Conditionally Activatable Visible-Light Photocages

Selective Binding and Light-Driven Release of Fluorous PF6- and Radioactive 99TcO4- Anions for All-to-Nothing Liquid-Liquid Extraction

The removal of anions from aqueous media using molecular receptors in liquid-liquid extraction is a long-standing strategy to clean up contaminated water sources. Therein, high selectivity is needed to remove specific ions from mixtures of other ions, and high affinity provides extractions at low concentrations. However, the high affinity creates a conundrum by impeding the release of the ions in any stripping steps needed for further processing. To circumvent this problem, light-responsive receptors have been proposed as candidates for turning off the binding, but they are currently untested in liquid-liquid extraction. We tested the feasibility of light-driven release using a cyanostar macrocycle. We demonstrate the selective extraction of PF6- anions over large excesses of competing anions (Cl-, NO3-, SO42-) followed by photodriven release for quantitative isolation of the target. Release relies on photoisomerization of the macrocycle's five stilbenes generating distorted isomers to turn off binding. With modest reversibility, only a single-shot release was demonstrated, akin to photodriven uncaging. These methods were extended to the capture and photodriven release of ReO4- and radioactive 99TcO4- anions at ∼90% efficiency. Extraction was demonstrated down to the highly dilute 4 ppb levels of the 99TcO4- anion. This proof-of-concept demonstration verifies the use of a large change in affinity for the all-to-nothing capture and release of target anions between liquid phases.

A hydrophobic photouncaging reaction to profile the lipid droplet interactome in tissues

Most bioorthogonal photouncaging reactions preferentially occur in polar environments to accommodate biological applications in the aqueous cellular milieu. However, they are not precisely designed to chemically adapt to the diverse microenvironments of the cell. Herein, we report a hydrophobic photouncaging reaction with tailored photolytic kinetics toward solvent polarity. Structural modulations of the aminobenzoquinone-based photocage reveal the impact of cyclic ring size, steric substituent, and electronic substituent on the individual uncaging kinetics (kH2O and kdioxane) and polarity preference (kdioxane/kH2O). Rational incorporation of optimized moieties leads to up to 20.2-fold nonpolar kinetic selectivity (kdioxane/kH2O). Further photochemical spectroscopic characterizations and theoretical calculations together uncover the mechanism underlying the polarity-dependent uncaging kinetics. The uncaged ortho-quinone methide product bears covalent reactivity toward diverse nucleophiles of a protein revealed by tandem mass spectrometry. Finally, we demonstrate the application of such lipophilic photouncaging chemistry toward selective labeling and profiling of proteins in proximity to lipid droplets inside human fatty liver tissues. Together, this work studies the solvent polarity effects of a photouncaging reaction and chemically adapts it toward suborganelle-targeted protein proximity labeling and profiling.

Thioketal-photocage: a universal modification strategy for constructing new photochemical tools for real-time imaging in living cells

Photoactivable fluorescent probes (photocages) are powerful tools for studying biological processes in living cells. We report a novel class of photodegradable thioketals that serve as photo-responsive elements and apply them to xanthene dyes to design photocages for live cell imaging. Compared with traditional thioketals, these compounds demonstrate the ability to undergo deprotection upon exposure to ultraviolet-visible light, independent of photosensitizers or external oxidants and relying solely on dissolved oxygen within the solvent. This photoreaction results in a remarkable 68-fold increase in fluorescence intensity. We verify that the uncaged product is the corresponding ketone, with high-performance liquid chromatography analysis, which indicates a yield of up to 80%. Furthermore, we extend this modification strategy to xanthene dyes substituted with various heteroatoms and confirm the universal applicability of this photoactivable strategy. These dyes exhibit good stability against reducing agents and metal ions, with carbon and silicon xanthene photocages also demonstrating commendable dark stability against reactive oxygen species. We apply these photocages for bioimaging and further modify them for selective labeling, activation, and imaging of specific organelles and intracellular proteins within living cells. This modification strategy offers high spatiotemporal selectivity and holds promise as a powerful tool for advanced biological studies.

Design strategies for tetrazine fluorogenic probes for bioorthogonal imaging

Tetrazine fluorogenic probes play a critical role in bioorthogonal chemistry, selectively activating fluorescence upon reaction to enhance precision in imaging and sensing within complex biological environments. Recent structural innovations-such as varied fluorophore choices, spacer optimization, and direct tetrazine integration within a fluorophore's π-conjugated system-have expanded their spectral range from visible to NIR, enhancing adaptability across various applications. This review examines advancements in the rational design and synthesis of these probes. We examine key fluorogenic mechanisms, such as energy transfer, internal conversion, and electron/charge transfer, that significantly influence fluorescence activation. We also highlight representative applications in live-cell imaging, super-resolution microscopy, and therapeutic monitoring, underscoring the expanding role of tetrazine probes in biomedical research and diagnostics. Collectively, these insights provide a strategic foundation for developing next-generation tetrazine probes with tailored properties to address evolving diagnostic and therapeutic challenges.

