Small molecule photocatalysis enables drug target identification via energy transfer

Abstract

The identification of cellular targets that can be exploited for therapeutic benefit, broadly known as target ID, remains a fundamental goal in drug discovery. In recent years, the application of new chemical and biological technologies that accelerate target ID has become commonplace within drug discovery programs, as a complete understanding of how molecules react in a cellular environment can lead to increased binding selectivity, improved safety profiles, and clinical efficacy. Established approaches using photoaffinity labelling (PAL) are often costly and time-consuming due to poor signal-to-noise coupled with extensive probe optimization. Such challenges are exacerbated when dealing with low abundance membrane proteins or multiple protein target engagement, typically rendering target ID unfeasible. Herein, we describe a general platform for photocatalytic small molecule target ID, which hinges upon the generation of high-energy carbene intermediates via visible light-mediated Dexter energy transfer. By decoupling the reactive warhead from the drug, catalytic signal amplification results in multiple labelling events per drug, leading to unprecedented levels of target enrichment. Through the development of cell permeable photocatalyst conjugates, this method has enabled the quantitative target and off target identification of several drugs including (+)-JQ1, paclitaxel, and dasatinib. Moreover, this methodology has led to the target ID of two GPCRs, ADORA2A and GPR40m, a class of drug target seldom successfully uncovered in small molecule PAL campaigns.

A genetically encoded photo-proximity labeling approach for mapping protein territories

“…16 However, the reliance of PPL strategies on peptide- or protein-based delivery modalities generally impedes application within living cells, although cell-permeable photocatalysts can still be used intracellularly in cases where prior conjugation to a targeting protein is not required. 17,18 In addition, unlike with genetically-encoded PL systems, supplementation of an exogenous photocatalyst could result in some off-target localization, increasing the PL background.…”

ICBS 2021: Looking Toward the Next Decade of Chemical Biology

“…This strategy could be extended to covalent labeling of cell surface targets such as the A2aR receptor, in a native cellular context. 57 Concurrent Session 3: Antimicrobial Discovery and Resistance, Tackling an Upcoming Health Crisis. This session, which highlighted one of the most urgent areas of contemporary drug discovery, was chaired by Claudia Jessen-Trefzer (University of Freiburg) and Stephan Hacker (Leiden University).…”

Drug interaction mapping with proximity dependent enzyme recruiting chimeras

“…One of the limitations of these strategies, however, is that they routinely identify large numbers of differentially regulated genes, often because of downstream effects of signaling or pathway modulation, resulting in uncertainty in the assignment of efficacy targets and MoA. Therefore, orthogonal molecular interaction focused chemo-proteomic approaches, such as affinity-based pulldowns 6 , photo-affinity labeling 7 , activity-based protein profiling 8 , and more recent methods like µMapping 9 have been used extensively to tackle these challenges by providing information on physical protein-drug interactions. While these approaches are invaluable tools for exploration of the target ID landscape, additional orthogonal tools are needed to tackle the unpredictable and fastidious nature of target ID.…”

“…For example, most covalent probes utilized in ABPP workflows target active site serine and cysteine residues and can therefore only be applied to a subset of targets. Similarly, PAL with minimalist diazirine linkers suffers from low conjugation efficiency as most probe molecules react with solvent, severely limiting sensitivity 9 . With these shortcomings in mind, an approach that provides generic targeting and simultaneously allowing for signal amplification based on proximity-dependent enzymatic labeling was devised.…”