Distribution of photo-cross-linked products from 3-aryl-3-trifluoromethyldiazirines and alcohols

Discovery of drug targets based on traditional Chinese medicine microspheres (TCM-MPs) fishing strategy combined with bio-layer interferometry (BLI) technology

Target discovery of natural products is a key step in the development of new drugs, and it is also a difficult speed-limiting step. In this study, a traditional Chinese medicine microspheres (TCM-MPs) target fishing strategy was developed to discover the key drug targets from complex system. The microspheres are composed of Fe3O4 magnetic nanolayer, oleic acid modified layer, the photoaffinity group (4- [3-(Trifluoromethyl)-3H-diazirin-3-yl] benzoic acid, TAD) layer and active small molecule layer from inside to outside. TAD produces highly reactive carbene under ultraviolet light, which can realize the self-assembly and fixation of drug active small molecules with non-selective properties. Here, taking Shenqi Jiangtang Granules (SJG) as an example, the constructed TCM-MPs was used to fish the related proteins of human glomerular mesangial cells (HMCs) lysate. 28 differential proteins were screened. According to the target analysis based on bioinformatics, GNAS was selected as the key target, which participated in insulin secretion and cAMP signaling pathway. To further verify the interaction effect of GNAS and small molecules, a reverse fishing technique was established based on bio-layer interferometry (BLI) coupled with UHPLC-Q/TOF-MS/MS. The results displayed that 26 small molecules may potentially interact with GNAS, and 7 of them were found to have strong binding activity. In vitro experiments for HMCs have shown that 7 active compounds can significantly activate the cAMP pathway by binding to GNAS. The developed TCM-MPs target fishing strategy combined with BLI reverse fishing technology to screen out key proteins that directly interact with active ingredients from complex target protein systems is significant for the discovery of drug targets for complex systems of TCM.

Identification of a Small Molecule That Enhances Ferroptosis via Inhibition of Ferroptosis Suppressor Protein 1 (FSP1)

Glutathione peroxidase 4 (GPX4) is an intracellular enzyme that oxidizes glutathione while reducing lipid peroxides and is a promising target for cancer therapy. To date, several GPX4 inhibitors have been reported to exhibit cytotoxicity against cancer cells. However, some cancer cells are less sensitive to the known GPX4 inhibitors. This study aimed to explore compounds showing synergistic effects with GPX4 inhibitors. We screened a chemical library and identified a compound named NPD4928, whose cytotoxicity was enhanced in the presence of a GPX4 inhibitor. Furthermore, we identified ferroptosis suppressor protein 1 as its target protein. The results indicate that NPD4928 enhanced the sensitivity of various cancer cells to GPX4 inhibitors, suggesting that the combination might have therapeutic potential via the induction of ferroptosis.

CaproGlu: Multifunctional tissue adhesive platform

Driven by the clinical need for a strong tissue adhesive with elastomeric material properties, a departure from legacy crosslinking chemistries was sought as a multipurpose platform for tissue mending. A fresh approach to bonding wet substrates has yielded a synthetic biomaterial that overcomes the drawbacks of free-radical and nature-inspired bioadhesives. A food-grade liquid polycaprolactone grafted with carbene precursors yields CaproGlu. The first-of-its-kind low-viscosity prepolymer is VOC-free and requires no photoinitiators. Grafted diazirine end-groups form carbene diradicals upon low energy UVA (365 nm) activation that immediately crosslink tissue surfaces; no pre-heating or animal-derived components are required. The hydrophobic polymeric environment enables metastable functional groups not possible in formulations requiring solvents or water. Activated diazirine within CaproGlu is uniquely capable of crosslinking all amino acids, even on wet tissue substrates. CaproGlu undergoes rapid liquid-to-biorubber transition within seconds of UVA exposure-features not found in any other bioadhesive. The exceptional shelf stability of CaproGlu allows gamma sterilization with no change in material properties. CaproGlu wet adhesiveness is challenged against current unmet clinical needs: anastomosis of spliced blood vessels, anesthetic muscle patches, and human platelet-mediating coatings. The versatility of CaproGlu enables both organic and inorganic composites for future bioadhesive platforms.

