Phosphinate-containing rhodol and fluorescein scaffolds for the development of bioprobes

Evaluation of the Cytosolic Uptake of HaloTag Using a pH-Sensitive Dye

The efficient cytosolic delivery of proteins is critical for advancing novel therapeutic strategies. Current delivery methods are severely limited by endosomal entrapment, and detection methods lack sophistication in tracking the fate of delivered protein cargo. HaloTag, a commonly used protein in chemical biology and a challenging delivery target, is an exceptional model system for understanding and exploiting cellular delivery. Here, we employed a combinatorial strategy to direct HaloTag to the cytosol. We established the use of Virginia Orange, a pH-sensitive fluorophore, and Janelia Fluor 585, a similar but pH-agnostic fluorophore, in a fluorogenic assay to ascertain protein localization within human cells. Using this assay, we investigated HaloTag delivery upon modification with cell-penetrating peptides, carboxyl group esterification, and cotreatment with an endosomolytic agent. We found efficacious cytosolic entry with two distinct delivery methods. This study expands the toolkit for detecting the cytosolic access of proteins and highlights that multiple intracellular delivery strategies can be used synergistically to effect cytosolic access. Moreover, HaloTag is poised to serve as a platform for the delivery of varied cargo into human cells.

Azaphosphinate Dyes: A Low Molecular Weight Near-Infrared Scaffold for Development of Photoacoustic or Fluorescence Imaging Probes

Near-infrared (NIR) dyes are desirable for biological imaging applications including photoacoustic (PA) and fluorescence imaging. Nonetheless, current NIR dyes are often plagued by relatively large molecular weights, poor water solubility, and limited photostability. Herein, we provide the first examples of azaphosphinate dyes which display desirable properties such as low molecular weight, absorption/emission above 750 nm, and remarkable water solubility. In PA imaging, an azaphosphinate dye exhibited a 4.1-fold enhancement in intensity compared to commonly used standards, the ability to multiplex with existing dyes in whole blood, imaging depths of 2.75 cm in a tissue model, and contrast in mice. An improved derivative for fluorescence imaging displayed a >10-fold reduction in photobleaching in water compared to the FDA-approved indocyanine green dye and could be visualized in mice. This new dye class provides a robust scaffold for the development of photoacoustic or NIR fluorescence imaging agents.

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.

Synthesis of Thioxanthone 10,10-Dioxides and Sulfone-Fluoresceins via Pd-Catalyzed Sulfonylative Homocoupling

Our report describes the facile and scalable preparation of 9H-thioxanthen-9-one 10,10-dioxides via Pd-catalyzed sulfonylative homocoupling of the appropriately substituted benzophenones. This transformation provides a straightforward route to previously unreported sulfone-fluoresceins and -fluorones. Several examples of these red fluorescent dyes have been prepared, characterized, and evaluated as live-cell permeant labels compatible with super-resolution fluorescence microscopy with 775 nm stimulated emission depletion.

Coerulein B: a water-soluble and water-compatible near-infrared photoredox catalyst

The recent expansion of photoredox catalysis into chemical biology has underscored the importance of photochemistry, attracting the attention of many researchers. On the other hand, as conventional photoredox catalysts were developed for organic synthesis, there is a necessity to develop biocompatible photoredox catalysts. Here, we show a water-soluble and water-compatible near-infrared (NIR) photoredox catalyst, coerulein B (CB). CB is a water-soluble molecule with a slightly twisted molecular structure, and its anionic species (CB-) exhibits NIR absorption and emission. We demonstrated that CB works as a water-compatible photoredox catalyst in the coupling reaction of pyridine hydrochloride and aryldiazonium salt. These results indicate that CB is one of the promising candidates for photocatalysts used in biological reactions.

