Abstract
Recently, a novel coronavirus (SARS-CoV-2) appeared which is conscientious for the current outbreak in China and rapidly spread worldwide. Unluckily, there is no approved vaccine found against SARS-CoV-2. Therefore, there is an urgent need for designing a suitable peptide vaccine constituent against the SARS-CoV-2. In this study, we characterized the spike glycoprotein of SARS-CoV-2 to obtain immunogenic epitopes. In addition, we used 58 SARS-CoV-2 isolates were retrieved from the Global Initiative on Sharing All Influenza Data (GISAID) and National Center for Biotechnology Information (NCBI), then aligned to obtain the conserved region of SARS-CoV-2 spike glycoprotein. The interaction between the conserved region with ACE2 receptor, a SARS-CoV-2 receptor on the host cell, has been evaluated through molecular docking approach. The B-cell epitope was identified using the immune epitope database (IEDB) web server. Interestingly, we recommend Pep_4 ADHQPQTFVNTELH as a epitope-based peptide vaccine candidate to deal with the SARS-CoV-2 outbreak. Pep_4 has a high level of immunogenicity and does not trigger autoimmune mechanisms. Pep_4 is capable of forming BCR/Fab molecular complexes with the lowest binding energy for activation of transduction signal the direct B-cell immune response. However, further study is suggested for confirmation (in vitro and in vivo).
Highlights
On 30 December 2019, Chinese government reported an outbreak of pneumonia disease in Wuhan (Lam et al, 2020)
We characterized the spike glycoprotein of SARS-CoV-2 to obtain immunogenic epitopes
We used 58 SARS-CoV-2 isolates were retrieved from the Global Initiative on Sharing All Influenza Data (GISAID) and National Center for Biotechnology Information (NCBI), aligned to obtain the conserved region of SARS-CoV-2 spike glycoprotein
Summary
On 30 December 2019, Chinese government reported an outbreak of pneumonia disease in Wuhan (Lam et al, 2020). The conserved domain in the SARS-CoV-2 viral spike glycoprotein sequences were identified through protein alignment with Molecular Evolutionary Genetics Analysis (MEGA) X, the 3D structure was modeled using the SWISSMODEL (https://swissmodel.expasy.org) with homology modeling approach (Schwede et al, 2003; Adianingsih and Kharisma, 2019). Molecular interaction simulation between the host cell receptor, angiotensinconverting enzyme 2 (ACE2), and SARS-CoV-2 spike glycoprotein during viral attachment and mechanism for binding peptide vaccine candidate with B-cell receptors (BCR), using the protein docking on the Cluspro 2.0 web server (https://cluspro.org/login.php). The complex of molecular docking displayed in PyMol with representative structures and color selections to identify between receptors (ACE2) and ligands (SARS-CoV-2 spike glycoprotein) (Fig. 2). The conserved domain on SARS-CoV-2 spike glycoproteins analyzed for the potential of B-cell immunogenicity to obtain specific peptides as vaccine candidates. Specific antibodies for neutralization of SARS-CoV-2 and the role of memory cells to keep the body formed from future infections
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