Recent studies have demonstrated the effectiveness of hybrid SARS-CoV-2
vaccines that combine the wild-type nucleocapsid (N) and Spike (S)
proteins. Based on this strategy, we have further enhanced the idea by
incorporating the spike protein with mutations from delta and post-delta
omicron variants of concern (VOC). Both delta and omicron mark the
transition of vaccine driven viral immunity and resistance, so their
mutations are highly crucial for future viral variants also.
Additionally, we have included certain nucleocapsid peptides, which have
clinically shown superior T-cell immunity being similar to homologous
sequences from other Human Coronaviruses (HuCoV). We have also carefully
selected an envelope peptide that elicits strong T-cell immune response.
These peptides are clustered in the hybrid spike’s cytoplasmic region
with non-immunogenic helical linkers, enabling systematic arrangement.
Through AlphaFold analysis, we have determined that the resulting domain
folds more efficiently when the construct lacks the transmembrane
domain. The AlphaFold designs were validated using the molecular
dynamics (MD) simulations and assessed various parameters of root mean
square deviation (RMSD), root mean square fluctuation (RMSF), radius of
gyration (Rg) and weighed the structural stability and conformational
dynamics. Interestingly, the dynamics revealed more insights into the
conformational changes in the structure overtime, more flexibility in
the C-terminus region, and overall compactness of the structures in a
time-based gradient indicating less fluctuation and transition in terms
of structure mobility and maintained a relatively compact fold
conformation throughout the simulation. Our proposed approach may
provide option for incorporating diverse anti-viral T-cell peptides,
similar to HuCoV, into linker regions, offering a versatile solution to
address outbreaks and challenges posed by various viruses, thereby
enabling effective management through multiepitope strategies in this
era of innovative vaccines.