Monitoring protein interactions and dynamics with solvatochromic fluorophores

Structure-function relationships in solvatochromic fluorophores targeting human and bovine carbonic anhydrases

The development of reversible, selective, small molecule fluorescent probes displaying high fluorescence turn-on responses and tight binding affinity with specific metalloenzymes requires consideration of multiple factors. In this study, we report a library of fluorescent probes for two carbonic anhydrases: human carbonic anhydrase II (hCAII) and bovine carbonic anhydrase II (bCAII) and compare differences in fluorescence turn-on and binding affinity with molecular docking to gain insight into structure-function relationships. We analyze the roles of electrostatics, hydrophobics, and sterics in influencing the fluorescence response of the probes with hCAII and bCAII which have 80 % sequence identity but drastically different fluorescence turn-on values with amino(na)phthalimide-based fluorophores.

Differentiating carrier protein interactions in biosynthetic pathways using dapoxyl solvatochromism

Carrier protein-dependent synthases are ubiquitous enzymes involved both in primary and secondary metabolism. Biocatalysis within these synthases is governed by key interactions between the carrier protein, substrate, and partner enzymes. The weak and transient nature of these interactions has rendered them difficult to study. Here we develop a useful fluorescent solvatochromic probe, dapoxyl-pantetheinamide, to monitor and quantify carrier protein interactions in vitro. Upon loading with target carrier proteins, we observe dramatic shifts in fluorescence emission wavelength and intensity and further demonstrate that this tool has the potential to be applied across numerous biosynthetic pathways. The environmental sensitivity of this probe allows rapid characterization of carrier protein interactions, with the ability to quantitatively determine inhibition of protein-protein interactions. We anticipate future application of these probes for inhibitor screening and in vivo characterization.

Design and synthesis of an environment-sensitive 3-methyleneisoindolin-1-one fluorophore for labeling DNA-interacting proteins

We designed 6-dimethylamino 3-methyleneisoindolin-1-one as an environment-sensitive fluorophore, examining its applications for protein labeling. Synthesized 3-methyleneisoindolin-1-one exhibits solvatochromic fluorescence (λemmax; 472 nm in 2-PrOH, 512 nm in H2O). A positive linear dependence between λemmax and solvent dielectric constant (DC), as well as between Stokes shift and DC, and a negative correlation between fluorescence quantum yield and DC are observed in protic solvents. These properties are similar to those of the oxygen isosteric fluorophore, 4-dimethylaminophthalimide, a slovatochromic fluorophore utilized for labeling oligodeoxynucleotides (ODNs) and peptides. Notably, fluorescence intensity of 3-methyleneisoindolin-1-one is higher than the phthalimide in protic solvents used in this study. The 3-methyleneisoindolin-1-one demonstrated the higher stability in pH 8 solution than in pH 6 solution in contrast to the stability profile of the phthalimide, which was stable at pH 6 but was hydrolyzed at pH 8. We also synthesized an o-keto benzaldehyde derivative that converts a primary amine to 6-dimethylamino 3-methyleneisoindolin-1-one under biocompatible conditions and introduced it into ODNs for turn-on fluorescent protein labeling. The synthesized ODN with a protein-binding sequence of Escherichia coli DnaA was employed to modify the DNA-binding domain of DnaA, and the fluorescent properties of the modified protein were investigated.

Regulation of Absorption and Emission in a Protein/Fluorophore Complex

Human cellular retinol binding protein II (hCRBPII) was used as a protein engineering platform to rationally regulate absorptive and emissive properties of a covalently bound fluorogenic dye. We demonstrate the binding of a thio-dapoxyl analog via formation of a protonated imine between an active site lysine residue and the chromophore's aldehyde. Rational manipulation of the electrostatics of the binding pocket results in a 204 nm shift in absorption and a 131 nm shift in emission. The protein is readily expressed in mammalian systems and binds with exogenously delivered fluorophore as demonstrated by live-cell imaging experiments.

Presenting a new fluorescent probe, methyl(10-phenylphenanthren-9-yl)sulfane sensitive to the polarity and rigidity of the microenvironment: applications toward microheterogeneous systems

A molecule, methyl(10-phenylphenanthren-9-yl)sulfane (MPPS), with a straightforward structure, has been synthesized, characterized, and explored as a new fluorescent probe for microheterogeneous systems. The photophysical properties of MPPS have been studied through experimental and theoretical calculations using the range-separated hybrid functional CAM-B3LYP in conjunction with a 6-311++g(d,p) basis set. Theoretical calculations show that the freely rotating phenyl ring forms a 94° dihedral angle with the phenanthrene ring in the ground state. Experimentally found two absorption bands correspond to the n → π* and π → π* transitions supported by the frontier molecular orbital calculations. Two excited singlet states, E-1 and E-2 (the former being more stable than the latter in the gas phase), exist with dihedral angles between the phenyl and phenanthrene rings as 142° and 133°, respectively, in the gas phase. Two emitting states in a condensed medium of varying polarities are supported by the steady-state fluorescence and fluorescence intensity decay data. Emission energies, fluorescence intensities, and excited singlet state lifetimes change with the polarity of the solvents. To support that the free rotation in the molecule is responsible for these changes, the fluorescence properties of another molecule, methyl(10-(o-tolyl)phenanthren-9-yl)sulfane (MTPS), with restricted rotation of the substituted benzene, i.e., o-tolyl ring have been studied. The fast-intensity decay component of MPPS is ascribed to the conformer in the E-1 state. The molecule has proved to be an excellent polarity probe explored to determine the critical micelle concentrations (cmc) values of different surfactants, which agree well with the literature reports. Different regions of binding isotherm (specific, non-cooperative, cooperative, and massive binding) of a gemini surfactant, 12-6-12,2Br- with bovine serum albumin (BSA) have been successfully demonstrated by the steady-state and time-resolved fluorescence and fluorescence anisotropic properties of MPPS. Docking results show that MPPS resides in the hydrophobic pocket of BSA. The fluorescence quenching of BSA by MPPS reveals the location of Trp residues of BSA. Thus, a polarity and molecular rigidity-sensitive fluorescent molecule, MPPS has been presented here that can potentially be used to monitor the changes in the microenvironment of biomolecules in different processes.