Conditional Relay Activation of Theranostic Prodrug by Pretargeting Bioorthogonal Trigger and Fluorescence-Guided Visible Light Irradiation

Bioorthogonalized light-responsive click-and-uncage platform has enabled precise cell surface engineering and timed payload release, but most of such photoactivatable prodrugs have "always-on" photoactivity leading to the dark toxicity. On the other hand, the conditionally activatable photocage is limited to the application of fluorogenic probe/photosensitizer liberation. Herein, we devise a conditionally activatable theranostic platform based on the tetrazine (Tz)-boron-dipyrromethene (BODIPY) construct, in which tetrazine serves as a quencher motif to disable both the fluorescence and photoresponsivity of BODIPY. The uncaged BODIPY upon the bioorthogonal transformation of the tetrazine reinstates fluorescence on-target to guide the subsequent visible light irradiation thereby releasing the therapeutic payload in situ. The proof of concept for such "light where is lit up"-activated theranostics was demonstrated by the tetrazine-BODIPY conjugated SN-38 (1) with masked fluorescence, up to 70 times-reduced cytotoxicity, and good photostability. Upon an inverse electron-demand Diels-Alder (IEDDA) reaction between tetrazine unit on 1 and a biotinylated trans-cyclooctene (biotin-TCO) as a pretargeted trigger on tumor cell surface, the green fluorescence from BODIPY was fully restored for cell-selective imaging, which guided the green light irradiation (500-520 nm) to activate the caged drug SN-38 exerting potent cytotoxicity against tumor cells, offering high spatiotemporal precision of disease diagnosis and therapy.

Unveiling the photophysical mechanistic mysteries of tetrazine-functionalized fluorogenic labels

Tetrazine-based fluorogenic labels are widely utilized in medical and biological studies, exhibiting substantial fluorescence enhancement (FE) following tetrazine degradation through bio-orthogonal reactions. However, the underlying mechanisms driving this fluorogenic response remain only partially resolved, particularly regarding the diminished FE efficiency in the deep-red and near-infrared (NIR) regions. This knowledge gap has impeded efforts to optimize these labels for extended emission wavelengths and improved FE ratios. This review offers a photophysical perspective, discussing the fluorescence quenching pathways (i.e., energy flows and charge separation) that regulate the fluorogenic properties exhibited in various types of tetrazine labels. Moreover, this work examines the emerging role of intramolecular rotations in certain tetrazine-based structures and the integration of additional quencher units. The proposed alternative quenching channel offers the potential to surpass traditional wavelength constraints while achieving improved FE. By examining these photophysical mechanisms, this review aims to advance the understanding of tetrazine-functionalized fluorogenic labels and provide guiding principles for their future design and practical applications.

Precise photorelease in living cells by high-viscosity activatable coumarin-based photocages

Intracellular viscosity is a critical microenvironmental factor in various biological systems, and its abnormal increase is closely linked to the progression of many diseases. Therefore, precisely controlling the release of bioactive molecules in high-viscosity regions is vital for understanding disease mechanisms and advancing their diagnosis and treatment. However, viscosity alone cannot directly trigger chemical reactions. Inspired by molecular rotor fluorophores, we have developed a series of high-viscosity activated photocages by modifying the C3 position of the coumarin scaffold with electron-withdrawing groups. In low-viscosity environments, both fluorescence and photocleavage of the photocages are inhibited by nonradiative decay caused by intramolecular free rotation. In contrast, in high-viscosity environments, the restriction of this intramolecular rotation restores fluorescence and photocleavage. These unique photolysis properties enable the selective photorelease of these photocages in high-viscosity conditions. As a proof of concept, we have developed a drug delivery system that targets abnormal mitochondria with high viscosity. This system demonstrates enhanced photolysis efficiency in abnormal mitochondria compared to normal ones, allowing for precise drug release in diseased mitochondria while ensuring excellent biological safety in healthy mitochondria. We anticipate that these photocages will serve as convenient and efficient tools for the precise release of active molecules in high-viscosity environments.

Bioorthogonal Activation of Deep Red Photoredox Catalysis Inducing Pyroptosis

The revolutionary impact of photoredox catalytic processes has ignited novel avenues for exploration, empowering us to delve into nature in unprecedented ways and to pioneer innovative biotechnologies for therapy and diagnosis. However, integrating artificial photoredox catalysis into living systems presents significant challenges, primarily due to concerns over low targetability, low compatibility with complex biological environments, and the safety risks associated with photocatalyst toxicity. To address these challenges, herein, we present a novel bioorthogonally activatable photoredox catalysis approach. In this approach, potent photocatalyst selection via atom replacement of the rhodamine core yielded the bioorthogonally activatable photocatalyst (PC-Tz). The introduction of 1,2,4,5-tetrazine quenched its photocatalytic properties, which were restored upon an intracellular inverse electron-demand Diels-Alder (iEDDA) reaction with trans-cyclooctene (TCO) localized in mitochondria. This reaction led to remarkable photocatalytic oxidation of nicotinamide adenine dinucleotide (NADH), effectively manipulating the mitochondrial electron transport chain (ETC) under hypoxic conditions in cancer cells. Additionally, photocatalytic pyroptotic cell death was observed through a caspase-3/gasdermin E (GSDME) pathway, achieving notable antitumor efficacy and adenosine triphosphate (ATP) reduction in tumor cells. To the best of our knowledge, this represents the first example of bioorthogonally activatable photoredox catalysis, opening new avenues for chemists to spatiotemporally control activity in specific cell organelles without disrupting other native biological processes.

