Activatable Optical Probes for the Detection of Enzymes

Tracking the Endosomal Escape: A Closer Look at Calcein and Related Reporters

Crossing the cellular membrane and delivering active pharmaceuticals or biologicals into the cytosol of cells is an essential step in the development of nanomedicines. One of the most important intracellular processes regarding the cellular uptake of biologicals is the endolysosomal pathway. Sophisticated nanocarriers have been developed overcoming a major hurdle, the endosomal entrapment, and delivering their cargo to the required site of action. In parallel, in vitro assays have been established analyzing the performance of these nanocarriers. Among them, the release of the membrane-impermeable dye calcein has become a popular and straightforward method. It is accessible for most researchers worldwide, allows for rapid conclusions about the release potential, and enables the study of release mechanisms. This review is intended to provide an overview and guidance for scientists applying the calcein release assay. It comprises a survey of several applications in the study of endosomal escape, considerations of potential pitfalls, challenges and limitations of the assay, and a brief summary of complementary methods. Based on this review, we hope to encourage further research groups to take advantage of the calcein release assay for their own purposes and help to create a database for more efficient cross-correlations between nanocarriers. This article is protected by copyright. All rights reserved.

Polymeric agents for activatable fluorescence, self-luminescence and photoacoustic imaging

Numerous polymeric agents have been widely applied in biology and medicine by virtue of the facile chemical modification, feasible nano-engineering approaches and fine-tuned pharmacokinetics. To endow polymeric imaging agents with ability to monitor and measure subtle molecular or cellular alterations at diseased sites, activatable polymeric probes that can elicit signal changes in response to biomolecular interactions or the analytes of interest have to be developed. Herein, this review aims to provide a systemic interpretation and summarization of the design methodology and imaging utility of recently emerged activatable polymeric probes. An introduction of activatable probes allowing for precise imaging and classification of polymeric imaging agents is reported first. Then, we give a detailed discussion of the contemporary design approaches toward activatable polymeric probes in diverse imaging modes for the detection of various stimuli and their imaging applications. Finally, current challenges and future advances are discussed and highlighted.

Turn-on Fluorescent Biosensors for Imaging Hypoxia-like Conditions in Living Cells

We present the synthesis, photophysical properties, and biological application of nontoxic 3-azo-conjugated BODIPY dyes as masked fluorescent biosensors of hypoxia-like conditions. The synthetic methodology is based on an operationally simple N=N bond-forming protocol, followed by a Suzuki coupling, that allows for a direct access to simple and underexplored 3-azo-substituted BODIPY. These dyes can turn on their emission properties under both chemical and biological reductive conditions, including bacterial and human azoreductases, which trigger the azo bond cleavage, leading to fluorescent 3-amino-BODIPY. We have also developed a practical enzymatic protocol, using an immobilized bacterial azoreductase that allows for the evaluation of these azo-based probes and can be used as a model for the less accessible and expensive human reductase NQO1. Quantum mechanical calculations uncover the restructuration of the topography of the S₁ potential energy surface following the reduction of the azo moiety and rationalize the fluorescent quenching event through the mapping of an unprecedented pathway. Fluorescent microscopy experiments show that these azos can be used to visualize hypoxia-like conditions within living cells.

Enzyme assays with supramolecular chemosensors - the label-free approach

Enzyme activity measurements are essential for many research areas, e.g., for the identification of inhibitors in drug discovery, in bioengineering of enzyme mutants for biotechnological applications, or in bioanalytical chemistry as parts of biosensors. In particular in high-throughput screening (HTS), sensitive optical detection is most preferred and numerous absorption and fluorescence spectroscopy-based enzyme assays have been developed, which most frequently require time-consuming fluorescent labelling that may interfere with biological recognition. The use of supramolecular chemosensors, which can specifically signal analytes with fluorescence-based read-out methods, affords an attractive and label-free alternative to more established enzyme assays. We provide herein a comprehensive review that summarizes the current state-of-the-art of supramolecular enzyme assays ranging from early examples with covalent chemosensors to the most recent applications of supramolecular tandem enzyme assays, which utilize common and often commercially available combinations of macrocyclic host molecules (e.g. cyclodextrins, calixarenes, and cucurbiturils) and fluorescent dyes as self-assembled reporter pairs for assaying enzyme activity.