Fluorometric Analysis of Carrier-Protein-Dependent Biosynthesis through a Conformationally Sensitive Solvatochromic Pantetheinamide Probe

Carrier proteins (CPs) play a fundamental role in the biosynthesis of fatty acids, polyketides, and non-ribosomal peptides, encompassing many medicinally and pharmacologically relevant compounds. Current approaches to analyze novel carrier-protein-dependent synthetic pathways are hampered by a lack of activity-based assays for natural product biosynthesis. To fill this gap, we turned to 3-methoxychromones, highly solvatochromic fluorescent molecules whose emission intensity and wavelength are heavily dependent on their immediate molecular environment. We have developed a solvatochromic carrier-protein-targeting probe which is able to selectively fluoresce when bound to a target carrier protein. Additionally, the probe displays distinct responses upon CP binding in carrier-protein-dependent synthases. This discerning approach demonstrates the design of solvatochromic fluorophores with the ability to identify biosynthetically active CP-enzyme interactions.

Cellular and Biophysical Applications of Genetic Code Expansion

Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.

Aromatic Alcohol-Based pH-Sensitive Chromophore with a Unique Near-Infrared Dual-Band Solvatochromic Property and Its Application as a Ratiometric Fluorescent Sensor for G-Quadruplexes

Solvatochromes have gained great attention because of their unique roles in monitoring biomolecular location, interaction, and dynamics. Particularly, solvatochromes presenting both red-shifting excitation and dual-band switchable emission are in great demand yet significantly difficult to come true. In this article, we disclose an aromatic alcohol-based pH-sensitive chromophore NIR-HBT that not only presents red-shifting excitation and solvent-dependent dual-band emission but also shows high photostability and excellent brightness. To the best of our knowledge, this is the first solvatochrome to simultaneously display these optical properties. Especially, in contrast to the reported dual-band solvatochromes whose solvatochromism is achieved by affecting their excited state behaviors, the solvatochromism of NIR-HBT is realized by modulating its ground state proton dissociation, which is a new solvatochromic mechanism that has not been reported. Furthermore, based on the dual-band solvatochromism of NIR-HBT and its intrinsic binding ability to GQs, near-infrared ratiometric detection of GQs is achieved. These results indicate that NIR-HBT is an attractive solvatochrome that can be used to develop near-infrared ratiometric biosensors for biological research. More broadly, the discovered solvatochromic mechanism can also open new horizons for exploring the solvatochrome.

Artificial Protein Crosstalk with a Molecule that Exchanges Binding Partners

Drawing inspiration from allosteric signaling enzymes, whose catalytic and regulatory units are non-covalently linked, we have devised a method to establish unnatural, effector-mediated enzyme activation within native cells. The feasibility of this approach is demonstrated by introducing a synthetic regulatory unit (sRU) onto glycogen synthase kinase 3 (GSK-3) through non-covalent means. Our study reveals that this synthetic regulator mediates an unnatural crosstalk between GSK-3 and lactate dehydrogenase A (LDHA), whose expression is regulated by cellular oxygen levels. Specifically, with this approach, the constitutively active GSK-3 is transformed into an activable enzyme, whereas LDHA is repurposed as an unnatural effector protein that controls the activity of the kinase, making it unnaturally dependent on the cell's hypoxic response. These findings demonstrate a step toward imitating the function of effector-regulated cell-signaling enzymes, which play a key biological role in mediating the response of cells to changes in their environment. In addition, at the proof-of-principle level, our results indicate the potential to develop a new class of protein inhibitors whose inhibitory effect in cells is dictated by the cell's environment and consequent protein expression profile.

In-situ quantification of lipids in live cells through imaging approaches

Lipids are important molecules that are widely distributed within the cell, and they play a crucial role in several biological processes such as cell membrane formation, signaling, cell motility and division. Monitoring the spatiotemporal dynamics of cellular lipids in real-time and quantifying their concentrations in situ is crucial since the local concentration of lipids initiates various signaling pathways that regulate cellular processes. In this review, we first introduced the historical background of lipid quantification methods. We then delve into the current state of the art of in situ lipid quantification, including the establishment and utility of fluorescence imaging techniques based on sensors of lipid-binding domains labeled with organic dyes or fluorescent proteins, and Raman and magnetic resonance imaging (MRI) techniques that do not require lipid labeling. Next, we highlighted the biological applications of live-cell lipid quantification techniques in the study of in situ lipid distribution, lipid transformation, and lipid-mediated signaling pathways. Finally, we discussed the technical challenges and prospects for the development of lipid quantification in live cells, with the aim of promoting the development of in situ lipid quantification in live cells, which may have a profound impact on the biological and medical fields.

