Organelle-Directed Staudinger Reaction Enabling Fluorescence-on Resolution of Mitochondrial Electropotentials via a Self-Immolative Charge Reversal Probe

AI-driven precision subcellular navigation with fluorescent probes

Precise navigation within intricate biological systems is pivotal for comprehending cellular functions and diagnosing diseases. Fluorescent molecular probes, designed to target specific biological molecules, are indispensable tools for this endeavor. This paper delves into the revolutionary potential of artificial intelligence (AI) in crafting highly precise and effective fluorescent probes. We will discuss how AI can be employed to: design new subcellular dyes by optimizing physicochemical properties; design prospective subcellular targeting probes based on specific receptors; quantitatively explore the potential chemical laws of fluorescent molecules to optimize the optical properties of fluorescent probes; optimize the comprehensive properties of the probe and guide the construction of multifunctional targeting probes. Additionally, we showcase recent AI-driven advancements in probe development and their successful biomedical applications, while addressing challenges and outlining future directions towards transforming subcellular research, diagnostics, and drug discovery.

Organelle-targeting ratiometric fluorescent probes: design principles, detection mechanisms, bio-applications, and challenges

Biological species, including reactive oxygen species (ROS), reactive sulfur species (RSS), reactive nitrogen species (RNS), F-, Pd2+, Cu2+, Hg2+, and others, are crucial for the healthy functioning of cells in living organisms. However, their aberrant concentration can result in various serious diseases. Therefore, it is essential to monitor biological species in cellular organelles such as the cell membrane, mitochondria, lysosome, endoplasmic reticulum, Golgi apparatus, and nucleus. Among various fluorescent probes for species detection within the organelles, ratiometric fluorescent probes have drawn special attention as a potential way to get beyond the drawbacks of intensity-based probes. This method depends on measuring the intensity change of two emission bands (caused by an analyte), which produces an efficient internal referencing that increases the detection's sensitivity. This review article discusses the literature publications (from 2015 to 2022) on organelle-targeting ratiometric fluorescent probes, the general strategies, the detecting mechanisms, the broad scope, and the challenges currently faced by fluorescent probes.

Membrane-Activated Fluorescent Probe for High-Fidelity Imaging of Mitochondrial Membrane Potential

Mitochondrial membrane potential (ΔΨ_m) is a key indicator of cell health or injury due to its vital roles in adenosine 5'-triphosphate synthesis. Thus, monitoring ΔΨ_m is of great significance for the assessment of cell status, diagnosis of diseases, and medicament screening. Cationic fluorescent probes suffer from severe photobleaching or false positive signals due to the luminescence of the probe on non-mitochondria. Herein, we report a lipophilic cationic fluorescent probe [1-methyl-2-(4-(1,2,2-triphenylvinyl)styryl)-β-naphthothiazol-1-ium trifluoromethanesulfonate (TPE-NT)] with the features of aggregation-induced emission and intramolecular charge transfer for imaging ΔΨ_m in live cells. TPE-NT is enriched on the surface of the mitochondrial inner membrane due to the negative ΔΨ_m, and its fluorescence is activated in the high-viscosity microenvironment. The false positive signals of emission from TPE-NT on non-mitochondria are therefore effectively eliminated. Moreover, TPE-NT exhibits a Stokes shift of >200 nm, near-infrared (∼675 nm) emission, excellent photostability, and low cytotoxicity, which facilitate real-time imaging in live cells. Cell imaging confirmed that the probe can rapidly and reliably report mitochondrial depolarization (decrement of ΔΨ_m) during cell damage caused by CCCP and H₂O₂ as well as mitochondrial polarization (increment of ΔΨ_m) by oligomycin. Furthermore, the probe successfully detected the reduction of ΔΨ_m in these cell models of hypoxia, heat damage, acidification, aging, inflammation, mitophagy, and apoptosis caused by hypoxia, heatstroke, lactate/pyruvate, doxorubicin, lipopolysaccharide, rapamycin, monensin, and nystatin, respectively.

