Coevolution based immunoinformatics approach considering variability of epitopes to combat different strains: A case study using spike protein of SARS-CoV-2.

Publication date: Jul 01, 2023

In the recent past several vaccines were developed to combat the COVID-19 disease. Unfortunately, the protective efficacy of the current vaccines has been reduced due to the high mutation rate in SARS-CoV-2. Here, we successfully implemented a coevolution based immunoinformatics approach to design an epitope-based peptide vaccine considering variability in spike protein of SARS-CoV-2. The spike glycoprotein was investigated for B- and T-cell epitope prediction. Identified T-cell epitopes were mapped on previously reported coevolving amino acids in the spike protein to introduce mutation. The non-mutated and mutated vaccine components were constructed by selecting epitopes showing overlapping with the predicted B-cell epitopes and highest antigenicity. Selected epitopes were linked with the help of a linker to construct a single vaccine component. Non-mutated and mutated vaccine component sequences were modelled and validated. The in-silico expression level of the vaccine constructs (non-mutated and mutated) in E. coli K12 shows promising results. The molecular docking analysis of vaccine components with toll-like receptor 5 (TLR5) demonstrated strong binding affinity. The time series calculations including root mean square deviation (RMSD), radius of gyration (RGYR), and energy of the system over 100 ns trajectory obtained from all atom molecular dynamics simulation showed stability of the system. The combined coevolutionary and immunoinformatics approach used in this study will certainly help to design an effective peptide vaccine that may work against different strains of SARS-CoV-2. Moreover, the strategy used in this study can be implemented on other pathogens.

Open Access PDF

Concepts Keywords
Covid Coevolution
Effective Immunoinformatics
K12 SARS-CoV-2
Mutation Spike protein
Vaccine Vaccine


Type Source Name
disease MESH COVID-19
disease MESH mutation rate
disease VO peptide vaccine
disease VO Glycoprotein
disease IDO cell
drug DRUGBANK Amino acids
disease VO vaccine
disease VO vaccine component
disease VO Toll-like receptor
disease VO time
disease VO effective
disease VO organization
disease MESH Syndrome
disease MESH viral infection
disease MESH emergency
disease VO Viruses
disease IDO infectivity
drug DRUGBANK Angiotensin II
disease IDO host
drug DRUGBANK Coenzyme M
disease IDO pathogen
disease VO therapeutic vaccine
disease VO West Nile virus vaccine
disease MESH infection
disease VO effectiveness
disease VO population
disease VO frequency

Original Article

(Visited 1 times, 1 visits today)

Leave a Comment

Your email address will not be published. Required fields are marked *