SCOTfluors: Small, Conjugatable, Orthogonal, and Tunable Fluorophores for In Vivo Imaging of Cell Metabolism

Photosensitizer-Amplified Antimicrobial Materials for Broad-Spectrum Ablation of Resistant Pathogens in Ocular Infections

The emergence of multidrug resistant (MDR) pathogens and the scarcity of new potent antibiotics and antifungals are one of the biggest threats to human health. Antimicrobial photodynamic therapy (aPDT) combines light and photosensitizers to kill drug-resistant pathogens; however, there are limited materials that can effectively ablate different classes of infective pathogens. In the present work, a new class of benzodiazole-paired materials is designed as highly potent PDT agents with broad-spectrum antimicrobial activity upon illumination with nontoxic light. The results mechanistically demonstrate that the energy transfer and electron transfer between nonphotosensitive and photosensitive benzodiazole moieties embedded within pathogen-binding peptide sequences result in increased singlet oxygen generation and enhanced phototoxicity. Chemical optimization renders PEP3 as a novel PDT agent with remarkable activity against MDR bacteria and fungi as well as pathogens at different stages of development (e.g., biofilms, spores, and fungal hyphae), which also prove effective in an ex vivo porcine model of microbial keratitis. The chemical modularity of this strategy and its general compatibility with peptide-based targeting agents will accelerate the design of highly photosensitive materials for antimicrobial PDT.

Recent advances in minimal fluorescent probes for optical imaging

Fluorescent probes have revolutionized biological imaging by enabling the real-time visualization of cellular processes under physiological conditions. However, their size and potential perturbative nature can pose challenges in retaining the integrity of biological functions. This manuscript highlights recent advancements in the development of small fluorescent probes for optical imaging studies. Single benzene-based fluorophores offer versatility with minimal disruption, exhibiting diverse properties like aggregation-induced emission and pH responsiveness. Fluorescent nucleobases enable precise labeling of nucleic acids without compromising function, offering high sensitivity and compatibility with biochemistry studies. Bright yet small fluorescent amino acids provide an interesting alternative to bulky fusion proteins, facilitating non-invasive imaging of cellular events with high precision. These miniaturized fluorophores promise enhanced capabilities for studying biological systems in a non-invasive manner, fostering further innovations in molecular imaging.

Fluorescent carbazole-derived α-amino acids: structural mimics of tryptophan

Fluorescent tags are commonly used for imaging of proteins and peptides during biological events; however, the large size of dyes can disrupt protein structure and function, and typically require the use of a chemical spacer. Herein, we report the synthesis of a new class of fluorescent unnatural α-amino acid, containing carbazole side-chains designed to mimic l-tryptophan and thus, readily incorporated into peptides. The amino acids were constructed using a Negishi cross-coupling reaction as the key step and exhibited strong fluorescent emission, with high quantum yields in both organic solvents and water. Compatible with solid phase peptide synthesis, the carbazole amino acids were used to replace tryptophan in a β-hairpin model peptide and shown to be a close structural mimic with retention of conformation. They were also found to be effective fluorescent molecular reporters for biological events. Incorporation into a proline-rich ligand of the WW domain protein demonstrated that the fluorescent properties of a carbazole amino acid could be used to measure the protein-protein binding interaction of this important biological signalling process.

Near-infrared II theranostic agents for the diagnosis and treatment of Alzheimer's disease

BACKGROUND

Near-infrared II theranostic agents have gained great momentum in the research field of AD owing to the appealing advantages. Recently, an array of activatable NIR-II fluorescence probes has been developed to specifically monitor pathological targets of AD. Furthermore, various NIR-II-mediated nanomaterials with desirable photothermal and photodynamic properties have demonstrated favorable outcomes in the management of AD.

METHODS

We summerized amounts of references and focused on small-molecule probes, nanomaterials, photothermal therapy, and photodynamic therapy based on NIR-II fluorescent imaging for the diagnosis and treatment in AD. In addition, design strategies for NIR-II-triggered theranostics targeting AD are presented, and some prospects are also addressed.

RESULTS

NIR-II theranostic agents including small molecular probes and nanoparticles have received the increasing attention for biomedical applications. Meanwhile, most of the theranostic agents exhibited the promising results in animal studies. To our surprise, the multifunctional nanoplatforms also show a great potential in the diagnosis and treatment of AD.

CONCLUSIONS

Although NIR-II theranostic agents showed the great potential in diagnosis and treatment of AD, there are still many challenges: 1) Faborable NIR-II fluorohpores are still lacking; 2) Biocompatibility, bioseurity and dosage of NIR-II theranostic agents should be further revealed; 3) New equipment and software associated with NIR-II imaging system should be explored.

Chemical Approaches to Optimize the Properties of Organic Fluorophores for Imaging and Sensing

Organic fluorophores are indispensable tools in cells, tissue and in vivo imaging, and have enabled much progress in the wide range of biological and biomedical fields. However, many available dyes suffer from insufficient performances, such as short absorption and emission wavelength, low brightness, poor stability, small Stokes shift, and unsuitable permeability, restricting their application in advanced imaging technology and complex imaging. Over the past two decades, many efforts have been made to improve these performances of fluorophores. Starting with the luminescence principle of fluorophores, this review clarifies the mechanisms of the insufficient performance for traditional fluorophores to a certain extent, systematically summarizes the modified approaches of optimizing properties, highlights the typical applications of the improved fluorophores in imaging and sensing, and indicates existing problems and challenges in this area. This progress not only proves the significance of improving fluorophores properties, but also provide a theoretical guidance for the development of high-performance fluorophores.

