Designing Novel Multi-Epitope Vaccine Construct against Prevotella intermedia-Interpain A: An Immunoinformatics Approach
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sequence Analysis
2.2. Prediction of Epitope
2.3. Population Coverage Analysis
2.4. Construction of Multi Epitope Vaccine
2.5. Structure Prediction and Validation
2.6. Molecular Docking Analysis
2.7. Molecular Dynamics Simulation
3. Results
3.1. Analysis of P. intermedia Peptide Sequences
3.2. Prediction and Assessment of T-Lymphocyte Epitope
3.3. Prediction and Assessment of B-Lymphocytes
3.4. Analysis of Population Coverage
3.5. Construction of Multi-Epitope Vaccine
3.6. Molecular Docking
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Allele | # | Peptide * | Core | Score | Score | Percentile Rank |
---|---|---|---|---|---|---|
HLA-A * 01:01 | 6 | SADFGNTTY | SADFGNTTY | SADFGNTTY | 0.976649 | 0.01 |
2 | TTWGQQMPY | TTWGQQMPY | TTWGQQMPY | 0.634927 | 0.12 | |
13 | LTKGHPLIY | LTKGHPLIY | LTKGHPLIY | 0.631891 | 0.12 | |
3 | TATAQVLNY | TATAQVLNY | TATAQVLNY | 0.466786 | 0.21 | |
15 | EQDMVRGVY | EQDMVRGVY | EQDMVRGVY | 0.46399 | 0.21 |
Allele | # | Start | End | Peptide * | Percentile Rank | Adjusted Rank |
---|---|---|---|---|---|---|
HLA-DRB1 * 01:01 | 1 | 55 | 69 | FKYPVRGIGSHTVHY | 8.40 | 8.40 |
1 | 98 | 112 | SGNYTEAEANAVATL | 8.70 | 8.70 | |
1 | 99 | 113 | GNYTEAEANAVATLM | 8.90 | 8.90 | |
1 | 6 | 20 | PSKYAAEVSTLLTTT | 8.90 | 8.90 | |
1 | 97 | 111 | YSGNYTEAEANAVAT | 9.70 | 9.70 |
Rank | Sequence | Start Position | Score * |
---|---|---|---|
1 | VRGIGSHTVHYPANDP | 59 | 0.93 |
2 | DFGNTTYDWANMKDNY | 82 | 0.90 |
3 | HPLIYGGVSPGSMGQD | 176 | 0.87 |
3 | SGAYMTDCAAGLRTYF | 131 | 0.87 |
4 | SGTAISADFGNTTYDW | 75 | 0.86 |
5 | GGPNEGSGAYMTDCAA | 125 | 0.84 |
No. | Start | End | Peptide | Length |
---|---|---|---|---|
1 | 5 | 11 | DPSKYAA | 7 |
2 | 21 | 36 | WGQQMPYNKLLPKTKK | 16 |
3 | 56 | 76 | KYPVRGIGSHTVHYPANDPSG | 21 |
4 | 85 | 104 | NTTYDWANMKDNYSGNYTEA | 20 |
5 | 122 | 133 | MQYGGPNEGSGA | 12 |
6 | 147 | 166 | GFTDAEYITRANYTDEQWMD | 20 |
7 | 185 | 192 | PGSMGQDA | 8 |
8 | 217 | 217 | V | 1 |
9 | 228 | 236 | PGNMYSFTA | 9 |
Peptide Sequence * | SVM Score | Hydrophobicity | Hydropathicity | Hydrophilicity | Charge |
---|---|---|---|---|---|
YAAEVSTLL | −1.36 | 0.12 | 1.01 | −0.61 | −1.00 |
TTWGQQMPY | −1.25 | −0.11 | −1.19 | −0.82 | 0.00 |
TATAQVLNY | −0.91 | −0.01 | 0.21 | −0.78 | 0.00 |
ATAQVLNYF | −0.90 | 0.08 | 0.60 | −1.01 | 0.00 |
GIGSHTVHY | −0.84 | 0.04 | −0.14 | −0.74 | 1.00 |
SADFGNTTY | −0.93 | −0.10 | −0.70 | −0.29 | −1.00 |
MKDNYSGNY | −0.90 | −0.32 | −1.81 | 0.09 | 0.00 |
YTEAEANAV | −0.99 | −0.08 | −0.32 | 0.06 | −2.00 |
MTDCAAGLR | −0.78 | −0.13 | 0.30 | 0.06 | 0.00 |
FTDAEYITR | −0.48 | −0.21 | −0.57 | 0.12 | −1.00 |
YTDEQWMDI | −1.28 | −0.17 | −1.17 | 0.00 | −3.00 |
WMDIVFSEL | −1.43 | 0.16 | 0.94 | −0.67 | −2.00 |
LTKGHPLIY | −1.28 | 0.02 | 0.11 | −0.62 | 1.50 |
WNGDVDGYY | −0.50 | −0.09 | −1.18 | −0.37 | −2.00 |
EQDMVRGVY | −1.42 | −0.25 | −0.71 | 0.29 | −1.00 |
Number of HLA Combinations Identified | Percent of Individuals | Cumulative Percent of Population Coverage (in %) |
---|---|---|
0 | 70.19 | 100 |
1 | 25.08 | 29.81 |
2 | 4.06 | 4.72 |
3 | 0.66 | 0.66 |
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Yadalam, P.K.; Anegundi, R.V.; Munawar, S.; Ramadoss, R.; Rengaraj, S.; Ramesh, S.; Aljeldah, M.; Shammari, B.R.A.; Alshehri, A.A.; Alwashmi, A.S.S.; et al. Designing Novel Multi-Epitope Vaccine Construct against Prevotella intermedia-Interpain A: An Immunoinformatics Approach. Medicina 2023, 59, 302. https://doi.org/10.3390/medicina59020302
Yadalam PK, Anegundi RV, Munawar S, Ramadoss R, Rengaraj S, Ramesh S, Aljeldah M, Shammari BRA, Alshehri AA, Alwashmi ASS, et al. Designing Novel Multi-Epitope Vaccine Construct against Prevotella intermedia-Interpain A: An Immunoinformatics Approach. Medicina. 2023; 59(2):302. https://doi.org/10.3390/medicina59020302
Chicago/Turabian StyleYadalam, Pradeep Kumar, Raghavendra Vamsi Anegundi, Safa Munawar, Ramya Ramadoss, Santhiya Rengaraj, Sindhu Ramesh, Mohammed Aljeldah, Basim R. Al Shammari, Ahmad A. Alshehri, Ameen S. S. Alwashmi, and et al. 2023. "Designing Novel Multi-Epitope Vaccine Construct against Prevotella intermedia-Interpain A: An Immunoinformatics Approach" Medicina 59, no. 2: 302. https://doi.org/10.3390/medicina59020302