Synthetic Homogeneous Glycoforms of the SARS‐CoV‐2 Spike Receptor‐Binding Domain Reveals Different Binding Profiles of Monoclonal Antibodies

AbstractMonoclonal antibodies against the SARS-CoV-2 spike protein, notably, those developed by Regeneron Pharmaceuticals and Eli Lilly and Company have proven to provide protection against severe COVID-19. The emergence of SARS-CoV-2 variants with heavily mutated spike proteins raises the concern that the therapy could become less effective if any of the mutations disrupt epitopes engaged by the antibodies. In this study, we tested monoclonal antibodies REGN10933 and REGN10987 that are used in combination, for their ability to neutralize SARS-CoV-2 variants B.1.1.7, B.1.351, mink cluster 5 and COH.20G/677H. We report that REGN10987 maintains most of its neutralization activity against viruses with B.1.1.7, B.1.351 and mink cluster 5 spike proteins but that REGN10933 has lost activity against B.1.351 and mink cluster 5. The failure of REGN10933 to neutralize B.1.351 is caused by the K417N and E484K mutations in the receptor binding domain; the failure to neutralize the mink cluster 5 spike protein is caused by the Y453F mutation. The REGN10933 and REGN10987 combination was 9.1-fold less potent on B.1.351 and 16.2-fold less potent on mink cluster 5, raising concerns of reduced efficacy in the treatment of patients infected with variant viruses. The results suggest that there is a need to develop additional monoclonal antibodies that are not affected by the current spike protein mutations.

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Key substitutions in the spike protein of SARS-CoV-2 variants can predict resistance to monoclonal antibodies, but other substitutions can modify the effects

10.1101/2021.07.16.452748 ◽

2021 ◽

Author(s):

Sabrina Lusvarghi ◽

Wei Wang ◽

Rachel Herrup ◽

Sabari Nath Neerukonda ◽

Russell Vassell ◽

...

Keyword(s):

Monoclonal Antibodies ◽

Receptor Binding ◽

Clinical Stage ◽

Binding Domain ◽

Spike Protein ◽

Receptor Binding Domain ◽

Therapeutic Antibodies ◽

Epistatic Interactions ◽

Neutralization Activity ◽

Virus Susceptibility

Mutations in the spike protein of SARS-CoV-2 variants can compromise the effectiveness of therapeutic antibodies. Most clinical-stage therapeutic antibodies target the spike receptor binding domain (RBD), but variants often have multiple mutations in several spike regions. To help predict antibody potency against emerging variants, we evaluated 25 clinical-stage therapeutic antibodies for neutralization activity against 60 pseudoviruses bearing spikes with single or multiple substitutions in several spike domains, including the full set of substitutions in B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.429 (Epsilon), B.1.526 (Iota), A.23.1 and R.1 variants. We found that 14 of 15 single antibodies were vulnerable to at least one RBD substitution, but most combination and polyclonal therapeutic antibodies remained potent. Key substitutions in variants with multiple spike substitutions predicted resistance, but the degree of resistance could be modified in unpredictable ways by other spike substitutions that may reside outside of the RBD. These findings highlight the importance of assessing antibody potency in the context of all substitutions in a variant and show that epistatic interactions in spike can modify virus susceptibility to therapeutic antibodies.

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On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2

10.1101/2020.04.05.026377 ◽

2020 ◽

Cited By ~ 2

Author(s):

Carolina Corrêa Giron ◽

Aatto Laaksonen ◽

Fernando L. Barroso da Silva

Keyword(s):

Monoclonal Antibodies ◽

Receptor Binding ◽

International Health ◽

Binding Domain ◽

Clinical Aspects ◽

Receptor Binding Domain ◽

Health Crisis ◽

Structural Modifications ◽

Constant Ph ◽

Promising Target

ABSTRACTA new betacoronavirus named SARS-CoV-2 has emerged as a new threat to global health and economy. A promising target for both diagnosis and therapeutics treatments of the new disease named COVID-19 is the coronavirus (CoV) spike (S) glycoprotein. By constant-pH Monte Carlo simulations and the PROCEEDpKa method, we have mapped the electrostatic epitopes for four monoclonal antibodies and the angiotensin-converting enzyme 2 (ACE2) on both SARS-CoV-1 and the new SARS-CoV-2 S receptor binding domain (RBD) proteins. We also calculated free energy of interactions and shown that the S RBD proteins from both SARS viruses binds to ACE2 with similar affinities. However, the affinity between the S RBD protein from the new SARS-CoV-2 and ACE2 is higher than for any studied antibody previously found complexed with SARS-CoV-1. Based on physical chemical analysis and free energies estimates, we can shed some light on the involved molecular recognition processes, their clinical aspects, the implications for drug developments, and suggest structural modifications on the CR3022 antibody that would improve its binding affinities for SARS-CoV-2 and contribute to address the ongoing international health crisis.

