Design and Immunoinformatic Assessment of Candidate Multivariant mRNA Vaccine Construct against Immune Escape Variants of SARS-CoV-2

Abstract

To effectively counter the evolving threat of SARS-CoV-2 variants, modifications and/or redesigning of mRNA vaccine construct are essentially required. Herein, the design and immunoinformatic assessment of a candidate novel mRNA vaccine construct, DOW-21, are discussed. Briefly, immunologically important domains, N-terminal domain (NTD) and receptor binding domain (RBD), of the spike protein of SARS-CoV-2 variants of concern (VOCs) and variants of interest (VOIs) were assessed for sequence, structure, and epitope variations. Based on the assessment, a novel hypothetical NTD (h-NTD) and RBD (h-RBD) were designed to hold all overlapping immune escape variations. The construct sequence was then developed, where h-NTD and h-RBD were intervened by 10-mer gly-ala repeat and the terminals were flanked by regulatory sequences for better intracellular transportation and expression of the coding regions. The protein encoded by the construct holds structural attributes (RMSD NTD: 0.42 Å; RMSD RBD: 0.15 Å) found in the respective domains of SARS-CoV-2 immune escape variants. In addition, it provides coverage to the immunogenic sites of the respective domains found in SARS-CoV-2 variants. Later, the nucleotide sequence of the construct was optimized for GC ratio (56%) and microRNA binding sites to ensure smooth translation. Post-injection antibody titer was also predicted (~12000 AU) to be robust. In summary, the construct proposed in this study could potentially provide broad spectrum coverage in relation to SARS-CoV-2 immune escape variants.

Advances of Reverse Vaccinology for mRNA Vaccine Design against SARS-CoV-2: A Review of Methods and Tools

“…Addressing the growing concern of SARS-CoV-2 variants, Hussain et al [33] unveiled DOW-21, a restructured mRNA vaccine construct. This design emphasizes the N-terminal domain (NTD) and the receptor-binding domain (RBD) of the spike protein, integrating variations from both variants of concern (VOCs) and variants of interest (VOIs).…”

“…The Virus Pathogen Database and Analysis Resource (ViPR) serves as another specialized repository with a focus on viral pathogens. Studies cited as Ahammad and Lira [27], ELKHOLY [28] leveraged ViPR for the purpose of sequence acquisition, whereas the Global Initiative for Sharing All Influenza Data (GISAID) was utilized in Oluwagbemi et al [30], Oladipo et al [32], Hussain et al [33] for the procurement of complete genomic sequences of SARS-CoV-2 and its associated variants. GISAID is particularly renowned for its expeditious data dissemination capabilities, rendering it indispensable for research endeavors necessitating real-time genomic data.…”

“…Similarly, Durojaye et al [34] integrated ABCpred, iBCE-EL, and Bepipred web servers. For the prediction of discontinuous B cell epitopes, Hussain et al [33] exploited the capabilities of DiscoTope v2. The multimethod approach, as shown by Pourseif et al [35], represents an advancement in prediction strategies, using Bepipred for continuous and Discotope for discontinuous epitopes.…”

“…Ahammad and Lira [27], ELKHOLY [28], and Oluwagbemi et al [30] discuss how specific linkers like GPGPG and (EAAK)2 are employed to optimize the vaccine's efficacy. Hussain et al [33] employs molecular modeling to assess the structural and thermodynamic attributes of the construct, a technique further refined by Durojaye et al [34] through the use of SimRNA for 3D structure prediction. Pourseif et al [35] add to the discussion by presenting two distinct vaccine constructs optimized for different platforms, showcasing the adaptability inherent in mRNA vaccine technology.…”

“…Using default parameters, these two servers calculate the percentage of 2D configurations such as alpha helix, random coil, and beta-turn. Moreover, specific servers for predicting RNA sequence structures, such as RNAfold and simRNA, were used by Hussain et al [33] and Durojaye et al [34], respectively [65,66]. The latter was proposed to predict the three-dimensional structure, but also provides additional results, including the secondary structure.…”