Execution and Design of an Anti HPIV-1 Vaccine with Multiple Epitopes Triggering Innate and Adaptive Immune Responses: An Immunoinformatic Approach
Abstract
:1. Introduction
2. Materials and Methods
2.1. Viral Proteins’ Sequence Retrieval
2.2. Antigenic Protein Identification
2.3. Physicochemical Analysis
2.4. Two-Dimensional (2D) and 3D Structural Analysis
2.5. B-Cell-Specific Epitopes Identification via IEDB Tools
2.6. Predicting T-Cells Restricted Epitopes
2.7. Selected Epitopes’ Population Coverage
2.8. Profiling of Predicted Epitopes
2.9. Vaccine Design and Profiling
2.10. Disulfide Engineering of Vaccine
2.11. Three-Dimensional (3D) Structural Analysis
2.12. Molecular Docking and Dynamics
2.13. Codon Improvement and Cloning
2.14. Immune Simulation
3. Results
3.1. Antigenicity, Structural and Physicochemical Analysis of Viral HN Protein
3.2. B-Cell-Restricted Epitope Predictions
3.3. Predicting T-Cells Restricted Epitopes
3.4. Filtration of Predicted Epitopes
3.5. Population-Coverage Analysis
3.6. Assembly of a Multi-Epitope Vaccine
3.7. Quality Check Analysis and Profiling of Designed Vaccine
3.8. Physicochemical Properties
3.9. Prediction of Secondary and Tertiary Structure
3.10. Tertiary Structure Refinement and Validation
3.11. Vaccine Stability by Disulfide Engineering
3.12. Molecular Docking of Designed Vaccine with Ligand Binding TLRs
3.13. Molecular Dynamic Simulations
3.14. Adaptation and Enhancement of Codon along with In-Silico Cloning
3.15. Immune Simulations
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Molecule | MW (Da) | Instability Index | Half-Life | Theoretical pI | AA No. | GRAVY | Aliphatic Index |
---|---|---|---|---|---|---|---|
HN protein | 63,981.34 | 36.48 | 30 h | 8.17 | 575 | −0.161 | 94.94 |
Vaccine | 69,661.70 | 33.32 | 3.5 h | 9.04 | 641 | −0.060 | 93.53 |
Start | End | Peptide | Length | Antigenicity Score |
---|---|---|---|---|
343 | 375 | TTPLQGDTKCVTNRCANVNQSVCNDALKITWLK | 33 | 0.5002 |
445 | 470 | MTIKWAPHEVLSRPGNQDCNWYNRCP | 26 | 0.8932 |
520 | 528 | RLKNVQLEA | 9 | 1.3398 |
Start | End | Allele | Peptide | Length | Antigenicity Score |
---|---|---|---|---|---|
MHC-I EPITOPES | |||||
399 | 407 | HLA-A * 26:01 | ETIPITQNY | 9 | 0.9982 |
150 | 159 | HLA-B * 57:01 | ISPLDPHDFW | 10 | 0.9645 |
150 | 159 | HLA-B * 58:01 | ISPLDPHDFW | 10 | 0.9538 |
94 | 102 | HLA-A * 68:02 | EVISRTINI | 9 | 0.9457 |
247 | 256 | HLA-A * 68:01 | HTYDINDNRK | 10 | 0.9373 |
305 | 313 | HLA-A * 24:02 | RYKNEDITF | 9 | 0.9317 |
41 | 49 | HLA-B * 57:01 | TTMHTILSF | 9 | 0.9105 |
