Simple and Versatile Method for Tagging Phenyldiazirine Photophores

Trace Hydrogen Sulfide Sensing Inspired by Polyoxometalate-Mediated Aerobic Oxidation

A high-performance chemiresistive gas sensor is described for the detection of hydrogen sulfide (H₂S), an acutely toxic and corrosive gas. The chemiresistor operates at room temperature with low power requirements potentially suitable for wearable sensors or for rapid in-field detection of H₂S in settings such as pipelines and wastewater treatment plants. Specifically, we report chemiresistors based on single-walled carbon nanotubes (SWCNTs) containing highly oxidizing platinum-polyoxometalate (Pt-POM) selectors. We show that by tuning the vanadium content and thereby the oxidation reactivity of the constituent POMs, an efficient chemiresistive sensor is obtained that is proposed to operate by modulating CNT doping during aerobic H₂S oxidation. The sensor shows exceptional sensitivity to trace H₂S in air with a ppb-level detection limit, multimonth stability under ambient conditions, and high selectivity for H₂S over a wide range of interferants, including thiols, thioethers, and thiophene. Finally, we demonstrate that the robust sensing material can be used to fabricate flexible devices by covalently immobilizing the SWCNT-P4VP network onto a polyimide substrate, further extending the potentially broad utility of the chemiresistors. The strategy presented herein highlights the applicability of concepts in molecular aerobic oxidation catalysis to the development of low-cost analyte detection technologies.

Structure-function relationships in aryl diazirines reveal optimal design features to maximize C-H insertion

Diazirine reagents allow for the ready generation of carbenes upon photochemical, thermal, or electrical stimulation. Because carbenes formed in this way can undergo rapid insertion into any nearby C-H, O-H or N-H bond, molecules that encode diazirine functions have emerged as privileged tools in applications ranging from biological target identification and proteomics through to polymer crosslinking and adhesion. Here we use a combination of experimental and computational methods to complete the first comprehensive survey of diazirine structure-function relationships, with a particular focus on thermal activation methods. We reveal a striking ability to vary the activation energy and activation temperature of aryl diazirines through the rational manipulation of electronic properties. Significantly, we show that electron-rich diazirines have greatly enhanced efficacy toward C-H insertion, under both thermal and photochemical activation conditions. We expect these results to lead to significant improvements in diazirine-based chemical probes and polymer crosslinkers.

Thermally-induced hyperbranching of bromine-containing polyesters by insertion of in situ generated chain-end carbenes

Hyperbranched, biodegradable PCL-based polymers are obtained through a random but invasive migration of an in situ generated carbene end group which is unmasked via the thermolysis of its precursor diazirine moiety. These hyperbranched cores are used as macroinitiators for 'grafting-from' polymerisation using controlled radical polymerisation to achieve amphiphilic copolymers which can subsequently be self-assembled into spherical core-shell micelles.

Recent progress in the use of diaziridine-based sweetener derivatives to elucidate the chemoreception mechanism of the sweet taste receptor

The review summarized recent progress for the elucidation of the chemoreception mechanism of sweet taste receptor–sweetener interactions with photoaffinity labeling.

Engineering bromodomains with a photoactive amino acid by engaging 'Privileged' tRNA synthetases

Site-specific placement of unnatural amino acids, particularly those responsive to light, offers an elegant approach to control protein function and capture their fleeting 'interactome'. Herein, we have resurrected 4-(trifluoromethyldiazirinyl)-phenylalanine, an underutilized photo-crosslinker, by introducing several key features including easy synthetic access, site-specific incorporation by 'privileged' synthetases and superior crosslinking efficiency, to develop photo-crosslinkable bromodomains suitable for 'interactome' profiling.

Understanding Cell Penetration of Cyclic Peptides

Approximately 75% of all disease-relevant human proteins, including those involved in intracellular protein-protein interactions (PPIs), are undruggable with the current drug modalities (i.e., small molecules and biologics). Macrocyclic peptides provide a potential solution to these undruggable targets because their larger sizes (relative to conventional small molecules) endow them the capability of binding to flat PPI interfaces with antibody-like affinity and specificity. Powerful combinatorial library technologies have been developed to routinely identify cyclic peptides as potent, specific inhibitors against proteins including PPI targets. However, with the exception of a very small set of sequences, the vast majority of cyclic peptides are impermeable to the cell membrane, preventing their application against intracellular targets. This Review examines common structural features that render most cyclic peptides membrane impermeable, as well as the unique features that allow the minority of sequences to enter the cell interior by passive diffusion, endocytosis/endosomal escape, or other mechanisms. We also present the current state of knowledge about the molecular mechanisms of cell penetration, the various strategies for designing cell-permeable, biologically active cyclic peptides against intracellular targets, and the assay methods available to quantify their cell-permeability.