Chronological development of functional fluorophores for bio-imaging

Functional fluorophores represent an emerging research field, distinguished by their diverse applications, especially in sensing and cellular imaging. After the discovery of quinine sulfate and subsequent elucidation of the fluorescence mechanism by Sir George Stokes, research in the field of fluorescence gained momentum. Over the past few decades, advancements in sophisticated instruments, including super-resolution microscopy, have further promoted cellular imaging using traditional fluorophores. These advancements include deciphering sensing mechanisms via photochemical reactions and scrutinizing the applications of fluorescent probes that specifically target organelles. This approach elucidates molecular interactions with biomolecules. Despite the abundance of literature illustrating different classes of probe development, a concise summary of newly developed fluorophores remains inadequate. In this review, we systematically summarize the chronological discovery of traditional fluorophores along with new fluorophores. We briefly discuss traditional fluorophores ranging from visible to near-infrared (NIR) in the context of cellular imaging and in vivo imaging. Furthermore, we explore ten new core fluorophores developed between 2007 and 2022, which exhibit advanced optical properties, providing new insights into bioimaging. We illustrate the utilization of new fluorophores in cellular imaging of biomolecules, such as reactive oxygen species (ROS), reactive nitrogen species (RNS), and proteins and microenvironments, especially pH and viscosity. Few of the fluorescent probes provided new insights into disease progression. Furthermore, we speculate on the potential prospects and significant challenges of existing fluorophores and their potential biomedical research applications. By addressing these aspects, we intend to illuminate the compelling advancements in fluorescent probe development and their potential influence across various fields.

meta-Fluorophores: an uncharted ocean of opportunities

meta-Fluorophores (MFs) are unique ultra-light (in terms of molecular weight (MW)) fluorophores exhibiting luminescence with a wide colour gamut ranging from blue to the NIR. Single benzenic MFs are easy to synthesize, are quite bright (with photoluminescence quantum yield (PLQY) as high as 63%) and exhibit very large Stokes shift (as high as 260 nm (8965 cm-1)), with large solvatochromic shift (as high as 175 nm), and very long excited-state-lifetime (as high as 26 ns) for such ultra-light fluorophores. An emission maximum of ≥600 nm has been achieved with an MF in a polar medium having a MW of only 177 g mol-1 and in a nonpolar medium having MW of only 255 g mol-1; therefore, a large-sized π-conjugated para-fluorophore is no longer a prerequisite for red/NIR emission. Structurally varied MFs pave the way for creating an ocean of opportunities and are thus promising for replacing para-fluorophores for different applications, ranging from bioimaging to LEDs.

Molecular engineering and bioimaging applications of C2-alkenyl indole dyes with tunable emission wavelengths covering visible to NIR light

As an important member of dyes, small-molecule fluorescent dyes show indispensable value in biomedical fields. Although various molecular dyes have been developed, full-color dyes covering blue to red region derived from a single chromophore are still in urgent demand. In this work, a series of dyes based on C2-alkenyl indole skeleton were synthesized, namely AI dyes, and their photophysical properties, cytotoxicity, and imaging capacity were verified to be satisfactory. Particularly, the maximal emission wavelengths of these dyes could cover a wide range from visible to NIR light with large Stokes shifts. Besides, the optical and structural discrepancies between the C2- and C3- alkenyl AI dyes were discussed in detail, and the theoretical calculations were conducted to provide insights on such structure-activity relationship. Finally, as a proof-of-concept, a fluorescent probe AI-Py-B capable of imaging endogenous ONOO- was presented, demonstrating the bioimaging potentials of these alkenyl indole dyes. This work is anticipated to open up new possibilities for developing dye engineering and bio-applications of natural indole framework.

Evidence of Cytolysin A nanopore incorporation in mammalian cells assessed by a graphical user interface

Technologies capable of assessing cellular metabolites with high precision and temporal resolution are currently limited. Recent developments in the field of nanopore sensors allow the non-stochastic quantification of metabolites, where a nanopore is acting as an electrical transducer for selective substrate binding proteins (SBPs). Here we show that incorporation of the pore-forming toxin Cytolysin A (ClyA) into the plasma membrane of Chinese hamster ovary cells (CHO-K1) results in the appearance of single-channel conductance amenable to multiplexed automated patch-clamp (APC) electrophysiology. In CHO-K1 cells, SBPs modify the ionic current flowing though ClyA nanopores, thus demonstrating its potential for metabolite sensing of living cells. Moreover, we developed a graphical user interface for the analysis of the complex signals resulting from multiplexed APC recordings. This system lays the foundation to bridge the gap between recent advances in the nanopore field (e.g., proteomic and transcriptomic) and potential cellular applications.

Burst of hopping trafficking correlated reversible dynamic interactions between lipid droplets and mitochondria under starvation

Dynamic membrane contacts between lipid droplets (LDs) and mitochondria play key roles in lipid metabolism and energy homeostasis. Understanding the dynamics of LDs under energy stimulation is thereby crucial to disclosing the metabolic mechanism. Here, the reversible interactions between LDs and mitochondria are tracked in real-time using a robust LDs-specific fluorescent probe (LDs-Tags). Through tracking the dynamics of LDs at the single-particle level, spatiotemporal heterogeneity is revealed. LDs in starved cells communicate and integrate their activities (i.e., lipid exchange) through a membrane contact site-mediated mechanism. Thus the diffusion is intermittently alternated between active and confined states. Statistical analysis shows that the translocation of LDs in response to starvation stress is non-Gaussian, and obeys nonergodic-like behavior. These results provide deep understanding of the anomalous diffusion of LDs in living cells, and also afford guidance for rationally designing efficient transporter.

Lipid-induced polymorphic amyloid fibril formation by α-synuclein

Many proteins that self-assemble into amyloid and amyloid-like fibers can adopt diverse polymorphic forms. These forms have been observed both in vitro and in vivo and can arise through variations in the steric-zipper interactions between β-sheets, variations in the arrangements between protofilaments, and differences in the number of protofilaments that make up a given fiber class. Different polymorphs arising from the same precursor molecule not only exhibit different levels of toxicity, but importantly can contribute to different disease conditions. However, the factors which contribute to formation of polymorphic forms of amyloid fibrils are not known. In this work, we show that in the presence of 1,2-dimyristoyl-sn-glycero-3-phospho-L-serine, a highly abundant lipid in the plasma membrane of neurons, the aggregation of α-synuclein is markedly accelerated and yields a diversity of polymorphic forms under identical experimental conditions. This morphological diversity includes thin and curly fibrils, helical ribbons, twisted ribbons, nanotubes, and flat sheets. Furthermore, the amyloid fibrils formed incorporate lipids into their structures, which corroborates the previous report of the presence of α-synuclein fibrils with high lipid content in Lewy bodies. Thus, the present study demonstrates that an interface, such as that provided by a lipid membrane, can not only modulate the kinetics of α-synuclein amyloid aggregation but also plays an important role in the formation of morphological variants by incorporating lipid molecules in the process of amyloid fibril formation.

