Intracellular Protein-Labeling Probes for Multicolor Single-Molecule Imaging of Immune Receptor-Adaptor Molecular Dynamics

Photoactive Arylamine Appended β-Naphthols via Friedel-Crafts Alkylation of Vinylidine Quinone Methides (VQMs)

Substituted naphthol derivatives have received significant attention due to their wide range of biological and pharmaceutical activities, and further extending the generation of naphthol with photoactive materials promotes optoelectronic applications. Nevertheless, the synthetic methodology of such materials hitherto unknown. In this study, we have adopted an efficient Friedel-Crafts reaction of ortho-alkynylnaphthols with N,N-disubstituted arylamines to generate arylamine-appended β-naphthol derivatives. This transformation features broad substrate scope, excellent yields, and high atom economy and the method was successfully adapted for late-stage functionalization of biomolecules and drug molecules with excellent yields. Further, UV-vis absorption and emission studies reveal that these materials have shown visible range absorption and blue emission with a quantum efficiency of 10%. Lately, photo-irradiation on arylamine leads to a charged state that facilitates the improvement of the electronic properties. Consequently, novel synthetic methodology of photoactive materials paves the way to generate new developments in the area of small molecule-derived optoelectronics.

Fluorescent probes in autoimmune disease research: current status and future prospects

Autoimmune diseases (AD) present substantial challenges for early diagnosis and precise treatment due to their intricate pathogenesis and varied clinical manifestations. While existing diagnostic methods and treatment strategies have advanced, their sensitivity, specificity, and real-time applicability in clinical settings continue to exhibit significant limitations. In recent years, fluorescent probes have emerged as highly sensitive and specific biological imaging tools, demonstrating substantial potential in AD research.This review examines the response mechanisms and historical evolution of various types of fluorescent probes, systematically summarizing the latest research advancements in their application to autoimmune diseases. It highlights key applications in biomarker detection, dynamic monitoring of immune cell functions, and assessment of drug treatment efficacy. Furthermore, this article analyzes the technical challenges currently encountered in probe development and proposes potential directions for future research. With ongoing advancements in materials science, nanotechnology, and bioengineering, fluorescent probes are anticipated to achieve higher sensitivity and enhanced functional integration, thereby facilitating early detection, dynamic monitoring, and innovative treatment strategies for autoimmune diseases. Overall, fluorescent probes possess substantial scientific significance and application value in both research and clinical settings related to autoimmune diseases, signaling a new era of personalized and precision medicine.

Non-invasive in vivo monitoring of PROTAC-mediated protein degradation using an environment-sensitive reporter

Proteolysis targeting chimeras (PROTACs) represent a groundbreaking therapeutic technology for selectively degrading proteins of interest (POIs). The structural variations in PROTACs unpredictably influence their protein degradation efficiency, which is predominantly assessed by quantifying POIs abundance through western blotting. This approach, however, falls short of enabling non-invasive monitoring of protein degradation within living cells let alone assessing directly the degradation effects in vivo. Herein, we develop an environment-sensitive reporter (ESR) for the quantification of protein degradation events triggered by PROTACs in vivo. By simultaneously integrating POIs targeting ligand and an environment-sensitive fluorophore, the ESR signals exhibit a strong fluorescence correlation with the levels of POIs. This non-invasive monitoring reporter offers a high-throughput and convenient way to screen POIs targeting degraders and predict PROTACs-mediated therapeutic outcomes in mouse models. These properties suggest the potential of ESR strategy as a general modular scheme for non-invasive quantification of protein degradation of cancer-related therapeutic targets.

An encodable amino acid for targeted photocatalysis

Photocatalysts are excellent scaffolds for the light-mediated control of bioactive molecules. Current photocatalytic structures are not compatible with genetic encoding and therefore cannot be directly incorporated into the sequences of native proteins. Herein, we developed new amino acids incorporating Si-rosamine photocatalytic units, and introduced them via aminoacylation of tRNAs into specific positions of different proteins to enable targeted photocatalytic reactions in defined populations of immune cells.

