Designing a Multi-Epitope Subunit Vaccine against VP1 Major Coat Protein of JC Polyomavirus
Abstract
:1. Introduction
2. Methodology
2.1. VP1 Protein Sequence Retrieval and Physicochemical Analysis
2.2. B Cell Epitopes Prediction
2.3. Helper T Lymphocyte (HTL) Epitopes Prediction
2.4. Cytotoxic T-Lymphocyte (CTL) Epitopes Prediction
2.5. Computational Construction of Vaccine and Its Physiochemical Analysis
2.6. Vaccine 3D Structure Prediction and Validation
2.7. Interaction of Vaccine with TLR-4 Using Docking
2.8. Molecular Dynamic (MD) Simulation
2.9. Immune Simulation Response of Vaccine Protein
3. Results and Discussion
3.1. Sequence Retrieval and Analysis
3.1.1. B Cell Epitope Prediction
3.1.2. HTL Epitope Prediction
3.1.3. CTL Epitope Prediction
3.1.4. Design of the Linear Vaccine Construct and Physiochemical Analysis
3.1.5. Vaccine Tertiary Structure Prediction and Validation
3.1.6. Binding Mode of Vaccine Construct with TLR-4
3.2. Molecular Dynamic Simulations
3.3. Immune System Simulation
4. Discussion
5. Conclusions
Limitation
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Peptide | Length | Antigenicity | Allergenicity | Toxicity |
---|---|---|---|---|
WEAVTLKTEVIGVT | 14 | Antigenic | Non-Allergen | Non-Toxin |
NPYPISFLLTD | 11 | Antigenic | Non-Allergen | Non-Toxic |
Peptide | Length | Antigenicity | Allergenicity | Toxicity |
---|---|---|---|---|
ENVPPVLHINTATT | 15 | Antigenic | Non-Allergen | Non-Toxin |
KRRVKNPYISFLLT | 15 | Antigenic | Non-Allergen | Non-Toxin |
LRKRRVKNPYISFL | 15 | Antigenic | Non-Allergen | Non-Toxin |
FGVGPLCKGDNLYLS | 15 | Antigenic | Non-Allergen | Non-Toxin |
GGEALELQGVLFNYR | 15 | Antigenic | Non-Allergen | Non-Toxin |
Peptide | Length | Antigenicity | Allergenicity | Toxicity |
---|---|---|---|---|
CGMFTKRSG | 9 | Antigenic | Non-Allergen | Non-Toxin |
DLTCGNILM | 9 | Antigenic | Non-Allergen | Non-Toxin |
ELQGVVFNYR | 10 | Antigenic | Non-Allergen | Non-Toxin |
GVEVLEVKTG | 10 | Antigenic | Non-Allergen | Non-Toxin |
GVVFNYRTK | 9 | Antigenic | Non-Allergen | Non-Toxin |
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Kanse, S.; Khandelwal, M.; Pandey, R.K.; Khokhar, M.; Desai, N.; Kumbhar, B.V. Designing a Multi-Epitope Subunit Vaccine against VP1 Major Coat Protein of JC Polyomavirus. Vaccines 2023, 11, 1182. https://doi.org/10.3390/vaccines11071182
Kanse S, Khandelwal M, Pandey RK, Khokhar M, Desai N, Kumbhar BV. Designing a Multi-Epitope Subunit Vaccine against VP1 Major Coat Protein of JC Polyomavirus. Vaccines. 2023; 11(7):1182. https://doi.org/10.3390/vaccines11071182
Chicago/Turabian StyleKanse, Sukhada, Mehak Khandelwal, Rajan Kumar Pandey, Manoj Khokhar, Neetin Desai, and Bajarang Vasant Kumbhar. 2023. "Designing a Multi-Epitope Subunit Vaccine against VP1 Major Coat Protein of JC Polyomavirus" Vaccines 11, no. 7: 1182. https://doi.org/10.3390/vaccines11071182
APA StyleKanse, S., Khandelwal, M., Pandey, R. K., Khokhar, M., Desai, N., & Kumbhar, B. V. (2023). Designing a Multi-Epitope Subunit Vaccine against VP1 Major Coat Protein of JC Polyomavirus. Vaccines, 11(7), 1182. https://doi.org/10.3390/vaccines11071182