A new efficient method of generating photoaffinity beads for drug target identification

Affinity purification is one of the most prevalent methods for the target identification of small molecules. Preparation of an appropriate chemical for immobilization, however, is a tedious and time-consuming process. A decade ago, a photoreaction method for generating affinity beads was reported, where compounds are mixed with agarose beads carrying a photoreactive group (aryldiazirine) and then irradiated with ultraviolet light under dry conditions to form covalent attachment. Although the method has proven useful for identifying drug targets, the beads suffer from inefficient ligand incorporation and tend to shrink and aggregate, which can cause nonspecific binding and low reproducibility. We therefore decided to craft affinity beads free from these shortcomings without compromising the ease of preparation. We herein report a modified method; first, a compound of interest is mixed with a crosslinker having an activated ester and a photoreactive moiety on each end. This mixture is then dried in a glass tube and irradiated with ultraviolet light. Finally, the conjugates are dissolved and reacted with agarose beads with a primary amine. This protocol enabled us to immobilize compounds more efficiently (approximately 500-fold per bead compared to the original method) and generated beads without physical deterioration. We herein demonstrated that the new FK506-immobilized beads specifically isolated more FKBP12 than the original beads, thereby proving our method to be applicable to target identification experiments.

A mild two-step propargylation of aromatic bioactive small molecules

A mild 2-step propargylation strategy for aromatic bioactive small molecules has been developed.

Photo-cross-linked small-molecule affinity matrix as a tool for target identification of bioactive small molecules

This review describes the status of the photo-cross-linked small-molecule affinity matrix while providing a useful tutorial for academic and industrial chemical biologists who are involved or interested in drug target identification.

6-Amidopyrene as a label-assisted laser desorption/ionization (LA-LDI) enhancing tag: development of photoaffinity pyrene derivative

Pyrene-conjugated compounds are detected by label-assisted laser desorption/ionization mass spectrometry (LA-LDI MS) without matrixes. We found that 6-amidopyrene derivatives were highly detectable by the LDI MS instrument equipped with a 355 nm laser. In a certain case of a 6-amidopyrene derivative, a molecular ion peak [M]^+• and a characteristic fragment ion peak [M–42]^+• were detected in an amount of only 10 fmol. The latter peak, corresponding to the 6-aminopyrene fragment, might be generated in situ by the removal of ketene (CH₂=C=O) from the parent molecule. A photoaffinity amidopyrene derivative of an antitumor macrolide aplyronine A (ApA–PaP) was synthesized, which showed potent cytotoxicity and actin-depolymerizing activity. In an LDI MS analysis of the MeOH- and water-adducts of ApA–PaP, oxime N–O bonds as well as amidopyrene N-acetyl moieties were preferentially cleaved, and their internal structures were confirmed by MS/MS analysis. Amidopyrene moiety might enhance fragmentation and stabilize the cleaved fragments by intramolecular or intermolecular weak interactions including hydrogen bonding. Our chemical probe methods might contribute to a detailed analysis of binding modes between various ligands and target biomacromolecules that include multiple and weak interactions.

Third generation photo-cross-linked small-molecule affinity matrix: a photoactivatable and photocleavable system enabling quantitative analysis of the photo-cross-linked small molecules and their target purification

The third generation of photoactivatable beads designed to capture bioactive small molecules in a chemo- and site-nonselective manner upon irradiation at 365 nm of UV light and release them as coumarin conjugates after exposure to UV light of 302 nm is described. These photoactivatable and photocleavable beads enable quantification of the amount and distribution of immobilized small molecules prior to the pull-down experiments to identify target protein(s) for the immobilized small molecules. The newly developed system was then used to analyze the functional group compatibility of the photo-cross-linking technology as well as the preferable nature of small molecules to be immobilized. As a result, compounds having a hydroxyl group, carboxylic acid, or aromatic ring were shown to give multiple conjugates, indicating that these compounds are well compatible with the photoactivatable beads system.

Affinity-based target identification for bioactive small molecules

A variety of new approaches of affinity-based target identification for bioactive small molecules are being developed, facilitating drug development and understanding complicated biological processes.

Photoactivation of (p-methoxyphenyl)(trifluoromethyl)diazirine in the presence of phenolic reaction partners

Shine light on your chemistry! Irradiating 3-(4-methoxyphenyl)-3-(trifluoromethyl)-3H-diazirine in the presence of equimolar solutions of phenol and tyrosine derivatives leads to Friedel-Crafts alkylations (see scheme), which suggests a strategy for the development of "cleaner" diazirines for chemical biology.

Target identification for small bioactive molecules: finding the needle in the haystack

Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.

