Illuminating the chemistry of life: design, synthesis, and applications of "caged" and related photoresponsive compounds

A Live-Cell Epigenome Manipulation by Photo-Stimuli-Responsive Histone Methyltransferase Inhibitor

Post-translational modifications on the histone H3 tail regulate chromatin structure, impact epigenetics, and hence the gene expressions. Current chemical modulation tools, such as unnatural amino acid incorporation, protein splicing, and sortase-based editing, have allowed for the modification of histones with various PTMs in cellular contexts, but are not applicable for editing native chromatin. The use of small organic molecules to manipulate histone-modifying enzymes alters endogenous histone PTMs but lacks precise temporal and spatial control. To date, there has been no achievement in modulating histone methylation in living cells with spatiotemporal resolution. In this study, a new method is presented for temporally manipulating histone dimethylation H3K9me2 using a photo-responsive inhibitor that specifically targets the methyltransferase G9a on demand. The photo-caged molecule is stable under physiological conditions and cellular environments, but rapidly activated upon exposure to light, releasing the bioactive component that can immediately inhibit the catalytic ability of the G9a in vitro. Besides, this masked compound could also efficiently reactivate the inhibition of methyltransferase activity in living cells, subsequently suppress H3K9me2, a mark that regulates various chromatin functions. Therefore, the chemical system will be a valuable tool for manipulating the epigenome for therapeutic purposes and furthering the understanding of epigenetic mechanisms.

A Site-Specific Cross-Linker for Visible-Light Control of Proteins

There is a need for photochemical tools that allow precise control of protein structure and function with visible light. We focus here on the s-tetrazine moiety, which can be installed at a specific protein site via the reaction between dichlorotetrazine and two adjacent sulfhydryl groups. Tetrazine's compact size enables structural mimicry of native amino acid linkages, such as an intramolecular salt bridge or disulfide bond. In this study, we investigated tetrazine installation in three different proteins, where it was confirmed that the cross-linking reaction is highly efficient in aqueous conditions and site-specific when two cysteines are located proximally: the S-S distance was 4-10 Å. As shown in maltose binding protein, the tetrazine cross-linker can replace an interdomain salt bridge crucial for xenon binding and serve as a visible-light photoswitch to modulate 129Xe NMR contrast. This work highlights the ease of aqueous tetrazine bioconjugation and its applications for protein photoregulation.

Recent advances in stimuli-responsive controlled release systems for neuromodulation

Neuromodulation aims to modulate the signaling activity of neurons or neural networks by the precise delivery of electrical stimuli or chemical agents and is crucial for understanding brain function and treating brain disorders. Conventional approaches, such as direct physical stimulation through electrical or acoustic methods, confront challenges stemming from their invasive nature, dependency on wired power sources, and unstable therapeutic outcomes. The emergence of stimulus-responsive delivery systems harbors the potential to revolutionize neuromodulation strategies through the precise and controlled release of neurochemicals in a specific brain region. This review comprehensively examines the biological barriers controlled release systems may encounter in vivo and the recent advances and applications of these systems in neuromodulation. We elucidate the intricate interplay between the molecular structure of delivery systems and response mechanisms to furnish insights for material selection and design. Additionally, the review contemplates the prospects and challenges associated with these systems in neuromodulation. The overarching objective is to propel the application of neuromodulation technology in analyzing brain functions, treating brain disorders, and providing insightful perspectives for exploiting new systems for biomedical applications.

Multi-Photon-Sensitive Chromophore for the Photorelease of Biologically Active Phenols

Phenols confer bioactivity to a plethora of organic compounds. Protecting the phenolic functionality with photoremovable protecting groups (PPGs) sensitive to two-photon excitation (2PE) can block the bioactivity and provide controlled release of these compounds in a spatially and temporally restricted manner by photoactivation with IR light. To develop an efficient 2PE-sensitive PPG for releasing phenols, the (8-cyano-7-hydroxyquinolin-2-yl)methyl (CyHQ) chromophore was functionalized at the C4 position with methyl, morpholine, methoxy, para-tolyl, and 3,4,5-trimethoxyphenyl groups to provide 4-methyl-CyHQ (Me-CyHQ), 4-morpholino-CyHQ (Mor-CyHQ), 4-methoxy-CyHQ (MeO-CyHQ), 4-(p-tolyl)-CyHQ (pTol-CyHQ), and 4-(3,4,5-trimethoxyphenyl)-CyHQ (TMP-CyHQ) PPGs. The probes possess attributes useful for biological use, including high quantum yield (Φu), hydrolytic stability, and good aqueous solubility in physiological conditions. The MeO-CyHQ PPG enhanced the two-photon uncaging action cross section (δu) of dopamine 3.5-fold (0.85 GM) compared to CyHQ (0.24 GM) at 740 nm and 1.49 GM at 720 nm. MeO-CyHQ was used to mediate photoactivation via 2PE of serotonin, rotigotine, N-vanillyl-nonanoylamide (VNA) (a capsaicin analogue), and eugenol. The constructs except rotigotine showed excellent efficiency in 2PE with δu ranging from 0.75 to 1.01 GM at 740 nm and from 1.31 to 1.36 GM at 720 nm high yielding release of the payloads. These probes also performed well by using conventional single photon excitation (1PE). The spatially and temporally controlled release of dopamine from CyHQ-DA and MeO-CyHQ-DA and serotonin (5-HT) from MeO-CyHQ-5HT was quantified in cell culture by using genetically encoded sensors for dopamine and serotonin, respectively. Calcium imaging was employed to quantify the release of VNA and eugenol (EG) from MeO-CyHQ-VNA and MeO-CyHQ-EG, respectively. These tools will enable experiments to understand the intricate mechanisms involved in neurological signaling and the roles played by neurotransmitters, such as dopamine and serotonin, in the activation of their respective receptors.

