A Mitochondrial Surface-Specific Fluorescent Probe Activated by Bioconversion

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.

Meso pyridinium BODIPY-based long wavelength infrared mitochondria-targeting fluorescent probe with high photostability

Mito-tracker deep red (MTDR) as a commercially available mitochondria-targeting probe was easily bleached upon imaging. We designed and synthesized a family of meso-pyridinium BODIPY and introduced lipophilic methyl or benzyl as the head moiety to develop a mitochondria-targeting deep red probe. Moreover, we changed the substitution of the 3,5-phenyl moieties with the methoxy or methoxyethoxyethyl group to balance hydrophilicity. The designed BODIPY dyes possessed long absorption and good fluorescence emission. Among them, meso ortho-pyridinium BODIPYs with benzyl head and glycol substitution on phenyl moiety (3h) with favorable Stokes shift were found to have the best mitochondrial targeting performance. 3h was easily uptaken by cells and was less toxic and more photostable than MTDR. An immobilizable probe (3i) was further developed, and nice mitochondria targeting properties under the damaging condition of mitochondria membrane potential were maintained. BODIPY 3h or 3i may become alternative long-wavelength mitochondria targeting probes apart from MTDR and be suitable for long-term mitochondrial tracking studies.

Photostable polymorphic organic cages for targeted live cell imaging

Fluorescent microscopy is a powerful tool for studying the cellular dynamics of biological systems. Small-molecule organic fluorophores are the most commonly used for live cell imaging; however, they often suffer from low solubility, limited photostability and variable targetability. Herein, we demonstrate that a tautomeric organic cage, OC1, has high cell permeability, photostability and selectivity towards the mitochondria. We further performed a structure–activity study to investigate the role of the keto–enol tautomerization, which affords strong and consistent fluorescence in dilute solutions through supramolecular self-assembly. Significantly, OC1 can passively diffuse through the cell membrane directly targeting the mitochondria without going through the endosomes or the lysosomes. We envisage that designing highly stable and biocompatible self-assembled fluorophores that can passively diffuse through the cell membrane while selectively targeting specific organelles will push the boundaries of fluorescent microscopy to visualize intricate cellular processes at the single molecule level in live samples.

In this article, we demonstrate the relatively unexplored potential of organic cages for use in targeted live cell imaging and highlight the importance of inter- and intramolecular interactions to stabilize and improve the performance of fluorophores.

Design, synthesis and imaging of a novel mitochondrial fluorescent nanoprobe based on distyreneanthracene-substituted triphenylphosphonium salt

Targeting and monitoring the dynamics of mitochondria are of great significance because mitochondria are involved in a variety of physiological and pathological processes. For achieving this purpose, highly sensitive, photostable, tolerance and specific fluorescent probe is necessary. To obtain a superior mitochondrial fluorescent probe, (4-distyreneanthracenoxybutyl) bis(triphenylphosphonium) bromide (DSA-TPP) with aggregation-induced emission (AIE) characteristic was designed and synthesized for mitochondrial targeting. DSA-TPP dots with high fluorescence quantum yield (Φ = 17.9) and small particle size (8 nm) can be easily prepared by self-assembly formation. DSA-TPP dots had the ability of lightning mitochondria in living cells with high brightness, superior photostability and strong tolerance to cell environment change.

FOXM1 inhibitors as potential diagnostic agents: 1st generation of a PET probe targeting FOXM1 to detect triple negative-breast cancer in vitro and in vivo

The FOXM1 protein controls the expression of essential genes related to cancer cell cycle progression, metastasis, and chemoresistance. We hypothesize that FOXM1 inhibitors could represent a novel approach to develop 18 F-based radiotracers for Positron Emission Tomography (PET). Therefore, in this report we describe the first attempt to use 18 F-labeled FOXM1 inhibitors to detect triple-negative breast cancer (TNBC). Briefly, we replaced the original amide group in the parent drug FDI-6 for a ketone group in the novel AF-FDI molecule, to carry out an aromatic nucleophilic ( 18 F)-fluorination. AF-FDI dissociated the FOXM1-DNA complex, decreased FOXM1 levels, and inhibited cell proliferation in a TNBC cell line (MDA-MB-231). [ 18 F]AF-FDI was internalized in MDA-MB-231 cells. Cell uptake inhibition experiments showed that AF-FDI and FDI-6 significantly decreased the maximum uptake of [ 18 F]AF-FDI, suggesting specificity towards FOXM1. [ 18 F]AF-FDI reached a tumor uptake of SUV = 0.31 in MDA-MB-231 tumor-bearing mice and was metabolically stable 60 min post-injection. These results provide preliminary evidence supporting the potential role of FOXM1 to develop PET radiotracers.

