Table_1_Functional and in silico Characterization of Neutralizing Interactions Between Antibodies and the Foot-and-Mouth Disease Virus Immunodominant Antigenic Site.DOCX

Molecular knowledge of virus–antibody interactions is essential for the development of better vaccines and for a timely assessment of the spread and severity of epidemics. For foot-and-mouth disease virus (FMDV) research, in particular, computational methods for antigen–antibody (Ag–Ab) interaction, and cross-antigenicity characterization and prediction are critical to design engineered vaccines with robust, long-lasting, and wider response against different strains. We integrated existing structural modeling and prediction algorithms to study the surface properties of FMDV Ags and Abs and their interaction. First, we explored four modeling and two Ag–Ab docking methods and implemented a computational pipeline based on a reference Ag–Ab structure for FMDV of serotype C, to be used as a source protocol for the study of unknown interaction pairs of Ag–Ab. Next, we obtained the variable region sequence of two monoclonal IgM and IgG antibodies that recognize and neutralize antigenic site A (AgSA) epitopes from South America serotype A FMDV and developed two peptide ELISAs for their fine epitope mapping. Then, we applied the previous Ag–Ab molecular structure modeling and docking protocol further scored by functional peptide ELISA data. This work highlights a possible different behavior in the immune response of IgG and IgM Ab isotypes. The present method yielded reliable Ab models with differential paratopes and Ag interaction topologies in concordance with their isotype classes. Moreover, it demonstrates the applicability of computational prediction techniques to the interaction phenomena between the FMDV immunodominant AgSA and Abs, and points out their potential utility as a metric for virus-related, massive Ab repertoire analysis or as a starting point for recombinant vaccine design.

病毒-抗体相互作用之分子知识对于疫苗研发以及疫情传播速度与严重性的及时评估至关重要。特别是在口蹄疫病毒（FMDV）的研究中，抗原-抗体（Ag-Ab）相互作用计算方法、交叉抗原性特征及其预测技术对于设计具有强大、持久和广泛免疫反应的工程疫苗极为关键。本研究整合了现有的结构建模和预测算法，以研究口蹄疫病毒Ag和Ab的表面性质及其相互作用。首先，我们探索了四种建模方法和两种Ag-Ab对接方法，并基于参考Ag-Ab结构建立了一个计算流程，用于C血清型FMDV的研究，以此作为未知Ag-Ab相互作用对研究的源协议。接着，我们从南美洲血清型A的FMDV中获取了识别和中和抗原位点A（AgSA）表位的两种单克隆IgM和IgG抗体的可变区序列，并为其开发了两种肽ELISA以进行精细表位映射。然后，我们将先前的Ag-Ab分子结构建模和对接协议应用于功能性肽ELISA数据。本研究突显了IgG和IgM抗体亚型在免疫反应中可能存在的不同行为。当前方法产生了具有不同表位和Ag相互作用拓扑结构的可靠抗体模型，并与它们的亚型类别相一致。此外，它证明了计算预测技术在FMDV免疫优势AgSA与抗体相互作用现象中的应用可行性，并指出其作为病毒相关大规模抗体库分析指标或重组疫苗设计起始点的潜在效用。