Immunoinformatics for Novel Multi-Epitope Vaccine Development in Canine Parvovirus Infections
Abstract
:1. Introduction
2. Materials and Methods
2.1. Retrieval of VP2-Protein Sequences from the Corresponding Gene Sequences of Local CPV-2 Strain
2.2. Topology and Antigenicity Screening
2.3. Identification of Homologous Proteins and Analysis of Conserved Regions
2.4. T-Cell Epitope Prediction, Trans-Membrane Topology Screening, and Antigenicity Analysis
2.5. Assessment of Allergenicity and Toxicity of T-Cell Epitopes
2.6. Identification of B-Cell Epitopes
2.7. Selection of the Superior Epitopes and Their Conservancy Analysis
2.8. 3D-Structure Predictions of Superior T-Cell Epitopes and Docking at the Allele Level
2.9. Vaccine Constructions
2.10. Physico-Chemical Analysis and Structure Prediction of the Vaccine Construct
2.11. Molecular Docking and Molecular Simulation against TLR-5
2.12. Disulfide Engineering of the Designed Vaccine
2.13. Codon Adaptations, In Silico Cloning, and Similarity Search with Host
3. Results
3.1. Identification of Protein Sequences and Antigenicity Screening
3.2. Identification of Homologous Protein Sets
3.3. T-Cell- and B-Cell-Epitope Prediction
3.4. Superior Epitope Selection and Conservancy Prediction
3.5. Molecular Docking with Dog Leukocyte Antigen (DLA) Molecules
3.6. Vaccine Construction
3.7. Physico-Chemical Analyses of Vaccine Construct and Secondary Structure Prediction
3.8. Tertiary-Structure Prediction
3.9. Binding Affinity and Stability of the Vaccine–TLR 5 Binding Complex
3.10. Disulfide Engineering of the Vaccine Construct
3.11. Codon Adaptation, In Silico Cloning, and Similarity Search with Host
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sl. No. | Sequence ID | Topology | VaxiJen Score |
---|---|---|---|
1 | DPHSAUBD11N001 | Outside | 0.5468 |
2 | DPHSAUBD11N008 | Outside | 0.5263 |
3 | DPHSAUBD11N013 | Outside | 0.5263 |
4 | DPHSAUBD12N042 | Outside | 0.5381 |
5 | DPHSAUBD12N044 | Outside | 0.4930 |
6 | DPHSAUBD12N067 | Outside | 0.4933 |
7 | DPHSAUBD13N069 | Outside | 0.5294 |
8 | DPHSAUBD13N073 | Outside | 0.5263 |
9 | DPHSAUBD13N081 | Outside | 0.5386 |
10 | DPHSAUBD13N100 | Outside | 0.5477 |
11 | DPHSAUBD21N118 | Outside | 0.5180 |
12 | DPHSAUBD21N125 | Outside | 0.5209 |
13 | DPHSAUBD21N147 | Outside | 0.5289 |
14 | DPHSAUBD22N163 | Outside | 0.5209 |
15 | DPHSAUBD12N056 | Outside | 0.5285 |
16 | DPHSAUBD22N169 | Outside | 0.5209 |
17 | DPHSAUBD22N170 | Outside | 0.5310 |
18 | DPHSAUBD22N196 | Outside | 0.5310 |
19 | DPHSAUBD23N200 | Outside | 0.5285 |
20 | DPHSAUBD23N213 | Outside | 0.5334 |
21 | DPHSAUBD23M249 | Outside | 0.4976 |
Sequence | Topology | VaxiJen Score |
---|---|---|
SGTPTNIYHGTDPDDVQ | Outside | 0.6334 |
EFATGTFYFDCKPCRLTHTWQTNRALGLPPFLNSLPQAEGGTNFGYIG | Outside | 0.7204 |
LLPTDPIGGKTGINYTN | Outside | 0.8635 |
VPPVYPNGQIWDKEFDTDLKP | Outside | 0.4321 |
Sl. No. | EPITOPE | VaxiJen Score | Allergenicity | Toxicity | Epitope Length | Conservancy |
---|---|---|---|---|---|---|
1 | DPIGGKTGI | 0.9259 | Non-allergenic | Non-Toxic | 9 | 100.00% |
