Monoclonal antibodies have proven to be a powerful tool in our ability to prevent and treat SARS-CoV-2 infections. The current epidemic is due in part to natural variants that evade monoclonal and vaccine-induced antibodies. The research focuses on broadly neutralizing antibodies. Here we describe such an antibody recently reported by Wang et al. in Japan.
In a previous study from earlier this year, Wang et al. attempted to discover broadly neutralizing monoclonal antibodies that would be effective against existing and future variants. Their experiments took place in the later stages of the Delta’s outbreak of infections. By sorting B cells for immune memory of the SARS-CoV-2 receptor binding domain, they found a match.
Wang et al. cloned the monoclonal antibody 35B5. They then analyzed the neutralization capacity, finding that 35B5 potently neutralized not only wild-type SARS-CoV-2, but also a wide range of variants, including Beta and Delta, leading the researchers to study the structural and functional mechanisms of 35B5 in greater detail.
35B5 also neutralizes Omicron
After the rise of the Omicron variant, Wang et al. repeated their experiments under the new variant. They observed 35B5 exhibiting 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 lower than that of the wild type, probably due to hydrogen bonding between the antibody and N481 in the receptor binding domain, which is impaired in the Omicron Fab interface.
In a neutralization test, they found that both pseudotype and authentic Omicron viruses were potently neutralized by 35B5. Although Omicron was not neutralized as effectively as Delta or wild type, it was still effective enough to deactivate the virus.
35B5 tailings target
Despite dozens of mutations in the Omicron Spike receptor binding domain and in the N-terminal domain, 35B5 still binds tightly across an interacting 29-residue footprint. These residues interact via 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 functions of glycans is to protect the virus particle underneath, but N165, along with N234, also has a unique responsibility. These two together act as a molecular switch to control the Spike conformational transition. The Spike alternates between the top and bottom conformation depending on whether it is currently infecting a host cell. The two glycans clamp both sides of the receptor binding domain and allow the trimer to change between up and down configurations, acting as a switch. The 35B5 antibody displaces N165 from its binding pocket, disabling the switch mechanism, like breaking a light switch lever.
If the Spike was in high configuration, Wang et al. found that the 35B5 antibody would continue to wreak havoc on the virus. When layered in the upward configuration, the researchers observed that the N165 and N234 glycans are displaced from their native binding pocket. This displacement results in significant dysfunction of the glycan switch necessary for the transition between high and low configurations, suggesting that the 35B5 antibody forces the trimer into the high 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 of 0.03%. The same can be said for N234, which only shows a mutation in 1,723 viruses or less than 0.02%. This suggests that 35B5 could have neutralized over 99% of viruses in circulation since the start of the pandemic, meaning it could be a great tool for future variants. Additionally, the mutations in Omicron are away from the 35B5 epitope, suggesting an additional advantage for 35B5. Since the 35B5 epitope residues are highly conserved, Omicron RBD mutations are unlikely to interfere with the neutralization of the 35B5 virus.
It is not the only antibody that recognizes highly conserved sequences in the Spike. We note that Zhou et al. describe two antibodies that target conserved sequences in the Omicron Spike: Ly-CoV1404 and S2E12. Moreover, Li et al. describe the CV3-25 antibody, which binds to a linear epitope in S2. We suggest that a combination of 35B5 and CV3-25 might be ideal for the prevention and treatment of Covid-19. Similar combination antibodies that bind both membrane-associated protein and receptor-binding protein exhibit broad neutralizing activity against most existing strains of Ebola. Such combination antibody therapy for Covid-19 could be a successful avenue for treatment and prophylaxis against current and future strains of the virus.