Small-molecule fluorophores and fluorescent probes for bioimaging

Recent development in dual function fluorescence probes for HOCl and interaction with different bioactive molecules

Reactive oxygen species (ROS), reactive sulfur species (RSS), metal ions, and nitrogen species (RNS) play important roles in a variety of biological processes, such as a signal transduction, inflammation, and neurodegenerative damage. These species, while essential for certain functions, can also induce stress-related diseases. The interrelation between ROS, RSS, Metal ions and RNS underscores the importance of quantifying their concentrations in live cells, tissues, and organisms. The review emphasizes the use of small-molecule-based fluorescent/chemodosimeter probes to effectively measure and map the species' distribution with high temporal and spatial precision, paying particular attention to in vitro and in vivo environments. These probes are recognized as valuable tools contributing to breakthroughs in modern redox biology. The review specifically addresses the relationship of HOCl/ClO‾ (hypochlorous acid/Hypochlorite) with other reactive species. (Dual sensing probes).

Folic acid-mediated enhancement of the diagnostic potential of luminescent europium-doped hydroxyapatite nanocrystals for cancer biomaging

Early and accurate cancer diagnosis is crucial for improving patient survival rates. Luminescent nanoparticles have emerged as a promising tool in fluorescence bioimaging for cancer diagnosis. To enhance diagnostic accuracy, ligands promoting endocytosis into cancer cells are commonly incorporated onto nanoparticle surfaces. Folic acid (FA) is one such ligand, known to specifically bind to folate receptors (FR) overexpressed in various cancer cells such as cervical and ovarian carcinoma. Therefore, surface modification of luminescent nanoparticles with FA can enhance both luminescence efficiency and diagnostic accuracy. In this study, luminescent europium-doped hydroxyapatite (EuHAp) nanocrystals were prepared via hydrothermal method and subsequently modified with (3-Aminopropyl)triethoxysilane (APTES) followed by FA to target FR-positive human cervical adenocarcinoma cell line (HeLa) cells. The sequential grafting of APTES and then FA formed a robust covalent linkage between the nanocrystals and FA. Rod-shaped FA-modified EuHAp nanocrystals, approximately 100 nm in size, exhibited emission peaks at 589, 615, and 650 nm upon excitation at 397 nm. Despite a reduction in photoluminescence intensity following FA modification, fluorescence microscopy revealed a remarkable 120-fold increase in intensity compared to unmodified EuHAp, attributed to the enhanced uptake of FA-modified EuHAp. Additionally, confocal microscope observations confirmed the specificity and the internalization of FA-modified EuHAp nanocrystals in HeLa cells. In conclusion, the modification of EuHAp nanocrystals with FA presents a promising strategy to enhance the diagnostic potential of cancer bioimaging probes.

Small Molecule Optical Probes for Detection of H2S in Water Samples: A Review

Hydrogen sulfide (H2S) is closely linked to not only environmental hazards, but also it affects human health due to its toxic nature and the exposure risks associated with several occupational settings. Therefore, detection of this pollutant in water sources has garnered immense importance in the analytical research arena. Several research groups have devoted great efforts to explore the selective as well as sensitive methods to detect H2S concentrations in water. Recent studies describe different strategies for sensing this ubiquitous gas in real-life water samples. Though many of the designed and developed H2S detection approaches based on the use of organic small molecules facilitate qualitative/quantitative detection of the toxic contaminant in water, optical detection has been acknowledged as one of the best, attributed to the simple, highly sensitive, selective, and good repeatability features of the technique. Therefore, this review is an attempt to offer a general perspective of easy-to-use and fast response optical detection techniques for H2S, fluorimetry and colorimetry, over a wide variety of other instrumental platforms. The review affords a concise summary of the various design strategies adopted by various researchers in constructing small organic molecules as H2S sensors and offers insight into their mechanistic pathways. Moreover, it collates the salient aspects of optical detection techniques and highlights the future scope for prospective exploration in this field based on the limitations of the existing H2S probes.

3-Amino-5,6,7,8-tetrahydrothieno[2,3-b]quinoline-2-carbonitrile: A fluorescent molecule that induces differentiation in PC12 cells

Neural differentiation is triggered by the activation of multiple signaling pathways initiated by various neurotrophic factors. An elucidation of these mechanisms is anticipated to facilitate the prevention of diseases and the development of novel therapeutic approaches. Alternative small-molecule inducers for neuroscience studies are required instead of protein-based reagents for more efficient and convenient experiments. We demonstrated that small molecules of thieno[2,3-b]pyridine derivatives that induce neural differentiation, compounds 3a and 9a in particular, exhibited significant neuritogenic activity in rat pheochromocytoma (PC12) cells. Moreover, 3a displayed pronounced fluorescence and a discernible Stokes shift. Furthermore, the outcome of the experiment conducted on the NGF-insensitive clones of rat PC12 cells, and the results of the intercellular uptake analyses suggested that the 3a-mediated activation of neural differentiation occurred independently of the TrkA receptor. Therefore, 3a portrays potential applicability both as a small molecule reagent to replace novel neurotrophic factors and as a potent fluorescent reagent for various techniques, including bioimaging.

Excited state hydrogen or proton transfer pathways in microsolvated n-cyanoindole fluorescent probes

The sensitivity of the fluorescence properties of n-cyanoindole (n-CNI) fluorescent probes to the microenvironment makes them potential reporters of protein conformation and hydration. The fluorescence intensity of 5-CNI, 6-CNI, and 7-CNI is quenched when exposed to water solvent whereas substitution on position 4 of indoles dramatically increases it. A potential mechanism for this sensitivity to water may be similar to that found in indole. The fluorescence of indole is found to be quenched when interacting with water and ammonia solvent molecules via radiationless decay through an S1 (πσ*)/S0 conical intersection caused by excited state proton or hydrogen transfer to the solvent molecules. In this study we examine this fluorescence quenching mechanism along the N-H bond stretch of n-CNI probes using water cluster models and quantum mechanical calculations of the excited states. We find that n-CNI-(H2O)1-2 clusters form cyclic or non-cyclic structures via hydrogen bonds which lead to different photochemical reaction paths that can potentially quench the fluorescence by undergoing internal conversion from S1 to S0. However, the existence of a high energy barrier along the potential energy surface of the S1 state in most cases prevents this from occurring. We show that substitution on position 4 leads to the highest energy barrier that prevents the fluorophore from accessing these non-radiative channels, in agreement with its high intensity. We also find that the energy barrier in the S1 state of non-cyclic 5-CNI-(H2O)1-2 excited complexes decreases as the number of water molecules increases, which suggests great sensitivity of the fluorescence quenching on the aqueous environment.