Current advances of carbene-mediated photoaffinity labeling in medicinal chemistry

Photoaffinity labeling (PAL) in combination with a chemical probe to covalently bind its target upon UV irradiation has demonstrated considerable promise in drug discovery for identifying new drug targets and binding sites. In particular, carbene-mediated photoaffinity labeling (cmPAL) has been widely used in drug target identification owing to its excellent photolabeling efficiency, minimal steric interference and longer excitation wavelength. Specifically, diazirines, which are among the precursors of carbenes and have higher carbene yields and greater chemical stability than diazo compounds, have proved to be valuable photolabile reagents in a diverse range of biological systems. This review highlights current advances of cmPAL in medicinal chemistry, with a focus on structures and applications for identifying small molecule-protein and macromolecule-protein interactions and ligand-gated ion channels, coupled with advances in the discovery of targets and inhibitors using carbene precursor-based biological probes developed in recent decades.

Fishing for Drug Targets: A Focus on Diazirine Photoaffinity Probe Synthesis

Target identification is a high-priority, albeit challenging, aspect of drug discovery. Diazirine-based photoaffinity probes (PAPs) can facilitate the process by covalently capturing transient molecular interactions. This can help identify target proteins and map the ligand's interactome. Diazirine probes have even been incorporated by cellular machinery into proteins. Embarking on the synthesis of customized PAPs, containing either an aliphatic or trifluoromethyl phenyl diazirine, can be a considerable endeavor, particularly for medicinal chemists and chemical biologists new to the field. This review takes a synthetic focus, aiming to summarize available routes, propose new avenues, and illuminate recent advances in diazirine synthesis. Select examples of diazirine photoaffinity labeling applications have been included throughout to provide instructive definition of the advantages and limitations of the technology while simultaneously highlighting how these reagents can be applied in a practical sense.

Dehydrogenation of the NH-NH Bond Triggered by Potassium tert-Butoxide in Liquid Ammonia

A novel strategy for the dehydrogenation of the NH-NH bond is disclosed using potassium tert-butoxide (tBuOK) in liquid ammonia (NH₃ ) under air at room temperature. Its synthetic value is well demonstrated by the highly efficient synthesis of aromatic azo compounds (up to 100 % yield, 3 min), heterocyclic azo compounds, and dehydrazination of phenylhydrazine. The broad application of this strategy and its benefit to chemical biology is proved by a novel, convenient, one-pot synthesis of aliphatic diazirines, which are important photoreactive agents for photoaffinity labeling.

Cosolvent-Promoted O-Benzylation with Silver(I) Oxide: Synthesis of 1'-Benzylated Sucrose Derivatives, Mechanistic Studies, and Scope Investigation

A cosolvent-promoted O-benzylation strategy with Ag2O was developed. The cosolvent consisting of CH2Cl2 and n-hexane can not only improve the reaction solubility for carbohydrates but also increase the benzylation efficiency. The formation of byproducts is greatly inhibited in the developed method. This method is simple, mild, and highly effective, and numerous 1'-benzylated sucrose derivatives were prepared including a photoreactive (trifluoromethyl)phenyldiazirine-based sucrose. The mechanisms of benzylation with primary and secondary benzyl bromides were also elaborated. Furthermore, the application scope with alcohols, glucose, and ribose derivatives was investigated.