Activation of apoptosis by rationally constructing NIR amphiphilic AIEgens: surmounting the shackle of mitochondrial membrane potential for amplified tumor ablation

In recent years, the use of aggregation-induced emission luminogens (AIEgens) for biological imaging and phototherapy has become an area of intense research. However, most traditional AIEgens suffer from undesired aggregation in aqueous media with "always on" fluorescence, or their targeting effects cannot be maintained accurately in live cells with the microenvironment changes. These drawbacks seriously impede their application in the fields of bio-imaging and antitumor therapy, which require a high signal-to-noise ratio. Herein, we propose a molecular design strategy to tune the dispersity of AIEgens in both lipophilic and hydrophilic systems to obtain the novel near-infrared (NIR, ∼737 nm) amphiphilic AIE photosensitizer (named TPA-S-TPP) with two positive charges as well as a triplet lifetime of 11.43 μs. The synergistic effects of lipophilicity, electrostatic interaction, and structure-anchoring enable the wider dynamic range of AIEgen TPA-S-TPP for mitochondrial targeting with tolerance to the changes of mitochondrial membrane potential (ΔΨ m). Intriguingly, TPA-S-TPP was difficult for normal cells to be taken up, indicative of low inherent toxicity for normal cells and tissues. Deeper insight into the changes of mitochondrial membrane potential and cleaved caspase 3 levels further revealed the mechanism of tumor cell apoptosis activated by AIEgen TPA-S-TPP under light irradiation. With its advantages of low dark toxicity and good biocompatibility, acting as an efficient theranostic agent, TPA-S-TPP was successfully applied to kill cancer cells and to efficiently inhibit tumor growth in mice. This study will provide a new avenue for researchers to design more ideal amphiphilic AIE photosensitizers with NIR fluorescence.

Chimeric Drug Design with a Noncharged Carrier for Mitochondrial Delivery

Recently, it was proposed that the thiophene ring is capable of promoting mitochondrial accumulation when linked to fluorescent markers. As a noncharged group, thiophene presents several advantages from a synthetic point of view, making it easier to incorporate such a side moiety into different molecules. Herein, we confirm the general applicability of the thiophene group as a mitochondrial carrier for drugs and fluorescent markers based on a new concept of nonprotonable, noncharged transporter. We implemented this concept in a medicinal chemistry application by developing an antitumor, metabolic chimeric drug based on the pyruvate dehydrogenase kinase (PDHK) inhibitor dichloroacetate (DCA). The promising features of the thiophene moiety as a noncharged carrier for targeting mitochondria may represent a starting point for the design of new metabolism-targeting drugs.

Fluorescent Benzoselenadiazoles: Synthesis, Characterization, and Quantification of Intracellular Lipid Droplets and Multicellular Model Staining

In this work, we described the synthesis of 10 new fluorescent 2,1,3-benzoselenadiazole small-molecule derivatives and their chemical- and photocharacterizations. The new derivatives could, for the first time, be successfully applied as selective live cell imaging probes (at nanomolar concentrations) and stained lipid-based structures preferentially. Density functional theory (DFT) calculations were used to help in understanding the photophysical data and the intramolecular charge-transfer (ICT) processes of the synthesized dyes. Some derivatives showed impressive cellular responses, allowing them to be tested as probes in a complex multicellular model (i.e., Caenorhabditis elegans). When compared with the commercially available dye, the new fluorescent compounds showed far better results both at the cellular level and inside the live worm. Inside the multicellular complex model, the tested probes also showed selectivity, a feature not observed when the commercial dye was used to carry out the bioimaging experiments.

Supramolecular β-Sheet Forming Peptide Conjugated with Near-Infrared Chromophore for Selective Targeting, Imaging, and Dysfunction of Mitochondria

