Small molecule photocatalysis enables drug target identification via energy transfer

Abstract

Over half of new therapeutic approaches fail in clinical trials due to a lack of target validation. As such, the development of new methods to improve and accelerate the identification of cellular targets, broadly known as target ID, remains a fundamental goal in drug discovery. While advances in sequencing and mass spectrometry technologies have revolutionized drug target ID in recent decades, the corresponding chemical-based approaches have not changed in over 50 y. Consigned to outdated stoichiometric activation modes, modern target ID campaigns are regularly confounded by poor signal-to-noise resulting from limited receptor occupancy and low crosslinking yields, especially when targeting low abundance membrane proteins or multiple protein target engagement. Here, we describe a broadly general platform for photocatalytic small molecule target ID, which is founded upon the catalytic amplification of target-tag crosslinking through the continuous generation of high-energy carbene intermediates via visible light-mediated Dexter energy transfer. By decoupling the reactive warhead tag from the small molecule ligand, catalytic signal amplification results in unprecedented levels of target enrichment, enabling the quantitative target and off target ID of several drugs including (+)-JQ1, paclitaxel (Taxol), dasatinib (Sprycel), as well as two G-protein-coupled receptors—ADORA2A and GPR40.

Photoaffinity Labeling Chemistries Used to Map Biomolecular Interactions

“…This platform was originally developed as a proximity labeling strategy to detect protein-protein interactions [83] and has since been applied to small molecule target identification experiments. [90] In this technique, a small molecule of interest is modified with an Ir catalyst, which spatiotemporally activates a biotin-diazirine probe via Dexter energy transfer for localized protein labeling (Figure 3B). Advantages of this approach include the Ir photocatalyst allows for multiple labeling events per small molecule-protein interaction and use of a less damaging blue light (450 nm) for activation of the Ir catalyst.…”

“…Recently, an Ir photocatalyst platform has been developed to activate aryl trifluoromethyl diazirines using blue light (Figure 3A). This platform was originally developed as a proximity labeling strategy to detect protein–protein interactions [83] and has since been applied to small molecule target identification experiments [90] . In this technique, a small molecule of interest is modified with an Ir catalyst, which spatiotemporally activates a biotin‐diazirine probe via Dexter energy transfer for localized protein labeling (Figure 3B).…”

Ligand-Directed Photocatalysts and Far-Red Light Enable Catalytic Bioorthogonal Uncaging inside Live Cells

“…The ability to mimic cellular compartmentalization with non-natural catalysts would provide a unique tool for regulating cellular processes. Recently, several groups have described photocatalytic proximity labeling as a chemoproteomic tool, − including the use of Ir photocatalysis to promote azide reduction/uncaging in live cells, where the positively charged Ir-catalyst was nonspecifically localized to the negatively charged environment of the mitochondria. Additionally, Ru-photocatalysis in the presence of cells has been used to promote a cellular effect via E- to Z- isomerization of a combretastatin analogue .…”

Switching of Photocatalytic Tyrosine/Histidine Labeling and Application to Photocatalytic Proximity Labeling

“…Proximity labeling has been widely investigated in recent years and is used to analyze protein–protein interactions in living cells [ 13 , 14 ], cell membranes [ 15 , 16 ], ligand recognition on cell membrane surfaces [ 17 , 18 ], and intercellular communication [ 19 ]. APEX and BioID are performed to chemically label proteins in proximity to a target protein to which an enzyme is fused [ 20 , 21 ].…”