Isoform-specific optical activation of kinase function reveals p38-ERK signaling crosstalk

Evolution has diversified the mammalian proteome by the generation of protein isoforms that originate from identical genes, e.g., through alternative gene splicing or post-translational modifications, or very similar genes found in gene families. Protein isoforms can have either overlapping or unique functions and traditional chemical, biochemical, and genetic techniques are often limited in their ability to differentiate between isoforms due to their high similarity. This is particularly true in the context of highly dynamic cell signaling cascades, which often require acute spatiotemporal perturbation to assess mechanistic details. To that end, we describe a method for the selective perturbation of the individual protein isoforms of the mitogen-activated protein kinase (MAPK) p38. The genetic installation of a photocaging group at a conserved active site lysine enables the precise light-controlled initiation of kinase signaling, followed by investigation of downstream events. Through optical control, we have identified a novel point of crosstalk between two major signaling cascades: the p38/MAPK pathway and the extracellular signal-regulated kinase (ERK)/MAPK pathway. Specifically, using the photoactivated p38 isoforms, we have found the p38γ and p38δ variants to be positive regulators of the ERK signaling cascade, while confirming the p38α and p38β variants as negative regulators.

Crystal Structure of an Archaeal Tyrosyl-tRNA Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-ray Crystallography

Genetically encoded caged amino acids can be used to control the dynamics of protein activities and cellular localization in response to external cues. In the present study, we revealed the structural basis for the recognition of O-(2-nitrobenzyl)-L-tyrosine (oNBTyr) by its specific variant of Methanocaldococcus jannaschii tyrosyl-tRNA synthetase (oNBTyrRS), and then demonstrated its potential availability for time-resolved X-ray crystallography. The substrate-bound crystal structure of oNBTyrRS at a 2.79 Å resolution indicated that the replacement of tyrosine and leucine at positions 32 and 65 by glycine (Tyr32Gly and Leu65Gly, respectively) and Asp158Ser created sufficient space for entry of the bulky substitute into the amino acid binding pocket, while Glu in place of Leu162 formed a hydrogen bond with the nitro moiety of oNBTyr. We also produced an oNBTyr-containing lysozyme through a cell-free protein synthesis system derived from the Escherichia coli B95. ΔA strain with the UAG codon reassigned to the nonnatural amino acid. Another crystallographic study of the caged protein showed that the site-specifically incorporated oNBTyr was degraded to tyrosine by light irradiation of the crystals. Thus, cell-free protein synthesis of caged proteins with oNBTyr could facilitate time-resolved structural analysis of proteins, including medically important membrane proteins.

Synthesis and mammalian cell compatibility of light-released glycan precursors for controlled metabolic engineering

Sugar additions to biomolecules, or glycans, are some of the most abundant biomolecule modifications in biology because they enable cells to adapt to changing nutrient and stress conditions. An unmet challenge for the field of glycobiology is the study of glycan biosynthetic pathways with chemical control, especially in live cell settings. The objective of this study was to create biocompatible glycan precursors with controlled release properties. Here, we report eleven "caged" sugar probes that release glycan biosynthetic precursor molecules upon light exposure. The specific sugar pathways we target with our probes regulate the addition of the N-acetyl sugars GlcNAc, GalNAc, and sialic acid onto biomolecules in cells, each of which has the potential to alter glycan processes involved in cell morphology, signaling, and behavior. We hypothesized that our glycan precursor probes would remain biologically inert until light-initiated decaging conditions were met, avoiding biological activities including metabolism and cytotoxicity. The photocaged analogs of GlcNAc, GalNAc, and ManNAc (sialic acid precursor) sugars, which we call "photo-sugars," were released within minutes of light exposure at their optimal wavelengths. During the course of the study, we characterized the cell compatibility of these sugars under their respective decaging conditions, and found highly cell compatible GlcNAc, GalNAc, and ManNAc photocaged precursors. Release of GlcNAc-1-phosphate precursors led to altered ATP levels in cells, demonstrating preliminary metabolic engineering. We envision these probes as useful additions to the chemical glycobiology field that will enable spatiotemporal control over glycosylation pathways in living mammalian cells.

Deactivation of a dimeric DNA-binding peptide through a palladium-mediated self-immolative cleavage

Herein, we describe an approach for the on-demand disassembly of dimeric peptides using a palladium-mediated cleavage of a designed self-immolative linker. The utility of the strategy is demonstrated for the case of dimeric basic regions of bZIP transcription factors. While the dimer binds designed DNA sequences with good affinities, the peptide-DNA complex can be readily dismounted by addition of palladium reagents that trigger the cleavage of the spacer, and the release of unfunctional monomeric peptides.

Molecular photoswitches in aqueous environments

Molecular photoswitches enable dynamic control of processes with high spatiotemporal precision, using light as external stimulus, and hence are ideal tools for different research areas spanning from chemical biology to smart materials. Photoswitches are typically organic molecules that feature extended aromatic systems to make them responsive to (visible) light. However, this renders them inherently lipophilic, while water-solubility is of crucial importance to apply photoswitchable organic molecules in biological systems, like in the rapidly emerging field of photopharmacology. Several strategies for solubilizing organic molecules in water are known, but there are not yet clear rules for applying them to photoswitchable molecules. Importantly, rendering photoswitches water-soluble has a serious impact on both their photophysical and biological properties, which must be taken into consideration when designing new systems. Altogether, these aspects pose considerable challenges for successfully applying molecular photoswitches in aqueous systems, and in particular in biologically relevant media. In this review, we focus on fully water-soluble photoswitches, such as those used in biological environments, in both in vitro and in vivo studies. We discuss the design principles and prospects for water-soluble photoswitches to inspire and enable their future applications.