Molecular fluorescent sensors for in vivo imaging

Small-molecule fluorophores are powerful tools for biological research. They have enabled researchers to study cellular architecture and decipher biological processes. Responsive fluorescent sensors have enabled the study of a wide range of analytes and their effects on biological phenomena in situ. The application of fluorescent sensors to studies in living organisms is complicated by challenges such as biocompatibility, chemostability, photostability and sufficient penetration of light through living tissues. Translation to in vivo imaging is therefore not straightforward and requires innovative approaches. Recent advances in the design of fluorophores with improved photophysical properties and the development of long-wavelength-emitting fluorophore scaffolds that can be modularly functionalised with targeting and sensing groups have allowed the application of fluorogenic, ratiometric and reversible sensors in vivo.

Loss of microglial MCT4 leads to defective synaptic pruning and anxiety-like behavior in mice

Microglia, the innate immune cells of the central nervous system, actively participate in brain development by supporting neuronal maturation and refining synaptic connections. These cells are emerging as highly metabolically flexible, able to oxidize different energetic substrates to meet their energy demand. Lactate is particularly abundant in the brain, but whether microglia use it as a metabolic fuel has been poorly explored. Here we show that microglia can import lactate, and this is coupled with increased lysosomal acidification. In vitro, loss of the monocarboxylate transporter MCT4 in microglia prevents lactate-induced lysosomal modulation and leads to defective cargo degradation. Microglial depletion of MCT4 in vivo leads to impaired synaptic pruning, associated with increased excitation in hippocampal neurons, enhanced AMPA/GABA ratio, vulnerability to seizures and anxiety-like phenotype. Overall, these findings show that selective disruption of the MCT4 transporter in microglia is sufficient to alter synapse refinement and to induce defects in mouse brain development and adult behavior.

Smart probes for optical imaging of T cells and screening of anti-cancer immunotherapies

T cells are an essential part of the immune system with crucial roles in adaptive response and the maintenance of tissue homeostasis. Depending on their microenvironment, T cells can be differentiated into multiple states with distinct functions. This myriad of cellular activities have prompted the development of numerous smart probes, ranging from small molecule fluorophores to nanoconstructs with variable molecular architectures and fluorescence emission mechanisms. In this Tutorial Review, we summarize recent efforts in the design, synthesis and application of smart probes for imaging T cells in tumors and inflammation sites by targeting metabolic and enzymatic biomarkers as well as specific surface receptors. Finally, we briefly review current strategies for how smart probes are employed to monitor the response of T cells to anti-cancer immunotherapies. We hope that this Review may help chemists, biologists and immunologists to design the next generation of molecular imaging probes for T cells and anti-cancer immunotherapies.

Environmentally sensitive photosensitizers enable targeted photodynamic ablation of Gram-positive antibiotic resistant bacteria

Bacterial infections remain among the biggest challenges to human health, leading to high antibiotic usage, morbidity, hospitalizations, and accounting for approximately 8 million deaths worldwide every year. The overuse of antibiotics and paucity of antimicrobial innovation has led to antimicrobial resistant pathogens that threaten to reverse key advances of modern medicine. Photodynamic therapeutics can kill bacteria but there are few agents that can ablate pathogens with minimal off-target effects. Methods: We describe nitrobenzoselenadiazoles as some of the first environmentally sensitive organic photosensitizers, and their adaptation to produce theranostics with optical detection and light-controlled antimicrobial activity. We combined nitrobenzoselenadiazoles with bacteria-targeting moieties (i.e., glucose-6-phosphate, amoxicillin, vancomycin) producing environmentally sensitive photodynamic agents. Results: The labelled vancomycin conjugate was able to both visualize and eradicate multidrug resistant Gram-positive ESKAPE pathogens at nanomolar concentrations, including clinical isolates and those that form biofilms. Conclusion: Nitrobenzoselenadiazole conjugates are easily synthesized and display strong environment dependent ROS production. Due to their small size and non-invasive character, they unobtrusively label antimicrobial targeting moieties. We envisage that the simplicity and modularity of this chemical strategy will accelerate the rational design of new antimicrobial therapies for refractory bacterial infections.

Late-stage peptide labeling with near-infrared fluorogenic nitrobenzodiazoles by manganese-catalyzed C-H activation

Late-stage diversification of structurally complex amino acids and peptides provides tremendous potential for drug discovery and molecular imaging. Specifically, labeling peptides with fluorescent tags is one of the most important methods for visualizing their mode of operation. Despite major recent advances in the field, direct molecular peptide labeling by C-H activation is largely limited to dyes with relatively short emission wavelengths, leading to high background signals and poor signal-to-noise ratios. In sharp contrast, here we report on the fluorescent labeling of peptides catalyzed by non-toxic manganese(i) via C(sp²)-H alkenylation in chemo- and site-selective manners, providing modular access to novel near-infrared (NIR) nitrobenzodiazole-based peptide fluorogenic probes.

Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity

Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.

