Chemical tools to expand the ligandable proteome: diversity-oriented synthesis-based photoreactive stereoprobes

Ogasawara, D.; Konrad, D.; Tan, Z. Y.; Carey, K.; Luo, J.; Won, S. J.; Li, H.; Carter, T.; DeMeester, K.; Njomen, E.; Schreiber, S.; Xavier, R.; Melillo, B.; Cravatt, B.

doi:10.1101/2024.02.27.582206

bioRxiv · 10.1101/2024.02.27.582206

Chemical tools to expand the ligandable proteome: diversity-oriented synthesis-based photoreactive stereoprobes

Ogasawara, D.·Konrad, D.·Tan, Z. Y.·Carey, K.·Luo, J.·Won, S. J.·Li, H.·Carter, T.·DeMeester, K.·Njomen, E.·Schreiber, S.·Xavier, R.·Melillo, B.·Cravatt, B.

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Abstract

Chemical proteomics enables the global assessment of small molecule-protein interactions in native biological systems and has emerged as a versatile approach for ligand discovery. The range of small molecules explored by chemical proteomics has, however, been limited. Here, we describe a diversity-oriented synthesis (DOS)-inspired library of stereochemically-defined compounds bearing diazirine and alkyne units for UV light-induced covalent modification and click chemistry enrichment of interacting proteins, respectively. We find that these photo-stereoprobes interact in a stereoselective manner with hundreds of proteins from various structural and functional classes in human cells and demonstrate that these interactions can form the basis for high-throughput screening-compatible nanoBRET assays. Integrated phenotypic analysis and chemical proteomics identified photo-stereoprobes that modulate autophagy by engaging the mitochondrial serine protease CLPP. Our findings show the utility of photo-stereoprobes for expanding the ligandable proteome, furnishing target engagement assays, and discovering and characterizing bioactive small molecules by cell-based screening.

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Ogasawara, D., Konrad, D., Tan, Z. Y., Carey, K., Luo, J., Won, S. J., Li, H., Carter, T., DeMeester, K., Njomen, E., Schreiber, S., Xavier, R., Melillo, B., Cravatt, B.. 2024-02-29. Chemical tools to expand the ligandable proteome: diversity-oriented synthesis-based photoreactive stereoprobes. https://doi.org/10.1101/2024.02.27.582206

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