Photoaffinity labelling strategies for mapping the small molecule–protein interactome

Abstract

We review the development of photoaffinity labeling (PAL) chemistries and the application of PAL to chemoproteomic target deconvolution for small molecules, lipids, and metabolites.

Developing Photoaffinity Probes for Dopamine Receptor D2 to Determine Targets of Parkinson’s Disease Drugs

“…Here, our work reinforces the notion that omics-based approaches which provide a broad picture of a molecule's "interactome" may also give insight into the pleiotropy of effects observed for a drug, or perhaps indicate new applications. 22,[57][58][59] Specifically, probes 5 and 7 bound other protein networks including the retrograde endocannabinoid signaling pathway, neuronal nitric oxide synthase, GABA receptor components, and muscarinic acetylcholine receptor M1. Follow-up analysis may yield insights into how this pathway relates specifically to Parkinson's disease symptoms or provide new targets for treatments.…”

“…For the photoaffinity moiety, two of the most common photocrosslinking groups are benzophenones and diazirines, which upon irradiation with UV light generate ketyl radicals and carbenes, respectively. 22 There are benefits and drawbacks to both groups, for example, the benzophenone generates a longer-lived reactive intermediate, and is relatively easy to synthesize, but is hampered by its large size. In contrast, the carbene is highly reactive and shorter-lived-which can be advantageous-but is relatively harder to synthesize in high yield and may degrade quickly.…”

Methods to characterize and discover molecular degraders in cells

“…12). 107 Similar to ABPP, PAL-assisted chemical proteomics allows for an unbiased identification of proteins interacting with the chemical probe, but is also able to visualize binding sites through photo-affinity labelling chemistry.…”

Chemical Probes and Activity-Based Protein Profiling for Cancer Research

“…On the other hand, affinity-based probes (AfBPs) consist of ligands for target binding and photoreactive groups for covalent bond formation, instead of electrophile warheads. The conjugation of a reporter tag with the target protein is primarily conducted by bio-orthogonal ligation, for example, of alkynes and azides, through click chemistry ( Figure 1 ) [ 8 ]. These probes must possess a highly light-responsive element or photoreactive group that demonstrates fluorogenic properties upon UV irradiation by forming a covalent bond with the protein of interest.…”