Single-cell analysis of regions of interest (SCARI) using a photosensitive tag

The functional activity and differentiation potential of cells are determined by their interactions with surrounding cells. Approaches that allow unbiased characterization of cell states while at the same time providing spatial information are of major value to assess this environmental influence. However, most current techniques are hampered by a tradeoff between spatial resolution and cell profiling depth. Here, we develop a photocage-based technology that allows isolation and in-depth analysis of live cells from regions of interest in complex ex vivo systems, including primary human tissues. The use of a highly sensitive 4-nitrophenyl(benzofuran) cage coupled to a set of nanobodies allows high-resolution photo-uncaging of different cell types in areas of interest. Single-cell RNA-sequencing of spatially defined CD8+ T cells is used to exemplify the feasibility of identifying location-dependent cell states. The technology described here provides a valuable tool for the analysis of spatially defined cells in diverse biological systems, including clinical samples.

Photo-induced variation of magnetism in coordination polymers with ligand-based electron transfer

Photo-induced variation of magnetism from ligand-based electron transfer has been extensively studied because of its potential applications in magneto-optical memory devices, light-responsive switches, and high-density information storage materials. In this review, we discussed the progress in the photo-induced variation of magnetism in coordination polymers with ligand-to-metal charge transfer (LMCT), ligand-to-ligand charge transfer (LLCT) and internal ligand charge transfer (ILCT), which provides fundamentals for the rational design of multi-functional materials. We also discussed the design and synthetic strategy of such molecule-based materials and gave views on the current challenges and growth trends in this field.

Caged Oxime Reactivators Designed for the Light Control of Acetylcholinesterase Reactivation†

Despite its promising role in the active control of biological functions by light, photocaging remains untested in acetylcholinesterase (AChE), a key enzyme in the cholinergic family. Here, we describe synthesis, photochemical properties and biochemical activities of two caged oxime compounds applied in the photocontrolled reactivation of the AChE inactivated by reactive organophosphate. Each of these consists of a photocleavable coumarin cage tethered to a known oxime reactivator for AChE that belongs in an either 2-(hydroxyimino)acetamide or pyridiniumaldoxime class. Of these, the first caged compound was able to successfully go through oxime uncaging upon irradiation at long-wavelength ultraviolet light (365 nm) or visible light (420 nm). It was further evaluated in AChE assays in vitro under variable light conditions to define its activity in the photocontrolled reactivation of paraoxon-inactivated AChE. This assay result showed its lack of activity in the dark but its induction of activity under light conditions only. In summary, this article reports a first class of light-activatable modulators for AChE and it offers assay methods and novel insights that help to achieve an effective design of caged compounds in the enzyme control.

Photocleavable proteins that undergo fast and efficient dissociation

Photocleavable molecules can enable the light-dependent modulation of biomolecular activities with high spatiotemporal precision. We have previously reported a photocleavable protein (PhoCl1) that, uniquely, is a fully genetically encoded photocleavable molecule that can be introduced into cells in the form of its corresponding gene to enable optogenetic control of biomolecular activities. However, the first generation PhoCl1 exhibited a relatively slow rate of dissociation, potentially limiting its utility. Here, we report the X-ray crystal structures of the PhoCl1 green state, red state, and cleaved empty barrel. Molecular dynamics (MD) simulations were performed to provide insight into the precise dissociation mechanism. Using structure-guided engineering and directed evolution, we have developed PhoCl2c with higher contrast ratio and PhoCl2f with faster dissociation. We characterized the performance of these new variants as purified proteins and in cultured cells. Our results demonstrate that PhoCl2 variants exhibit faster and more efficient dissociation, which should enable improved optogenetic manipulations of protein localization and protein-protein interactions in living cells.

Targeted Cancer Therapy Using Compounds Activated by Light

Cancer chemotherapy is affected by a modest selectivity and toxic side effects of pharmacological interventions. Among novel approaches to overcome this limitation and to bring to therapy more potent and selective agents is the use of light for selective activation of anticancer compounds. In this review, we focus on the anticancer applications of two light-activated approaches still in the experimental phase: photoremovable protecting groups ("photocages") and photoswitches. We describe the structural considerations behind the development of novel compounds and the plethora of assays used to confirm whether the photochemical and pharmacological properties are meeting the stringent criteria for an efficient in vivo light-dependent activation. Despite its immense potential, light activation brings many challenges, and the complexity of the task is very demanding. Currently, we are still deeply in the phase of pharmacological tools, but the vivid research and rapid development bring the light of hope for potential clinical use.

Small GTPases modulate intrinsic and extrinsic forces that control epithelial folding in Drosophila embryos

Epithelial folding is a common means to execute morphogenetic movements. The gastrulating Drosophila embryo offers many examples of epithelial folding events, including the ventral, cephalic, and dorsal furrows. Each of these folding events is associated with changes in intracellular contractility and/or cytoskeleton structures that autonomously promote epithelial folding. Here, we review accumulating evidence that suggests the progression and final form of ventral, cephalic, and dorsal furrows are also influenced by the behaviour of cells neighbouring these folds. We further discuss the prevalence and importance of junctional rearrangements during epithelial folding events, suggesting adherens junction components are prime candidates to modulate the transmission of the intercellular forces that influence folding events. Finally, we discuss how recently developed methods that enable precise spatial and/or temporal control of protein activity allow direct testing of molecular models of morphogenesis in vivo.