Syndecan-4 Is a Receptor for Clathrin-Mediated Endocytosis of Arginine-Rich Cell-Penetrating Peptides

Arginine-rich cell-penetrating peptides (CPPs) such as Tat and oligoarginine peptides have been widely used as carriers for intracellular delivery of bioactive molecules. Despite accumulating evidence for involvement of endocytosis in the cellular uptake of arginine-rich CPPs, the primary cell-surface receptors for these peptide carriers that would initiate endocytic processes leading to intracellular delivery of bioactive cargoes have remained poorly understood. Our previous attempt to identify membrane receptors for octa-arginine (R8) peptide, one of the representative arginine-rich CPPs, using the photo-cross-linking probe bearing a photoreactive diazirine was not successful due to considerable amounts of cellular proteins nonspecifically bound to the affinity beads. To address this issue, here we developed a photo-cross-linking probe in which a cleavable linker of a diazobenzene moiety was employed to allow selective elution of cross-linked proteins by reducing agent-mediated cleavage. We demonstrated that introduction of the diazobenzene moiety into the photoaffinity probe enables efficient purification of cross-linked proteins with significant reduction of nonspecific binding proteins, leading to successful identification of 17 membrane-associated proteins that would interact with R8 peptide. RNAi-mediated knockdown experiments in combination with the pharmacological inhibitors revealed that, among the proteins identified, syndecan-4, one of the heparan sulfate proteoglycans, is an endogenous membrane-associated receptor for the cellular uptake of R8 peptide via clathrin-mediated endocytosis. This syndecan-4-dependent pathway was also involved in the intracellular delivery of bioactive proteins mediated by R8 peptide. These results reveal that syndecan-4 is a primary cell-surface target for R8 peptide that allows intracellular delivery of bioactive cargo molecules via clathrin-mediated endocytosis.

HIV-1 drug discovery: targeting folded RNA structures with branched peptides

Human immunodeficiency virus type 1 (HIV-1) is an RNA virus that is prone to high rates of mutation. While the disease is managed with current antiretroviral therapies, drugs with a new mode of action are needed. A strategy towards this goal is aimed at targeting the native three-dimensional fold of conserved RNA structures. This perspective highlights medium-sized peptides and peptidomimetics used to target two conserved RNA structures of HIV-1. In particular, branched peptides have the capacity to bind in a multivalent fashion, utilizing a large surface area to achieve the necessary affinity and selectivity toward the target RNA.

Alternative one-pot synthesis of (trifluoromethyl)phenyldiazirines from tosyloxime derivatives: application for new synthesis of optically pure diazirinylphenylalanines for photoaffinity labeling

Alternative one-pot synthesis of 3-(trifluoromethyl)-3-phenyldiazirine derivatives from corresponding tosyloximes is developed. The deprotonation of intermediate diaziridine by NH2(-) is a new approach for construction of diazirine. Moreover, a novel synthesis of optically pure (trifluoromethyl)diazirinylphenylalanine derivatives was attempted involving these methods.

Utilization of acidic α-amino acids as acyl donors: an effective stereo-controllable synthesis of aryl-keto α-amino acids and their derivatives

Aryl-keto-containing α-amino acids are of great importance in organic chemistry and biochemistry. They are valuable intermediates for the construction of hydroxyl α-amino acids, nonproteinogenic α-amino acids, as well as other biofunctional components. Friedel-Crafts acylation is an effective method to prepare aryl-keto derivatives. In this review, we summarize the preparation of aryl-keto containing α-amino acids by Friedel-Crafts acylation using acidic α-amino acids as acyl-donors and Lewis acids or Brönsted acids as catalysts.

Analysis of amyloid nanostructures using photo-cross-linking: in situ comparison of three widely used photo-cross-linkers

Photoinduced cross-linking (PIC) has become a powerful tool in chemical biology for the identification and mapping of stable or transient interactions between biomacromolecules and their (unknown) ligands. However, the value of PIC for in vitro and in vivo structural proteomics can be realized only if cross-linking reports accurately on biomacromolecule secondary, tertiary, and quaternary structures with residue-specific resolution. Progress in this area requires rigorous and comparative studies of PIC reagents, but despite widespread use of PIC, these have rarely been performed. The use of PIC to report reliably on noncovalent structure is therefore limited, and its potentials have yet to be fully realized. In the present study, we compared the abilities of three probes, phenyl trifluoromethyldiazirine (TFMD), benzophenone (BP), and phenylazide (PA), to record structural information within a biomolecular complex. For this purpose, we employed a self-assembled amyloid-like peptide nanostructure as a tightly and specifically packed model environment in which to photolyze the reagents. Information about PIC products was gathered using mass spectrometry and ion mobility spectrometry, and the data were interpreted using a mechanism-oriented approach. While all three PIC groups appeared to generate information within the packed peptide environment, the data highlight technical limitations of BP and PA. On the other hand, TFMD displayed accuracy and generated straightforward results. Thus TFMD, with its robust and rapid photochemistry, was shown to be an ideal probe for cross-linking of peptide nanostructures. The implications of our findings for detailed analyses of complex systems, including those that are transiently populated, are discussed.

