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Inform."],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background and objectives<\/jats:title>\n                    <jats:p>Squamous cell carcinoma antigen recognized by T-cells 3 (SART3) has emerged as a promising target for cancer immunotherapy, given its overexpression in various malignancies and low or absent expression in non-tumorous tissues. This study aimed to design rationally and in silico evaluate a multi-epitope T cell vaccine targeting SART3, incorporating a TLR4 agonist adjuvant. The vaccine\u2019s predicted immunogenicity, physicochemical properties, structural stability, and interaction with TLR4 were comprehensively assessed. Additional assessments of cytokine-inducing potential, B-cell epitopes, and disulfide engineering opportunities were also executed.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Potential T-cell epitopes from SART3 were identified using IEDB and screened for antigenicity (VaxiJen), toxicity (ToxinPred), and MHC-I\/II binding affinity. Cytokine-inducing epitopes were evaluated using IL4pred, IL-10Pred, and IFNepitope servers. B-cell epitopes were predicted using ElliPro. The vaccine underwent comprehensive physicochemical, structural (I-TASSER\/GalaxyRefine), molecular docking (HDOCK), molecular dynamics simulations, and disulfide engineering (Disulfide by Design 2.0) analyses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The optimized 344-residue vaccine demonstrated non-allergenicity, high stability (instability index 17.16), antigenicity (Vaxijen 0.67), and solubility (SOLpro 0.96). HDOCK predicted favorable vaccine\u2013TLR4 binding (\u0394G\u2009= \u2212\u2009265.61\u00a0kcal\/mol, confidence 91%). MD simulations confirmed complex stability. Cytokine analysis revealed the potential to induce IL-4 and IL-10. The Val80\u2013Ala123 pair exhibited the lowest bond energy (1.16\u00a0kcal\/mol), indicating the optimal geometry for disulfide bond formation. The in silico immune simulations demonstrated a robust immune response following vaccine administration.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>This rationally designed SART3-targeted multi-epitope vaccine exhibits promising in silico characteristics across immunogenicity, physicochemical, cytokine-inducing, B-cell epitope, structural, and disulfide engineering profiles, warranting experimental validation for cancer immunotherapy development.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s44342-026-00068-5","type":"journal-article","created":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T13:54:47Z","timestamp":1777643687000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A bioinformatics pipeline for the design of a SART3-targeted cancer vaccine with enhanced immunogenicity"],"prefix":"10.1186","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5579-2082","authenticated-orcid":false,"given":"Zeynab","family":"Bayat","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8239-7068","authenticated-orcid":false,"given":"Faezeh","family":"Mahdian-Khoo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4128-165X","authenticated-orcid":false,"given":"Lida","family":"Samie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6546-8785","authenticated-orcid":false,"given":"Amir","family":"Taherkhani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,5,1]]},"reference":[{"key":"68_CR1","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1016\/j.lfs.2016.02.062","volume":"149","author":"A Whitmill","year":"2016","unstructured":"Whitmill A, Timani KA, Liu Y, He JJ. 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