Potent NTD-Targeting Neutralizing Antibodies against SARS-CoV-2 Selected from a Synthetic Immune System

Area of Science:

• Immunology
• Virology
• Structural Biology

Background:

• Most SARS-CoV-2 neutralizing antibodies target the spike protein's receptor-binding domain (RBD).
• The RBD is highly variable, developing mutations to evade immune responses and vaccines.
• Targeting non-RBD regions offers an alternative strategy for developing robust neutralizing antibodies.

Purpose of the Study:

• To identify novel neutralizing antibodies targeting non-RBD regions of the SARS-CoV-2 spike protein.
• To characterize the binding and neutralization capabilities of these antibodies against SARS-CoV-2 and its variants.

Main Methods:

• Screening of a pre-pandemic combinatorial antibody library (10^11) using a strategy of alternating negative and positive selection.
• Identification and characterization of 11 non-RBD-targeting antibodies, including SA3 which targets the N-terminal domain (NTD).
• Assessment of SA3's binding to the spike protein in different conformational states and its neutralization efficacy against wild-type and B.1.351 (Beta) SARS-CoV-2 pseudoviruses, both alone and in combination with an RBD-targeting antibody (S-E6).

Main Results:

• Eleven non-RBD-targeting antibodies were identified, including SA3 which binds the NTD.
• SA3 binds to both open and closed conformations of the spike protein and does not compete with ACE2 receptor binding.
• SA3 demonstrated neutralization activity against wild-type and B.1.351 SARS-CoV-2 pseudoviruses, comparable to the RBD-targeting antibody S-E6.
• The combination of SA3 and S-E6 exhibited synergistic neutralization, overcoming a 10-fold loss in efficacy against the B.1.351 variant.

Conclusions:

• Non-RBD targeting antibodies, such as SA3 against the NTD, represent a promising strategy for developing SARS-CoV-2 therapeutics.
• SA3's ability to neutralize variants and its synergistic effect with RBD-targeting antibodies highlight its potential therapeutic value.
• Combination therapy using antibodies targeting different spike protein regions may be effective in combating SARS-CoV-2 evolution and immune escape.