Functionalized Phytochemicals-Embedded Carbon Dots Derived from Medicinal Plant for Bioimaging Application

Precise visualization of biological processes necessitates reliable coloring technologies, and fluorescence imaging has emerged as a powerful method for capturing dynamic cellular events. Low emission intensity and solubility of intrinsic fluorescence are still challenging, hindering their application in the biomedical field. The nanostructurization and functionalization of the insoluble phytochemicals, such as chlorophyll and curcumin, into carbon dots (CDs) were conducted to address these challenges. Due to their unique fluorescence characteristics and biocompatibility, CDs derived from medicinal plants hold promise as bioimaging agents. Further, the nitrogen in situ functionalization of the as-synthesized CDs offered tunable optical properties and enhanced solubility. The surface modification aims to achieve a more positive zeta potential, facilitating penetration through biological membranes. This work provides valuable insights into utilizing functionalized phytochemical-embedded carbon dots for bioimaging applications. The doping of nitrogen by adding urea showed an alteration of surface charge, which is more positive based on zeta potential measurement. The more positive CD particles showed that Andrographis paniculata-urea-based CDs were the best particles to penetrate cells than others related to the alteration of the surface charge and the functional group of the CDs, with the optimum dose of 12.5 μg/mL for 3 h of treatment for bioimaging assay.

Autofluorescent antimalarials by hybridization of artemisinin and coumarin: in vitro/in vivo studies and live-cell imaging

Malaria is one of our planet's most widespread and deadliest diseases, and there is an ever-consistent need for new and improved pharmaceuticals. Natural products have been an essential source of hit and lead compounds for drug discovery. Antimalarial drug artemisinin (ART), a highly effective natural product, is an enantiopure sesquiterpene lactone and occurs in Artemisia annua L. The development of improved antimalarial drugs, which are highly potent and at the same time inherently fluorescent is particularly favorable and highly desirable since they can be used for live-cell imaging, avoiding the requirement of the drug's linkage to an external fluorescent label. Herein, we present the first antimalarial autofluorescent artemisinin-coumarin hybrids with high fluorescence quantum yields of up to 0.94 and exhibiting excellent activity in vitro against CQ-resistant and multidrug-resistant P. falciparum strains (IC50 (Dd2) down to 0.5 nM; IC50 (K1) down to 0.3 nM) compared to reference drugs CQ (IC50 (Dd2) 165.3 nM; IC50 (K1) 302.8 nM) and artemisinin (IC50 (Dd2) 11.3 nM; IC50 (K1) 5.4 nM). Furthermore, a clear correlation between in vitro potency and in vivo efficacy of antimalarial autofluorescent hybrids was demonstrated. Moreover, deliberately designed autofluorescent artemisinin-coumarin hybrids, were not only able to overcome drug resistance, they were also of high value in investigating their mode of action via time-dependent imaging resolution in living P. falciparum-infected red blood cells.

Evaluation of intracellular lipid droplets viscosity by a probe with high fluorescence quantum yield

BACKGROUND

Lipid droplets (LDs) are an important organelle as the main energy storage site in cells. LDs viscosity controls the material and energy exchange between it and other organelles. Furthermore, the LDs metabolic abnormalities, cell dysfunction, some diseases may be attributed to the singular LDs viscosity. Currently, the fluorescent probes for sensing the variations of LDs viscosity are still scarce and expose some drawbacks of low fluorescence quantum yield, low sensitivity and LDs polarity interference. Thus, the development of high performance probes is significant to detect LDs viscosity.

RESULTS

We hereby provide a lipophilic fluorescent probe (TPE-BET) with high fluorescence quantum yield (Φf, 0.91 in glycerol) for imaging LDs viscosity in living cells. With the increase of viscosity from 0.54 cp to 934 cp, the fluorescence at λex/λem = 405/520 nm and the fluorescence quantum yield of TPE-BET linearly increased by 64.9 and 128.5 folds, respectively. Meanwhile, the outstanding LDs staining capability of TPE-BET may provide a high spatial resolution for LDs imaging. The cell imaging of TPE-BET not only successfully observed the viscosity variations of LDs in cell stress models, e.g., ferroptosis, inflammation and mitophagy, but also revealed the increased viscosity and extracellular delivery of LDs in heavy metal cell injury models (Hg/As) for the first time, which may supply concrete evidence for understanding the structure and function of LDs.

SIGNIFICANCE

This represents a new fluorescent probe TPE-BET with high fluorescence quantum yield for imaging LDs viscosity, which may decrease the dose of probe and excitation light intensity along with the improvement on signal noise ratio (S/N). The imaging results of TPE-BET clarified that LDs viscosity may be an appraisal index on cell differentiation, state evaluation and drug screening.

Biodistribution and toxicity assessment of methoxyphenyl phosphonium carbosilane dendrimers in 2D and 3D cell cultures of human cancer cells and zebrafish embryos

The consideration of human and environmental exposure to dendrimers, including cytotoxicity, acute toxicity, and cell and tissue accumulation, is essential due to their significant potential for various biomedical applications. This study aimed to evaluate the biodistribution and toxicity of a novel methoxyphenyl phosphonium carbosilane dendrimer, a potential mitochondria-targeting vector for cancer therapeutics, in 2D and 3D cancer cell cultures and zebrafish embryos. We assessed its cytotoxicity (via MTT, ATP, and Spheroid growth inhibition assays) and cellular biodistribution. The dendrimer cytotoxicity was higher in cancer cells, likely due to its specific targeting to the mitochondrial compartment. In vivo studies using zebrafish demonstrated dendrimer distribution within the vascular and gastrointestinal systems, indicating a biodistribution profile that may be beneficial for systemic therapeutic delivery strategies. The methoxyphenyl phosphonium carbosilane dendrimer shows promise for applications in cancer cell delivery, but additional studies are required to confirm these findings using alternative labelling methods and more physiologically relevant models. Our results contribute to the growing body of evidence supporting the potential of carbosilane dendrimers as vectors for cancer therapeutics.

