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Government of Khyber Pakhtunkhwa, Pakistan","award":["2023YFE0199200"],"award-info":[{"award-number":["2023YFE0199200"]}]},{"name":"DG(R), L&amp;DD Department, and CCGR Project-Phase-II, Government of Khyber Pakhtunkhwa, Pakistan","award":["32070662"],"award-info":[{"award-number":["32070662"]}]},{"name":"DG(R), L&amp;DD Department, and CCGR Project-Phase-II, Government of Khyber Pakhtunkhwa, Pakistan","award":["32030063"],"award-info":[{"award-number":["32030063"]}]},{"name":"Intergovernmental International Scientific and Technological Innovation and Cooperation Program of the National Key R&amp;D Program","award":["A0130713808"],"award-info":[{"award-number":["A0130713808"]}]},{"name":"Intergovernmental International Scientific and Technological Innovation and Cooperation Program of the National Key R&amp;D Program","award":["46\/220020"],"award-info":[{"award-number":["46\/220020"]}]},{"name":"Intergovernmental International Scientific and Technological Innovation and Cooperation Program of the National Key R&amp;D Program","award":["2023YFE0199200"],"award-info":[{"award-number":["2023YFE0199200"]}]},{"name":"Intergovernmental International Scientific and Technological Innovation and Cooperation Program of the National Key R&amp;D Program","award":["32070662"],"award-info":[{"award-number":["32070662"]}]},{"name":"Intergovernmental International Scientific and Technological Innovation and Cooperation Program of the National Key R&amp;D Program","award":["32030063"],"award-info":[{"award-number":["32030063"]}]},{"name":"National Science Foundation of China","award":["A0130713808"],"award-info":[{"award-number":["A0130713808"]}]},{"name":"National Science Foundation of China","award":["46\/220020"],"award-info":[{"award-number":["46\/220020"]}]},{"name":"National Science Foundation of China","award":["2023YFE0199200"],"award-info":[{"award-number":["2023YFE0199200"]}]},{"name":"National Science Foundation of China","award":["32070662"],"award-info":[{"award-number":["32070662"]}]},{"name":"National Science Foundation of China","award":["32030063"],"award-info":[{"award-number":["32030063"]}]},{"name":"Khyber Medical University Publication Fund","award":["A0130713808"],"award-info":[{"award-number":["A0130713808"]}]},{"name":"Khyber Medical University Publication Fund","award":["46\/220020"],"award-info":[{"award-number":["46\/220020"]}]},{"name":"Khyber Medical University Publication Fund","award":["2023YFE0199200"],"award-info":[{"award-number":["2023YFE0199200"]}]},{"name":"Khyber Medical University Publication Fund","award":["32070662"],"award-info":[{"award-number":["32070662"]}]},{"name":"Khyber Medical University Publication Fund","award":["32030063"],"award-info":[{"award-number":["32030063"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Vaccines"],"abstract":"<jats:p>Background: Newcastle disease virus (NDV) is a highly contagious and economically devastating pathogen affecting poultry worldwide, leading to significant losses in the poultry industry. Despite existing vaccines, outbreaks continue to occur, highlighting the need for more effective vaccination strategies. Developing a multi-epitopic peptide vaccine offers a promising approach to enhance protection against NDV. Objectives: Here, we aimed to design and evaluate a multi-epitopic vaccine against NDV using molecular dynamics (MD) simulation. Methodology: We retrieved NDV sequences for the fusion (F) protein and hemagglutinin\u2013neuraminidase (HN) protein. Subsequently, B-cell and T-cell epitopes were predicted. The top potential epitopes were utilized to design the vaccine construct, which was subsequently docked against chicken TLR4 and MHC1 receptors to assess the immunological response. The resulting docked complex underwent a 1 microsecond (1000 ns) MD simulation. For experimental evaluation, the vaccine\u2019s efficacy was assessed in mice and chickens using a controlled study design, where animals were randomly divided into groups receiving either a local ND vaccine or the peptide vaccine or a control treatment. Results: The 40 amino acid peptide vaccine demonstrated strong binding affinity and stability within the TLR4 and MHC1 receptor\u2013peptide complexes. The root mean square deviation of peptide vaccine and TLR4 receptor showed rapid stabilization after an initial repositioning. The root mean square fluctuation revealed relatively low fluctuations (below 3 \u00c5) for the TLR4 receptor, while the peptide exhibited higher fluctuations. The overall binding energy of the peptide vaccine with TLR4 and MHC1 receptors amounted to \u221215.7 kcal\u00b7mol\u22121 and \u221236.8 kcal\u00b7mol\u22121, respectively. For experimental evaluations in mice and chicken, the peptide vaccine was synthesized using services of GeneScript Biotech\u00ae (Singapore) PTE Limited. Experimental evaluations showed a significant immune response in both mice and chickens, with the vaccine eliciting robust antibody production, as evidenced by increasing HI titers over time. Statistical analysis was performed using an independent t-test with Type-II error to compare the groups, calculating the p-values to determine the significance of the immune response between different groups. Conclusions: Multi-epitopic peptide vaccine has demonstrated a good immunological response in natural hosts.<\/jats:p>","DOI":"10.3390\/vaccines12111250","type":"journal-article","created":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T11:53:43Z","timestamp":1730462023000},"page":"1250","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Multi-Epitopic Peptide Vaccine Against Newcastle Disease Virus: Molecular Dynamics Simulation and Experimental Validation"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6051-1596","authenticated-orcid":false,"given":"Muhammad Tariq","family":"Zeb","sequence":"first","affiliation":[{"name":"Department of Molecular Biology and Genetics, Institute of Basic Medical Sciences, Khyber Medical University, Phase-V, Hayatabad Peshawar, Peshawar 25100, Pakistan"},{"name":"Genomic Laboratory, Veterinary Research Institute, Bacha Khan Chowk, Charsadda Road, Peshawar 25100, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2359-111X","authenticated-orcid":false,"given":"Elise","family":"Dumont","sequence":"additional","affiliation":[{"name":"Institut de Chimie de Nice, Universit\u00e9 C\u00f4te d\u2019Azur, CNRS, UMR 7272, 06108 Nice, France"},{"name":"Institut Universitaire de France, 5 Rue Descartes, 75005 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1158-2133","authenticated-orcid":false,"given":"Muhammad Tahir","family":"Khan","sequence":"additional","affiliation":[{"name":"Institute of Molecular Biology & Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore 54000, Pakistan"},{"name":"State Key Laboratory of Respiratory Disease, Guangzhou Key Laboratory of Tuberculosis Research, Department of Clinical Laboratory, Guangzhou Chest Hospital, Institute of Tuberculosis, Guangzhou Medical University, Guangzhou 510180, China"},{"name":"Qihe Laboratory, Qishui Guang East, Qibin District, Hebi 458030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aroosa","family":"Shehzadi","sequence":"additional","affiliation":[{"name":"Institute of Molecular Biology & Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore 54000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irshad","family":"Ahmad","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Genetics, Institute of Basic Medical Sciences, Khyber Medical University, Phase-V, Hayatabad Peshawar, Peshawar 25100, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.virusres.2014.02.016","article-title":"Newcastle Disease Virus: Current Status and Our Understanding","volume":"184","author":"Ganar","year":"2014","journal-title":"Virus Res."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Mansour, S.M.G., ElBakrey, R.M., Mohamed, F.F., Hamouda, E.E., Abdallah, M.S., Elbestawy, A.R., Ismail, M.M., Abdien, H.M.F., and Eid, A.A.M. 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