mRNA Vaccine Designing Using Chikungunya Virus E Glycoprotein through Immunoinformatics-Guided Approaches
Abstract
:1. Introduction
2. Materials and Methods
2.1. Retrieval of Envelope Glycoprotein Sequence
2.2. MSA and Determination of Consensus Sequence
2.3. T-Lymphocytes Epitopes Prediction
2.4. T-Lymphocytes Predicted Epitopes Analysis
2.5. Population Coverage Analysis (PCA) of T-Lymphocytes
2.6. B-Lymphocytes Epitopes Prediction and Analysis
2.7. Multi-Epitope Vaccine Construct Design
2.8. Peptide Vaccine Construct Analysis
2.9. Prediction of Secondary and Tertiary Structures of the Vaccine Construct
2.10. Conformational B-Cell Epitopes Prediction
2.11. Molecular Docking and Dynamic Simulation Studies
2.12. Immune Simulation Studies
2.13. Back-Translation and Codon Optimization of Vaccine Construct
2.14. Secondary Structure Prediction of mRNA Sequence
2.15. mRNA Vaccine Construct Design
2.16. In Silico Plasmid Design for Cloning
3. Results
3.1. Determination of Consensus Sequence
3.2. T-Lymphocytes Epitopes Determination
3.3. Population Coverage Analysis (PCA) of Selected T-Lymphocyte Epitopes
3.4. B-Lymphocytes Epitopes Determination
3.5. Peptide Vaccine Construction and Analysis
3.6. Peptide Vaccine Structure Prediction and Validation
3.7. Conformational B-Cell Epitopes Prediction
3.8. Docking and MD Simulation
3.9. Immune Simulation
3.10. Optimized mRNA Determination
3.11. Secondary Structure Prediction of Optimized mRNA
3.12. mRNA Vaccine Construct Design
3.13. rPlasmid Design for In Vitro Cloning
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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Alleles | Start | End | Epitopes | Score | Rank | Conservancy | Antigenicity | Toxicity | Allergenicity |
---|---|---|---|---|---|---|---|---|---|
HLA-C*14:02 | 186 | 194 | YYNWHHGAV | 0.553042 | 0.15 | 100.00% | Antigen | Non-Toxin | Allergen |
HLA-B*58:02 | 253 | 261 | ITPEGAEEW | 0.191746 | 0.06 | 88.89% | Non-Antigen | Non-Toxin | Allergen |
HLA-C*15:02 | 1170 | 1178 | ASAEFRVQV | 0.910008 | 0.01 | 77.78% | Antigen | Non-Toxin | Non-Allergen |
HLA-B*35:03 | 772 | 780 | IPLAALIVL | 0.819695 | 0.05 | 88.89% | Antigen | Non-Toxin | Allergen |
HLA-C*07:01 | 719 | 727 | RRCITPYEL | 0.309353 | 0.05 | 88.89% | Antigen | Non-Toxin | Non-Allergen |
HLA-A*24:02 | 195 | 203 | QYSGGRFTI | 0.779379 | 0.06 | 88.89% | Non-Antigen | Non-Toxin | Allergen |
HLA-A*30:02 | 653 | 661 | VTWGNNEPY | 0.46361 | 0.2 | 77.78% | Antigen | Non-Toxin | Allergen |
HLA-C*12:03 | 672 | 680 | TAHGHPHEI | 0.919117 | 0.01 | 77.78% | Non-Antigen | Non-Toxin | Non-Allergen |
HLA-A*32:01 | 888 | 896 | KVFTGVYPF | 0.959162 | 0.01 | 88.89% | Non-Antigen | Non-Toxin | Allergen |
HLA-B*35:01 | 816 | 824 | IPNTVGVPY | 0.986276 | 0.01 | 88.89% | Antigen | Non-Toxin | Allergen |
HLA-C*15:02 | 1222 | 1230 | ITGGVGLVV | 0.442712 | 0.17 | 88.89% | Antigen | Non-Toxin | Allergen |
HLA-B*51:01 | 430 | 438 | CPKGETLTV | 0.706451 | 0.07 | 88.89% | Antigen | Non-Toxin | Non-Allergen |
HLA-B*08:01 | 219 | 227 | DNKGRVVAI | 0.789156 | 0.04 | 88.89% | Antigen | Non-Toxin | Allergen |
HLA-C*14:02 | 683 | 691 | YYYELYPTM | 0.960772 | 0.01 | 88.89% | Antigen | Non-Toxin | Allergen |
HLA-A*33:01 | 385 | 393 | DSHDWTKLR | 0.815075 | 0.03 | 88.89% | Non-Antigen | Non-Toxin | Allergen |
