Attenuated Subcomponent Vaccine Design Targeting the SARS-CoV-2 Nucleocapsid Phosphoprotein RNA Binding Domain: In silico analysis

The lack of effective vaccines against the novel corona virus (SARS-CoV-2) initiates a search for new approaches to overcoming this problem. We therefore design a subcomponent antigenic peptide vaccine specifically targeting the N-terminal (NTD) and C-terminal (CTD) RNA domains that aid in the viral...

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Bibliographic Details
Published in:bioRxiv 2020-07
Main Authors: Chukwudozie, Onyeka S, Chukwuanukwu, Rebecca C, Onyekachi, Iroanya O, Daniel, Eze M, Vincent, Duru C, Onaopemipo, Dele-Alimi T, David, Kehinde B, Taiwo, Bankole T, Perpetua, Obi C, Elizabeth, Okinedo U
Format: Article
Language:English
Subjects:
Allergenicity
Antigenicity
CD4 antigen
CD8 antigen
Epitopes
Hypersensitivity
Immunogenicity
Informatics
Lymphocytes B
Lymphocytes T
Major histocompatibility complex
Nucleocapsids
Peptides
Ribonucleic acid
RNA
Severe acute respiratory syndrome coronavirus 2
Toll-like receptors
Toxicity
Vaccines
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Summary:The lack of effective vaccines against the novel corona virus (SARS-CoV-2) initiates a search for new approaches to overcoming this problem. We therefore design a subcomponent antigenic peptide vaccine specifically targeting the N-terminal (NTD) and C-terminal (CTD) RNA domains that aid in the viral replication. Promising antigenic B-cells and T cell epitopes were predicted using immuno-informatics pipelines. The peptides RIRGGDGKMKDL and AFGRRGPEQTQGNFG were the B cell linear epitopes with a good antigenic index and non-allergenic property. Two CD8+ and Three CD4+ T-cell epitopes were also selected considering their immunogenic profiling such as allergenicity, antigen level conservancy, antigenicity, peptide toxicity and putative restrictions to a number of MHC-I and II alleles. With these selected epitopes, a non-allergenic chimeric peptide vaccine with the inability of inducing a Type II hypersensitivity reaction was constructed. The molecular interaction between the Toll like receptor-5 which was triggered by the vaccine was analyzed by molecular docking, and scrutinize using the dynamics simulation. Finally, in silico cloning was performed to ensure the expression and translation efficiency of the vaccine, utilizing pET-28a vector. This research, therefore, provides a guide for experimental investigations and validations. Competing Interest Statement The authors have declared no competing interest.
DOI:10.1101/2020.06.30.176537