Engineering a SARS-CoV-2 Vaccine Targeting the Receptor-Binding Domain Cryptic-Face via Immunofocusing

Theodora U J Bruun; Jonathan Do; Payton A-B Weidenbacher; Ashley Utz; Peter S Kim

doi:10.1021/acscentsci.4c00722

Engineering a SARS-CoV-2 Vaccine Targeting the Receptor-Binding Domain Cryptic-Face via Immunofocusing

ACS Cent Sci. 2024 Sep 17;10(10):1871-1884. doi: 10.1021/acscentsci.4c00722. eCollection 2024 Oct 23.

Authors

Theodora U J Bruun^{1

2}, Jonathan Do^{1

2}, Payton A-B Weidenbacher^{1

3}, Ashley Utz^{1

4

5}, Peter S Kim^{1

2

6}

Affiliations

¹ Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States.
² Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States.
³ Department of Chemistry, Stanford University, Stanford, California 94305, United States.
⁴ Stanford Biophysics Program, Stanford University School of Medicine, Stanford, California 94305, United States.
⁵ Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, California 94305, United States.
⁶ Chan Zuckerberg Biohub, San Francisco, California 94158, United States.

Abstract

The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is the main target of neutralizing antibodies. Although they are infrequently elicited during infection or vaccination, antibodies that bind to the conformation-specific cryptic face of the RBD display remarkable breadth of binding and neutralization across Sarbecoviruses. Here, we employed the immunofocusing technique PMD (protect, modify, deprotect) to create RBD immunogens (PMD-RBD) specifically designed to focus the antibody response toward the cryptic-face epitope recognized by the broadly neutralizing antibody S2X259. Immunization with PMD-RBD antigens induced robust binding titers and broad neutralizing activity against homologous and heterologous Sarbecovirus strains. A serum-depletion assay provided direct evidence that PMD successfully skewed the polyclonal antibody response toward the cryptic face of the RBD. Our work demonstrates the ability of PMD to overcome immunodominance and refocus humoral immunity, with implications for the development of broader and more resilient vaccines against current and emerging viruses with pandemic potential.