Structure-Based Design of SARS-CoV-2 Spike Immunogens Stabilized in the RBD-All Down Conformation

SARS-CoV-2 has emerged as a global pathogen, sparking urgent vaccine development efforts. The trimeric SARS-CoV-2 spike appears to be a leading vaccine antigen. However, the inability of antibodies such as CR3022, which binds tightly to a cryptic spike epitope, to neutralize SARS-CoV-2 suggests a spike-based means of neutralization escape.

Researchers at the Vaccine Research Center (VRC) of the National Institute of Allergy and Infectious Diseases (NIAID) sought to understand how antibodies with high affinity fail to neutralize the SARS-CoV-2. To that end, the researchers characterized the SARS-CoV-2 spike protein conformational changes as a function of pH and observed that at endosomal pH the spike protein has a conformation in which all of the receptor binding domains (RBD) are in a down conformation which could explain the virus' ability to escape neutralization in the endosome.

Hypothesizing that SARS-CoV-2 escapes neutralization through pH-dependent conformational masking, the researchers designed spike proteins with mutations to stabilize the spike in the RBD-all down conformation. Such designs include cavity-filling mutations, disulfides, aspartic acid to asparagine mutations, proline mutations, and other sequence modifications to fix the spike protein in its RBD-all down conformation so that immunization at a physiological pH will elicit antibodies that can recognize the low pH-stabilized all RBD-down conformation of the spike protein and no longer be susceptible to pH-induced neutralization escape.

Immunogenicity studies are underway to determine which of the designs will yield a neutralizing immune response in mice. Pending results in mice, a lead candidate will be selected for studies in nonhuman primates.

This technology is available for licensing for commercial development in accordance with 35 U.S.C. § 209 and 37 CFR Part 404.