Lactam-fused tropolones: a new tunable, environmentally sensitive fluorophore class

Fluorescent small-molecules capable of altering their profiles in response to environmental changes are exceptionally valuable tool compounds throughout the scientific community. The following manuscriipt describes a new class of fluorescent small molecules based on lactam-fused tropolones that are responsive to a dynamic range of environmental changes. These molecules can be easily obtained through a rapid annulation procedure between appropriately functionalized tropolones and primary amines, which is often complete within minutes at room temperature. Molecules generated through this approach have been identified with fluoresence emission across the visible light spectra, and can be tuned based on either the tropolone or amine component. They are also highly responsive to changes in solvent, pH, and certain divalent metal ions. Tropolone-fused lactams thus represent a new class of tunable fluorescent small molecules that could find value throughout the scientific community.

Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching

Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl can optimize color switching by altering fluorophore conformational equilibria in the apo and glucose-bound proteins. A commonly accepted view is that Prodan derivatives report on protein conformations via solvatochromic effects due to changes in the dielectric of their local environment. Here we show that instead Prodan carbonyl twisting controls color switching. These insights enable structure-based biosensor design by coupling ligand-mediated protein conformational changes to internal chromophore twists through specific steric interactions between fluorophore and protein.

Genetic Targeting of Solvatochromic Dyes for Probing Nanoscale Environments of Proteins in Organelles

A variety of protein tags are available for genetically encoded protein labeling, which allow their precise localization and tracking inside the cells. A new dimension in protein imaging can be offered by combining protein tags with polarity-sensitive fluorescent probes, which provide information about local nanoscale environments of target proteins within the subcellular compartments (organelles). Here, we designed three fluorescent probes based on solvatochromic nile red dye, conjugated to a HaloTag reactive targeting group through polyethylene glycol linkers of varying lengths. The probe with medium linker length, NR12-Halo, was found to label specifically a large variety of proteins localized in defined cell compartments, such as plasma membranes (outer and inner leaflets), endoplasmic reticulum, Golgi apparatus, cytosol, microtubules, actin, and chromatin. Owing to its polarity-sensitive fluorophore, the probe clearly distinguished the proteins localized within apolar lipid membranes from other proteins. Moreover, it revealed dramatic changes in the environment during the life cycle of proteins from biosynthesis to their expected localization and, finally, to recycling inside lysosomes. Heterogeneity in the local polarity of some membrane proteins also suggested a formation of low-polar protein aggregates, for example, within cell-cell contacts. The approach also showed that mechanical stress (cell shrinking by osmotic shock) induced a general polarity decrease in membrane proteins, probably due to the condensation of biomolecules. Finally, the nanoenvironment of some membrane proteins was affected by a polyunsaturated fatty acid diet, which provided the bridge between organization of lipids and proteins. The developed solvatochromic HaloTag probe constitutes a promising tool for probing nanoscale environments of proteins and their interactions within subcellular structures.

Autoregulation of GPCR signalling through the third intracellular loop

The third intracellular loop (ICL3) of the G protein-coupled receptor (GPCR) fold is important for the signal transduction process downstream of receptor activation1-3. Despite this, the lack of a defined structure of ICL3, combined with its high sequence divergence among GPCRs, complicates characterization of its involvement in receptor signalling4. Previous studies focusing on the β2 adrenergic receptor (β2AR) suggest that ICL3 is involved in the structural process of receptor activation and signalling5-7. Here we derive mechanistic insights into the role of ICL3 in β2AR signalling, observing that ICL3 autoregulates receptor activity through a dynamic conformational equilibrium between states that block or expose the receptor's G protein-binding site. We demonstrate the importance of this equilibrium for receptor pharmacology, showing that G protein-mimetic effectors bias the exposed states of ICL3 to allosterically activate the receptor. Our findings additionally reveal that ICL3 tunes signalling specificity by inhibiting receptor coupling to G protein subtypes that weakly couple to the receptor. Despite the sequence diversity of ICL3, we demonstrate that this negative G protein-selection mechanism through ICL3 extends to GPCRs across the superfamily, expanding the range of known mechanisms by which receptors mediate G protein subtype selective signalling. Furthermore, our collective findings suggest ICL3 as an allosteric site for receptor- and signalling pathway-specific ligands.

Configuration-Induced Multichromism of Phenanthridine Derivatives: A Type of Versatile Fluorescent Probe for Microenvironmental Monitoring

Fluorescent probes are attractive in diagnosis and sensing. However, most reported fluorophores can only detect one or few analytes/parameters, notably limiting their applications. Here we have designed three phenanthridine-based fluorophores (i.e., B1, F1, and T1 with 1D, 2D, and 3D molecular configuration, respectively) capable of monitoring various microenvironments. In rigidifying media, all fluorophores show bathochromic emissions but with different wavelength and intensity changes. Under compression, F1 shows a bathochromic emission of over 163 nm, which results in organic fluorophore-based full-color piezochromism. Moreover, both B1 and F1 exhibit an aggregation-caused quenching (ACQ) behavior, while T1 is an aggregation-induced emission (AIE) fluorophore. Further, F1 and T1 selectively concentrate in cell nucleus, whereas B1 mainly stains the cytoplasm in live cell imaging. This work provides a general design strategy of versatile fluorophores for microenvironmental monitoring.