Optical control of purinergic signaling

Purinergic signaling plays a pivotal role in physiological processes and pathological conditions. Over the past decades, conventional pharmacological, biochemical, and molecular biology techniques have been utilized to investigate purinergic signaling cascades. However, none of them is capable of spatially and temporally manipulating purinergic signaling cascades. Currently, optical approaches, including optopharmacology and optogenetic, enable controlling purinergic signaling with low invasiveness and high spatiotemporal precision. In this mini-review, we discuss optical approaches for controlling purinergic signaling and their applications in basic and translational science.

Inducible CRISPR-dCas9 Transcriptional Systems for Sensing and Genome Regulation

The clustered, regularly interspaced short palindromic repeats-associated protein 9 endonuclease (CRISPR-Cas9) and the nuclease-deactivated Cas9 (dCas9) systems have revolutionized our ability to precisely engineer and regulate genomes. Inducible CRISPR-dCas9-based transcriptional systems have been rapidly developed to conditionally control genetic manipulation. Current strategies mainly focus on conditional control of gRNA function and dCas9 protein using exogenous and endogenous triggers, including external light, small molecules, synthetic and intracellular oligonucleotides. These strategies have established novel platforms for the spatiotemporal regulation of genome activation and repression, epigenome editing, and so on. Herein, we summarize the recent progress in conditionally controlling CRISPR-dCas9 transcriptional systems through gRNA modulation and dCas9 protein engineering.

Efficient implementation of isotropic cubic response functions for two-photon absorption cross sections within the self-consistent field approximation

Within the self-consistent field approximation, computationally tractable expressions for the isotropic second-order hyperpolarizability have been derived and implemented for the calculation of two-photon absorption cross sections. The novel tensor average formulation presented in this work allows for the evaluation of isotropic damped cubic response functions using only ∼3.3% (one-photon off-resonance regions) and ∼10% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of the two-photon absorption cross section in the one-photon off-resonance and resonance regions are provided for alanine-tryptophan and 2,5-dibromo-1,4-bis(2-(4-diphenylaminophenyl)vinyl)-benzene. Furthermore, a benchmark set of 22 additional small- and medium-sized organic molecules is considered. In all these calculations, a quantitative assessment is made of the reduced and approximate forms of the cubic response function in the one-photon off-resonance regions and results demonstrate a relative error of less than ∼5% when using the reduced expression as compared to the full form of the isotropic cubic response function.

Visible-to-NIR-Light Activated Release: From Small Molecules to Nanomaterials

Photoactivatable (alternatively, photoremovable, photoreleasable, or photocleavable) protecting groups (PPGs), also known as caged or photocaged compounds, are used to enable non-invasive spatiotemporal photochemical control over the release of species of interest. Recent years have seen the development of PPGs activatable by biologically and chemically benign visible and near-infrared (NIR) light. These long-wavelength-absorbing moieties expand the applicability of this powerful method and its accessibility to non-specialist users. This review comprehensively covers organic and transition metal-containing photoactivatable compounds (complexes) that absorb in the visible- and NIR-range to release various leaving groups and gasotransmitters (carbon monoxide, nitric oxide, and hydrogen sulfide). The text also covers visible- and NIR-light-induced photosensitized release using molecular sensitizers, quantum dots, and upconversion and second-harmonic nanoparticles, as well as release via photodynamic (photooxygenation by singlet oxygen) and photothermal effects. Release from photoactivatable polymers, micelles, vesicles, and photoswitches, along with the related emerging field of photopharmacology, is discussed at the end of the review.

Site-Specific Incorporation of a Photoactivatable Fluorescent Amino Acid

Photoactivatable fluorophores are emerging optical probes for biological applications. Most photoactivatable fluorophores are relatively large in size and need to be activated by ultraviolet light; this dramatically limits their applications. To introduce photoactivatable fluorophores into proteins, recent investigations have explored several protein-labeling technologies, including fluorescein arsenical hairpin (FlAsH) Tag, HaloTag labeling, SNAPTag labeling, and other bioorthogonal chemistry-based methods. However, these technologies require a multistep labeling process. Here, by using genetic code expansion and a single sulfur-for-oxygen atom replacement within an existing fluorescent amino acid, we have site-specifically incorporated the photoactivatable fluorescent amino acid thioacridonylalanine (SAcd) into proteins in a single step. Moreover, upon exposure to visible light, SAcd can be efficiently desulfurized to its oxo derivatives, thus restoring the strong fluorescence of labeled proteins.

Engineering Photosensory Modules of Non-Opsin-Based Optogenetic Actuators

Optogenetic (photo-responsive) actuators engineered from photoreceptors are widely used in various applications to study cell biology and tissue physiology. In the toolkit of optogenetic actuators, the key building blocks are genetically encodable light-sensitive proteins. Currently, most optogenetic photosensory modules are engineered from naturally-occurring photoreceptor proteins from bacteria, fungi, and plants. There is a growing demand for novel photosensory domains with improved optical properties and light-induced responses to satisfy the needs of a wider variety of studies in biological sciences. In this review, we focus on progress towards engineering of non-opsin-based photosensory domains, and their representative applications in cell biology and physiology. We summarize current knowledge of engineering of light-sensitive proteins including light-oxygen-voltage-sensing domain (LOV), cryptochrome (CRY2), phytochrome (PhyB and BphP), and fluorescent protein (FP)-based photosensitive domains (Dronpa and PhoCl).

