Ex Tenebris Lux: Illuminating Reactive Oxygen and Nitrogen Species with Small Molecule Probes

Reactive oxygen and nitrogen species are small reactive molecules derived from elements in the air─oxygen and nitrogen. They are produced in biological systems to mediate fundamental aspects of cellular signaling but must be very tightly balanced to prevent indiscriminate damage to biological molecules. Small molecule probes can transmute the specific nature of each reactive oxygen and nitrogen species into an observable luminescent signal (or even an acoustic wave) to offer sensitive and selective imaging in living cells and whole animals. This review focuses specifically on small molecule probes for superoxide, hydrogen peroxide, hypochlorite, nitric oxide, and peroxynitrite that provide a luminescent or photoacoustic signal. Important background information on general photophysical phenomena, common probe designs, mechanisms, and imaging modalities will be provided, and then, probes for each analyte will be thoroughly evaluated. A discussion of the successes of the field will be presented, followed by recommendations for improvement and a future outlook of emerging trends. Our objectives are to provide an informative, useful, and thorough field guide to small molecule probes for reactive oxygen and nitrogen species as well as important context to compare the ecosystem of chemistries and molecular scaffolds that has manifested within the field.

Machine-Learning-Assisted Rational Design of Si─Rhodamine as Cathepsin-pH-Activated Probe for Accurate Fluorescence Navigation

High-performance fluorescent probes stand as indispensable tools in fluorescence-guided imaging, and are crucial for precise delineation of focal tissue while minimizing unnecessary removal of healthy tissue. Herein, machine-learning-assisted strategy to investigate the current available xanthene dyes is first proposed, and a quantitative prediction model to guide the rational synthesis of novel fluorescent molecules with the desired pH responsivity is constructed. Two novel Si─rhodamine derivatives are successfully achieved and the cathepsin/pH sequentially activated probe Si─rhodamine─cathepsin-pH (SiR─CTS-pH) is constructed. The results reveal that SiR─CTS-pH exhibits higher signal-to-noise ratio of fluorescence imaging, compared to single pH or cathepsin-activated probe. Moreover, SiR─CTS-pH shows strong differentiation abilities for tumor cells and tissues and accurately discriminates the complex hepatocellular carcinoma tissues from normal ones, indicating its significant application potential in clinical practice. Therefore, the continuous development of xanthene dyes and the rational design of superior fluorescent molecules through machine-learning-assisted model broaden the path and provide more advanced methods to researchers.

Effect of spirocyclization of xanthene dyes on linear and nonlinear optical properties by considering D-π-A and D-A-D Systems: DFT and TD-DFT approach

Spirocyclization, a unique feature of xanthene dyes, makes it a promising candidate for developing fluorescent ratiometric probes for sensing, imaging, tracking, and labeling. How will this feature of xanthene dyes influence the linear and nonlinear optical properties? To examine the effect of spirocyclization of xanthene dyes, we have selected both the open-close form of rhodamine B and π-extended xanthene dyes substituted with thienyl and thieno[3,2-b]thienyl group at position 3 and 6. Here, rhodamine B will serve as the (Donor)D-π-A(Acceptor) system and thiophene-substituted xanthene dyes will serve as the D-A-D system. The geometry optimization of the close-open form of xanthene dyes at B3LYP/6-311++G(d,p) and CAM-B3LYP/6-311++G(d,p) revealed that the open form is energetically more stable in the S0 state than the closed form. The vertical excitation energy (ΔE), from Time-Dependent-Density Functional Theory (TD-DFT) calculation at B3LYP/6-311++G(d,p), CAM-B3LYP/6-311++G(d,p), ωB97XD/6-311++G(d,p) revealed that (ΔE)open < (ΔE)close. Further, the open form of xanthene dyes displays red-shifted absorption compared to the closed form. The λVt of xanthene dyes (open-close forms) is mainly assigned to HOMO → LUMO transition (S0 → S1) with % orbital contribution for open form ∼ 90 % and close form ∼ 60 %. The oscillator strength of xanthene dyes is obtained in the range of 0.01 - 1.74. The λVt of xanthene dyes is in agreement with experimental absorption. The static polarizability (α0), first-order hyperpolarizability (β0), second-order hyperpolarizability (γ), molecular hyperpolarizability (µβ0), and frequency-dependent hyperpolarizability (β1064), of the open form of xanthene dyes, were found to be higher than the close form. Thus, the open form of xanthene dyes will show superior linear and nonlinear optical properties than the closed form. The thienyl[3, 2-b] thieno substituted xanthene dye with red-shifted absorption shows higher α0, β0, γ, µβ0, β1064, and γ values, show better linear and NLO properties than thienyl and diethylamine substituted xanthene dyes.