Live Detection of Intracellular Chitin in Butterfly Wing Epithelial Cells In Vivo Using Fluorescent Brightener 28: Implications for the Development of Scales and Color Patterns

Chitin is the major component of the extracellular cuticle and plays multiple roles in insects. In butterflies, chitin builds wing scales for structural colors. Here, we show that intracellular chitin in live cells can be detected in vivo with fluorescent brightener 28 (FB28), focusing on wing epithelial cells of the small lycaenid butterfly Zizeeria maha immediately after pupation. A relatively small number of cells at the apical surface of the epithelium were strongly FB28-positive in the cytosol and seemed to have extensive ER-Golgi networks, which may be specialized chitin-secreting cells. Some cells had FB28-positive tadpole-tail-like or rod-like structures relative to the nucleus. We detected FB28-positive hexagonal intracellular objects and their associated structures extending toward the apical end of the cell, which may be developing scale bases and shafts. We also observed FB28-positive fibrous intracellular structures extending toward the basal end. Many cells were FB28-negative in the cytosol, which contained FB28-positive dots or discs. The present data are crucial to understanding the differentiation of the butterfly wing epithelium, including scale formation and color pattern determination. The use of FB28 in probing intracellular chitin in live cells may be applicable to other insect systems.

Real-time spatial quantification of gastric acid diffusion in whey protein gels with different NaCl concentrations by wide-field fluorescence microscopy

Gastric acid diffusion and penetration constitute an essential process in the structural breakdown and enzymatic hydrolysis of solid food during digestion. This study aimed to quantify the real-time diffusion and spatial distribution of gastric acids in whey protein isolate (WPI) gels in the presence of 0-0.05 M NaCl during simulated digestion using a wide-field fluorescence microscope. For all the gels regardless of NaCl concentration, the outer surface rapidly developed a near-saturated layer, resulting in a higher normalized gastric acid concentration in the outer layer than in the inner layer. The pH decrease was more significant for the gels at a higher NaCl concentration (i.e., 0.05 M) due to the formation of a more discontinuous and looser network structure that would facilitate acid diffusion into the gel matrix and decrease the gel buffering capacity. Consistently, the effective diffusion coefficient (D_A) estimated via the Fick diffusion model was 6.19 × 10^-10 m²/s for 0.05 M WPI-RITC gels, significantly higher than 0.015 M (4.46 × 10^-10 m²/s) and 0 M (3.54 × 10^-10 m²/s) gels. The present study has provided a quantitative understanding of the diffusion process and spatial distribution of gastric acids within the WPI gel matrix in real-time during in vitro gastric digestion as influenced by NaCl concentration.

A fluorescent probe for lipid droplet polarity imaging with low viscosity crosstalk

Monitoring the variations of lipid droplet (LD) polarity is of great significance for the investigation of LD-related cellular metabolism and function. We hereby report a lipophilic fluorescent probe (BTHO) with the feature of intramolecular charge transfer (ICT) for imaging the LD polarity in living cells. BTHO exhibits an obvious attenuation of fluorescence emission in response to the increase of environmental polarity. The linear response range of BTHO to polarity (ε, the dielectric constant of solvents) is derived to be 2.21-24.40, and the fluorescence of BTHO in glyceryl trioleate falls in this range. Furthermore, BTHO has high molecular brightness, which may effectively improve the signal to noise ratio, along with the decrease of phototoxicity. BTHO exhibits excellent photostability and targeting capability to LDs with low cytotoxicity, which is satisfactory in long-term imaging in live cells. The probe was successfully applied for imaging LD polarity variation in live cells caused by oleic acid (OA), methyl-β-cyclodextrin (MβCD), H₂O₂, starvation, lipopolysaccharide (LPS), nystatin, and erastin. The low crosstalk caused by viscosity to BTHO measuring the LD polarity was confirmed from a calculation result.

Red-Emitting Dithienothiophene S,S-Dioxide Dyes for Cellular Membrane Staining

A series of dithienothiophene S,S-dioxide (DTTDO) dyes was designed, synthesized, and investigated for their suitability in fluorescent cell imaging. Synthetized (D-π-A-π-D)-type DTTDO derivatives have molecule lengths close to the thickness of the phospholipid membrane, and they contain on both ends two positively charged or neutral polar groups to increase their solubility in water and to ensure simultaneous interaction with polar groups of the inner and outer part of the cellular membrane. DTTDO derivatives exhibit absorbance and emission maxima in the 517-538 nm and 622-694 nm range, respectively, and a large Stokes shift up to 174 nm. Fluorescence microscopy experiments revealed that these compounds selectively intercalate into cell membranes. Moreover, a cytotoxicity assay conducted on a model human live cells indicates low toxicity of these compounds at the concentrations required for effective staining. With suitable optical properties, low cytotoxicity, and high selectivity against cellular structures, DTTDO derivatives are proven to be attractive dyes for fluorescence-based bioimaging.

Characterizing the binding of glycoprotein VI with nanobody 35 reveals a novel monomeric structure of glycoprotein VI where the conformation of D1+D2 is independent of dimerization

BACKGROUND

The platelet-signaling receptor glycoprotein VI (GPVI) is a promising antithrombotic target. We have previously raised a series of high-affinity nanobodies (Nbs) against GPVI and identified Nb2, Nb21, and Nb35 as potent GPVI inhibitors. The Nb2 binding site has been mapped to the D1 domain, which is directly adjacent to the CRP binding site. Ligand-binding complementary determining region 3 has only 15% conservation between all 3 Nbs.

OBJECTIVES

To map the binding sites of Nb21 and Nb35 on GPVI.

METHODS

We determined the X-ray crystal structure of the D1 and D2 extracellular domains of the GPVI-Nb35 complex. We then looked at the effects of various GPVI mutations on the ability of Nbs to inhibit collagen binding and GPVI signaling using surface binding assays and transfected cell lines.