389 | 397 | HLA-A * 02:03 | YLSDRPKIV | 9 | 0.8992 |
305 | 313 | HLA-A * 23:01 | RYKNEDITF | 9 | 0.8926 |
364 | 373 | HLA-B * 57:01 | VCNDALKITW | 10 | 0.8925 |
2 | 11 | HLA-B * 44:03 | AEKGKTNSSY | 10 | 0.8767 |
2 | 11 | HLA-B * 44:02 | AEKGKTNSSY | 10 | 0.8757 |
150 | 159 | HLA-B * 53:01 | ISPLDPHDFW | 10 | 0.8588 |
367 | 375 | HLA-A * 68:01 | DALKITWLK | 9 | 0.8520 |
41 | 49 | HLA-B * 58:01 | TTMHTILSF | 9 | 0.8503 |
290 | 298 | HLA-A * 68:01 | LVFDILDLK | 9 | 0.8461 |
MHC-II EPITOPES | |||||
46 | 60 | HLA-DRB4 * 01:01 | ILSFIIMILCIDLII | 14 | 0.08 |
45 | 59 | HLA-DRB4 * 01:01 | TILSFIIMILCIDL | 14 | 0.08 |
96 | 110 | HLA-DRB4 * 01:01 | ISRTINIQSSVQSGI | 14 | 0.15 |
95 | 109 | HLA-DRB4 * 01:01 | VISRTINIQSSVQSG | 14 | 0.2 |
94 | 108 | HLA-DRB4 * 01:01 | EVISRTINIQSSVQS | 14 | 0.23 |
166 | 180 | HLA-DRB3 * 02:02 | PLLSNNPNISLLPGP | 14 | 0.46 |
44 | 58 | HLA-DRB4 * 01:01 | HTILSFIIMILCIDL | 14 | 0.76 |
514 | 528 | HLA-DRB4 * 01:01 | EIINMLRLKNVQLEA | 14 | 1.2 |
515 | 529 | HLA-DRB4 * 01:01 | IINMLRLKNVQLEAA | 14 | 1.2 |
516 | 530 | HLA-DRB4 * 01:01 | INMLRLKNVQLEAAY | 14 | 1.4 |
415 | 429 | HLA-DRB1 * 15:01 | LKLGKKIYIYTRSSG | 14 | 1.5 |
43 | 57 | HLA-DRB1 * 15:01 | MHTILSFIIMILCID | 14 | 1.6 |
43 | 57 | HLA-DRB4 * 01:01 | MHTILSFIIMILCID | 14 | 2.3 |
517 | 531 | HLA-DRB4 * 01:01 | NMLRLKNVQLEAAYT | 14 | 2.6 |
511 | 525 | HLA-DRB4 * 01:01 | NTSEIINMLRLKNVQ | 14 | 2.9 |
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Naveed, M.; Yaseen, A.R.; Khalid, H.; Ali, U.; Rabaan, A.A.; Garout, M.; Halwani, M.A.; Al Mutair, A.; Alhumaid, S.; Al Alawi, Z.; et al. Execution and Design of an Anti HPIV-1 Vaccine with Multiple Epitopes Triggering Innate and Adaptive Immune Responses: An Immunoinformatic Approach. Vaccines 2022, 10, 869. https://doi.org/10.3390/vaccines10060869
Naveed M, Yaseen AR, Khalid H, Ali U, Rabaan AA, Garout M, Halwani MA, Al Mutair A, Alhumaid S, Al Alawi Z, et al. Execution and Design of an Anti HPIV-1 Vaccine with Multiple Epitopes Triggering Innate and Adaptive Immune Responses: An Immunoinformatic Approach. Vaccines. 2022; 10(6):869. https://doi.org/10.3390/vaccines10060869
Chicago/Turabian StyleNaveed, Muhammad, Allah Rakha Yaseen, Hira Khalid, Urooj Ali, Ali A. Rabaan, Mohamed Garout, Muhammad A. Halwani, Abbas Al Mutair, Saad Alhumaid, Zainab Al Alawi, and et al. 2022. "Execution and Design of an Anti HPIV-1 Vaccine with Multiple Epitopes Triggering Innate and Adaptive Immune Responses: An Immunoinformatic Approach" Vaccines 10, no. 6: 869. https://doi.org/10.3390/vaccines10060869