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.

A Case-Study on the Photophysics of Chalcogen-Substituted Zinc(II) Phthalocyanines

Singlet dioxygen has been widely applied in different disciplines such as medicine (photodynamic therapy or blood sterilization), remediation (wastewater treatment) or industrial processes (fine chemicals synthesis). Particularly, it can be conveniently generated by energy transfer between a photosensitizer's triplet state and triplet dioxygen upon irradiation with visible light. Among the best photosensitizers, substituted zinc(II) phthalocyanines are prominent due to their excellent photophysical properties, which can be tuned by structural modifications, such as halogen- and chalcogen-atom substitution. These patterns allow for the enhancement of spin-orbit coupling, commonly attributed to the heavy atom effect, which correlates with the atomic number ( Z ${Z}$ ) and the spin-orbit coupling constant ( ζ ${\zeta }$ ) of the introduced heteroatom. Herein, a fully systematic analysis of the effect exerted by chalcogen atoms on the photophysical characteristics (absorption and fluorescence properties, lifetimes and singlet dioxygen photogeneration), involving 30 custom-made β-tetrasubstituted chalcogen-bearing zinc(II) phthalocyanines is described and evaluated regarding the heavy atom effect. Besides, the intersystem crossing rate constants are estimated by several independent methods and a quantitative profile of the heavy atom is provided by using linear correlations between relative intersystem crossing rates and relative atomic numbers. Good linear trends for both intersystem crossing rates (S1-T1 and T1-S0) were obtained, with a dependency on the atomic number and the spin-orbit coupling constant scaling asZ 0 . 4 ${{Z}^{0.4}}$ andζ 0 . 2 ${{\zeta }^{0.2}}$ , respectively The trend shows to be independent of the solvent and temperature.

OregonFluor enables quantitative intracellular paired agent imaging to assess drug target availability in live cells and tissues

Non-destructive fluorophore diffusion across cell membranes to provide an unbiased fluorescence intensity readout is critical for quantitative imaging applications in live cells and tissues. Commercially available small-molecule fluorophores have been engineered for biological compatibility, imparting high water solubility by modifying rhodamine and cyanine dye scaffolds with multiple sulfonate groups. The resulting net negative charge, however, often renders these fluorophores cell-membrane-impermeant. Here we report the design and development of our biologically compatible, water-soluble and cell-membrane-permeable fluorophores, termed OregonFluor (ORFluor). By adapting previously established ratiometric imaging methodology using bio-affinity agents, it is now possible to use small-molecule ORFluor-labelled therapeutic inhibitors to quantitatively visualize their intracellular distribution and protein target-specific binding, providing a chemical toolkit for quantifying drug target availability in live cells and tissues.

Photophysical Rate Constants and Oxygen Dependence for Si and Ge Rhodamine Zwitterions

The family of group XIV rhodamine zwitterions are fluorescence probes with carbon, silicon, germanium, or tin substituted in the 10-position of the xanthene ring. Because of their inherent near-infrared fluorescence, photostability and high quantum yields in aqueous solutions, the Si and Ge containing fluorophores in this class have become increasingly important for fluorescent labeling of proteins and biological molecules. This study fully characterizes photophysical rates derived from a model consisting of a singlet ground state, the lowest singlet excited state, and the lowest triplet excited state for two exemplar group XIV rhodamine zwitterions, one containing Si and the other Ge. Within a simple Jablonski diagram, all radiative and non-radiative rates, including intersystem crossing and triplet depopulation rates, were measured as a function of oxygen concentration. It was shown that the triplet depopulation rates are intrinsically fast in comparison with traditional xanthene containing fluorophores, probably due to the increased spin-obit coupling from the Si and Ge substitution in the xanthene ring. Dissolved oxygen increases both the intersystem crossing and triplet depopulation rates. Stern-Volmer analysis was conducted to estimate rates of quenching by oxygen. The experimental data was used to estimate the initial rates for reactive oxygen production by Si and Ge containing fluorophores in aqueous solutions containing different concentrations of dissolved O₂. These estimates showed a significantly slower initial rate of reactive oxygen production in comparison with rhodamine 6G. This goes a long way to explaining their inherent photostability. Spectroscopic experiments were also conducted in 77 K viscous aqueous glasses where it was observed that the fluorescence spectra remained unchanged, and the quantum yields increased from 0.53 to 0.84 and from 0.52 to 0.89 for the Si and Ge containing fluorophores respectively; no phosphorescence was observed. All intersystem crossing and triplet depopulation rates were measured using fluorescence correlation spectroscopy (FCS) and analyzed using a new method that extrapolated the power dependence of the FCS curves to optical saturation. This method was verified using published data.