Stereochemistry-Dependent Labeling of Organelles with a Near-Infrared-Emissive Phosphorus-Bridged Rhodamine Dye in Live-Cell Imaging

The development of near-infrared (NIR) fluorophores that have both excellent chemical stability and photostability, as well as efficient cell permeability, is highly demanded. In this study, we present phospha-rhodamine (POR) dyes which display significantly improved performance for protein labeling. This is achieved by incorporating a 2-carboxy-3-benzothiophenyl group at the 9-position of the xanthene scaffold. The resulting cis and trans isomers were successfully isolated and structurally characterized using X-ray diffraction. The HaloTag ligand conjugates of the two isomers exhibited different staining abilities in live cells. While the cis isomer showed non-specific accumulation on the organelle membranes, the trans isomer selectively labeled the HaloTag-fused proteins, enabling the long-term imaging of cell division and the 5-color imaging of cell organelles. Molecular dynamics simulations of the HaloTag ligand conjugates within the lipid membrane suggested that the cis isomer is more prone to forming oligomers in the membrane. In contrast, the oligomerization of the trans isomer is effectively suppressed by its interaction with the lipid molecules. By taking advantage of the superior labeling performance of the trans isomer and its NIR-emissive properties, multi-color time-lapse super-resolution 3D imaging, namely super-resolution 5D-imaging, of the interconnected network between the endoplasmic reticulum and microtubules was achieved in living cells.

A Substituted-Rhodamine-Based Reversible Fluorescent Probe for In Vivo Quantification of Glutathione

Quantifying glutathione (GSH) in cells and organisms is of great significance for understanding the mechanism of oxidative stress in various physiological and pathological processes. However, the quantification by fluorescence bioimaging in living tissues has much stricter requirements than the "Petri dish"-cultured cells in flat plates. Based on the evaluation of the electronic structure and steric hindrance-tuned reactivity of phospha-substituted rhodamine with GSH, a reversible Förster resonance energy transfer (FRET) probe ZpSiP with a distinct performance (K_d =4.9 mM, t_1/2 =0.57 s, k=81 M^-1  s^-1 ) is developed for real time quantifying GSH in living cells. Furthermore, the near-infrared (NIR) probe succeeded in sensitively tracking the dynamics of GSH in the real organisms bearing tumors, chronic renal failure, and liver fibrosis for unveiling the related pathological processes. We believe that the advance in chemistry with quantitative analysis methods will initiate more promising progress and broad applications.

Solvent-controlled regioselective arylation of indoles and mechanistic explorations

A new reaction for the regioselective arylation of indoles at C2 or C3 positions achieved by adjusting the solvent and with P(O)tBu2 as an auxiliary group is reported. And the experimental results and DFT confirmed the process.

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.

Copper-catalyzed arylation of polycyclic aromatic hydrocarbons by the P[double bond, length as m-dash]O group

The first example of a directed and regioselective arylation of polycyclic aromatic hydrocarbons (PAHs) by using a P[double bond, length as m-dash]O directing group is reported herein. The protocol uses a cheap copper catalyst, and results in a breakthrough meta-selective C-H functionalization of arylphosphine oxide compounds. Substrates with potential fluorescence properties, for example, pyrene and fluoranthene, were successfully arylated under the system, thus achieving an efficient modification of fluorescent molecules containing the P[double bond, length as m-dash]O functional group.

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.

Effects of Amino Group Substitution on the Photophysical Properties and Stability of Near-Infrared Fluorescent P-Rhodamines

A series of phosphine oxide-bridged rhodamines (P-rhodamines) bearing various acyclic and cyclic amine moieties, including dimethyl- and diethylamine, azetidine, pyrrolidine and 7-azabicyclo[2,2,1]heptane (7ABH), have been synthesized. The photophysical properties as well as chemical and photostability of these dyes have been studied in detail. Among these dyes, the 7ABH-substituted dye shows stronger fluorescence in the near-infrared (NIR) region, relative to the other P-rhodamines. This dye could be applied to live-cell imaging, wherein lysosomes were selectively stained in a pH-independent manner. It was also found that the ring fusion of the amine moieties gives rise to remarkably redshifted spectra, with absorption and emission maxima at 770 and 820 nm, respectively, spectrally close to that of indocyanine green (ICG). Importantly, the ring-fused P-rhodamines showed much higher photostability than ICG, indicative of their promising utility as the NIR-emissive dyes.

