the cellular receptor angiotensin-converting enzyme 2 (ACE2). A competition assay indicated different epitopes on the RBD for these two antibodies, making them a potentially promising virus-targeting monoclonal antibody pair for avoiding immune escape in future clinical applications. Moreover, a therapeutic study in a mouse model validated that these antibodies can reduce virus titers in infected lungs. The RBD-B38 complex structure revealed that most residues on the epitope overlap with the RBD-ACE2 binding interface, explaining the blocking effect and neutralizing capacity. Our results highlight the promise of antibody-based therapeutics and provide a structural basis for rational vaccine design.

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A non-competing pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2

10.1101/2020.05.01.20077743 ◽

2020 ◽

Cited By ~ 12

Author(s):

Yan Wu ◽

Feiran Wang ◽

Chenguang Shen ◽

Weiyu Peng ◽

Delin Li ◽

...

Keyword(s):

Monoclonal Antibodies ◽

Neutralizing Antibodies ◽

Immune Escape ◽

Structural Basis ◽

Cellular Receptor ◽

Virus Binding ◽

Reduction Activity ◽

Binding Interface ◽

Neutralizing Capacity

AbstractNeutralizing antibodies could be antivirals against COVID-19 pandemics. Here, we report the isolation of four human-origin monoclonal antibodies from a convalescent patient in China. All of these isolated antibodies display neutralization abilities in vitro. Two of them (B38 and H4) block the binding between RBD and vial cellular receptor ACE2. Further competition assay indicates that B38 and H4 recognize different epitopes on the RBD, which is ideal for a virus-targeting mAb-pair to avoid immune escape in the future clinical applications. Moreover, therapeutic study on the mouse model validated that these two antibodies can reduce virus titers in the infected mouse lungs. Structure of RBD-B38 complex revealed that most residues on the epitope are overlapped with the RBD-ACE2 binding interface, which explained the blocking efficacy and neutralizing capacity. Our results highlight the promise of antibody-based therapeutics and provide the structural basis of rational vaccine design.One Sentence SummaryA pair of human neutralizing monoclonal antibodies against COVID-19 compete cellular receptor binding but with different epitopes, and with post-exposure viral load reduction activity.

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Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants

Science ◽

10.1126/science.abi9745 ◽

2021 ◽

pp. eabi9745

Author(s):

Yongfei Cai ◽

Jun Zhang ◽

Tianshu Xiao ◽

Christy L. Lavine ◽

Shaun Rawson ◽

...

Keyword(s):

Immune Evasion ◽

Neutralizing Antibodies ◽

Viral Fitness ◽

Structural Basis ◽

Amino Acid Substitutions ◽

Receptor Binding Domain ◽

Angiotensin Converting Enzyme 2 ◽

Antigenic Properties ◽

Structural Details ◽

Fast Spreading

Several fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have become the dominant circulating strains in the COVID-19 pandemic. We report here cryo-EM structures of the full-length spike (S) trimers of the B.1.1.7 and B.1.351 variants, as well as their biochemical and antigenic properties. Amino acid substitutions in the B.1.1.7 protein increase the accessibility of its receptor binding domain and also the binding affinity for receptor angiotensin-converting enzyme 2 (ACE2). The enhanced receptor engagement may account for the increased transmissibility. The B.1.351 variant has evolved to reshape antigenic surfaces of the major neutralizing sites on the S protein, making it resistant to some potent neutralizing antibodies. These findings provide structural details on how SARS-CoV-2 has evolved to enhance viral fitness and immune evasion.

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Inter-Molecular Electrostatic Interactions Stabilizing the Structure of the PD-1/PD-L1 Axis: A Structural Evolutionary Perspective

10.20944/preprints202001.0130.v1 ◽

2020 ◽

Author(s):

Wei Li

Keyword(s):

Natural Selection ◽

Tumor Cell ◽

Tumor Immunity ◽

Electrostatic Interactions ◽

Immune Escape ◽

Complex Structure ◽

Evolutionary Perspective ◽

Binding Interface ◽

First Time ◽

Structural Hypothesis

PD-1/PD-L1 axis is one key therapeutic target against tumor cell immune escape. Structurally essential to the PD-1/PD-L1-linked immune escape is the binding interface of the PD-1/PD-L1 complex structure. Incorporating currently available PD-1/PD-L1-related experimental structures, this article unveils two sets of experimentally observed inter-molecular electrostatic interactions which stabilize the binding interface of the PD-1/PD-L1 complex structure. For the first time, this article proposes an evolutionary structural hypothesis that, as a result of natural selection, PD-1 is able to genetically mutate itself to structurally disrupt the PD-1/PD-L1 axis towards the restoration of T cell-mediated anti-tumor immunity.

