Chemistry & Chemical Biology Seminar - Green Ahn - "Precision reprogramming of cellular pathways through chemical and computational design"

Repurposing endogenous machinery to degrade disease-driving proteins is a promising therapeutic strategy. We harnessed cellular lysosomal trafficking pathway to induce targeted degradation of extracellular and membrane proteins. Lysosome targeting chimeras (LYTACs) couple a lysosomal trafficking receptor to an extracellular target to drive degradation. We identified key genetic regulators of LYTAC activity through a genome-wide CRISPR screen, and elucidated pathways that are essential for efficient lysosomal trafficking. These insights have broad implications for diverse therapeutics that rely on cell-surface to lysosome trafficking, such as enzyme replacement therapies, nucleic acid delivery, and antibody-drug conjugates. Achieving precise control over cell surface machinery requires approaches that extend beyond existing ligands. De novo protein design allows targeting virtually any epitope on a given protein. We employed computational protein design to develop endocytosis triggering proteins (EndoTags) that engage endogenous internalizing receptors for cell-type-specific degradation and delivery of protein-based nanocages. Designed EndoTags exhibited in vivo efficacy and demonstrated conditional activation through logic gating. To further enhance the precision of designed proteins, we sought to program selective responsiveness to native environmental cues that define cellular state and location. Among these cues, pH is dynamically regulated during endocytic trafficking and metabolic rewiring in tumors. We developed machine learning (ML)-driven computational methods to rationally design pH-responsive proteins, uncovering general molecular principles for encoding pH-sensitivity. These pH-responsive designs enable durable and selective activation of protein-based therapeutics. Together, these efforts establish a foundation for employing molecular engineering and ML-driven protein design to create precision molecules that reprogram cellular processes.