Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2

Abstract

Background: Coronavirus disease 2019 (COVID-19) linked with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause severe illness and life-threatening pneumonia in humans. The current COVID-19 pandemic demands an effective vaccine to acquire protection against the infection. Therefore, the present study was aimed to design a multiepitope-based subunit vaccine (MESV) against COVID-19.

Methods: Structural proteins (Surface glycoprotein, Envelope protein, and Membrane glycoprotein) of SARS-CoV-2 are responsible for its prime functions. Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast B- and T- cell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV.

Results: Predicted epitopes suggested high antigenicity, conserveness, substantial interactions with the human leukocyte antigen (HLA) binding alleles, and collective global population coverage of 88.40%. Taken together, 276 amino acids long MESV was designed by connecting 3 cytotoxic T lymphocytes (CTL), 6 helper T lymphocyte (HTL) and 4 B-cell epitopes with suitable adjuvant and linkers. The MESV construct was non-allergenic, stable, and highly antigenic. Molecular docking showed a stable and high binding affinity of MESV with human pathogenic toll-like receptors-3 (TLR3). Furthermore, in silico immune simulation revealed significant immunogenic response of MESV. Finally, MEV codons were optimized for its in silico cloning into the Escherichia coli K-12 system, to ensure its increased expression.

Conclusion: The MESV developed in this study is capable of generating immune response against COVID-19. Therefore, if designed MESV further investigated experimentally, it would be an effective vaccine candidate against SARS-CoV-2 to control and prevent COVID-19.

Keywords: COVID-19; Epitope; Immunoinformatics; Multiepitope-based subunit vaccine; SARS-CoV-2; Structural protein; Vaccine.

Fig. 1

The schematic workflow used to develop MESV construct against SARS-CoV-2 structural proteins

Fig. 2

Population coverage of MESV epitopes around the globe predicted by IEDB population coverage tool

Fig. 3

Schematic diagram of MESV construct: It has 276 amino acids, consisting of an adjuvant (orange) linked at N-terminal of MEV with the aid of EAAAK linker (yellow). AAY linkers (blue) used to join the CTL epitopes, GPGPG linkers (green) used to join the HTL epitopes and KK linkers (gray) used to join the B-cell epitopes

Fig. 4

a MESV construct sequence. Epitopes sequence is in black. The adjuvant sequence is highlighted in brown color, EAAAK linker sequence is highlighted in blue, AAY linkers are highlighted with orange, GPGPG linkers are highlighted with green and KK linkers are highlighted with maroon color; b MESV construct refined 3D structure pipes representation (alpha helix: green; beta strands: blue; loops: gray); c Ramachandran plot analysis of predicted structure shows 89.4% residues are present in the favored region

Fig. 5

TLR3-MESV docked complex shown at the left in cartoon representation. Interacting residues of MESV are highlighted at right side. MESV vaccine construct displayed with blue color and TLR3 displayed with green color. Salt bridges are displayed with red color lines; other contacts are shown with orange color lines, and hydrogen bonds are displayed with blue color lines. The colors of interacting residues are interpreting the characteristics of amino acids (neutral: green, Cys: yellow, aromatic: pink, aliphatic: grey, positive: blue, negative: red, and Pro&Gly: orange)

Fig. 6

In silico immune response using MESV as antigen. a The antibodies, and b cytokines and interleukins

Fig. 7

In silico cloning of codon optimized MESV into E. coli K12 expression system. The plasmid back-bone is kept in black color while the inserted DNA sequence is shown in green color