Comprehensive Investigation of Parameters Influencing Fluorescence Lifetime Imaging Microscopy in Frequency- and Time-Domain Illustrated by Phasor Plot Analysis

Having access to fluorescence lifetime, researchers can reveal in-depth details about the microenvironment as well as the physico-chemical state of the molecule under investigation. However, the high number of influencing factors might be an explanation for the strongly deviating values of fluorescent lifetimes for the same fluorophore reported in the literature. This could be the reason for the impression that inconsistent results are obtained depending on which detection and excitation scheme is used. To clarify this controversy, the two most common techniques for measuring fluorescence lifetimes in the time-domain and in the frequency-domain were implemented in one single microscopy setup and applied to a variety of fluorophores under different environmental conditions such as pH-value, temperature, solvent polarity, etc., along with distinct state forms that depend, for example, on the concentration. From a vast amount of measurement results, both setup- and sample-dependent parameters were extracted and represented using a single display form, the phasor-plot. The measurements showed consistent results between the two techniques and revealed which of the tested parameters has the strongest influence on the fluorescence lifetime. In addition, quantitative guidance as to which technique is most suitable for which research task and how to perform the experiment properly to obtain consistent fluorescence lifetimes is discussed.

Development of Fluorescent Turn-On Probes for CAG-RNA Repeats

Fluorescent sensing of nucleic acids is a highly sensitive and efficient bioanalytical method for their study in cellular processes, detection and diagnosis in related diseases. However, the design of small molecule fluorescent probes for the selective binding and detection of RNA of a specific sequence is very challenging because of their diverse, dynamic, and flexible structures. By modifying a bis(amidinium)-based small molecular binder that is known to selectively target RNA with CAG repeats using an environment-sensitive fluorophore, a turn-on fluorescent probe featuring aggregation-induced emission (AIE) is successfully developed in this proof-of-concept study. The probe (DB-TPE) exhibits a strong, 19-fold fluorescence enhancement upon binding to a short CAG RNA, and the binding and fluorescence response was found to be specific to the overall RNA secondary structure with A·A mismatches. These promising analytical performances suggest that the probe could be applied in pathological studies, disease progression monitoring, as well as diagnosis of related neurodegenerative diseases due to expanded CAG RNA repeats.

A fluorogenic probe for predicting treatment response in non-small cell lung cancer with EGFR-activating mutations

Therapeutic responses of non-small cell lung cancer (NSCLC) to epidermal growth factor receptor (EGFR) - tyrosine kinase inhibitors (TKIs) are known to be associated with EGFR mutations. However, a proportion of NSCLCs carrying EGFR mutations still progress on EGFR-TKI underlining the imperfect correlation. Structure-function-based approaches have recently been reported to perform better in retrospectively predicting patient outcomes following EGFR-TKI treatment than exon-based method. Here, we develop a multicolor fluorescence-activated cell sorting (FACS) with an EGFR-TKI-based fluorogenic probe (HX103) to profile active-EGFR in tumors. HX103-based FACS shows an overall agreement with gene mutations of 82.6%, sensitivity of 81.8% and specificity of 83.3% for discriminating EGFR-activating mutations from wild-type in surgical specimens from NSCLC patients. We then translate HX103 to the clinical studies for prediction of EGFR-TKI sensitivity. When integrating computed tomography imaging with HX103-based FACS, we find a high correlation between EGFR-TKI therapy response and probe labeling. These studies demonstrate HX103-based FACS provides a high predictive performance for response to EGFR-TKI, suggesting the potential utility of an EGFR-TKI-based probe in precision medicine trials to stratify NSCLC patients for EGFR-TKI treatment.

Alkoxy-Substituted Quadrupolar Fluorescent Dyes

Polar and polarizable π-conjugated organic molecules containing push-pull chromophores have been investigated extensively in the past. Identifying unique backbones and building blocks for fluorescent dyes is a timely exercise. Here, we report the synthesis and characterization of a series of fluorescent dyes containing quadrupolar A-D-A constitutions (where A = acceptor and D = donor), which exhibit fluorescence emission at a variety of different wavelengths. We have investigated the effects of different electron-withdrawing groups, located at both termini of a para-terphenylene backbone, by steady-state UV/vis and fluorescence spectroscopy. Pyridine and substituted pyridinium units are also introduced during the construction of the quadrupolar backbones. Depending on the quadrupolarity, fluorescence emission wavelengths cover from 380 to 557 nm. Time-resolved absorption and emission spectroscopy reveal that the photophysical properties of those quadrupolar dyes result from intramolecular charge transfer. One of the dyes we have investigated is a symmetrical box-like tetracationic cyclophane. Its water-soluble tetrachloride, which is non-cytotoxic to cells up to a loading concentration of 1 μM, has been employed in live-cell imaging. When taken up by cells, the tetrachloride emits a green fluorescence emission without any hint of photobleaching or disruption of normal cell behavior. We envision that our design strategy of modifying molecules through the functionalization of the quadrupolar building blocks as chromophores will lead to future generations of fluorescent dyes in which these A-D-A constitutional fragments are incorporated into more complex molecules and polymers for broader photophysical and biological applications.

In vivo visualization of fluorescence reflecting CDK4 activity in a breast cancer mouse model

The CDK4/6-Rb axis is a crucial target of cancer therapy and several selective inhibitors of it have been approved for clinical application. However, current therapeutic efficacy evaluation mostly relies on anatomical imaging, which cannot directly reflect changes in drug targets, leading to a delay in the selection of optimal treatment. In this study, we constructed a novel fluorescent probe, CPP30-Lipo/CDKACT4, for real-time monitoring of CDK4 activity and the therapeutic efficacy of its inhibitor in HR+/HER2- breast cancer. CPP30-Lipo/CDKACT4 exhibited good optical stability and targetability. The signal of the probe in living cells decreased after CDK4 knockdown or palbociclib treatment. Moreover, the fluorescence intensity of the tumors after 7 days of palbociclib treatment was significantly lower than that before treatment, while no significant change in tumor diameter was observed under magnetic resonance imaging. Overall, we developed an innovative fluorescent probe that can monitor CDK4 activity and the early therapeutic response to CDK4 inhibitors in living cells and in vivo. It may provide a new strategy for evaluating antitumor therapeutic efficacy in a clinical context and for drug development.

