Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), a public health emergency of international concerns declared by the World Health Organization (WHO). An immuno-informatics approach along with comparati...
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| Format: | Article |
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PeerJ Inc.
2020-07-01
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| Online Access: | https://peerj.com/articles/9572.pdf |
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| author | M. Shaminur Rahman M. Nazmul Hoque M. Rafiul Islam Salma Akter A. S. M. Rubayet-Ul-Alam Mohammad Anwar Siddique Otun Saha Md. Mizanur Rahaman Munawar Sultana Keith A. Crandall M. Anwar Hossain |
| author_facet | M. Shaminur Rahman M. Nazmul Hoque M. Rafiul Islam Salma Akter A. S. M. Rubayet-Ul-Alam Mohammad Anwar Siddique Otun Saha Md. Mizanur Rahaman Munawar Sultana Keith A. Crandall M. Anwar Hossain |
| author_sort | M. Shaminur Rahman |
| collection | DOAJ |
| description | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), a public health emergency of international concerns declared by the World Health Organization (WHO). An immuno-informatics approach along with comparative genomics was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M, and E proteins. The tertiary structure was predicted, refined and validated using advanced bioinformatics tools. The candidate vaccine showed an average of ≥90.0% world population coverage for different ethnic groups. Molecular docking and dynamics simulation of the chimeric vaccine with the immune receptors (TLR3 and TLR4) predicted efficient binding. Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2. It also increased the proliferation of T-helper cells and cytotoxic T-cells along with the increased IFN-γ and IL-2 cytokines. The codon optimization and mRNA secondary structure prediction revealed that the chimera is suitable for high-level expression and cloning. Overall, the constructed recombinant chimeric vaccine candidate demonstrated significant potential and can be considered for clinical validation to fight against this global threat, COVID-19. |
| first_indexed | 2024-03-09T06:59:43Z |
| format | Article |
| id | doaj.art-068374fcab0648cb8e0fe6f9c53a4c91 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:59:43Z |
| publishDate | 2020-07-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-068374fcab0648cb8e0fe6f9c53a4c912023-12-03T09:54:59ZengPeerJ Inc.PeerJ2167-83592020-07-018e957210.7717/peerj.9572Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approachM. Shaminur Rahman0M. Nazmul Hoque1M. Rafiul Islam2Salma Akter3A. S. M. Rubayet-Ul-Alam4Mohammad Anwar Siddique5Otun Saha6Md. Mizanur Rahaman7Munawar Sultana8Keith A. Crandall9M. Anwar Hossain10Department of Microbiology, University of Dhaka, Dhaka, BangladeshDepartment of Microbiology, University of Dhaka, Dhaka, BangladeshDepartment of Microbiology, University of Dhaka, Dhaka, BangladeshDepartment of Microbiology, University of Dhaka, Dhaka, BangladeshDepartment of Microbiology, Jashore University of Science and Technology, Jashore, BangladeshDepartment of Microbiology, University of Dhaka, Dhaka, BangladeshDepartment of Microbiology, University of Dhaka, Dhaka, BangladeshDepartment of Microbiology, University of Dhaka, Dhaka, BangladeshDepartment of Microbiology, University of Dhaka, Dhaka, BangladeshComputational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, Washington D.C., United States of AmericaDepartment of Microbiology, University of Dhaka, Dhaka, BangladeshSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), a public health emergency of international concerns declared by the World Health Organization (WHO). An immuno-informatics approach along with comparative genomics was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M, and E proteins. The tertiary structure was predicted, refined and validated using advanced bioinformatics tools. The candidate vaccine showed an average of ≥90.0% world population coverage for different ethnic groups. Molecular docking and dynamics simulation of the chimeric vaccine with the immune receptors (TLR3 and TLR4) predicted efficient binding. Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2. It also increased the proliferation of T-helper cells and cytotoxic T-cells along with the increased IFN-γ and IL-2 cytokines. The codon optimization and mRNA secondary structure prediction revealed that the chimera is suitable for high-level expression and cloning. Overall, the constructed recombinant chimeric vaccine candidate demonstrated significant potential and can be considered for clinical validation to fight against this global threat, COVID-19.https://peerj.com/articles/9572.pdfSARS-CoV-2Muti-epitopeChimeric Peptide VaccineB-cell EpitopeT-cell Epitope |
| spellingShingle | M. Shaminur Rahman M. Nazmul Hoque M. Rafiul Islam Salma Akter A. S. M. Rubayet-Ul-Alam Mohammad Anwar Siddique Otun Saha Md. Mizanur Rahaman Munawar Sultana Keith A. Crandall M. Anwar Hossain Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach PeerJ SARS-CoV-2 Muti-epitope Chimeric Peptide Vaccine B-cell Epitope T-cell Epitope |
| title | Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach |
| title_full | Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach |
| title_fullStr | Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach |
| title_full_unstemmed | Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach |
| title_short | Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach |
| title_sort | epitope based chimeric peptide vaccine design against s m and e proteins of sars cov 2 etiologic agent of global pandemic covid 19 an in silico approach |
| topic | SARS-CoV-2 Muti-epitope Chimeric Peptide Vaccine B-cell Epitope T-cell Epitope |
| url | https://peerj.com/articles/9572.pdf |
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