Glycosylated AIE-active Red Light-triggered Photocage with Precisely Tumor Targeting Capability for Synergistic Type I Photodynamic Therapy and CPT Chemotherapy

Photocaging is an emerging protocol for precisely manipulating spatial and temporal behaviors over biological activity. However, the red/near-infrared light-triggered photolysis process of current photocage is largely singlet oxygen (1O2)-dependent and lack of compatibility with other reactive oxygen species (ROS)-activated techniques, which has proven to be the major bottleneck in achieving efficient and precise treatment. Herein, we reported a lactosylated photocage BT-LRC by covalently incorporating camptothecin (CPT) into hybrid BODIPY-TPE fluorophore via the superoxide anion radical (O2 -⋅)-cleavable thioketal bond for type I photodynamic therapy (PDT) and anticancer drug release. Amphiphilic BT-LRC could be self-assembled into aggregation-induced emission (AIE)-active nanoparticles (BT-LRCs) owing to the regulation of carbohydrate-carbohydrate interactions (CCIs) among neighboring lactose units in the nanoaggregates. BT-LRCs could simultaneously generate abundant O2 -⋅ through the aggregation modulated by lactose interactions, and DNA-damaging agent CPT was subsequently and effectively released. Notably, the type I PDT and CPT chemotherapy collaboratively amplified the therapeutic efficacy in HepG2 cells and tumor-bearing mice. Furthermore, the inherent AIE property of BT-LRCs endowed the photocaged prodrug with superior bioimaging capability, which provided a powerful tool for real-time tracking and finely tuning the PDT and photoactivated drug release behavior in tumor therapy.

Bioorthogonally activated probes for precise fluorescence imaging

Over the past two decades, bioorthogonal chemistry has undergone a remarkable development, challenging traditional assumptions in biology and medicine. Recent advancements in the design of probes tailored for bioorthogonal applications have met the increasing demand for precise imaging, facilitating the exploration of complex biological systems. These state-of-the-art probes enable highly sensitive, low background, in situ imaging of biological species and events within live organisms, achieving resolutions comparable to the size of the biomolecule under investigation. This review provides a comprehensive examination of various categories of bioorthogonally activated in situ fluorescent labels. It highlights the intricate design and benefits of bioorthogonal chemistry for precise in situ imaging, while also discussing future prospects in this rapidly evolving field.

Optically Controlled Drug Delivery Through Microscale Brain-Machine Interfaces Using Integrated Upconverting Nanoparticles

The aim of this work is to incorporate lanthanide-cored upconversion nanoparticles (UCNP) into the surface of microengineered biomedical implants to create a spatially controlled and optically releasable model drug delivery device in an integrated fashion. Our approach enables silicone-based microelectrocorticography (ECoG) implants holding platinum/iridium recording sites to serve as a stable host of UCNPs. Nanoparticles excitable in the near-infrared (lower energy) regime and emitting visible (higher energy) light are utilized in a study. With the upconverted higher energy photons, we demonstrate the induction of photochemical (cleaving) reactions that enable the local release of specific dyes as a model system near the implant. The modified ECoG electrodes can be implanted in brain tissue to act as an uncaging system that releases small amounts of substance while simultaneously measuring the evoked neural response upon light activation. In this paper, several technological challenges like the surface modification of UCNPs, the immobilization of particles on the implantable platform, and measuring the stability of integrated UCNPs in in vitro and in vivo conditions are addressed in detail. Besides the chemical, mechanical, and optical characterization of the ready-to-use devices, the effect of nanoparticles on the original electrophysiological function is also evaluated. The results confirm that silicone-based brain-machine interfaces can be efficiently complemented with UCNPs to facilitate local model drug release.

Coumarin-Derived Caging Groups in the Spotlight: Tailoring Physiochemical and Photophysical Properties

The development of light-responsive molecular tools enables spatiotemporal control of biochemical processes with superior precision. Amongst these molecular tools, photolabile caging groups are employed to prevent critical binding interactions between a bioactive molecule and its corresponding target. Only upon irradiation with light, the bioactive is released in its 'active' form and is now readily available to bind to its target. Coumarin-derived caging groups constitute one of the most popular classes of photolabile protecting groups, due to their facile synthetic accessibility, ease of tuning photophysical properties via structural modification and rapid photolysis reactions. Herein, we highlight the recent progress made on the development of coumarin-derived caging groups, in which the red-shifting of absorption spectra, improving aqueous solubility and tailoring sub-cellular localisation has been of particular interest.

Triphenylamine Sensitized 8-Dimethylaminoquinoline: An Efficient Two-Photon Caging Group for Intracellular Delivery

Triphenylamine-sensitized 8-dimethylaminoquinoline (TAQ) probes showed fair two-photon absorption and fragmentation cross sections in releasing kainate and GABA ligands. The water-soluble PEG and TEG-analogs allowed cell internalization and efficient light-gated liberation of the rhodamine reporter under UV and two-photon (NIR) irradiation conditions.

A Photoredox Thiol-yne Reaction for the Synthesis of Vinyl Sulfide-Based Coumarins and its Effect on Fluorescence Properties

Coumarins still remain one of the most widely explored fluorescent dyes, with a broad spectrum of applications spanning various fields, such as molecular imaging, bioorganic chemistry, materials chemistry, or medical sciences. Their fluorescence is strongly based on a push-pull mechanism involving an electron-donating group (EDG), mainly located at the C7 or C8 positions of the dye core. Unfortunately, up to now, these positions have been very limited to hydroxyl or amino groups. In this study, we present in detail the synthesis of the first series of coumarins bearing a vinyl sulfide as the EDG at the C7 position. These derivatives were prepared by thiol-yne reaction, promoted by ruthenium- or porphyrin-based photoredox catalysis, enabling rapid late-stage diversification. We also functionalized coumarins with short peptides, and BSA protein as a proof-of-concept study, in a single-step process. This strategy, capable of proceeding under aqueous conditions, overcomes the protection/deprotection steps usually required by traditional methods, which also use strong bases and organic solvents. Moreover, the photophysical properties such as absorption and emission of obtained coumarins (for 3-CF3, 3-benzothiazole, 6-8-difluoro derivatives), predominantly exhibited large Stokes shifts (up to 204 nm) and maintained intramolecular charge transfer (ICT) characteristics.

