Peptide-Based Vaccine against SARS-CoV-2: Peptide Antigen Discovery and Screening of Adjuvant Systems

Abstract

The SARS-CoV-2 virus has caused a global crisis, resulting in 0.5 billion infections and over 6 million deaths as of March 2022. Fortunately, infection and hospitalization rates were curbed due to the rollout of DNA and mRNA vaccines. However, the efficacy of these vaccines significantly drops a few months post immunization, from 88% down to 47% in the case of the Pfizer BNT162 vaccine. The emergence of variant strains, especially delta and omicron, have also significantly reduced vaccine efficacy. We propose peptide vaccines as a potential solution to address the inadequacies of the current vaccines. Peptide vaccines can be easily modified to target emerging strains, have greater stability, and do not require cold-chain storage. We screened five peptide fragments (B1–B5) derived from the SARS-CoV-2 spike protein to identify neutralizing B-cell peptide antigens. We then investigated adjuvant systems for efficient stimulation of immune responses against the most promising peptide antigens, including liposomal formulations of polyleucine (L10) and polymethylacrylate (PMA), as well as classical adjuvants (CFA and MF59). Immune efficacy of formulations was evaluated using competitive ELISA, pseudovirion neutralization, and live virus neutralization assays. Unfortunately, peptide conjugation to L10 and PMA dramatically altered the secondary structure, resulting in low antibody neutralization efficacy. Of the peptides tested, only B3 administered with CFA or MF59 was highly immunogenic. Thus, a peptide vaccine relying on B3 may provide an attractive alternative to currently marketed vaccines.

The potential of developing a protective peptide‐based vaccines against SARS‐CoV‐2

“…Further, several neutralizing Abs that were directed against RBM remained potently neutralizing against emerging SARS‐2 variant lineages (Stamatatos et al, 2021 ), as only four RBM residues, R 452 L, K 478 T, K/Q 484 E, and N 501 Y, were altered in emergent variant lineages (Figure 1c ). The RBM‐derived epitopes were also found to be neutralizing (e.g., SARS‐2‐S 451–470 and S 491–510 ) in mice when conjugated to diphtheria toxoid and adjuvanted with alum or emulsion‐based adjuvants (Pandey et al, 2021 ; Shalash et al, 2022 ). When sera of mice immunized with two different epitopes were combined, synergistically inhibited RBD/ACE2 binding when examined using competitive ELISA (Pandey et al, 2021 ; Shalash et al, 2021a ).…”

“…Short RBD‐derived epitopes were considered to be of insufficient length to produce potently neutralizing nAbs, which have only been observed with protein/RNA subunit vaccines so far. Therefore, longer peptides could be employed to provide the highly discontinuous epitopes needed to trigger the production of potently neutralizing Abs (Shalash et al, 2022 ; Shalash et al, 2021b ). Furthermore, recently complete Freund (CFA)‐adjuvanted, long RBM‐derived, peptide epitope (S 444–483 ) demonstrated potent neutralization (serum nAb titers ≈300), against S‐protein pseudotyped‐virions, which was equivalent to CFA‐adjuvanted RBD protein in BALB/c mice (Shalash et al, 2022 ).…”

“…Therefore, longer peptides could be employed to provide the highly discontinuous epitopes needed to trigger the production of potently neutralizing Abs (Shalash et al, 2022 ; Shalash et al, 2021b ). Furthermore, recently complete Freund (CFA)‐adjuvanted, long RBM‐derived, peptide epitope (S 444–483 ) demonstrated potent neutralization (serum nAb titers ≈300), against S‐protein pseudotyped‐virions, which was equivalent to CFA‐adjuvanted RBD protein in BALB/c mice (Shalash et al, 2022 ). EpiVacCorona (Vektor State Research Centre, Russia) is a peptide vaccine composed of three short peptides derived from SARS‐2‐S (S 454–478 , S 1181–1202 , and S 1191–1211 ) conjugated to SARS‐2 nucleocapsid protein.…”

“…Vaccine antigen selection should not only focus on original SARS‐2 lineage sequences, but also consider new mutant variant sequences; especially, as several mutations have increased the virulence and also have compromised the efficacy of approved vaccines. Several in vitro methods have been employed to evaluate SARS‐2‐S neutralization efficacy (Shalash et al, 2021a , 2021b ; Shalash et al, 2022 ), and these methods can be adapted to evaluate vaccine efficacy against emerging variants. Further, since the immune correlates of protection of several approved vaccines were evaluated in animal infection challenge models (e.g., ferrets and non‐human primates) and in humans, validation of a translation model is possible to infer higher confidence in the relevance of animal infection challenge outcomes to efficacy in humans (Shalash et al, 2021b ).…”

“…SARS-2-S neutralization efficacy (Shalash et al, 2021a(Shalash et al, , 2021bShalash et al, 2022), and these methods can be adapted to evaluate vaccine efficacy against emerging variants. Further, since the immune correlates of protection of several approved vaccines were evaluated in animal infection challenge models (e.g., ferrets and non-human primates) and in humans, validation of a translation model is possible to infer higher confidence in the relevance of animal infection challenge outcomes to efficacy in humans (Shalash et al, 2021b).…”