Reverse Vaccinology Integrated with Biophysics Techniques for Designing a Peptide-Based Subunit Vaccine for Bourbon Virus
Abstract
1. Introduction
2. Materials and Methods
2.1. Identification of Antigenic Protein
2.2. Predicting Immunologically Potent Epitopes
2.3. B-Cell Antigenic Region Prediction
2.4. Constructing a Multi-Epitope Vaccine
2.5. Examination of Physiochemical Characteristics
2.6. Secondary and Three-Dimensional Structural Predictive Modeling
2.7. Validation of Tertiary Structure
2.8. Molecular Docking of Epitopes with HLAs and TLR4
2.9. Simulation-Based Computational Approach
2.10. Computational Cloning and Sequence Refinement
2.11. MD Simulation
2.12. Analysis of MMGBSA Binding Energy
3. Results
3.1. Protein Retrieval
3.2. Immunogenic Epitope Profiling
3.3. Development of a MEVC Construct
3.4. Physicochemical Properties
3.5. Secondary and 3D Structural Modeling
3.6. Docking Simulations Among Peptides and MEVC
3.7. Codon Optimization of the Comple Vaccine Construct
3.8. Immune Simulation
3.9. Molecular Docking
3.10. MD Simulation
3.11. Binding Free Energy Calculations
4. Discussion
5. Conclusions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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(A) | ||||||
---|---|---|---|---|---|---|
Protein | Peptide | Affinity | Cleavage | Tap Score | Combined Score | |
Nucleoprotein | LVDALNAEF | 0.2994 | 0.9286 | 2.5550 | 1.5382 | |
GVSPVCEPY | 0.1263 | 0.9660 | 2.9280 | 0.8276 | ||
GVRTTYNQY | 0.1057 | 0.9748 | 3.0650 | 0.7483 | ||
Polymerase subunit PA | PTDMEWLTL | 0.2933 | 0.8914 | 0.4090 | 1.3995 | |
RFSPATLEY | 0.1405 | 0.9767 | 3.3020 | 0.9083 | ||
IIRVLCIEY | 0.0817 | 0.7837 | 3.0690 | 0.6178 | ||
(B) | ||||||
Protein | Allele | Peptide | Score | Allergenicity | IFN | |
Nucleoprotein | HLA-DRB1*15:01 | YNIKDKLKKSRPLSI | 1.22 | Nill | Yes | |
HLA-DRB1*15:01 | KAQMVSLANKAKVDM | 0.34 | Nill | Yes | ||
HLA-DRB1*15:01 | VGKGKKLSQRAAAGI | 0.25 | Nill | Yes | ||
Polymerase subunit PA | HLA-DRB1*15:01 | HEDVLVRVTSIAKYK | 0.53 | Nill | Yes | |
HLA-DRB1*15:01 | QLWGFVIIGPHHVKQ | 0.67 | Nill | Yes | ||
HLA-DRB1*15:01 | LAVEALLLQDTDLDL | 1.78 | Nill | Yes | ||
(C) | ||||||
Protein | Position | Peptide | Score | |||
Nucleoprotein | 24 | RSKIEVDPLANKRKYE | 0.91 | |||
1 | MQSSRKAPNPRSSNDE | 0.91 | ||||
307 | MAQILIHCTFRSMHED | 0.85 | ||||
Polymerase subunit PA | 295 | TKIQEDLQAFGVGIKK | 0.87 | |||
62 | TWCPKEVVDSIMRQNQ | 0.85 | ||||
132 | TLEYLDQSQSQDVRNF | 0.83 |
Energy Parameter | Vaccine–TLR4 Complex |
---|---|
Van der Waals Energy (kcal/mol) | −120.56 |
Columbic Energy (kcal/mol) | −45.69 |
Total Gas-Phase Energy (kcal/mol) | −166.25 |
Total Solvation Energy (kcal/mol) | 31.42 |
Net Energy (kcal/mol) | −134.83 |
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Almanaa, T.N. Reverse Vaccinology Integrated with Biophysics Techniques for Designing a Peptide-Based Subunit Vaccine for Bourbon Virus. Bioengineering 2024, 11, 1056. https://doi.org/10.3390/bioengineering11111056
Almanaa TN. Reverse Vaccinology Integrated with Biophysics Techniques for Designing a Peptide-Based Subunit Vaccine for Bourbon Virus. Bioengineering. 2024; 11(11):1056. https://doi.org/10.3390/bioengineering11111056
Chicago/Turabian StyleAlmanaa, Taghreed N. 2024. "Reverse Vaccinology Integrated with Biophysics Techniques for Designing a Peptide-Based Subunit Vaccine for Bourbon Virus" Bioengineering 11, no. 11: 1056. https://doi.org/10.3390/bioengineering11111056
APA StyleAlmanaa, T. N. (2024). Reverse Vaccinology Integrated with Biophysics Techniques for Designing a Peptide-Based Subunit Vaccine for Bourbon Virus. Bioengineering, 11(11), 1056. https://doi.org/10.3390/bioengineering11111056