An immunoinformatics study on the spike protein of SARS-CoV-2 revealing potential epitopes as vaccine candidates

Abstract

Background The pandemic situation of SARS-CoV-2 infection has sparked global concern due to the disease COVID-19 caused by it. Since the first cluster of confirmed cases in China in December 2019, the infection has been reported across the continents and inflicted upon a substantial number of populations. Method This study is focused on immunoinformatics analyses of the SARS-CoV-2 spike glycoprotein (S protein) which is key for the viral attachment to human host cells. Computational analyses were carried out for the prediction of B-cell and T-cell (MHC class I and II) epitopes of S protein and the analyses were extended further for the prediction of their immunogenic properties. The interaction and binding affinity of T-cell epitopes with HLA-B7 were also investigated by molecular docking. Result Three distinct epitopes for vaccine design were predicted from the sequence of S protein. The potential B-cell epitope was KNHTSPDVDLG possessing the highest antigenicity score of 1.4039 among other B-cell epitopes. T-cell epitope for human MHC class I was VVVLSFELL with an antigenicity score of 1.0909 and binding ability to 29 MHC-I alleles. The predicted T-cell epitope for human MHC class II molecule was VVIGIVNNT with a corresponding 1.3063 antigenicity score, less digesting enzymes, and 7 MHC-II alleles binding ability. All these three peptides were predicted to be highly antigenic, non-allergenic, and non-toxic. Analyses of the physiochemical properties of these predicted epitopes indicate their stable nature for plausible vaccine design. Furthermore, molecular docking investigation between the MHC class-I epitopes and human HLA-B7 reflects the stable interaction with high affinity among them. Conclusion The present study posits three potential epitopes of S protein of SARS-CoV-2 predicted by immunoinformatic methods based on their immunogenic properties and interactions with the host counterpart that can facilitate the development of vaccine against SARS-CoV-2. This study can act as the springboard for the future development of the COVID-19 vaccine.

Immunoinformatics based prediction of recombinant multi-epitope vaccine for the control and prevention of SARS-CoV-2

“…The epitopes were linked with GPGPG linker to make a peptide. The GPGPG linker has already used in other SARS-CoV-2 vaccines [45] , [46] , [47] .…”

“…Moreover, it was concluded that HLA-B7 plays a major role in MERS-CoV infections and HIV [49] . The HLA-B7 is the most favorable and used haplotype in the prediction of HLA binding to coronavirus peptides [45] , [50] .…”

Mutation profile of SARS-CoV-2 spike protein and identification of potential multiple epitopes within spike protein for vaccine development against SARS-CoV-2

“…is capable of binding to the viral antigen presented by MHC II molecules, then it leads to activation of B-cells that identifies the antigen by causing them to clonally proliferate and secrete antibodies to target different parts of the SARS-CoV-2 virus [25]. Some memory B-cells procured from the plasma B-cells keep the invader's memory to exhibit faster recognition and quick response during subsequent encounters with the invader [2]. The T-cell mediated response in SARS-CoV-2 is shown in Fig.…”

Bioinformatics Prediction of SARS-CoV-2 Epitopes as Vaccine Candidates for the Colombian Population

“…Several authors have reported epitope-based vaccine candidates by using inmmunoinformatic approaches [ 18 ]. These have predicted peptides with potential to interact with Human Leukocyte Antigen class I (HLA I) and class II (HLA II), and exhibited immunogenic responses, non-toxicity and non-allergenicity [ 19 ].…”