Structural and Computational Design of a SARS-2 Spike Antigen with Increased Receptor Binding Domain Exposure and Improved Immunogenicity

Abstract

Emerging SARS-CoV-2 variants of concern challenge the efficacy of approved vaccines and emphasize the need for improved antigens. Using an evolutionary-based design approach starting from the widely used engineered Spike antigen, S-2P, we sought to increase antigen production levels and the exposure of highly conserved and neutralization sensitive receptor-binding domain (RBD) epitopes. Thirty-six prototypes were generatedin silico, of which fifteen were produced and tested in biochemical assays. Design S2D14, which contains 20 mutations within the Spike S2 domain, showed a 6-fold increase in expression while preserving similar thermal stability and antigenicity as S-2P. Cryo-EM structures indicate that the dominant populations of S2D14 particles have RBDs in exposed states, and analysis of these structures revealed how modifications within the S2 domain balance trimer stability and RBD accessibility through formation and removal of hydrogen bonds and surface charge alterations. Importantly, vaccination of mice with adjuvanted S2D14 resulted in higher levels of neutralizing antibodies than adjuvanted S-2P against SARS-CoV-2 Wuhan strain and four variants of concern. These results can guide the design of next generation vaccines to combat current, and future coronaviruses and the approaches used may be broadly applicable to streamline the successful design of vaccine antigens.

Computational Protein Design for COVID-19 Research and Emerging Therapeutics

“…S2D14 elicited nAbs against the SARS-CoV-2 Wuhan-Hu1 strain and four VOCs in vaccinated mice. 55 Most monoclonal antibodies (mAbs) developed as COVID-19 prophylaxis block RBD-ACE2 binding. Mutations in the viral protein confer resistance toward these neutralizing antibodies (nAbs).…”

“…In another study, they incorporated point mutations to these peptides to design three peptides (SPB25 Q22R , SPB25 F8R/K11W/L25R , and SPB25 F8R/K11F/Q22R/L25R ) with binding affinities ( K D ) greater than that of ACE2. , Williams et al recently employed Protein Repair One-Stop Shop (PROSS), an evolution-based design approach, to design a novel prefusion S-antigen, S2D14, having 20 mutations in the S2 domain of S-protein. S2D14 elicited nAbs against the SARS-CoV-2 Wuhan-Hu1 strain and four VOCs in vaccinated mice …”