Viral escape-inspired framework for structure-guided dual bait protein biosensor design

A generalizable computational platform, CTRL-V (Computational TRacking of Likely Variants), is introduced to design selective binding (dual bait) biosensor proteins. The iteratively evolving receptor binding domain (RBD) of SARS-CoV-2 spike protein has been construed as a model dual bait biosensor which has iteratively evolved to distinguish and selectively bind to human entry receptors and avoid binding neutralizing antibodies. Spike RBD prioritizes mutations that reduce antibody binding while enhancing/ retaining binding with the ACE2 receptor. CTRL-V's through iterative design cycles was shown to pinpoint 20% (of the 39) reported SARS-CoV-2 point mutations across 30 circulating, infective strains as responsible for immune escape from commercial antibody LY-CoV1404. CTRL-V successfully identifies ~70% (five out of seven) single point mutations (371F, 373P, 440K, 445H, 456L) in the latest circulating KP.2 variant and offers detailed structural insights to the escape mechanism. While other data-driven viral escape variant predictor tools have shown promise in predicting potential future viral variants, they require massive amounts of data to bypass the need for physics of explicit biochemical interactions. Consequently, they cannot be generalized for other protein design applications. The publicly availably viral escape data was leveraged as in vivo anchors to streamline a computational workflow that can be generalized for dual bait biosensor design tasks as exemplified by identifying key mutational loci in Raf kinase that enables it to selectively bind Ras and Rap1a GTP. We demonstrate three versions of CTRL-V which use a combination of integer optimization, stochastic sampling by PyRosetta, and deep learning-based ProteinMPNN for structure-guided biosensor design.