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Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016

10.1101/2021.02.17.431683 ◽

2021 ◽

Cited By ~ 10

Author(s):

Tyler N. Starr ◽

Allison J. Greaney ◽

Adam S. Dingens ◽

Jesse D. Bloom

Keyword(s):

Monoclonal Antibody ◽

Monoclonal Antibodies ◽

Amino Acid ◽

Receptor Binding ◽

Binding Domain ◽

Single Amino Acid ◽

Receptor Binding Domain ◽

Antigenic Evolution

AbstractMonoclonal antibodies and antibody cocktails are a promising therapeutic and prophylaxis for COVID-19. However, ongoing evolution of SARS-CoV-2 can render monoclonal antibodies ineffective. Here we completely map all mutations to the SARS-CoV-2 spike receptor binding domain (RBD) that escape binding by a leading monoclonal antibody, LY-CoV555, and its cocktail combination with LY-CoV016. Individual mutations that escape binding by each antibody are combined in the circulating B.1.351 and P.1 SARS-CoV-2 lineages (E484K escapes LY-CoV555, K417N/T escape LY-CoV016). Additionally, the L452R mutation in the B.1.429 lineage escapes LY-CoV555. Furthermore, we identify single amino acid changes that escape the combined LY-CoV555+LY-CoV016 cocktail. We suggest that future efforts should diversify the epitopes targeted by antibodies and antibody cocktails to make them more resilient to antigenic evolution of SARS-CoV-2.

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Effect of RBD (Y453F) mutation in spike glycoprotein of SARS-CoV-2 on neutralizing IgG affinity

10.1101/2021.01.28.21250577 ◽

2021 ◽

Author(s):

Takuma Hayashi ◽

Nobuo Yaegashi ◽

Ikuo Konishi

Keyword(s):

Monoclonal Antibodies ◽

Structural Analysis ◽

Severe Acute Respiratory Syndrome ◽

Receptor Binding ◽

Neutralizing Antibodies ◽

Virus Disease ◽

Three Dimensional ◽

Binding Domain ◽

Receptor Binding Domain ◽

Spike Glycoprotein

AbstractBackgroundInfection with receptor binding domain (RBD) mutant (Y453F) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from farmed minks is known to widely spread among humans.MethodsWe investigated the characteristics of SARS-CoV-2 RBD Y453F mutant using three- dimensional structural analysis. We investigated the effect of the RBD Y453F mutant of SARS-CoV- 2 on neutralizing antibodies in serum derived from Corona virus Disease 2019 (COVID-19) positive patients.ResultsOur studies suggest that virus variants with RBD Y453F mutation partially escaped detection by four neutralizing monoclonal antibodies and neutralizing antibodies in serum.ConclusionsConsequently, raising a concern that infection of SARS-CoV-2 mutants that cause serious symptoms in humans may spread globally.

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Considerable escape of SARS-CoV-2 variant Omicron to antibody neutralization

10.1101/2021.12.14.472630 ◽

2021 ◽

Author(s):

Delphine Planas ◽

Nell Saunders ◽

Piet Maes ◽

Florence Guivel Benhassine ◽

Cyril Planchais ◽

...