HLA-C*15:02 | 1140 | 1148 | HSMTNAVTI | 0.500844 | 0.14 | 88.89% | Non-Antigen | Non-Toxin | Non-Allergen |
HLA-C*14:02 | 612 | 620 | LYPDHPTLL | 0.969246 | 0.01 | 88.89% | Non-Antigen | Non-Toxin | Non-Allergen |
HLA-B*08:01 | 1052 | 1060 | WLKERGASL | 0.974106 | 0.01 | 88.89% | Antigen | Non-Toxin | Non-Allergen |
HLA-A*68:02 | 1062 | 1070 | HTAPFGCQI | 0.79801 | 0.05 | 88.89% | Antigen | Non-Toxin | Allergen |
HLA-B*08:01 | 593 | 601 | VPKARNPTV | 0.792978 | 0.04 | 88.89% | Non-Antigen | Non-Toxin | Non-Allergen |
HLA-C*15:02 | 845 | 853 | VTLEPTLSL | 0.887273 | 0.01 | 88.89% | Antigen | Non-Toxin | Non-Allergen |
*HLA-C*04:01 | 159 | 167 | KYDLECAQI | 0.366935 | 0.11 | 100.00% | Antigen | Non-Toxin | Non-Allergen |
Alleles | Start | End | Peptide | Rank | Conservancy | Antigenicity | Toxicity | Allergenicity | IL4 Inducer | IL10 Inducer |
---|---|---|---|---|---|---|---|---|---|---|
HLA-DPA1*01:03/DPB1*02:01 | 677 | 691 | PHEIILYYYELYPTM | 0.04 | 66.67% | Antigen | Non-Toxin | Non-Allergen | IL4 inducer | IL10 non-inducer |
HLA-DQA1*05:01/DQB1*03:01 | 1219 | 1233 | VQKITGGVGLVVAVA | 0.85 | 86.67% | Non-Antigen | Non-Toxin | Non-Allergen | Non IL4 inducer | IL10 non-inducer |
HLA-DRB1*09:01 | 723 | 737 | TPYELTPGATVPFLL | 0.88 | 93.33% | Antigen | Non-Toxin | Non-Allergen | Non IL4 inducer | IL10 non-inducer |
*HLA-DRB1*13:02 | 213 | 227 | SGRPIFDNKGRVVAI | 2 | 93.33% | Antigen | Non-Toxin | Non-Allergen | IL4 inducer | IL10 non-inducer |
HLA-DQA1*01:02/DQB1*06:02 | 230 | 244 | GGANEGARTALSVVT | 1.1 | 93.33% | Non-Antigen | Non-Toxin | Allergen | IL4 inducer | IL10 non-inducer |
HLA-DRB3*02:02 | 405 | 419 | RAGLFVRTSAPCTIT | 1.1 | 86.67% | Antigen | Non-Toxin | Non-Allergen | IL4 inducer | IL10 non-inducer |
HLA-DQA1*01:02/DQB1*06:02 | 1137 | 1151 | CAVHSMTNAVTIREA | 0.86 | 93.33% | Non-Antigen | Non-Toxin | Non-Allergen | Non IL4 inducer | IL10 non-inducer |
HLA-DRB1*04:04 | 1234 | 1248 | ALILIVVLCVSFSRH | 1.1 | 93.33% | Antigen | Non-Toxin | Allergen | Non IL4 inducer | IL10 inducer |
*HLA-DRB3*01:01 | 103 | 117 | ERMCMKIENDCIFEV | 2 | 100.00% | Antigen | Non-Toxin | Non-Allergen | IL4 inducer | IL10 inducer |
HLA-DRB3*02:02 | 557 | 571 | HKKWQYNSPLVPRNA | 1.6 | 86.67% | Antigen | Non-Toxin | Non-Allergen | IL4 inducer | IL10 non-inducer |
*HLA-DRB1*04:05 | 856 | 870 | ITCEYKTVIPSPYVK | 1.4 | 93.33% | Antigen | Non-Toxin | Non-Allergen | IL4 inducer | IL10 non-inducer |
*HLA-DRB3*01:01 | 988 | 1002 | VYKGDVYNMDYPPFG | 1.8 | 93.33% | Antigen | Non-Toxin | Non-Allergen | IL4 inducer | IL10 non-inducer |
HLA-DRB1*11:01 | 821 | 835 | GVPYKTLVNRPGYSP | 1.4 | 93.33% | Non-Antigen | Non-Toxin | Allergen | Non IL4 inducer | IL10 inducer |
HLA-DPA1*02:01/DPB1*14:01 | 929 | 943 | SAYRAHTASASAKLR | 0.74 | 86.67% | Antigen | Non-Toxin | Non-Allergen | Non IL4 inducer | IL10 non-inducer |
HLA-DRB3*02:02 | 599 | 613 | PTVTYGKNQVIMLLY | 1.7 | 86.67% | Antigen | Non-Toxin | Allergen | Non IL4 inducer | IL10 non-inducer |
HLA-DRB4*01:01 | 365 | 379 | EATDGTLKIQVSLQI | 0.61 | 93.33% | Antigen | Non-Toxin | Non-Allergen | Non IL4 inducer | IL10 non-inducer |
HLA-DRB5*01:01 | 1039 | 1053 | HVPYSQAPSGFKYWL | 0.37 | 93.33% | Non-Antigen | Non-Toxin | Non-Allergen | IL4 inducer | IL10 non-inducer |
HLA-DRB1*07:01 | 1155 | 1169 | VEGNSQLQISFSTAL | 0.27 | 86.67% | Antigen | Non-Toxin | Non-Allergen | IL4 inducer | IL10 inducer |
