Research exhibits structural and practical points of the antibody neutralization of the SARS-CoV-2-Omicron variant

In a study recently published on the bioRxiv * pre-print server, a team of researchers showed the neutralization of the Omicron (B.1.1.529) variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by selected antibodies and used cryogenic electron microscopy (cryo-EM) structures to uncover structural mechanisms for maintaining effective neutralization against emerging SARS-CoV-2 variants of concern (VOC).

Study: Structural basis for a potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529. Image source: CKA / Shutterstock

Omicron has a higher transmission and has an increased resistance to host immunity. Of the 37 reported mutations in its spike (S) protein, 15 are within the receptor binding domain (RBD), which is the main target for neutralizing antibodies. It is therefore important to understand the mechanisms by which these mutations develop and, based on that understanding, develop effective antibody therapeutics and vaccines.

About the study

Researchers used a range of functional and structural analyzes to determine the differences in neutralization of various VOCs, identify antibodies and antibody combinations that are capable of effectively neutralizing emerging VOCs, including Omicron. To functionally frame their analyzes, they used the Barnes Classification, which categorizes antibodies based on their binding to the ACE2 binding site and the location of RBD.

The researchers collected single particle cryo-EM data to obtain a structure of the trimeric ectodomain of the S protein with a resolution of 3.29. They next used a flow cytometric assay to assess the binding of human ACE2 to cells expressing variant S proteins.

In total, they purified 17 high-potency antibodies targeting the S RBD, including 13 antibodies currently in clinical trials or approved by the US Food and Drug Administration (FDA) for use under an Extended Approval (EUA) are.

results

The two Supersite antibodies, VH1-58, B1-182.1 and S2E12, showed about a 6-fold difference in Omicron neutralization, and these two antibodies remained highly potent. The study results showed that Omicron requires a number of mutations to reduce the effectiveness of an antibody, and VH1-58 antibodies could mitigate the effects of Omicron mutations by reducing the size of its CDR H3 residue 100C.

The researchers also evaluated two Class II antibodies, LY-CoV555 and A19-46.1, and determined the functional basis of Omicron neutralization and escape. The results indicated that either E484A or Q493R RBD mutations from Omicron resulted in a complete loss of LYCoV555 neutralization, while the same mutations did not affect A19-46.1.

Next, they assessed the structural basis of the A19-46.1 neutralization from Omicron, for which they obtained the cryo-EM structure of the Omicron S in complex with Fab A19-46.1. This structure indicated that A19-46.1 binds to an RBD region that is generally directed by the class II antibodies at an angle of approximately 45 degrees to the virus membrane. Binding involved latching light chain CDRs to the outer edge of the RBD, which provided ~ 70% of the binding surface area, and A19-46.1 used its 17 residue CDR H3 to form parallel strand interactions with RBD residues 345-350 . It showed how the bound antibody collided with ACE2 and provided the structural basis for its neutralization of B.1.1.529.

Among the class III antibodies tested, A19-61.1 completely lost neutralization activity due to the change in the G446S amino acid in Omicron RBD. While S309 exhibited moderate neutralizing activity against Omicron, the S371L amino acid change completely abolished its neutralizing ability, suggesting that combinations of S371L with other Omicron mutations may result in structural changes in S that allowed S309 to experience the effects of the Overcome S371L substitution. Likewise, no amino acid change / mutation affected the high effectiveness of LY-CoV1404 against all tested VOCs, including Omicron. The analysis also showed that S309 and COV2-2196 class III antibodies were neutralized to a similar extent.

The study also identified antibody combinations, suggesting the possibility of synergistic neutralization against Omicron. Of the 10 antibody combinations examined, only COV2-2196 / COV2-2130, B1-182.1 / A19-46.1 and B1-182.1 / S309 neutralized Omicron. Interestingly, each used a VH-158 Supersite antibody and showed a 5- to 115-fold improvement in potency against each antibody component.

Conclusions

The study provides detailed insights into the neutralization activity of several classes of anti-SARS-CoV-2 antibodies. The study showed that the VH1-58 supersite is common to the strongest and most neutralizing anti-SARS-CoV-2 antibodies, suggesting the development of structure-based designs of existing antibodies to target SARS-CoV-2 mutations through targeting to weaken to these amino acid positions.

The study results also suggested using potent Class III antibodies to induce structure-based vaccine designs that mask residue 446 in RBD. In addition, the study results demonstrated the existence of G446S sensitive and resistant antibodies with significant epitope overlap, suggesting the use of S with G446S substitution to assess the quality of the class III immune response in serum-based epitope mapping assays. The B1-182.1 antibody derived from VH1-58 was unaffected by the S371L substitution and the preferred RBD-up conformation and was able to break the interaction to induce the 3-RBD-up conformation, thereby binding other antibodies who need the RBD-up will be reinforced-quality (like A19-46.1).

The study also emphasizes the identification of SARS-CoV-2 monoclonal antibodies that could act synergistically (as seen with other viruses) that can be used in combinations to increase overall effectiveness and reduce the risk of SARS-CoV-2 escaping. To reduce variants.

*Important NOTE

bioRxiv publishes preliminary scientific reports that have not been peer reviewed and therefore should not be considered conclusive, that guide clinical practice / health-related behavior or should be treated as established information.