Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics

Abstract

The emergence and rapid expansion of the coronavirus disease (COVID-19) require the development of effective countermeasures especially a vaccine to provide active acquired immunity against the virus. This study presented a comprehensive vaccinomics approach applied to the complete protein data published so far in the National Center for Biotechnological Information (NCBI) coronavirus data hub. We identified non-structural protein 8 (Nsp8), 3C-like proteinase, and spike glycoprotein as potential targets for immune responses to COVID-19. Epitopes prediction illustrated both B-cell and T-cell epitopes associated with the mentioned proteins. The shared B and T-cell epitopes: DRDAAMQRK and QARSEDKRA of Nsp8, EDMLNPNYEDL and EFTPFDVVR of 3C-like proteinase, and VNNSYECDIPI of the spike glycoprotein are regions of high potential interest and have a high likelihood of being recognized by the human immune system. The vaccine construct of the epitopes shows stimulation of robust primary immune responses and high level of interferon gamma. Also, the construct has the best conformation with respect to the tested innate immune receptors involving vigorous molecular mechanics and solvation energy. Designing of vaccination strategies that target immune response focusing on these conserved epitopes could generate immunity that not only provide cross protection across Betacoronaviruses but additionally resistant to virus evolution.

Keywords: 3C-like proteinase; Coronavirus disease (COVID-19); Non-structural protein 8; Spike glycoprotein; Vaccinomics.

Graphical abstract

Fig. 1

Designed workflow for in silico vaccine engineering against COVID-19.

Fig. 2

The final set of potential vaccine candidates filtered through several in silico checks presented as interactive Venn. The total number of proteins (TPs), filtered to 191 host non-homologous proteins (HNHPs), 174 mouse non-similar proteins (MNSPs), 26 adhesive proteins (APs), 7 antigenic proteins and finally to 3 potential vaccine candidates (PVCs).

Fig. 3

Schematic representation of the designed MEPVC.

Fig. 4

A. The tertiary structure of the designed MEPVC. The red, green, purple, and yellow colors represent AAY linkers, epitopes, adjuvant, and EAAK linkers, respectively. B. The z-score plot indicating the overall good quality of the MEPVC. The z-score of the input MEPVC is shown by a black dot, validating the score within the range revealed for similar size proteins. C. Ramachandran plot for the MEPVC illustrating distribution of torsion angles (blue squares) comparative to the core (shown in red) and allowed (shown in brown) regions. Residues in the generously allowed region are shown in dark yellow whereas disallowed regions are depicted in pale yellow.

Fig. 5

Disulfide engineering of the MEPVC. The yellow spheres represent mutated residues.

Fig. 6

In silico restriction cloning of the MEPVC into pET28a(+) vector. The insert is shown in red.

Fig. 7

Binding conformation of MEPVC with respect to TLR3 innate immune receptor. The yellow labeled region pointing to the residues involved in both hydrophobic and hydrophilic interactions with MEPVC.

Fig. 8

Binding conformation of MEPVC with respect to TLR4 innate immune receptor. The yellow labeled region pointing to the residues involved in both hydrophobic and hydrophilic interactions with MEPVC.

Fig. 9

In silico simulation of the host immune system using MEPVS as an antigen. A. Antibodies titer (A) and cytokines and interleukins (B) in response to the antigen.

Fig. 10

MD trajectories based calculation of Cα RMSD (top left), RMSD (top right), Rg (bottom left), and β-factor (bottom right).

Fig. 11

Binding mode of MEPVC at different snapshots at the TLR3 docked side.

Fig. 12

Binding mode of MEPVC at different snapshots at the TLR4 docked side.

Fig. 13

The number of hydrogen bonds formed during simulation between MEPVC and TLR3 and TLR4 receptors.