*HLA-DRB1*03:01 | 126 | 140 | YACLVGDKVMKPAHV | 1.1 | 93.33% | Antigen | Non-Toxin | Non-Allergen | IL4 inducer | IL10 inducer |
HLA-DRB1*12:01 | 146 | 160 | NADLAKLAFKRSSKY | 1.9 | 86.67% | Antigen | Non-Toxin | Non-Allergen | IL4 inducer | IL10 non-inducer |
Start | End | Epitopes | Score | Antigenicity | Allergenicity | Toxicity | Conservancy |
---|---|---|---|---|---|---|---|
198 | 217 | GGRFTIPTGAGKPGDSGRPI | 1 | Non-Antigen | Non-Allergen | Non-Toxin | 95.00% |
993 | 1012 | VYNMDYPPFGAGRPGQFGDI | 1 | Antigen | Allergen | Non-Toxin | 90.00% |
490 | 509 | EEIEVHMPPDTPDRTLMSQQ | 0.996 | Non-Antigen | Non-Allergen | Non-Toxin | 85.00% |
447 | 466 | SHSCTHPFHHDPPVIGREKF | 0.983 | Antigen | Non-Allergen | Toxin | 80.00% |
242 | 261 | VVTWNKDIVTKITPEGAEEW | 0.98 | Non-Antigen | Allergen | Non-Toxin | 90.00% |
1058 | 1077 | *ASLQHTAPFGCQIATNPVRA | 0.976 | Antigen | Non-Allergen | Non-Toxin | 95.00% |
972 | 991 | *VGPMSSAWTPFDNKIVVYKG | 0.974 | Antigen | Non-Allergen | Non-Toxin | 95.00% |
177 | 196 | *KFTHEKPEGYYNWHHGAVQY | 0.968 | Antigen | Non-Allergen | Non-Toxin | 95.00% |
654 | 673 | TWGNNEPYKYWPQLSTNGTA | 0.958 | Non-Antigen | Non-Allergen | Non-Toxin | 90.00% |
1149 | 1168 | REAEIEVEGNSQLQISFSTA | 0.925 | Antigen | Non-Allergen | Non-Toxin | 85.00% |
856 | 875 | ITCEYKTVIPSPYVKCCGTA | 0.917 | Non-Antigen | Allergen | Toxin | 80.00% |
807 | 826 | VSAYEHVTVIPNTVGVPYKT | 0.912 | Antigen | Non-Allergen | Non-Toxin | 90.00% |
1037 | 1056 | TVHVPYSQAPSGFKYWLKER | 0.875 | Non-Antigen | Non-Allergen | Non-Toxin | 95.00% |
883 | 902 | PDYSCKVFTGVYPFMWGGAY | 0.819 | Antigen | Allergen | Non-Toxin | 95.00% |
360 | 379 | *ERIRNEATDGTLKIQVSLQI | 0.812 | Antigen | Non-Allergen | Non-Toxin | 95.00% |
715 | 734 | *MCARRRCITPYELTPGATVP | 0.757 | Antigen | Non-Allergen | Non-Toxin | 95.00% |
129 | 148 | LVGDKVMKPAHVKGTIDNAD | 0.752 | Non-Antigen | Allergen | Non-Toxin | 95.00% |
Physiochemical Properties | Measurement | Indication |
---|---|---|
Total Number of Amino Acids | 631 | Appropriate |
Molecular Weight | 70,036.77 | Appropriate |
Theoretical pI | 8.52 | Basic |
Total Number of Negatively Charged Residues (Asp + Glu) | 82 | - |
Total Number of Positively Charged Residues (Arg + Lys) | 90 | - |
Aliphatic Index (AI) | 80.55 | Thermostable |
Grand Average of Hydropathicity (GRAVY) | –0.361 | Hydrophilic |
Antigenicity (using Vaxijen) | 0.4711 | Antigenic |
Solubility upon overexpression | 0.722294 | Soluble |
Allergenicity | Non-allergen | Non-Allergenic |
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Jaan, S.; Zaman, A.; Ahmed, S.; Shah, M.; Ojha, S.C. mRNA Vaccine Designing Using Chikungunya Virus E Glycoprotein through Immunoinformatics-Guided Approaches. Vaccines 2022, 10, 1476. https://doi.org/10.3390/vaccines10091476
Jaan S, Zaman A, Ahmed S, Shah M, Ojha SC. mRNA Vaccine Designing Using Chikungunya Virus E Glycoprotein through Immunoinformatics-Guided Approaches. Vaccines. 2022; 10(9):1476. https://doi.org/10.3390/vaccines10091476
Chicago/Turabian StyleJaan, Samavia, Aqal Zaman, Sarfraz Ahmed, Mohibullah Shah, and Suvash Chandra Ojha. 2022. "mRNA Vaccine Designing Using Chikungunya Virus E Glycoprotein through Immunoinformatics-Guided Approaches" Vaccines 10, no. 9: 1476. https://doi.org/10.3390/vaccines10091476