Exploring SARS-COV-2 structural proteins to design a multi-epitope vaccine using immunoinformatics approach: An in silico study

Abstract

In December 2019, a new virus called SARS-CoV-2 was reported in China and quickly spread to other parts of the world. The development of SARS-COV-2 vaccines has recently received much attention from numerous researchers. The present study aims to design an effective multi-epitope vaccine against SARS-COV-2 using the reverse vaccinology method. In this regard, structural proteins from SARS-COV-2, including the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins, were selected as target antigens for epitope prediction. A total of five helper T lymphocytes (HTL) and five cytotoxic T lymphocytes (CTL) epitopes were selected after screening the predicted epitopes for antigenicity, allergenicity, and toxicity. Subsequently, the selected HTL and CTL epitopes were fused via flexible linkers. Next, the cholera toxin B-subunit (CTxB) as an adjuvant was linked to the N-terminal of the chimeric structure. The proposed vaccine was analyzed for the properties of physicochemical, antigenicity, and allergenicity. The 3D model of the vaccine construct was predicted and docked with the Toll-like receptor 4 (TLR4). The molecular dynamics (MD) simulation was performed to evaluate the stable interactions between the vaccine construct and TLR4. The immune simulation was also conducted to explore the immune responses induced by the vaccine. Finally, in silico cloning of the vaccine construct into the pET-28 (+) vector was conducted. The results obtained from all bioinformatics analysis stages were satisfactory; however, in vitro and in vivo tests are essential to validate these results.

IDbSV: An Open-Access Repository for Monitoring SARS-CoV-2 Variations and Evolution

“…Yet we revealed a median variation rate of 18.6 variations per genome with an increasing rate of one more variation every 12.5 days, which is expectedly higher than what identified in earlier studies ( 36 , 37 ). Noteworthy, 27.8% of variations were identified in regions coding for structural proteins, this put more emphasis on the importance of monitoring SARS-CoV-2 variations especially in these regions, as these structural proteins are the main targets of the currently developed vaccines) ( 38 , 39 ).…”

Daphnoretin from Carthamus tinctorius as a Potential Inflammatory Inhibitor in COVID-19 by Binding to Toll-like Receptor-4: An in silico Molecular Docking Study

“…A different approach has been taken in several studies to search for potential vaccine candidates by targeting TLR4 to bind the epitope of the SARS-CoV2 spike protein [32], [34], [35]. Several studies on SARS-CoV2 have shown the importance of TLR4 in generating an effective immune response [36], [37].…”

Severe acute respiratory syndrome coronavirus-2: An era of struggle and discovery leading to the emergency use authorization of treatment and prevention measures based on computational analysis

“…The antigen analysis, for example, helps to determine immunological epitopes that can trigger an immune response without causing the reversal of viral pathogenesis ( Dhama et al, 2020 , Mishra et al, 2020 ) In silico proteome analysis of the SARS-CoV-2 genome ( Mishra et al, 2020 , Wu et al, 2020 ) identified 29 encoded proteins ( Baruah et al, 2020 ). There are 14 open reading frames (ORFs): ORF1a, ORF1b, ORF 14, 9b, 8b, 7b, 7a, p6, 3a (papain-like protease), and 3b ( Baruah et al, 2020 , Sanami et al, 2021 ). ORF1a and ORF1b encode 16 different nonstructural proteins (NSPs) ( Baruah et al, 2020 , Tan et al, 2005 ).…”

“…ORF1a and ORF1b encode 16 different nonstructural proteins (NSPs) ( Baruah et al, 2020 , Tan et al, 2005 ). Other proteins that are encoded by the virus genome are the envelope protein (E), the membrane protein (M), spike glycoprotein S, and the nucleocapsid protein (N) ( Baruah et al, 2020 , Sanami et al, 2021 , Tan et al, 2005 ).…”

“…Due to this emergency, health scientists have focused on the identification of ideal and efficient vaccine candidates ( Mishra et al, 2020 ). With the urgent need to develop multiepitope vaccines and the high pathogenicity of SARS-CoV-2, a lucrative in silico analysis was implemented for predicting active antigenic epitopes ( Mishra et al, 2020 , Sanami et al, 2021 ). One of the methods for vaccine development used was immunoinformatics ( Mishra et al, 2020 ) and the reverse vaccinology method.…”