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

J Immunol Res. 2020 Sep 17;2020:2837670. doi: 10.1155/2020/2837670. eCollection 2020.


The novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has previously never been identified with humans, thereby creating devastation in public health. The need for an effective vaccine to curb this pandemic cannot be overemphasized. In view of this, we designed a subcomponent antigenic peptide vaccine targeting the N-terminal (NT) and C-terminal (CT) RNA binding domains of the nucleocapsid protein that aid in viral replication. Promising antigenic B cell and T cell epitopes were predicted using computational pipelines. The peptides "RIRGGDGKMKDL" and "AFGRRGPEQTQGNFG" were the B cell linear epitopes with good antigenic index and nonallergenic property. Two CD8+ and Three CD4+ T cell epitopes were also selected considering their safe immunogenic profiling such as allergenicity, antigen level conservancy, antigenicity, peptide toxicity, and putative restrictions to a number of MHC-I and MHC-II alleles. With these selected epitopes, a nonallergenic chimeric peptide vaccine incapable of inducing a type II hypersensitivity reaction was constructed. The molecular interaction between the Toll-like receptor-5 (TLR5) which was triggered by the vaccine was analyzed by molecular docking and scrutinized using dynamics simulation. Finally, in silico cloning was performed to ensure the expression and translation efficiency of the vaccine, utilizing the pET-28a vector. This research, therefore, provides a guide for experimental investigation and validation.

MeSH terms

  • Betacoronavirus / immunology*
  • CD4-Positive T-Lymphocytes / immunology
  • CD8-Positive T-Lymphocytes / immunology
  • COVID-19
  • Coronavirus Infections / prevention & control*
  • Epitopes, B-Lymphocyte / genetics
  • Epitopes, B-Lymphocyte / immunology
  • Epitopes, T-Lymphocyte / genetics
  • Epitopes, T-Lymphocyte / immunology
  • Humans
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Nucleocapsid / immunology*
  • Nucleocapsid Proteins / immunology*
  • Nucleocapsid Proteins / metabolism
  • Pandemics / prevention & control*
  • Pneumonia, Viral / prevention & control*
  • RNA Recognition Motif Proteins / immunology
  • RNA-Binding Motifs / immunology
  • SARS-CoV-2
  • Toll-Like Receptor 5 / metabolism
  • Vaccines, Attenuated / immunology
  • Vaccines, Subunit / immunology
  • Viral Vaccines / immunology*


  • Epitopes, B-Lymphocyte
  • Epitopes, T-Lymphocyte
  • Nucleocapsid Proteins
  • RNA Recognition Motif Proteins
  • TLR5 protein, human
  • Toll-Like Receptor 5
  • Vaccines, Attenuated
  • Vaccines, Subunit
  • Viral Vaccines