Development of practical red fluorescent probe for cytoplasmic calcium ions with greatly improved cell-membrane permeability

BODIPY-based photocages: rational design and their biomedical application

Photocages, also known as photoactivated protective groups (PPGs), have been utilized to achieve controlled release of target molecules in a non-invasive and spatiotemporal manner. In the past decade, BODIPY fluorophores, a well-established class of fluorescent dyes, have emerged as a novel type of photoactivated protective group capable of efficiently releasing cargo species upon irradiation. This is due to their exceptional properties, including high molar absorption coefficients, resistance to photochemical and thermal degradation, multiple modification sites, favorable uncaging quantum yields, and highly adjustable spectral properties. Compared to traditional photocages that mainly absorb UV light, BODIPY-based photocages that absorb visible/near-infrared (Vis/NIR) light offer advantages such as deeper tissue penetration and reduced bio-autofluorescence, making them highly suitable for various biomedical applications. Consequently, different types of photoactivated protective groups based on the BODIPY skeleton have been established. This highlight provides a comprehensive overview of the strategies employed to construct BODIPY photocages by substituting leaving groups at different positions within the BODIPY fluorophore, including the meso-methyl position, boron position, 2,6-position, and 3,5-position. Furthermore, the application of these BODIPY photocages in biomedical fields, such as fluorescence imaging and controlled release of active species, is discussed.

Design and One-Pot Ultrasound Synthesis of Inorganic Base-Promoted Fluorescent Ligand-Gated Ion Channel Fused Arylpyrazole Sulfonamide Skeletons to Enhance Phloem Mobility and Insecticidal Activity as GABA and nACh Receptors Inhibitors

Ligand-gated ion channels are essential in living organisms, and sulfonamides have antibacterial effects and can be readily coordinated with metal ions with good biological activity. A series of fluorescent ligand-gated ion channel fused arylpyrazole sulfonamide skeletons (APSnM) were synthesized based on a one-pot ultrasound strategy promoted by an inorganic base. APSnM had a high fluorescence quantum yield and a large Stokes shift in ethanol solvent. The ligand bonded ions took on a different color from the ligand and can be used as a probe to detect their own residue on plant surfaces. Their hydrophobic parameters and the fluorescence distribution in Chinese cabbage leaves indicated that APSnM significantly increased the phloem mobility of the plant. The insecticidal activity of APS3Na was higher (LC50 = 7.2423 μg/mL) than that of fipronil (15.2312 μg/mL) against Plutella xylostella, and the mechanism of high insecticidal activity of APS3Na was simulated by molecular docking, which confirmed its strong interactions with the GABA and nACh receptors of Plutella xylostella. Analysis of the crystal structure of these ligand-gated ion channels further confirmed the consistency of their structure and biological activity.

Fluorogenic and genetic targeting of a red-emitting molecular calcium indicator

We introduce a strategy for the fluorogenic and genetic targeting of a calcium indicator by combining a protein fluorogen with the BAPTA sensing group. The resulting dual-input probe acts like a fluorescent AND logic gate with a Ca²⁺-sensitive red emission that is activated only upon reaction with HaloTag with a 25-fold intensity enhancement and can be used for wash-free calcium imaging in HeLa cells. The modular all-molecular design relying on a well-established self-labeling protein tag opens future possibilities for tuning the photophysical properties or targeting different analytes.

Design, Synthesis, and Anticancer Activity of Triptycene-Peptide Hybrids that Induce Paraptotic Cell Death in Cancer Cells

We report on the design and synthesis of triptycene-peptide hybrids (TPHs), 5, syn-6, and anti-6, which are conjugates of a triptycene core unit with two or three cationic KKKGG peptides (K: lysine and G: glycine) through a C₈ alkyl chain. It was discovered that syn-6 and anti-6 induce paraptosis, a type of programmed cell death (PCD), in Jurkat cells (leukemia T-lymphocytes). Mechanistic studies indicate that these TPHs induce the transfer of Ca²⁺ from the endoplasmic reticulum (ER) to mitochondria, a loss of mitochondrial membrane potential (ΔΨ_m), tethering of the ER and mitochondria, and cytoplasmic vacuolization in the paraptosis processes.