A thiomorpholine-based fluorescent probe for the far-red hypochlorous acid monitoring

A simple thiomorpholine-based fluorescent probe was designed and synthesized by combining thiomorpholine (TM) and nitrobenzenoselenadiazoles fluorophore (NBD-Se). The thiomorpholine group quenches the fluorescence of NBD-Se efficiently through the photoinduced electron transfer (PET) effect. Hypochlorous acid (HOCl) oxidizes the NBD-Se-TM probe to its fluorescent S-oxide (NBD-Se-TSO) with a 1:1 stoichiometry. The desirable features of NBD-Se-TM for detecting HOCl in aqueous solutions, such as its high sensitivity and selectivity, reliability at physiological pH, and rapid fluorescence response, enabled its application in the detection of HOCl produced by myeloperoxidase. The results proved that NBD-Se-TM is a promising fluorescent probe that can be used in screening assays for MPO inhibitors. Its high reaction rate constant with HOCl (²k = 2.0 × 10⁷M^-1s^-1) indicates the possibility of application in more complex biological systems.

Light induced diversity-oriented synthesis (DOS) library of annulated indolizine fluorophores for imaging non-lysosomal lipid droplets (LDs)

We report the design, synthesis, and biological evaluation of a novel class of annulated indolizines as fluorescent probes. The compounds were generated through an eco-friendly, blue LED-induced domino reaction in ethyl acetate. A library of 24 coloured compounds exhibited tuneable emissions. One of the compounds (which we call DASS-fluor) proved to be an excellent polarity sensing probe. It is biocompatible, photostable, and detects specific types of lipid droplets (LDs in response to oleic acid, stress, and drug-induced autophagy in lungs and hepatic carcinoma cells). In comparison to Nile Red (a commercial probe), DASS-fluor can differentiate non-lysosomal LDs from lysosomal LDs and offers an advantage in precisely mapping drug-induced lipidosis caused by increased non-lysosomal LDs in cancerous cells. This unique probe could be a potential fluorescent marker for specific types of lipidosis induced by drugs.

Small Fluorogenic Amino Acids for Peptide-Guided Background-Free Imaging

The multiple applications of super-resolution microscopy have prompted the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. Many fluorescent reporters display limitations (e.g., large and charged scaffolds, non-specific binding) as building blocks for the construction of fluorogenic peptides. Herein we have built a library of benzodiazole amino acids and systematically examined them as reporters for background-free fluorescence microscopy. We have identified amine-derivatized benzoselenadiazoles as scalable and photostable amino acids for the straightforward solid-phase synthesis of fluorescent peptides. Benzodiazole amino acids retain the binding capabilities of bioactive peptides and display excellent signal-to-background ratios. Furthermore, we have demonstrated their application in peptide-PAINT imaging of postsynaptic density protein-95 nanoclusters in the synaptosomes from mouse brain tissues.

Small Fluorogenic Amino Acids for Peptide-Guided Background-Free Imaging

The multiple applications of super-resolution microscopy have prompted the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. Many fluorescent reporters display limitations (e.g., large and charged scaffolds, non-specific binding) as building blocks for the construction of fluorogenic peptides. Herein we have built a library of benzodiazole amino acids and systematically examined them as reporters for background-free fluorescence microscopy. We have identified amine-derivatized benzoselenadiazoles as scalable and photostable amino acids for the straightforward solid-phase synthesis of fluorescent peptides. Benzodiazole amino acids retain the binding capabilities of bioactive peptides and display excellent signal-to-background ratios. Furthermore, we have demonstrated their application in peptide-PAINT imaging of postsynaptic density protein-95 nanoclusters in the synaptosomes from mouse brain tissues.

Fluorescently Labeled Ceramides and 1-Deoxyceramides: Synthesis, Characterization, and Cellular Distribution Studies

Ceramides (Cer) are bioactive sphingolipids that have been proposed as potential disease biomarkers since they are involved in several cellular stress responses, including apoptosis and senescence. 1-Deoxyceramides (1-deoxyCer), a particular subtype of noncanonical sphingolipids, have been linked to the pathogenesis of type II diabetes. To investigate the metabolism of these bioactive lipids, as well as to have a better understanding of the signaling processes where they participate, it is essential to expand the toolbox of fluorescent sphingolipid probes exhibiting complementary subcellular localization. Herein, we describe a series of new sphingolipid probes tagged with two different organic fluorophores, a far-red/NIR-emitting coumarin derivative (COUPY) and a green-emitting BODIPY. The assembly of the probes involved a combination of olefin cross metathesis and click chemistry reactions as key steps, and these fluorescent ceramide analogues exhibited excellent emission quantum yields, being the Stokes' shifts of the COUPY derivatives much higher than those of the BODIPY counterparts. Confocal microscopy studies in HeLa cells confirmed an excellent cellular permeability for these sphingolipid probes and revealed that most of the vesicles stained by COUPY probes were either lysosomes or endosomes, whereas BODIPY probes accumulated either in Golgi apparatus or in nonlysosomal intracellular vesicles. The fact that the two sets of fluorescent Cer probes have such different staining patterns indicates that their subcellular distribution is not entirely defined by the sphingolipid moiety but rather influenced by the fluorophore.

A multicomponent reaction platform towards multimodal near-infrared BODIPY dyes for STED and fluorescence lifetime imaging

We report a platform combining multicomponent reaction synthesis and automated cell-based screening to develop biocompatible NIR-BODIPY fluorophores. From a library of over 60 fluorophores, we optimised compound NIRBD-62c as a multimodal probe with suitable properties for STED super-resolution and fluorescence lifetime imaging. Furthermore, we employed NIRBD-62c for imaging trafficking inside cells and to examine how pharmacological inhibitors can alter the vesicular traffic between intracellular compartments and the plasma membrane.

Single cell metabolism: current and future trends

Single cell metabolomics is an emerging and rapidly developing field that complements developments in single cell analysis by genomics and proteomics. Major goals include mapping and quantifying the metabolome in sufficient detail to provide useful information about cellular function in highly heterogeneous systems such as tissue, ultimately with spatial resolution at the individual cell level. The chemical diversity and dynamic range of metabolites poses particular challenges for detection, identification and quantification. In this review we discuss both significant technical issues of measurement and interpretation, and progress toward addressing them, with recent examples from diverse biological systems. We provide a framework for further directions aimed at improving workflow and robustness so that such analyses may become commonly applied, especially in combination with metabolic imaging and single cell transcriptomics and proteomics.