The Journey of 1-Keto-1,2,3,4-Tetrahydrocarbazole Based Fluorophores: From Inception to Implementation

Carbazole is a unique template associated with several biological activities. It is due to the diverse and versatile biological properties of carbazole derivatives that they are of immense interest to the research community. 1-keto-1,2,3,4-tetrahydrocarbazoles are important synthetic intermediates to obtain carbazole derivatives. Several members of this family emit fluorescence on photoexcitation. In the context of biochemical and biophysical research, designing and characterising small molecule environment sensitive fluorophores is extremely significant. This article aims to be a state of the art review with synthetic and photophysical details of a variety of fluorophores based on 1-keto-1,2,3,4-tetrahydrocarbazole skeleton.

Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications

Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.

Discovery of Environment-Sensitive Fluorescent Ligands of β-Adrenergic Receptors for Cell Imaging and NanoBRET Assay

By fusing several environment-sensitive fluorophores to the pharmacophore mirabegron, a series of new fluorescent ligands for β-adrenergic receptors (β-ARs) were produced with a turn-on mechanism and high binding affinity to β-ARs efficiently. Compound L5 with the pyridinium moiety possessed the most favorable combination of properties after systematic comparison and optimization, including high affinity and acceptable cytotoxicity, remarkable fluorescence enhancement (up to 30-fold) upon binding with β-ARs, and feasible visualizing ability of β-ARs in living cells under no-wash conditions. Furthermore, a NanoLuc-based bioluminescence resonance energy transfer (NanoBRET) binding assay based on compound L5 was developed and may be used in high-throughput screening (HTS) in the drug discovery of β-ARs due to its unique fluorescence spectroscopic features. Overall, as the first environment-sensitive fluorescent ligand, molecule L5 could be a useful tool for understanding the pharmacology of β-ARs.

Shining Light on Protein Kinase Biomarkers with Fluorescent Peptide Biosensors

Protein kinases (PKs) are established gameplayers in biological signalling pathways, and a large body of evidence points to their dysregulation in diseases, in particular cancer, where rewiring of PK networks occurs frequently. Fluorescent biosensors constitute attractive tools for probing biomolecules and monitoring dynamic processes in complex samples. A wide variety of genetically encoded and synthetic biosensors have been tailored to report on PK activities over the last decade, enabling interrogation of their function and insight into their behaviour in physiopathological settings. These optical tools can further be used to highlight enzymatic alterations associated with the disease, thereby providing precious functional information which cannot be obtained through conventional genetic, transcriptomic or proteomic approaches. This review focuses on fluorescent peptide biosensors, recent developments and strategies that make them attractive tools to profile PK activities for biomedical and diagnostic purposes, as well as insights into the challenges and opportunities brought by this unique toolbox of chemical probes.

Application of a novel fluorescence intensity assay: identification of distinct fatty acetates as volatile compounds that bind specifically to amino acid region 149-168 of a transmembrane receptor CD36

The cluster of differentiation 36 (CD36) is a transmembrane receptor expressed in various cells and has diverse lipid ligands. The expression of CD36 in the murine olfactory epithelium and its ability to recognize certain species of fatty aldehydes, a class of odor-active volatile compounds, have suggested a role for this receptor in the capture of specific odorants in the nasal cavity of mammals. However, the spectrum of CD36-recognizable volatile compounds is poorly understood. In this study, we employed our recently devised assay with fluorescently labeled peptides as probes (fluorescence intensity assay) and identified distinct fatty acetates as volatile compounds that bind specifically to amino acid region 149-168 of CD36 (eg dodecyl and tetradecyl acetates). The present findings demonstrate the utility of our assay for the discovery of novel CD36 ligands and support the notion that the receptor functions as a captor of volatile compounds in the mammalian olfactory system.

Visualizing the Multistep Process of Protein Aggregation in Live Cells

Protein aggregation is a biological phenomenon in which aberrantly processed or mutant proteins misfold and assemble into a variety of insoluble aggregates. Decades of studies have delineated the structure, interaction, and activity of proteins in either their natively folded structures or insoluble aggregates such as amyloid fibrils. However, a variety of intermediate species exist between these two extreme states in the protein folding landscape. Herein, we collectively term these intermediate species as misfolded protein oligomers, including soluble oligomers and preamyloid oligomers that are formed by unfolded or misfolded proteins. While extensive tools have been developed to study folded proteins or amyloid fibrils, research to understand the properties and activities of misfolded protein oligomers has been limited by the lack of methods to detect and interrogate these species in live cells.In this Account, we describe our efforts in the development of chemical methods that allow for the characterization of the multistep protein aggregation process, in particular the misfolded protein oligomers, in living cells. As the start of this journey, we attempted to develop a fluorogenic method wherein the misfolded oligomers could turn on the fluorescence of chemical probes that are conjugated to the protein-of-interest (POI). To this end, we produced a series of destabilized HaloTag variants, formulating the primary component of the AgHalo sensor, which misfolds and aggregates when cells are subjected to stress. When AgHalo is covalently conjugated with a solvatochromic fluorophore, misfolding of the AgHalo conjugate would activate fluorescence, resulting in the observation of misfolded oligomers. Following this work, we extended the scope of detection from AgHalo to any protein-of-interest via the AggTag method, wherein the POIs are genetically fused to self-labeling protein tags (HaloTag or SNAP-tag). Focusing on the molecular rotor-based fluorophores, we applied the modulated fluorescent protein (FP) chromophore core as a prototype for the AggTag probes, to enable the fluorogenic detection of misfolded soluble oligomers of multiple proteins in live cells. Next, we further developed the AggTag method to distinguish insoluble aggregates from misfolded oligomers, using two classes of probes that activate different fluorescence emission toward these two conformations. To enable this goal, we applied physical organic chemistry and computational chemistry to discover a new category of triode-like fluorophores, wherein the π orbitals of either an electron density regulator or the donor-acceptor linkages are used to control the rotational barriers of fluorophores in the excited states. This mechanism allows us to rationally design molecular rotor-based fluorophores that have desired responses to viscosity, thus extending the application of the AggTag method.In summary, our work allows the direct monitoring of the misfolded protein oligomers and differentiation of insoluble aggregates from other conformations in live cells, thus enabling studies of many currently unanswered questions in protein aggregation. Future directions are to develop methods that enable quantitative analyses of the protein aggregation process. Further, new methods are needed to detect and to quantify the formation and maturation of protein or RNA condensates that form membraneless organelles.

