Xanthene-based functional dyes: towards new molecules operating in the near-infrared region

Xanthene-based functional dyes have diverse applications in life science and materials science. A current challenge is to develop new dyes with suitable physicochemical properties, including near-infrared (NIR) operation, for advanced biological applications such as medical diagnostics and molecular imaging. In this review, we first present an overview of xanthene-based functional dyes and then focus on synthetic strategies for modulating the absorption and fluorescence of dyes that operate in the NIR wavelength region with bright emission and good photostability. We also introduce our work on aminobenzopyranoxanthenes (ABPXs) and bridged tetra-aryl-p-quinodimethanes (BTAQs) as new xanthene-based far-red (FR)/NIR absorbing/emitting molecules whose absorption/fluorescence wavelengths change in response to external stimuli.

Combination of changeable π-conjugation and hydrophilic groups for developing water-soluble small-molecule NIR-II fluorogenic probes

Small-molecule probes emitting in the second near-infrared window (NIR-II) are attracting great attention because of their deep-tissue imaging ability. However, developing NIR-II fluorogenic (off-on) probes with good water solubility remains a great challenge due to the lack of a facile approach. Herein we first report the combination of changeable π-conjugation and hydrophilic groups as an effective strategy for developing water-soluble NIR-II fluorogenic probes. With the strategy, new water-soluble NIR-II fluorophores are prepared, among which NIR-II-F2 and NIR-II-F3 show superior stability and bright fluorescence in aqueous media, and are thus used to design two water-soluble NIR-II fluorogenic probes for leucine aminopeptidase (LAP). The excellent performance in real aqueous bio-environments is demonstrated by imaging mouse vasculatures and organs with NIR-II-F2, and LAP in drug-induced liver injury mice with one of the enzymatic probes; however, water-insoluble dyes cannot achieve such in vivo imaging under the same conditions. Our strategy may be helpful for further developing water-soluble organic NIR-II fluorogenic probes for in vivo imaging of other analytes.

Mechanism of Absorption Wavelength Shift Depending on the Protonation State of the Acrylate Group in Chlorophyll c

Diatoms can use light in the blue-green region because they have chlorophyll c (Chlc) in light-harvesting antenna proteins, fucoxanthin and chlorophyll a/c-binding protein (FCP). Chlc has a protonatable acrylate group (-CH═CH-COOH/COO-) conjugated to the porphyrin ring. As the absorption wavelength of Chlc changes upon the protonation of the acrylate group, Chlc is a candidate component that is responsible for photoprotection in diatoms, which switches the FCP function between light-harvesting and energy-dissipation modes depending on the light intensity. Here, we investigate the mechanism by which the absorption wavelength of Chlc changes owing to the change in the protonation state of the acrylate group, using a quantum mechanical/molecular mechanical approach. The calculated absorption wavelength of the Soret band of protonated Chlc is ∼25 nm longer than that of deprotonated Chlc, which is due to the delocalization of the lowest (LUMO) and second lowest (LUMO+1) unoccupied molecular orbitals toward the acrylate group. These results suggest that in FCP, the decrease in pH on the lumenal side under high-light conditions leads to protonation of Chlc and thereby a red shift in the absorption wavelength.

Force-Induced Synergetic Pigmentary and Structural Color Change of Liquid Crystalline Elastomer with Nanoparticle-Enhanced Mechanosensitivity

The ability of some animals to rapidly change their colors can greatly improve their chances of escaping predators or hunting prey. A classic example is cephalopods, which can rapidly shift through a wide range of colors. This ability is based on the synergetic effect of the change of pigmentary and structural colors exhibited by their own two categories of color-changing cells: supernatant chromatophores offer various pigmentary colors and lower iridophores or leucophores reflect the different structural colors by adjusting their periodicities. Here, a mechanochromic liquid crystalline elastomer with force-induced synergetic pigmentary and structural color change, whose mechanosensitivity is enhanced by the stress-concentration induced by the doped nanoparticle, is presented. The materials have a large color-changing gamut and high mechanochromic sensitivity, which exhibit great potential in the field of mechanical detectors, sensors, and anti-counterfeiting materials.

