Direct ring-strain loading for visible-light accelerated bioorthogonal ligation via diarylsydnone-dibenzo[b,f ][1,4,5]thiadiazepine photo-click reactions

Photo-activatable Reagents for Bioorthogonal Ligation Reactions

Light-induced bioorthogonal reactions offer spatiotemporal control over selective biomolecular labeling. This review covers the recent advances in the design of photo-activatable reagents for bioorthogonal conjugation reactions in living systems. These reagents are stable in the absence of light, but transformed into reactive species upon light illumination, which then undergo rapid ligation reactions. The light wavelength has been tuned from ultraviolet to near infrared to enable efficient photo-activation in reactions in deep tissues. The most prominent photo-activatable reagents are presented, including tetrazoles, tetrazines, 9,10-phenanthrenequinone, diarylsydnones, and others. A particular focus is on the strategies for improving reaction kinetics and biocompatibility accomplished through careful molecular engineering. The utilities of these photo-activatable reagents are illustrated through a broad range of biological applications, including in vivo protein labeling, positron emission tomography (PET) imaging, responsive hydrogels, and fluorescence microscopy. The further development and optimization of these biocompatible photo-activatable reagents should lead to new chemical biology strategies for studying biomolecular structure and function in living systems.

Photoswitchable and long-lived seven-membered cyclic singlet diradicals for the bioorthogonal photoclick reaction

Annularly 1,3-localized singlet diradicals are energetic and homolytic intermediates, but commonly too short-lived for widespread utilization. Herein, we describe a direct observation of a long-lived and seven-membered singlet diradical, oxepine-3,6-dione-2,7-diyl (OXPID), via spectroscopic experiments and also theoretical evidence from computational studies, which is generated via photo-induced ring-expansion of 2,3-diaryl-1,4-naphthoquinone epoxide (DNQO). The photo-generated OXPID reverts to the thermally stable σ-bonded DNQO with t1/2 in the μs level, thus constituting a novel class of T-type molecular photoswitches with high light-energy conversion efficiency (η = 7.8-33%). Meanwhile, the OXPID is equilibrated to a seven-membered cyclic 1,3-dipole as an electronic tautomer that can be captured by ring-strained dipolarophiles with an ultrafast cycloaddition rate (k2CA up to 109 M-1 s-1). The T-type photoswitchable DNQO is then exploited to be a highly selective and recyclable photoclick reagent, enabling spatiotemporal-resolved bioorthogonal ligation on living cell membranes via a tailored DNQO-Cy3 probe.

Establishing PQ-ERA photoclick reactions with unprecedented efficiency by engineering of the nature of the phenanthraquinone triplet state

The light-induced photocycloaddition of 9,10-phenanthrenequinone (PQ) with electron-rich alkenes (ERA), known as the PQ-ERA reaction, is a highly attractive photoclick reaction characterized by high selectivity, external non-invasive control with light and biocompatibility. The conventionally used PQ compounds show limited reactivity, which hinders the overall efficiency of the PQ-ERA reaction. To address this issue, we present in this study a simple strategy to boost the reactivity of the PQ triplet state to further enhance the efficiency of the PQ-ERA reaction, enabled by thiophene substitution at the 3-position of the PQ scaffold. Our investigations show that this substitution pattern significantly increases the population of the reactive triplet state (³ππ*) during excitation of 3-thiophene PQs. This results in a superb photoreaction quantum yield (Φ_P, up to 98%), high second order rate constants (k₂, up to 1974 M^-1 s^-1), and notable oxygen tolerance for the PQ-ERA reaction system. These results have been supported by both experimental transient absorption data and theoretical calculations, providing further evidence for the effectiveness of this strategy, and offering fine prospects for fast and efficient photoclick transformations.

Ligand-Directed Photocatalysts and Far-Red Light Enable Catalytic Bioorthogonal Uncaging inside Live Cells

