Fluorogenic “photoclick” labelling of DNA using a Cy3 dye

Two 2′-deoxyuridines as new building blocks for automated DNA synthesis carry a small aryltetrazole as a “photoclickable” group at their 5-positions.

Developments of bioorthogonal handle-containing photo-crosslinkers for photoaffinity labeling

Photoaffinity labeling (PAL) has been widely applied in various research areas such as medicinal chemistry, chemical biology and structural biology, owing to its capability of investigating non-covalent ligand-protein interactions under native environments and elucidating protein structures, functions etc. One important application of this technique is to use affinity-based proteome profiling (AfBP) coupled with bioimaging for profiling drug-target interactions in situ. In order to accurately report drug-target interactions via these approaches, several considerations as follows need to be made: (1) maximally retaining bioactivities of photoprobes upon functionalization with a photoreactive group and a reporter tag from a parental compound; (2) performing proteome profiling and imaging in situ simultaneously, to monitor drug-target interactions in different manners; and (3) developing excellent photo-crosslinkers capable of photo-crosslinking and fluorescence turn-on at the same time. With these considerations in mind, we have developed three versions of "minimalist" bioorthogonal handle-containing photo-crosslinkers (L3-L6) during the years and successfully applied them in all kinds of small bioactive molecules for protein labeling and cellular imaging studies. In this mini-review, the features and functions of these linkers are specifically highlighted and summarized.

Covalent Probe Finds Carboxylic Acid

In this issue of Cell Chemical Biology, Martín-Gago et al. (2017a) disclose a new strategy for the selective covalent targeting of binding site carboxylic acids within the proteome using the isoxazolium salt as a warhead. This discovery paves the way for developing new protein ligation methods as well as covalent drug candidates.

Ligand-free Cu(ii)-mediated aerobic oxidations of aldehyde hydrazones leading to N,N'-diacylhydrazines and 1,3,4-oxadiazoles

A Cu(ii)-mediated synthesis of N,N'-diacylhydrazines and 1,3,4-oxadiazoles from aldehyde hydrazones has been developed. This is the first time that the synthesis of N,N'-diacylhydrazines and 1,3,4-oxadiazoles using N,N-dimethylamides as the acylation reagent and O₂ in air as the oxidation reagent is reported. These reactions offered several advantages including simple workups, ligand-free inexpensive metal salts as mediators, high yields, and wide scope of substrates.

Photochemistry of 1- and 2-Methyl-5-aminotetrazoles: Structural Effects on Reaction Pathways

The influence of the position of the methyl substituent in 1- and 2-methyl-substituted 5-aminotetrazoles on the photochemistry of these molecules is evaluated. The two compounds were isolated in an argon matrix (15 K) and the matrix was subjected to in situ narrowband UV excitation at different wavelengths, which induce selectively photochemical transformations of different species (reactants and initially formed photoproducts). The progress of the reactions was followed by infrared spectroscopy, supported by quantum chemical calculations. It is shown that the photochemistries of the two isomers, 1-methyl-(1H)-tetrazole-5-amine (1a) and 2-methyl-(2H)-tetrazole-5-amine (1b), although resulting in a common intermediate diazirine 3, which undergoes subsequent photoconversion into 1-amino-3-methylcarbodiimide (H₂N-N═C═N-CH₃), show marked differences: formation of the amino cyanamide 4 (H₂N-N(CH₃)-C≡N) is only observed from the photocleavage of the isomer 1a, whereas formation of the nitrile imine 2 (H₂N-C^-═N⁺═N-CH₃) is only obtained from photolysis of 1b. The exclusive formation of nitrile imine from the isomer 1b points to the possibility that only the 2H-tetrazoles forms can give a direct access to nitrile imines, while observation of the amino cyanamide 4 represents a novel reaction pathway in the photochemistry of tetrazoles and seems to be characteristic of 1H-tetrazoles. The structural and vibrational characterization of both reactants and photoproducts has been undertaken.

Studying epigenetic complexes and their inhibitors with the proteomics toolbox

Some epigenetic modifier proteins have become validated clinical targets. With a few small molecule inhibitors already approved by national health administrations and many more in the pharmaceutical industry pipelines, there is a need for technologies that can promote full comprehension of the molecular action of these drugs. Proteomics, with its relatively unbiased nature, can contribute to a thorough understanding of the complexity of the megadalton complexes, which write, read and erase the histone code, and it can help study the on-target and off-target effect of the drugs designed to modulate their action. This review on the one hand gathers the published affinity probes able to decipher small molecule targets and off-targets in a close-to-native environment. These are small molecule analogues of epigenetic drugs conceived as protein target enrichment tools after they have engaged them in cells or lysates. Such probes, which have been designed for deacetylases, bromodomains, demethylases, and methyltransferases not only enrich their direct protein targets but also their stable interactors, which can be identified by mass spectrometry. Hence, they constitute a tool to study the epigenetic complexes together with other techniques also reviewed here: immunoaffinity purification with antibodies against native protein complex constituents or epitope tags, affinity matrices designed to bind recombinantly tagged protein, and enrichment of the complexes using histone tail peptides as baits. We expect that this toolbox will be adopted by more and more researchers willing to harness the spectacular advances in mass spectrometry to the epigenetic field.

Zinc and cadmium complexes based on bis-(1H-tetrazol-5-ylmethyl/ylethyl)-amine ligands: structures and photoluminescence properties

Nine zinc and cadmium coordination compounds with bis-(1H-tetrazol-5-ylmethyl/ylethyl)-amine were synthesized and structurally characterized, and the fluorescent emission and fluorescence lifetime of complexes 1–9 have been investigated and discussed.