Herein, conjugation of the amyloid-β (Aβ) peptide fragment, Lys-Leu-Val-Phe-Phe (KLVFF, fragment of Aβ_16-20), with an unsymmetrical near-infrared (NIR) cyanine-5 (Cy-5) chromophore is achieved using microwave-assisted solid phase synthesis on 2-chlorotrityl chloride resin. Selective mitochondria tracking and staining in human carcinoma cells are accomplished by the KLVFF/Cy-5 conjugate containing triphenylphosphonium functionality, and this is compared to a control molecule KLVFF/Cy-5c. Mitochondrial target specificity of KLVFF/Cy-5 is established by the colocalization assay using mitochondria selective probe MitoTracker Red, which is monitored by confocal laser scanning microscope and shows a high Pearson's correlation coefficient. The KLVFF/Cy-5 conjugate has high photostability, NIR absorption/emission, high molar extinction coefficient, narrow absorption/emission band, high fluorescence lifetime, and high fluorescence quantum yield. Moreover, mitochondria targeting KLVFF/Cy-5 conjugate reaches the critical aggregation concentration inside the mitochondria of cancer cells due to the strong negative inner mitochondrial membrane potential [(ΔΨ_m)_cancer -220 mV] and self-assembles to form amyloid fibrils at the target site, which is responsible for the mitochondrial dysfunction and cytotoxicity. Annexin V-FITC/PI apoptosis detection assay is used to determine the signal pathway of mitochondria targeted cellular dysfunction.

Targeting and Imaging of Mitochondria Using Near-Infrared Cyanine Dye and Its Application to Multicolor Imaging

Herein, we report water-soluble mitochondria-selective molecules that consist of a target-specific moiety conjugated with a near-infrared (NIR) imaging agent through variable spacer length. The presented NIR fluorescent cyanine-5 (Cy-5) chromophore exhibits excellent photostability, narrow NIR absorption and emission bands, high molar extinction coefficient, high fluorescence quantum yield, and long fluorescence lifetime. The biological compatibility and negligible cytotoxicity further make the dye an attractive choice for biological applications. Confocal fluorescence microscopic studies in the fixed human lung carcinoma cell line (A549) stained with the targeting NIR Cy-5 dyes (Cy-5a and Cy-5b) at 700 nM concentration show their cellular uptake and localization, which is compared with the nontargeting Cy-5c. Mitochondrial target specificity is demonstrated by colocalization experiments using the mitochondrion-tracking probe, MitoTracker Red and lysosome-tracking probe, LysoTracker Green. Multicolor imaging of cellular organelles in A549 cells is achieved in combination with suitable target-specific dyes with distinct excitation and emission, such as green emitting FM 1-43FX to selectively image the plasma membrane, blue-fluorescent DAPI to stain the nucleus, and the synthesized NIR Cy-5 to image the mitochondria. Higher accumulation of the dye inside the cancer cell mitochondria compared to the noncancerous cell is also demonstrated.

Solubilization of Pyridone-Based Fluorescent Tag by Complexation in Cucurbit[7]uril

Aimed at further exploring the hosting properties of cucurbit[7]uril (CB7), we have exploited the spectroscopic and photophysical properties of a known fluorescent label as the guest molecule, namely, 3-cyano-6-(2-thienyl)-4-trifluoromethyl pyridine (TFP), in neat solvents. The formation of an inclusion host-guest complex with CB7 was checked by UV-vis absorption spectroscopy, and the value of binding constant (9.7 × 10⁵ M^-1) was extracted from the spectrophotometric data. The modulation of keto-enol equilibrium in TFP by the local environment is governed by the interplay between dimerization through intermolecular hydrogen bonding between individual solute molecules, favoring the enol form, and intermolecular hydrogen bonding between TFP and the surrounding solvents, favoring the keto form. Time-resolved fluorescence results established that the macromolecular CB7 host stabilizes preferentially the neutral enol form over the keto form of TFP. Unprecedentedly, our results reveal a linear dependence of the amplitudes of the extracted decay-associated spectra from the time-resolved fluorescence spectra of TFP on the sum of polarity/polarizability and hydrogen bonding parameters of the local environment, confirming that TFP at micromolar concentration in the CB7 complexes is experiencing a methanol-like environment. The results rationalized the 42-fold enhancement in the solubility of TFP in water media by complexation in CB7.

Ionic Pyridinium-Oxazole Dyads: Design, Synthesis, and Application in Mitochondrial Imaging