A near-infrared light-mediated cleavable linker strategy using the heptamethine cyanine chromophore

Optical methods offer the potential to manipulate living biological systems with exceptional spatial and temporal control. Caging bioactive molecules with photocleavable functional groups is an important strategy that could be applied to a range of problems, including the targeted delivery of otherwise toxic therapeutics. However existing approaches that require UV or blue light are difficult to apply in organismal settings due to issues of tissue penetration and light toxicity. Photocaging groups built on the heptamethine cyanine scaffold enable the targeted delivery of bioactive molecules using near-IR light (up to 780nm) in live animal settings. Here we provide a detailed procedure demonstrating the utility of the heptamethine cyanine caging group to create a light-cleavable linker between an antibody, panitumumab, and a therapeutic small molecule in the duocarmycin class of natural products. Descriptions of the design and synthesis of the small molecule component, assembly of the antibody conjugate, in vitro analysis of uncaging, in vivo imaging, and impact on tumor progression are provided.

Synthesis of hydrophilic caged DAG-lactones for chemical biology applications

The 6-bromo-7-hydroxy-coumarin-4-ylmethyl (Bhc) group has been used widely in cage chemistry because of its high molar absorptivity and photolytic efficiency. One of the drawbacks of coumarins however is their low aqueous solubility. Aqueous solubility is important in the behavior of caged compounds because hydrophobic caged compounds might be aggregated in physiological conditions and consequently the photocleavage would be impaired. The 8-azacoumarin-4-ylmethyl derivatives with bromine (8-aza-Bhc) or iodine (8-aza-Ihc), which were previously developed in this laboratory, have aqueous solubilities that are higher than those of related coumarins. Here, to improve the hydrophilicity and management of caged diacylglycerol lactones (DAG-lactones), 8-aza-Bhc and 8-aza-Ihc were introduced into the DAG-lactone structure. The synthesized caged compounds showed high hydrophilicity compared with the parent Bhc-caged DAG-lactone, and the 8-aza-Ihc-caged DAG-lactone (2) showed excellent photolytic efficiency, which allows rapid release of the DAG-lactone (1) by brief photoirradiation. The 8-aza-7-hydroxy-6-iodo-coumarin-4-ylmethyl group might be useful for caging of bioactive compounds, especially hydrophobic compounds.

Diffusion of DNA-Binding Species in the Nucleus: A Transient Anomalous Subdiffusion Model

Single-particle tracking experiments have measured escape times of DNA-binding species diffusing in living cells: CRISPR-Cas9, TetR, and LacI. The observed distribution is a truncated power law. Working backward from the experimental results, the observed distribution appears inconsistent with a Gaussian distribution of binding energies. Working forward, the observed distribution leads to transient anomalous subdiffusion, in which diffusion is anomalous at short times and normal at long times, here only mildly anomalous. Monte Carlo simulations are used to characterize the time-dependent diffusion coefficient D(t) in terms of the anomalous exponent α, the crossover time tcross, and the limits D(0) and D(∞) and to relate these quantities to the escape time distribution. The simplest interpretations identify the escape time as the actual binding time to DNA or the period of one-dimensional diffusion on DNA in the standard model combining one-dimensional and three-dimensional search, but a more complicated interpretation may be required. The model has several implications for cell biophysics. 1) The initial anomalous regime represents the search of the DNA-binding species for its target DNA sequence. 2) Non-target DNA sites have a significant effect on search kinetics. False positives in bioinformatic searches of the genome are potentially rate-determining in vivo. For simple binding, the search would be speeded if false-positive sequences were eliminated from the genome. 3) Both binding and obstruction affect diffusion. Obstruction ought to be measured directly, using as the primary probe the DNA-binding species with the binding site inactivated and eGFP as a calibration standard among laboratories and cell types. 4) Overexpression of the DNA-binding species reduces anomalous subdiffusion because the deepest binding sites are occupied and unavailable. 5) The model provides a coarse-grained phenomenological description of diffusion of a DNA-binding species, useful in larger-scale modeling of kinetics, FCS, and FRAP.

Substrate-Photocaged Enzymatic Fluorogenic Probe Enabling Sequential Activation for Light-Controllable Monitoring of Intracellular Tyrosinase Activity

Tyrosinase (TYR) is a crucial enzyme involved in melanogenesis, and its overexpression is closely associated with melanoma. To precisely monitor intracellular TYR activity, remote control of a molecule imaging tool is highly meaningful but remains to be explored. In this work, we present the first photocaged tyrosinase fluorogenic probe by caging the substrate of the enzymatic probe with a photolabile group. Because of the sequential light and enzyme-activation feature, this probe exhibits photocontrollable "turn on" response toward TYR with good selectivity and high sensitivity (detection limit: 0.08 U/mL). Fluorescence imaging results validate that the caged probe possesses the capability of visualizing intracellular endogenous tyrosinase activity in a photocontrol fashion, thus offering a promising molecule imaging tool for investigating TYR-related physiological function and pathological role. Moreover, our sequential activation strategy has great potential for developing more photocontrollable enzymatic fluorogenic probes with spatiotemporal resolution.

Optofluidic control of rodent learning using cloaked caged glutamate

Glutamate is the major excitatory neurotransmitter in the brain, and photochemical release of glutamate (or uncaging) is a chemical technique widely used by biologists to interrogate its physiology. A basic prerequisite of these optical probes is bio-inertness before photolysis. However, all caged glutamates are known to have strong antagonism toward receptors of γ-aminobutyric acid, the major inhibitory transmitter. We have developed a caged glutamate probe that is inert toward these receptors at concentrations that are effective for photolysis with violet light. Pharmacological tests in vitro revealed that attachment of a fifth-generation (G5) dendrimer (i.e., cloaking) to the widely used 4-methoxy-7-nitro-indolinyl(MNI)-Glu probe prevented such off-target effects while not changing the photochemical properties of MNI-Glu significantly. G5-MNI-Glu was used with optofluidic delivery to stimulate dopamine neurons of the ventral tegmental area of freely moving mice in a conditioned place-preference protocol so as to mediate Pavlovian conditioning.

