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Design of antibody structure-guided epitope vaccines in silico to induce potent immune responses against emerging viruses

Xue-Feng Wei,Liang Zhao,Zhao Zhao,Yu-Ming Gong,Yu-Ying Zheng,Gao-feng Cheng,Gao-Xue Wang,Bin Zhu,Weiguang Kong

Published 2025 in Journal of Virology

ABSTRACT

ABSTRACT The severe damage caused by public health emergencies in recent years indicates that epitope identification and vaccine development remain potential strategies to stop viral epidemics. Despite challenges such as comprehensive virus analysis, computer simulations and antibody-based reverse vaccinology can rapidly localize antigenic epitopes without the need to resolve protein functions, thereby supporting vaccine design. In previous studies, we developed a strategy for peptide vaccine design based on simulated epitopes for tilapia lake virus (TiLV). To further improve vaccine immunogenicity and capitalize on the significance of antibodies for epitope screening, this study presents a structural modification strategy based on antigen-antibody docking for reverse vaccinology in conjunction with single amino acid mutagenesis inducing a robust immune response in tilapia. A high-affinity scFv1 was obtained through screening from the constructed single-chain antibody fragment (scFv) library targeting TiLV. Subsequently, the key dominant epitope 385GYQLASEIRGTIPLSS400 was identified through alanine scanning and antibody binding assays based on the docking. Based on the epitope and scFv1 structure, an enhanced epitope vaccine, S390F, was obtained through single amino acid random mutation modification. Boost immunizations of tilapia elicited significant responses in IgM levels and non-specific immune enzyme activities, upregulated the expression of immune-related genes, and improved RPS of TiLV infection by approximately 25%, effectively preventing viral attack. Meanwhile, S390F activated the expression of the co-stimulatory molecule CD40, suggesting a response from immune cells. The development of peptide-based vaccines through computer-aided design effectively highlights the importance of antibodies and offers valuable insights for the control of emerging diseases. IMPORTANCE Public health emergencies pose significant threats to both human and environmental health, and the rapid control of emerging diseases often remains challenging due to their unknown characteristics. In this context, vaccines have historically been instrumental in the fight against major diseases, with epitope vaccines emerging as a preferred approach due to their precision and efficacy. In previous studies, we developed a strategy for peptide vaccine design based on simulated epitopes for tilapia lake virus (TiLV). To further improve vaccine immunogenicity and capitalize on the significance of antibodies for epitope screening, this study presents a structural modification strategy based on antigen-antibody docking for reverse vaccinology in conjunction with single amino acid mutagenesis inducing a robust immune response in tilapia. We believe that our findings are highly relevant to the field and contribute to the ongoing efforts to combat public health threats. Public health emergencies pose significant threats to both human and environmental health, and the rapid control of emerging diseases often remains challenging due to their unknown characteristics. In this context, vaccines have historically been instrumental in the fight against major diseases, with epitope vaccines emerging as a preferred approach due to their precision and efficacy. In previous studies, we developed a strategy for peptide vaccine design based on simulated epitopes for tilapia lake virus (TiLV). To further improve vaccine immunogenicity and capitalize on the significance of antibodies for epitope screening, this study presents a structural modification strategy based on antigen-antibody docking for reverse vaccinology in conjunction with single amino acid mutagenesis inducing a robust immune response in tilapia. We believe that our findings are highly relevant to the field and contribute to the ongoing efforts to combat public health threats.

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