The synthesis and application of a diazirine-modified uridine analogue for investigating RNA–protein interactions

A uridine analogue equipped with a photoactive diazirine unit was generated and incorporated into RNA either syntheticallyviaphosphoramidite chemistry or by enzymatic polymerization. The new analogue was developed to identify and investigate RNA–protein interactions.

Novel microarrays for simultaneous serodiagnosis of multiple antiviral antibodies

We developed an automated diagnostic system for the detection of virus-specific immunoglobulin Gs (IgGs) that was based on a microarray platform. We compared efficacies of our automated system with conventional enzyme immunoassays (EIAs). Viruses were immobilized to microarrays using a radical cross-linking reaction that was induced by photo-irradiation. A new photoreactive polymer containing perfluorophenyl azide (PFPA) and poly(ethylene glycol) methacrylate was prepared and coated on plates. Inactivated measles, rubella, mumps, Varicella-Zoster and recombinant Epstein-Barr viruse antigen were added to coated plates, and irradiated with ultraviolet light to facilitate immobilization. Virus-specific IgGs in healthy human sera were assayed using these prepared microarrays and the results obtained compared with those from conventional EIAs. We observed high correlation (0.79-0.96) in the results between the automated microarray technique and EIAs. The microarray-based assay was more rapid, involved less reagents and sample, and was easier to conduct compared with conventional EIA techniques. The automated microarray system was further improved by introducing reagent storage reservoirs inside the chamber, thereby conserving the use of expensive reagents and antibodies. We considered the microarray format to be suitable for rapid and multiple serological diagnoses of viral diseases that could be developed further for clinical applications.

Distinct metabolites for photoreactive L-phenylalanine derivatives in Klebsiella sp. CK6 isolated from rhizosphere of a wild dipterocarp sapling

Photoaffinity labeling is a reliable analytical method for biological functional analysis. Three major photophores—aryl azide, benzophenone and trifluoromethyldiazirine—are utilized in analysis. Photophore-bearing l-phenylalanine derivatives, which are used for biological functional analysis, were inoculated into a Klebsiella sp. isolated from the rhizosphere of a wild dipterocarp sapling in Central Kalimantan, Indonesia, under nitrogen-limiting conditions. The proportions of metabolites were quite distinct for each photophore. These results indicated that photophores affected substrate recognition in rhizobacterial metabolic pathways, and differential photoaffinity labeling could be achieved using different photophore-containing l-phenylalanine derivatives.

Diazirine based photoaffinity labeling

Diazirines are among the smallest photoreactive groups that form a reactive carbene upon light irradiation. This feature has been widely utilized in photoaffinity labeling to study ligand-receptor, ligand-enzyme and protein-protein interactions, and in the isolation and identification of unknown proteins. This review summarizes recent advances in the use of diazirines in photoaffinity labeling.

Rapidly photoactivatable ATP probes for specific labeling of tropomyosin within the actomyosin protein complex

Tropomyosin-specific photoaffinity adenosine triphosphate (ATP) probes have been first developed, in which a diazirine moiety is incorporated into the γ-phosphate group as a rapidly carbene-generating photophore. These probes clearly labeled tropomyosin in the presence of other actomyosin components, that is, myosin, actin, and troponins. The specific labeling of tropomyosin was easily identified by selective trapping of the photo-incorporated ATP probe on Fe(3+)-immobilized metal ion affinity chromatography (IMAC) beads. The characteristic nature of tropomyosin-specific photocross-linking was further confirmed with a biotin-carrying derivative of the ATP probe. These data suggest that the tropomyosin on the actin filament assembly is located in close proximity to the ATP binding cavity of myosin.