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Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies

PLoS Pathogens ◽

10.1371/journal.ppat.1009772 ◽

2021 ◽

Vol 17 (8) ◽

pp. e1009772

Author(s):

Marta Alenquer ◽

Filipe Ferreira ◽

Diana Lousa ◽

Mariana Valério ◽

Mónica Medina-Lopes ◽

...

Keyword(s):

Amino Acid ◽

Immune Evasion ◽

Neutralizing Antibodies ◽

Immune Escape ◽

Host Immunity ◽

Arms Race ◽

Spike Protein ◽

Antibody Neutralization ◽

Angiotensin Converting Enzyme 2 ◽

The Core

Understanding SARS-CoV-2 evolution and host immunity is critical to control COVID-19 pandemics. At the core is an arms-race between SARS-CoV-2 antibody and angiotensin-converting enzyme 2 (ACE2) recognition, a function of the viral protein spike. Mutations in spike impacting antibody and/or ACE2 binding are appearing worldwide, imposing the need to monitor SARS-CoV2 evolution and dynamics in the population. Determining signatures in SARS-CoV-2 that render the virus resistant to neutralizing antibodies is critical. We engineered 25 spike-pseudotyped lentiviruses containing individual and combined mutations in the spike protein, including all defining mutations in the variants of concern, to identify the effect of single and synergic amino acid substitutions in promoting immune escape. We confirmed that E484K evades antibody neutralization elicited by infection or vaccination, a capacity augmented when complemented by K417N and N501Y mutations. In silico analysis provided an explanation for E484K immune evasion. E484 frequently engages in interactions with antibodies but not with ACE2. Importantly, we identified a novel amino acid of concern, S494, which shares a similar pattern. Using the already circulating mutation S494P, we found that it reduces antibody neutralization of convalescent and post-immunization sera, particularly when combined with E484K and with mutations able to increase binding to ACE2, such as N501Y. Our analysis of synergic mutations provides a signature for hotspots for immune evasion and for targets of therapies, vaccines and diagnostics.

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Structural basis for bivalent binding and inhibition of SARS-CoV-2 infection by human potent neutralizing antibodies

Cell Research ◽

10.1038/s41422-021-00487-9 ◽

2021 ◽

Author(s):

Renhong Yan ◽

Ruoke Wang ◽

Bin Ju ◽

Jinfang Yu ◽

Yuanyuan Zhang ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Clinical Intervention ◽

Structural Features ◽

Full Length ◽

Structural Basis ◽

Receptor Binding Domain ◽

S Protein ◽

Angiotensin Converting Enzyme 2 ◽

Neutralizing Activity ◽

Potent Neutralization

AbstractNeutralizing monoclonal antibodies (nAbs) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represent promising candidates for clinical intervention against coronavirus disease 2019 (COVID-19). We isolated a large number of nAbs from SARS-CoV-2-infected individuals capable of disrupting proper interaction between the receptor binding domain (RBD) of the viral spike (S) protein and the receptor angiotensin converting enzyme 2 (ACE2). However, the structural basis for their potent neutralizing activity remains unclear. Here, we report cryo-EM structures of the ten most potent nAbs in their native full-length IgG-form or in both IgG-form and Fab-form bound to the trimeric S protein of SARS-CoV-2. The bivalent binding of the full-length IgG is found to associate with more RBDs in the “up” conformation than the monovalent binding of Fab, perhaps contributing to the enhanced neutralizing activity of IgG and triggering more shedding of the S1 subunit from the S protein. Comparison of a large number of nAbs identified common and unique structural features associated with their potent neutralizing activities. This work provides a structural basis for further understanding the mechanism of nAbs, especially through revealing the bivalent binding and its correlation with more potent neutralization and the shedding of S1 subunit.

