In Silico Designed Multi-Epitope Vaccine Based on the Conserved Fragments in Viral Proteins for Broad-Spectrum Protection Against Porcine Reproductive and Respiratory Syndrome Virus
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Retrieval of PRRSV Protein Sequence
2.2. Step-by-Step Selection of Epitopes
2.3. Design and Assembly of Candidate Vaccines
2.4. Evaluation of Candidate Vaccines in Physicochemical and Immune Properties
2.5. Prediction and Validation of Molecular Structure for Candidate Vaccines
2.6. Molecular Docking and Dynamic Analysis of Vaccine-TLR (Toll-like Receptors) Complexes
2.7. Immune Simulation of Candidate Vaccines
2.8. In Silico Cloning of Selected Vaccine Candidate
3. Results
3.1. Extraction of Conserved Fragments from PRRSV Protein Sequences Collected Worldwide
3.2. Prediction and Evaluation of Epitopes for B Cells, CTLs, and HTLs
3.3. Design of Three Candidate Vaccines
- PRRSV-V-1: Core antigen attached with S50 L7/12 ribosomal protein on N-terminal.
- PRRSV-V-2: Core antigen attached with β-defensin on the N-terminal.
- PRRSV-V-3: Core antigen attached with HBHA adjuvant on N-terminal.
3.4. Properties of Candidate Vaccines in Physicochemical and Immunology
3.5. Prediction and Refinement of Secondary and Tertiary Structure
3.6. Molecular Docking and Dynamics Simulation for Complexes of Vaccine-Immune Receptor
3.7. Simulation of Immune Responses Post-Vaccination
3.8. Codon Optimization of the Final Vaccine Candidate
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
PRRSV | Porcine respiratory and reproductive syndrome virus |
PRRSV-V | Porcine respiratory and reproductive syndrome virus-vaccine |
SLA | Swine Leukocyte Antigen |
HLA | Human Leukocyte Antigen |
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Genotype | Protein | Start –End | Epitopes | Length | Antigenicity Score | Allergenicity /Toxicity | Intra/Inter Conservancy |
---|---|---|---|---|---|---|---|
PRRSV1 | ORF2A | 57–66 | APRYSVRALP | 10 | 0.8784 | Non/Non | 75.00% /20.00% |
PRRSV2 | GP3 | 38–45 | LVRGNFSF | 8 | 1.7037 | Non/Non | 100.00% /33.33% |
PRRSV2 | GP4 | 44–57 | QHTQQHHLVIDHIR | 14 | 0.5457 | Non/Non | 100.00% /33.33% |
PRRSV1 | GP5 | 49–61 | LNGTDWLDKRFDW | 13 | 1.7333 | Non/Non | 75.00% /20.00% |
PRRSV2 | M | 131–144 | RKPGLTSVNGTLV | 13 | 0.8659 | Non/Non | 100.00% /33.33% |
PRRSV1 | N | 6–13 | HFPLAAED | 8 | 0.9417 | Non/Non | 66.00% /22.22% |
Genotype | Protein | HLA- Allele | Epitope | Antigenicity | Allergenicity/Toxicity | IL-4/IFN- γ Induction | Intra/Inter Conservancy |
---|---|---|---|---|---|---|---|
PRRSV1 | ORF1a | DPA1*02:01 DPB1*05:01 | GVAPAVRIAERYRGR | 0.9596 | Non/Non | Inducer /Inducer | 100.00% /13.33% |
PRRSV1 | ORF1a | DRB4*01:04 | KPIAYANLDEKKISA | 0.9123 | Non/Non | Inducer /Inducer | 100.00% /13.33% |
PRRSV2 | ORF1b | DRB1*12:04 | CLGDFKQLHPVGFDS | 1.2326 | Non/Non | Inducer /Inducer | 95.24% /20.00% |
PRRSV2 | GP2a | DPA1*02:01 DPB1*04:01 | LSFASDWFAPRYSVR | 0.5461 | Non/Non | Inducer /Inducer | 75.00% /20.00% |
PRRSV2 | GP2b | DRB1*04:04 | VFCIRLVCSAIHRSR | 1.3347 | Non/Non | Inducer /Inducer | 100.00% /20.00% |
PRRSV2 | GP3 | DPA1*02:01 DPB1*04:01 | NWFHLEWLRPFFSSW | 0.4583 | Non/Non | Inducer /Inducer | 75.00% /20.00% |
PRRSV1 | GP4 | DRB5*01:03 | ACVNFTDYVAHVTQH | 1.0257 | Non/Non | Inducer /Inducer | 75.00% /13.33% |
PRRSV2 | GP5 | DPA1*01:03 DPB1*01:01 | WRYSCTRYTNFLLDT | 0.5114 | Non/Non | Inducer /Inducer | 100.00% /13.33% |
PRRSV1 | M | DPA1*02:01 DPB1*02:01 | LAFSITYTPIIYALK | 1.4017 | Non/Non | Inducer /Inducer | 100.00% /13.33% |
PRRSV2 | N | DQA1*01:01 DQB1*02:01 | PHFPLATEDDVRHHF | 0.4807 | Non/Non | Inducer /Inducer | 66.67% /26.67% |