Fluorescent glutamine and asparagine as promising probes for chemical biology

Fluorescent probes have become valuable tools in chemical biology, providing interesting inferences for unfolding the complexities of natural biochemical processes. In this study, we report the synthesis and characterization of fluorescent labelled glutamine (Gln) and asparagine (Asn) derivatives via traceless Staudinger ligation, which exhibited high fluorescence quantum yields, excellent photostabilities and emission of blue fluorescence in the visible region. The successful permeation of these fluorescent amino acids into cellular components proved their potential as fluorescent probes for chemical biology.

Gold-Bipyramid-Based Nanothernostics: FRET-Mediated Protein-Specific Sialylation Visualization and Oxygen-Augmenting Phototherapy against Hypoxic Tumor

Despite several attempts, incorporating biological detection that supplies necessary biological information into therapeutic nanotheranostics for hypoxic tumor treatments is considered to be in its infancy. It is therefore imperative to consolidate biological detection and desirable phototherapy into a single nanosystem for maximizing theranostic advantages. Herein, we develop a versatile nanoprobe through combined fluorescence resonance energy transfer (FRET) and oxygen-augmenting strategy, namely APT, which enables glycosylation detection, O₂ self-sufficiency, and collaborative phototherapy. Such APT nanoprobes were constructed by depositing platinum onto gold nano-bipyramids (Au NBPs), linking FITC fluorophore-labeled AS1411 aptamers for introducing FRET donors, and by conjugating G-quadruplex intercalated with TMPyP4 to their surfaces via the SH-DNA chain. By installing FRET acceptors on the glycan of targeted EpCAM glycoprotein using the metabolic glycan labeling and click chemistry, FRET signals appear on the cancerous cell membranes, not normal cells, when donors and acceptors are within an appropriate distance. This actualizes protein-specific glycosylation visualization while revealing glycan-based changes correlated with tumor progression. Interestingly, the deposited platinum scavenges excessive H₂O₂ as artificial nanoenzymes to transform O₂ that alleviates tumor hypoxia and simultaneously elevates singlet oxygen (¹O₂) for inducing cancer cell apoptosis. Notably, the significant hyperthermia devastation was elicited via APT nanoprobes with phenomenal photothermal therapy (PTT) efficiency (71.8%) for thermally ablating cancer cells, resulting in synergistically enhanced photodynamic-hyperthermia therapy. Consequently, APT nanoprobes nearly actualized thorough tumor ablation while demonstrating highly curative biosafety. This work offers a new paradigm to rationally explore a combined FRET and oxygen-augmenting strategy with a focus on nanotheranostics for hypoxic tumor elimination.

Optical Manipulation of Subcellular Protein Translocation Using a Photoactivatable Covalent Labeling System

The photoactivatable chemically induced dimerization (photo-CID) technique for tag-fused proteins is one of the most promising methods for regulating subcellular protein translocations and protein-protein interactions. However, light-induced covalent protein dimerization in living cells has yet to be established, despite its various advantages. Herein, we developed a photoactivatable covalent protein-labeling technology by applying a caged ligand to the BL-tag system, a covalent protein labeling system that uses mutant β-lactamase. We further developed CBHD, a caged protein dimerizer, using caged BL-tag and HaloTag ligands, and achieved light-induced protein translocation from the cytoplasm to subcellular regions. In addition, this covalent photo-CID system enabled quick protein translocation to a laser-illuminated microregion. These results indicate that the covalent photo-CID system will expand the scope of CID applications in the optical manipulation of cellular functions.