Planar Chiral Analogues of PRODAN Based on a [2.2]Paracyclophane Scaffold: Synthesis and Photophysical Studies

We describe the synthesis and photophysical characterization of differently substituted planar chiral analogues of PRODAN based on a [2.2]paracyclophane scaffold. This experimental and theoretical study highlights that the (chir)optical properties of the new "phane" compounds, which incorporate an electron-withdrawing propionyl moiety and an electron-donating dimethylamino group at their para or pseudo-para positions, strongly depend on their substitution patterns. In particular, for this series of molecules, a more pronounced solvatochromism and clear chiroptical behaviors are observed when the two substituents are placed on the two rings of the pCp core in a non-"co-planar" arrangement (pseudo-para derivative). This observation may help design new pCp-based luminophores with finely tuned photophysical properties.

Environment-Sensitive Fluorescent Labelling of Peptides by Luciferin Analogues

Environment-sensitive fluorophores are very valuable tools in the study of molecular and cellular processes. When used to label proteins and peptides, they allow for the monitoring of even small variations in the local microenvironment, thus acting as reporters of conformational variations and binding events. Luciferin and aminoluciferin, well known substrates of firefly luciferase, are environment-sensitive fluorophores with unusual and still-unexploited properties. Both fluorophores show strong solvatochromism. Moreover, luciferin fluorescence is influenced by pH and water abundance. These features allow to detect local variations of pH, solvent polarity and local water concentration, even when they occur simultaneously, by analyzing excitation and emission spectra. Here, we describe the characterization of (amino)luciferin-labeled derivatives of four bioactive peptides: the antimicrobial peptides GKY20 and ApoB_L, the antitumor peptide p53pAnt and the integrin-binding peptide RGD. The two probes allowed for the study of the interaction of the peptides with model membranes, SDS micelles, lipopolysaccharide micelles and Escherichia coli cells. K_d values and binding stoichiometries for lipopolysaccharide were also determined. Aminoluciferin also proved to be very well-suited to confocal laser scanning microscopy. Overall, the characterization of the labeled peptides demonstrates that luciferin and aminoluciferin are previously neglected environment-sensitive labels with widespread potential applications in the study of proteins and peptides.

Site-Specific Labeling of Endogenous Proteins Using CoLDR Chemistry

Chemical modifications of native proteins can affect their stability, activity, interactions, localization, and more. However, there are few nongenetic methods for the installation of chemical modifications at a specific protein site in cells. Here we report a covalent ligand directed release (CoLDR) site-specific labeling strategy, which enables the installation of a variety of functional tags on a target protein while releasing the directing ligand. Using this approach, we were able to label various proteins such as BTK, K-Ras^G12C, and SARS-CoV-2 PL^pro with different tags. For BTK we have shown selective labeling in cells of both alkyne and fluorophores tags. Protein labeling by traditional affinity methods often inhibits protein activity since the directing ligand permanently occupies the target binding pocket. We have shown that using CoLDR chemistry, modification of BTK by these probes in cells preserves its activity. We demonstrated several applications for this approach including determining the half-life of BTK in its native environment with minimal perturbation, as well as quantification of BTK degradation by a noncovalent proteolysis targeting chimera (PROTAC) by in-gel fluorescence. Using an environment-sensitive “turn-on” fluorescent probe, we were able to monitor ligand binding to the active site of BTK. Finally, we have demonstrated efficient CoLDR-based BTK PROTACs (DC₅₀ < 100 nM), which installed a CRBN binder onto BTK. This approach joins very few available labeling strategies that maintain the target protein activity and thus makes an important addition to the toolbox of chemical biology.

A Solvatochromic Fluorescent Probe Reveals Polarity Heterogeneity upon Protein Aggregation in Cells

We report a crystallization-induced emission fluorophore to quantitatively interrogate the polarity of aggregated proteins. This solvatochromic probe, namely "AggRetina" probe, inherently binds to aggregated proteins and exhibits both a polarity-dependent fluorescence emission wavelength shift and a viscosity-dependent fluorescence intensity increase. Regulation of its polarity sensitivity was achieved by extending the conjugation length. Different proteins bear diverse polarity upon aggregation, leading to different resistance to proteolysis. Polarity primarily decreases during protein misfolding but viscosity mainly increases upon the formation of insoluble aggregates. We quantified the polarity of aggregated protein-of-interest in live cells via HaloTag bioorthogonal labeling, revealing polarity heterogeneity within cellular aggregates. The enriched micro-environment details inside misfolded and aggregated proteins may correlate to their bio-chemical properties and pathogenicity.