Structurally Redesigned Bioorthogonal Reagents for Mitochondria-Specific Prodrug Activation

The development of abiotic chemical reactions that can be performed in an organelle-specific manner can provide new opportunities in drug delivery and cell and chemical biology. However, due to the complexity of the cellular environment, this remains a significant challenge. Here, we introduce structurally redesigned bioorthogonal tetrazine reagents that spontaneously accumulate in mitochondria of live mammalian cells. The attributes leading to their efficient accumulation in the organelle were optimized to include the right combination of lipophilicity and positive delocalized charge. The best performing mitochondriotropic tetrazines enable subcellular chemical release of TCO-caged compounds as we show using fluorogenic substrates and mitochondrial uncoupler niclosamide. Our work demonstrates that a shrewd redesign of common bioorthogonal reagents can lead to their transformation into organelle-specific probes, opening the possibility to activate prodrugs and manipulate biological processes at the subcellular level by using purely chemical tools.

Organelle-Redirected Chameleon Sensor-Enabled Live Cell Imaging of Mitochondrial DNA

Mitochondrial DNA (mtDNA) plays important roles in diverse physiological processes and myriad diseases. We herein report mtDNA imaging with a chameleon sensor containing a cationic rhodamine B (RB) entity for mitochondria targeting and a fluorogenic SYBR Green-I (SG) entity for DNA sensing. SG-RB selectively binds to mtDNA and gives green SG fluorescence in mitochondria of living cells but gives red RB fluorescence upon delivery of mitochondria into lysosomes in mitophagy. With the dual-color imaging, mtDNA aggregation and elevated mitophagy were identified in HeLa cells stressed with anticancer doxorubicin. These results suggest the utility of organelle-redirected DNA sensors for live cell imaging of mtDNA involved in myriad pathological disorders.

Fluorescent probes for organelle-targeted bioactive species imaging

The dynamic fluctuations of bioactive species in living cells are associated with numerous physiological and pathological phenomena. The emergence of organelle-targeted fluorescent probes has significantly facilitated our understanding on the biological functions of these species. This review describes the design, applications, challenges and potential directions of organelle-targeted bioactive species probes.

Bioactive species, including reactive oxygen species (ROS, including O₂˙^–, H₂O₂, HOCl, ¹O₂, ˙OH, HOBr, etc.), reactive nitrogen species (RNS, including ONOO^–, NO, NO₂, HNO, etc.), reactive sulfur species (RSS, including GSH, Hcy, Cys, H₂S, H₂S_n, SO₂ derivatives, etc.), ATP, HCHO, CO and so on, are a highly important category of molecules in living cells. The dynamic fluctuations of these molecules in subcellular microenvironments determine cellular homeostasis, signal conduction, immunity and metabolism. However, their abnormal expressions can cause disorders which are associated with diverse major diseases. Monitoring bioactive molecules in subcellular structures is therefore critical for bioanalysis and related drug discovery. With the emergence of organelle-targeted fluorescent probes, significant progress has been made in subcellular imaging. Among the developed subcellular localization fluorescent tools, ROS, RNS and RSS (RONSS) probes are highly attractive, owing to their potential for revealing the physiological and pathological functions of these highly reactive, interactive and interconvertible molecules during diverse biological events, which are rather significant for advancing our understanding of different life phenomena and exploring new technologies for life regulation. This review mainly illustrates the design principles, detection mechanisms, current challenges, and potential future directions of organelle-targeted fluorescent probes toward RONSS.

Aryl Azides as Phosphine-Activated Switches for Small Molecule Function

Engineered small molecule triggers are important tools for the control and investigation of biological processes, in particular protein function. Staudinger reductions of aryl azides to amines through the use of phosphines can trigger an elimination reaction, and thereby activation of a functional molecule, if an appropriately positioned leaving group is present. We conducted detailed investigations of the effect of aryl azide and phosphine structure on both the mechanism and kinetics of these reaction-induced eliminations and identified phosphine/azide pairs that enable complete activation within minutes under physiologically relevant conditions.