Genetically Encoded Supramolecular Targeting of Fluorescent Membrane Tension Probes within Live Cells: Precisely Localized Controlled Release by External Chemical Stimulation

To image membrane tension in selected membranes of interest (MOI) inside living systems, the field of mechanobiology requires increasingly elaborated small-molecule chemical tools. We have recently introduced HaloFlipper, i.e., a mechanosensitive flipper probe that can localize in the MOI using HaloTag technology to report local membrane tension changes using fluorescence lifetime imaging microscopy. However, the linker tethering the probe to HaloTag hampers the lateral diffusion of the probe in all the lipid domains of the MOI. For a more global membrane tension measurement in any MOI, we present here a supramolecular chemistry strategy for selective localization and controlled release of flipper into the MOI, using a genetically encoded supramolecular tag. SupraFlippers, functionalized with a desthiobiotin ligand, can selectively accumulate in the organelle having expressed streptavidin. The addition of biotin as a biocompatible external stimulus with a higher affinity for Sav triggers the release of the probe, which spontaneously partitions into the MOI. Freed in the lumen of endoplasmic reticulum (ER), SupraFlippers report the membrane orders along the secretory pathway from the ER over the Golgi apparatus to the plasma membrane. Kinetics of the process are governed by both the probe release and the transport through lipid domains. The concentration of biotin can control the former, while the expression level of a transmembrane protein (Sec12) involved in the stimulation of the vesicular transport from ER to Golgi influences the latter. Finally, the generation of a cell-penetrating and fully functional Sav-flipper complex using cyclic oligochalcogenide (COC) transporters allows us to combine the SupraFlipper strategy and HaloTag technology.

Late-stage peptide and protein modifications through phospha-Michael addition reaction

We developed a late-stage modification strategy by a phospha-Michael addition reaction between various functional phosphines and unprotected dehydroalanine (Dha) peptides and proteins under mild conditions. This strategy was applied to generate a staple peptide to enhance its cell membrane penetrability, and it was also able to regulate α-synuclein aggregation properties and morphological characteristics with the addition of different charges.

Near-infrared fluorescent probes: a next-generation tool for protein-labeling applications

The development of near-infrared (NIR) fluorescent probes over the past few decades has changed the way that biomolecules are imaged, and thus represents one of the most rapidly progressing areas of research. Presently, NIR fluorescent probes are routinely used to visualize and understand intracellular activities. The ability to penetrate tissues deeply, reduced photodamage to living organisms, and a high signal-to-noise ratio characterize NIR fluorescent probes as efficient next-generation tools for elucidating various biological events. The coupling of self-labeling protein tags with synthetic fluorescent probes is one of the most promising research areas in chemical biology. Indeed, at present, protein-labeling techniques are not only used to monitor the dynamics and localization of proteins but also play a more diverse role in imaging applications. For instance, one of the dominant technologies employed in the visualization of protein activity and regulation is based on protein tags and their associated NIR fluorescent probes. In this mini-review, we will discuss the development of several NIR fluorescent probes used for various protein-tag systems.

HaloFlippers: A General Tool for the Fluorescence Imaging of Precisely Localized Membrane Tension Changes in Living Cells