RESULTS

The crystal structure of GPVI bound to Nb35 was solved. GPVI was present as a monomer, and the D1+D2 conformation was comparable to that in the dimeric structure. Arg46, Tyr47, and Ala57 are common residues on GPVI targeted by both Nb2 and Nb35. Mutating Arg46 to an Ala abrogated the ability of Nb2, Nb21, and Nb35 to inhibit collagen-induced GPVI signaling and blocked the binding of all 3 Nbs. In addition, Arg60 was found to reduce Nb21 inhibition but not the inhibition Nb2 or Nb35.

CONCLUSIONS

These findings reveal key residues involved in the high-affinity binding of GPVI inhibitors and negate the idea that GPVI dimerization induces a conformational change required for ligand binding.

The Contribution of Cell Imaging to the Study of Anterior Pituitary Function and Its Regulation

Advances in the knowledge of the neuroendocrine system are closely related to the development of cellular imaging and labeling techniques. This synergy ranges from the staining techniques that allowed the first characterizations of the anterior pituitary gland, its relationship with the hypothalamus, and the birth of neuroendocrinology; through the development of fluorescence microscopy applications, specific labeling strategies, transgenic systems, and intracellular calcium sensors that enabled the study of processes and dynamics at the cellular and tissue level; until the advent of super-resolution microscopy, miniscopes, optogenetics, fiber photometry, and other imaging methods that allowed high spatiotemporal resolution and long-term three-dimensional cellular activity recordings in living systems in a conscious and freely moving condition. In this review, we briefly summarize the main contributions of cellular imaging techniques that have allowed relevant advances in the field of neuroendocrinology and paradigm shifts that have improved our understanding of the function of the hypothalamic-pituitary axes. The development of these methods and equipment is the result of the integration of knowledge achieved by the integration of several disciplines and effort to solve scientific questions and problems of high impact on health and society that this system entails.

Development of Fluorescent Turn-On Probes for CAG-RNA Repeats

Fluorescent sensing of nucleic acids is a highly sensitive and efficient bioanalytical method for their study in cellular processes, detection and diagnosis in related diseases. However, the design of small molecule fluorescent probes for the selective binding and detection of RNA of a specific sequence is very challenging because of their diverse, dynamic, and flexible structures. By modifying a bis(amidinium)-based small molecular binder that is known to selectively target RNA with CAG repeats using an environment-sensitive fluorophore, a turn-on fluorescent probe featuring aggregation-induced emission (AIE) is successfully developed in this proof-of-concept study. The probe (DB-TPE) exhibits a strong, 19-fold fluorescence enhancement upon binding to a short CAG RNA, and the binding and fluorescence response was found to be specific to the overall RNA secondary structure with A·A mismatches. These promising analytical performances suggest that the probe could be applied in pathological studies, disease progression monitoring, as well as diagnosis of related neurodegenerative diseases due to expanded CAG RNA repeats.

Bioimaging of Lysosomes with a BODIPY pH-Dependent Fluorescent Probe

Fluorescence-based probes represent a powerful tool for noninvasive imaging of living systems in real time and with a high temporal and spatial resolution. Amongst several known fluorophores, 3-difluoroborodipyrromethene (BODIPY) derivatives have become a cornerstone for innovative fluorescent labelling applications, mainly due to their advantageous features including their facile synthesis, structural versatility and exceptional photophysical properties. In this context, we report a BODIPY-based fluorescent probe for imaging of lysosomes in living cells. The BODIPY derivative displayed a remarkable fluorescence enhancement at low pH values with a pK_a* of 3.1. In vitro studies by confocal microscopy in HeLa cells demonstrated that the compound was able to permeate cell membrane and selectively label lysosome whilst remaining innocuous to the cell culture at the maximum concentration tested. Herein, the BODIPY derivative holds the promise of investigating lysosomal dynamics and function in living cells through fluorescence imaging.

Evaluating the Effect of Dye-Dye Interactions of Xanthene-Based Fluorophores in the Fluorosequencing of Peptides

A peptide sequencing scheme utilizing fluorescence microscopy and Edman degradation to determine the amino acid position in fluorophore-labeled peptides was recently reported, referred to as fluorosequencing. It was observed that multiple fluorophores covalently linked to a peptide scaffold resulted in a decrease in the anticipated fluorescence output and worsened the single-molecule fluorescence analysis. In this study, we report an improvement in the photophysical properties of fluorophore-labeled peptides by incorporating long and flexible (PEG)₁₀ linkers at the peptide attachment points. Long linkers to the fluorophores were installed using copper-catalyzed azide-alkyne cycloaddition conditions. The photophysical properties of these peptides were analyzed in solution and immobilized on a microscope slide at the single-molecule level under peptide fluorosequencing conditions. Solution-phase fluorescence analysis showed improvements in both quantum yield and fluorescence lifetime with the long linkers. While on the solid support, photometry measurements showed significant increases in fluorescence brightness and 20 to 60% improvements in the ability to determine the amino acid position with fluorosequencing. This spatial distancing strategy demonstrates improvements in the peptide sequencing platform and provides a general approach for improving the photophysical properties in fluorophore-labeled macromolecules.

Stereoselective Synthesis of Atropisomeric Acridinium Salts by the Catalyst‐Controlled Cyclization of ortho ‐Quinone Methide Iminiums

Quinone methides are fundamental intermediates for a wide range of reactions in which catalyst stereocontrol is often achieved by hydrogen bonding. Herein, we describe the feasibility of an intramolecular Friedel–Crafts 6π electrocyclization through ortho‐quinone methide iminiums stereocontrolled by a contact ion pair. A disulfonimide catalyst activates racemic trichloroacetimidate substrates and imparts stereocontrol in the cyclization step, providing a new avenue for selective ortho‐quinone methide iminium functionalization. A highly stereospecific oxidation readily transforms the enantioenriched acridanes into rotationally restricted acridiniums. Upon ion exchange, the method selectively affords atropisomeric acridinium tetrafluoroborate salts in high yields and an enantioenrichment of up to 93 : 7 e.r. We envision that ion‐pairing catalysis over ortho‐quinone methide iminiums enables the selective synthesis of a diversity of heterocycles and aniline derivatives with distinct stereogenic units.