Covalent cross-linking within supramolecular peptide structures

β-Sheet peptide nanostructures (e.g., amyloid fibrils) are recognized as important entities in biological systems and as functional materials in their own right. Their unique physical properties and architectural complexity, however, present a challenge for structure determination at atomic resolution. Covalent cross-linking and mass spectrometry are appealing methods for this endeavor because, potentially, a large amount of information can be extracted from a small sample in a single experiment. Previously, we described preliminary studies on the use of a photoreactive diazirine-containing amino acid to cross-link peptide monomers in nanostructures, together with the integrated separation and analysis of the products using ion mobility spectrometry coupled to conventional mass spectrometry. Here, a pH-switchable system (Aβ(16-22), a sequence from the amyloid-β peptide) was used to examine cross-linking chemistry in morphologically distinct supramolecular structures containing, or entirely composed of, diazirine-functionalized peptides. We examine the relationship between cross-linker chemistry, covalent cross-links (identified using chemical derivatization and tandem mass spectrometry), and noncovalent structure, and report differences in the site of cross-linking that can only be explained by supramolecular templating. The results demonstrate the applicability of the approach for obtaining structural restraints in ordered supramolecular assemblies, provided that a considered evaluation of the cross-linked products is undertaken.

Preparation of photo-cross-linked small molecule affinity matrices for affinity selection of protein targets for biologically active small molecules

Small molecule-immobilized affinity matrices are indispensable tools in chemical genomics to screen and purify protein targets for biologically active small molecules. Usually, prior to immobilization, small -molecules have to be derivatized at a position that does not significantly abrogate the intrinsic biological activity, or chemically synthesized to have an appropriate functional group for the immobilization chemistry. Here, we describe a photo-cross-linking technique to immobilize biologically active small molecules for protein target screening, without the need for chemical derivatization.

Using the Man(9)(GlcNAc)(2)-DC-SIGN pairing to probe specificity in photochemical immobilization

We demonstrate the expected preference of an immobilised oligosaccharide Man(9)(GlcNAc)(2) upon a 96-well photochemical array, for its known receptor, the cell-surface lectin Dendritic Cell-Specific ICAM3 Grabbing Nonintegrin (DC-SIGN) when compared to immobilised competing monosaccharides.

Construction of photo-cross-linked microarrays of small molecules

Small molecule microarrays are one of the most promising approaches to screen ligand molecules for individual proteins of interest. However, their potential has not been fully realized due to the limited number of methods to introduce small molecules onto the solid surfaces. To expand the compatibility of small molecule microarrays, we have developed a unique photo-cross-linking approach for immobilizing various small molecules, including natural products, on glass slides.

Diazirine-modified gold nanoparticle: template for efficient photoinduced interfacial carbene insertion reactions

Photolysis of a 3-aryl-3-(trifluoromethyl)diazirine-modified monolayer-protected gold nanoparticles (2-C(12)MPNs), with a core size of 1.8 ± 0.3 nm, in the presence of model carbene trapping reagents leads to efficient, essentially quantitative, modification of the interface via carbene insertion reactions. The utility of carbene insertion reactions as a general approach for the modification of Au-MPNs to provide a breadth of new structures available was demonstrated using acetic acid, methanol, benzyl alcohol, phenol, benzylamine, methyl acrylate, and styrene (10a-g, respectively) as electrophilic carbene trapping agents to form the corresponding modified 3a-g-C(12)MPNs. The 1.8 ± 0.3 nm gold nanoparticles bearing a diazirine group (2-C(12)MPNs) were synthesized using the ligand exchange reaction with the requisite 3-aryl-3-(trifluoromethyl)diazirinealkylthiol. The 2-C(12)MPNs and the resulting products of the reaction on the MPN (3a-g-C(12)MPN) were fully characterized by IR, (1)H NMR, and (19)F NMR spectroscopy and, when applicable, transmission electron microscopy (TEM). Verification for the 3a-g-C(12)MPNs was accomplished by comparison of the spectral data to those of obtained for the photoreactions of 3-(3-methoxyphenyl)-3-(trifluoromethyl)-3H-diazirine as a model with 10a-g.

Cleavable linker for photo-cross-linked small-molecule affinity matrix

The introduction of a cleavable site in a photoactivatable linker, which is used to immobilize small molecules on an affinity matrix via a site-nonselective carbene addition/insertion reaction, makes it possible to verify the presence of the immobilized small molecule on the affinity matrix. It also permits the efficient detection of proteins covalently bound to the immobilized small molecule.