An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-CoV-2

Abstract

COVID-19 is a new viral emergent disease caused by a novel strain of coronavirus. This virus has caused a huge problem in the world as millions of people are affected by this disease. We aimed at designing a peptide vaccine for COVID-19 particularly for the envelope protein using computational methods to predict epitopes inducing the immune system. The envelope protein sequence of SARS-CoV-2 has been retrieved from the NCBI database. The bioinformatics analysis was carried out by using the Immune Epitope Database (IEDB) to predict B- and T-cell epitopes. The predicted HTL and CTL epitopes were docked with HLA alleles and binding energies were evaluated. The allergenicity of predicted epitopes was analyzed, the conservancy analysis was performed, and the population coverage was determined throughout the world. Some overlapped CTL, HTL, and B-cell epitopes were suggested to become a universal candidate for peptide-based vaccine against COVID-19. This vaccine peptide could simultaneously elicit humoral and cell-mediated immune responses. We hope to confirm our findings by adding complementary steps of both in vitro and in vivo studies to support this new universal predicted candidate.

Immunoinformatics Analysis of SARS-CoV-2 ORF1ab Polyproteins to Identify Promiscuous and Highly Conserved T-Cell Epitopes to Formulate Vaccine for Indonesia and the World Population

“…There have been several reports employing immunoinformatics to identify T-cell epitopes and formulate a vaccine for SARS-CoV-2 infection. PubMed search using keywords 'peptide-based vaccine', 'SARS-CoV-2', and 'immunoinformatics' conducted on 14 October 2021 resulted in 15 research articles [94][95][96][97][98][99][100][101][102][103][104][105][106][107][108]. In this study, we made a prediction based on the HLA alleles that are present with at least 5% frequency in the Indonesian population.…”

Untitled

“…Numerous efforts have been made in determining vaccine targets for SARS-CoV-2 using computational methods. These methods are based on B cell and T cell epitope prediction [7][8][9][10][11][12][13][14] and indeed extend beyond SARS-CoV-2 to encompass prediction of the pathogen-based immune response more generically [15][16][17][18][19] . In the current study, we explored this approach by investigating in silico the binding affinities of all linear 15-, 18and 22-amino acid long epitopes of S natural and its 5 variants (S D614G , S B.1.1.7 , S B.1.351 , S P.1 , S P.167.2 ) to 66 common HLA Class II alleles with global frequencies of ≥ 0.01.…”

Immunoinformatics Identification of B- and T-Cell Epitopes in the RNA-Dependent RNA Polymerase of SARS-CoV-2

“…ese vaccine candidates can be designed to encompass multiple determinants from various pathogens or multiple epitopes from the same pathogenic organism. In silico epitope-based vaccines have a remarkable advantage over the conventional methods of vaccine development because they are found to be highly specific, capable of avoiding unwanted immune responses, eliciting long-lasting innate and adaptive immunity, safe and less time-consuming, and are reasonably cheaper [16].…”