C(sp3)-H cyclizations of 2-(2-vinyl)phenoxy-tert-anilines

1,5-hydride transfer-triggered cyclization reactions offering a robust method for C(sp3)-C(sp3) coupling and the synthesis of e.g. tetrahydroquinolines have been thoroughly investigated in the literature. Catalysts allowing milder reaction conditions or the development of enantioselective processes were important recent contributions to the field, as well as the studies on subtrates with oxygen or sulfur heteroatoms (besides the originally described nitrogen heterocycles). In a series of studies, we focused on expanded, higher order H-transfers/cyclizations by positioning the interacting substituents on distanced rings. Cyclizations of appropriately functionalized biaryl and fused bicyclic systems led to 7-9 membered rings. In the frame of this research, we set out to study the feasibility of the cyclization and the factors affecting it by in silico methods. The conclusions drawn from computational studies were complemented by cyclization screens on 2-(2-vinyl)phenoxy-tert-anilines and their CH2-expanded analogues, the results of which are presented here. Besides isolating the expected oxazonine products in several cases, we also observed a unique dimer formation, leading to an interesting 5-6-5 ring system.

All-photonic kinase inhibitors: light-controlled release-and-report inhibition

Light-responsive molecular tools targeting kinases affords one the opportunity to study the underlying cellular function of selected kinases. In efforts to externally control lymphocyte-specific protein tyrosine kinase (LCK) activity, the development of release-and-report LCK inhibitors is described, in which (i) the release of the active kinase inhibitor can be controlled externally with light; and (ii) fluorescence is employed to report both the release and binding of the active kinase inhibitor. This introduces an unprecedented all-photonic method for users to both control and monitor real-time inhibitory activity. A functional cellular assay demonstrated light-mediated LCK inhibition in natural killer cells. The use of coumarin-derived caging groups resulted in rapid cellular uptake and non-specific intracellular localisation, while a BODIPY-derived caging group predominately localised in the cellular membrane. This concept of release-and-report inhibitors has the potential to be extended to other biorelevant targets where both spatiotemporal control in a cellular setting and a reporting mechanism would be beneficial.

Synthesis and Pharmacological Characterization of New Photocaged Agonists for Histamine H3 and H4 Receptors

The modulation of biological processes with light-sensitive chemical probes promises precise temporal and spatial control. Yet, the design and synthesis of suitable probes is a challenge for medicinal chemists. This article introduces a photocaging strategy designed to modulate the pharmacology of histamine H3 receptors (H3R) and H4 receptors (H4R). Employing the photoremovable group BODIPY as the caging entity for two agonist scaffolds-immepip and 4-methylhistamine-for H3R and H4R, respectively, we synthesized two BODIPY-caged compounds, 5 (VUF25657) and 6 (VUF25678), demonstrating 10-100-fold reduction in affinity for their respective receptors. Notably, the caged H3R agonist, VUF25657, exhibits approximately a 100-fold reduction in functional activity. The photo-uncaging of VUF25657 at 560 nm resulted in the release of immepip, thereby restoring binding affinity and potency in functional assays. This approach presents a promising method to achieve optical control of H3R receptor pharmacology.

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.

Photochemically Controlled Release of the Glucose Transporter 1 Inhibitor for Glucose Deprivation Responses and Cancer Suppression Research

Cancer cells need a greater supply of glucose mainly due to their aerobic glycolysis, known as the Warburg effect. Glucose transport by glucose transporter 1 (GLUT1) is the rate-limiting step for glucose uptake, making it a potential cancer therapeutic target. However, GLUT1 is widely expressed and performs crucial functions in a variety of cells, and its indiscriminate inhibition will cause serious side effects. In this study, we designed and synthesized a photocaged GLUT1 inhibitor WZB117-PPG to suppress the growth of cancer cells in a spatiotemporally controllable manner. WZB117-PPG exhibited remarkable photolysis efficiency and substantial cytotoxicity toward cancer cells under visible light illumination with minimal side effects, ensuring its safety as a potential cancer therapy. Furthermore, our quantitative proteomics data delineated a comprehensive portrait of responses in cancer cells under glucose deprivation, underlining the mechanism of cell death via necrosis rather than apoptosis. We reason that our study provides a potentially reliable cancer treatment strategy and can be used as a spatiotemporally controllable trigger for studying nutrient deprivation-related stress responses.

Genetically Encoded Photocatalysis Enables Spatially Restricted Optochemical Modulation of Neurons in Live Mice

Light provides high temporal precision for neuronal modulations. Small molecules are advantageous for neuronal modulation due to their structural diversity, allowing them to suit versatile targets. However, current optochemical methods release uncaged small molecules with uniform concentrations in the irradiation area, which lack spatial specificity as counterpart optogenetic methods from genetic encoding for photosensitive proteins. Photocatalysis provides spatial specificity by generating reactive species in the proximity of photocatalysts. However, current photocatalytic methods use antibody-tagged heavy-metal photocatalysts for spatial specificity, which are unsuitable for neuronal applications. Here, we report a genetically encoded metal-free photocatalysis method for the optochemical modulation of neurons via deboronative hydroxylation. The genetically encoded photocatalysts generate doxorubicin, a mitochondrial uncoupler, and baclofen by uncaging stable organoboronate precursors. The mitochondria, nucleus, membrane, cytosol, and ER-targeted drug delivery are achieved by this method. The distinct signaling pathway dissection in a single projection is enabled by the dual optogenetic and optochemical control of synaptic transmission. The itching signaling pathway is investigated by photocatalytic uncaging under live-mice skin for the first time by visible light irradiation. The cell-type-specific release of baclofen reveals the GABABR activation on NaV1.8-expressing nociceptor terminals instead of pan peripheral sensory neurons for itch alleviation in live mice.

