Harnessing Hydrophobic Interactions for Photocaging and Photoproximity Labeling

About This Grant

Project Summary. In recent years, the catalytic proximity labeling (CPL) approaches have emerged as viable tools for in situ biological study that can capture and identify the collection of proteins from a particular cellular location or interaction. The proximity labeling largely relies on combined H-bonding, ionic interaction, and hydrophobic force between ligands and biomolecules. It is noteworthy that many biological interactions are dominated by hydrophobic interactions. For example, such interactions are heavily involved in lipid-protein and recent emerged hydrophobic tag (HyT) based protein degrader. However, the exploration of hydrophobic interactions in CPL is a largely untapped area while offering unique opportunities to gain (new) insights of lipid- proteomic networks and understand the unknown mechanism of action in HyT degraders. The goal of this application is to develop photocatalytic proximity labeling (PPL) platforms to map protein interactions in lipid and HyT-based protein degraders, and to develop new ‘hydrophobic interactions photocaging’ strategy for spatiotemporal modulation of lipid signaling and HyT-based protein degradation in living cells. In Aim 1, I will develop an unprecedented near-infrared (NIR) -responsive photocaging methods to modulate HyT-based protein degradation and lipid signaling. The conceptually innovative ‘photocaging hydrophobic interaction’ method provides a new platform to probe the role of hydrophobic interactions in biological systems. In Aim 2, I will develop NIR-activated proximity labeling platforms to comprehensively map lipid–protein interactions. This light-responsive platform will address the limitations of conventional diazirine-based photoaffinity labeling method and has potential to uncover new drug targets and lipid-binding proteins. In Aim 3, I will further profile HyT degrader interactomes using NIR-triggered proximity labeling. Hydrophobic tag (HyT)-based degraders offer a promising alternative to PROTACs due to their lower molecular weight and improved pharmacokinetics. However, the mechanistic basis of HyT-induced protein degradation remains poorly understood. These studies will provide mechanistic insight into HyT-mediated degradation and inform rational design of next-generation degraders. The proposed studies will be conducted at UC San Diego, an internationally recognized research university distinguished by its collaborative culture, interdisciplinary strengths, and state-of-the-art core facilities. Throughout the K99/R00 phase, I will benefit from the mentorship of my advisory committee, including Dr. Benjamin Cravatt, a pioneer in chemical biology and proteomics, Dr. Eric Bennett, an expert in protein quality control and proteomics, and Dr. Fleur Ferguson, a leader in targeted protein degradation. Their collective guidance in scientific training and career development, together with the structured training afforded by the K99/R00, will provide the critical foundation for me to launch an independent research program at the interface of chemical biology, proteomics, and photochemistry.