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Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike

10.1101/2020.07.09.193680 ◽

2020 ◽

Cited By ~ 4

Author(s):

Ahmad Reza Mehdipour ◽

Gerhard Hummer

Keyword(s):

Neutralizing Antibodies ◽

Neutralizing Antibody ◽

Md Simulations ◽

Spike Protein ◽

Dual Nature ◽

Angiotensin Converting Enzyme 2 ◽

Fusion Inhibitors ◽

Binding Interface ◽

Glycosylation Sites ◽

Cryptic Epitope

AbstractBinding of the spike protein of SARS-CoV-2 to the human angiotensin converting enzyme 2 (ACE2) receptor triggers translocation of the virus into cells. Both the ACE2 receptor and the spike protein are heavily glycosylated, including at sites near their binding interface. We built fully glycosylated models of the ACE2 receptor bound to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Using atomistic molecular dynamics (MD) simulations, we found that the glycosylation of the human ACE2 receptor contributes substantially to the binding of the virus. Interestingly, the glycans at two glycosylation sites, N90 and N322, have opposite effects on spike protein binding. The glycan at the N90 site partly covers the binding interface of the spike RBD. Therefore, this glycan can interfere with the binding of the spike protein and protect against docking of the virus to the cell. By contrast, the glycan at the N322 site interacts tightly with the RBD of the ACE2-bound spike protein and strengthens the complex. Remarkably, the N322 glycan binds into a conserved region of the spike protein identified previously as a cryptic epitope for a neutralizing antibody. By mapping the glycan binding sites, our MD simulations aid in the targeted development of neutralizing antibodies and SARS-CoV-2 fusion inhibitors.

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Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants

10.1101/2021.04.13.439709 ◽

2021 ◽

Author(s):

Yongfei Cai ◽

Jun Zhang ◽

Tianshu Xiao ◽

Christy L. Lavine ◽

Shaun Rawson ◽

...

Keyword(s):

Immune Evasion ◽

Neutralizing Antibodies ◽

Rapid Evolution ◽

Cell Types ◽

Viral Fitness ◽

Structural Basis ◽

Angiotensin Converting Enzyme 2 ◽

Risk Of Mortality ◽

Antigenic Properties ◽

Additional Cell

Several fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have become the dominant circulating strains that continue to fuel the COVID-19 pandemic despite intensive vaccination efforts throughout the world. We report here cryo-EM structures of the full-length spike (S) trimers of the B.1.1.7 and B.1.351 variants, as well as their biochemical and antigenic properties. Mutations in the B.1.1.7 protein increase the accessibility of its receptor binding domain and also the binding affinity for receptor angiotensin-converting enzyme 2 (ACE2). The enhanced receptor engagement can account for the increased transmissibility and risk of mortality as the variant may begin to infect efficiently infect additional cell types expressing low levels of ACE2. The B.1.351 variant has evolved to reshape antigenic surfaces of the major neutralizing sites on the S protein, rendering complete resistance to some potent neutralizing antibodies. These findings provide structural details on how the wide spread of SARS-CoV-2 enables rapid evolution to enhance viral fitness and immune evasion. They may guide intervention strategies to control the pandemic.

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Molecular mechanism of SHP2 activation by PD-1 stimulation

Science Advances ◽

10.1126/sciadv.aay4458 ◽

2020 ◽

Vol 6 (5) ◽

pp. eaay4458 ◽

Cited By ~ 23

Author(s):

M. Marasco ◽

A. Berteotti ◽

J. Weyershaeuser ◽

N. Thorausch ◽

J. Sikorska ◽

...