Single Atom Stabilization of Phosphinate Ester-Containing Rhodamines Yields Cell Permeable Probes for Turn-On Photoacoustic Imaging

Photoacoustic imaging (PAI) is an emerging imaging technique that uses pulsed laser excitation with near-infrared (NIR) light to elicit local temperature increases through non-radiative relaxation events, ultimately leading to the production of ultrasound waves. The classical xanthene dye scaffold has found numerous applications in fluorescence imaging, however, xanthenes are rarely utilized for PAI since they do not typically display NIR absorbance. Herein, we report the ability of Nebraska Red (NR) xanthene dyes to produce photoacoustic (PA) signal and provide a rational design approach to reduce the hydrolysis rate of ester containing dyes, affording cell permeable probes. To demonstrate the utility of this approach, we construct the first cell permeable rhodamine-based, turn-on PAI imaging probe for hypochlorous acid (HOCl) with maximal absorbance within the range of commercial PA instrumentation. This probe, termed SNR700 -HOCl, is capable of detecting exogenous HOCl in mice. This work provides a new set of rhodamine-based PAI agents as well as a rational design approach to stabilize esterified versions of NR dyes with desirable properties for PAI. In the long term, the reagents described herein could be utilized to enable non-invasive imaging of HOCl in disease-relevant model systems.

Strategies to convert organic fluorophores into red/near-infrared emitting analogues and their utilization in bioimaging probes

Organic fluorophores aided by current microscopy imaging modalities are essential for studying biological systems. Recently, red/near-infrared emitting fluorophores have attracted great research efforts, as they enable bioimaging applications with reduced autofluorescence interference and light scattering, two significant obstacles for deep-tissue imaging, as well as reduced photodamage and photobleaching. Herein, we analyzed the current strategies to convert key organic fluorophores bearing xanthene, coumarin, and naphthalene cores into longer wavelength-emitting derivatives by focussing on their effectiveness and limitations. Together, we introduced typical examples of how such fluorophores can be used to develop molecular probes for biological analytes, along with key sensing features. Finally, we listed several critical issues to be considered in developing new fluorophores.

THQ-Xanthene: An Emerging Strategy to Create Next-Generation NIR-I/II Fluorophores

Near-infrared fluorescence imaging is vital for exploring the biological world. The short emissions (<650 nm) and small Stokes shifts (<30 nm) of current xanthene dyes obstruct their biological applications since a long time. Recently, a potent and universal THQ structural modification technique that shifts emission to the NIR-I/II range and enables a substantial Stokes shift (>100 nm) for THQ-modified xanthene dyes is established. Thus, a timely discussion of THQ-xanthene and its applications is extensive. Hence, the advent, working principles, development trajectory, and biological applications of THQ-xanthene dyes, especially in the fields of fluorescence probe-based sensing and imaging, cancer theranostics, and super-resolution imaging, are introduced. It is envisioned that the THQ modification tactic is a simple yet exceptional approach to upgrade the performance of conventional xanthene dyes. THQ-xanthene will advance the strides of xanthene-based potentials in early fluorescent diagnosis of diseases, cancer theranostics, and imaging-guided surgery.

Experimentally Calibrated Computational Prediction Enables Accurate Fine-Tuning of Near-Infrared Rhodamines for Multiplexing

A significant barrier inhibiting multiplexed imaging in the near-infrared (NIR) is the extensive trial and error associated with fine-tuning NIR dyes. In particular, the need to synthesize and experimentally evaluate dye derivatives in order to empirically identify those that can be used in multiplexing applications, requires a large investment of time. While coarse-tuning efforts benefit from computational prediction that can be used to identify target dye structures for synthetic campaigns, errors in computational prediction remain too large to accurately parse modifications aimed at fine-tuning changes in dye absorbance and emission. To address this issue, we screened different levels of theory and identified a time-dependent density functional theory (TD-DFT) approach that can rapidly, as opposed to synthesis and experimental evaluation, estimate absorbance and emission. By calibrating these computational estimations of absorbance and emission to experimentally determined parameters for a panel of existing NIR dyes, we obtain calibration curves that can be used to accurately predict the effect of fine-tuning modifications in new dyes. We demonstrate the predictive power of this calibrated dataset using seven previously unreported dyes, obtaining mean percent errors in absorbance and emission of 2.2 and 2.8 %, respectively. This approach provides a significant timesavings, relative to synthesis and evaluation of dye derivatives, and can be used to focus synthetic campaigns on the most promising dye structures. The new dyes described herein can be utilized for multiplexed imaging, and the experimentally calibrated dataset will provide the dye chemistry community with a means to rapidly identify fine-tuned NIR dyes in silico to guide subsequent synthetic campaigns.