We recently developed an oxidative intramolecular 1,2-amino-oxygenation reaction, combining gold(I)/gold(III) catalysis, for accessing structurally unique ionic pyridinium-oxazole dyads (PODs) with tunable emission wavelengths. On further investigation, these fluorophores turned out to be potential biomarkers; in particular, the one containing -NMe₂ functionality (NMe₂-POD) was highly selective for mitochondrial imaging. Of note, because of mitochondria's involvement in early-stage apoptosis and degenerative conditions, tracking the dynamics of mitochondrial morphology with such imaging technology has attracted much interest. Along this line, we wanted to build a library of such PODs which are potential mitochondria trackers. However, Au/Selecfluor, our first-generation catalyst system, suffers from undesired fluorination of electronically rich PODs resulting in an inseparable mixture (1:1) of the PODs and their fluorinated derivatives. In our attempt to search for a better alternative to circumvent this issue, we developed a second-generation approach for the synthesis of PODs by employing Cu(II)/PhI(OAC)₂-mediated oxidative 1,2-amino-oxygenation of alkynes. Thes newly synthesized PODs exhibit tunable emissions as well as excellent quantum efficiency up to 0.96. Further, this powerful process gives rapid access to a library of NMe₂-PODs which are potential mitochondrial imaging agents. Out of the library, the randomly chosen POD-3g was studied for cell-imaging experiments which showed high mitochondrial specificity, superior photostability, and appreciable tolerance to microenvironment changes with respect to commercially available MitoTracker green.

When the strategies for cellular selectivity fail. Challenges and surprises in the design and application of fluorescent benzothiadiazole derivatives for mitochondrial staining

Design, synthesis, molecular architecture and the unexpected behavior of fluorescent benzothiadiazole for selective mitochondrial and plasma membrane staining are investigated.

Development and sensing applications of fluorescent motifs within the mitochondrial environment

The potential use of fluorescent molecular probes to measure ions and biomolecules has contributed incessantly to the understanding of chemical and biological systems. The approach has many advantages such as high sensitivity, simplicity and non-destructive cellular imaging that offer visible information about the targeted species. In this article, our objective is to discuss fluorescent probes that have sensing applications within the mitochondrial environment. Mitochondria are cellular organelles which are well known for their unique physiological functions and have been found to be associated with various diseases and disorders. It is therefore, important to develop new tools and tactics that can provide useful information concerning the mitochondrial environment which in turn is essential to understand its biophysical functioning and related diseases.

A Set of Organelle-Localizable Reactive Molecules for Mitochondrial Chemical Proteomics in Living Cells and Brain Tissues

Protein functions are tightly regulated by their subcellular localization in live cells, and quantitative evaluation of dynamically altered proteomes in each organelle should provide valuable information. Here, we describe a novel method for organelle-focused chemical proteomics using spatially limited reactions. In this work, mitochondria-localizable reactive molecules (MRMs) were designed that penetrate biomembranes and spontaneously concentrate in mitochondria, where protein labeling is facilitated by the condensation effect. The combination of this selective labeling and liquid chromatography-mass spectrometry (LC-MS) based proteomics technology facilitated identification of mitochondrial proteomes and the profile of the intrinsic reactivity of amino acids tethered to proteins expressed in live cultured cells, primary neurons and brain slices. Furthermore, quantitative profiling of mitochondrial proteins whose expression levels change significantly during an oxidant-induced apoptotic process was performed by combination of this MRMs-based method with a standard quantitative MS technique (SILAC: stable isotope labeling by amino acids in cell culture). The use of a set of MRMs represents a powerful tool for chemical proteomics to elucidate mitochondria-associated biological events and diseases.

Unparalleled Ease of Access to a Library of Biheteroaryl Fluorophores via Oxidative Cross-Coupling Reactions: Discovery of Photostable NIR Probe for Mitochondria

The development of straightforward accesses to organic functional materials through C-H activation is a revolutionary trend in organic synthesis. In this article, we propose a concise strategy to construct a large library of donor-acceptor-type biheteroaryl fluorophores via the palladium-catalyzed oxidative C-H/C-H cross-coupling of electron-deficient 2H-indazoles with electron-rich heteroarenes. The directly coupled biheteroaryl fluorophores, named Indazo-Fluors, exhibit continuously tunable full-color emissions with quantum yields up to 93% and large Stokes shifts up to 8705 cm(-1) in CH2Cl2. By further fine-tuning of the substituent on the core skeleton, Indazo-Fluor 3l (FW = 274; λem = 725 nm) is obtained as the lowest molecular weight near-infrared (NIR) fluorophore with emission wavelength over 720 nm in the solid state. The NIR dye 5h specifically lights up mitochondria in living cells with bright red luminescence. Typically, commercially available mitochondria trackers suffer from poor photostability. Indazo-Fluor 5h exhibits superior photostability and very low cytotoxicity, which would be a prominent reagent for in vivo mitochondria imaging.

Fluorescent probes for the selective detection of chemical species inside mitochondria

This feature article systematically summarizes the development of fluorescent probes for the selective detection of chemical species inside mitochondria.

