The design of immunogens for the SARS-CoV-2 spike protein using structure-guided epitope grafting and scaffolding methods

In a recent study posted to the bioRxiv* preprint server, researchers designed an efficient vaccine design against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections.

Study: Adaptation-proof SARS-CoV-2 vaccine design. Image Credit: Kateryna Kon/Shutterstock

The development of coronavirus disease 2019 (COVID-19) vaccines has been instrumental in curbing widespread transmission of SARS-CoV-2. However, emerging reports of immune evasion and increased transmissibility by novel SARS-CoV-2 variants have highlighted the need for newer and more efficient vaccines.

About the study

In the present study, researchers designed immunogens against the SARS-CoV-2 spike (S) glycoprotein using computational methods, including scaffolding and structure-guided epitope grafting.

The team first evaluated the evolutionary conservation score corresponding to each amino acid related to the viral S protein. Epitope conservation was assessed using multiple sequence alignment while the area in the protein surface accessible to the test solvent was calculated using Gaia and Chiron. The team also identified scaffold proteins that could be used for subsequent grafting. The coordinates corresponding to the backbone atoms were also extracted for the identified viral S proteins.

The scaffolds were subsequently redesigned using a computational platform called Eris that performed side-chain repacking as well as backbone relaxation before calculating the alterations in free energy after mutations. This was followed by exposing the generated scaffolds to solvent residues found within each corresponding epitope.

The structural rigidity of the models was estimated by performing discrete molecular dynamics (DMD) simulation, which calculated atomic collisions resulting in discrete potential energy. The team also conducted three independent simulations per design for a total of 107 steps. The resulting trajectories were assessed to describe data related to the average structure, energy, radius of gyration, root-mean-square deviation (RMSD), and root-mean-square fluctuations (RMSF).

Furthermore, the team obtained genes that encoded the designed proteins and transformed each of the protein constructs into Escherichia coli (E. coli) strains. The bicinchoninic acid (BCA) assay subsequently purified and analyzed these proteins to determine the protein concentrations.


The study results showed that the team identified a total of three epitope regions in the SARS-CoV-2 spike protein S2 domain. These epitopes were characterized by high conservation of sequences and high exposure to solvent on the spike surface area. The team noted that all the residues found in epitopes 1 and 2 were located on the alpha-helices of the protein, while the epitope 3 residues were on the loop region of the protein. The researchers also designed immunogens that were similar to the three epitopes by finding acceptor proteins with backbone structures comparable to the identified epitopes.

The side-chain grafting method was used to replace the amino acids found on the epitope match region within each acceptor protein with residues that corresponded to the spike epitope sequences. The team generated 15 epitope-scaffold designs and evaluated the alterations in free energy after substitutions. Furthermore, the conformational stabilities of the epitope scaffolds were determined by DMD simulations, and only the scaffolds having significant rigidity around the grafted area were selected.

A total of seven chimeric immunogens were expressed along with their corresponding scaffolds in E. coli. Five epitope scaffolds were soluble proteins and exhibited chromatography spectra aligned with the designed topology. The team noted that a comparison of the secondary structures of the epitope-scaffold designs and the E. coli scaffolds resulted in insignificant changes.

When the crystal structures of the epitope-scaffolds were solved, the structure of epitope-scaffold 1 had a dimer while size exclusion chromatography (SEC) detected a monomer. Moreover, the comparison of epitope-scaffold 1 with the spike protein showed that all the grafted residues found in the epitope-scaffold 1 structure had conformations similar to the corresponding residue of the viral spike protein. RMSD also suggested a high degree of mimicry among the epitope regions of the epitope-scaffold 1 structure and the spike protein.

The immunogenicity assessment of the four stable epitope scaffolds in the mouse models showed the presence of epitope-specific antibodies. The designs of epitope-scaffold 1 and 3 resulted in low levels of epitope-specific immunoglobulin (IgG) response, while the epitope-scaffold 2 showed significantly higher levels of antigen-specific IgG response. On the other hand, epitope-scaffold 5 had an intermediate IgG response.

Epitope-scaffold 2 antisera showed significant binding to the SARS-CoV-2 spike protein. On further analysis of whether humans could generate antibodies specific for the epitope-scaffold 2, the team observed a substantial level of binding in SARS-CoV-2 positive samples compared to healthy samples.


Overall, the study findings showed the development of epitope scaffolds that could target conserved SARS-CoV-2 epitopes and enable the generation of a universal CoV vaccine design.

*Important notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

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