Fluorogenic Sydnone-Modified Coumarins Switched-On by Copper-Free Click Chemistry

Bioorthogonal Reactions in Bioimaging

Visualization of biomolecules in their native environment or imaging-aided understanding of more complex biomolecular processes are one of the focus areas of chemical biology research, which requires selective, often site-specific labeling of targets. This challenging task is effectively addressed by bioorthogonal chemistry tools in combination with advanced synthetic biology methods. Today, the smart combination of the elements of the bioorthogonal toolbox allows selective installation of multiple markers to selected targets, enabling multicolor or multimodal imaging of biomolecules. Furthermore, recent developments in bioorthogonally applicable probe design that meet the growing demands of superresolution microscopy enable more complex questions to be addressed. These novel, advanced probes enable highly sensitive, low-background, single- or multiphoton imaging of biological species and events in live organisms at resolutions comparable to the size of the biomolecule of interest. Herein, the latest developments in bioorthogonal fluorescent probe design and labeling schemes will be discussed in the context of in cellulo/in vivo (multicolor and/or superresolved) imaging schemes. The second part focuses on the importance of genetically engineered minimal bioorthogonal tags, with a particular interest in site-specific protein tagging applications to answer biological questions.

An Efficient One-Pot Synthesis of Pyrido[2,3-c]coumarins via Serial Catalysis and Its Application in Concise Formal Synthesis of Santiagonamine

Versatile and high-yielding one-pot synthesis of polysubstituted pyrido[2,3-c]coumarins from N-Boc-N-coumarinyl propargylamine derivatives was achieved via serial catalysis using AgSbF6. Using this approach, the concise formal synthesis of santiagonamine was successfully accomplished. This simple and versatile method could be used to increase the potential of the pyrido[2,3-c]coumarin scaffold for diverse synthetic and biological applications.

Bioorthogonal chemistry: Bridging chemistry, biology, and medicine

As chemical biologists sought methods to modify and study biomolecules in their native environments, the need for bioorthogonal chemical reactions emerged. These fast and selective reactions between otherwise inert, abiotic functional groups have enabled exploration of some of the most intriguing and challenging questions in chemical biology. Further, the ability to perform organic reactions in cells and organisms has led to important applications in clinical spaces, and one reaction is now an integral part of a phase 2 trial for treating solid tumors. Given that bioorthogonal chemistry was a recipient of the 2022 Nobel Prize, we expect this field to be even more energized. Here, we highlight some of the most recent studies in this sphere and how these set the stage for where bioorthogonal chemistry is headed.

Sydnone: Synthesis, Reactivity and Biological Activities

Sydnones are among the most well-known mesoionic compounds. Since their synthesis in 1935 by Earl and Mecknay, numerous researches have shown that the chemical behavior, physical and biological properties of sydnones make them the most useful compounds in organic chemistry. Sydnones undergo thermal 1,3-dipolar cycloaddition reaction with dipolarophiles (alkynes or alkenes) to give exclusively derivatives containing a pyrazole moiety exhibiting numerous applications, such as pharmaceuticals and agrochemicals. However, the sydnone cycloaddition reaction with alkynes requires harsh conditions, like high temperatures and long reaction times, giving poor regioselectivity to the resulting products. To overcome these constraints, new reactions named CuSAC (Copper- Catalyzed Sydnone-Alkyne Cycloaddition) and SPSAC (Strain-Promoted Sydnone- Alkyne Cycloaddition) have been developed, leading to pyrazoles with interesting constant kinetics.

Recent Advances in Organic Synthesis of 3-Amino- or 4-Aminocoumarins

:

Coumarin is a privileged scaffold that contains the unique 2H-chromen-2-one motif, and its derivatives are widely distributed in nature, especially in plants. In recent years, due to their diverse pharmacological activities and remarkable photochemical properties, they have attracted significant attention from scientists, which has also prompted the research on the synthesis approaches and the availability of substrates for these compounds. This article is a brief description of the methods for the synthesis of various coumarin derivatives via two- or multi-component reactions involving 3-amino or 4-aminocoumarin reported during 2015-2021. This review may help expand the development of various analogues with coumarin as the basic unit.