Strategy of De Novo Design toward First-In-Class Imaging Agents for Simultaneously Differentiating Glioma Boundary and Grades

The extent of resection and tumor grade are two predominant prognostic factors for glioma. Fluorescent imaging is promising to facilitate accurate resection and simultaneous tumor grading. However, no probe fulfilling this task has been reported. Herein, we proposed a strategy of de novo design toward first-in-class fluorescent probes for simultaneously differentiating glioma boundary and grades. By bioinformatics analysis in combination with experimental validation, platelet-derived growth factor receptor β (PDGFRβ) was revealed as a promising biomarker for glioma imaging and grading. Then, fluorogenic probe PDGFP 1 was designed, guided by the structure-activity relationship study. Finally, the probe was demonstrated to stain glioma cells and tissues in the mice orthotopic glioma model with high selectivity over normal brain cells or tissues. Meanwhile, ex vivo experiments using patient-derived samples indicated that the fluorescence was significantly positively correlated with the tumor grades. This result highlighted the feasibility of the three-step de novo probe design strategy and suggested PDGFP 1 as a promising probe for simultaneously differentiating glioma boundary and grades, showing prospects of clinical translation.

Design of Large Stokes Shift Fluorescent Proteins Based on Excited State Proton Transfer of an Engineered Photobase

The incredible potential for fluorescent proteins to revolutionize biology has inspired the development of a variety of design strategies to address an equally broad range of photophysical characteristics, depending on potential applications. Of these, fluorescent proteins that simultaneously exhibit high quantum yield, red-shifted emission, and wide separation between excitation and emission wavelengths (Large Stokes Shift, LSS) are rare. The pursuit of LSS systems has led to the formation of a complex, obtained from the marriage of a rationally engineered protein (human cellular retinol binding protein II, hCRBPII) and different fluorogenic molecules, capable of supporting photobase activity. The large increase in basicity upon photoexcitation leads to protonation of the fluorophore in the excited state, dramatically red-shifting its emission, leading to an LSS protein/fluorophore complex. Essential for selective photobase activity is the intimate involvement of the target protein structure and sequence that enables Excited State Proton Transfer (ESPT). The potential power and usefulness of the strategy was demonstrated in live cell imaging of human cell lines.

Assessment of direct binding interaction between CD36 and its potential lipid ligands using a peptide mimic of the receptor labeled with a fluorophore

Cluster of differentiation 36 (CD36) is a cell-surface receptor that recognizes diverse substances. We have presented indirect evidence that a short segment of the receptor comprising amino acids 149-168 contains a site for binding of its lipid ligands (e.g., distinct fatty acids and aldehydes). However, experimental support for their direct interactions is yet to be achieved. For this, we devised a fluorescence intensity assay, where a synthetic peptide consisting of CD36 amino acids 149-168 labeled with fluorescein isothiocyanate (FITC-CD36_149-168) and its variant peptides were used as positive and negative probes, respectively. First, we obtained results indicating that 1-palmitoyl-2-(5-keto-6-octenedioyl)phosphatidylcholine (an established CD36 ligand) but not 1-palmitoyl-2-arachidonyl-phosphatidylcholine (a non-ligand of the receptor) bound in a saturable and specific manner to FITC-CD36_149-168. Strikingly, the assay allowed us to provide the first evidence supporting direct and specific binding between the CD36 segment and fatty aldehydes (e.g., Z-11-hexadecenal). However, this method failed to illustrate specific interactions of the segment with fatty acids, such as oleic acid. Nonetheless, our findings offer further insight into the biologically relevant ligands and the role of CD36. In addition, we suggest that this fluorescence-based technique provides a convenient means to evaluate protein (peptide)-lipid interactions.

Fluorescent Peptide Biosensors for Probing CDK Kinase Activity in Cell Extracts

Fluorescent biosensors can report on the relative abundance, activity, or conformation of biomolecules and analytes through changes in fluorescence emission. A wide variety of genetically-encoded and synthetic biosensors have been developed to monitor protein kinase activity. We have focused on the design, engineering and characterization of fluorescent peptide biosensors of cyclin-dependent kinases (CDKs) that constitute attractive cancer biomarkers and pharmacological targets. In this chapter, we describe the CDKACT fluorescent peptide biosensor technology and its application to assess the relative kinase activity of CDKs in vitro, either using recombinant proteins or cell extracts as a more complex source of kinase. This technology offers a straightforward means of comparing CDK activity in different cell lines and evaluating the specific impact of treatments intended to target kinase activity in a physiologically relevant environment.

Enantioselective Synthesis and Application of Small and Environmentally Sensitive Fluorescent Amino Acids for Probing Biological Interactions

Environmentally sensitive fluorescent amino acids (FlAAs) have been used extensively to probe biological interactions. However, most of these amino acids are large and do not resemble amino acid side chains. Here, we report the enantioselective synthesis of two small and environmentally sensitive fluorescent amino acids bearing 7-dialkylaminocoumarin side chains by alkylation of a Ni(II) glycine Schiff base complex. These amino acids exhibit a large increase in fluorescence as environment polarity decreases. One of these FLAAs was incorporated into a highly active analog of the cyclic lipopeptide antibiotic paenibacterin by Fmoc solid-phase peptide synthesis via a new and very efficient route. This peptide was used to probe the interaction of the antibiotic with model liposomes, lipopolysaccharides, and live bacteria.

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.

