Novel prefusion S antigen designed by the mutation of the SARS-CoV-2 Spike protein’s trimeric structure

Novel prefusion S antigen designed by the mutation of the SARS-CoV-2 Spike protein’s trimeric structure

In a current examine posted to the bioRxiv* server, researchers mutated the extreme acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein’s trimeric construction to design a novel prefusion S antigen, S2D14.

Study: Structural and Computational Design of a SARS-2 Spike Antigen with Increased Receptor Binding Domain Exposure and Improved Immunogenicity. Image Credit: creativeneko/Shutterstock
Examine: Structural and Computational Design of a SARS-2 Spike Antigen with Elevated Receptor Binding Area Publicity and Improved Immunogenicity. Picture Credit score: creativeneko/Shutterstock


Amid rising considerations that at present used coronavirus illness 2019 (COVID-19)  vaccines are dropping efficacy in opposition to new SARS-CoV-2 variants, corresponding to Omicron, there’s a essential want for extra S-2P-like S protein antigens. Utilizing improved S antigens in future vaccines would broaden safety in opposition to rising SARS-CoV-2 variants of concern (VOCs), together with Omicron.

In regards to the examine

All at present used COVID-19 vaccines are prefusion stabilized S protein antigen, S-2P-based. S2-P, in a prefusion state, is engineered by a structure-based design technique. Step one requires the insertion of two proline residues, Ok986P and V987P (S-2P), harbored between the central helix area (CH) and heptad repeat area 1 (HR1), and additional modified by insertion of further prolines, F817P, A892P, A899P, A942P (HexaPro). The final step is essential, for it requires testing a whole lot of single-point mutations to determine an antigen with the popular stability, conformation, and expression ranges.

For this, the researchers tailored a design algorithm, Protein Restore One-Cease Store (PROSS), that makes use of multi-sequence alignment (evolutionary data) of a protein, on this case, associated betacoronavirus glycoproteins, to determine extra purposeful amino acid residues in a protein. Rosetta combinatorial sequence optimization generated constructs with extra favorable power profiles than the unique S antigen mannequin.

The crew narrowed the variety of design methods to a few to acquire 12 design constructs per technique for testing. Additional, they chose one design from every group for manufacturing, purification, and in vitro evaluation. Design 14 displayed a six-fold larger expression relative to S-2P. It certain the human angiotensin-converting enzyme 2 (ACE2) receptor with an equilibrium dissociation binding fixed (KD) within the picomolar vary and binding affinity akin to S-2P.

The differential scanning fluorimetry (DSF) assay revealed that melting transition (Tm1) values for design 14, indicating improved thermal stability, had been akin to S-2P. Cryogenic electron microscope (cryo-EM) micrographs of design 14 additionally confirmed anticipated particle dimension and secondary structural options.

The resultant novel prefusion S antigen, now known as S2D14, confirmed superior biochemical and biophysical properties than S-2P, plus the next functionality of eliciting neutralizing antibodies (nAbs) in opposition to SARS-CoV-2 Wuhan-Hu1 ancestral pressure and VOCs in mice.

For in vivo experiments to evaluate the immunogenicity of S2D14 vs. S-12P, researchers used seven to eight weeks outdated feminine BALB/c mice and vaccinated them with three micrograms (μg) or 0.three μg of AS03-adjuvanted S proteins, admixed shortly earlier than intramuscular administration. They administered the vaccine twice, three weeks aside. They collected serum samples from all mice twice, three weeks after the primary vaccination (post-I) and two weeks after the second vaccination (post-II).

They assessed S-2P-specific antibody responses utilizing a Wuhan pressure pseudo-virus neutralization (PVN) assay. Likewise, they used an enzyme-linked immunosorbent assay (ELISA) to measure immunoglobulin G (IgG)-binding antibodies within the sera of check animals. They moreover measured neutralizing antibodies in post-II serum samples utilizing a PVN assay with the Alpha, Beta, Delta, and Omicron VOCs.

For comparative evaluation of IgG binding and neutralization information from S-2P and S2D14 vaccinated teams, the crew used an  ANOVA mannequin fitted on log10-transformed information. It accounted for the vaccine kind, dosage, time, and interplay information as mounted elements and regarded the homogeneity of variances between teams. This mannequin in contrast responses to S-2P and S2D14 vaccines by dose and computed geometric technique of titers (GMT) and geometric imply ratios (GMR) with corresponding 95% confidence intervals (CIs).

Examine findings

Though vaccination of mice with S2D14 or S-2P elicited comparable IgG titers, S2D14 elicited the next purposeful response that extra successfully neutralized the Wuhan-Hu1 pressure and Alpha, Beta, and Delta VOCs than S-2P. The S2D14-elicited purposeful response, when mixed with its enhanced expression, may translate into dose-sparing results. It may also translate to a decrease dose when delivered by various platforms, corresponding to messenger ribonucleic acid (mRNA) or replication-competent viral vectors.

In comparison with S-2P, immunization of mice with the 0.three µg dose of S2D14 elicited ~10-fold larger nAb titers in opposition to the Omicron pressure than the Wuhan-Hu1 pressure, thereby pointing to utilizing S2D14 as a scaffold for extra modifications which may enhance nAb responses in opposition to Omicron or different rising SARS-CoV-2 variants.


The current examine stuffed the data hole of the molecular determinants of improved S antigens, which might show priceless in informing the design of future S-based vaccines with the power to elicit broad safety in opposition to rising SARS-CoV-2 variants.

A complete molecular map of the immune response elicited by S2D14 may additionally assist comparisons between polyclonal specificities elicited post-vaccination or pure an infection, which, in flip, may additional inform future vaccine designs. Future research ought to study whether or not mutations in S2D14 would possibly introduce new epitopes and assess their impression on T cell immunity.

*Vital discover

bioRxiv publishes preliminary scientific studies that aren’t peer-reviewed and, subsequently, shouldn’t be thought to be conclusive, information medical observe/health-related habits, or handled as established data.

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