Pathological structural conversion of α-synuclein at the mitochondria induces neuronal toxicity

Aggregation of alpha-synuclein (α-Syn) drives Parkinson's disease (PD), although the initial stages of self-assembly and structural conversion have not been directly observed inside neurons. In this study, we tracked the intracellular conformational states of α-Syn using a single-molecule Förster resonance energy transfer (smFRET) biosensor, and we show here that α-Syn converts from a monomeric state into two distinct oligomeric states in neurons in a concentration-dependent and sequence-specific manner. Three-dimensional FRET-correlative light and electron microscopy (FRET-CLEM) revealed that intracellular seeding events occur preferentially on membrane surfaces, especially at mitochondrial membranes. The mitochondrial lipid cardiolipin triggers rapid oligomerization of A53T α-Syn, and cardiolipin is sequestered within aggregating lipid-protein complexes. Mitochondrial aggregates impair complex I activity and increase mitochondrial reactive oxygen species (ROS) generation, which accelerates the oligomerization of A53T α-Syn and causes permeabilization of mitochondrial membranes and cell death. These processes were also observed in induced pluripotent stem cell (iPSC)-derived neurons harboring A53T mutations from patients with PD. Our study highlights a mechanism of de novo α-Syn oligomerization at mitochondrial membranes and subsequent neuronal toxicity.

Miniaturized Chemical Tags for Optical Imaging

Recent advances in optical bioimaging have prompted the need for minimal chemical reporters that can retain the molecular recognition properties and activity profiles of biomolecules. As a result, several methodologies to reduce the size of fluorescent and Raman labels to a few atoms (e.g., single aryl fluorophores, Raman‐active triple bonds and isotopes) and embed them into building blocks (e.g., amino acids, nucleobases, sugars) to construct native‐like supramolecular structures have been described. The integration of small optical reporters into biomolecules has also led to smart molecular entities that were previously inaccessible in an expedite manner. In this article, we review recent chemical approaches to synthesize miniaturized optical tags as well as some of their multiple applications in biological imaging.

Triazole-derivatized near-infrared cyanine dyes enable local functional fluorescent imaging of ocular inflammation

Near-infrared (NIR) chemical fluorophores are promising tools for in-vivo imaging in real time but often succumb to rapid photodegradation. Indocyanine green (ICG) is the only NIR dye with regulatory approval for ocular imaging in humans; however, ICG, when employed for applications such as labelling immune cells, has limited sensitivity and does not allow precise detection of specific inflammatory events, for example leukocyte recruitment during uveitic flare-ups. We investigated the potential use of photostable novel triazole NIR cyanine (TNC) dyes for detecting and characterising activated T-cell activity within the eye. Three TNC dyes were evaluated for ocular cytotoxicity in-vitro using a MTT assay and optimised concentrations for intraocular detection within ex-vivo porcine eyes after topical application or intracameral injections of the dyes. TNC labelled T-cell tracking experiments and mechanistic studies were also performed in-vitro. TNC-1 and TNC-2 dyes exhibited greater fluorescence intensity than ICG at 10 μM, whereas TNC-3 was only detectable at 100 μM within the porcine eye. TNC dyes did not demonstrate any ocular cell toxicity at working concentrations of 10 μM. CD4⁺T-cells labelled with TNC-1 or TNC-2 were detected within the porcine eye, with TNC-1 being brighter than TNC-2. Detection of TNC-1 and TNC-2 into CD4⁺T-cells was prevented by prior incubation with dynole 34-2 (50 μM), suggesting active uptake of these dyes via dynamin-dependent processes. The present study provides evidence that TNC dyes are suitable to detect activated CD4⁺T-cells within the eye with potential as a diagnostic marker for ocular inflammatory diseases.

N-Methyl deuterated rhodamines for protein labelling in sensitive fluorescence microscopy

Rhodamine fluorophores are setting benchmarks in fluorescence microscopy. Herein, we report the deuterium (d12) congeners of tetramethyl(silicon)rhodamine, obtained by isotopic labelling of the four methyl groups, show improved photophysical parameters (i.e. brightness, lifetimes) and reduced chemical bleaching. We explore this finding for SNAP- and Halo-tag labelling in live cells, and highlight enhanced properties in several applications, such as fluorescence activated cell sorting, fluorescence lifetime microscopy, stimulated emission depletion nanoscopy and single-molecule Förster-resonance energy transfer. We finally extend this idea to other dye families and envision deuteration as a generalizable concept to improve existing and to develop new chemical biology probes.

Activatable Fluorophores for Imaging Immune Cell Function

Optical imaging has become an essential tool to study biomolecular processes in live systems with unprecedented spatial resolution. New fluorescent technologies and advances in optical microscopy have revolutionized the ways in which we can study immune cells in real time. For example, activatable fluorophores that emit signals after target recognition have enabled direct imaging of immune cell function with enhanced readouts and minimal background. In this Account, we summarize recent advances in the chemical synthesis and implementation of activatable fluorescent probes to monitor the activity and the role of immune cells in different pathological processes, from infection to inflammatory diseases or cancer. In addition to the contributions that our group has made to this field, we review the most relevant literature disclosed over the past decade, providing examples of different activatable architectures and their application in diagnostics and drug discovery. This Account covers the imaging of the three major cell types in the immune system, that is, neutrophils, macrophages, and lymphocytes. Attracted by the tunability and target specificity of peptides, many groups have designed strategies based on fluorogenic peptides whose fluorescence emission is regulated by the reaction with enzymes (e.g., MMPs, cathepsins, granzymes), or through Förster resonance energy transfer (FRET) mechanisms. Selective imaging of immune cells has been also achieved by targeting different intracellular metabolic routes, such as lipid biogenesis. Other approaches involve the implementation of diversity-oriented fluorescence libraries or the use of environmentally sensitive fluorescent scaffolds (e.g., molecular rotors). Our group has made important progress by constructing probes to image metastasis-associated macrophages in tumors, apoptotic neutrophils, or cytotoxic natural killer (NK) cells against cancer cells, among other examples. The chemical probes covered in this Account have been successfully validated in vitro in cell culture systems, and in vivo in relevant models of inflammation and cancer. Overall, the range of chemical structures and activation mechanisms reported to sense immune cell function is remarkable. However, the emergence of new strategies based on new molecular targets or activatable mechanisms that are yet to be discovered will open the door to track unexplored roles of immune cells in different biological systems. We anticipate that upcoming generations of activatable probes will find applications in the clinic to help assessing immunotherapies and advance precision medicine. We hope that this Account will evoke new ideas and innovative work in the design of fluorescent probes for imaging cell function.