A preliminary study for the development of cleavable linkers using activatable fluorescent probes targeting leucine aminopeptidase

The Kinetic and ex vivo stability studies of LAP-responsive fluorescent probes demonstrated that the stability and intrinsic drug releasing activity of the cleavalbe linker can be evaluated by a peptidase-responsive activatable fluorescent probe.

qDNase assay: A quantitative method for real-time assessment of DNase activity on coated surfaces

DNase coatings show great potential to prevent biofilm formation in various applications of the medical implant, food and marine industry. However, straightforward and quantitative methods to characterize the enzymatic activity of these coatings are currently not available. We here introduce the qDNase assay, a quantitative, real-time method to characterize the activity of DNase coatings. The assay combines (1) the use of an oligonucleotide probe, which fluoresces upon cleavage by coated DNases, and (2) the continuous read-out of the fluorescent signal within a microplate fluorometer format. The combination of these two properties results in a real-time fluorescent signal that is used to directly quantify the activity of DNase coatings. As a proof of concept, bovine DNase I coatings were immobilized on titanium by means of chemical grafting and their activity was estimated at 3.87 × 10^-4 U. To our knowledge, the qDNase assay provides the first approach to report the activity of a DNase coating in absolute DNase activity units. This assay will not only serve to compare existing DNase coating methods more accurately, but will also enable the rational design of new DNase coating methods in the future.

Interaction of Cucurbit[7]uril With Protease Substrates: Application to Nanosecond Time-Resolved Fluorescence Assays

We report the use of the macrocyclic host cucurbit[7]uril (CB7) as a supramolecular additive in nanosecond time-resolved fluorescence (Nano-TRF) assays for proteases to enhance the discrimination of substrates and products and, thereby, the sensitivity. A peptide substrate was labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a long-lived (>300 ns) fluorescent probe and 3-nitrotyrosine was established as a non-fluorescent fluorescence resonance energy transfer (FRET) acceptor that acts as a “dark quencher.” The substrate was cleaved by the model proteases trypsin and chymotrypsin and the effects of the addition of CB7 to the enzyme assay mixture were investigated in detail using UV/VIS absorption as well as steady-state and time-resolved fluorescence spectroscopy. This also allowed us to identify the DBO and nitrotyrosine residues as preferential binding sites for CB7 and suggested a hairpin conformation of the peptide, in which the guanidinium side chain of an arginine residue is additionally bound to a vacant ureido rim of one of the CB7 hosts.

Fluorescence for biological logic gates

Biological logic gates are smart probes able to respond to biological conditions in behaviors similar to computer logic gates, and they pose a promising challenge for modern medicine. Researchers are creating many kinds of smart nanostructures that can respond to various biological parameters such as pH, ion presence, and enzyme activity. Each of these conditions alone might be interesting in a biological sense, but their interactions are what define specific disease conditions. Researchers over the past few decades have developed a plethora of stimuli-responsive nanodevices, from activatable fluorescent probes to DNA origami nanomachines, many explicitly defining logic operations. Whereas many smart configurations have been explored, in this review we focus on logic operations actuated through fluorescent signals. We discuss the applicability of fluorescence as a means of logic gate implementation, and consider the use of both fluorescence intensity as well as fluorescence lifetime.

Emerging Approaches for Fluorescence-Based Newborn Screening of Mucopolysaccharidoses

Interest in newborn screening for mucopolysaccharidoses (MPS) is growing, due in part to ongoing efforts to develop new therapies for these disorders and new screening assays to identify increased risk for the individual MPSs on the basis of deficiency in the cognate enzyme. Existing tests for MPSs utilize either fluorescence or mass spectrometry detection methods to measure biomarkers of disease (e.g., enzyme function or glycosaminoglycans) using either urine or dried blood spot (DBS) samples. There are currently two approaches to fluorescence-based enzyme function assays from DBS: (1) manual reaction mixing, incubation, and termination followed by detection on a microtiter plate reader; and (2) miniaturized automation of these same assay steps using digital microfluidics technology. This article describes the origins of laboratory assays for enzyme activity measurement, the maturation and clinical application of fluorescent enzyme assays for MPS newborn screening, and considerations for future expansion of the technology.