Tools to image membrane tension in response to mechanical stimuli are badly needed in mechanobiology. We have recently introduced mechanosensitive flipper probes to report quantitatively global membrane tension changes in fluorescence lifetime imaging microscopy (FLIM) images of living cells. However, to address specific questions on physical forces in biology, the probes need to be localized precisely in the membrane of interest (MOI). Herein we present a general strategy to image the tension of the MOI by tagging our newly introduced HaloFlippers to self-labeling HaloTags fused to proteins in this membrane. The critical challenge in the construction of operational HaloFlippers is the tether linking the flipper and the HaloTag: It must be neither too taut nor too loose, be hydrophilic but lipophilic enough to passively diffuse across membranes to reach the HaloTags, and allow partitioning of flippers into the MOI after the reaction. HaloFlippers with the best tether show localized and selective fluorescence after reacting with HaloTags that are close enough to the MOI but remain nonemissive if the MOI cannot be reached. Their fluorescence lifetime in FLIM images varies depending on the nature of the MOI and responds to myriocin-mediated sphingomyelin depletion as well as to osmotic stress. The response to changes in such precisely localized membrane tension follows the validated principles, thus confirming intact mechanosensitivity. Examples covered include HaloTags in the Golgi apparatus, peroxisomes, endolysosomes, and the ER, all thus becoming accessible to the selective fluorescence imaging of membrane tension.

Experimental and theoretical study on the cyclic(alkyl)(amino)carbene-copper catalyzed Friedel-Crafts reaction of N,N-dialkylanilines with styrenes

The Friedel-Crafts reaction of alkalinous substrates is challenging because of the coordination between amines and traditional acid catalysts. Based on theoretical research, we designed a catalytic process for the Friedel-Crafts reactions of N,N-dialkylanilines in the presence of CAAC-CuCl [CAAC = cyclic(alkyl)(amino)carbene] and KB(C₆F₅)₄. Experimental results show that the catalytic system is suitable for a series of N,N-dialkylanilines and styrenes with good to excellent yields of para-selectivity products. The results are comparable to those obtained in carbene-gold catalyzed processes.

Large-scale single-molecule imaging aided by artificial intelligence

Single-molecule imaging analysis has been applied to study the dynamics and kinetics of molecular behaviors and interactions in living cells. In spite of its high potential as a technique to investigate the molecular mechanisms of cellular phenomena, single-molecule imaging analysis has not been extended to a large scale of molecules in cells due to the low measurement throughput as well as required expertise. To overcome these problems, we have automated the imaging processes by using computer operations, robotics and artificial intelligence (AI). AI is an ideal substitute for expertise to obtain high-quality images for quantitative analysis. Our automated in-cell single-molecule imaging system, AiSIS, could analyze 1600 cells in 1 day, which corresponds to ∼ 100-fold higher efficiency than manual analysis. The large-scale analysis revealed cell-to-cell heterogeneity in the molecular behavior, which had not been recognized in previous studies. An analysis of the receptor behavior and downstream signaling was accomplished within a significantly reduced time frame and revealed the detailed activation scheme of signal transduction, advancing cell biology research. Furthermore, by combining the high-throughput analysis with our previous finding that a receptor changes its behavioral dynamics depending on the presence of a ligand/agonist or inhibitor/antagonist, we show that AiSIS is applicable to comprehensive pharmacological analysis such as drug screening. This AI-aided automation has wide applications for single-molecule analysis.

Covalently Tethered Rhodamine Voltage Reporters for High Speed Functional Imaging in Brain Tissue

Voltage-sensitive fluorophores enable the direct visualization of membrane potential changes in living systems. To pair the speed and sensitivity of chemically synthesized fluorescent indicators with cell-type specific genetic methods, we here develop Rhodamine-based Voltage Reporters (RhoVR) that can be covalently tethered to genetically encoded, self-labeling enzymes. These chemical-genetic hybrids feature a photoinduced electron transfer triggered RhoVR voltage-sensitive indicator coupled to a chloroalkane HaloTag ligand through a long, water-soluble polyethylene glycol linker (RhoVR-Halo). When applied to cells, RhoVR-Halo dyes selectively and covalently bind to surface-expressed HaloTag enzyme on genetically modified cells. RhoVR-Halo dyes maintain high voltage sensitivities-up to 34% ΔF/F per 100 mV-and fast response times typical of untargeted RhoVRs, while gaining the selectivity of genetically encodable voltage indicators. We show that RhoVR-Halos can record action potentials in single trials from cultured rat hippocampal neurons and can be used in concert with green-fluorescent Ca2+ indicators like GCaMP to provide simultaneous voltage and Ca2+ imaging. In a brain slice, RhoVR-Halos provide exquisite labeling of defined cells and can be imaged using epifluorescence, confocal, or two-photon microscopy. Using high-speed epifluorescence microscopy, RhoVR-Halos provide a read-out of action potentials from labeled cortical neurons in a rat brain slice, without the need for trial averaging. These results demonstrate the potential of hybrid chemical-genetic voltage indicators to combine the optical performance of small-molecule chromophores with the inherent selectivity of genetically encodable systems, permitting imaging modalities inaccessible to either technique individually.

