Monoclonal antibodies have proven to be a powerful tool in our ability to prevent and treat SARS-CoV-2 infections. The current epidemic is driven in part by natural variants that elude monoclonal and vaccine-induced antibodies. The search is focused on broadly neutralizing antibodies. Here we describe one such antibody recently reported by Wang et al. in Japan.
In an earlier study from earlier this year, Wang et al. attempted to discover broadly neutralizing monoclonal antibodies that would be effective against existing and future variants. His experiments took place in the later stages of the wave of Delta infections. By sorting B cells for the immune memory of the SARS-CoV-2 receptor-binding domain, they found a match.
Wang et al. cloned the monoclonal antibody 35B5. They then looked at neutralization ability and found that 35B5 potently neutralized not only wild-type SARS-CoV-2 but also a broad spectrum of variants, including Beta and Delta, prompting the researchers to investigate the structural and functional mechanisms of SARS-CoV-2. 35B5 to a greater extent. detail.
35B5 also neutralizes Omicron
After the rise of the Omicron variant, Wang and others. they repeated their experiments in the context of the new variant. They found that 35B5 displayed Omicron-binding efficiency comparable to Delta and wild-type SARS-CoV-2, as well as trimer dissociation. The authors note that the binding efficiency of Omicron with 35B5 is slightly weaker than that of wild-type, probably due to a hydrogen bond between the antibody and N481 in the receptor-binding domain, which is impaired at the Fab interface of . Omicron.
In a neutralization assay, they found that both pseudotypes and authentic Omicron viruses were potently neutralized by 35B5. While Omicron was not neutralized as effectively as Delta or the wild type, it was efficient enough to disable the virus.
35B5 waste target
Despite dozens of mutations in the Omicron Spike receptor binding domain and N-terminal domain, 35B5 still binds tightly over a footprint of 29 interacting residues. These residues interact through salt bridges and hydrogen bonds to allow interaction between the antibody and the Spike.
A crucial glycan that 35B5 interacts with is N165. One of the glycans’ roles is to protect the virus particle below, but N165, along with N234, also has a unique responsibility. These two act together as a molecular switch to control Spike’s conformational transition. The Spike alternates between up and down conformation based on whether it is currently infecting a host cell. The two glycans clamp the two sides of the receptor-binding domain and allow the trimer to toggle between up- and down-configurations, acting as a switch. The 35B5 antibody displaces N165 from its binding pocket, deactivating the switch mechanism, as if a light switch lever were broken.
If the Spike were on the top setting, Wang et al. found that the 35B5 antibody would go on to wreak havoc on the virus. When superimposed on the upstream configuration, the researchers observed that the N165 and N234 glycans are displaced from their native binding pocket. This shift results in significant dysfunction of the glycan switch necessary for the transition between upstream and downstream configurations, suggesting that the 35B5 antibody forces the trimer into the upstream configuration, thereby destabilizing the Spike.
What makes this antibody so exciting is the conservation of N-glycans in SARS-CoV-2 genomes. Of the 10.5 million SARS-CoV-2 genomes in the GISAID database, only 3,129 contain a mutation at position N165 or less than 0.03%. The same can be said for N234, which shows only one mutation in 1723 viruses or less than 0.02%. This suggests that 35B5 could have neutralized more than 99% of the viruses that have circulated since the beginning of the pandemic, which means that it could be a great tool for variants to come. Furthermore, the mutations in Omicron are far from the 35B5 epitope, suggesting an additional advantage for 35B5. Because residues of the 35B5 epitope are highly conserved, Omicron RBD mutations are unlikely to interfere with 35B5 virus neutralization.
This is not the only antibody that recognizes highly conserved sequences in Spike. We note that Zhou et al. describe two antibodies that target conserved sequences in Omicron Spike: Ly-CoV1404 and S2E12. Also, Li et al. describe the CV3-25 antibody, which binds to a linear epitope on S2. We suggest that a combination of 35B5 and CV3-25 could be ideal for the prevention and treatment of Covid-19. Similar combinations of antibodies that bind to both membrane-associated protein and receptor-binding protein show broad neutralizing activity against most existing strains of Ebola. Such a combination antibody therapy for Covid-19 could be a successful path for treatment and prophylaxis against current and future strains of the virus.