Sulfatase-cleavable linkers for antibody-drug conjugates

Antibody-drug conjugates (ADCs) are a class of targeted drug delivery agents combining the cell-selectivity of monoclonal antibodies (mAbs) and the cytotoxicity of small molecules. These two components are joined by a covalent linker, whose nature is critical to the efficacy and safety of the ADC. Enzyme-cleavable dipeptidic linkers have emerged as a particularly effective ADC linker type due to their ability to selectively release the payload in the lysosomes of target cells. However, these linkers have a number of drawbacks, including instability in rodent plasma and their inherently high hydrophobicity. Here we show that arylsulfate-containing ADC linkers are cleaved by lysosomal sulfatase enzymes to tracelessly release their payload, while circumventing the instability problems associated with dipeptide-linkers. When incorporated with trastuzumab and the highly potent monomethyl auristatin E (MMAE) payload, the arylsulfate-containing ADC 2 and ADC 3 were more cytotoxic than the non-cleavable ADC 4 against HER2-positive cells, while maintaining selectivity over HER2-negative cells. We propose that the stability, solubility and synthetic tractability of our arylsulfate linkers make them an attractive new motif for cleavable ADC linkers, with clear benefits over the widely used dipeptidic linkers.

Deeper insight into protease-sensitive "covalent-assembly" fluorescent probes for practical biosensing applications

We report a rational and systematic study devoted to the structural optimisation of a novel class of protease-sensitive fluorescent probes that we recently reported (S. Debieu and A. Romieu, Org. Biomol. Chem., 2017, 15, 2575-2584), based on the "covalent-assembly" strategy and using the targeted enzyme penicillin G acylase as a model protease to build a fluorescent pyronin dye by triggering a biocompatible domino cyclisation-aromatisation reaction. The aim is to identify ad hoc probe candidate(s) that might combine fast/reliable fluorogenic "turn-on" response, full stability in complex biological media and ability to release a second molecule of interest (drug or second fluorescent reporter), for applications in disease diagnosis and therapy. We base our strategy on screening a set of active methylene compounds (C-nucleophiles) to convert the parent probe to various pyronin caged precursors bearing Michael acceptor moieties of differing reactivities. In vitro stability and fluorescent enzymatic assays combined with HPLC-fluorescence analyses provide data useful for defining the most appropriate structural features for these fluorogenic scaffolds depending on the specifications inherent to biological application (from biosensing to theranostics) for which they will be used.

Environment-specific spectral modeling: A new tool for the analysis of biological specimens

The recent discovery of fluorescent dyes for improving pathologic tissues identification has highlighted the need of robust methods for performance validation especially in the field of fluorescence-guided surgery. Optical imaging of excised tissue samples is the reference tool to validate the association between dyes localization and the underlying histology in a controlled environment. Spectral unmixing may improve the validation process discriminating dye from endogenous signal. Here, an innovative spectral modeling approach that weights the spectral shifts associated with changes in chemical environment is described. The method is robust against spectral shift variations and its application leads to unbiased spectral weights estimates as demonstrated by numerical simulations. Finally, spectral shifts values computed pixel-wise from spectral images are used to display additional information with potential diagnostic value.

Smart fluorescent probes for in situ imaging of enzyme activity: design strategies and applications

Enzymes play critical roles in the physiological and pathological processes of living systems. To provide detailed pictures of enzyme activity at the molecular and cellular levels, interdisciplinary studies of chemistry and biology have led to the emergence of many smart fluorescent probes, which emit fluorescence or show a shifted signal only upon interaction with their targets. With distinct advantage of a higher signal-to-noise ratio than traditional ‘always on’ probes, smart fluorescent probes enable sensitive detection of enzymes with clinical significance. In this review, we summarize the design strategies and selected applications of smart fluorescent probes for in situ imaging of enzyme activity. Current challenges and future developments in this field are also discussed.

