Systematic Proteomic Characterization of EV‐A71‐Infected Mice Identifies Dynamic Molecular Changes and Therapeutic Targets

Enterovirus A71 (EV-A71) is recognized as the primary causative agent of hand, foot, and mouth disease (HFMD) and is prevalent worldwide. However, the precise pathogenic mechanisms of EV-A71 remain unclear, and specific drugs targeting it have yet to be successfully developed. To explore the mechanisms underlying EV-A71 pathogenesis and to identify potential therapeutic opportunities, we performed a comprehensive proteogenomic characterization of muscle tissues from BALB/c mice infected with EV-A71, integrating transcriptomic, proteomic, and phosphoproteomic analyses. Our results showed that phagosome, complement, and coagulation cascade pathway-related molecules were activated, and the expression of cell growth-related molecules was downregulated. Concurrently, a rapid activation of the neutrophil extracellular trap pathway was observed at the protein level. Additionally, we mapped the global phosphorylation profiles to dysregulated kinases, predicting 32 drugs corresponding to 27 kinases. We found that kinase inhibitors have antiviral activity in vitro; vandetanib, nintedanib, dasatinib, avitinib, and nilotinib can inhibit virus replication in mice to some extent. Overall, this study provides a multi-omics resource for elucidating EV-A71-induced alterations in target tissues and for linking omics-based target discovery with drug screening and functional validation, providing new insights into both pathogenesis and therapeutic exploration.