Development of an effective protein-labeling system based on smart fluorogenic probes

Proteins are an important component of living systems and play a crucial role in various physiological functions. Fluorescence imaging of proteins is a powerful tool for monitoring protein dynamics. Fluorescent protein (FP)-based labeling methods are frequently used to monitor the movement and interaction of cellular proteins. However, alternative methods have also been developed that allow the use of synthetic fluorescent probes to target a protein of interest (POI). Synthetic fluorescent probes have various advantages over FP-based labeling methods. They are smaller in size than the fluorescent proteins, offer a wide variety of colors and have improved photochemical properties. There are various chemical recognition-based labeling techniques that can be used for labeling a POI with a synthetic probe. In this review, we focus on the development of protein-labeling systems, particularly the SNAP-tag, BL-tag, and PYP-tag systems, and understanding the fluorescence behavior of the fluorescently labeled target protein in these systems. We also discuss the smart fluorogenic probes for these protein-labeling systems and their applications. The fluorogenic protein labeling will be a useful tool to investigate complex biological phenomena in future work on cell biology.

Perfluorocarbon-Based 19 F MRI Nanoprobes for In Vivo Multicolor Imaging

In vivo multicolor imaging is important for monitoring multiple biomolecular or cellular processes in biology. 19 F magnetic resonance imaging (MRI) is an emerging in vivo imaging technique because it can non-invasively visualize 19 F nuclei without endogenous background signals. Therefore, 19 F MRI probes capable of multicolor imaging are in high demand. Herein, we report five types of perfluorocarbon-encapsulated silica nanoparticles that show 19 F NMR peaks with different chemical shifts. Three of the nanoprobes, which show spectrally distinct 19 F NMR peaks with sufficient sensitivity, were selected for in vivo multicolor 19 F MRI. The nanoprobes exhibited 19 F MRI signals with three colors in a living mouse. Our in vivo multicolor system could be utilized for evaluating the effect of surface functional groups on the hepatic uptake in a mouse. This novel multicolor imaging technology will be a practical tool for elucidating in vivo biomolecular networks by 19 F MRI.

Dual-functional protein for one-step production of a soluble and targeted fluorescent dye

Low water solubility and poor selectivity are two fundamental limitations that compromise applications of near-infrared (NIR) fluorescent probes. Methods: Here, a simple strategy that can resolve these problems simultaneously was developed by using a novel hybrid protein named RGD-HFBI that is produced by fusion of hydrophobin HFBI and arginine-glycine-aspartic acid (RGD) peptide. This unique hybrid protein inherits self-assembly and targeting functions from HFBI and RGD peptide respectively. Results: Boron-dipyrromethene (BODIPY) used as a model NIR dye can be efficiently dispersed in the RGD-HFBI solution by simple mixing and sonication for 30 min. The data shows that self-assembled RGD-HFBI forms a protein nanocage by using the BODIPY as the assembly template. Cell uptake assay proves that RGD-HFBI/BODIPY can efficiently stain αvβ3 integrin-positive cancer cells. Finally, in vivo affinity tests fully demonstrate that the soluble RGD-HFBI/BODIPY complex selectively targets and labels tumor sites of tumor-bearing mice due to the high selectivity of the RGD peptide. Conclusion: Our one-step strategy using dual-functional RGD-HFBI opens a novel route to generate soluble and targeted NIR fluorescent dyes in a very simple and efficient way and may be developed as a general strategy to broaden their applications.