Fast and sensitive near-infrared fluorescent probes for ALP detection and 3d printed calcium phosphate scaffold imaging in vivo

Alkaline phosphatase (ALP) is a critical biological marker for osteoblast activity during early osteoblast differentiation, but few biologically compatible methods are available for its detection. Here, we describe the discovery of highly sensitive and rapidly responsive novel near-infrared (NIR) fluorescent probes (NIR-Phos-1, NIR-Phos-2) for the fluorescent detection of ALP. ALP cleaves the phosphate group from the NIR skeleton and substantially alters its photophysical properties, therefore generating a large "turn-on" fluorescent signal resulted from the catalytic hydrolysis on fluorogenic moiety. Our assay quantified ALP activity from 0 to 1.0UmL^-1 with a 10^-5-10^-3UmL^-1 limit of detection (LOD), showing a response rate completed within 1.5min. A potentially powerful approach to probe ALP activity in biological systems demonstrated real-time monitoring using both concentration- and time-dependent variations of endogenous ALP in live cells and animals. Based on high binding affinity to bone tissue of phosphate moiety, bone-like scaffold-based ALP detection in vivo was accessed using NIR probe-labeled three-dimensional (3D) calcium deficient hydroxyapatite (CDHA) scaffolds. They were subcutaneously implanted into mice and monitored ALP signal changes using a confocal imaging system. Our results suggest the possibility of early-stage ALP detection during neo-bone formation inside a bone defect, by in vivo fluorescent evaluation using 3D CDHA scaffolds.

In situ formation of pyronin dyes for fluorescence protease sensing

A cutting-edge strategy for fluorogenic sensing of proteases (leucine aminopeptidase for the proof of concept) and based on the “covalent-assembly” principle is reported. Non-fluorescent mixed bis-aryl ethers are readily converted into a fluorescent pyronin through a domino process triggered by the peptide bond cleavage event caused by the targeted enzyme.

Highly selective and rapidly activatable fluorogenic Thrombin sensors and application in human lung tissue

A fast and selective fluorogenic probe for Thrombin is reported and applied in ex vivo fibrotic human lung tissue.

Fluorescence switchable probes based on a molecular rotor for selective detection of proteins and small molecules

In this communication, we report a general strategy to create fluorescence switchable probes, where a small molecule ligand is conjugated to a fluorescent molecular rotor, for the selective detection of proteins through a non-enzymatic process. In the presence of target proteins, bond rotation of the molecular rotor is restricted, thereby triggering the emission of strong fluorescence.

Nanomaterial-based activatable imaging probes: from design to biological applications

Activatable imaging probes as alternatives to "always on" imaging probes have attracted more and more attention due to their improved sensitivity and specificity. They are commonly designed to amplify or boost imaging signals only in response to specific biomolecular recognition or interaction. Thus, the design strategies play a vital role in the fabrication of activatable imaging probes. In this review, we focus on the design mechanisms and biological applications of those nanomaterial-based activatable imaging probes reported in the past five years, benefitting greatly from the good development of nanotechnology. These probes not only include the most studied activatable fluorescence imaging probes, but also cover more activatable MR imaging probes based on nanoparticle contrast agents and activatable photoacoustic imaging probes, providing more bases for clinical translation.

Two-Photon Small Molecule Enzymatic Probes

Enzymes are essential for life, especially in the development of disease and on drug effects, but as we cannot yet directly observe the inside interactions and only partially observe biochemical outcomes, tools "translating" these processes into readable information are essential for better understanding of enzymes as well as for developing effective tools to fight against diseases. Therefore, sensitive small molecule probes suitable for direct in vivo monitoring of enzyme activities are ultimately desirable. For fulfilling this desire, two-photon small molecule enzymatic probes (TSMEPs) producing amplified fluorescent signals based on enzymatic conversion with better photophysical properties and deeper penetration in intact tissues and whole animals have been developed and demonstrated to be powerful in addressing the issues described above. Nonetheless, currently available TSMEPs only cover a small portion of enzymes despite the distinct advantages of two-photon fluorescence microscopy. In this Account, we would like to share design principles for TSMEPs as potential indicators of certain pathology-related biomarkers together with their applications in disease models to inspire more elegant work to be done in this area. Highlights will be addressed on how to equip two-photon fluorescent probes with features amenable for direct assessment of enzyme activities in complex pathological environments. We give three recent examples from our laboratory and collaborations in which TSMEPs are applied to visualize the distribution and activity of enzymes at cellular and organism levels. The first example shows that we could distinguish endogenous phosphatase activity in different organelles; the second illustrates that TSMEP is suitable for specific and sensitive detection of a potential Parkinson's disease marker (monoamine oxidase B) in a variety of biological systems from cells to patient samples, and the third identifies that TSMEPs can be applied to other enzyme families (proteases). Indeed, TSMEPs have helped to uncover new biological roles and functions of a series of enzymes; therefore, we hope to encourage more TSMEPs to be developed for diverse enzymes. Meanwhile, improvements in the TSMEP properties (such as new two-photon fluorophores with longer excitation and emission wavelengths and strategies allowing high specificity) are also indispensable for producing high-fidelity information inside biological systems. We are enthusiastic however that, with these efforts and wider applications of TSMEPs in both research studies and further clinical diagnoses, comprehensive knowledge of enzyme contributions to various physiologies will be obtained.

