Rational design 2.0: transitioning from static structural biology to computational prioritization and iterative...

Respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract disease (LRTD) in infants and older adults worldwide. Although vaccines based on the fusion (F) protein have shown progress, their efficacy remains limited by antigenic instability and viral evolution. The metastable transition of the F protein between prefusion (preF) and postF conformations critically determines the exposure of neutralizing epitopes, with most potent antibodies targeting preF-specific sites. In addition, the glycosylated G protein contributes to immune evasion through glycan shielding and CX3C-mediated immunomodulation. Recent advances in structural biology and computational protein design have improved the stabilization of preF conformations; however, these approaches do not fully address antigenic variability. Emerging methods, including protein language models (PLMs) and structure prediction frameworks, enable antigen design to be guided by sequence-structure relationships, allowing researchers to prioritize candidate antigens with favorable stability profiles. Here, we propose the term "Rational Design 2.0" to describe this emerging framework. By integrating structural information with evolutionary and sequence-level constraints, Rational Design 2.0 extends RSV vaccine design beyond static structural optimization and provides a conceptual framework for future vaccine-development strategies.