Research progress in pharmacological activities and structure-activity relationships of tetralone scaffolds as pharmacophore and fluorescent skeleton

The tetralone and tetralone derivatives, as crucial structural scaffolds of potential novel drugs targeted at multiple biological end-points, are normally found in several natural compounds and also, it can be used as parental scaffold and/or intermediate for the synthesis of a series of pharmacologically active compounds with a broad-spectrum of bioactivities including antibacterial, antitumor, CNS effect and so on. Meanwhile, SAR information of its analogues has drawn attentions among medicinal chemists, which could contribute to the further research related to tetralone derivatives aimed at multiple targets. This review encompasses pharmacological activities, SAR analysis and docking study of tetralone and its derivatives, expecting to provide a general retrospect and prospect on tetralone derivatives.

Hemicyanine-Based Near-Infrared Activatable Probes for Imaging and Diagnosis of Diseases

Molecular activatable probes with near-infrared (NIR) fluorescence play a critical role in in vivo imaging of biomarkers for drug screening and disease diagnosis. With structural diversity and high fluorescence quantum yields, hemicyanine dyes have emerged as a versatile scaffold for the construction of activatable optical probes. This Review presents a survey of hemicyanine-based NIR activatable probes (HNAPs) for in vivo imaging and early diagnosis of diseases. The molecular design principles of HNAPs towards activatable optical signaling against various biomarkers are discussed with a focus on their broad applications in the detection of diseases including inflammation, acute organ failure, skin diseases, intestinal diseases, and cancer. This progress not only proves the unique value of HNAPs in preclinical research but also highlights their high translational potential in clinical diagnosis.

Synthesis of Profluorescent Strigolactone Probes for Biochemical Studies

In this chapter, we will describe a method we set up to synthesize two profluorescent strigolactone (SL) mimic probes (GC240 and GC242) and the optimized protocols developed to study the enzymatic properties of various strigolactone receptors. The Arabidopsis AtD14 SL receptor is used here as a model for this purpose.

NIR-Light-Activated Ratiometric Fluorescent Hybrid Micelles for High Spatiotemporally Controlled Biological Imaging and Chemotherapy

Intelligent-responsive imaging-therapy strategy has shown great significance for biomedicine. However, it is still a challenge to construct spatiotemporally controlled imaging-therapy systems triggered by near infrared (NIR) light. In this work, NIR-light-activated ratiometric fluorescent hybrid micelles (RFHM) are prepared via the co-assembly of upconversion nanoparticles (UCNPs), doxorubicin (DOX), and UV-light-responsive amphiphilic block copolymer for the spatiotemporally controlled imaging and chemotherapy. Upon NIR light irradiation, UCNPs can convert NIR light to UV light. The emitted UV light induces the photoreaction of copolymer to further trigger ratiometric fluorescence imaging and degradation of hybrid micelles, resulting in rapid DOX release from hybrid micelles for antitumor therapy. The animal experiments reveal that NIR light can not only remotely regulate the ratiometric fluorescence imaging of RFHM in tumor tissue, but also trigger DOX release from RFHM to inhibit tumor growth. Therefore, this study provides a new strategy to achieve high spatial-temporal-controlled biological imaging and chemotherapy.

Microbial nitroreductases: A versatile tool for biomedical and environmental applications

Nitroreductases, enzymes found mostly in bacteria and also in few eukaryotes, use nicotinamide adenine dinucleotide (NADH) or nicotinamide adenine dinucleotide phosphate (NADPH) as a cofactor for their activity and metabolize an enormous list of a diverse nitro group-containing compounds. Nitroreductases that are capable of metabolizing nitroaromatic and nitro heterocyclic compounds have drawn great attention in recent years owing to their biotechnological, biomedical, environmental, and human impact. These enzymes attracted medicinal chemists and pharmacologists because of their prodrug selectivity for activation/reduction of nitro compounds that wipe out pathogens/cancer cells, leaving the host/normal cells unharmed. It is applied in diverse fields of study like prodrug activation in treating cancer and leishmaniasis, designing fluorescent probes for hypoxia detection, cell imaging, ablation of specific cell types, biodegradation of nitro-pollutants, and interpretation of mutagenicity of nitro compounds. Keeping in view the immense prospects of these enzymes and a large number of research contributions in this area, the present review encompasses the enzymatic reaction mechanism, their role in antibiotic resistance, hypoxia sensing, cell imaging, cancer therapy, reduction of recalcitrant nitro chemicals, enzyme variants, and their specificity to substrates, reaction products, and their applications.

Organocatalytic 1,4-Addition of Azadienes with 3-Homoacyl Coumarins toward Highly Enantioenriched Benzofuran Coumarin Skeletons

A highly enantioselective 1,4-addition reaction of azadiene with 3-homoacyl coumarin has been accomplished by low amounts of bifunctional cinchona alkaloid catalysis under mild conditions. Varieties of benzofuran coumarin skeletons were obtained in moderate to high yields (up to 99%) with excellent enantioselectivities (up to 99% ee) and complete diastereoselectivity.