An ultra-sensitive dual-mode imaging system using metal-enhanced fluorescence in solid phantoms

In this study we developed a highly sensitive dual modal imaging system designed for gold nanoparticles (GNPs) conjugated to various fluorophores in solid phantoms. The system consists of fluorescence lifetime imaging microscopy (FLIM) for surface imaging, diffusion reflection (DR) for deep tissue imaging (up to 1cm), and metal enhanced fluorescence (MEF). We detected quenching in fluorescent intensity (FI) for the conjugation of gold nanospheres (GNS) as well as gold nanorods (GNRs) to Fluorescein, which has an excitation peak at a wavelength shorter than the surface plasmon resonance (SPR) of both types of GNPs, and enhanced FI in conjugation to Rhodamine B and Sulforhodamine B, both with excitation peaks in the GNPs' SPR. The enhanced FI was detected in solution as well as in solid phantoms from FLIM measurements. DR measurements detected GNR presence within the solid phantoms by recording dropped rates of light scattering using wavelengths corresponding to the GNRs' absorption. With the inclusion of MEF, this promising dual modal imaging technique enables efficient and sensitive molecular and functional imaging.

Towards aspirin-inspired self-immolating molecules which target the cyclooxygenases

Cyclooxygenases (COXs) are enzymes that play a vital role in the inflammatory cascade through the generation of prostaglandins. Their over-expression has been implicated in numerous diseases. In particular, over-expression of COX-2 has been shown to be a predictive biomarker for progression of pre-malignant lesions towards invasive cancer in various tissues. This makes the early detection of COX-2 expressing lesions of high clinical relevance. Herein we describe the development of the first self-immolating trigger which targets COXs. We incorporated our trigger design into 2 activatable fluorogenic probes and demonstrated COX-specific activation in vitro. Experimental data revealed probe activation was likely caused by solvent-exposed amino acids on the surface of the COXs. Overall, the probes reported here mark the first step towards developing self-immolating imaging/therapeutic agents targeted to specific COXs.

Recent advances in the development of synthetic chemical probes for glycosidase enzymes

The emergence of synthetic glycoconjugates as chemical probes for the detection of glycosidase enzymes has resulted in the development of a range of useful chemical tools with applications in glycobiology, biotechnology, medical and industrial research. Critical to the function of these probes is the preparation of substrates containing a glycosidic linkage that when activated by a specific enzyme or group of enzymes, irreversibly releases a reporter molecule that can be detected. Starting from the earliest examples of colourimetric probes, increasingly sensitive and sophisticated substrates have been reported. In this review we present an overview of the recent advances in this field, covering an array of strategies including chromogenic and fluorogenic substrates, lanthanide complexes, gels and nanoparticles. The applications of these substrates for the detection of various glycosidases and the scope and limitations for each approach are discussed.

Enzyme-Specific Doxorubicin Drug Beacon as Drug-Resistant Theranostic Molecular Probes

We report here on the use of anticancer drug doxorubicin (Dox) to construct a Förster resonance energy transfer (FRET)-based theranostic molecular probe by covalently linking together through a lysine junction a fluorescent drug, a black hole quencher, and a cell-penetrating peptide. We show that upon cleavage by the target lysosomal protease cathepsin B (CatB) the designed drug beacon could release the fluorescent drug serving as an indicator for CatB. Our cell studies suggest that the drug-beacon design can help to circumvent the Dox drug resistance in NCI/ADR-Res ovarian cancer cells, showing significant improvement in cell cytotoxicity compared to the free drug. We believe our design opens up new opportunities to exploit the new functional and structural features of anticancer drugs in addition to their characteristic cytotoxicity.