Ketone Incorporation Extends the Emission Properties of the Xanthene Scaffold Beyond 1000 nm

Imaging in the shortwave-infrared region (SWIR, λ = 1000-2500 nm) has the potential to enable deep tissue imaging with high resolution. Critical to the development of these methods is the identification of low molecular weight, biologically compatible fluorescent probes that emit beyond 1000 nm. Exchanging the bridging oxygen atom on the xanthene scaffold (C10' position) with electron withdrawing groups has been shown to lead to significant redshifts in absorbance and emission. Guided by quantum chemistry computational modeling studies, we investigated the installation of a ketone bridge at the C10' position. This simple modification extends the absorbance maxima to 860 nm and the emission beyond 1000 nm, albeit with reduced photon output. Overall, these studies demonstrate that broadly applied xanthene dyes can be extended into the SWIR range.

Late-stage functionalisation of alkyne-modified phospha-xanthene dyes: lysosomal imaging using an off-on-off type of pH probe

Near-infrared (NIR) fluorescent molecules are of great importance for the visualisation of biological processes. Among the most promising dye scaffolds for this purpose are P[double bond, length as m-dash]O-substituted phospha-xanthene (POX) dyes, which show NIR emission with high photostability. Their practical utility for in vitro and in vivo imaging has recently been demonstrated. Although classical modification methods have been used to produce POX-based fluorescent probes, it is still a challenge to introduce additional functional groups to control the localisation of the probe in cells. Herein, we report on the development of POXs that bear a 4-ethynylphenyl group on the phosphorus atom. These dyes can subsequently be functionalised with azide-tagged biomolecules via a late-stage Cu-catalysed azide/alkyne cycloaddition (CuAAC) reaction, thus achieving target-selective labelling. To demonstrate the practical utility of the functionalised POXs, we designed a sophisticated NIR probe that exhibits a bell-shaped off-on-off pH-response and is able to assess the degree of endosomal maturation.

Asymmetric bismuth-rhodamines as an activatable fluorogenic photosensitizer

Bismuth-rhodamine compounds stand out for their unique excitable photosensitizing properties and concomitant fluorescence; however, further knowledge of the structure-property relationship is required to expand the scope of their practical application. With this aim, this study describes the first examples of asymmetric bismuth-incorporated rhodamines, BiRNH and BiRAc, including their synthesis, photophysical properties, and photosensitizing abilities. Upon red light excitation, BiRNH exhibits detectable emission and photosensitizing properties, while the N-acetylated derivative BiRAc shows a hypsochromic shift in the absorption wavelength and attenuation of emission and photosensitizing ability. These significantly different photophysical properties enabled us to design an activatable fluorogenic photosensitizer, BiRGlu, which bears a γ-glutamyl group instead of the acetyl group in BiRAc. The γ-glutamyl group can be cleaved by γ-glutamyl transpeptidase (GGT) to produce BiRNH, which acts as a red-light-excitable fluorophore and photosensitizer. A cell study revealed that the phototoxicity and fluorescence of BiRGlu could be simultaneously and selectively activated in the cells with high GGT activity. Thus, we established that BiRNH could be envisaged as a versatile scaffold for activatable fluorogenic photosensitizers.

Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes

The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10'. After a short introduction, we will focus on applications like the interaction of probes with enzymes and targeted labeling of organelles and proteins, detection of small molecules, as well as their use in therapeutics or diagnostics and super-resolution microscopy. Furthermore, the last part will summarize recent advances in the synthesis and understanding of their structure-behavior relationship including novel computational approaches.

Imaging GPCR internalization using near-infrared Nebraska red-based reagents

Internalization of G protein-coupled receptor (GPCRs) represents a nearly universal pathway for receptor downregulation. Imaging this process provides a means for the identification of pharmaceutical agents as well as potential ligands for orphan receptors. However, there is a need for the further development of near-infrared (NIR) probes capable of monitoring internalization in order to enable multiplexing with existing green fluorescent GPCR activity assays. Our laboratory has recently described a series of near-infrared (NIR) fluorophores in which a phosphinate functionality is inserted at the bridging position of the xanthene scaffold. These fluorophores, termed Nebraska Red (NR) dyes, provide attractive reagents for imaging protein localization. Herein, we disclose the development of NR-based HaloTag ligands for imaging membrane proteins on living cells. These new probes are utilized to image membrane pools of the human orexin type 2 receptor, an established target for the treatment of insomnia. We demonstrate the ability of fetal bovine serum (FBS) to noncovalently associate with a spirolactonized NR probe, enabling no-wash imaging with a 45-fold enhancement of fluorescence. Furthermore, we characterize the utility of NR-based HaloTag ligands for real-time monitoring of receptor internalization upon agonist stimulation. These new reagents enable potential multiplexing with existing GPCR activity assays in order to identify new modulators of GPCR activity as well as ligands for orphan receptors.