A Clickable Bioorthogonal Sydnone‐Aglycone for the Facile Preparation of a Core 1 O ‐Glycan‐Array

Protein‐O‐glycosylation has been shown to be essential for many biological processes. However, determining the exact relationship between O‐glycan structures and their biological activity remains challenging. Here we report that, unlike azides, sydnones can be incorporated as an aglycon into core 1 O‐glycans early‐on in their synthesis since it is compatible with carbohydrate chemistry and enzymatic glycosylations, allowing us to generate a small library of sydnone‐containing core 1 O‐glycans by chemoenzymatic synthesis. The sydnone‐aglycon was then employed for the facile preparation of an O‐glycan array, via bioorthogonal strain‐promoted sydnone‐alkyne cycloaddition click reaction, and in turn was utilized for the high‐throughput screening of O‐glycan‐lectin interactions. This sydnone‐aglycon, particularly adapted for O‐glycomics, is a valuable chemical tool that complements the limited technologies available for investigating O‐glycan structure‐activity relationships.

Fluorogenic Cyclopropenones for Multicomponent, Real-Time Imaging

Fluorogenic bioorthogonal reactions enable biomolecule visualization in real time. These reactions comprise reporters that "light up" upon reaction with complementary partners. While the spectrum of fluorogenic chemistries is expanding, few transformations are compatible with live cells due to cross-reactivities or insufficient signal turn-on. To address the need for more suitable chemistries for cellular imaging, we developed a fluorogenic reaction featuring cyclopropenone reporters and phosphines. The transformation involves regioselective activation and cyclization of cyclopropenones to form coumarin products. With optimal probes, the reaction provides >1600-fold signal turn-on, one of the highest fluorescence enhancements reported to date. The bioorthogonal motifs were evaluated in vitro and in cells. The reaction was also found to be compatible with other common fluorogenic transformations, enabling multicomponent, real-time imaging. Collectively, these data suggest that the cyclopropenone-phosphine reaction will bolster efforts to track biomolecule targets in their native settings.

Fast and Efficient Postsynthetic DNA Labeling in Cells by Means of Strain-Promoted Sydnone-Alkyne Cycloadditions

Sydnones are highly stable mesoionic 1,3‐dipoles that react with cyclooctynes through strain‐promoted sydnone‐alkyne cycloaddition (SPSAC). Although sydnones have been shown to be valuable bioorthogonal chemical reporters for the labeling of proteins and complex glycans, nucleic acids have not yet been tagged by SPSAC. Evaluation of SPSAC kinetics with model substrates showed fast reactions with cyclooctyne probes (up to k=0.59 M⁻¹ s⁻¹), and two different sydnones were effectively incorporated into both 2’‐deoxyuridines at position 5, and 7‐deaza‐2’‐deoxyadenosines at position 7. These modified nucleosides were synthetically incorporated into single‐stranded DNAs, which were successfully postsynthetically labeled with cyclooctyne probes both in vitro and in cells. These results show that sydnones are versatile bioorthogonal tags and have the premise to become essential tools for tracking DNA and potentially RNA in living cells.

Impacting Bacterial Sialidase Activity by Incorporating Bioorthogonal Chemical Reporters onto Mammalian Cell-Surface Sialosides

Bioorthogonal chemical reporters, in synergy with click chemistry, have emerged as a key technology for tagging complex glycans in living cells. This strategy relies on the fact that bioorthogonal chemical reporters are highly reactive species while being biologically noninvasive. Here, we report that chemical reporters and especially sydnones may have, on the contrary, enormous impact on biomolecule processing enzymes. More specifically, we show that editing cell-surface sialic acid-containing glycans (sialosides) with bioorthogonal chemical reporters can significantly affect the activity of bacterial sialidases, enzymes expressed by bacteria during pathogenesis for cleaving sialic acid sugars from mammalian cell-surface glycans. Upon screening various chemical reporters, as well as their position on the sialic acid residue, we identified that pathogenic bacterial sialidases were unable to cleave sialosides displaying a sydnone at the 5-position of sialic acids in vitro as well as in living cells. This study highlights the importance of investigating more systematically the metabolic fate of glycoconjugates modified with bioorthogonal reporters.

A Dansyl Amide N-Oxide Fluorogenic Probe Based on a Bioorthogonal Decaging Reaction

A smart fluorescence "turn-on" probe which contained a dansyl amide fluorophore and an N-oxide group was designed based on the bioorthogonal decaging reaction between N-oxide and the boron reagent. The reaction proceeds in a rapid kinetics (k2 =57.1±2.5 m-1  s-1 ), and the resulting reduction product showcases prominent fluorescence enhancement (up to 72-fold). Time dependent density functional theoretical (TD-DFT) calculation revealed that the process of photoinduced electron transfer (PET) from the N-oxide moiety to the dansyl amide fluorophore accounts for the quenching mechanism of N-oxide. This probe also showed high selectivity over various nucleophilic amino acids and good biocompatibility in physiological conditions. The successful application of the probe in HaloTag protein labeling and HepG2 live-cell imaging proves it a valuable tool for visualization of biomolecules.

