Structural and computational design of a SARS-CoV-2 spike antigen with improved expression and immunogenicity

Sci Adv. 2023 Jun 9;9(23):eadg0330. doi: 10.1126/sciadv.adg0330. Epub 2023 Jun 7.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern challenge the efficacy of approved vaccines, emphasizing the need for updated spike antigens. Here, we use an evolutionary-based design aimed at boosting protein expression levels of S-2P and improving immunogenic outcomes in mice. Thirty-six prototype antigens were generated in silico and 15 were produced for biochemical analysis. S2D14, which contains 20 computationally designed mutations within the S2 domain and a rationally engineered D614G mutation in the SD2 domain, has an ~11-fold increase in protein yield and retains RBD antigenicity. Cryo-electron microscopy structures reveal a mixture of populations in various RBD conformational states. Vaccination of mice with adjuvanted S2D14 elicited higher cross-neutralizing antibody titers than adjuvanted S-2P against the SARS-CoV-2 Wuhan strain and four variants of concern. S2D14 may be a useful scaffold or tool for the design of future coronavirus vaccines, and the approaches used for the design of S2D14 may be broadly applicable to streamline vaccine discovery.

MeSH terms

  • Animals
  • Antibodies, Viral
  • COVID-19*
  • Cryoelectron Microscopy
  • Mice
  • Neutralization Tests
  • SARS-CoV-2*

Substances

  • Antibodies, Viral