Stabilized SARS-CoV-2 spike S2 immunogens designed using insights from enhanced sampling molecular dynamics simulations

The SARS-CoV-2 spike protein is an important molecular machine that facilitates membrane fusion to host cells and is the major antigenic component of vaccines. Notably, full-length prefusion-stabilized spike proteins produce a strong neutralizing antibody response against S1, which contains the N-terminal domain (NTD) and receptor binding domain (RBD). Unfortunately, emerging variants of concern contain numerous mutations, insertions, and deletions within S1 that impact the binding of neutralizing antibodies which may diminish the efficacy of current vaccines. In contrast, S2 is the most conserved region of the spike and is capable of eliciting antibodies that bind broadly to diverse β-coronavirus spikes. Although S2-based immunogens may have potential benefits, a challenge to its usage as an alternative vaccine strategy is the general instability of S2 in the absence of S1. Using enhanced sampling molecular dynamics simulations, we observed that the S2 head adopts an open conformation where individual protomers separate from one another at the apex. Extensive contact map analysis reveals that the formation and breakage of contacts between three helices mediates these opening motions. Through introducing mutations in these helices, we designed a stabilized S2 construct that maintains a closed conformation and has enhanced thermal stability and protein expression. These studies represent the first simulations characterizing S2 conformational dynamics and demonstrate the potential of using enhanced sampling molecular dynamics simulations in the design of stabilized SARS-CoV-2 S2 immunogens.