Described are ligand-directed catalysts for live-cell, photocatalytic activation of bioorthogonal chemistry. Catalytic groups are localized via a tethered ligand either to DNA or to tubulin, and red light (660 nm) photocatalysis is used to initiate a cascade of DHTz oxidation, intramolecular Diels-Alder reaction, and elimination to release phenolic compounds. Silarhodamine (SiR) dyes, more conventionally used as biological fluorophores, serve as photocatalysts that have high cytocompatibility and produce minimal singlet oxygen. Commercially available conjugates of Hoechst dye (SiR-H) and docetaxel (SiR-T) are used to localize SiR to the nucleus and microtubules, respectively. Computation was used to assist the design of a new class of redox-activated photocage to release either phenol or n-CA4, a microtubule-destabilizing agent. In model studies, uncaging is complete within 5 min using only 2 μM SiR and 40 μM photocage. In situ spectroscopic studies support a mechanism involving rapid intramolecular Diels-Alder reaction and a rate-determining elimination step. In cellular studies, this uncaging process is successful at low concentrations of both the photocage (25 nM) and the SiR-H dye (500 nM). Uncaging n-CA4 causes microtubule depolymerization and an accompanying reduction in cell area. Control studies demonstrate that SiR-H catalyzes uncaging inside the cell, and not in the extracellular environment. With SiR-T, the same dye serves as a photocatalyst and the fluorescent reporter for microtubule depolymerization, and with confocal microscopy, it was possible to visualize microtubule depolymerization in real time as the result of photocatalytic uncaging in live cells.

Photoswitchable Oxidopyrylium Ylide for Photoclick Reaction with High Spatiotemporal Precision: A Dynamic Switching Strategy to Compensate for Molecular Diffusion

We describe a novel type of photoclick reaction between 2,3-diaryl indenone epoxide (DIO) and ring-strained dipolarophiles, in which DIO serves as a P-type photoswitch to produce mesoionic oxidopyrylium ylide (PY) to initiate an ultra-fast [5+2] cycloaddition (k_2hν =1.9×10⁵  M^-1  s^-1 ). The photoisomerization between DIO and PY can be tightly controlled by either 365 or 520 nm photo-stimulation, which allows reversion or regeneration of the reactive PY dipole on demand. Thus, this reversible photoactivation was exploited to increase the chemoselectivity of the [5+2] cycloaddition in complex environments via temporal dual-λ stimulation sequences and to recycle the DIO reagent for batch-wise protein conjugation. A dynamic photoswitching strategy is also proposed to compensate for molecular diffusion of PY in aqueous solution, enhancing the spatial resolution of lithographic surface decoration and bioorthogonal labeling on living cells via a spatiotemporal dual-λ photo-modulation.

A facile and light-controllable drug combination for enhanced photopharmacology

We investigated the feasibility of creating cyclic azobenzene/azobenzene-based photo-switchable drugs that can fine-tune antibacterial activity against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) with light dependence. Furthermore, a "light-controlled drug combination" of these obtained drugs could be reversibly controlled to efficiently improve the antibiotic effect so as to reduce the minimum inhibitory concentrations (MICs) with different wavelength light illumination. Importantly, their antimicrobial activity could be easily manipulated by using light in bacterial patterning studies with high spatiotemporal precision, which might allow for localized activation of drugs and provide an alternative solution for practical clinical application in photopharmacology.

Fluorescence turn-on by photoligation - bright opportunities for soft matter materials

Photochemical ligation has become an indispensable tool for applications that require spatially addressable functionalisation, both in biology and materials science. Interestingly, a number of photochemical ligations result in fluorescent products, enabling a self-reporting function that provides almost instantaneous visual feedback of the reaction's progress and efficiency. Perhaps no other chemical reaction system allows control in space and time to the same extent, while concomitantly providing inherent feedback with regard to reaction success and location. While photoactivable fluorescent properties have been widely used in biology for imaging purposes, the expansion of the array of photochemical reactions has further enabled its utility in soft matter materials. Herein, we concisely summarise the key developments of fluorogenic-forming photoligation systems and their emerging applications in both biology and materials science. We further summarise the current challenges and future opportunities of exploiting fluorescent self-reporting reactions in a wide array of chemical disciplines.

Seeking Citius: Photochemical Access of Reactive Intermediates for Faster Bioorthogonal Reactions

Fast bioorthogonal reactions are sought after because of their superior performance in labeling low-abundance biomolecules in native cellular environments. An attractive strategy to increase reaction kinetics is to access the reactive intermediates through photochemical activation. To this end, significant progress was made in the last few years in harnessing two highly reactive intermediates-nitrile imine and tetrazine-generated through photoinduced ring rupture and catalytic photooxidation, respectively. The efficient capture of these reactive intermediates by their cognate reaction partners has enabled bioorthogonal fluorescent labeling of biomolecules in live cells.