Direct visualization and profiling of protein misfolding and aggregation in live cells

Over the past few years, research tools have been developed to monitor the multistep protein aggregation process in live cells, a process that has been associated with a growing number of human diseases. Herein, we describe recent advances in methods that can either survey the distribution of aggregation at the level of the cellular proteome using mass spectroscopy or discern the multistep aggregation process of specific proteins of interest via fluorescence signals. Future development and application of such technologies are expected to provide insights on mechanisms, diagnosis, and treatment of diseases rooted in protein aggregation.

Developing Bright Green Fluorescent Protein (GFP)-like Fluorogens for Live-Cell Imaging with Nonpolar Protein-Chromophore Interactions

Fluorescence-activating proteins (FAPs) that bind a chromophore and activate its fluorescence have gained popularity in bioimaging. The fluorescence-activating and absorption-shifting tag (FAST) is a light-weight FAP that enables fast reversible fluorogen binding, thus advancing multiplex and super-resolution imaging. However, the rational design of FAST-specific fluorogens with large fluorescence enhancement (FE) remains challenging. Herein, a new fluorogen directly engineered from green fluorescent protein (GFP) chromophore by a unique double-donor-one-acceptor strategy, which exhibits an over 550-fold FE upon FAST binding and a high extinction coefficient of approximately 100,000 M^-1  cm^-1 , is reported. Correlation analysis of the excited state nonradiative decay rates and environmental factors reveal that the large FE is caused by nonpolar protein-fluorogen interactions. Our deep insights into structure-function relationships could guide the rational design of bright fluorogens for live-cell imaging with extended spectral properties such as redder emissions.

Quantitative interrogation of protein co-aggregation using multi-color fluorogenic protein aggregation sensors

Co-aggregation of multiple pathogenic proteins is common in neurodegenerative diseases but deconvolution of such biochemical process is challenging. Herein, we developed a dual-color fluorogenic thermal shift assay to simultaneously report on the aggregation of two different proteins and quantitatively study their thermodynamic stability during co-aggregation. Expansion of spectral coverage was first achieved by developing multi-color fluorogenic protein aggregation sensors. Orthogonal detection was enabled by conjugating sensors of minimal fluorescence crosstalk to two different proteins via sortase-tag technology. Using this assay, we quantified shifts in melting temperatures in a heterozygous model protein system, revealing that the thermodynamic stability of wild-type proteins was significantly compromised by the mutant ones but not vice versa. We also examined how small molecule ligands selectively and differentially interfere with such interplay. Finally, we demonstrated these sensors are suited to visualize how different proteins exert influence on each other upon their co-aggregation in live cells.

Broad Applications of Thiazole Orange in Fluorescent Sensing of Biomolecules and Ions

Fluorescent sensing of biomolecules has served as a revolutionary tool for studying and better understanding various biological systems. Therefore, it has become increasingly important to identify fluorescent building blocks that can be easily converted into sensing probes, which can detect specific targets with increasing sensitivity and accuracy. Over the past 30 years, thiazole orange (TO) has garnered great attention due to its low fluorescence background signal and remarkable 'turn-on' fluorescence response, being controlled only by its intramolecular torsional movement. These features have led to the development of numerous molecular probes that apply TO in order to sense a variety of biomolecules and metal ions. Here, we highlight the tremendous progress made in the field of TO-based sensors and demonstrate the different strategies that have enabled TO to evolve into a versatile dye for monitoring a collection of biomolecules.

Testing the Limitations of MD-Based Local Electric Fields Using the Vibrational Stark Effect in Solution: Penicillin G as a Test Case

Noncovalent interactions underlie nearly all molecular processes in the condensed phase from solvation to catalysis. Their quantification within a physically consistent framework remains challenging. Experimental vibrational Stark effect (VSE)-based solvatochromism can be combined with molecular dynamics (MD) simulations to quantify the electrostatic forces in solute-solvent interactions for small rigid molecules and, by extension, when these solutes bind in enzyme active sites. While generalizing this approach toward more complex (bio)molecules, such as the conformationally flexible and charged penicillin G (PenG), we were surprised to observe inconsistencies in MD-based electric fields. Combining synthesis, VSE spectroscopy, and computational methods, we provide an intimate view on the origins of these discrepancies. We observe that the electric fields are correlated to conformation-dependent effects of the flexible PenG side chain, including both the local solvation structure and solute conformational sampling in MD. Additionally, we identified that MD-based electric fields are consistently overestimated in three-point water models in the vicinity of charged groups; this cannot be entirely ameliorated using polarizable force fields (AMOEBA) or advanced water models. This work demonstrates the value of the VSE as a direct method for experiment-guided refinements of MD force fields and establishes a general reductionist approach to calibrating vibrational probes for complex (bio)molecules.

Synthesis of a Coumarin-Based PPARγ Fluorescence Probe for Competitive Binding Assay

Peroxisome proliferator-activated receptor γ (PPARγ) is a molecular target of metabolic syndrome and inflammatory disease. PPARγ is an important nuclear receptor and numerous PPARγ ligands were developed to date; thus, efficient assay methods are important. Here, we investigated the incorporation of 7-diethylamino coumarin into the PPARγ agonist rosiglitazone and used the compound in a binding assay for PPARγ. PPARγ-ligand-incorporated 7-methoxycoumarin, 1, showed weak fluorescence intensity in a previous report. We synthesized PPARγ-ligand-incorporating coumarin, 2, in this report, and it enhanced the fluorescence intensity. The PPARγ ligand 2 maintained the rosiglitazone activity. The obtained partial agonist 6 appeared to act through a novel mechanism. The fluorescence intensity of 2 and 6 increased by binding to the ligand binding domain (LBD) of PPARγ and the affinity of reported PPARγ ligands were evaluated using the probe.