Integrated Immuno and bioinformatics assisted novel epitope vaccine against HIV infection: a study based on complete genome
Abstract Background As the HIV-based complication is still going on with the high infection and mortality rate, it requires a novel strategy to combat this infection due to the unavailability of proper therapeutic. Therefore, we utilize integrated immuno and bioinformatics approaches in this study t...
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| Format: | Article |
| Language: | English |
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BMC
2025-07-01
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| Series: | Virology Journal |
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| Online Access: | https://doi.org/10.1186/s12985-025-02764-0 |
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| author | Saurav Kumar Mishra Abdelkrim Guendouzi Neeraj Kumar Ganesh Sharma Taha Alqahtani Magdi E. A. Zaki Md. Abdullah Al mashud Yewulsew Kebede Tiruneh John J. Georrge |
| author_facet | Saurav Kumar Mishra Abdelkrim Guendouzi Neeraj Kumar Ganesh Sharma Taha Alqahtani Magdi E. A. Zaki Md. Abdullah Al mashud Yewulsew Kebede Tiruneh John J. Georrge |
| author_sort | Saurav Kumar Mishra |
| collection | DOAJ |
| description | Abstract Background As the HIV-based complication is still going on with the high infection and mortality rate, it requires a novel strategy to combat this infection due to the unavailability of proper therapeutic. Therefore, we utilize integrated immuno and bioinformatics approaches in this study to design a peptide vaccine against HIV infection by targeting its complete genome. Methods The complete genome sequence was analyzed, and the potential B and T cells were predicted. Among the predicted epitopes, the promising ones were selected and further used with the adjuvant and linker to formulate a vaccine candidate. The vaccine was modeled, and its activity and stability towards the TLRs were analyzed via docking and dynamics (500ns). The vaccine-generated immune activity and expression via in-silico cloning were also evaluated. Results A total of 6 B cells, 7 CTL, and 6 HTL were identified as an immunodominant epitope and used for vaccine formulation. These epitopes were fused together via linkers, and their efficiency and constancy were enhanced with Adjuvant, PADRE epitope, and His-tag. Further, the formulated vaccine shows high population coverage and stable features based on the 2D and 3D assessments. The docking investigation demonstrated the strong activity of the vaccine towards the TLR2 and TLR3, having binding affinity − 10.8 kcal/mol-1 and − 15.8 kcal/mol-1, and also disclosed remarkable constancy based on the 500ns simulation period. The vaccine-assisted immune simulation and expression level in the vector revealed a robust immune response towards the host based on the vaccination and a significant expression level. Conclusions Based on the integrated approach and validation steps, the overall finding suggests that the formulated vaccine may have strongly immunodominant properties and could combat the infection. |
| format | Article |
| id | doaj-art-da716dbd9e7b46d69406d584909c9b8d |
| institution | Kabale University |
| issn | 1743-422X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj-art-da716dbd9e7b46d69406d584909c9b8d2025-08-20T03:42:34ZengBMCVirology Journal1743-422X2025-07-0122111710.1186/s12985-025-02764-0Integrated Immuno and bioinformatics assisted novel epitope vaccine against HIV infection: a study based on complete genomeSaurav Kumar Mishra0Abdelkrim Guendouzi1Neeraj Kumar2Ganesh Sharma3Taha Alqahtani4Magdi E. A. Zaki5Md. Abdullah Al mashud6Yewulsew Kebede Tiruneh7John J. Georrge8Department of Bioinformatics, University of North BengalLaboratory of Chemistry: Synthesis, Properties and Application, Faculty of Sciences and Technology, University of SaidaDepartment of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Bhupal Nobles’ UniversityDepartment of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Bhupal Nobles’ UniversityDepartment of Pharmacology, College of Pharmacy, King Khalid UniversityDepartment of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU)Biophysics and Biomedicine Research Lab, Department of Electrical and Electronic Engineering, Islamic UniversityDepartment of Biology, Biomedical Sciences Stream, Bahir Dar UniversityDepartment of Bioinformatics, University of North BengalAbstract Background As the HIV-based complication is still going on with the high infection and mortality rate, it requires a novel strategy to combat this infection due to the unavailability of proper therapeutic. Therefore, we utilize integrated immuno and bioinformatics approaches in this study to design a peptide vaccine against HIV infection by targeting its complete genome. Methods The complete genome sequence was analyzed, and the potential B and T cells were predicted. Among the predicted epitopes, the promising ones were selected and further used with the adjuvant and linker to formulate a vaccine candidate. The vaccine was modeled, and its activity and stability towards the TLRs were analyzed via docking and dynamics (500ns). The vaccine-generated immune activity and expression via in-silico cloning were also evaluated. Results A total of 6 B cells, 7 CTL, and 6 HTL were identified as an immunodominant epitope and used for vaccine formulation. These epitopes were fused together via linkers, and their efficiency and constancy were enhanced with Adjuvant, PADRE epitope, and His-tag. Further, the formulated vaccine shows high population coverage and stable features based on the 2D and 3D assessments. The docking investigation demonstrated the strong activity of the vaccine towards the TLR2 and TLR3, having binding affinity − 10.8 kcal/mol-1 and − 15.8 kcal/mol-1, and also disclosed remarkable constancy based on the 500ns simulation period. The vaccine-assisted immune simulation and expression level in the vector revealed a robust immune response towards the host based on the vaccination and a significant expression level. Conclusions Based on the integrated approach and validation steps, the overall finding suggests that the formulated vaccine may have strongly immunodominant properties and could combat the infection.https://doi.org/10.1186/s12985-025-02764-0Acquired immunodeficiency syndromeDockingHuman immunodeficiency virusSimulationVaccine |
| spellingShingle | Saurav Kumar Mishra Abdelkrim Guendouzi Neeraj Kumar Ganesh Sharma Taha Alqahtani Magdi E. A. Zaki Md. Abdullah Al mashud Yewulsew Kebede Tiruneh John J. Georrge Integrated Immuno and bioinformatics assisted novel epitope vaccine against HIV infection: a study based on complete genome Virology Journal Acquired immunodeficiency syndrome Docking Human immunodeficiency virus Simulation Vaccine |
| title | Integrated Immuno and bioinformatics assisted novel epitope vaccine against HIV infection: a study based on complete genome |
| title_full | Integrated Immuno and bioinformatics assisted novel epitope vaccine against HIV infection: a study based on complete genome |
| title_fullStr | Integrated Immuno and bioinformatics assisted novel epitope vaccine against HIV infection: a study based on complete genome |
| title_full_unstemmed | Integrated Immuno and bioinformatics assisted novel epitope vaccine against HIV infection: a study based on complete genome |
| title_short | Integrated Immuno and bioinformatics assisted novel epitope vaccine against HIV infection: a study based on complete genome |
| title_sort | integrated immuno and bioinformatics assisted novel epitope vaccine against hiv infection a study based on complete genome |
| topic | Acquired immunodeficiency syndrome Docking Human immunodeficiency virus Simulation Vaccine |
| url | https://doi.org/10.1186/s12985-025-02764-0 |
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