Keyword(s):

South Africa ◽

Monoclonal Antibodies ◽

Receptor Binding ◽

Binding Domain ◽

Viral Fitness ◽

Receptor Binding Domain ◽

Antibody Neutralization ◽

Neutralizing Activity ◽

Terminal Domain ◽

Therapeutic Monoclonal Antibodies

The SARS-CoV-2 Omicron variant was first identified in November 2021 in Botswana and South Africa. It has in the meantime spread to many countries and is expected to rapidly become dominant worldwide. The lineage is characterized by the presence of about 32 mutations in the Spike, located mostly in the N-terminal domain (NTD) and the receptor binding domain (RBD), which may enhance viral fitness and allow antibody evasion. Here, we isolated an infectious Omicron virus in Belgium, from a traveller returning from Egypt. We examined its sensitivity to 9 monoclonal antibodies (mAbs) clinically approved or in development, and to antibodies present in 90 sera from COVID-19 vaccine recipients or convalescent individuals. Omicron was totally or partially resistant to neutralization by all mAbs tested. Sera from Pfizer or AstraZeneca vaccine recipients, sampled 5 months after complete vaccination, barely inhibited Omicron. Sera from COVID-19 convalescent patients collected 6 or 12 months post symptoms displayed low or no neutralizing activity against Omicron. Administration of a booster Pfizer dose as well as vaccination of previously infected individuals generated an anti-Omicron neutralizing response, with titers 5 to 31 fold lower against Omicron than against Delta. Thus, Omicron escapes most therapeutic monoclonal antibodies and to a large extent vaccine-elicited antibodies.

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Effect of RBD mutations in spike glycoprotein of SARS-CoV-2 on neutralizing IgG affinity

10.21203/rs.3.rs-363352/v1 ◽

2021 ◽

Author(s):

Takuma Hayashi ◽

Nobuo Yaegashi ◽

Ikuo Konishi

Keyword(s):

Monoclonal Antibodies ◽

Structural Analysis ◽

Receptor Binding ◽

Neutralizing Antibodies ◽

Three Dimensional ◽

Binding Domain ◽

Receptor Binding Domain ◽

Spike Glycoprotein ◽

Mutant Strains

Abstract Background: Certain mutant strains of SARS-CoV-2 are known to spread widely among humans, including the receptor binding domain (RBD) mutant, Y453F, from farmed minks, and the RBD mutant, N501Y, a mutation common to three major SARS-CoV-2 subspecies (B.1.1.7, B.1.351, and B.1.1.248). Methods: We investigated the characteristics of the RBD mutants, Y453F and N501Y, using three-dimensional structural analysis. We also investigated the effect of Y453F and N501Y on neutralizing antibodies in serum derived from COVID-19-positive patients. Results: Our results suggest that SARS-CoV-2 subspecies with the RBD mutations Y453F or N501Y partially escaped detection by 4 neutralizing monoclonal antibodies and 21 neutralizing antibodies in serums derived from COVID-19-positive patients.Conclusions: Infection with SARS-CoV-2 subspecies that cause serious symptoms in humans may spread globally.

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Reduced sensitivity of infectious SARS-CoV-2 variant B.1.617.2 to monoclonal antibodies and sera from convalescent and vaccinated individuals

10.1101/2021.05.26.445838 ◽

2021 ◽

Author(s):

Delphine Planas ◽

David Veyer ◽

Artem Baidaliuk ◽

Isabelle Staropoli ◽

Florence Guivel-Benhassine ◽

...

Keyword(s):

Monoclonal Antibodies ◽

Receptor Binding ◽

Immune Evasion ◽

Binding Domain ◽

The Other ◽

Receptor Binding Domain ◽

Terminal Domain

The SARS-CoV-2 B.1.617 lineage emerged in October 2020 in India. It has since then become dominant in some indian regions and further spread to many countries. The lineage includes three main subtypes (B1.617.1, B.1617.2 and B.1.617.3), which harbour diverse Spike mutations in the N-terminal domain (NTD) and the receptor binding domain (RBD) which may increase their immune evasion potential. B.1.617.2 is believed to spread faster than the other versions. Here, we isolated infectious B.1.617.2 from a traveller returning from India. We examined its sensitivity to monoclonal antibodies (mAbs) and to antibodies present in sera from COVID-19 convalescent individuals or vaccine recipients, in comparison to other viral lineages. B.1.617.2 was resistant to neutralization by some anti-NTD and anti-RBD mAbs, including Bamlanivimab, which were impaired in binding to the B.1.617.2 Spike. Sera from convalescent patients collected up to 12 months post symptoms and from Pfizer Comirnaty vaccine recipients were 3 to 6 fold less potent against B.1.617.2, relative to B.1.1.7. Sera from individuals having received one dose of AstraZeneca Vaxzevria barely inhibited B.1.617.2. Thus, B.1.617.2 spread is associated with an escape to antibodies targeting non-RBD and RBD Spike epitopes.

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