Origins of Ca2+ Imaging with Fluorescent Indicators

In 1980, Roger Tsien published a paper, in this journal [Tsien, R. Y. (1980) Biochemistry, 19 (11), 2396], titled "New calcium indicators and buffers with high selectivity against magnesium and protons: design, synthesis, and properties of prototype structures". These new buffers included 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid, or BAPTA, which is still widely used today. And so, the world was set alight with new ways in which to visualize Ca²⁺. The ability to watch fluctuations in intracellular Ca²⁺ revolutionized the life sciences, although the fluorescent indicators used today, particularly in neurobiology, no longer rely exclusively on BAPTA but on genetically encoded fluorescent Ca²⁺ indicators. In this Perspective, we reflect on the origins of Ca²⁺ imaging with a special focus on the contributions made by Roger Tsien, from the early concept of selective Ca²⁺ binding described in Biochemistry to optical Ca²⁺ indicators based on chemically synthesized fluorophores to genetically encoded fluorescent Ca²⁺ indicators.

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.

Detection of Tyrosinase in Real Food Samples and Living Cells by a Novel Near-Infrared Fluorescence Probe

A new near-infrared fluorescence probe was developed and applied to the fluorescence detection of tyrosinase in real food samples and living cells. The probe (E)-2-(2-(6-((3-hydroxybenzyloxy)carbonylamino)-2,3-dihydro-1H-xanthen-4-yl)vinyl)-3,3-dimethyl-1-propyl-3H-indolium (1) was designed and synthesized by coupling 3-hydroxybenzyl alcohol via carbamate bond with an amino hemicyanine skeleton, based on the high anti-interference ability of 3-hydroxybenzyl alcohol to reactive oxygen species and its binding affinity to tyrosinase. Compared with the existing tyrosinase probes, the proposed probe exhibits superior analytical performance, such as high selectivity, high sensitivity, superior spatiotemporal sampling ability, fluorescence signal switching at 706 nm, and low detection limit of 0.36 U mL^-1. More importantly, the probe has been successfully used to monitor tyrosinase in the browning of apple slices for the first time, and the results indicated that the strongest fluorescence intensity could be achieved at 2.5 h to realize precise visual recognition of tyrosinase. Notably, the probe determined tyrosinase in real food samples (apple, banana, cheese, and red wine) with a stable average recovery range of 95.7-108.3% and has been successfully used to monitor tyrosinase in the living B16 cells. The superior properties of the probe make it of great potential use in food nutritional value evaluation and clinical diagnosis of melanin-related diseases.

Rational Design of a Near-infrared Fluorescence Probe for Ca2+ Based on Phosphorus-substituted Rhodamines Utilizing Photoinduced Electron Transfer

Fluorescence imaging in the near-infrared (NIR) region (650-900 nm) is useful for bioimaging because background autofluorescence is low and tissue penetration is high in this range. In addition, NIR fluorescence is useful as a complementary color window to green and red for multicolor imaging. Here, we compared the photoinduced electron transfer (PeT)-mediated fluorescence quenching of silicon- and phosphorus-substituted rhodamines (SiRs and PRs) in order to guide the development of improved far-red to NIR fluorescent dyes. The results of density functional theory calculations and photophysical evaluation of a series of newly synthesized PRs confirmed that the fluorescence of PRs was more susceptible than that of SiRs to quenching via PeT. Based on this, we designed and synthesized a NIR fluorescence probe for Ca²⁺ , CaPR-1, and its membrane-permeable acetoxymethyl derivative, CaPR-1 AM, which is distributed to the cytosol, in marked contrast to our previously reported Ca²⁺ far-red to NIR fluorescence probe based on the SiR scaffold, CaSiR-1 AM, which is mainly localized in lysosomes as well as cytosol in living cells. CaPR-1 showed longer-wavelength absorption and emission (up to 712 nm) than CaSiR-1. The new probe was able to image Ca²⁺ at dendrites and spines in brain slices, and should be a useful tool in neuroscience research.

A cytosolically localized far-red to near-infrared rhodamine-based fluorescent probe for calcium ions

We developed the cytosolically localized far-red to NIR fluorescent probe for Ca²⁺,CaSiR-2 AM, utilizing the rhodamine scaffold.