Perfluorophenyl azides: new applications in surface functionalization and nanomaterial synthesis

A major challenge in materials science is the ongoing search for coupling agents that are readily synthesized, capable of versatile chemistry, able to easily functionalize materials and surfaces, and efficient in covalently linking organic and inorganic entities. A decade ago, we began a research program investigating perfluorophenylazides (PFPA) as the coupling agents in surface functionalization and nanomaterial synthesis. The p-substituted PFPAs are attractive heterobifunctional coupling agents because of their two distinct and synthetically distinguishable reactive centers: (i) the fluorinated phenylazide, which is capable of forming stable covalent adducts, and (ii) the functional group R, which can be tailored through synthesis. Two approaches have been undertaken for material synthesis and surface functionalization. The first method involves synthesizing PFPA bearing the first molecule or material with a functional linker R and then attaching the resulting PFPA to the second material by activating the azido group. In the second approach, the material surface is first functionalized with PFPA via functional center R, and coupling of the second molecule or material is achieved with the surface azido groups. In this Account, we review the design and protocols of the two approaches, providing examples in which PFPA derivatives were successfully used in material surface functionalization, ligand conjugation, and the synthesis of hybrid nanomaterials. The methods developed have proved to be general and versatile, and they are applicable to a wide range of materials (especially those that lack reactive functional groups or are difficult to derivatize) and to various substrates of polymers, oxides, carbon materials, and metal films. The coupling chemistry can be initiated by light, heat, and electrons. Patterned structures can be generated by selectively activating the areas of interest. Furthermore, the process is easy to perform, and light activation occurs in minutes, greatly facilitating the efficiency of the reaction. PFPAs indeed demonstrate many benefits as versatile surface coupling agents and offer opportunities for further exploration.

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.

Identification of a substrate-binding site in a peroxisomal beta-oxidation enzyme by photoaffinity labeling with a novel palmitoyl derivative

Peroxisomes play an essential role in a number of important metabolic pathways including beta-oxidation of fatty acids and their derivatives. Therefore, peroxisomes possess various beta-oxidation enzymes and specialized fatty acid transport systems. However, the molecular mechanisms of these proteins, especially in terms of substrate binding, are still unknown. In this study, to identify the substrate-binding sites of these proteins, we synthesized a photoreactive palmitic acid analogue bearing a diazirine moiety as a photophore, and performed photoaffinity labeling of purified rat liver peroxisomes. As a result, an 80-kDa peroxisomal protein was specifically labeled by the photoaffinity ligand, and the labeling efficiency competitively decreased in the presence of palmitoyl-CoA. Mass spectrometric analysis identified the 80-kDa protein as peroxisomal multifunctional enzyme type 2 (MFE2), one of the peroxisomal beta-oxidation enzymes. Recombinant rat MFE2 was also labeled by the photoaffinity ligand, and mass spectrometric analysis revealed that a fragment of rat MFE2 (residues Trp(249) to Arg(251)) was labeled by the ligand. MFE2 mutants bearing these residues, MFE2(W249A) and MFE2(R251A), exhibited decreased labeling efficiency. Furthermore, MFE2(W249G), which corresponds to one of the disease-causing mutations in human MFE2, also exhibited a decreased efficiency. Based on the crystal structure of rat MFE2, these residues are located on the top of a hydrophobic cavity leading to an active site of MFE2. These data suggest that MFE2 anchors its substrate around the region from Trp(249) to Arg(251) and positions the substrate along the hydrophobic cavity in the proper direction toward the catalytic center.

Synthesis and evaluation of photoreactive tetrazole amino acids

Six photoreactive tetrazole amino acids were efficiently synthesized either by the de novo Kakehi tetrazole synthesis method or by alkylation of a glycine Schiff base with tetrazole-containing alkyl halides, and four of them showed excellent reactivity toward a simple alkene in the photoinduced 1,3-dipolar cycloaddition reaction in acetonitrile/PBS buffer (1:1) mixture.

Photocrosslinking of RNA and photoMet-containing amphiphilic alpha-helical peptides

Discovering RNA-protein interactions: A library of photoMet-containing peptides was synthesized by using an Arg- and Leu-rich alpha-helical amphiphilic peptide. Irradiation of mixtures of these peptides and Rev-responsive element (RRE) hairpin RNA promoted formation of covalent adducts. Analysis of one adduct showed that U26 in the bulged stem is responsible for covalent bond formation with the carbene intermediate. This strategy can provide important structural information about RNA-peptide interactions.