De novo protein design has enabled the construction of functional proteins with tailored tertiary structures from scratch, moving beyond traditional simulations to machine learning (ML)-driven approaches. Key case studies from our research will be highlighted: 1) BBB-penetrating therapeutics: designing protein shuttles for CNS drug delivery in collaboration with Imnewrun. 2) Narcotic & viral neutralization: engineering high-affinity binders for narcotic drugs and respiratory viruses, including COVID-19, Influenza, and RSV. Our workflow bridges computational design with synthetic biology, utilizing yeast surface display for high-throughput screening and validating candidates through antibody-fusion and mRNA-based delivery in in vivo models. Furthermore, we emphasize the industrial impact of generative models in streamlining the drug discovery process. By significantly reducing the time and cost associated with lead optimization, these AI-driven platforms enable the rapid generation of "developable" biologics with superior pharmacokinetics. This paradigm shift from serendipitous discovery to intentional design represents a transformative leap for the biopharmaceutical industry, providing a scalable solution for the hit-to-clinic transition of novel protein modalities.
AI-Enabled Generative Protein Design for Virus-Neutralizing Therapeutics
ArTemIS: Architecture of Templating for Interaction-driven Scaffolds