Rapid and sensitive detection of dextran sulfate sodium based on supramolecular self-assembly of a perylene diimide derivative in aqueous solution

Dextran sulfate sodium (DSS) is a heparin polysaccharide, whose overuse would cause many adverse effects, such as stiff and painful joints and loss of hair. It is crucial to search after a rapid and accurate approach for the determination of DSS in the clinical treatment and diagnosis. Regrettably, there are few literatures about analytical methods for detecting DSS at present. In this research, a sensitive and selective method for detecting DSS based on the hydrosoluble perylene diimide (PDI) derivative was established in pure aqueous solution. The sensing mechanism and performance of PDI-PdEC were systematically investigated by ultraviolet and fluorescence spectroscopy. Non-covalent interactions between DSS and PDI-PdEC, like π-π stacking, electrostatic and hydrophobic interaction, promote the aggregation of PDI-PdEC and form supramolecular aggregates, which realize the sensitive and rapid detection of DSS in aqueous system. The detection limit for DSS is as low as 5.51 ng/mL and the linear range is 20-500 ng/mL. Furthermore, this probe was triumphantly applied in the detecting of DSS in serum. To the best of our knowledge, this is the first fluorescent probe for detecting DSS in aqueous media. We consider that our study will not only broaden the range of applications of perylene diimide fluorescent sensors, but also provide valuable reference for the design of new sensors for the rapid determination method of DSS.

HDAC Inhibitors: Innovative Strategies for Their Design and Applications

Histone deacetylases (HDACs) are a large family of epigenetic metalloenzymes that are involved in gene transcription and regulation, cell proliferation, differentiation, migration, and death, as well as angiogenesis. Particularly, disorders of the HDACs expression are linked to the development of many types of cancer and neurodegenerative diseases, making them interesting molecular targets for the design of new efficient drugs and imaging agents that facilitate an early diagnosis of these diseases. Thus, their selective inhibition or degradation are the basis for new therapies. This is supported by the fact that many HDAC inhibitors (HDACis) are currently under clinical research for cancer therapy, and the Food and Drug Administration (FDA) has already approved some of them. In this review, we will focus on the recent advances and latest discoveries of innovative strategies in the development and applications of compounds that demonstrate inhibitory or degradation activity against HDACs, such as PROteolysis-TArgeting Chimeras (PROTACs), tumor-targeted HDACis (e.g., folate conjugates and nanoparticles), and imaging probes (positron emission tomography (PET) and fluorescent ligands).

Computational Methods for Single-Cell Imaging and Omics Data Integration

Integrating single cell omics and single cell imaging allows for a more effective characterisation of the underlying mechanisms that drive a phenotype at the tissue level, creating a comprehensive profile at the cellular level. Although the use of imaging data is well established in biomedical research, its primary application has been to observe phenotypes at the tissue or organ level, often using medical imaging techniques such as MRI, CT, and PET. These imaging technologies complement omics-based data in biomedical research because they are helpful for identifying associations between genotype and phenotype, along with functional changes occurring at the tissue level. Single cell imaging can act as an intermediary between these levels. Meanwhile new technologies continue to arrive that can be used to interrogate the genome of single cells and its related omics datasets. As these two areas, single cell imaging and single cell omics, each advance independently with the development of novel techniques, the opportunity to integrate these data types becomes more and more attractive. This review outlines some of the technologies and methods currently available for generating, processing, and analysing single-cell omics- and imaging data, and how they could be integrated to further our understanding of complex biological phenomena like ageing. We include an emphasis on machine learning algorithms because of their ability to identify complex patterns in large multidimensional data.

Recent Efforts and Milestones for Simulating Nucleic Acid FRET Experiments through Computational Methods

Computational methods can greatly aid nucleic acid fluorescence experiments by either offering fully detailed atomic insights into the conformations and interactions present in the studied system or by providing accurate simulations of the fundamental parameters. Fluorescence-based optical biosensors show great potential for clinical diagnosis of life-altering diseases with a very high specificity. Many of the designs for such rely on the concept of Förster resonance energy transfer (FRET). Currently, the methods used experimentally make use of theoretical assumptions which fundamentally affect the results. Having a detailed atomistic overview or significant simulated parameters could improve the understanding of the calculations and provide much more accurate outcomes. However, there are many challenges that need to be addressed before standardized computational protocols can be employed. This review is meant to highlight the progress made for computational methods used to simulate FRET experiments for nucleic acid probes. Recent advances have been made in computational tools, such as force field parametrizations and improved protocols. Complementary simulations to experimental data are also comprised in the this review.

Label-free bioassay with graphene oxide-based fluorescent aptasensors: A review

Bioassays using a fluorophore and DNA aptamer have been extensively developed due to the ultrasensitivity of fluorophores and recognition ability of DNA aptamers. Conventional fluorescent aptamer-based sensors (aptasensors) require chemical labeling between the fluorophore and aptamer and is technologically impracical for various sensing and assay applications. A simple "mix and go" strategy has been introduced that uses label-free technology as a platform for sensor development. The biosensors comprise a fluorophore, a ssDNA aptamer, and eco-friendly graphene oxide (GO). In the absence of the sensor target, GO quenches the fluorescence of the fluorophore and single-strand DNA aptamer complex. When the target is added, the DNA aptamer conformationally turns into a duplex, G-quadruplexe, or other secondary structure. This structure change leads to release of GO by the fluorophore-aptamer-target complex, generating dramatic fluorescence recovery and amplification. With this sensing method, the DNA aptamer does not need to be chemically labeled. Therefore, flexible fluorophore indicators and ssDNA aptamers can be used in this label-free aptasensing strategy. In this review, we discuss various unlabeled fluorophores, including synthetic small molecular fluorophores and genetically encoded fluorescent proteins, as indicators for generating GO-based fluorescent DNA aptasensors for label-free bioassay.

Practicable Applications of Aggregation-Induced Emission with Biomedical Perspective

Considerable efforts have been made into developing aggregation-induced emission fluorogens (AIEgens)-containing nano-therapeutic systems due to the excellent properties of AIEgens. Compared to other fluorescent molecules, AIEgens have advantages including low background, high signal-to-noise ratio, good sensitivity, and resistance to photobleaching, in addition to being exempt from concentration quenching or aggregation-caused quenching effects. The present review outlines the major developments in the biomedical applications of AIEgens-containing systems. From a literature survey, the recent AIE works are reviewed and the reasons why AIEgens are chosen in various biomedical applications are highlighted. The research activities on AIEgens-containing systems are increasing rapidly, therefore, the present review is timely.

