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Structural mechanism of anti-SARS-CoV-2 neutralizing antibodies targeting separate spike epitopes




Since 2020, variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have become a global threat. The first subspecies (alpha subspecies) was discovered in the United Kingdom and soon became globally dominant. Since then, more and more variants have been discovered, including beta, gamma, and variants that now account for over 90% of cases, delta variants.

study: Structural Mechanism of SARS-CoV-2 Neutralization by Two Mouse Antibodies Targeting RBD.. Image Credit: ktsdesign / Shutterstock

New mutants are recognized by highly glycosylated mutations Spike protein.. This protein is the leading cause of SARS-CoV-2 pathogenicity. The receptor binding domain (RBD) within the N-terminal S1 subunit of the peplomer binds to the ACE2 receptor presented by human cells, allowing viral entry.

Changes caused by mutations in this protein can reduce the effectiveness of treatments such as monoclonal antibodies and reduce the effectiveness of vaccines. Both the Pfizer and Modana vaccines have been shown to be up to one-twelfth less effective against beta mutants.

In a treatise published in Cell reportResearchers at the University of Washington School of Medicine have identified a way a subset of Variant of Concern (VOC) avoids two neutralizations. Neutralizing antibody –2B04 and 2H04.

the study

Two conformations, “top” and “bottom”, are observed in the RBD. Since peplomer is a trimer, this allows for four configurations for each peaplomer. All up (UUU), all down (DDD), 1 up 2 down (UDD), or 2 up 1 down (UUD). Most trimers assume DDD or UDD. This is considered an evolutionary strategy to avoid the immune response. Some of the more infectious variants show more monomers that take an upward position, allowing for increased binding to ACE2.

Researchers investigated two monoclonal antibodies with strong neutralizing activity, 2B04 and 2H04, and used cryo-electron microscopy (cryo-EM) to characterize the epitopes targeted by these antibodies. They also sought to identify possible viral mutations that could lead to the virus’s ability to evade neutralization of these antibodies.

Researchers first elucidated the structure of the 2B04 bound to the UDD conformation by collecting data from a frozen complex on a lace-like carbon grid covered with an ultrathin carbon film. .. This allowed us to overcome the problems of using standard racing carbon grids. This tended to indicate a strong top-down priority, hindering reliable model building. After also unraveling the structure of 2H04, they discovered that it was normally bound to the particles of the DDD conformation. However, both antibodies were able to bind to the peplomer regardless of the RBD conformation.

Graphical Summary: Structural Mechanism of SARS-CoV-2 Neutralization by Two Mouse Antibodies Targeting RBDGraphical abstraction: Structural Mechanism of SARS-CoV-2 Neutralization by Two Mouse Antibodies Targeting RBD

Scientists have used maps generated by local modifications to discover specific residues and strands that form the interface of the complex of both monoclonal antibodies. 2B04 binds to the receptor binding motif (RBM), and the heavy chain presses the RBM loop. Light chains also bind to RBM, but most contacts come from heavy chains. 2H04 binds to the region adjacent to the RBM, with both heavy and light chains in contact with the loop.

To examine the ability of the virus to escape neutralization from these antibodies, scientists Pseudovirus Selective reduction from both antibodies. Several mutations occurred, but upon further investigation they were identical to the naturally occurring mutations. These mutations are outside the ACE2 binding site and alter the epitopes of 2H04 and 2B04. Although not sufficient to prevent neutralization alone, this indicates a mechanism by which the virus evolves to evade host immunity.


Researchers emphasize the importance of research that helps to better understand the epitopes that antibodies produced against SARS-CoV-2 target. This information can be important in helping healthcare professionals provide information and directing further research and drug development to combat pandemics.

Knowing both the mechanism by which antibodies target SARS-CoV-2 and how to evade its immunity allows researchers to attempt to mimic the effects of the immune system when creating new drugs. Knowing the mechanisms may be able to initiate action against new variants before they emerge. Creating successful treatments for new strains of COVID-19 could be the key to ending a pandemic, especially as mass vaccination programs are beginning to stagnate around the world.





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