Design Strategies of Photoacoustic Molecular Probes

Photoacoustic (PA) probes have been developed very quickly and applied in broad areas in recent years. Most of them are constructed based on organic dyes with intrinsic near-infrared (NIR) absorption properties. To increase PA contrast and improve imaging resolution and the sensitivity of detection, various methods for the design of PA probes have been developed. This minireview mainly focuses on the development and design strategies of activatable small-molecule PA probes in four aspects: reaction-cleavage, metal ion chelation, photoswitch, and protonation-deprotonation. It highlights some key points of designing PA probes corresponding to their properties and applications. The challenges and perspectives for small-molecule PA probes are also discussed.

One-step synthesis of rhodamine-based Fe3+ fluorescent probes via Mannich reaction and its application in living cell imaging

Four rhodamine-based fluorescent probes M1-M4 were synthesized in one step using Mannich reaction. The Mannich reaction based approach has the advantages of simplicity, good yield and excellent atomic economy. The structures were determined by ¹H NMR, ¹³C NMR, IR and HRMS. The probe M3 as a representative compound was characterized by single-crystal X-ray analyses. The fluorescence and absorbance spectra research of the probes demonstrated that they could be used as Fe³⁺-selective fluorescent probes with good sensitivity, excellent linearity, and outstanding anti-interference in acetonitrile/Tris-HCl buffer solution (3:7, V/V; pH = 7.4). Moreover, confocal laser scanning microscopy experiments have proven that the probe M3 was successfully used for fluorescence imaging in MCF-7 cells.

Deeper insight into protease-sensitive "covalent-assembly" fluorescent probes for practical biosensing applications

We report a rational and systematic study devoted to the structural optimisation of a novel class of protease-sensitive fluorescent probes that we recently reported (S. Debieu and A. Romieu, Org. Biomol. Chem., 2017, 15, 2575-2584), based on the "covalent-assembly" strategy and using the targeted enzyme penicillin G acylase as a model protease to build a fluorescent pyronin dye by triggering a biocompatible domino cyclisation-aromatisation reaction. The aim is to identify ad hoc probe candidate(s) that might combine fast/reliable fluorogenic "turn-on" response, full stability in complex biological media and ability to release a second molecule of interest (drug or second fluorescent reporter), for applications in disease diagnosis and therapy. We base our strategy on screening a set of active methylene compounds (C-nucleophiles) to convert the parent probe to various pyronin caged precursors bearing Michael acceptor moieties of differing reactivities. In vitro stability and fluorescent enzymatic assays combined with HPLC-fluorescence analyses provide data useful for defining the most appropriate structural features for these fluorogenic scaffolds depending on the specifications inherent to biological application (from biosensing to theranostics) for which they will be used.

Recognition Moieties of Small Molecular Fluorescent Probes for Bioimaging of Enzymes

Enzymes are a class of important substances for life, and their abnormal levels are associated with many diseases. Thus, great progress has been made in the past decade in detecting and imaging enzymes in living biosystems, and in this respect fluorescent probes combined with confocal microscopy have attracted much attention because of their high sensitivity and unrivaled spatiotemporal resolution. Fluorescent probes are usually composed of three moieties: a signal or fluorophore moiety, a recognition or labeling moiety, and an appropriate linker to connect the two aforementioned moieties. At present, however, research and reviews on enzymatic probes mostly focus on fluorophores and/or linkers, whereas those on the recognition moiety are relatively few. Moreover, current enzymatic probes with some recognition moieties have drawbacks such as poor selectivity, high background fluorescence, or/and low sensitivity and are unsatisfactory for practical applications. Thus, developing new recognition moieties with higher specificity or/and sensitivity to the enzyme of interest is very desirable but still challenging. In this Account, we introduce the recognition moieties of fluorescent probes for several enzymes, including tyrosinase, monoamine oxidase A (MAO-A), nitroreductase (NTR), and aminopeptidases. Highlights are given on how new specific recognition moieties of tyrosinase and MAO-A were designed to eliminate the interference by reactive oxygen species (ROS) and MAO-B, respectively. Here we present four recent examples in which designed fluorescent probes are employed to image enzymes in living biosystems. The first example shows that 3-hydroxyphenyl can serve as a new and more specific recognition moiety than the traditional 4-hydroxyphenyl group for tyrosinase, enabling the development of a highly selective fluorescent probe for imaging of tyrosinase without interference by ROS. The second presents a general design strategy for fluorescent probes specific for an enzyme, which involves combining the characteristic structure of an inhibitor of the target enzyme along with its traditional reactive group as a new recognition moiety, and successfully demonstrates it by selective detection of MAO-A in the presence of its isomeric MAO-B. The third mainly illustrates that 5-nitrothiophen-2-yl alcohol with a stronger electron-donating S atom is a better fluorescence quenching and recognition moiety than 5-nitrofuran-2-yl alcohol for NTR, leading to the development of a highly sensitive method for NTR assay. Lastly, on the basis of known observations, we show that besides the specific interaction with the target, another function of some recognition moieties may be responsible for tuning the fluorescence signal, which is exemplified by the linking of several aminopeptidases' recognition moieties to the free hydroxyl or amino group of different fluorophores. It is our wish that this Account will promote the appearance of more specific recognition moieties and fluorescent probes with excellent properties and that new biofunctions of the enzymes will be uncovered.