Highly specific probe for dual-emissive mitochondrial imaging based on a photostable and aqueous-soluble phosphonium fluorophore

In recent years, fluorescent mitochondrial imaging has emerged as a powerful tool for monitoring the biological processes of mitochondria with high spatial and temporal resolution.

New photostable naphthalimide-based fluorescent probe for mitochondrial imaging and tracking

Monitoring mitochondria morphological changes temporally and spatially exhibits significant importance for diagnosing, preventing and treating various diseases related to mitochondrial dysfunction. However, the application of commercially available mitochondria trackers is limited due to their poor photostability. To overcome these disadvantages, we designed and synthesized a mitochondria-localized fluorescent probe by conjugating 1,8-naphthalimide with triphenylphosphonium (i.e. NPA-TPP). The structure and characteristic of NPA-TPP was characterized by UV-vis, fluorescence spectroscopy, (1)HNMR, (13)CNMR, FTIR, MS, etc. The photostability and cell imaging were performed on the laser scanning confocal microscopy. Moreover, the cytotoxicity of NPA-TPP on cells was evaluated using (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay. The results showed that NPA-TPP not only has high sensitivity and specificity to mitochondria, but also exhibits super-high photostability, negligible cytotoxicity and good water solubility. In short, NPA-TPP indicates great potential for targeting mitochondria and enables a real-time and long-term tracking mitochondrial dynamics changes.

Design and synthesis of fluorenone-based dyes: two-photon excited fluorescent probes for imaging of lysosomes and mitochondria in living cells

Three fluorenone-based two-photon fluorescent probes for specific targeting of lysosomes and mitochondria in cancer cells.

Real-time monitoring of the mitophagy process by a photostable fluorescent mitochondrion-specific bioprobe with AIE characteristics

A tetraphenylethene-based AIE bioprobe is developed for mitochondrial imaging. The probe shows high brightness, tolerance to environmental changes and photostability, making it promising for monitoring of mitophagy process.

Synthesis and structure-activity relationship study of chemical probes as hypoxia induced factor-1α/malate dehydrogenase 2 inhibitors

A structure-activity relationship study of hypoxia inducible factor-1α inhibitor 3-aminobenzoic acid-based chemical probes, which were previously identified to bind to mitochondrial malate dehydrogenase 2, was performed to provide a better understanding of the pharmacological effects of LW6 and its relation to hypoxia inducible factor-1α (HIF-1α) and malate dehydrogenase 2 (MDH2). A variety of multifunctional probes including the benzophenone or the trifluoromethyl diazirine for photoaffinity labeling and click reaction were prepared and evaluated for their biological activity using a cell-based HRE-luciferase assay as well as a MDH2 assay in human colorectal cancer HCT116 cells. Among them, the diazirine probe 4a showed strong inhibitory activity against both HIF-1α and MDH2. Significantly, the inhibitory effect of the probes on HIF-1α activity was consistent with that of the MDH2 enzyme assay, which was further confirmed by the effect on in vitro binding activity to recombinant human MDH2, oxygen consumption, ATP production, and AMP activated protein kinase (AMPK) activation. Competitive binding modes of LW6 and probe 4a to MDH2 were also demonstrated.

A chemical probe that labels human pluripotent stem cells

A small-molecule fluorescent probe specific for human pluripotent stem cells would serve as a useful tool for basic cell biology research and stem cell therapy. Screening of fluorescent chemical libraries with human induced pluripotent stem cells (iPSCs) and subsequent evaluation of hit molecules identified a fluorescent compound (Kyoto probe 1 [KP-1]) that selectively labels human pluripotent stem cells. Our analyses indicated that the selectivity results primarily from a distinct expression pattern of ABC transporters in human pluripotent stem cells and from the transporter selectivity of KP-1. Expression of ABCB1 (MDR1) and ABCG2 (BCRP), both of which cause the efflux of KP-1, is repressed in human pluripotent stem cells. Although KP-1, like other pluripotent markers, is not absolutely specific for pluripotent stem cells, the identified chemical probe may be used in conjunction with other reagents.

[Control and analysis of cells by synthetic small molecules]

In human history, small organic molecules have been utilized for improving human health and for revealing secrets of life. Discovery or design of small organic molecules with unique biological activity permits small-molecule-initiated exploration of biology. Our laboratory has been discovering and designing bioactive small synthetic molecules to use them as tools to analyze or modulate biological processes. This personal perspective summarizes our contributions to chemical biology, particularly in the fields of gene transcription, cell therapy, growth factor signaling, and target identification.