Excavating SARS‐coronavirus 2 genome for epitope‐based subunit vaccine synthesis using immunoinformatics approach

Abstract

Since the outbreak of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in December 2019 in China, there has been an upsurge in the number of deaths and infected individuals throughout the world, thereby leading to the World Health Organization declaration of a pandemic. Since no specific therapy is currently available for the same, the present study was aimed to explore the SARS-CoV-2 genome for the identification of immunogenic regions using immunoinformatics approach. A series of computational tools were applied in a systematic way to identify the epitopes that could be utilized in vaccine development. The screened-out epitopes were passed through several immune filters, such as promiscuousity, conservancy, antigenicity, nonallergenicity, population coverage, nonhomologous to human proteins, and affinity with human leukocyte antigen alleles, to screen out the best possible ones. Further, a construct comprising 11 CD4, 12 CD8, 3 B cell, and 3 interferon-γ epitopes, along with an adjuvant β-defensin, was designed in silico, resulting in the formation of a multiepitope vaccine. The in silico immune simulation and population coverage analysis of the vaccine sequence showed its capacity to elicit cellular, humoral, and innate immune cells and to cover up a worldwide population of more than 97%. Further, the interaction analysis of the vaccine construct with Toll-like receptor 3 (immune receptor) was carried out by docking and dynamics simulations, revealing high affinity, constancy, and pliability between the two. The overall findings suggest that the vaccine may be highly effective, and is therefore required to be tested in the lab settings to evaluate its efficacy.

Engineering a multi epitope vaccine against SARS-CoV-2 by exploiting its non structural and structural proteins

“…In the present study we have proposed a non allergenic and non toxic vaccine construct with acceptable physiological properties, which is composed of highly immunogenic B and T cell epitopes from two structural and three non-structural proteins of SARS-CoV-2. In comparison to our study with other similar reports where both classes of proteins have been utilized (Ahmad et al, 2020 ; Chauhan et al, 2021 ; Enayatkhani et al, 2021 ; Srivastava et al, 2020 ), we found that our proposed candidate exhibits enhanced immunogenic potential on account of its predicted antigenicity score. Moreover, the combinations of proteins/epitopes that we have utilized have not been explored by any other immunoinformatics study so far.…”

“…Several groups have utilized this approach in developing candidate vaccines to combat Covid-19. Most of these immunoinformatics studies have focussed on prediction of epitopes from a single protein, majorly the surface spike glycoprotein (Abraham Peele et al, 2020 ; Bhatnager et al, 2020 ; Bhattacharya et al, 2020 ; Kar et al, 2020 ; Naz et al, 2020 ; Rahman et al, 2020 ; Samad et al, 2020 ; Sanami et al, 2020 ) or a single category of proteins, either structural or non-structural (Kalita et al, 2020 ; Ojha et al, 2020 ; Sarkar & Ullah, 2020 ); relatively few are focused on a candidate that utilizes both these classes of proteins (Ahmad et al, 2020 ; Chauhan et al, 2021 ; Enayatkhani et al, 2021 ; Srivastava et al, 2020 ; Tahir et al, 2020 ).Some others have employed only CTL epitopes leaving the significant B-cell or HTL epitopes (Mishra, 2020 ). In the present study we have proposed a non allergenic and non toxic vaccine construct with acceptable physiological properties, which is composed of highly immunogenic B and T cell epitopes from two structural and three non-structural proteins of SARS-CoV-2.…”

Immunoinformatics-guided designing and in silico analysis of epitope-based polyvalent vaccines against multiple strains of human coronavirus (HCoV)

“…The B-cells mediate the humoral immune response by producing antibodies and keeping the memory of a previous infection. However, the humoral immune response provided by the B-cells may get weaker overtime and pathogens or antigens can easily overcome the humoral immune response [ 124 ]. In such cases, the cell-mediated immune response can provide much broader, often life-long immunity by secreting antiviral cytokines and specifically identifying and destroying the infected cells.…”

Development of an in silico multi-epitope vaccine against SARS-COV-2 by précised immune-informatics approaches

“…By combining all of the possible CTL, HTL, and LBL epitopes with suitable adjuvant and flexible linkers, a multi-epitope vaccine was constructed [ 62 , 63 ]. Based on the immunological filters mentioned above, the best potential epitopes were screened and combined to produce a single peptide chain [ 64 ]. Because peptides are not immunogenic on their own, an adjuvant is necessary to stimulate the immune response [ 65 , 66 ].…”