Development of a unique reversible fluorescent probe for tracking endogenous sulfur dioxide and formaldehyde fluctuation in vivo

A FRET-based reversible fluorescent probe for sensing SO₂ and FA was designed. The probe was first used for imaging endogenous SO₂ and FA in vitro and in vivo. Moreover, we first found that the interaction of SO₂ and FA can reduce the cytotoxicity.

Synthesis of 4-styrylcoumarins via FeCl3-promoted cascade reactions of propargylamines with β-keto esters

A versatile and highly regioselective FeCl₃-promoted tandem cyclization reaction of in situ generated alkynyl o-quinone methides (o-AQMs) with β-keto esters has been developed.

Emerging trends in sensors based on carbon nitride materials

A new class of functional materials, carbon nitrides, has recently attracted the attention of researchers.

3-Homoacyl coumarin: an all carbon 1,3-dipole for enantioselective concerted (3+2) cycloaddition

A new type of all-carbon 1,3-dipole precursor, 3-homoacylcoumarin, was employed for the stereoselective (3+2) cycloaddition with indandione alkylidenes to generate a series of coumarin/indandione-fused spirocyclopentanes bearing four contiguous stereogenic centers. While two reaction pathways progressed simultaneously, detailed mechanistic investigation revealed that the highly efficient stereoselective concerted route dominated the extremely slow stepwise pathway.

Electrospun nanofibers decorated with bio-sonochemically synthesized gold nanoparticles as an ultrasensitive probe in amalgam-based mercury (II) detection system

In this study, bio-ultrasound-assisted synthesized gold nanoparticles using Gracilaria canaliculata algae have been immobilized on a polymeric support and used as a glassy probe chemosensor for detection and rapid removal of Hg²⁺ ions. The function of the suggested chemosensor has been explained based on gold-amalgam formation and its catalytic role on the reaction of sodium borohydride and rhodamine B (RhB) with fluorescent and colorimetric sensing function. The catalyzed reduction of RhB by the gold amalgam led to a distinguished color change from red and yellow florescence to colorless by converting the amount of Hg²⁺ deposited on Au-NPs. The detection limit of the colorimetric and fluorescence assays for Hg²⁺ was 2.21 nM and 1.10 nM respectively. By exposing the mentioned colorless solution to air for at least 2 h, unexpectedly it was observed that the color and fluorescence of RhB were restored. Have the benefit of the above phenomenon a recyclable and portable glass-based sensor has been provided by immobilizing the Au-NPs and RB on the glass slide using electrospinning. Moreover, the introduced combinatorial membrane has facilitated the detection and removal of Hg²⁺ ions in various Hg (II)-contaminated real water samples with efficiency of up to 99%.

Advances in targeting the folate receptor in the treatment/imaging of cancers

The folate receptor (FR) is a recognised biomarker for tumour cells due to its overexpression on a large number of tumours. Consequently, the FR has been exploited by many diagnostic and therapeutic tools to allow targeted delivery to, and imaging of, cancer cells. Herein, we describe the many different approaches by which this has been achieved, including the attachment of folate to potent chemotherapeutic drugs to form FR-targeting small molecule-drug conjugates (SMDCs), FR-targeting antibodies (as antibody alone and as an antibody-drug conjugate), and in the form of complementary nanotechnology-folate platforms; as well as imaging variants thereof. The potential of exploiting the FR for targeted therapy/imaging has the potential to revolutionise the way several cancers are treated. These FR-targeted technologies can also pave the way for inspiring further sophisticated drug conjugates, especially as this receptor is being targeted by use of several complementary technologies: small molecule, nanoparticle and protein-based - thus providing broad and distinct knowledge in the area.

pH-Responsive diblock copolymers with two different fluorescent labels for simultaneous monitoring of micellar self-assembly and degree of protonation

Facile labelling of both blocks of a pH-responsive diblock copolymer with different fluorophores allows monitoring of polymer aggregation and deprotonation.

