Developing Isoxazole as a Native Photo‐Cross‐Linker for Photoaffinity Labeling and Chemoproteomics

Photoaffinity labeling is a powerful technique to interrogate drug‐protein interactions in native cellular environments. Photo‐cross‐linkers are instrumental for this technique. However, the introduction of unnatural photo‐cross‐linkers may significantly reduce the bioactivity of the drug, thus impairing the chemoproteomic outcomes. Herein, we developed a common pharmacophore, isoxazole, into a natively embedded photo‐cross‐linker for chemoproteomics, which minimally perturbs the drug structure. The photo‐cross‐linking reactions of the isoxazole were thoroughly investigated for the first time. Functionalized isoxazoles were then designed and applied to protein labeling, demonstrating the superior photo‐cross‐linking efficiency. Subsequently, two isoxazole‐based drugs, Danazol and Luminespib, were employed in chemoproteomic studies, revealing their potential cellular targets. These results provide valuable strategies for future chemoproteomic study and drug development. Isoxazole is an essential pharmacophore in drug discovery. In this study, we investigated the photochemistry of isoxazole with biomolecules and developed it as a natively embedded photo‐cross‐linker for chemoproteomics and drug discovery. With this strategy, two isoxazole‐containing drugs were successfully applied to chemoproteomic platforms to uncover their cellular targets and interactions.