MMP-2/9-Specific Activatable Lifetime Imaging Agent

Optical (molecular) imaging can benefit from a combination of the high signal-to-background ratio of activatable fluorescence imaging with the high specificity of luminescence lifetime imaging. To allow for this combination, both imaging techniques were integrated in a single imaging agent, a so-called activatable lifetime imaging agent. Important in the design of this imaging agent is the use of two luminophores that are tethered by a specific peptide with a hairpin-motive that ensured close proximity of the two while also having a specific amino acid sequence available for enzymatic cleavage by tumor-related MMP-2/9. Ir(ppy)3 and Cy5 were used because in close proximity the emission intensities of both luminophores were quenched and the influence of Cy5 shortens the Ir(ppy)3 luminescence lifetime from 98 ns to 30 ns. Upon cleavage in vitro, both effects are undone, yielding an increase in Ir(ppy)3 and Cy5 luminescence and a restoration of Ir(ppy)3 luminescence lifetime to 94 ns. As a reference for the luminescence activation, a similar imaging agent with the more common Cy3-Cy5 fluorophore pair was used. Our findings underline that the combination of enzymatic signal activation with lifetime imaging is possible and that it provides a promising method in the design of future disease specific imaging agents.

Detecting enzyme activities with exogenous MRI contrast agents

This review focuses on exogenous magnetic resonance imaging (MRI) contrast agents that are responsive to enzyme activity. Enzymes can catalyze a change in water access, rotational tumbling time, the proximity of a (19)F-labeled ligand, the aggregation state, the proton chemical-exchange rate between the agent and water, or the chemical shift of (19)F, (31)P, (13)C or a labile (1)H of an agent, all of which can be used to detect enzyme activity. The variety of agents attests to the creativity in developing enzyme-responsive MRI contrast agents.

Bright building blocks for chemical biology

Small-molecule fluorophores manifest the ability of chemistry to solve problems in biology. As we noted in a previous review (Lavis, L. D.; Raines, R. T. ACS Chem. Biol. 2008, 3, 142-155), the extant collection of fluorescent probes is built on a modest set of "core" scaffolds that evolved during a century of academic and industrial research. Here, we survey traditional and modern synthetic routes to small-molecule fluorophores and highlight recent biological insights attained with customized fluorescent probes. Our intent is to inspire the design and creation of new high-precision tools that empower chemical biologists.

Photoacoustic lifetime contrast between methylene blue monomers and self-quenched dimers as a model for dual-labeled activatable probes

Activatable photoacoustic probes efficiently combine the high spatial resolution and penetration depth of ultrasound with the high optical contrast and versatility of molecular imaging agents. Our approach is based on photoacoustic probing of the excited-state lifetime of methylene blue (MB), a fluorophore widely used in clinical therapeutic and diagnostic applications. Upon aggregation, static quenching between the bound molecules dramatically shortens their lifetime by three orders of magnitude. We present preliminary results demonstrating the ability of photoacoustic imaging to probe the lifetime contrast between monomers and dimers with high sensitivity in cylindrical phantoms. Gradual dimerization enhancement, driven by the addition of increasing concentrations of sodium sulfate to a MB solution, showed that lifetime-based photoacoustic probing decreases linearly with monomer concentration. Similarly, the addition of 4 mM sodium dodecyl sulfate, a concentration that amplifies MB aggregation and reduces the monomer concentration by more than 20-fold, led to a signal decrease of more than 20 dB compared to a solution free of surfactant. These results suggest that photoacoustic imaging can be used to selectively detect the presence of monomers. We conclude by discussing the implementation of the monomer-dimer contrast mechanism for the development of an enzyme-specific activatable probe.

The chemistry of small-molecule fluorogenic probes

Chemical fluorophores find wide use in biology to detect and visualize different phenomena. A key advantage of small-molecule dyes is the ability to construct compounds where fluorescence is activated by chemical or biochemical processes. Fluorogenic molecules, in which fluorescence is activated by enzymatic activity, light, or environmental changes, enable advanced bioassays and sophisticated imaging experiments. Here, we detail the collection of fluorophores and highlight both general strategies and unique approaches that are employed to control fluorescence using chemistry.