A novel turn-on type AIE fluorescent probe for highly selective detection of cysteine/homocysteine and its application in living cells

Biothiols, associated with multiple physiological and pathological processes, have structural similarities. Monitoring Biothiols selectively in organisms is of great significance. Burdened by the aggregation-caused quenching (ACQ) effect, the applications of conventional biothiols fluorescent probes are extremely limited. Herein, we developed a "turn-on" type aggregation-induced emission (AIE) fluorescent probe BQM-NBD, which was composed of a BQM-OH fluorophore molecule with AIE effect and the recognition group 7-nitro-1,2,3-benzoxadiazole (NBD). Non-fluorescent BQM-NBD produces strong fluorescence after the addition of cysteine (Cys) or homocysteine (Hcy). BQM-NBD exhibited excellent linearity for selective detection of Cys (0-100 Μm) and Hcy (0-50 μM) with detection limits of 6.0 × 10^-8 M and 8.4 × 10^-8 M, respectively. Simultaneously, after treatment with glutathione (GSH), it appeared no fluorescence. The results demonstrated BQM-NBD exhibited good selectivity to Cys/Hcy. Furthermore, BQM-NBD was successfully performed in the imaging of Cys in living cells with low cytotoxicity, which provides a feasible strategy for the selective detection of Cys in the living system.

A Molecular-Splicing Strategy for Constructing a Near-Infrared Fluorescent Probe for UDP-Glucuronosyltransferase 1A1

UDP-glucuronosyltransferase 1A1 (UGT1A1) is a vital metabolic enzyme responsible for the clearance of endogenous substances and drugs. Hitherto, the development of fluorescent probes for UGTs was severely restricted due to the poor isoform selectivity and on-off or blue-shifted fluorescence response. Herein, we established a novel "molecular-splicing" strategy to construct a highly selective near-infrared (NIR) fluorescent probe, HHC, for UGT1A1, which exhibited a NIR signal at 720 nm after UGT1A1 metabolism. HHC was then successfully used for the real-time imaging of endogenous UGT1A1 in living cells and animals and to monitor the bile excretion function. In summary, an isoform-specific NIR fluorescent probe has been developed for monitoring UGT1A1 activity in living systems, high-throughput screening of novel UGT1A1 inhibitors and visual evaluation of bile excretion function.

Fluorescence Approaches for Characterizing Ion Channels in Synthetic Bilayers

Ion channels are membrane proteins that play important roles in a wide range of fundamental cellular processes. Studying membrane proteins at a molecular level becomes challenging in complex cellular environments. Instead, many studies focus on the isolation and reconstitution of the membrane proteins into model lipid membranes. Such simpler, in vitro, systems offer the advantage of control over the membrane and protein composition and the lipid environment. Rhodopsin and rhodopsin-like ion channels are widely studied due to their light-interacting properties and are a natural candidate for investigation with fluorescence methods. Here we review techniques for synthesizing liposomes and for reconstituting membrane proteins into lipid bilayers. We then summarize fluorescence assays which can be used to verify the functionality of reconstituted membrane proteins in synthetic liposomes.

Recent Advances in Small Molecule-Based Intracellular pH Probes

Intracellular pH plays an important role in many biological and pathological processes. Small-molecule based pH probes are found to be the most effective for pH sensing because of ease of preparation, high sensitivity, and quick response. They have many advantages such as small perturbation to the functions of the target, functional adaptability, cellular component-specific localization, etc. The present review highlights the flurry of recent activity in the development of such probes. The probes are categorized based on the type of fluorophore used like quinoline, coumarin, BODIPY, rhodamine, indolium, naphthalimide, etc., and their analytical performance is discussed.

Ultrahigh-Throughput Detection of Enzymatic Alcohol Dehydrogenase Activity in Microfluidic Droplets with a Direct Fluorogenic Assay

The exploration of large DNA libraries of metagenomic or synthetic origin is greatly facilitated by ultrahigh‐throughput assays that use monodisperse water‐in‐oil emulsion droplets as sequestered reaction compartments. Millions of samples can be generated and analysed in microfluidic devices at kHz speeds, requiring only micrograms of reagents. The scope of this powerful platform for the discovery of new sequence space is, however, hampered by the limited availability of assay substrates, restricting the functions and reaction types that can be investigated. Here, we broaden the scope of detectable biochemical transformations in droplet microfluidics by introducing the first fluorogenic assay for alcohol dehydrogenases (ADHs) in this format. We have synthesized substrates that release a pyranine fluorophore (8‐hydroxy‐1,3,6‐pyrenetrisulfonic acid, HPTS) when enzymatic turnover occurs. Pyranine is well retained in droplets for >6 weeks (i. e. 14‐times longer than fluorescein), avoiding product leakage and ensuring excellent assay sensitivity. Product concentrations as low as 100 nM were successfully detected, corresponding to less than one turnover per enzyme molecule on average. The potential of our substrate design was demonstrated by efficient recovery of a bona fide ADH with an >800‐fold enrichment. The repertoire of droplet screening is enlarged by this sensitive and direct fluorogenic assay to identify dehydrogenases for biocatalytic applications.

Targeted optical fluorescence imaging: a meta-narrative review and future perspectives

Purpose

The aim of this review is to give an overview of the current status of targeted optical fluorescence imaging in the field of oncology, cardiovascular, infectious and inflammatory diseases to further promote clinical translation.

Methods

A meta-narrative approach was taken to systematically describe the relevant literature. Consecutively, each field was assigned a developmental stage regarding the clinical implementation of optical fluorescence imaging.

Results

Optical fluorescence imaging is leaning towards clinical implementation in gastrointestinal and head and neck cancers, closely followed by pulmonary, neuro, breast and gynaecological oncology. In cardiovascular and infectious disease, optical imaging is in a less advanced/proof of concept stage.

Conclusion

Targeted optical fluorescence imaging is rapidly evolving and expanding into the clinic, especially in the field of oncology. However, the imaging modality still has to overcome some major challenges before it can be part of the standard of care in the clinic, such as the provision of pivotal trial data. Intensive multidisciplinary (pre-)clinical joined forces are essential to overcome the delivery of such compelling phase III registration trial data and subsequent regulatory approval and reimbursement hurdles to advance clinical implementation of targeted optical fluorescence imaging as part of standard practice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00259-021-05504-y.

