Superior Fluorogen-Activating Protein Probes Based on 3-Indole–Malachite Green

Azetidinyl Malachite Green: a superior fluorogen-activating protein probe for live-cell and dynamic SIM imaging

Malachite Green (MG) and its fluorogen-activating protein (FAP) pair are valuable tools for live-cell and super-resolution fluorescence imaging due to their unique near-infrared absorption and signal enhancement. However, the low brightness and photostability of MG have limited its use in dynamic imaging. In this study, we introduce a novel derivative, azetidinly Malachite Green (Aze-MG), which enhances the brightness of the MG-FAP complex by 2.6-fold. This enhancement is achieved by replacing the N,N-dimethylamino group in MG with an azetidine group, which suppresses the twisted intramolecular charge transfer (TICT) effect, leading to improved quantum yield and photostability. Additionally, the reduced binding affinity of Aze-MG for FAP enables a buffering strategy, allowing the reversible exchange of photobleached fluorogens with free fluorogens, thereby ensuring stable fluorescence over time. This combination of improved brightness and buffering capability makes Aze-MG an ideal probe for live-cell and dynamic SIM imaging.

Hybrid Small-Molecule/Protein Fluorescent Probes

Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.

Characterization of Chlorogenic Acid as a Two-Photon Fluorogenic Probe that Regulates Glycolysis in Tumor Cells under Hypoxia

High levels of steady-state mitochondrial reactive oxygen species (ROS) and glycolysis are hallmarks of cancer. An improved understanding of interactions between tumor energetics and mitochondrial ROS modulation is useful for the development of new anticancer strategies. Here, we show that the natural product chlorogenic acid (CGA) specifically scavenged abnormally elevated mitochondrial O₂^•- and exhibited a two-photon fluorescence turn-on response to tumor cells under hypoxia and tumor tissues in vivo. Furthermore, we illustrated that CGA treatment reduced O₂^•- levels in cells, hampered activation of AMP-activated protein kinase (AMPK), and shifted metabolism from glycolysis to oxidative phosphorylation (OXPHOS), resulting in inhibition of tumor growth under hypoxia. This study demonstrates an efficient two-photon fluorescent tool for real-time assessment of mitochondrial O₂^•- and a clear link between reducing intracellular ROS levels by CGA treatments and regulating metabolism, as well as undeniably helpful insights for the development of new anticancer strategies.

Eosin Y-Containing Metal-Organic Framework as a Heterogeneous Catalyst for Direct Photoactivation of Inert C-H Bonds

Xanthene dyes as a class of ideal organic homogeneous photocatalyst have received significant attention in C-H bond activation; however, the inherent nature of fast carrier recombination/deactivation and low stability limits their practical applications. Herein, by the ingenious decoration of eosin Y into a porous metal-organic framework (MOF), a high-performance heterogeneous MOF-based photocatalyst was prepared to efficiently activate inert C-H bonds on the reactants via the hydrogen atom transfer pathway for the functionalization of the C-H bonds. Taking advantage of the fixation effect of a rigid framework, the incorporation of eosin Y into MOF leads to great enhancement of their chemical durability. More importantly, by the introduction of the second auxiliary ligand, the carbonyl groups of xanthene on the eosin Y dyes were perfectly retained and periodically aligned within the confined channels of this rigid framework, which could effectively form excited state radicals to prompt inert C-H bond activation, promoting reaction efficiency by the host-guest supramolecular interaction. New eosin Y-based MOFs were recyclable for six times without reducing photocatalytic activity. This eosin Y functionalized MOF-based heterogeneous photocatalytic system provides an availably catalytic avenue to develop a scalable and sustainable synthetic strategy for the practical application of organic dyes.

Developing fluoromodule-based probes for in vivo monitoring the bacterial infections and antibiotic responses

Recently, antibiotic resistant has become a serious public health concern, which warrants new generations of antibiotics to be developed. Pharmacodynamic evaluation is crucial in drug discovery processes. Despite numerous advanced imaging systems are available nowadays, technologies for the sensitive in vivo diagnosis of bacterial infections and direct visualization of drug efficacy are yet to be developed. In this study, we have developed novel near-infrared (NIR) fluorogenic probes. These probes are dark in solution but highly fluorescent when bound to the cognate reporter, fluorogen-activating protein (FAP). We established the in vivo bacterial infection model using FAP_dH6.2 recombinantly expressed E. coli and applied this NIR fluoromodule-based system for diagnosing bacterial infections and monitoring disease progressions and its responses to a type of antibiotics through classic mechanism of membrane lysis. This NIR fluoromodule-based system will discover new information on bacterial infections and identify newer antibacterial entities.

Genetically Encoded Activators of Small Molecules for Imaging and Drug Delivery

Chemical biologists have developed many tools based on genetically encoded macromolecules and small, synthetic compounds. The two different approaches are extremely useful, but they have inherent limitations. In this Minireview, we highlight examples of strategies that combine both concepts to tackle challenging problems in chemical biology. We discuss applications in imaging, with a focus on super-resolved techniques, and in probe and drug delivery. We propose future directions in this field, hoping to inspire chemical biologists to develop new combinations of synthetic and genetically encoded probes.