Blue and Green Light Responsive Caged Glutamate

Glutamate (Glu) is an excitatory neurotransmitter that plays a critical role in memory. Brain mapping activities of such pathways relied heavily on the ability to release Glu with spatiotemporal precision. Several photo-protecting groups (PPGs), referred to as photocages or cages, were designed to accomplish the release of Glu upon irradiation. Previously reported Glu cages responded to UV upon irradiation with single photons, which limited their use in vivo experiments due to cytotoxicity. Other caged designs suffered from lower quantum efficiency (QE) of release necessitating higher concentrations and/or longer photoirradiation times. There have been limited examples of cages that respond to visible light with single photon irradiation. Herein, we report the efficient preparation of 11 caged Glu examples that respond to two visible wavelengths, 467 nm (thiocoumarin based) and 515-540 nm (BODIPY based). The kinetics of photouncaging were studied for all caged designs, and we report all quantum efficiencies, i.e., quantum yields (Φ), that ranged from 0.0001-0.65. Two of the BODIPY cages are reported here for the first time, and one, Me-BODIPY-Br-Glu, shows the most efficient Glu release with a QE of 0.65. Similar caged designs can be extended to the inhibitory neurotransmitter, GABA. This would enable the use of two visible wavelengths to modulate the release of excitatory and inhibitory neurotransmitters upon demand via optical control.

Allosteric regulation of kinase activity in living cells

The dysregulation of protein kinases is associated with multiple diseases due to the kinases' involvement in a variety of cell signaling pathways. Manipulating protein kinase function, by controlling the active site, is a promising therapeutic and investigative strategy to mitigate and study diseases. Kinase active sites share structural similarities, making it difficult to specifically target one kinase, and allosteric control allows specific regulation and study of kinase function without directly targeting the active site. Allosteric sites are distal to the active site but coupled via a dynamic network of inter-atomic interactions between residues in the protein. Establishing an allosteric control over a kinase requires understanding the allosteric wiring of the protein. Computational techniques offer effective and inexpensive mapping of the allosteric sites on a protein. Here, we discuss the methods to map and regulate allosteric communications in proteins, and strategies to establish control over kinase functions in live cells and organisms. Protein molecules, or 'sensors,' are engineered to function as tools to control allosteric activity of the protein as these sensors have high spatiotemporal resolution and help in understanding cell phenotypes after immediate activation or inactivation of a kinase. Traditional methods used to study protein functions, such as knockout, knockdown, or mutation, cannot offer a sufficiently high spatiotemporal resolution. We discuss the modern repertoire of tools to regulate protein kinases as we enter a new era in deciphering cellular signaling and developing novel approaches to treat diseases associated with signal dysregulation.

Allosteric regulation of kinase activity in living cells

The dysregulation of protein kinases is associated with multiple diseases due to the kinases' involvement in a variety of cell signaling pathways. Manipulating protein kinase function, by controlling the active site, is a promising therapeutic and investigative strategy to mitigate and study diseases. Kinase active sites share structural similarities making it difficult to specifically target one kinase, allosteric control allows specific regulation and study of kinase function without directly targeting the active site. Allosteric sites are distal to the active site but coupled via a dynamic network of inter-atomic interactions between residues in the protein. Establishing an allosteric control over a kinase requires understanding the allosteric wiring of the protein. Computational techniques offer effective and inexpensive mapping of the allosteric sites on a protein. Here, we discuss methods to map and regulate allosteric communications in proteins, and strategies to establish control over kinase functions in live cells and organisms. Protein molecules, or "sensors" are engineered to function as tools to control allosteric activity of the protein as these sensors have high spatiotemporal resolution and help in understanding cell phenotypes after immediate activation or inactivation of a kinase. Traditional methods used to study protein functions, such as knockout, knockdown, or mutation, cannot offer a sufficiently high spatiotemporal resolution. We discuss the modern repertoire of tools to regulate protein kinases as we enter a new era in deciphering cellular signaling and developing novel approaches to treat diseases associated with signal dysregulation.

Evaluation of bioorthogonally applicable tetrazine-Cy3 probes for fluorogenic labeling schemes

The fluorogenic features of three sets of tetrazine-Cy3 probes were evaluated in bioorthogonal tetrazine-cyclooctyne ligation schemes. These studies revealed that the more efficient, internal conversion-based quenching of fluorescence by the tetrazine modul is translated to improved fluorogenicity compared to the more conventional, energy transfer-enabled design. Furthermore, a comparison of directly conjugated probes and vinylene-linked tetrazine-Cy3 probes revealed that more intimate conjugation of the tetrazine and the chromophore results in more efficient IC-based quenching even in spectral ranges where tetrazine exhibits diminished modulation efficiency. The applicability of these tetrazine-quenched fluorogenic Cy3 probes was demonstrated in the fluorogenic labeling schemes of the extra- and intracellular proteins of live cells.

Spatiotemporal Investigation of Intercellular Heterogeneity via Multiple Photocaged Probes

Intercellular heterogeneity occurs widely under both normal physiological environments and abnormal disease-causing conditions. Several attempts to couple spatiotemporal information to cell states in a microenvironment were performed to decipher the cause and effect of heterogeneity. Furthermore, spatiotemporal manipulation can be achieved with the use of photocaged/photoactivatable molecules. Here, we provide a platform to spatiotemporally analyze differential protein expression in neighboring cells by multiple photocaged probes coupled with homemade photomasks. We successfully established intercellular heterogeneity (photoactivable ROS trigger) and mapped the targets (directly ROS-affected cells) and bystanders (surrounding cells), which were further characterized by total proteomic and cysteinomic analysis. Different protein profiles were shown between bystanders and target cells in both total proteome and cysteinome. Our strategy should expand the toolkit of spatiotemporal mapping for elucidating intercellular heterogeneity.