Synthesis and Spectroscopic Properties of 1,2,3-Triazole BOPAHY Dyes and Their Water-Soluble Triazolium Salts

Water-soluble BOPAHY fluorophores have not yet been reported. The potential of 1,2,3-triazolium salts for the formation of water-soluble chromophores is explored. 1,2,3-Triazole-substituted pyrroles were synthesized in a metal-free pathway and alkylated to obtain water-soluble 1,2,3-triazolium BOPAHY dyes. High fluorescence quantum yields were observed for triazole-bridged BOPAHY dyes in DCM and moderate fluorescence quantum yields for 1,2,3-triazolium-bridged BOPAHY chromophores in DCM and water. The fluorescence of the freely rotatable 1,2,3-triazolium-linked BOPAHYs is partially quenched in water.

Lighting up ATP in cells and tissues using a simple aptamer-based fluorescent probe

Extracellular ATP as a purinergic signaling molecule, together with ATP receptor, are playing an important role in tumor growth, therapy resistance, and host immunity suppression. Meanwhile ATP is a crucial indicator for cellular energy status and viability, thus a vital variable for tissue regeneration and in vitro tissue engineering. Most recent studies on COVID-19 virus suggest infection caused ATP deficit and release as a major characterization at the early stage of the disease and major causes for disease complications. Thus, imaging ATP molecule in both cellular and extracellular contexts has many applications in biology, engineering, and clinics. A sensitive and selective fluorescence “signal-on” probe for ATP detection was constructed, based on the base recognition between a black hole quencher (BHQ)-labeled aptamer oligonucleotide and a fluorophore (Cy5)-labeled reporter flare. The probe was able to detect ATP in solution with single digit µM detection limit. With the assistance of lipofectamine, this probe efficiently entered and shined in the model cells U2OS within 3 h. Further application of the probe in specific scenery, cardio-tissue engineering, was also tested where the ATP aptamer complex was able to sense cellular ATP status in a semi-quantitative manner, representing a novel approach for selection of functional cardiomyocytes for tissue engineering. At last a slight change in probe configuration in which a flexible intermolecular A14 linker was introduced granted regeneration capability. These data support the application of this probe in multiple circumstances where ATP measurement or imaging is on demand.

A highly effective "turn-on" camphor-based fluorescent probe for rapid and sensitive detection and its biological imaging of Fe2

In this work, a novel fluorescent probe CBO was synthesized for detecting Fe²⁺ using the natural monoterpenketone camphor as the starting material. The probe CBO displayed turn-on fluorescence to Fe²⁺ accompanied by the solution change from colorless to green. As expected, there was an excellent linear relationship between the fluorescence intensity of probe CBO and the concentration of Fe²⁺ (0-20 μM), and the detection limit was as low as 1.56×10^-8 M. In particular, CBO could selectively sense Fe²⁺ more than other analytes (Fe³⁺ included) through the N-oxide strategy, and quickly responded to Fe²⁺ (60 s) over a wide pH (4-14) range. Additionally, based on the rapid fluorescence response of CBO to Fe²⁺, a simple test strip-based detector was designed for boosting practical applicability. The probe CBO had been successfully applied to the fluorescence imaging of Fe²⁺ in onion cells and living zebrafish. The probe CBO was a powerful tool of detecting Fe²⁺ level in organisms, which was of significance to understand the role of Fe²⁺ in Fe²⁺-related physical processes and diseases.

Selective Mitochondrial Protein Labeling Enabled by Biocompatible Photocatalytic Reactions inside Live Cells

Biocompatible reactions are powerful tools to probe protein functions in their native environment. Due to the difficulty of penetrating the live-cell membrane and the complex intracellular environment, the biocompatible reactions inside live cells are challenging, especially at the subcellular level with spatial resolution. Here we report the first biocompatible photocatalytic azide conjugation reaction inside live cells to achieve the mitochondria-selective proteins labeling. The organic dyes acridine orange, fluorescein, and rhodamine 123 were developed as the biocompatible photocatalysts for the proteins labeling with aryl azides, which yielded benzazirines and ketenimines from triplet nitrenes for the protein nucleophilic residue trapping. The photocatalytic azide conjugation reaction with rhodamine 123 selectively labeled the mitochondrial proteins via the organic dye's mitochondrial localization. In response to the mitochondrial stress induced by rotenone, this photocatalytic azide-promoted labeling method mapped the dynamic mitochondrial proteome changes with high temporal-spatial precision and identified several potential mitochondrial stress-response proteins for the first time. The high temporal-spatial precision of this photocatalytic azide-promoted labeling method holds excellent potential for intracellular protein network investigations.

The design, synthesis and cellular imaging of a tumor-anchored, potent and cell-permeable BRD4-targeted fluorescent ligands

Bromodomain 4 (BRD4) proteins play an important role in histone post-translational modifications and facilitate several important physiological and pathological processes, including cancers. The inhibition of BRD4 by small molecule inhibitors shows promise as a therapeutic strategy for cancer treatment. However, their clinical applications were limited, which is largely hampered by off-target effects-induced toxicity. We herein report the design, synthesis, and cellular imaging of a set of tumor-anchored and BRD4-targeted fluorescent ligands by introducing selective and potent BRD4 inhibitor into different fluorophores via variable linkers. One of the fluorescent conjugates (compound 6) was demonstrated to be cell-permeable and low cytotoxic, preferentially accumulated in cancer cells, and display pronounced fluorescent signal. More importantly, 6 was identified to show specific BRD4 engagement in the cellular content. Collectively, this study provides a pathway for developing labeled BRD4 ligands and highlights that compound 6 may represent a valuable tool for explorative learning and target delivery study of BRD4.

