An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Bijan Soleymani
Corresponding Author
Ali Najafi
Corresponding Author
Ebrahim Barzegari
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
One of the strategies against the lack of data and short onset time of the ongoing COVID-19 disease is the use of computational methods in the field of drug and vaccine design. Though demanding experimental validations, these methods can greatly reduce the time and cost of the immunogenic development projects. In this protocol, we describe the use of various immunoinformatics tools to design a multi-epitope vaccine polypeptide with the highest potential for activating the human immune system against SARS-CoV-2. The initial epitope set was extracted from the whole set of viral structural proteins. Their potential non-toxic and non-allergenic T-cell and B-cell binding and cytokine inducing epitopes were then identified through a priori immunoinformatic prediction. Selected epitopes were bonded to each other with appropriate links. A suitable adjuvant was added to the N-terminus of the vaccine polypeptide sequence to increase its immunogenicity. Molecular modelling of the 3D structure of the vaccine polypeptide, docking, molecular dynamics simulations and free energy calculations were used to confirm stability and receptor affinity. Time taken to complete: 43 days.
Keywords
SARS-CoV-2, Multi-epitope Vaccine, Molecular Dynamics Simulations, Toll-like Receptor 3, Immunoinformatics
The authors declare no competing financial interests.
Loading...
Version History
CURRENT STATUS: Posted
Version 1
Posted 02 Dec, 2020
Community comments: 1
Metrics
Comments: 0
HTML Views: ...
Associated Publications
An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Bijan Soleymani
Corresponding Author
Ali Najafi
Corresponding Author
Ebrahim Barzegari
Corresponding Author
Version History
CURRENT STATUS: Posted
Version 1
Posted 02 Dec, 2020
Community comments: 1
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
One of the strategies against the lack of data and short onset time of the ongoing COVID-19 disease is the use of computational methods in the field of drug and vaccine design. Though demanding experimental validations, these methods can greatly reduce the time and cost of the immunogenic development projects. In this protocol, we describe the use of various immunoinformatics tools to design a multi-epitope vaccine polypeptide with the highest potential for activating the human immune system against SARS-CoV-2. The initial epitope set was extracted from the whole set of viral structural proteins. Their potential non-toxic and non-allergenic T-cell and B-cell binding and cytokine inducing epitopes were then identified through a priori immunoinformatic prediction. Selected epitopes were bonded to each other with appropriate links. A suitable adjuvant was added to the N-terminus of the vaccine polypeptide sequence to increase its immunogenicity. Molecular modelling of the 3D structure of the vaccine polypeptide, docking, molecular dynamics simulations and free energy calculations were used to confirm stability and receptor affinity. Time taken to complete: 43 days.
The authors declare no competing financial interests.
Loading...