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

ABSTRACT: The COVID-19 pandemic worldwide has resulted in over 176 million cases and roughly 3.8 million deaths so far. We could analyze mutation dynamics across the genome from countries such as the USA, Italy, the UK, France, Brazil, and India considering the rapid mutations of the SARS-CoV-2 genome. The analysis would help us to understand the genome diversity, the implications of the mutations in protein stability, and viral transmission. Among the 11 genes, surface glycoprotein (S) was singled out because of its crucial function associated with the entry of virion into the human cell upon binding with the hACE2 receptor. 749 S protein sequences from India were retrieved from the NCBI database for our study. The S protein is an important antigenic component responsible for inducing host immune responses, neutralizing antibodies, and providing protective immunity against viral infection. During an epitope prediction from a mutation-prone S-protein region, it is necessary to ascertain how new mutations significantly change the S protein, such that our vaccine is effective against all the mutated strains as well. The S1 region of the S protein had been our prime focus for identifying immune epitopes against SARS-COV-2. Antigenic B- cell epitopes were YYPDKVF from NTD and LFRKSNLKP from RBD. Cytotoxic T-cell epitopes WTAGAAAYY (within NTD) and CVADYSVLY (within RBD) exhibited binding with a maximum number of MHC I alleles. The T-cell epitopes which showed a maximum affinity for MHC II alleles were FLPFFSNVT within NTD and YFPLQSYGF within RBD. Furthermore, the best epitopes were characterized in terms of their physicochemical properties to establish their potentiality.

SUBMITTER: Paul D

PROVIDER: S-EPMC8569294 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundThe 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.MethodThis 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.ResultThree 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.ConclusionThe 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.

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

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