Real-time probing of mercury using an efficient “turn-on” strategy with potential as in-field mapping kit and in live cell imaging

Based on a rhodamine scaffold as a fluorophore and 2-aminothiazole as a receptor, we present a highly selective and sensitive sensor (TS).

Light-Up of Rhodamine Hydrazide to Generate Emissive Initiator for Polymerization and to Afford Photochromic Polypeptide Metal Complex

Ring-opening polymerization (ROP) of cyclic peptide monomer of γ-propargyl-l-glutamate N-carboxyanhydride (PLG⁻NCA) was originally initiated by non-emissive, ring-close rhodamine 6G hydrazide (R-C). However, instantaneously after adding PLG⁻NCA to R-C, the spirolactam ring of R-C was opened by PLG⁻NCA, rendering emissive, ring-open R-O to initiate ROP of PLG⁻NCA. The emissive R-O moiety therefore produced fluorescent R⁻PLG with aggregation-induced emission (AIE) properties. Moreover, R⁻PLG was found to exhibit photochromic properties with good fatigue resistance and long lifetime when forming metal complexes with Sn(II) and Fe(III). In the dark, irradiated metal complexes slowly (~50 min) restored to the initial state. This research provides foundation for the development of new photochromic materials with long lifetime.

Chemical Probes for Visualizing Intact Animal and Human Brain Tissue

Newly developed tissue clearing techniques can be used to render intact tissues transparent. When combined with fluorescent labeling technologies and optical sectioning microscopy, this allows visualization of fine structure in three dimensions. Gene-transfection techniques have proved very useful in visualizing cellular structures in animal models, but they are not applicable to human brain tissue. Here, we discuss the characteristics of an ideal chemical fluorescent probe for use in brain and other cleared tissues, and offer a comprehensive overview of currently available chemical probes. We describe their working principles and compare their performance with the goal of simplifying probe selection for neuropathologists and stimulating probe development by chemists. We propose several approaches for the development of innovative chemical labeling methods which, when combined with tissue clearing, have the potential to revolutionize how we study the structure and function of the human brain.

Gold nanoparticles and the corresponding filter membrane as chemosensors and adsorbents for dual signal amplification detection and fast removal of mercury(ii)

Nowadays, the development of a multifunction system for the simultaneous multiple signal amplification detection and fast removal of Hg²⁺ remains a major challenge. Herein, we for the first time used gold nanoparticles (Au NPs) and the corresponding filter membrane as chemosensors and adsorbents for dual signal amplification detection and fast removal of Hg²⁺. Such a system was based on the formation of gold amalgam and a gold amalgam-based reaction between rhodamine B (RhB) and NaBH₄ with fluorescence and colorimetric sensing functions. When the gold amalgam catalyzes the reduction of RhB, the red color and orange fluorescence of RhB gradually changed to colorless by switching the amount of Hg²⁺ deposited on 13 nm Au NPs. The detection limit of the fluorescence assay and colorimetric assay is 1.16 nM and 2.54 nM for Hg²⁺, respectively. Interestingly, the color and fluorescence of RhB could be recovered when the above colorless reaction solution was exposed to air for about 2 hours. Taking advantage of the above optical phenomenon, a recyclable paper-based sensor has been developed by immobilizing the Au NPs and RhB dye on filter paper and has been successfully used for detection of Hg²⁺ in real water samples. In addition, the filter membrane immobilized Au NPs could allow fast removal of mercury ions in Yellow river water and tap water with the removal efficiency close to 99%.

In situ formation of pyronin dyes for fluorescence protease sensing

A cutting-edge strategy for fluorogenic sensing of proteases (leucine aminopeptidase for the proof of concept) and based on the “covalent-assembly” principle is reported. Non-fluorescent mixed bis-aryl ethers are readily converted into a fluorescent pyronin through a domino process triggered by the peptide bond cleavage event caused by the targeted enzyme.