Sydnone Methides-A Forgotten Class of Mesoionic Compounds for the Generation of Anionic N-Heterocyclic Carbenes

Sydnone methides are described from which only one single example has been mentioned in the literature so far. Their deprotonation gave anions which can be formulated as π-electron rich anionic N-heterocyclic carbenes. Sulfur and selenium adducts were stabilized as their methyl ethers, and mercury, gold as well as rhodium complexes of the sydnone methide carbenes were prepared. Sydnone methide anions also undergo C-C coupling reactions with 1-fluoro-4-iodobenzene under Pd(PPh3 )4 and CuBr catalysis. 77 Se NMR resonance frequencies and 1 JC4-Se as well as 1 JC4-H coupling constants have been determined to gain knowledge about the electronic properties of the anionic N-heterocyclic carbenes. The carbene carbon atom of the sydnone methide anion 3 j resonates at δ=155.2 ppm in 13 C NMR spectroscopy at -40 °C which is extremely shifted upfield in comparison to classical N-heterocyclic carbenes.

Photoclick Chemistry: A Bright Idea

At its basic conceptualization, photoclick chemistry embodies a collection of click reactions that are performed via the application of light. The emergence of this concept has had diverse impact over a broad range of chemical and biological research due to the spatiotemporal control, high selectivity, and excellent product yields afforded by the combination of light and click chemistry. While the reactions designated as "photoclick" have many important features in common, each has its own particular combination of advantages and shortcomings. A more extensive realization of the potential of this chemistry requires a broader understanding of the physical and chemical characteristics of the specific reactions. This review discusses the features of the most frequently employed photoclick reactions reported in the literature: photomediated azide-alkyne cycloadditions, other 1,3-dipolarcycloadditions, Diels-Alder and inverse electron demand Diels-Alder additions, radical alternating addition chain transfer additions, and nucleophilic additions. Applications of these reactions in a variety of chemical syntheses, materials chemistry, and biological contexts are surveyed, with particular attention paid to the respective strengths and limitations of each reaction and how that reaction benefits from its combination with light. Finally, challenges to broader employment of these reactions are discussed, along with strategies and opportunities to mitigate such obstacles.

Click and Bio-Orthogonal Reactions with Mesoionic Compounds

Click and bio-orthogonal reactions are dominated by cycloaddition reactions in general and 1,3-dipolar cycloadditions in particular. Among the dipoles routinely used for click chemistry, azides, nitrones, isonitriles, and nitrile oxides are the most popular. This review is focused on the emerging click chemistry that uses mesoionic compounds as dipole partners. Mesoionics are a very old family of molecules, but their use as reactants for click and bio-orthogonal chemistry is quite recent. The facility to derivatize these dipoles and to tune their reactivity toward cycloaddition reactions makes mesoionics an attractive opportunity for future click chemistry development. In addition, some compounds from this family are able to undergo click-and-release reactions, finding interesting applications in cells, as well as in animals. This review covers the synthetic access to main mesoionics, their reaction with dipolarophiles, and recent applications in chemical biology and heterocycle synthesis.

To View Your Biomolecule, Click inside the Cell

The surging development of bioorthogonal chemistry has profoundly transformed chemical biology over the last two decades. Involving chemical partners that specifically react together in highly complex biological fluids, this branch of chemistry now allows researchers to probe biomolecules in their natural habitat through metabolic labelling technologies. Chemical reporter strategies include metabolic glycan labelling, site-specific incorporation of unnatural amino acids in proteins, and post-synthetic labelling of nucleic acids. While a majority of literature reports mark cell-surface exposed targets, implementing bioorthogonal ligations in the interior of cells constitutes a more challenging task. Owing to limiting factors such as membrane permeability of reagents, fluorescence background due to hydrophobic interactions and off-target covalent binding, and suboptimal balance between reactivity and stability of the designed molecular reporters and probes, these strategies need mindful planning to achieve success. In this review, we discuss the hurdles encountered when targeting biomolecules localized in cell organelles and give an easily accessible summary of the strategies at hand for imaging intracellular targets.

Design of Nitroso-Modified Naphthylene-Based Fluorophores as Photoactivatable Bioorthogonal Turn-On Probes

We reported a series of nitroso-modified naphthylene-based fluorophores as novel bioorthogonal fluorescence turn-on probes. The cycloadducts from nitroso-diene Diels-Alder reaction could be either photochemically or spontaneously transformed into highly fluorescent rearrangement products with remarkable photophysical properties including significant fluorescence enhancement, large Stokes shift, high fluorescence quantum yield, superior photostability, and distinct solvatochromic effect. This strategy is suitable for selective labeling of diene-modified proteins and visualizing specific organelles in live mammalian cells under no-wash conditions.