Spacer-Mediated Control of Coumarin Uncaging for Photocaged Thymidine

Despite its importance in the design of photocaged molecules, less attention is focused on linker chemistry than the cage itself. Here, we describe unique uncaging properties displayed by two coumarin-caged thymidine compounds, each conjugated with (2) or without (1) an extended, self-immolative spacer. Photolysis of 1 using long-wavelength UVA (365 nm) or visible (420, 455 nm) light led to the release of free thymidine along with the competitive generation of a thymidine-bearing recombination product. The occurrence of this undesired side reaction, which is previously unreported, was not present with the photolysis of 2, which released thymidine exclusively with higher quantum efficiency. We propose that the spatial separation between the cage and the substrate molecule conferred by the extended linker can play a critical role in circumventing this unproductive reaction. This report reinforces the importance of linker selection in the design of coumarin-caged oligonucleosides and other conjugates.

Water-Soluble BODIPY Photocages with Tunable Cellular Localization

Photoactivation of bioactive molecules allows manipulation of cellular processes with high spatiotemporal precision. The recent emergence of visible-light excitable photoprotecting groups has the potential to further expand the established utility of the photoactivation strategy in biological applications by offering higher tissue penetration, diminished phototoxicity, and compatibility with other light-dependent techniques. Nevertheless, a critical barrier to such applications remains the significant hydrophobicity of most visible-light excitable photocaging groups. Here, we find that applying the conventional 2,6-sulfonation to meso-methyl BODIPY photocages is incompatible with their photoreaction due to an increase in the excited state barrier for photorelease. We present a simple, remote sulfonation solution to BODIPY photocages that imparts water solubility and provides control over cellular permeability while retaining their favorable spectroscopic and photoreaction properties. Peripherally disulfonated BODIPY photocages are cell impermeable, making them useful for modulation of cell-surface receptors, while monosulfonated BODIPY retains the ability to cross the cellular membrane and can modulate intracellular targets. This new approach is generalizable for controlling BODIPY localization and was validated by sensitization of mammalian cells and neurons by visible-light photoactivation of signaling molecules.

Engineered BRET-Based Biologic Light Sources Enable Spatiotemporal Control over Diverse Optogenetic Systems

Light-inducible optogenetic systems offer precise spatiotemporal control over a myriad of biologic processes. Unfortunately, current systems are inherently limited by their dependence on external light sources for their activation. Further, the utility of laser/LED-based illumination strategies are often constrained by the need for invasive surgical procedures to deliver such devices and local heat production, photobleaching and phototoxicity that compromises cell and tissue viability. To overcome these limitations, we developed a novel BRET-activated optogenetics (BEACON) system that employs biologic light to control optogenetic tools. BEACON is driven by self-illuminating bioluminescent-fluorescent proteins that generate "spectrally tuned" biologic light via bioluminescence resonance energy transfer (BRET). Notably, BEACON robustly activates a variety of commonly used optogenetic systems in a spatially restricted fashion, and at physiologically relevant time scales, to levels that are achieved by conventional laser/LED light sources.

Synthesis and activation of an iron oxide immobilized drug-mimicking reporter under conventional and pulsed X-ray irradiation conditions

An efficient nano-sized delivery system is presented here allowing the immobilized, picolinium-tethered organic ligand to be released by X-ray irradiation. A marked difference was observed in the fragmentation efficiency by using conventional Cs-137 vs. pulsed sources.

The nano-sized delivery system allowed releasing complex organic ligands by X-ray irradiation. Marked difference was observed in the release efficiency by using conventional Cs-137 vs. pulsed sources.

Tumor targeting vitamin B12 derivatives for X-ray induced treatment of pancreatic adenocarcinoma

BACKGROUND

X-Ray induced phototherapy is highly sought after as it provides a deep tissue, synergistic method of treating cancers via standard-of-care radiotherapy. When this is combined with releasable chemotherapy agents, it can provide high target selectivity, with reduced off-target organ effects that limit current systemic therapies. We have recently developed a unique light-activated drug delivery system whereby the drug is conjugated to an alkylcobalamin scaffold. Alkylcobalamins are actively transported into cells by transcobalamin receptors (TCblR), which are overexpressed in a variety of cancer types. We hope to utilize this cobalamin scaffold technology for drug delivery in pancreatic adenocarcinoma (PDAC) cancer.

METHODS

The ability of the cobalamin scaffold to selectively target PDAC was investigated by treating mice that had MIA PaCa-2 xenografts with an alkylcobalamin labeled with the fluorophore Bodipy650 (Bodipy650-cobalamin). The mice were imaged alive and organs as well as tumors were subsequently imaged ex vivo. In addition, we examined the potential of the cobalamin scaffold to deliver drugs to orthotopic pancreas MIA PaCa-2 tumors with Bodipy650-cobalamin. We determined the light dose required for release of cargo from the cobalamin scaffold by examining the fluorescence increase of Bodipy650-cobalamin in response to red light (650 nm). Finally, we probed the ability of the cobalamin scaffold to release cargo with increasing X-ray doses from a clinical linear accelerator.

RESULTS

We have found that Bodipy650-cobalamin was shown to localize in MIA PaCa-2 tumors, both in flank and orthotopic models. We quantified a light dose for red light release from the cobalamin scaffold that is within normal clinical doses required for photodynamic therapy. This derivative was also activated with clinical X-ray doses from a linear accelerator.