2 | KEFDTDLKP | 0.9968 | Non-allergenic | Non-Toxic | 9 | 100.00% |
3 | GTDPDDVQ | 0.9231 | Non-allergenic | Non-Toxic | 8 | 100.00% |
4 | GGTNFGYIG | 1.9328 | Non-allergenic | Non-Toxic | 9 | 100.00% |
5 | GTFYFDCKP | 1.5199 | Non-allergenic | Non-Toxic | 9 | 100.00% |
6 | NRALGLPP | 1.3745 | Non-allergenic | Non-Toxic | 8 | 100.00% |
7 | SGTPTN | 0.9542 | Non-allergenic | Non-Toxic | 6 | 100.00% |
8 | LGLPPFLNSL | 0.4422 | Non-allergenic | Non-Toxic | 10 | 100.00% |
9 | IGGKTG | 1.5579 | Non-allergenic | Non-Toxic | 6 | 100.00% |
10 | VPPVYPN | 0.9901 | Non-allergenic | Non-Toxic | 7 | 100.00% |
Epitope | Global Energy | Hydrogen Bond Energy | ACE * | Score | Area |
---|---|---|---|---|---|
DPIGGKTGI | −40.88 | −1.45 | −2.66 | 7456 | 839.80 |
KEFDTDLKP | −4.44 | 0.00 | −1.05 | 7506 | 1012.50 |
GTDPDDVQ | −14.84 | −1.82 | 1.17 | 6786 | 852.50 |
GGTNFGYIG | −50.33 | −5.65 | −8.81 | 7152 | 903.70 |
GTFYFDCKP | −55.54 | −1.05 | −9.60 | 8484 | 81,119.50 |
NRALGLPP | −14.84 | −2.37 | 6.23 | 6910 | 846.30 |
Epitope | Global Energy | Hydrogen Bond Energy | ACE | Score | Area |
---|---|---|---|---|---|
DPIGGKTGI | −28.98 | −0.50 | −2.00 | 7650 | 979.60 |
KEFDTDLKP | −24.03 | −2.90 | 7.58 | 8850 | 1026.00 |
GTDPDDVQ | −29.84 | −3.54 | 0.50 | 7080 | 826.60 |
GGTNFGYIG | −49.95 | −2.71 | −7.60 | 7516 | 895.60 |
GTFYFDCKP | −30.79 | −2.33 | −5.91 | 9338 | 1134.70 |
NRALGLPP | −36.67 | −2.58 | −4.98 | 7576 | 979.10 |
Vaccine Construct | Properties | Value |
---|---|---|
MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTGGSAKFVAAWTLKAAAGGSDPIGGKTGIGGSKEFDTDLKPGGSGTDPDDVQGGSGGTNFGYIGGGSGTFYFDCKPGGSNRALGLPPGGSSGTPTNGGSLGLPPFLNSLGGSIGGKTGGGSVPPVYPN | Length | 272 |
Molecular weight | 27,388.01 | |
Aliphatic index | 73.97 | |
Theoretical pI | 5.51 | |
GRAVY value | −0.388 | |
Instability index | 30.77 (stable) | |
Extinction coefficients | 9970 | |
Estimated half-life | >20 h (yeast, in vivo) >10 h (Escherichia coli, in vivo) | |
Antigenicity | 0.5696 (Probable ANTIGEN) | |
Solubility | 0.627 | |
Allergenicity | Probable NON-ALLERGEN |
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Paul, B.; Alam, J.; Hossain, M.M.K.; Hoque, S.F.; Bappy, M.N.I.; Akter, H.; Ahmed, N.; Akter, M.; Ali Zinnah, M.; Das, S.; et al. Immunoinformatics for Novel Multi-Epitope Vaccine Development in Canine Parvovirus Infections. Biomedicines 2023, 11, 2180. https://doi.org/10.3390/biomedicines11082180
Paul B, Alam J, Hossain MMK, Hoque SF, Bappy MNI, Akter H, Ahmed N, Akter M, Ali Zinnah M, Das S, et al. Immunoinformatics for Novel Multi-Epitope Vaccine Development in Canine Parvovirus Infections. Biomedicines. 2023; 11(8):2180. https://doi.org/10.3390/biomedicines11082180
Chicago/Turabian StylePaul, Bashudeb, Jahangir Alam, Mridha Md. Kamal Hossain, Syeda Farjana Hoque, Md. Nazmul Islam Bappy, Hafsa Akter, Nadim Ahmed, Margia Akter, Mohammad Ali Zinnah, Shobhan Das, and et al. 2023. "Immunoinformatics for Novel Multi-Epitope Vaccine Development in Canine Parvovirus Infections" Biomedicines 11, no. 8: 2180. https://doi.org/10.3390/biomedicines11082180