Rationales Design von Phe-BODIPY-Aminosäuren als fluorogene Bausteine für den peptidbasierten Nachweis von Candida-Infektionen im Harntrakt

Pilzinfektionen, die durch Candida‐Arten verursacht werden, gehören zu den häufigsten Infektionen bei Krankenhauspatienten. Die derzeitigen Methoden zum Nachweis von Candida‐Pilzzellen in klinischen Proben beruhen jedoch auf zeitaufwändigen Analysen, die eine schnelle und zuverlässige Diagnose erschweren. In diesem Beitrag beschreiben wir die rationale Entwicklung neuer Phe‐BODIPY‐Aminosäuren als kleine fluorogene Bausteine und ihre Anwendung zur Erzeugung fluoreszierender antimikrobieller Peptide für die schnelle Markierung von Candida‐Zellen im Urin. Mit Hilfe von computergestützten Berechnungen haben wir das fluorogene Verhalten von BODIPY‐substituierten aromatischen Aminosäuren analysiert und Bioaktivitäts‐ und konfokale Mikroskopieexperimente bei verschiedenen Stämmen durchgeführt, um den Nutzen und die Vielseitigkeit von Peptiden mit Phe‐BODIPYs zu bestätigen. Schließlich haben wir einen einfachen und sensitiven fluoreszensbasierten Test zum Nachweis von Candida albicans in menschlichen Urinproben entwickelt.

Rational Design of Phe‐BODIPY Amino Acids as Fluorogenic Building Blocks for Peptide‐Based Detection of Urinary Tract Candida Infections

Fungal infections caused by Candida species are among the most prevalent in hospitalized patients. However, current methods for the detection of Candida fungal cells in clinical samples rely on time‐consuming assays that hamper rapid and reliable diagnosis. Herein, we describe the rational development of new Phe‐BODIPY amino acids as small fluorogenic building blocks and their application to generate fluorescent antimicrobial peptides for rapid labelling of Candida cells in urine. We have used computational methods to analyse the fluorogenic behaviour of BODIPY‐substituted aromatic amino acids and performed bioactivity and confocal microscopy experiments in different strains to confirm the utility and versatility of peptides incorporating Phe‐BODIPYs. Finally, we have designed a simple and sensitive fluorescence‐based assay for the detection of Candida albicans in human urine samples.

Thiourea‐ and Amino‐Substituted Benzoxadiazole Dyes with Large Stokes Shifts as Red‐Emitting Probe Monomers for Imprinted Polymer Layers Targeting Carboxylate‐Containing Antibiotics

Bifunctional fluorescent molecular oxoanion probes based on the benzoxadiazole (BD) chromophore are described which integrate a thiourea binding motif and a polymerizable 2‐aminoethyl methacrylate unit in the 4,7‐positions of the BD core. Concerted charge transfer in this electron donor‐acceptor‐donor architecture endows the dyes with strongly Stokes shifted (up to >250 nm) absorption and fluorescence. Binding of electron‐rich carboxylate guests at the thiourea receptor leads to further analyte‐induced red‐shifts of the emission, shifting the fluorescence maximum of the complexes to ≥700 nm. Association constants for acetate are ranging from 1–5×10⁵ M⁻¹ in acetonitrile. Integration of one of the fluorescent probes through its polymerizable moiety into molecularly imprinted polymers (MIPs) grafted from the surface of submicron silica cores yielded fluorescent MIP‐coated particle probes for the selective detection of antibiotics containing aliphatic carboxylate groups such as enoxacin (ENOX) at micromolar concentrations in highly polar solvents like acetonitrile.

Fluorescent probe strategy for live cell distinction

Live cell discrimination is the first and essential step to understand complex biosystems. Conventional cell discrimination involving various antibodies relies on selective surface biomarkers. Compared to antibodies, the fluorescent probe strategy allows the utilisation of intracellular biomarkers, providing broader options with unique chemical principles to achieve the live cell distinction. In general, fluorescent probes can be retained in cells by interacting with biomolecules, accumulating via transporters, and participating in metabolism. Based on the target difference, fluorescent probe strategy can be divided into several categories: protein-oriented live cell distinction (POLD), carbohydrate-oriented live cell distinction (COLD), DNA-oriented live cell distinction (DOLD), gating-oriented live cell distinction (GOLD), metabolism-oriented live cell distinction (MOLD) and lipid-oriented live cell distinction (LOLD). In this review, we will outline the concepts and mechanisms of different strategies, introduce their applications in cell-type discrimination, and discuss their advantages and challenges in this area. We expect this tutorial will provide a new perspective on the mechanisms of fluorescent probe strategy and facilitate the development of cell-type-specific probes.