Expanding the functionality of proteins with genetically encoded dibenzo[b,f][1,4,5]thiadiazepine: a photo-transducer for photo-click decoration

Genetic incorporation of novel noncanonical amino acids (ncAAs) that are specialized for the photo-click reaction allows the precisely orthogonal and site-specific functionalization of proteins in living cells under photo-control. However, the development of a r̲ing-strain i̲n situ l̲oadable d̲ipolarophile (RILD) as a genetically encodable reporter for photo-click bioconjugation with spatiotemporal controllability is quite rare. Herein, we report the design and synthesis of a photo-switchable d̲ib̲enzo[b,f][1,4,5]t̲hiad̲iazepine-based a̲lanine (DBTDA) ncAA, together with the directed evolution of a pyrrolysyl-tRNA synthetase/tRNA_CUA pair (PylRS/tRNA_CUA), to encode the DBTDA into recombinant proteins as a RILD in living E. coli cells. The fast-responsive photo-isomerization of the DBTDA residue can be utilized as a converter of photon energy into ring-strain energy to oscillate the conformational changes of the parent proteins. Due to the photo-activation of RILD, the photo-switching of the DBTDA residue on sfGFP and OmpC is capable of promoting the photo-click ligation with diarylsydnone (DASyd) derived probes with high efficiency and selectivity. We demonstrate that the genetic code expansion (GCE) with DBTDA benefits the studies on the distribution of decorated OmpC-DBTD on specific E. coli cells under a spatiotemporal resolved photo-stimulation. The GCE for encoding DBTDA enables further functional diversity of artificial proteins in living systems.

Catalytic Activation of Bioorthogonal Chemistry with Light (CABL) Enables Rapid, Spatiotemporally Controlled Labeling and No-Wash, Subcellular 3D-Patterning in Live Cells Using Long Wavelength Light

Described is the spatiotemporally controlled labeling and patterning of biomolecules in live cells through the catalytic activation of bioorthogonal chemistry with light, referred to as "CABL". Here, an unreactive dihydrotetrazine (DHTz) is photocatalytically oxidized in the intracellular environment by ambient O2 to produce a tetrazine that immediately reacts with a trans-cyclooctene (TCO) dienophile. 6-(2-Pyridyl)dihydrotetrazine-3-carboxamides were developed as stable, cell permeable DHTz reagents that upon oxidation produce the most reactive tetrazines ever used in live cells with Diels-Alder kinetics exceeding k2 of 106 M-1 s-1. CABL photocatalysts are based on fluorescein or silarhodamine dyes with activation at 470 or 660 nm. Strategies for limiting extracellular production of singlet oxygen are described that increase the cytocompatibility of photocatalysis. The HaloTag self-labeling platform was used to introduce DHTz tags to proteins localized in the nucleus, mitochondria, actin, or cytoplasm, and high-yielding subcellular activation and labeling with a TCO-fluorophore were demonstrated. CABL is light-dose dependent, and two-photon excitation promotes CABL at the suborganelle level to selectively pattern live cells under no-wash conditions. CABL was also applied to spatially resolved live-cell labeling of an endogenous protein target by using TIRF microscopy to selectively activate intracellular monoacylglycerol lipase tagged with DHTz-labeled small molecule covalent inhibitor. Beyond spatiotemporally controlled labeling, CABL also improves the efficiency of "ordinary" tetrazine ligations by rescuing the reactivity of commonly used 3-aryl-6-methyltetrazine reporters that become partially reduced to DHTzs inside cells. The spatiotemporal control and fast rates of photoactivation and labeling of CABL should enable a range of biomolecular labeling applications in living systems.

Water-Involved Ring-Opening of 4-Phenyl-1,2,4-triazoline-3,5-dione for "Photo-Clicked" Access to Carbamoyl Formazan Photoswitches In Situ

Cyclic azodicarbonyl derivatives, particularly 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD), commonly serve as arenophile, dienophile, enophile and electrophile. Perplexed by its instability in aqueous environment, there are few studies focused on the transient intermediate produced by hydrolysis of PTAD to achieve synthetic significance. Herein, we describe a "photo-click" method that involves nitrile imine (NI) from diarylsydnone to capture the diazenecarbonyl-phenyl-carbamic acid (DACPA) generated by water-promoted ring-opening of PTAD. DFT calculation reveal that H-bonding interactions between PTAD and water are vital to form DACPA which exhibited an umpolung effect during ligation by nature bond orbit (NBO) analysis. The ultra-fast ligation resulted in carbamoyl formazans, as a unique Z↔E photo-switchable linker on target molecules, including peptide and drugs, with excellent anti-fatigue performance. This strategy is showcased to construct highly functionalized carbamoyl formazans in situ for photo-pharmacology and material studies, which also expands the chemistry of PTAD in aqueous media.

Visible-Light-Mediated Modification and Manipulation of Biomacromolecules

Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.