Modulating Secondary Structure Motifs Through Photo-Labile Peptide Staples

Peptide-protein interactions (PPIs) are facilitated by the well-defined three-dimensional structure of bioactive peptides, interesting compounds for the development of new therapeutic agents. Their secondary structure and thus their propensity to engage in PPIs can be influenced by the introduction of peptide staples on the side chains. In particular, light-controlled staples based on azobenzene photoswitches and their structural influence on helical peptides have been studied extensively. In contrast, photolabile staples bearing photocages as a structural key motif, have mainly been used to block supramolecular interactions. Their influence on the secondary structure of the target peptide is under-investigated. Thus, in this study we use a combination of spectroscopic techniques and in silico simulations to systematically study a series of helical peptides with varying length of the photo-labile staple to obtain a detailed insight into the structure-property relationship in such photoresponsive biomolecules.

Bioorthogonally Assisted Phototherapy: Recent Advances and Prospects

Photoresponsive materials offer excellent spatiotemporal control over biological processes and the emerging phototherapeutic methods are expected to have significant effects on targeted cancer therapies. Recent examples show that combination of photoactivatable approaches with bioorthogonal chemistry enhances the precision of targeted phototherapies and profound implications are foreseen particularly in the treatment of disperse/diffuse tumors. The extra level of on-target selectivity and improved spatial/temporal control considerably intensified related bioorthogonally assisted phototherapy research. The anticipated growth of further developments in the field justifies the timeliness of a brief summary of the state of the art.

Phototriggered structures: Latest advances in biomedical applications

Non-invasive control of the drug molecules accessibility is a key issue in improving diagnostic and therapeutic procedures. Some studies have explored the spatiotemporal control by light as a peripheral stimulus. Phototriggered drug delivery systems (PTDDSs) have received interest in the past decade among biological researchers due to their capability the control drug release. To this end, a wide range of phototrigger molecular structures participated in the DDSs to serve additional efficiency and a high-conversion release of active fragments under light irradiation. Up to now, several categories of PTDDSs have been extended to upgrade the performance of controlled delivery of therapeutic agents based on well-known phototrigger molecular structures like o-nitrobenzyl, coumarinyl, anthracenyl, quinolinyl, o-hydroxycinnamate and hydroxyphenacyl, where either of one endows an exclusive feature and distinct mechanistic approach. This review conveys the design, photochemical properties and essential mechanism of the most important phototriggered structures for the release of single and dual (similar or different) active molecules that have the ability to quickly reason of the large variety of dynamic biological phenomena for biomedical applications like photo-regulated drug release, synergistic outcomes, real-time monitoring, and biocompatibility potential.

Solid-Phase Synthesis of s-Tetrazines

An efficient synthesis of s-tetrazines by solid-phase methods is described. This synthesis route was compatible with different solid-phase resins and linkers and did not require metal catalysts or high temperatures. Monosubstituted tetrazines were routinely synthesized using thiol-promoted chemistry, using dichloromethane as a carbon source, while disubstituted unsymmetrical aryl or alkyl tetrazines were synthesized using readily available nitriles. This efficient approach enabled the synthesis of s-tetrazines in high yields (70-94%), eliminating the classical solution-phase problems of mixtures of symmetrical and unsymmetrical tetrazines, with only a single final purification step required, and paves the way to the rapid synthesis of s-tetrazines with various applications in bioorthogonal chemistry and beyond.

Activatable dual-functional molecular agents for imaging-guided cancer therapy

Theranostics has attracted great attention due to its ability to combine the real-time diagnosis of cancers with efficient treatment modalities. Activatable dual-functional molecular agents could be synthesized by covalently conjugating imaging agents, therapeutic agents, stimuli-responsive linkers and/or targeting molecules together. They could be selectively activated by overexpressed physiological stimuli or external triggers at the tumor sites to release imaging agents and cytotoxic drugs, thus offering many advantages for tumor imaging and therapy, such as a high signal-to-noise ratio, low systemic toxicity, and improved therapeutic effects. This review summarizes the recent advances of dual-functional molecular agents that respond to various physiological or external stimuli for cancer theranostics. The molecular designs, synthetic strategies, activatable mechanisms, and biomedical applications of these molecular agents are elaborated, followed by a brief discussion of the challenges and opportunities in this field.

Wavelength-Dependent, Orthogonal Photoregulation of DNA Liberation for Logic Operations

In this study, we synthesized two phosphoramidites based on 2,7-bis-{4-nitro-8-[3-(2-propyl)-styryl]}-9,9-bis-[1-(3,6-dioxaheptyl)]-fluorene (BNSF) and 4,4'-bis-{8-[4-nitro-3-(2-propyl)-styryl]}-3,3'-di-methoxybiphenyl (BNSMB) structures as visible light-cleavable linkers for oligonucleotide conjugation. In addition to the commercial ultraviolet (UV) photocleavable (PC) linker, the BNSMB linker was further applied as a building component to construct photoregulated DNA devices as duplex structures, which are functionalized with fluorophores and quenchers. Selective cleavage of PC and BNSMB is achieved in response to ultraviolet (UV) and visible light irradiations as two inputs, respectively. This leads to controllable dissociation of pieces of DNA fragments, which is followed by changes of fluorescence emission as signal outputs of the system. By tuning the number and position of the photocleavable molecules, fluorophores, and quenchers, various DNA devices were developed, which mimic the functions of Boolean logic gates and achieve logic operations in AND, OR, NOR, and NAND gates in response to two different wavelengths of light inputs. By sequence design, the photolysis products can be precisely programmed in DNA devices and triggered to release in a selective and/or sequential manner. Thus, this photoregulated DNA device shows potential as a wavelength-dependent drug delivery system for selective control over the release of multiple individual therapeutic oligonucleotide-based drugs. We believe that our work not only enriches the library of photocleavable phosphoramidites available for bioconjugation but also paves the way for developing spatiotemporal-controlled, orthogonal-regulated DNA-based logic devices for a range of applications in materials science, polymers, chemistry, and biology.