Fluorogen activating protein toolset for protein trafficking measurements

Throughout the past decade the use of fluorogen activating proteins (FAPs) has expanded with several unique reporter dyes that support a variety of methods to specifically quantify protein trafficking events. The platform's capabilities have been demonstrated in several systems and shared for widespread use. This review will highlight the current FAP labeling techniques for protein traffic measurements and focus on the use of the different designed fluorogenic dyes for selective and specific labeling applications.

Perylenequinone-based "turn on" fluorescent probe for hydrogen sulfide with high sensitivity in living cells

Hydrogen sulfide (H₂S) is a kind of gaseous signal molecule in many physiological processes. In order to detect H₂S, a novel "turn on" fluorescent probe 6,12-dihydroxyperylene-1,7-dione (DPD) was designed and synthesized. The probe DPD is fluorescence silence, while the addition of H₂S induces an obvious green fluorescence with an obvious color change from dark blue to yellow-green. The probe shows excellent selectivity, fast response (2.5min) and linear curve (0-90μM) in wide effective pH range (4-10). Competition experiments are also revealed in corresponding studies and the detection limit is 3.6μM. The response mechanism is proved to be the reduction of the probe by H₂S, which is confirmed by ¹H NMR. Furthermore, through the fluorescence turn-on signal toward H₂S in Hela cells, probe DPD was successfully applied to monitor H₂S in living Hela cells.

A coumarin-based dual optical probe for homocysteine with rapid response time, high sensitivity and selectivity

In this study, a new coumarin-based fluorescent and chromogenic dual channel probe (DC) was used for the selective detection of homocysteine (Hcy) over other amino acids, especially for cysteine (Cys) and glutathione (GSH). When Hcy is present in the solution, the remarkable fluorescence enhancement and obvious blue shift in UV-vis spectra can be observed. In addition, the color change from purple to yellow can be observed clearly by unaided eyes. This probe DC has fast response time, excellent sensitivity and selectivity to Hcy. A linear relationship exists between the ratio of emissions at 486 and 625 nm, and Hcy can be detected in a wide concentration range (0-200 μM). The signal-to-background ratio of fluorescence at 486 nm can reach 8.4, and the detection limit is calculated to be 3.5 µM. The response mechanism is proved to be the Michael addition reaction by Hcy. Preliminary results on cell imaging enable the practical application of Hcy tracing in living cells.

Self-Reporting Chemically Induced Protein Proximity System Based on a Malachite Green Derivative and the L5** Fluorogen Activating Protein

A unique chemically induced proximity method is engineered based on mutant antibody VL domain using a fluorogenic malachite green derivative as the inducer, which gives fluorescent signals upon VL domain dimerization while simultaneously inducing downstream biological effects.

Fluorogen-activating proteins: beyond classical fluorescent proteins

Fluorescence imaging is a powerful technique for the real-time noninvasive monitoring of protein dynamics. Recently, fluorogen activating proteins (FAPs)/fluorogen probes for protein imaging were developed. Unlike the traditional fluorescent proteins (FPs), FAPs do not fluoresce unless bound to their specific small-molecule fluorogens. When using FAPs/fluorogen probes, a washing step is not required for the removal of free probes from the cells, thus allowing rapid and specific detection of proteins in living cells with high signal-to-noise ratio. Furthermore, with different fluorogens, living cell multi-color proteins labeling system was developed. In this review, we describe about the discovery of FAPs, the design strategy of FAP fluorogens, the application of the FAP technology and the advances of FAP technology in protein labeling systems.

Gadolinium-Labeled Aminoglycoside and Its Potential Application as a Bacteria-Targeting Magnetic Resonance Imaging Contrast Agent

Magnetic resonance imaging (MRI) is a powerful diagnostic technique that can penetrate deep into tissue providing excellent spatial resolution without the need for ionizing radiation or harmful radionuclides. However, diagnosing bacterial infections in vivo with clinical MRI is severely hampered by the lack of contrast agents with high relaxivity, targeting capabilities, and bacterial penetration and specificity. Here, we report the development of the first gadolinium (Gd)-based bacteria-specific targeting MRI contrast agent, probe 1, by conjugating neomycin, an aminoglycoside antibiotic, with Dotarem (Gd-DOTA, an FDA approved T₁-weighted MRI contrast agent). The T₁ relaxivity of probe 1 was found to be comparable to that of Gd-DOTA; additionally, probe 1-treated bacteria generated a significantly brighter T₁-weighted MR signal than Gd-DOTA-treated bacteria. More importantly, in vitro cellular studies and preliminary in vivo MRI demonstrated probe 1 exhibits the ability to efficiently target bacteria over macrophage-like cells, indicating its great potential for high-resolution imaging of bacterial infections in vivo.

Real time detection of ESKAPE pathogens by a nitroreductase-triggered fluorescence turn-on probe

The identification of bacterial pathogens is the critical first step in conquering infection diseases. A novel turn-on fluorescent probe for the selective sensing of nitroreductase (NTR) activity and its initial applications in rapid, real-time detection and identification of ESKAPE pathogens have been reported.