Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2
Abstract
:1. Introduction
2. Methodology
2.1. Protein Sequence Retrieval and Determination of Antigenicity
2.2. B Cell Epitope Prediction
2.3. Prediction of Helper T Lymphocyte (HTL) Epitopes and Their Screening
2.4. Prediction of Cytotoxic T Lymphocyte (CTL) Epitopes
2.5. Toxicity Assessment and Prediction of the Allergenicity of the Screened Epitopes
2.6. Construction of Multi-Epitope-Based Vaccine
2.7. Prediction of Antigenicity and Allergenicity of the Designed Vaccine Candidate
2.8. Physiochemical Properties and Secondary Structure Prediction of the Constructed Vaccine
2.9. Disorder Profile Generation
2.10. Tertiary Structure Prediction and Validation
2.11. Molecular Interaction of the Designed Multi-Epitope Vaccine with TLR-3
2.12. In Silico Immune Stimulation Assay
3. Results
3.1. B-Cell Epitopes
3.2. HTL Epitopes
3.3. CTL Epitopes
3.4. Multi-Epitope Vaccine Design
3.5. Prediction of the Antigenicity and Allergenicity of the Constructed Vaccine
3.6. Physiochemical Characterization of the Designed Vaccine
3.7. Prediction of Secondary Structure and Disordered Residues
3.8. Prediction and Quality Assurance of the Tertiary Structure of the Designed Vaccine
3.9. Molecular Docking of the Vaccine Construct with TLR-3
3.10. In Silico Immunogenicity of the Designed Vaccine
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
References
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S No | Starting Amino Acid Position | Peptide Epitope | Bcpreds Server Score | Antigenicity Score (On Vaxijen V2.0) |
---|---|---|---|---|
1 | 443 | AQDGNAAISDYDYYRY | 0.987 | 0.5716 |
2 | 477 | DKYFDCYDGGCINANQ | 0.973 | 0.6443 |
3 | 347 | HFRELGVVHNQDVNLH | 0.938 | 1.4181 |
S No. | Peptide Epitope | Starting Amino Acid Position | Percentile Rank | Antigenicity Score (On Vaxijen V2.0) |
---|---|---|---|---|
1 | NMLRIMASLVLARKH | 208 | 0.01 | 0.4897 |
2 | PNMLRIMASLVLARK | 207 | 0.01 | 0.4128 |
3 | QMNLKYAISAKNRAR | 121 | 0.07 | 1.5044 |
4 | MNLKYAISAKNRART | 122 | 0.08 | 1.4377 |
5 | NLKYAISAKNRARTV | 123 | 0.15 | 1.3422 |
6 | DSYYSLLMPILTLTR | 25 | 0.16 | 0.5134 |
7 | MLRIMASLVLARKHT | 209 | 0.22 | 0.5283 |
8 | LRIMASLVLARKHTT | 210 | 0.32 | 0.6646 |
9 | LMPILTLTRALTAES | 31 | 0.37 | 0.4225 |
10 | ITQMNLKYAISAKNR | 119 | 0.41 | 1.5061 |
S No | Start | Peptide Epitope | Supertype | Antigenicity Score (On Vaxijen V2.0) |
---|---|---|---|---|
1 | 899 | MLDMYSVML | A2 | 0.5626 |
2 | 467 | RQLLFVVEV | A2 | 0.816 |
3 | 654 | RLANECAQV | A2 | 0.9246 |
4 | 784 | SVLYYQNNV | A2 | 0.5524 |
5 | 365 | RLSFKELLV | A2 | 0.864 |
6 | 366 | LSFKELLVY | A3 | 0.723 |
7 | 409 | TVKPGNFNK | A3 | 1.378 |
8 | 10 | RVCGVSAAR | A3 | 0.608 |
9 | 585 | ATVVIGTSK | A3 | 0.757 |
10 | 543 | NLKYAISAK | A3 | 1.351 |
11 | 365 | RLSFKELLV | A3 | 0.864 |
12 | 341 | VVSTGYHFR | A3 | 1.474 |
13 | 890 | KLHDELTGH | A3 | 0.4147 |
14 | 581 | ATRGATVVI | B7 | 0.569 |
15 | 242 | MPILTLTRA | B7 | 0.806 |
16 | 579 | IAATRGATV | B7 | 0.8883 |
17 | 399 | AALTNNVAF | B7 | 0.638 |
18 | 528 | FAYTKRNVI | B7 | 1.0296 |
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Mir, S.A.; Alaidarous, M.; Alshehri, B.; Bin Dukhyil, A.A.; Banawas, S.; Madkhali, Y.; Alsagaby, S.A.; Al Othaim, A. Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2. Vaccines 2022, 10, 1660. https://doi.org/10.3390/vaccines10101660
Mir SA, Alaidarous M, Alshehri B, Bin Dukhyil AA, Banawas S, Madkhali Y, Alsagaby SA, Al Othaim A. Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2. Vaccines. 2022; 10(10):1660. https://doi.org/10.3390/vaccines10101660
Chicago/Turabian StyleMir, Shabir Ahmad, Mohammed Alaidarous, Bader Alshehri, Abdul Aziz Bin Dukhyil, Saeed Banawas, Yahya Madkhali, Suliman A. Alsagaby, and Ayoub Al Othaim. 2022. "Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2" Vaccines 10, no. 10: 1660. https://doi.org/10.3390/vaccines10101660