Trends in small organic fluorescent scaffolds for detection of oxidoreductase

Oxidoreductases are diverse class of enzymes engaged in modulating the redox homeostasis and cellular signaling cascades. Abnormal expression of oxidoreductases including thioredoxin reductase, azoreductase, cytochrome oxidoreductase, tyrosinase and monoamine oxidase leads to the initiation of numerous disorders. Thus, enzymes are the promising biomarkers of the diseased cells and their accurate detection has utmost significance for clinical diagnosis. The detection method must be extremely selective, sensitive easy to use, long self-life, mass manufacturable and disposable. Fluorescence assay approach has been developed potential substitute to conventional techniques used in enzyme's quantification. The fluorescent probes possess excellent stability, high spatiotemporal ratio and reproducibility represent applications in real sample analysis. Therefore, the enzymatic transformations have been monitored by small activatable organic fluorescent probes. These probes are generally integrated with enzyme's substrate/inhibitors to improve their binding affinity toward the enzyme's catalytic site. As the recognition unit bio catalyzed, the signaling unit produces the readout signals and provides novel insights to understand the biochemical reactions for diagnosis and development of point of care devices. Several structural modifications are required in fluorogenic scaffolds to tune the selectivity for a particular enzyme. Hence, the fluorescent probes with their structural features and enzymatic reaction mechanism of oxidoreductase are the key points discussed in this review. The basic strategies to detect each enzyme are discussed. The selectivity, sensitivity and real-time applications are critically compared. The kinetic parameters and futuristic opportunities are present, which would be enormous benefits for chemists and biologists to understand the facts to design and develop unique fluorophore molecules for clinical applications.

Recent progress in developing fluorescent probes for imaging cell metabolites

Cellular metabolites play a crucial role in promoting and regulating cellular activities, but it has been difficult to monitor these cellular metabolites in living cells and in real time. Over the past decades, iterative development and improvements of fluorescent probes have been made, resulting in the effective monitoring of metabolites. In this review, we highlight recent progress in the use of fluorescent probes for tracking some key metabolites, such as adenosine triphosphate, cyclic adenosine monophosphate, cyclic guanosine 5'-monophosphate, Nicotinamide adenine dinucleotide (NADH), reactive oxygen species, sugar, carbon monoxide, and nitric oxide for both whole cell and subcellular imaging.

A facile combinatorial approach to construct a ratiometric fluorescent sensor: application for the real-time sensing of cellular pH changes

Realtime monitoring of the cellular environment, such as the intracellular pH, in a defined cellular space provides a comprehensive understanding of the dynamics processes in a living cell. Considering the limitation of spatial resolution in conventional microscopy measurements, multiple types of fluorophores assembled within that space would behave as a single fluorescent probe molecule. Such a character of microscopic measurements enables a much more flexible combinatorial design strategy in developing fluorescent probes for given targets. Nanomaterials with sizes smaller than the microscopy spatial resolution provide a scaffold to assemble several types of fluorophores with a variety of optical characteristics, therefore providing a convenient strategy for designing fluorescent pH sensors. In this study, fluorescein (CF) and tetramethylrhodamine (CR) were assembled on a DNA nanostructure with controlling the number of each type of fluorophore. By taking advantage of the different responses of CF and CR emissions to the pH environment, an appropriate assembly of both CF and CR on DNA origami enabled a controlled intensity of fluorescence emission and ratiometric pH monitoring within the space defined by DNA origami. The CF and CR-assembled DNA origami was successfully applied for monitoring the intracellular pH changes.

BODIPY-based fluorescent polymeric probes for selective detection of Fe3+ ions in aqueous solution

It is of scientific and practical significance to sense and to remove heavy metal ions in the environment. In this work, four BODIPY-based fluorescent polymeric probes with the ability to sense and separate Fe3+ ions have been prepared via thiol-ene click reaction. The polymers have good thermal stability. Meanwhile, the results show that they have selective recognition capabilities only for Fe3+, which are mainly manifested as significant quenching of fluorescence and color modulation under visible light. The sensitivity is good, and the limit of detection reaches as low as 0.14 µM. They can also be used as reversible chemical probes to detect Fe3+. Therefore, the click reaction provides us with a facile method for preparing fluorescent polymer probes.

Investigating the Nonradiative Decay Pathway in the Excited State of Silepin Derivatives: A Study with Second-Order Multireference Perturbation Wavefunction Theory

The fluorescence quantum yield for fluorescent organic molecules is an important molecular property, and tuning it up is desired for various applications. For the computational estimation of the fluorescence quantum yield, the theoretical prediction of the nonradiative decay rate constant has become an attractive subject of study. The rate constant of thermally activated nonradiative decay is related to the activation energy in the photoreaction; thus, the accuracy and reliability of the excited-state potential energies in the quantum chemical computation are critical. In this study, we employed a second-order multireference perturbation wavefunction theory for studying the thermally activated decay via conical intersection (CI) of 1,1-dimethyldibenzo[b,f]silepin derivatives. The correlation between the computed activation energy to reach the CI geometry in the S₁ state and the experimentally determined fluorescence quantum yield implied that silepins nonradiatively decay via the CI triggered by the twisting of the central C-C bond. Geometry optimization of the transition state using multireference perturbation theory drastically reduced the estimated activation energy. Our computation gave reasonable predictions of the activation free energies of photoexcited 1,1-dimethyldibenzo[b,f]silepin. The energy profiles and geometry optimizations using proper quantum chemical methods played a critical role in reliable estimation of the rate constant and fluorescence quantum yield.

Bicyclic 1,3a,6a-Triazapentalene Chromophores: Synthesis, Spectroscopy and Their Use as Fluorescent Sensors and Probes

The 1,3a,6a-triazapentalene (TAP) is an aromatic heterocyclic fluorescent dye with interesting features such as its small size, large Stokes shift, solvatochromism, and emission wavelengths that are spread across the visible spectrum. TAPs have been synthesized via different synthetic strategies involving click−cyclization−aromatization domino reactions, gold-catalyzed cyclization of propargyl triazoles or triazolization of acetophenones. As a result, TAPs with diverse substitution patterns were obtained, showing varying fluorescence properties. Based on these properties, several TAPs have been selected and studied as fluorescent imaging probes in living cells and as sensors. This mini review provides an overview of the research on the bicyclic TAPs and does not comment on the literature about benzo or otherwise fused systems. The synthetic methodologies for the preparation of TAPs, the substituent effects on the fluorescence properties, and the behavior of the TAP core as an element of biological imaging probes and sensors are discussed.

Novel PET-pperated rosamine pH-sensor dyes with substitution pattern-tunable pKa values and temperature sensitivity

We present the synthesis and characterization of a family of regioisomerically pure pH-sensitive rosamine fluorophores consisting of xanthene fluorophore cores and differently substituted phenol moieties.