Intelligent antigen design combined with yeast display enhances targeted immune responses

Inducing strong and targeted humoral immune responses, a central goal of next-generation vaccine development, involves a complex series of interconnected steps. However, a comprehensive study that addresses and integrates all steps is still missing. Here, we present a study that addresses these steps to elicit precise neutralizing antibody (nAb) responses targeting focused epitope motifs. We present a new protein design model called EpiTopoFold for constructing a topology that precisely accommodates and stabilizes the epitope motif. After ten thousand in silico simulations, we designed a de novo antigen L9, which structurally incorporated three epitope motifs from the receptor-binding domain (RBD) of the coronavirus spike protein. To enhance antigen immunogenicity, we displayed L9 on the surface of yeast (Saccharomyces cerevisiae). In mice, the yeast-displayed L9 induced stronger and broader neutralizing responses than the alum-adjuvanted L9 or commercial RBD protein. Together, this work establishes a proof-of-concept framework that integrates intelligent antigen design with yeast surface display to enable robust and targeted nAb responses for next-generation vaccine development.