Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein

The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants...

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Published inVaccines (Basel) Vol. 11; no. 2; p. 399
Main Authors Umitaibatin, Ramadhita, Harisna, Azza Hanif, Jauhar, Muhammad Miftah, Syaifie, Putri Hawa, Arda, Adzani Gaisani, Nugroho, Dwi Wahyu, Ramadhan, Donny, Mardliyati, Etik, Shalannanda, Wervyan, Anshori, Isa
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 01.02.2023
MDPI
Subjects
Amino acids
Antibodies
Antigenic determinants
antigenic epitope
Antigens
Binding sites
CD4 antigen
CD8 antigen
Coronaviruses
COVID-19
COVID-19 vaccines
Cytotoxicity
Design
Dynamic stability
epitope prediction
Epitopes
Glycoproteins
Health aspects
LR-4
Lymphocytes
Lymphocytes B
Lymphocytes T
Molecular docking
Molecular dynamics
Mutation
Phylogenetics
Population
Proteins
Severe acute respiratory syndrome coronavirus 2
Side effects
Simulation
Spike glycoprotein
Spike protein
TLR-3
Vaccines
Vectors (Biology)
Viral diseases
Viral infections
γ-Interferon
Indonesia
epitope prediction
antigenic epitope
TLR-3
spike glycoprotein
LR-4
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Abstract The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population using an immunoinformatic approach. This study was conducted using the SARS-CoV-2 spike glycoprotein sequences from Indonesia that were retrieved from the GISAID database. Three SARS-CoV-2 sequences, with IDs of EIJK-61453, UGM0002, and B.1.1.7 were selected. The CD8+ cytotoxic T-cell lymphocyte (CTL) epitope, CD4+ helper T lymphocyte (HTL) epitope, B-cell epitope, and IFN-γ production were predicted. After modeling the vaccines, molecular docking, molecular dynamics, in silico immune simulations, and plasmid vector design were performed. The designed vaccine is antigenic, non-allergenic, non-toxic, capable of inducing IFN-γ with a population reach of 86.29% in Indonesia, and has good stability during molecular dynamics and immune simulation. Hence, this vaccine model is recommended to be investigated for further study.
AbstractList The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population using an immunoinformatic approach. This study was conducted using the SARS-CoV-2 spike glycoprotein sequences from Indonesia that were retrieved from the GISAID database. Three SARS-CoV-2 sequences, with IDs of EIJK-61453, UGM0002, and B.1.1.7 were selected. The CD8+ cytotoxic T-cell lymphocyte (CTL) epitope, CD4+ helper T lymphocyte (HTL) epitope, B-cell epitope, and IFN-γ production were predicted. After modeling the vaccines, molecular docking, molecular dynamics, in silico immune simulations, and plasmid vector design were performed. The designed vaccine is antigenic, non-allergenic, non-toxic, capable of inducing IFN-γ with a population reach of 86.29% in Indonesia, and has good stability during molecular dynamics and immune simulation. Hence, this vaccine model is recommended to be investigated for further study.
The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population using an immunoinformatic approach. This study was conducted using the SARS-CoV-2 spike glycoprotein sequences from Indonesia that were retrieved from the GISAID database. Three SARS-CoV-2 sequences, with IDs of EIJK-61453, UGM0002, and B.1.1.7 were selected. The CD8+ cytotoxic T-cell lymphocyte (CTL) epitope, CD4+ helper T lymphocyte (HTL) epitope, B-cell epitope, and IFN-γ production were predicted. After modeling the vaccines, molecular docking, molecular dynamics, in silico immune simulations, and plasmid vector design were performed. The designed vaccine is antigenic, non-allergenic, non-toxic, capable of inducing IFN-γ with a population reach of 86.29% in Indonesia, and has good stability during molecular dynamics and immune simulation. Hence, this vaccine model is recommended to be investigated for further study.The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population using an immunoinformatic approach. This study was conducted using the SARS-CoV-2 spike glycoprotein sequences from Indonesia that were retrieved from the GISAID database. Three SARS-CoV-2 sequences, with IDs of EIJK-61453, UGM0002, and B.1.1.7 were selected. The CD8+ cytotoxic T-cell lymphocyte (CTL) epitope, CD4+ helper T lymphocyte (HTL) epitope, B-cell epitope, and IFN-γ production were predicted. After modeling the vaccines, molecular docking, molecular dynamics, in silico immune simulations, and plasmid vector design were performed. The designed vaccine is antigenic, non-allergenic, non-toxic, capable of inducing IFN-γ with a population reach of 86.29% in Indonesia, and has good stability during molecular dynamics and immune simulation. Hence, this vaccine model is recommended to be investigated for further study.
Audience Academic
Author Ramadhan, Donny
Anshori, Isa
Syaifie, Putri Hawa
Nugroho, Dwi Wahyu
Harisna, Azza Hanif
Umitaibatin, Ramadhita
Shalannanda, Wervyan
Arda, Adzani Gaisani
Mardliyati, Etik
Jauhar, Muhammad Miftah
AuthorAffiliation 1 Lab-on-Chip Group, Department of Biomedical Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
2 Nano Center Indonesia, Jl. Raya Puspiptek, South Tangerang 15314, Indonesia
5 Department of Telecommunication Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
4 Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
3 Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
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Issue 2
Keywords epitope prediction
antigenic epitope
TLR-3
spike glycoprotein
LR-4
Language English
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SSID ssj0000913867
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Snippet The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a...
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SubjectTerms Amino acids
Antibodies
Antigenic determinants
antigenic epitope
Antigens
Binding sites
CD4 antigen
CD8 antigen
Coronaviruses
COVID-19
COVID-19 vaccines
Cytotoxicity
Design
Dynamic stability
epitope prediction
Epitopes
Glycoproteins
Health aspects
LR-4
Lymphocytes
Lymphocytes B
Lymphocytes T
Molecular docking
Molecular dynamics
Mutation
Phylogenetics
Population
Proteins
Severe acute respiratory syndrome coronavirus 2
Side effects
Simulation
Spike glycoprotein
Spike protein
TLR-3
Vaccines
Vectors (Biology)
Viral diseases
Viral infections
γ-Interferon
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Title Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein
URI https://www.ncbi.nlm.nih.gov/pubmed/36851275
https://www.proquest.com/docview/2779669395
https://www.proquest.com/docview/2780762683
https://pubmed.ncbi.nlm.nih.gov/PMC9964839
https://doaj.org/article/582dd036fdc84c99ad6e6d68fd8244f2
Volume 11
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