Structure-assisted ligand-binding analysis using fluorogenic photoaffinity labeling

Fluorescent Labeling of a Target Protein with an Alkyl Diazirine Photocrosslinker Bearing a Cinnamate Moiety

A novel fluorogenic alkyl diazirine photocrosslinker bearing an o-hydroxycinnamate moiety has been developed for identification of the targets of bioactive molecules. The o-hydroxycinnamate moiety can be converted to the corresponding 7-hydroxycoumarin derivative, which should be created on the interacting site within the photocaptured target protein. The label yield and fluorescence intensity have been immensely improved in comparison with our previous aromatic crosslinkers to facilitate target identification in small quantities.

Lessons in Organic Fluorescent Probe Discovery

Fluorescent probes have gained profound use in biotechnology, drug discovery, medical diagnostics, molecular and cell biology. The development of methods for the translation of fluorophores into fluorescent probes continues to be a robust field for medicinal chemists and chemical biologists, alike. Access to new experimental designs has enabled molecular diversification and led to the identification of new approaches to probe discovery. This review provides a synopsis of the recent lessons in modern fluorescent probe discovery.

In situ formation of pyronin dyes for fluorescence protease sensing

A cutting-edge strategy for fluorogenic sensing of proteases (leucine aminopeptidase for the proof of concept) and based on the “covalent-assembly” principle is reported. Non-fluorescent mixed bis-aryl ethers are readily converted into a fluorescent pyronin through a domino process triggered by the peptide bond cleavage event caused by the targeted enzyme.

Kinetic controlled affinity labeling of target enzyme with thioester chemistry

High specificity has been an important feature in affinity labeling for target profiling. Especially, to label targets via rapidly progressing reactions with consumption of ligand (probe), high specificity of reaction with common functional groups of target protein should be achieved without reactions with similar groups of non-target proteins. Herein, we demonstrate the kinetic controlled affinity labeling of acyl CoA synthetase using a fatty acid analogue containing a phenylthioester linkage. High specificity was attained by accelerating the labeling rate in the binding pocket. This approach could be useful for profiling a series of target enzymes and transporters in signal transduction pathways.

Paramagnetic Ligand Tagging To Identify Protein Binding Sites

Transient biomolecular interactions are the cornerstones of the cellular machinery. The identification of the binding sites for low affinity molecular encounters is essential for the development of high affinity pharmaceuticals from weakly binding leads but is hindered by the lack of robust methodologies for characterization of weakly binding complexes. We introduce a paramagnetic ligand tagging approach that enables localization of low affinity protein–ligand binding clefts by detection and analysis of intermolecular protein NMR pseudocontact shifts, which are invoked by the covalent attachment of a paramagnetic lanthanoid chelating tag to the ligand of interest. The methodology is corroborated by identification of the low millimolar volatile anesthetic interaction site of the calcium sensor protein calmodulin. It presents an efficient route to binding site localization for low affinity complexes and is applicable to rapid screening of protein–ligand systems with varying binding affinity.

Hide and seek: Identification and confirmation of small molecule protein targets

Target identification and confirmation for small molecules is often the rate limiting step in drug discovery. A robust method to identify proteins addressed by small molecules is affinity chromatography using chemical probes. These usually consist of the compound of interest equipped with a linker molecule and a proper tag. Recently, methods emerged that allow the identification of protein targets without prior functionalization of the small molecule of interest. The digest offers an update on the newest developments in the area of target identification with special focus on confirmation techniques.