CONCLUSIONS

Tumor selectivity combined with fluorescence detection demonstrates the effectiveness of the vitamin B₁₂ scaffold as a theranostic targeting agent. The activation of this scaffold with radiation from a linear accelerator shows potential for action as radiation-induced chemotherapy.

Development of Prodrugs for PDT-Based Combination Therapy Using a Singlet-Oxygen-Sensitive Linker and Quantitative Systems Pharmacology

Photodynamic therapy (PDT) has become an effective treatment for certain types of solid tumors. The combination of PDT with other therapies has been extensively investigated in recent years to improve its effectiveness and expand its applications. This focused review summarizes the development of a prodrug system in which anticancer drugs are activated locally at tumor sites during PDT treatment. The development of a singlet-oxygen-sensitive linker that can be conveniently conjugated to various drugs and efficiently cleaved to release intact drugs is recapitulated. The initial design of prodrugs, preliminary efficacy evaluation, pharmacokinetics study, and optimization using quantitative systems pharmacology is discussed. Current treatment optimization in animal models using physiologically based a pharmacokinetic (PBPK) modeling approach is also explored.

Development of Chemical Biology Tools Focusing on Peptide/Amide Bond Cleavage Reaction

Peptides and proteins are involved in almost all biological events. In this review, three chemical biology tools, which were developed for peptide/protein sciences from a viewpoint of peptide/amide bond cleavage, are overviewed. First, study on an artificial amino acid that enables stimulus-responsive functional control of peptides/proteins is briefly described. Two N-S acyl transfer reaction-based tools, one a linker molecule for facile identification of target proteins of bioactive compounds and the other a reagent for selective labeling of proteins of interest, are then discussed.

Photo-triggered Drug Delivery Systems for Neuron-related Applications

The development of materials, chemistry and genetics has created a great number of systems for delivering antibiotics, neuropeptides or other drugs to neurons in neuroscience research, and has also provided important and powerful tools in neuron-related applications. Although these drug delivery systems can facilitate the advancement of neuroscience studies, they still have limited applications due to various drawbacks, such as difficulty in controlling delivery molecules or drugs to the target region, and trouble of releasing them in predictable manners. The combination of optics and drug delivery systems has great potentials to address these issues and deliver molecules or drugs to the nervous system with extraordinary spatiotemporal selectivity triggered by light. In this review, we will introduce the development of photo-triggered drug delivery systems in neuroscience research and their neuron-related applications including regulating neural activities, treating neural diseases and inducing nerve regenerations.

Development of photolabile protecting groups and their application to the optochemical control of cell signaling

Many biological processes are naturally regulated with spatiotemporal control. In order to perturb and investigate them, optochemical tools have been developed that convey similar spatiotemporal precision. Pivotal to optochemical probes are photolabile protecting groups, so called caging groups, and recent developments have enabled new applications to cellular processes, including cell signaling. This review focuses on the advances made in the field of caging groups and their application in cell signaling through caged molecules such as neurotransmitters, lipids, secondary messengers, and proteins.

Crystal structure of a domain-swapped photoactivatable sfGFP variant provides evidence for GFP folding pathway

Photoactivatable fluorescent proteins (PA-FPs) are a powerful non-invasive tool in high-resolution live-cell imaging. They can be converted from an inactive to an active form by light, enabling the spatial and temporal trafficking of proteins and cell dynamics. PA-FPs have been previously generated by mutating selected residues in the chromophore or in its close proximity. A new strategy to generate PA-FPs is the genetic incorporation of unnatural amino acids (UAAs) containing photocaged groups using unique suppressor tRNA/aminoacyl-tRNA synthetase pairs. We set out to develop a photoactivatable GFP variant suitable for time-resolved structural studies. Here, we report the crystal structure of superfolder GFP (sfGFP) containing the UAA ortho-nitrobenzyl-tyrosine (ONBY) at position 66 and its spectroscopic characterization. Surprisingly, the crystal structure (to 2.7 Å resolution) reveals a dimeric domain-swapped arrangement of sfGFP66ONBY with residues 1-142 of one molecule associating with residues 148-234 from another molecule. This unusual domain-swapped structure supports a previously postulated GFP folding pathway that proceeds via an equilibrium intermediate.

A Cyanine Photooxidation/β-Elimination Sequence Enables Near-infrared Uncaging of Aryl Amine Payloads

Uncaging strategies that use near-infrared wavelengths can enable the highly targeted delivery of biomolecules in complex settings. Many methods, including an approach we developed using cyanine photooxidation, are limited to phenol-containing payloads. Given the critical role of amines in diverse biological processes, we sought to use cyanine photooxidation to initiate the release of aryl amines. Heptamethine cyanines substituted with an aryl amine at the C4' position undergo only inefficient release, likely due electronic factors. We then pursued the hypothesis that the carbonyl products derived from cyanine photooxidation could undergo efficient β-elimination. After examining both symmetrical and unsymmetrical scaffolds, we identify a merocyanine substituted with indolenine and coumarin heterocycles that undergoes efficient photooxidation and aniline uncaging. In total, these studies provide a new scheme-cyanine photooxidation followed by β-elimination-through which to design photocages with efficient uncaging properties.