Genotype | Protein | SLA-Allele | Epitope | Antigenicity /Immunogenicity | Allergenicity /Toxicity | Intra/Inter Conservancy |
---|---|---|---|---|---|---|
PRRSV1 | ORF1a | 1*1101 | AALTGRTL | 1.2071 /0.14994 | Non/Non | 100.00% /25.00% |
PRRSV1 | ORF1a | 3*0501 | HQKPIAYANL | 1.1782 /0.1123 | Non/Non | 100.00% /20.00% |
PRRSV2 | ORF2b | 3*0701 | TRARHAIF | 1.0977 /0.31383 | Non/Non | 95.24% /25.00% |
PRRSV2 | GP2a | 3*0401 | SVRALPFTL | 1.5046 /0.15641 | Non/Non | 75.00% /22.22% |
PRRSV1 | GP2b | 2*0101 | IFLAILFGF | 0.7123 /0.27353 | Non/Non | 75.00% /22.22% |
PRRSV2 | GP3 | 2*0101 | YAWLAFLSF | 1.1215 /0.10302 | Non/Non | 100.00% /22.22% |
PRRSV2 | GP4 | 1*0702 | SACVNFTDY | 1.6035 /0.17366 | Non/Non | 66.67% /22.22% |
PRRSV2 | GP5 | 3*0101 | TRYTNFLL | 1.2753 /0.1324 | Non/Non | 66.67% /25.00% |
PRRSV1 | M | 2*1201 | FSITYTPII | 1.4228 /0.1836 | Non/Non | 66.67% /22.22% |
PRRSV1 | N | 2*1101 | FPLATEDDVRHHF | 0.4645 /0.34939 | Non/Non | 50.00% /38.46% |
Parameters | PRRSV-V-1 Vaccine | PRRSV-V-2 Vaccine | PRRSV-V-3 Vaccine |
---|---|---|---|
No. of amino acids | 531 | 448 | 551 |
Molecular weight | 57,526.93 kDa | 49,446.89 kDa | 60,733.93 kDa |
Instability index | 22.04 | 25.72 | 28.66 |
Aliphatic index | 81.02 | 80.91 | 77.04 |
Half-life | 30 h (mammalian reticulocytes, in vitro). >20 h (yeast, in vivo). >10 h (Escherichia coli, in vivo) | 30 h (mammalian reticulocytes, in vitro). >20 h (yeast, in vivo). >10 h (Escherichia coli, in vivo) | 30 h (mammalian reticulocytes, in vitro). >20 h (yeast, in vivo). >10 h (Escherichia coli, in vivo) |
Solubility | 0.979905 | 0.975094 | 0.986037 |
GRAVY | −0.054 | −0.191 | −0.249 |
Theoretical pI | 9.12 | 9.82 | 9.17 |
Antigenicity | 0.61 | 0.68 | 0.63 |
Allergenicity | Non-allergenic | Non-allergenic | Non-allergenic |
Toxicity | Non-toxic | Non-toxic | Non-toxic |
Vaccine–Receptor Complex | Docking Score | Number of Residues in Interface | Area of Interface (Å2) | Number of Salt Bridges | Number of Hydrogen Bonds | Number of Non-Covalent Interactions |
---|---|---|---|---|---|---|
PRRSV-V-1 TLR-3 | −196.74 | 15 20 | 1104 1114 | 2 | 3 | 121 |
PRRSV-V-1 TLR-8 | −190.43 | 10 14 | 791 870 | 0 | 2 | 87 |
PRRSV-V-2 TLR-3 | −308.16 | 20 15 | 939 1063 | 3 | 6 | 155 |
PRRSV-V-2 TLR-8 | −263.17 | 21 22 | 1010 975 | 1 | 9 | 176 |
PRRSV-V-3 TLR-3 | −260.99 | 30 37 | 2129 1943 | 4 | 3 | 316 |
PRRSV-V-3 TLR-8 | −335.61 | 34 37 | 2340 2211 | 1 | 3 | 282 |
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Ullah, S.; Ullah, H.; Fatima, K.; Lei, T. In Silico Designed Multi-Epitope Vaccine Based on the Conserved Fragments in Viral Proteins for Broad-Spectrum Protection Against Porcine Reproductive and Respiratory Syndrome Virus. Vet. Sci. 2025, 12, 577. https://doi.org/10.3390/vetsci12060577
Ullah S, Ullah H, Fatima K, Lei T. In Silico Designed Multi-Epitope Vaccine Based on the Conserved Fragments in Viral Proteins for Broad-Spectrum Protection Against Porcine Reproductive and Respiratory Syndrome Virus. Veterinary Sciences. 2025; 12(6):577. https://doi.org/10.3390/vetsci12060577
Chicago/Turabian StyleUllah, Shaukat, Hikmat Ullah, Kainat Fatima, and Tan Lei. 2025. "In Silico Designed Multi-Epitope Vaccine Based on the Conserved Fragments in Viral Proteins for Broad-Spectrum Protection Against Porcine Reproductive and Respiratory Syndrome Virus" Veterinary Sciences 12, no. 6: 577. https://doi.org/10.3390/vetsci12060577
APA StyleUllah, S., Ullah, H., Fatima, K., & Lei, T. (2025). In Silico Designed Multi-Epitope Vaccine Based on the Conserved Fragments in Viral Proteins for Broad-Spectrum Protection Against Porcine Reproductive and Respiratory Syndrome Virus. Veterinary Sciences, 12(6), 577. https://doi.org/10.3390/vetsci12060577