IndiFluors: A New Full-Visible Color-Tunable Donor-Acceptor-Donor (D1-A-D2) Fluorophore Family for Ratiometric pH Imaging during Mitophagy

Full-visible color-tunable new fluorophores are essential in bioimaging research. However, it is significantly challenging to design fluorophores with the desired optical and biological properties owing to their structural complexity. We report a unified design of an interesting molecular framework, IndiFluors, based on the principle of a donor-acceptor-donor (D1-A-D2) system. The IndiFluors comprise pyrylium, pyridinium, and pyridine derivatives, which exhibit full-visible emission color (375-700 nm) by varying donor and acceptor strengths of the core scaffolds. With a minimal change of structure, the bright fluorophores (Φ: 0.96) can be tuned to become nonfluorescent (Φ: 0.01), which is well explained by time-dependent density functional theory (TD-DFT/PCM) by oscillator strengths in the S1 state. Within IndiFluors, pyridinium offers several advantages, including a large Stokes shift (∼154 nm) and excellent stability, compared to pentacyclic pyrylium fluorophores. Especially, the designed probe, PM-Mito-OH, demonstrated specific colocalization in mitochondria and a monitored ratiometric pH change during mitochondrial damage, autolysosomes, and the mitophagy process. Hence, IndiFluors and the derived probe show great potential for cellular pH imaging in live cells while exhibiting minimal cytotoxicity.

A Bivalent Activatable Fluorescent Probe for Screening and Intravital Imaging of Chemotherapy-Induced Cancer Cell Death

The detection and quantification of apoptotic cells is a key process in cancer research, particularly during the screening of anticancer therapeutics and in mechanistic studies using preclinical models. Intravital optical imaging enables high-resolution visualisation of cellular events in live organisms; however, there are few fluorescent probes that can reliably provide functional readouts in situ without interference from tissue autofluorescence. We report the design and optimisation of the fluorogenic probe Apotracker Red for real-time detection of cancer cell death. The strong fluorogenic behaviour, high selectivity, and excellent stability of Apotracker Red make it a reliable optical reporter for the characterisation of the effects of anticancer drugs in cells in vitro and for direct imaging of chemotherapy-induced apoptosis in vivo in mouse models of breast cancer.

Rational Design and Synthesis of Large Stokes Shift 2,6-Sulphur-Disubstituted BODIPYs for Cell Imaging

Five new disubstituted 2,6-thioaryl-BODIPY dyes were synthesized via selective aromatic electrophilic substitution from commercially available thiophenols. The analysis of the photophysical properties via absorption and emission spectroscopy showed unusually large Stokes shifts for BODIPY fluorophores (70–100 nm), which makes them suitable probes for bioimaging. Selected compounds were evaluated for labelling primary immune cells as well as different cancer cell lines using confocal fluorescence microscopy.

Truly-Biocompatible Gold Catalysis Enables Vivo-Orthogonal Intra-CNS Release of Anxiolytics

Being recognized as the best-tolerated of all metals, the catalytic potential of gold (Au) has thus far been hindered by the ubiquitous presence of thiols in organisms. Herein we report the development of a truly-catalytic Au-polymer composite by assembling ultrasmall Au-nanoparticles at the protein-repelling outer layer of a co-polymer scaffold via electrostatic loading. Illustrating the in vivo-compatibility of the novel catalysts, we show their capacity to uncage the anxiolytic agent fluoxetine at the central nervous system (CNS) of developing zebrafish, influencing their swim pattern. This bioorthogonal strategy has enabled -for the first time- modification of cognitive activity by releasing a neuroactive agent directly in the brain of an animal.

Truly-Biocompatible Gold Catalysis Enables Vivo-Orthogonal Intra-CNS Release of Anxiolytics

Being recognized as the best-tolerated of all metals, the catalytic potential of gold (Au) has thus far been hindered by the ubiquitous presence of thiols in organisms. Herein we report the development of a truly-catalytic Au-polymer composite by assembling ultrasmall Au-nanoparticles at the protein-repelling outer layer of a co-polymer scaffold via electrostatic loading. Illustrating the in vivo-compatibility of the novel catalysts, we show their capacity to uncage the anxiolytic agent fluoxetine at the central nervous system (CNS) of developing zebrafish, influencing their swim pattern. This bioorthogonal strategy has enabled -for the first time- modification of cognitive activity by releasing a neuroactive agent directly in the brain of an animal.

Sulfonated red and far-red rhodamines to visualize SNAP- and Halo-tagged cell surface proteins

The (in)ability to permeate membranes is a key feature of chemical biology probes that defines their suitability for specific applications. Here we report sulfonated rhodamines that endow xanthene dyes with cellular impermeability for analysis of surface proteins. We fuse charged sulfonates to red and far-red dyes to obtain Sulfo549 and Sulfo646, respectively, and further link these to benzylguanine and choloralkane substrates for SNAP-tag and Halo-tag labelling. Sulfonated rhodamine-conjugated fluorophores maintain desirable photophysical properties, such as brightness and photostability. While transfected cells with a nuclear localized SNAP-tag remain unlabelled, extracellular exposed tags can be cleanly visualized. By multiplexing with a permeable rhodamine, we are able to differentiate extra- and intracellular SNAP- and Halo-tags, including those installed on the glucagon-like peptide-1 receptor, a prototypical class B G protein-coupled receptor. Sulfo549 and Sulfo646 also labelled transfected neurons derived from induced pluripotent stem cells (iPSCs), allowing STED nanoscopy of the axonal membrane. Together, this work provides a new avenue for rendering dyes impermeable for exclusive extracellular visualization via self-labelling protein tags. We anticipate that Sulfo549, Sulfo646 and their congeners will be useful for a number of cell biology applications where labelling of intracellular sites interferes with accurate surface protein analysis.

Sulfonated rhodamine dyes allow SNAP- and Halo-tag labelling of cell surface protein fusions. A far-red version can be used for STED nanoscopy.

A Bioorthogonal Chemical Reporter for the Detection and Identification of Protein Lactylation

L-Lactylation is a recently discovered post-translational modification occurring on histone lysine residues to regulate gene expression. However, the substrate scope of lactylation, especially that in non-histone proteins, remains unknown, largely...

Full-Color Emission in Multicomponent Metal-Organic Frameworks via Linker Installation

Herein, we demonstrate that linker installation (LI) through postsynthesis is an effective strategy to insert emissive second linkers into single-linker-based metal-organic frameworks (MOFs) to tune the emission properties of multicomponent MOFs. Full-color emission, including white-light emission, can be achieved via such a LI process.

