Substituted meso-vinyl-BODIPY as thiol-selective fluorogenic probes for sensing unfolded proteins in the endoplasmic reticulum

A reductively convertible nickel phthalocyanine precursor as a biological thiol-responsive turn-on photoacoustic contrast agent

A nickel phthalocyanine precursor bearing poly(ethylene glycol) as a turn-on contrast agent for photoacoustic imaging was prepared. The water-soluble polymeric chains were smoothly eliminated through thiol-mediated reductive aromatization in cancer cells, enabling the detection of endogenous biological thiols in vitro and in vivo.

An epoxide-based covalent sensor to detect cardiac proteome aggregation in a cardio-oncology model

Covalent sensors to detect and capture aggregated proteome in stressed cells are rare. Herein, we construct a series of covalent fluorogenic sensors for aggregated proteins by structurally modulating GFP chromophore and arming it with an epoxide warhead. Among them, P2 probe selectively modifies aggregated proteins over folded ones and turns on fluorescence as evidenced by biochemical and mass spectrometry results. The coverage of this epoxide-based covalent chemistry is demonstrated using different types of aggregated proteins. Finally, the covalent fluorescent sensor P2 allows for direct visualization and capture of aggregated proteome in stressed cardiomyocytes and cardiac tissue samples from a cardio-oncology mouse model. The epoxide-based covalent sensor developed herein may become useful for future chemical proteomics analysis of aggregated proteins to dissect the mechanism underlying cardio-oncology.

Tailoring the Amphiphilicity of Fluorescent Protein Chromophores to Detect Intracellular Proteome Aggregation in Diverse Biological Samples

The formation of amorphous misfolded and aggregated proteins is a hallmark of proteome stress in diseased cells. Given its lack of defined targeting sites, the rational design of intracellular proteome aggregation sensors has been challenging. Herein, we modulate the amphiphilicity of fluorescent protein chromophores to enable selective detection of aggregated proteins in different biological samples, including recombinant proteins, stressed live cells, intoxicated mouse liver tissue, and human hepatocellular carcinoma tissue. By tuning the number of hydroxyl groups, we optimize the selectivity of fluorescent protein chromophores toward aggregated proteins in these biological samples. In recombinant protein applications, the most hydrophobic P0 (cLogP = 5.28) offers the highest fold change (FC = 31.6), sensitivity (LLOD = 0.1 μM), and brightness (Φ = 0.20) upon binding to aggregated proteins. In contrast, P4 of balanced amphiphilicity (cLogP = 2.32) is required for selective detection of proteome stresses in live cells. In mouse and human liver histology tissues, hydrophobic P1 exhibits the best performance in staining the aggregated proteome. Overall, the amphiphilicity of fluorescent chromophores governs the sensor's performance by matching the diverse nature of different biological samples. Together with common extracellular amyloid sensors (e.g., Thioflavin T), these sensors developed herein for intracellular amorphous aggregation complement the toolbox to study protein aggregation.

Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity

Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.

BODIPY-Ethynylestradiol molecular rotors as fluorescent viscosity probes in endoplasmic reticulum

Due to their capability for sensing changes in viscosity, fluorescent molecular rotors (FMRs) have emerged as potential tools to develop several promising viscosity probes; most of them, however, localize non-selectively within cells, precluding changes in the viscosity of specific cellular microdomains to be studied by these means. Following previous reports on enhanced fluorophore uptake efficiency and selectivity by incorporation of biological submolecular fragments, here we report two potential BODIPY FMRs based on an ethynylestradiol spindle, a non-cytotoxic semisynthetic estrogen well recognized by human cells. A critical evaluation of the potential of these fluorophores for being employed as FMRs is presented, including the photophysical characterization of the probes, SXRD studies and TD-DFT computations, as well as confocal microscopy imaging in MCF-7 (breast cancer) cells.

Photophysical properties of furan-bridged dimeric boron-dipyrromethene derivatives (BODIPYs)

In order to investigate the changes in the spectroscopic properties of dimeric boron-dipyrromethenes (BODIPYs), four BODIPY derivatives are synthesized, including a monomer BODIPY in which a furyl group is substituted at the meso position and a dimer BODIPY with a furan group as a bridge. The four synthesized BODIPY derivatives are characterized through nuclear magnetic resonance and mass spectrometry. Photophysical properties such as ultraviolet–visible absorbance and the fluorescence emission of monomers (mT1 and mT2) and dimers (biT1 and biT2) are studied in eight different solvents. In addition, the relationship of their structural properties and optical properties are also considered through density functional theory calculations. The covalent link between the two BODIPY units using a furan group has a profound effect on the optical properties of the dimeric BODIPYs. We believe that an understanding of the synthesis and physical properties of dimeric BODIPYs will have a promising perspective in designing new BODIPY derivatives and predicting their spectroscopic characteristics in the future.