Keyword(s):

T Cell ◽

Immune Escape ◽

Complex Structure ◽

Structural Basis ◽

Immune Receptor ◽

Sh2 Domains ◽

T Cell Stimulation ◽

Programmed Death ◽

Programmed Death 1 ◽

Src Homology

In cancer, the programmed death-1 (PD-1) pathway suppresses T cell stimulation and mediates immune escape. Upon stimulation, PD-1 becomes phosphorylated at its immune receptor tyrosine–based inhibitory motif (ITIM) and immune receptor tyrosine–based switch motif (ITSM), which then bind the Src homology 2 (SH2) domains of SH2-containing phosphatase 2 (SHP2), initiating T cell inactivation. The SHP2–PD-1 complex structure and the exact functions of the two SH2 domains and phosphorylated motifs remain unknown. Here, we explain the structural basis and provide functional evidence for the mechanism of PD-1-mediated SHP2 activation. We demonstrate that full activation is obtained only upon phosphorylation of both ITIM and ITSM: ITSM binds C-SH2 with strong affinity, recruiting SHP2 to PD-1, while ITIM binds N-SH2, displacing it from the catalytic pocket and activating SHP2. This binding event requires the formation of a new inter-domain interface, offering opportunities for the development of novel immunotherapeutic approaches.

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Structural basis for bivalent binding and inhibition of SARS-CoV-2 infection by human potent neutralizing antibodies

10.1101/2020.10.13.336800 ◽

2020 ◽

Author(s):

Renhong Yan ◽

Ruoke Wang ◽

Bin Ju ◽

Jinfang Yu ◽

Yuanyuan Zhang ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Clinical Intervention ◽

Structural Features ◽

Full Length ◽

Structural Basis ◽

Virus Infections ◽

Virus Diseases ◽

S Protein ◽

Angiotensin Converting Enzyme 2 ◽

Potent Neutralization

AbstractNeutralizing monoclonal antibodies (nAbs) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represent promising candidates for clinical intervention against coronavirus virus diseases 2019 (COVID-19). We isolated a large number of nAbs from SARS-CoV-2 infected individuals capable of disrupting proper interaction between the receptor binding domain (RBD) of the viral spike (S) protein and the receptor angiotensin converting enzyme 2 (ACE2). In order to understand the mechanism of these nAbs on neutralizing SARS-CoV-2 virus infections, we have performed cryo-EM analysis and here report cryo-EM structures of the ten most potent nAbs in their native full-length IgG or Fab forms bound to the trimeric S protein of SARS-CoV-2. The bivalent binding of the full-length IgG is found to associate with more RBD in the “up” conformation than the monovalent binding of Fab, perhaps contributing to the enhanced neutralizing activity of IgG and triggering more shedding of the S1 subunit from the S protein. Comparison of large number of nAbs identified common and unique structural features associated with their potent neutralizing activities. This work provides structural basis for further understanding the mechanism of nAbs, especially through revealing the bivalent binding and their correlation with more potent neutralization and the shedding of S1 subunit.

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Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2100425118 ◽

2021 ◽

Vol 118 (19) ◽

pp. e2100425118

Author(s):

Ahmad Reza Mehdipour ◽

Gerhard Hummer

Keyword(s):

Neutralizing Antibodies ◽

Neutralizing Antibody ◽

Md Simulations ◽

Spike Protein ◽

Dual Nature ◽

Angiotensin Converting Enzyme 2 ◽

Fusion Inhibitors ◽

Binding Interface ◽

Glycosylation Sites ◽

Cryptic Epitope

Binding of the spike protein of SARS-CoV-2 to the human angiotensin-converting enzyme 2 (ACE2) receptor triggers translocation of the virus into cells. Both the ACE2 receptor and the spike protein are heavily glycosylated, including at sites near their binding interface. We built fully glycosylated models of the ACE2 receptor bound to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Using atomistic molecular dynamics (MD) simulations, we found that the glycosylation of the human ACE2 receptor contributes substantially to the binding of the virus. Interestingly, the glycans at two glycosylation sites, N90 and N322, have opposite effects on spike protein binding. The glycan at the N90 site partly covers the binding interface of the spike RBD. Therefore, this glycan can interfere with the binding of the spike protein and protect against docking of the virus to the cell. By contrast, the glycan at the N322 site interacts tightly with the RBD of the ACE2-bound spike protein and strengthens the complex. Remarkably, the N322 glycan binds to a conserved region of the spike protein identified previously as a cryptic epitope for a neutralizing antibody. By mapping the glycan binding sites, our MD simulations aid in the targeted development of neutralizing antibodies and SARS-CoV-2 fusion inhibitors.

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