Designing a prototype spike protein vaccine for SARS-CoV-2

A recent study published on the preprint server bioRxiv* in June 2020 reports the development of a prototype vaccine containing multiple antigenic sites, based on the spike protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is causing the current COVID-19 pandemic. If successful, this could lead to the development of an effective, non-allergenic vaccine that induces both humoral and cellular immunity.

Measures to Contain the Pandemic’s Impact

The rapid spread of COVID-19 is countered only by the effective application of non-pharmacological measures like contact tracing and isolation, quarantine of individuals with suspected exposure to infectious cases, social distancing, and in many countries, lockdowns. The emergence of an effective vaccine or therapeutic drug is eagerly awaited, to provide the hope of a point when these precautions can be relaxed and life return to the old normal.

Many older drugs are being tested for their potential as repurposed drugs against COVID-19, including the combination of lopinavir and ritonavir, hydroxychloroquine, and remdesivir. However, none of them have been found to have highly significant activity against the virus.

The Way Out: Vaccine Development

Prevention of infection is, therefore, the most effective strategy at present. The induction of neutralizing antibodies is the goal of vaccine development. Various vaccine candidates are being tested in preclinical and early clinical trials all over the world.

This process may take at least 12-18 months from the first step to the market availability of a vaccine. Moreover, live attenuated virus vaccines require highly skilled technical staff, advanced laboratory facilities, and biosafety level 3 norms.

Using Bioinformatics to Reduce Vaccine Development Time

The current paper by a researcher at Savitribai Phule Pune University, India, reports the use of bioinformatics to speed up this process using algorithms to predict viral peptides that are capable of inducing immunity successfully. This approach has been used to develop vaccines against earlier epidemic viruses such as the Ebola and Middle East Respiratory Syndrome (MERS) viruses.

Bioinformatic approaches have three advantages: high efficacy, shorter development cycle, and a low production cost. These may be key in producing a low-cost, highly available vaccine for use at the population level.

SARS-CoV-2 has three types of proteins – structural, non-structural, and accessory. Several of these proteins are key to its pathogenicity, such as the nucleocapsid (N) protein that is required for RNA binding, replication and transcription; the envelope (E) and membrane (M) proteins needed for virus assembly and virulence, as well as for inducing the immune response; and the spike (S) protein required for the binding of the virus to the host ACE2 receptor, the fusion of the virus with the cell membrane which paves the way for subsequent viral entry into the cell, and activation of the host T cell response.

Illustration of SARS-CoV-2, 2019 nCoV virusImage Credit: Orpheus FX / Shutterstock
Illustration of SARS-CoV-2, 2019 nCoV virusImage Credit: Orpheus FX / Shutterstock O By

One earlier vaccine candidate expressed the whole S protein in chimpanzee adeno 38 (ChAd)-vector, conferring protection against SARS-CoV-2 in mice and in rhesus monkeys via humoral and cellular immunity.

Designing the Vaccine

The current study is based on the use of multiple epitopes of the S protein in a designer vaccine, which is meant to have a long shelf life at room temperature, to induce high levels of immunity, to contain potent antigens and be non-allergenic. It contains epitopes that are uniformly effective in stimulating both humoral and cell-mediated immunity.

The steps followed in designing this vaccine may be summarized as follows:

  • Selecting four perfectly conserved epitopes to be presented to the T cell receptor (TCR)
  • Analysis of TCR epitopes for immunogenicity, allergenicity, antigenicity, and toxicity showed that all were predicted to be immunogenic and non-allergenic
  • Selecting epitopes for the B cell receptor (BCR) by six methods, with the condition that selected regions needed to qualify by at least four of the six methods
  • Designing the vaccine sequence that contains two BCR and three TCR epitopes, linked appropriately to form a 451-amino acid sequence, and linked with a suitable adjuvant for greater immunogenicity

Predicting the Vaccine’s Characteristics

The chimeric peptide vaccine was then tested for its antigenicity and allergenicity, which can be predicted with significant reliability using different online tools. These showed that it was likely to be antigenic but not allergenic.

Its physical and chemical characteristics were predicted as well as the secondary and tertiary structure. It was predicted to be a slightly basic 48.5 KDa peptide, hydrophilic in nature, and very stable.

Various other online tools were used to predict the presence of discontinuous B cell epitopes, which are located on different parts of the peptide sequence and brought into proximity by the folding of the protein.

The docking of the designer vaccine with the receptor called TLR4 was then simulated using a molecular docking server, to visualize how they would interact. Stable interaction indicates that the proteins activate the TLR4 in response to PAMPs (pathogen-associated molecular patterns). This triggers dendritic cell (DC) activation, antigen processing, and presentation to the T cells on the DC surface.

Finally, the cloning of the vaccine construct was predicted by another online tool.

Predicting the Vaccine’s Performance

The immune simulator webserver C-ImmSim predicted a good performance for the vaccine, with high IgM levels in the first week following immunization. Secondary and tertiary phases of immunity were also predicted with a rise in the B cell count, and increasing IgM, IgG, and reducing levels of antigens.

The B cell isotypes also showed a shift, indicating that memory cells were being formed. Th and Tc cells were also predicted at high levels, indicating memory development.

Macrophage activity was boosted by each dose of the antigen but declined with antigen clearance. Dendritic cells were also increased, as was the IFNγ and IL2 expression. These are antiviral cytokines that support Th activation to ensure that antibody production continues at a high level. The low Simpson index showed that antibody production was going on at adequate levels, indicating a good humoral immune response.

The researcher Gunderao H Kathwate concludes: “Although in silico results point out the effectiveness of the vaccine, efficacy needs to be analyzed by performing laboratory experiments and animal model studies.”

*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.

Journal reference:
Dr. Liji Thomas

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.


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