Bioorthogonally activatable cyanine dye with torsion-induced disaggregation for in vivo tumor imaging

Advancement of bioorthogonal chemistry in molecular optical imaging lies in expanding the repertoire of fluorophores that can undergo fluorescence signal changes upon bioorthogonal ligation. However, most available bioorthogonally activatable fluorophores only emit shallow tissue-penetrating visible light via an intramolecular charge transfer mechanism. Herein, we report a serendipitous "torsion-induced disaggregation (TIDA)" phenomenon in the design of near-infrared (NIR) tetrazine (Tz)-based cyanine probe. The TIDA of the cyanine is triggered upon Tz-transcyclooctene ligation, converting its heptamethine chain from S-trans to S-cis conformation. Thus, after bioorthogonal reaction, the tendency of the resulting cyanine towards aggregation is reduced, leading to TIDA-induced fluorescence enhancement response. This Tz-cyanine probe sensitively delineates the tumor in living mice as early as 5 min post intravenous injection. As such, this work discovers a design mechanism for the construction of bioorthogonally activatable NIR fluorophores and opens up opportunities to further exploit bioorthogonal chemistry in in vivo imaging.

Blue or Near-Infrared Light-Triggered Release of Halogens via Blebbistatin Photocage

Photocages can provide spatial and temporal control to accurately release the various chemicals and bioactive groups when excited by light. Although the absorption spectra of most photocages are in the ultraviolet absorption region, only a few absorb in the visible or near-infrared region. Blebbistatin (Bleb) would release a hydroxyl radical under blue one-photon or two-photon near-infrared light (800 nm) irradiation. In this work, typical chlorine and bromine as leaving groups substituted hydroxyl compounds (Bleb-Cl, Bleb-Br) are synthesized to evaluate the photocage's capability of Bleb's platform. Driven by the excited-state charge transfer, Bleb-Cl and Bleb-Br show good photolysis quantum yield to uncage the halogen anion and the uncaging process would be accelerated in water solution. The photochemical reaction, final product's analysis, and femtosecond transient absorption studies on Bleb-Cl/Bleb-Br demonstrate that Bleb can act as a photocage platform to release the halogen ion via heterolytic reaction when irradiated by blue or near-infrared light. Therefore, Bleb can be a new generation of visible or near-infrared light-triggered photocage.

Bioorthogonal Ligation-Activated Fluorogenic FRET Dyads

An energy transfer-based signal amplification relay concept enabling transmission of bioorthogonally activatable fluorogenicity of blue-excitable coumarins to yellow/red emitting cyanine frames is presented. Such relay mechanism resulted in improved cyanine fluorogenicities together with increased photostabilities and large apparent Stokes-shifts allowing lower background fluorescence even in no-wash bioorthogonal fluorogenic labeling schemes of intracellular structures in live cells. These energy transfer dyads sharing the same donor moiety together with their parent donor molecule allowed three-color imaging of intracellular targets using one single excitation source with separate emission windows. Sub-diffraction imaging of intracellular structures using the bioorthogonally activatable FRET dyads by STED microscopy is also presented.

A Bioorthogonal Double Fluorogenic Probe to Visualize Protein–DNA Interaction

Two sets of bioorthogonally applicable, double fluorogenic probes, capable of sensing DNA–protein interactions, were prepared by installing an azide or tetrazine motif onto structurally fluorogenic, DNA sensitive frames. Installation of these bioorthogonal functions onto DNA intercalating dyes furnished these scaffolds with reactivity based fluorogenicity, rendering these probes double-fluorogenic, AND-type logic switches that require the simultaneous occurrence of a bioorthogonal reaction and interaction with DNA to trigger high intensity fluorescence. The probes were evaluated for double fluorogenic behavior in the presence/absence of DNA and a complementary bioorthogonal function. Our studies revealed that azide and tetrazine appending thiazole orange frames show remarkable double fluorogenic features. One of these probes, a membrane permeable tetrazine modified thiazole orange derivative was further tested in live cell labeling studies. Cells expressing bioorthogonalized DNA-binding proteins showed intensive fluorescence characteristics of the localization of the proteins upon treatment with our double fluorogenic probe. On the contrary, labeling similarly bioorthogonalized cytosolic proteins did not result in the appearance of the fluorescence signal. These studies suggest that such double-fluorogenic probes are indeed capable of sensing DNA–protein interactions in cells.

