Bioinformatics Analysis of SARS-CoV-2 to Approach an Effective Vaccine Candidate Against COVID-19

Abstract

The emerging Coronavirus Disease 2019 (COVID-19) pandemic has posed a serious threat to the public health worldwide, demanding urgent vaccine provide. According to the virus feature as an RNA virus, a high rate of mutations imposes some vaccine design difficulties. Bioinformatics tools have been widely used to make advantage of conserved regions as well as immunogenicity. In this study, we aimed at immunoinformatic evaluation of SARS-CoV-2 proteins conservancy and immunogenicity to design a preventive vaccine candidate. Spike, Membrane and Nucleocapsid amino acid sequences were obtained, and four possible fusion proteins were assessed and compared in terms of structural features and immunogenicity, and population coverage. MHC-I and MHC-II T-cell epitopes, the linear and conformational B-cell epitopes were evaluated. Among the predicted models, the truncated form of Spike in fusion with M and N protein applying AAY linker has high rate of MHC-I and MCH-II epitopes with high antigenicity and acceptable population coverage of 82.95% in Iran and 92.51% in Europe. The in silico study provided truncated Spike-M-N SARS-CoV-2 as a potential preventive vaccine candidate for further in vivo evaluation.

Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach

“…Unfortunately, the entire length of the S-protein structure is not available in the protein data bank. We have used the earlier proved studies [ [33] , [34] , [35] , [36] , [37] , [38] ] to fix this issue. Hence, we have preferred the I-TASSER online server to predict the 3D structure of the S-protein.…”

“…Some of the collected SNP residue positions do not present in the existed PDB structures. To fix this issue, we have used the previous research studies as an example and implemented them in this study to construct the three-dimensional (3-D) conformation of the native S-protein [ [33] , [34] , [35] , [36] , [37] , [38] ]. Hence, we used the I-TASSER server [ 39 ] to model the native S-protein.…”

“…It is a threading-based structure prediction program which used to generate the three-dimensional structure of proteins from their amino acid sequence. Some recent studies opted for the threading approach to model the protein to check the interaction with other biological molecules [ [33] , [34] , [35] , [36] , [37] , [38] ]. I-TASSER produces great quality model predictions of three-dimensional structures from amino acid sequences.…”

Comparing Outcomes of Two Antiviral Therapy Combinations among COVID‐19 Patients

“…Coronavirus Disease 2019 (COVID-19) started in late 2019 in Wuhan, China, which then spread rapidly to many countries worldwide [ 1 , 2 ]. This pandemic disease has infected more than 200 million people worldwide [ 2 , 3 ] caused by a single-stranded RNA virus with human and animal hosts [ 4 – 6 ]. The average incubation period of the disease is between 4 and 5 days, but it may last up to 14 days.…”

In silico approach to design a multi-epitopic vaccine candidate targeting the non-mutational immunogenic regions in envelope protein and surface glycoprotein of SARS-CoV-2

“…Multi-epitopic vaccines with T-cell and B-cell epitopes are capable to evoke both cell mediated and humoral immune response without resulting in any immune complications. Moreover, the effectiveness of the vaccine can be regulated by selecting the epitopes that binds with large number of alleles resulting in diverse immune response (Elfiky, 2021 ; Foged, 2011 ; Sadat et al, 2021 ; Yang et al, 2021 ).…”