Visible-light induced photo-click and release strategy between monoarylsydnone and phenoxylfumarate

We report a visible-light induced photo-click and release platform between monoarylsydnone (MASyd) and phenoxylfumarates. The pyrazoline produced by the cycloaddition undergoes a photo-aromatization to form a fluorescent pyrazole. Meanwhile, the photo-aromatization also serves as the driving force to release fluorophores that are quenched in the form of phenoxylfumarates.

Enabling In Vivo Photocatalytic Activation of Rapid Bioorthogonal Chemistry by Repurposing Silicon-Rhodamine Fluorophores as Cytocompatible Far-Red Photocatalysts

Chromophores that absorb in the tissue-penetrant far-red/near-infrared window have long served as photocatalysts to generate singlet oxygen for photodynamic therapy. However, the cytotoxicity and side reactions associated with singlet oxygen sensitization have posed a problem for using long-wavelength photocatalysis to initiate other types of chemical reactions in biological environments. Herein, silicon-Rhodamine compounds (SiRs) are described as photocatalysts for inducing rapid bioorthogonal chemistry using 660 nm light through the oxidation of a dihydrotetrazine to a tetrazine in the presence of trans-cyclooctene dienophiles. SiRs have been commonly used as fluorophores for bioimaging but have not been applied to catalyze chemical reactions. A series of SiR derivatives were evaluated, and the Janelia Fluor-SiR dyes were found to be especially effective in catalyzing photooxidation (typically 3%). A dihydrotetrazine/tetrazine pair is described that displays high stability in both oxidation states. A protein that was site-selectively modified by trans-cyclooctene was quantitatively conjugated upon exposure to 660 nm light and a dihydrotetrazine. By contrast, a previously described methylene blue catalyst was found to rapidly degrade the protein. SiR-red light photocatalysis was used to cross-link hyaluronic acid derivatives functionalized by dihydrotetrazine and trans-cyclooctenes, enabling 3D culture of human prostate cancer cells. Photoinducible hydrogel formation could also be carried out in live mice through subcutaneous injection of a Cy7-labeled hydrogel precursor solution, followed by brief irradiation to produce a stable hydrogel. This cytocompatible method for using red light photocatalysis to activate bioorthogonal chemistry is anticipated to find broad applications where spatiotemporal control is needed in biological environments.

Spatiotemporal Resolved Live Cell Membrane Tracking through Photo-click Reactions Enriched in Lipid Phase

A set of photo-switchable monopeptides derived from cis-β-dibenzodiazocine-l-alanine (cis-DBDAA) have been designed and synthesized, which are capable of photo-click reacting with diaryltetrazoles or diarylsydnones in a hydrophobic phospholipid bilayer environment. The DBDAA monopeptides include both a hydrophobic tail on C-terminal, providing high affinity toward lipid membrane, and a modularized functional moiety on N-terminal, enabling rapid optimization of the self-assembly strength to form multifunctional supramolecules. With the cis-DBDAA monopeptides photo-switched into trans-configuration, we were able to disrupt the supramolecular assembly through an efficient photo-click reaction across the lipid bilayer of liposomes. We reveal that the performance of the photo-click reactions between the monopeptides and photo-generated nitrile imine intermediates is significantly enhanced by enrichment of both reactants in the hydrophobic membrane lamel of liposomes. Enrichment of the DBDAA monopeptide in lipid phase serves as a convenient method to introduce bioorthogonal chemical handles on live cell membranes, which enables fluorescence labelling of single cell's membrane with high spatiotemporal resolution to facilitate the studies on cell membrane dynamics.

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.

Light-Triggered Click Chemistry

The merging of click chemistry with discrete photochemical processes has led to the creation of a new class of click reactions, collectively known as photoclick chemistry. These light-triggered click reactions allow the synthesis of diverse organic structures in a rapid and precise manner under mild conditions. Because light offers unparalleled spatiotemporal control over the generation of the reactive intermediates, photoclick chemistry has become an indispensable tool for a wide range of spatially addressable applications including surface functionalization, polymer conjugation and cross-linking, and biomolecular labeling in the native cellular environment. Over the past decade, a growing number of photoclick reactions have been developed, especially those based on the 1,3-dipolar cycloadditions and Diels-Alder reactions owing to their excellent reaction kinetics, selectivity, and biocompatibility. This review summarizes the recent advances in the development of photoclick reactions and their applications in chemical biology and materials science. A particular emphasis is placed on the historical contexts and mechanistic insights into each of the selected reactions. The in-depth discussion presented here should stimulate further development of the field, including the design of new photoactivation modalities, the continuous expansion of λ-orthogonal tandem photoclick chemistry, and the innovative use of these unique tools in bioconjugation and nanomaterial synthesis.

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.