Design and Applications of Small Molecular Probes for Calcium Detection

The physiological significance of calcium ions such as the role in cellular signalling, cell growth, etc. have driven the development of methods to detect and monitor the level of Ca²⁺ ions, both in vivo and in vitro. Although various approaches for the detection of calcium ions have been reported, methods based on small molecular fluorescent probes have unique advantages including small probe size, easy monitoring of detection processes and applicability in biological systems. In this review article, we will discuss the progress in the development of Ca²⁺ -binding fluorescent probes by taking into account the types of chelating groups that have been employed for Ca²⁺ binding.

Preparation of cationized gelatin nanospheres incorporating molecular beacon to visualize cell apoptosis

The objective of this study is to prepare cationized gelatin nanospheres (cGNS) incorporating a molecular beacon (MB), and visualize cellular apoptosis. Two types of MB to detect the messenger RNA (mRNA) of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (GAP MB), and caspase-3 (casp3 MB) were incorporated in cGNS, respectively. MB incorporated in cGNS showed the DNA sequence specificity in hybridization. The cGNS incorporation enabled MB to enhance the stability against nuclease to a significantly great extent compared with free MB. The cGNS incorporating GAP MB were internalized into the KUM6 of a mouse bone marrow-derived stem cell by an endocytotic pathway. The cGNS were not distributed at the lysosomes. After the incubation with cGNS, the cell apoptosis was induced at different concentrations of camptothecin. No change in the intracellular fluorescence was observed for cGNS_GAPMB. On the other hand, for the cGNS_casp3MB, the fluorescent intensity significantly enhanced by the apoptosis induction of cells. It is concluded that cGNS incorporating MB is a promising system for the visualization of cellular apoptosis.

A far-red fluorescent probe based on a phospha-fluorescein scaffold for cytosolic calcium imaging

The far-red emissive fluorescent probe CaPF-1 based on a phospha-fluorescein scaffold enables the detection of cytosolic calcium ions in living cells. The probe can be excited in the red region (λ_abs = 636 nm) and exhibits a sufficiently high fluorescence turn-on response in the far-red region (λ_em = 663 nm) upon complexation with calcium ions. The hydrophilic and anionic characteristics of this phospha-fluorescein fluorophore allowed the cytosolic localization of CaPF-1. Moreover, it was possible to visualize histamine-induced calcium oscillation in HeLa cells using CaPF-1.

PEGylated Red-Emitting Calcium Probe with Improved Sensing Properties for Neuroscience

Monitoring calcium concentration in the cytosol is of main importance as this ion drives many biological cascades within the cell. To this end, molecular calcium probes are widely used. Most of them, especially the red emitting probes, suffer from nonspecific interactions with inner membranes due to the hydrophobic nature of their fluorophore. To circumvent this issue, calcium probes conjugated to dextran can be used to enhance the hydrophilicity and reduce the nonspecific interaction and compartmentalization. However, dextran conjugates also feature important drawbacks including lower affinity, lower dynamic range, and slow diffusion. Herein, we combined the advantage of molecular probes and dextran conjugate without their drawbacks by designing a new red emitting turn-on calcium probe based on PET quenching, Rhod-PEG, in which the rhodamine fluorophore bears four PEG₄ units. This modification led to a high affinity calcium probe (K_d = 748 nM) with reduced nonspecific interactions, enhanced photostability, two-photon absorbance, and brightness compared to the commercially available Rhod-2. After spectral characterizations, we showed that Rhod-PEG quickly and efficiently diffused through the dendrites of pyramidal neurons with an enhanced sensitivity (ΔF/F₀) at shorter time after patching compared to Rhod-2.

Synthesis of practical red fluorescent probe for cytoplasmic calcium ions with greatly improved cell-membrane permeability

In this data article, we described the detailed synthetic procedure and the experimental data for the synthesis of a red-fluorescent probe for calcium ions (Ca²⁺) with improved water solubility. This Ca²⁺ red-fluorescent probe CaTM-3 AM could be applied to fluorescence imaging of physiological Ca²⁺ concentration changes in not only live cells, but also brain slices, with high cell-membrane permeability leading to bright fluorescence in biosamples. The data provided herein are in association with the research article "The Development of Practical Red Fluorescent Probe for Cytoplasmic Calcium Ions with Greatly Improved Cell-membrane Permeability" in Cell Calcium (Hirabayashi et al., 2016) [1].

Ca-NIR: a ratiometric near-infrared calcium probe based on a dihydroxanthene-hemicyanine fluorophore

Ca-NIR is the first ratiometric fluorescent calcium probe emitting in the near infrared.