Far-red imaging of β-galactosidase through a phospha-fluorescein

The introduction of phosphine oxide into a fluorescein scaffold has yielded phospha-fluorescein with bathochromically shifted spectra, reliable photostability and solubility. Moreover, ratiometric and turn-on fluorescence in the decaging process has ensured that the phospha-fluorescein is a unique scaffold for fluorescence bioimaging. Probe DiMe-PF-Gal without further structural decoration was designed for accurately monitoring β-galactosidase in vivo.

Ratiometric pH Imaging Using a 1,2-Dioxetane Chemiluminescence Resonance Energy Transfer Sensor in Live Animals

Regulation of physiological pH is integral for proper whole body and cellular function, and disruptions in pH homeostasis can be both a cause and effect of disease. In light of this, many methods have been developed to monitor pH in cells and animals. In this study, we report a chemiluminescence resonance energy transfer (CRET) probe Ratio-pHCL-1, composed of an acrylamide 1,2-dioxetane chemiluminescent scaffold with an appended pH-sensitive carbofluorescein fluorophore. The probe provides an accurate measurement of pH between 6.8 and 8.4, making it a viable tool for measuring pH in biological systems. Further, its ratiometric output is independent of confounding variables. Quantification of pH can be accomplished using both common luminescence spectroscopy and advanced optical imaging methods. Using an IVIS Spectrum, pH can be measured through tissue with Ratio-pHCL-1, which is shown in vitro and calibrated in sacrificed mouse models. Intraperitoneal injections of Ratio-pHCL-1 into live mice show high photon outputs and consistent increases in the flux ratio when measured at pH 6, 7, and 8.

Core remodeling leads to long wavelength fluoro-coumarins

Low molecular weight, uncharged far-red and NIR dyes would be enabling for a range of imaging applications. Rational redesign of the coumarin scaffold leads to Fluoro-Coumarins (FCs), the lowest molecular weight dyes with emission maxima beyond 700, 800, and 900 nm. FCs display large Stokes shifts and high environmental sensitivity, with a 40-fold increase in emission intensity in hydrophobic solvents. Untargeted variants exhibit selective lipid droplet and nuclear staining in live cells. Furthermore, sulfo-lipid derivatization enables active targeting to the plasma membrane. Overall, these studies report a promising platform for the development of biocompatible, context-responsive imaging agents.

Fluoro-Coumarins are a novel class of far-red and near-infrared solvent sensitive dyes of exceptionally low molecular weight.

A rhodol-enone dye platform with dual reaction triggers for specific detection of Cys

In this work, we have developed a rhodol-enone dye platform with bis-reaction-triggers for the selective detection of Cys.

Rational Design of Fluorogenic and Spontaneously Blinking Labels for Super-Resolution Imaging

Rhodamine dyes exist in equilibrium between a fluorescent zwitterion and a nonfluorescent lactone. Tuning this equilibrium toward the nonfluorescent lactone form can improve cell-permeability and allow creation of "fluorogenic" compounds-ligands that shift to the fluorescent zwitterion upon binding a biomolecular target. An archetype fluorogenic dye is the far-red tetramethyl-Si-rhodamine (SiR), which has been used to create exceptionally useful labels for advanced microscopy. Here, we develop a quantitative framework for the development of new fluorogenic dyes, determining that the lactone-zwitterion equilibrium constant (K _L-Z) is sufficient to predict fluorogenicity. This rubric emerged from our analysis of known fluorophores and yielded new fluorescent and fluorogenic labels with improved performance in cellular imaging experiments. We then designed a novel fluorophore-Janelia Fluor 526 (JF₅₂₆)-with SiR-like properties but shorter fluorescence excitation and emission wavelengths. JF₅₂₆ is a versatile scaffold for fluorogenic probes including ligands for self-labeling tags, stains for endogenous structures, and spontaneously blinking labels for super-resolution immunofluorescence. JF₅₂₆ constitutes a new label for advanced microscopy experiments, and our quantitative framework will enable the rational design of other fluorogenic probes for bioimaging.