Optogenetic perturbation of the biochemical pathways that control cell behavior

Optogenetic tools provide a level of spatial and temporal resolution needed to shed new light on dynamic intercellular processes. In this chapter we outline specific protocols for applying these tools to cell motility (optogenetic cofilin), apoptosis [optogenetic Bcl-like protein 4 (Bax)], and protein kinase-mediated signaling pathways [optogenetic cAMP-dependent protein kinase (PKA)]. The activity of these optogenetic species is regulated by the light-mediated dimerization of a cryptochrome/Cib protein pair, which controls the intracellular positioning of the protein of interest. The light induced recruitment of cofilin to the cytoskeleton is utilized for directed migration studies and filopodial dynamics. Light-triggered migration of Bax to the outer mitochondrial membrane induces cellular collapse and eventual apoptosis. Finally, the light-mediated movement of PKA to specific intracellular compartments offers the means to assess the consequences of PKA activity in a site-specific fashion via phosphoproteomic analysis.

Protected 5-(hydroxymethyl)uracil nucleotides bearing visible-light photocleavable groups as building blocks for polymerase synthesis of photocaged DNA

Nucleosides, nucleotides and 2'-deoxyribonucleoside triphosphates (dNTPs) containing 5-(hydroxymethyl)uracil protected with photocleavable groups (2-nitrobenzyl-, 6-nitropiperonyl or 9-anthrylmethyl) were prepared and tested as building blocks for the polymerase synthesis of photocaged oligonucleotides and DNA. Photodeprotection (photorelease) reactions were studied in detail on model nucleoside monophosphates and their photoreaction quantum yields were determined. Photocaged dNTPs were then tested and used as substrates for DNA polymerases in primer extension or PCR. DNA probes containing photocaged or free 5-hydroxymethylU in the recognition sequence of restriction endonucleases were prepared and used for the study of photorelease of caged DNA by UV or visible light at different wavelengths. The nitropiperonyl-protected nucleotide was found to be a superior building block because the corresponding dNTP is a good substrate for DNA polymerases, and the protecting group is efficiently cleavable by irradiation by UV or visible light (up to 425 nm).

Light-triggered release of photocaged therapeutics - Where are we now?

The current available therapeutics face several challenges such as the development of ideal drug delivery systems towards the goal of personalized treatments for patients benefit. The application of light as an exogenous activation mechanism has shown promising outcomes, owning to the spatiotemporal confinement of the treatment in the vicinity of the diseased tissue, which offers many intriguing possibilities. Engineering therapeutics with light responsive moieties have been explored to enhance the bioavailability, and drug efficacy either in vitro or in vivo. The tailor-made character turns the so-called photocaged compounds highly desirable to reduce the side effects of drugs and, therefore, have received wide research attention. Herein, we seek to highlight the potential of photocaged compounds to obtain a clear understanding of the mechanisms behind its use in therapeutic delivery. A deep overview on the progress achieved in the design, fabrication as well as current and possible future applications in therapeutics of photocaged compounds is provided, so that novel formulations for biomedical field can be designed.

Photocatalysis Enables Visible-Light Uncaging of Bioactive Molecules in Live Cells

The photo-manipulation of bioactive molecules provides unique advantages due to the high temporal and spatial precision of light. The first visible-light uncaging reaction by photocatalytic deboronative hydroxylation in live cells is now demonstrated. Using Fluorescein and Rhodamine derivatives as photocatalysts and ascorbates as reductants, transient hydrogen peroxides were generated from molecular oxygen to uncage phenol, alcohol, and amine functional groups on bioactive molecules in bacteria and mammalian cells, including neurons. This effective visible-light uncaging reaction enabled the light-inducible protein expression, the photo-manipulation of membrane potentials, and the subcellular-specific photo-release of small molecules.

Optoregulated Biointerfaces to Trigger Cellular Responses

Optoregulated biointerfaces offer the possibility to manipulate the interactions between cell membrane receptors and the extracellular space. This Invited Feature Article summarizes recent efforts by our group and others during the past decade to develop light-responsive biointerfaces to stimulate cells and elicit cellular responses using photocleavable protecting groups (PPG) as our working tool. This article begins by providing a brief introduction to available PPGs, with a special focus on the widely used o-nitrobenzyl family, followed by an overview of molecular design principles for the control of bioactivity in the context of cell-material interactions and the characterization methods to use in following the photoreaction at surfaces. We present various light-guided cellular processes using PPGs, including cell adhesion, release, migration, proliferation, and differentiation, both in vitro and in vivo. Finally, this Invited Feature Article closes with our perspective on the current status and future challenges of this topic.

Palladium-mediated enzyme activation suggests multiphase initiation of glycogenesis

Biosynthesis of glycogen, the essential glucose (and hence energy) storage molecule in humans, animals and fungi¹, is initiated by the glycosyltransferase enzyme, glycogenin (GYG). Deficiencies in glycogen formation cause neurodegenerative and metabolic disease^2-4, and mouse knockout⁵ and inherited human mutations⁶ of GYG impair glycogen synthesis. GYG acts as a 'seed core' for the formation of the glycogen particle by catalysing its own stepwise autoglucosylation to form a covalently bound gluco-oligosaccharide chain at initiation site Tyr 195. Precise mechanistic studies have so far been prevented by an inability to access homogeneous glycoforms of this protein, which unusually acts as both catalyst and substrate. Here we show that unprecedented direct access to different, homogeneously glucosylated states of GYG can be accomplished through a palladium-mediated enzyme activation 'shunt' process using on-protein C-C bond formation. Careful mimicry of GYG intermediates recapitulates catalytic activity at distinct stages, which in turn allows discovery of triphasic kinetics and substrate plasticity in GYG's use of sugar substrates. This reveals a tolerant but 'proof-read' mechanism that underlies the precision of this metabolic process. The present demonstration of direct, chemically controlled access to intermediate states of active enzymes suggests that such ligation-dependent activation could be a powerful tool in the study of mechanism.