Tuning and Directing Energy Transfer in the Whole Visible Spectrum through Linker Installation in Metal-Organic Frameworks

While limited choice of emissive organic linkers with systematic emission tunability presents a great challenge to investigate energy transfer (ET) over the whole visible light range with designable directions, luminescent metal-organic frameworks (LMOFs) may serve as an ideal platform for such study due to their tunable structure and composition. Herein, five Zr₆ cluster-based LMOFs, HIAM-400X (X=0, 1, 2, 3, 4) are prepared using 2,1,3-benzothiadiazole and its derivative-based tetratopic carboxylic acids as organic linkers. The accessible unsaturated metal sites confer HIAM-400X as a pristine scaffold for linker installation. Six full-color emissive 2,1,3-benzothiadiazole and its derivative-based dicarboxylic acids (L) were successfully installed into HIAM-400X matrix to form HIAM-400X-L, in which the ET can be facilely tuned by controlling its direction, either from the inserted linkers to pristine MOFs or from the pristine MOFs to inserted linkers, and over the whole range of visible light. The combination of the pristine MOFs and the second linkers via linker installation creates a powerful two-dimensional space in tuning the emission via ET in LMOFs.

A Bivalent Activatable Fluorescent Probe for Screening and Intravital Imaging of Chemotherapy-induced Cancer Cell Death

The detection and quantification of apoptotic cells is a key process in cancer research, particularly during the screening of anticancer therapeutics and in mechanistic studies using preclinical models. Intravital optical imaging enables high‐resolution visualisation of cellular events in live organisms; however, there are few fluorescent probes that can reliably provide functional readouts in situ without interference from tissue autofluorescence. We report the design and optimisation of the fluorogenic probe Apotracker Red for real‐time detection of cancer cell death. The strong fluorogenic behaviour, high selectivity, and excellent stability of Apotracker Red make it a reliable optical reporter for the characterisation of the effects of anticancer drugs in cells in vitro and for direct imaging of chemotherapy‐induced apoptosis in vivo in mouse models of breast cancer.

Potent strategy towards strongly emissive nitroaromatics through a weakly electron-deficient core

Nitroaromatics seldom fluoresce. The importance of electron-deficient (n-type) conjugates, however, has inspired a number of strategies for suppressing the emission-quenching effects of the strongly electron-withdrawing nitro group. Here, we demonstrate how such strategies yield fluorescent nitroaryl derivatives of dipyrrolonaphthyridinedione (DPND). Nitro groups near the DPND core quench its fluorescence. Conversely, nitro groups placed farther from the core allow some of the highest fluorescence quantum yields ever recorded for nitroaromatics. This strategy of preventing the known processes that compete with photoemission, however, leads to the emergence of unprecedented alternative mechanisms for fluorescence quenching, involving transitions to dark nπ* singlet states and aborted photochemistry. Forming nπ* triplet states from ππ* singlets is a classical pathway for fluorescence quenching. In nitro-DPNDs, however, these ππ* and nπ* excited states are both singlets, and they are common for nitroaryl conjugates. Understanding the excited-state dynamics of such nitroaromatics is crucial for designing strongly fluorescent electron-deficient conjugates.

Making Nitronaphthalene Fluoresce

Nitroaromatic compounds are inherently nonfluorescent, and the subpicosecond lifetimes of the singlet excited states of many small nitrated polycyclic aromatic hydrocarbons, such as nitronaphthalenes, render them unfeasible for photosensitizers and photo-oxidants, despite their immensely beneficial reduction potentials. This article reports up to a 7000-fold increase in the singlet-excited-state lifetime of 1-nitronaphthalene upon attaching an amine or an N-amide to the ring lacking the nitro group. Varying the charge-transfer (CT) character of the excited states and the medium polarity balances the decay rates along the radiative and the two nonradiative pathways and can make these nitronaphthalene derivatives fluoresce. The strong electron-donating amine suppresses intersystem crossing (ISC) but accommodates CT pathways of nonradiate deactivation. Conversely, the N-amide does not induce a pronounced CT character but slows down ISC enough to achieve relatively long lifetimes of the singlet excited state. These paradigms are key for the pursuit of electron-deficient (n-type) organic conjugates with promising optical characteristics.

Altered substrate metabolism in neurodegenerative disease: new insights from metabolic imaging

Neurodegenerative diseases (NDs), such as Alzheimer's disease (AD), Parkinson's disease (PD) and multiple sclerosis (MS), are relatively common and devastating neurological disorders. For example, there are 6 million individuals living with AD in the United States, a number that is projected to grow to 14 million by the year 2030. Importantly, AD, PD and MS are all characterized by the lack of a true disease-modifying therapy that is able to reverse or halt disease progression. In addition, the existing standard of care for most NDs only addresses the symptoms of the disease. Therefore, alternative strategies that target mechanisms underlying the neuropathogenesis of disease are much needed. Recent studies have indicated that metabolic alterations in neurons and glia are commonly observed in AD, PD and MS and lead to changes in cell function that can either precede or protect against disease onset and progression. Specifically, single-cell RNAseq studies have shown that AD progression is tightly linked to the metabolic phenotype of microglia, the key immune effector cells of the brain. However, these analyses involve removing cells from their native environment and performing measurements in vitro, influencing metabolic status. Therefore, technical approaches that can accurately assess cell-specific metabolism in situ have the potential to be transformative to our understanding of the mechanisms driving AD. Here, we review our current understanding of metabolism in both neurons and glia during homeostasis and disease. We also evaluate recent advances in metabolic imaging, and discuss how emerging modalities, such as fluorescence lifetime imaging microscopy (FLIM) have the potential to determine how metabolic perturbations may drive the progression of NDs. Finally, we propose that the temporal, regional, and cell-specific characterization of brain metabolism afforded by FLIM will be a critical first step in the rational design of metabolism-focused interventions that delay or even prevent NDs.