Selective strain-promoted azide-alkyne cycloadditions through transient protection of bicyclo[6.1.0]nonynes with silver or gold

Complexation of bicyclo[6.1.0]nonynes with a cationic silver or gold salt results in protection from a click reaction with azides. The cycloalkyne protection using the silver or gold salt enables selective strain-promoted azide-alkyne cycloadditions of diynes keeping the bicyclo[6.1.0]nonyne moiety unreacted.

Core remodeling leads to long wavelength fluoro-coumarins

Low molecular weight, uncharged far-red and NIR dyes would be enabling for a range of imaging applications. Rational redesign of the coumarin scaffold leads to Fluoro-Coumarins (FCs), the lowest molecular weight dyes with emission maxima beyond 700, 800, and 900 nm. FCs display large Stokes shifts and high environmental sensitivity, with a 40-fold increase in emission intensity in hydrophobic solvents. Untargeted variants exhibit selective lipid droplet and nuclear staining in live cells. Furthermore, sulfo-lipid derivatization enables active targeting to the plasma membrane. Overall, these studies report a promising platform for the development of biocompatible, context-responsive imaging agents.

Fluoro-Coumarins are a novel class of far-red and near-infrared solvent sensitive dyes of exceptionally low molecular weight.

Fluorogenic iminosydnones: bioorthogonal tools for double turn-on click-and-release reactions

Iminosydnones are able to quench two fluorophores when connected to their core structure. Bioorthogonal click and release reaction with cyclooctynes provokes significant fluorescence enhancement of the two products, allowing their tracking in cells.

Selective Engineering of Linkage-Specific α2,6-N-Linked Sialoproteins Using Sydnone-Modified Sialic Acid Bioorthogonal Reporters

The metabolic oligosaccharide engineering (MOE) strategy using unnatural sialic acids has recently enabled the visualization of the sialome in living systems. However, MOE only reports on global sialylation and dissected information regarding subsets of sialosides is missing. Described here is the synthesis and utilization of sialic acids modified with a sydnone reporter for the metabolic labeling of sialoconjugates. The positioning of the reporter on the sugar significantly altered its metabolic fate. Further in vitro enzymatic assays revealed that the 9-modified neuraminic acid is preferentially accepted by the sialyltransferase ST6Gal-I over ST3Gal-IV, leading to the favored incorporation of the reporter into linkage-specific α2,6-N-linked sialoproteins. This sydnone sugar presents the possibility of investigating the roles of specific sialosides.

Development of 4-oxime-1,8-naphthalimide as a bioorthogonal turn-on probe for fluorogenic protein labeling

We report 4-oxime-1,8-naphthalimide as a novel bioorthogonal turn-on probe based on cascade 1,3-dipolar cycloaddition and photoisomerization for fluorogenic protein labeling.

Sydnone-based turn-on fluorogenic probes for no-wash protein labeling and in-cell imaging

Fluorogenic sydnone-based turn-on probes allow efficient labeling of proteins and cell imaging through a bioorthogonal strained promoted sydnone–alkyne cycloaddition reaction.

A strained alkyne-containing bipyridine reagent; synthesis, reactivity and fluorescence properties

We report the synthesis of a bipyridyl reagent containing a strained alkyne, which significantly restricts its flexibility. Upon strain-promoted alkyne-azide cycloaddition (SPAAC) with an azide, which does not require a Cu catalyst, the structure becomes significantly more flexible and an increase in fluorescence is observed. Upon addition of Zn(ii), the fluorescence is enhanced further. The reagent has the potential to act as a fluorescent labelling agent with azide-containing substrates, including biological molecules.

A bipyridyl reagent containing a strained alkyne 7, reacts with benzyl azide to give a significantly more flexible product 10 and an increase in fluorescence is observed. Upon addition of Zn(ii), the fluorescence is enhanced further.

A fluorogenic C4N4 probe for azide-based labelling

A new fluorogenic probe based on the recently identified 2,5-diaminopyrimidine (C4N4) fluorophore is introduced for azide-specific labelling.

Synthesis and evaluation of photo-activatable β-diarylsydnone-l-alanines for fluorogenic photo-click cyclization of peptides

β-Diarylsydnone-l-alanines were designed and introduced into peptides allowing photo-cyclization only in phosphate containing buffer with concomitant fluorescence generation in live cells.

Sydnone-coumarins as clickable turn-on fluorescent sensors for molecular imaging

Sydnone-coumarin compounds are interesting turn-on fluorogenic probes for protein labeling.