Conditionally Activatable Photoredox Catalysis in Living Systems

The transformational effect of photoredox catalytic chemistries has inspired new opportunities, enabling us to interrogate nature in ways that are not possible otherwise and to unveil new biotechnologies in therapy and diagnosis. However, the deployment of artificial photoredox catalysis in living systems remains challenging, mired by the off-target risk and safety concerns of photocatalyst toxicity. Here, we present an appealing approach, namely conditionally activatable photoredox catalysis (ConAPC), and as a proof of concept design the first ConAPC architecture (Se-NO2) based upon classic self-immolative chemistry, in which the inherent photocatalytic properties can be temporarily caged while the species becomes active only at the tumor sites via sensing to specific biomarkers. Such a masking strategy allows a spatial-temporal control of photoresponsivity in vitro and in vivo. In particular, for ConAPC design, a new biologically benign metal-free photocatalyst (Se-NH2), which is able to initiate NIR photoredox catalysis to manipulate the cellular electron pool in an O2-independent mechanism of action, is identified. With this unique strategy, potent tumor-specific targeting photocatalytic eradication (TGI: 95%) is obtained in a mouse model. Impressively, favorable features such as high-resolution tumor recognition (SBR: 33.6) and excellent biocompatibility and safety are also achieved. This work therefore offers a new possibility for chemists to leverage artificial photocatalytic reactions toward the development of facile and intelligent photocatalytic theranostics.

Superfast Tetrazole-BCN Cycloaddition Reaction for Bioorthogonal Protein Labeling on Live Cells

Here we report the design of a superfast bioorthogonal ligation reactant pair comprising a sterically shielded, sulfonated tetrazole and bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN). The design involves placing a pair of water-soluble N-sulfonylpyrrole substituents at the C-phenyl ring of diphenyltetrazoles to favor the photoinduced cycloaddition reaction over the competing nucleophilic additions. First-principles computations provide vital insights into the origin of the tetrazole-BCN cycloaddition's superior kinetics compared to the tetrazole-spirohexene cycloaddition. The tetrazole-BCN cycloaddition also enabled rapid bioorthogonal labeling of glucagon receptors on live cells in as little as 15 s.

Derivatization based on tetrazine scaffolds: synthesis of tetrazine derivatives and their biomedical applications

The recent advances in tetrazine scaffold-based derivatizations have been summarized. The advantages and limitations of derivatization methods and applications of the developed tetrazine derivatives in bioorthogonal chemistry have been highlighted.

Click chemistry for fluorescence imaging via combination of a BODIPY-based ‘turn-on’ probe and a norbornene glucosamine

In the present study, we synthesized a novel near-infrared turn-on BODIPY probe and a new norbornene-modified glucosamine derivative.

A nitroreductase responsive and photoactivated fluorescent probe for dual-controlled tumor hypoxia imaging

Tumor hypoxia has great importance in tumor progression and resistance to antitumor therapies. To precisely monitor tumor hypoxia, a controllable hypoxia imaging method is meaningful but still lacking. Herein, we develop a dual-controlled tumor hypoxia probe (TNB) by introducing a nitrophenol group and methyltetrazine group to the boron-dipyrromethene (BODIPY) dye. The fluorescence-quenching group nitrophenol is reduced to aminophenol by upregulated nitroreductase in hypoxic tumors, and the photocage methyltetrazine is cleaved by light irradiation. Hence the fluorescence of TNB is dual-controlled by hypoxia and photoactivation. We first evaluated TNB's potential for controllable hypoxia imaging in solution and tumor cells. The fluorescence of TNB under nitroreductase incubation and photoactivation increased more than 60 fold over that which was untreated or only treated with nitroreductase. Furthermore, results validate that TNB possesses photo-controllable activation features in tumor sections. We believe that the probe design based on enzyme and photoactivation responsiveness provides potential for spatiotemporal detection of other biomarkers.

Tumor hypoxia has great importance in tumor progression and resistance to antitumor therapies.

Molecular platforms based on biocompatible photoreactions for photomodulation of biological targets

Photoirradiation provides a convenient and biocompatible approach for spatiotemporal modulation of biological systems with photoresponsive components. The construction of molecular platforms with a photoresponse to be integrated into biomolecules for photomodulation has been of great research interest in optochemical biology. In this review, we summarize typical molecular platforms that are integratable with biomolecules for photomodulation purposes. We categorize these molecular platforms according to their excitation light source, namely ultraviolet (UV), visible (Vis) or near-infrared (NIR) light. The protype chemistry of these molecular platforms is introduced along with an overview of their most recent applications for spatiotemporal regulation of biomolecular function in living cells or mice models. Challenges and the outlook are also presented. We hope this review paper will contribute to further progress in the development of molecular platforms and their biomedical use.

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.

IEDDA: An Attractive Bioorthogonal Reaction for Biomedical Applications

The pretargeting strategy has recently emerged in order to overcome the limitations of direct targeting, mainly in the field of radioimmunotherapy (RIT). This strategy is directly dependent on chemical reactions, namely bioorthogonal reactions, which have been developed for their ability to occur under physiological conditions. The Staudinger ligation, the copper catalyzed azide-alkyne cycloaddition (CuAAC) and the strain-promoted [3 + 2] azide–alkyne cycloaddition (SPAAC) were the first bioorthogonal reactions introduced in the literature. However, due to their incomplete biocompatibility and slow kinetics, the inverse-electron demand Diels-Alder (IEDDA) reaction was advanced in 2008 by Blackman et al. as an optimal bioorthogonal reaction. The IEDDA is the fastest bioorthogonal reaction known so far. Its biocompatibility and ideal kinetics are very appealing for pretargeting applications. The use of a trans-cyclooctene (TCO) and a tetrazine (Tz) in the reaction encouraged researchers to study them deeply. It was found that both reagents are sensitive to acidic or basic conditions. Furthermore, TCO is photosensitive and can be isomerized to its cis-conformation via a radical catalyzed reaction. Unfortunately, the cis-conformer is significantly less reactive toward tetrazine than the trans-conformation. Therefore, extensive research has been carried out to optimize both click reagents and to employ the IEDDA bioorthogonal reaction in biomedical applications.