Recent progress in small-molecule fluorescent probes for endoplasmic reticulum imaging in biological systems

Endoplasmic reticulum (ER) is an indispensable organelle in eukaryotic cells involved in protein synthesis and processing, as well as calcium storage and release. Therefore, maintaining the quality of ER is of great importance for cellular homeostasis. Aberrant fluctuations of bioactive species in the ER will result in homeostasis disequilibrium and further cause ER stress, which has evolved to contribute to the pathogenesis of various diseases. Therefore, the real-time monitoring of various bioactive species in the ER is of high priority to ascertain the mysterious roles of ER, which will contribute to unveiling the corresponding mechanism of organism disturbances. Recently, fluorescence imaging has emerged as a robust technique for the direct visualization of molecular events due to its outstanding sensitivity, high temporal-spatial resolution and noninvasive nature. In this review, we comprehensively summarize the recent progress in design strategies, bioimaging applications, potential directions and challenges of ER-targetable small-molecular fluorescent probes.

Biosensors for Studying Neuronal Proteostasis

Cellular health depends on the integrity and functionality of the proteome. Each cell is equipped with a protein quality control machinery that maintains protein homeostasis (proteostasis) by helping proteins adopt and keep their native structure, and ensuring the degradation of damaged proteins. Postmitotic cells such as neurons are especially vulnerable to disturbances of proteostasis. Defects of protein quality control occur in aging and have been linked to several disorders, including neurodegenerative diseases. However, the exact nature and time course of such disturbances in the context of brain diseases remain poorly understood. Sensors that allow visualization and quantitative analysis of proteostasis capacity in neurons are essential for gaining a better understanding of disease mechanisms and for testing potential therapies. Here, I provide an overview of available biosensors for assessing the functionality of the neuronal proteostasis network, point out the advantages and limitations of different sensors, and outline their potential for biological discoveries and translational applications.

Chemical Biology Toolbox to Visualize Protein Aggregation in Live Cells

Protein misfolding and aggregation is a complex biochemical process and has been associated with numerous human degenerative diseases. Developing novel chemical and biological tools and approaches to visualize aggregated proteins in live cells is in high demand for mechanistic studies, diagnostics, and therapeutics. In this review, we summarize the recent developments in the chemical biology toolbox applied to protein aggregation studies in live cells. These methods exploited fluorescent protein tags, fluorescent chemical tags, and small-molecule probes to visualize the protein-aggregation process, detect proteome stresses, and quantify the protein homeostasis network capacity. Inspired by these seminal works, we have generalized design principles for the development of new detection methods and probes in the future that will illuminate this important biological process.

A novel methylenemalononitrile-BODIPY-based fluorescent probe for highly selective detection of hydrogen peroxide in living cells

Hydrogen peroxide (H₂O₂) plays vital roles in oxidative stress and signal transduction in living organisms, and its abnormal levels could be linked to many diseases. Despite numerous efforts spent, it is still urgent and of high importance to develop better H₂O₂ probes with good selectivity, high sensitivity and low backgrounds. To this end, a novel boron dipyrromethene (BODIPY)-based fluorescent probe with an electron-withdrawing methylenemalononitrile at the meso position has been rationally designed, successfully synthesized and investigated for detection of H₂O₂ in aqueous solutions and living cells, which exhibited high selectivity and sensitivity, fluorescent "turn-on" phenomenon at 540 nm, and ratiometric changes from 506 to 540 nm. Upon exposure to H₂O₂, a strong fluorescent emission at 540 nm appeared and the corresponding quantum yields changed from 0.009 to 0.13. The detection limit towards H₂O₂ was calculated to be 31 nM by the linear fluorescence change at 540 nm in the H₂O₂-concentration ranging from 2 to 10 μM. This probe was applicable in a pH range from 6 to 10. Meanwhile, the sensing mechanism was also confirmed by the ¹H NMR and mass spectrometry, suggesting that the above changes might be ascribed to the quick addition and oxidization of the double bond. Furthermore, confocal imaging results also showed great enhancement of intracellular fluorescence upon exposure to H₂O₂ and PMA in RAW264.7 cells, unambiguously confirming its great potentials as a fluorescent probe for highly sensitive detection of both exogenous and endogenous H₂O₂ in living cells.

Illuminating Protein Phase Separation: Reviewing Aggregation-Induced Emission, Fluorescent Molecular Rotor and Solvatochromic Fluorophore based Probes

Protein phase separation process involving protein unfolding, misfolding, condensation and aggregation etc. has been associated with numerous human degenerative diseases. The complexity in protein conformational transitions results in multi-step and multi-species biochemical pathways upon protein phase separation. Recent progresses in designing novel fluorescent probes have unraveled the enriched details of phase separated proteins and provided mechanistic insights towards disease pathology. In this review, we summarized the design and characterizations of fluorescent probes that selectively illuminate proteins at different phase separated states with a focus on aggregation-induced emission probes, fluorescent molecular rotors, and solvatochromic fluorophores. Inspired by these pioneering works, a design blueprint was proposed to further develop fluorescent probes that can potentially shed light on the unresolved protein phase separated states in the future.