Robust synthesis of NIR-emissive P-rhodamine fluorophores

P-Rhodamines were accessed by implementing a robust three step sequence consisting of (i) addition of m-metallated anilines to dichlorophosphine oxides, (ii) selective dibromination, and (iii) cyclization of the diaryllithium reagents derived from the dibromides to form the dihydroacridophosphine core of P-rhodamines. A modified route was developed to produce non-symmetric P-rhodamines. A library of prepared P-rhodamines provides first insight into dependence of fluorophore properties on the structure of P-rhodamines. A P-rhodamine with highest batochromic shifts and quantum yields in the class was identified.

Near-infrared fluorescein dyes containing a tricoordinate boron atom

Tricoordinate boron imparts near-infrared absorption/emission and unusual multi-stage changes in the photophysical properties to fluorescein dyes.

Bora-fluoresceins (BFs), fluorescein analogues containing a tricoordinate boron atom instead of an oxygen atom at the 10-position of the fluorescein skeleton, were synthesized as a new family of fluorescein analogues. The deprotonated BFs exhibited absorption and fluorescence in the near-infrared region, which were significantly red-shifted relative to those of hitherto-known heteroatom-substituted fluorescein analogues on account of the orbital interaction between the tricoordinate boron atom and the fluorescein skeleton. BFs also showed multi-stage changes resulting from a Lewis acid–base equilibrium at the boron center in combination with a Brønsted acid–base equilibrium at the phenolic hydroxy group.

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

A series of phosphinate-containing rhodol and fluorescein dyes are disclosed. These new fluorophores increase the color palette of phosphinate-based xanthenes in the far-red spectral region. The new chemical functionality of these scaffolds is leveraged to produce a sensitive, no-wash imaging probe for cellular esterase activity. The reported phosphinate-containing dyes provide platforms for the further development of imaging probes and self-reporting delivery vehicles.

A Phosphinate-Containing Fluorophore Capable of Selectively Inducing Apoptosis in Cancer Cells

Chemotherapeutic agents generally suffer from off-target cytotoxicity in noncancerous cell types, leading to undesired side effects. As a result, significant effort has been put into identifying compounds that are selective for cancerous over noncancerous cell types. Our laboratory has recently developed a series of near-infrared (NIR) fluorophores containing a phosphinate functionality at the bridging position of a xanthene scaffold, termed Nebraska Red (NR) fluorophores. Herein, we report the selective cytotoxicity of one NR derivative, NR₇₄₄ , against HeLa (cervical cancer) cells versus NIH-3T3 (noncancerous fibroblast) cells. Mechanistic studies based on the NIR fluorescence signal of NR₇₄₄ showed distinct subcellular localization in HeLa (mitochondrial) versus NIH-3T3 (lysosomal) that resulted from the elevated mitochondrial potential in HeLa cells. This study provides a new, NIR scaffold for the further development of reagents for targeted cancer therapy.

MoS2 quantum dots as a unique fluorescent "turn-off-on" probe for the simple and rapid determination of adenosine triphosphate

We report a one-step hydrothermal method for the preparation of fluorescent molybdenum disulfide quantum dots (MoS₂ QDs) and demonstrate the feasibility of fluorescent "turn-off-on" sensing of adenosine triphosphate (ATP) by using the MoS₂ QDs. MoS₂ QDs having strong blue-green fluorescence at 506 nm and good water-solubility were successfully synthesized by using ammonium tetrathiomolybdate as a single precursor. The fluorescence of MoS₂ QDs was first quenched by Fe³⁺ through the formation of a MoS₂ QDs/Fe³⁺ complex. ATP with the ability to coordinate with Fe³⁺ caused the dissociation of MoS₂ QDs/Fe³⁺, resulting in the final release of MoS₂ QDs and the recovery of fluorescence through a one-step competitive chelating process that took only 10 min to reach equilibrium at room temperature (RT). Facile and rapid sensing of Fe³⁺ and ATP could thus be achieved through the fluorescent "turn-off-on" strategy. Good linear relationships were obtained over the concentration ranges of 0-200 μM for Fe³⁺ and 0-140 μM for ATP with a lowest detectable concentration of 5 μM for ATP. Satisfactory results were obtained when the method was applied to a standard addition recovery trial of ATP in human serum samples. No complex surface modification during the preparation or detection process was needed based on the fluorescent "turn-off-on" method of the MoS₂ QDs, which suggests its great potential in fluorescent sensing.