Systematic investigation of the aza-Cope reaction for fluorescence imaging of formaldehyde in vitro and in vivo

Development of a urea-bond cleavage reaction induced by nitric oxide for fluorescence imaging

Nitric oxide (NO) is a multifunctional signalling molecule with indispensable roles in physiological processes, but its abnormal production is implicated in various disease conditions. Detecting NO is crucial for interrogating its biological roles. Although many o-phenylenediamine-based fluorescent probes have been developed, only a small fraction has been employed in vivo. Moreover, these probes largely require direct modifications of the fluorophore backbones to render NO responsiveness, which restricts the general applicability of o-phenylenediamine-based probe designs to other types of fluorophores. Here, we report the rational development, optimization, and application of a NO-induced urea-bond cleavage reaction for selective fluorescence detection and imaging of NO in living systems. Through rational design and extensive screening, we identified a 2-aminophenylurea-derived functionality that can react with NO through N-nitrosation, acyltriazole formation, and hydrolysis to induce the cleavage of the urea bond and release of the amino-containing coumarin fluorophore. By caging different amino-containing fluorophore scaffolds with the 2-aminophenylurea-derived functionality, we modularly developed a series of NO fluorescent probes with different excitation and emission profiles for the detection of NO in aqueous solutions and live cells. Among these probes, the near-infrared probe has been demonstrated to enable in vivo fluorescence visualization of elevated endogenous levels of NO in a murine inflammation model. Overall, this study provides a NO-induced urea-bond cleavage reaction and establishes the utility of this reaction for the general and modular development of NO fluorescent probes, thus opening new opportunities for studying and manipulating NO in biological systems.

Formaldehyde quantification using gas chromatography-mass spectrometry reveals high background environmental formaldehyde levels

Formaldehyde (HCHO) is a human toxin that is both a pollutant and endogenous metabolite. HCHO concentrations in human biological samples are reported in the micromolar range; however, accurate quantification is compromised by a paucity of sensitive analysis methods. To address this issue, we previously reported a novel SPME-GC-MS-based HCHO detection method using cysteamine as an HCHO scavenger. This method showed cysteamine to be a more efficient scavenger than the widely used O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine, and enabled detection of aqueous HCHO in the nanomolar range and quantification in the micromolar range. However, quantification in this range required immersive extraction of the HCHO-derived thiazolidine, while a high background signal was also observed. Following on from these studies, we now report an optimised head-space extraction SPME-GC-MS method using cysteamine, which provides similarly sensitive HCHO quantification to the immersive method but avoids extensive wash steps and is therefore more amenable to screening applications. However, high background HCHO levels were still observed A Complementary GC-MS analyses using a 2-aza-Cope-based HCHO scavenger also revealed high background HCHO levels; therefore, the combined results suggest that HCHO exists in high (i.e. micromolar) concentration in aqueous samples that precludes accurate quantification below the micromolar range. This observation has important implications for ongoing HCHO quantification studies in water, including in biological samples.

Progress in the Study of Optical Probes for the Detection of Formaldehyde

Formaldehyde, one of the simplest reactive carbonyl substances, is involved in many physiological and pathological processes in living organisms. There is a large amount of data showing that abnormal elevation of formaldehyde is associated with a variety of diseases in the body, such as neurodegenerative diseases, Alzheimer's disease, cardiovascular diseases and cancer, and is also a representative carcinogen, so monitoring formaldehyde is of great importance for disease diagnosis and treatment. In this review, In this paper, we summarize and classify the last ten years of probes for the detection of formaldehyde according to different reaction mechanisms and discuss the structures and applications of the probes. Finally, we briefly describe the challenges and possible solutions in this field. We believe that more new probes provide powerful tools to study the function of formaldehyde in living systems.

Modular Development of Enzyme-Activatable Proteolysis Targeting Chimeras for Selective Protein Degradation and Cancer Targeting

As an emerging therapeutic modality, proteolysis targeting chimeras (PROTACs) indiscriminately degrade proteins in both healthy and diseased cells, posing a risk of on-target off-site toxicity in normal tissues. Herein, we present the modular development of enzyme-activatable PROTACs, which utilize enzyme-recognition moieties to block protein degradation activities and can be specifically activated by elevated enzymes in cancer cells to enable cell-selective protein degradation and cancer targeting. We identified the methylene alkoxy carbamate (MAC) unit as an optimal self-immolative linker, possessing high stability and release efficiency for conjugating enzyme-recognition moieties with PROTACs. Leveraging the MAC linker, we developed a series of enzyme-activatable PROTACs, harnessing distinct enzymes for cancer-cell-selective protein degradation. Significantly, we introduced the first dual-enzyme-activatable PROTAC that requires the presence of two cancer-associated enzymes for activation, demonstrating highly selective protein degradation in cancer cells over nonmalignant cells, potent in vivo antitumor efficacy, and no off-tumor toxicity to normal tissues. The broad applicability of enzyme-activatable PROTACs was further demonstrated by caging other PROTACs via the MAC linker to target different proteins and E3 ligases. Our work underscores the substantial potential of enzyme-activatable PROTACs in overcoming the off-site toxicity associated with conventional PROTACs and offers new opportunities for targeted cancer treatment.

Modular development of organelle-targeting fluorescent probes for imaging formaldehyde in live cells

Formaldehyde (FA) is endogenously generated via fundamental biological processes in living systems. Aberrant FA homeostasis in subcellular microenvironments is implicated in numerous pathological conditions. Fluorescent probes for detecting FA in specific organelles are thus of great research interest. Herein, we present a modular strategy to construct diverse organelle-targeting FA probes by incorporating selective organelle-targeting moieties into the scaffold of a 1,8-naphthalimide-derived FA fluorescent probe. These probes react with FA through the 2-aza-Cope arrangement and exhibit highly selective fluorescence increases for detecting FA in aqueous solutions. Moreover, these organelle-targeting probes, i.e., FFP551-Nuc, FFP551-ER, FFP551-Mito, and FFP551-Lyso, allow selective localization and imaging of FA in the nucleus, endoplasmic reticulum, mitochondria, and lysosomes of live mammalian cells, respectively. Furthermore, FFP551-Nuc has been successfully employed to monitor changes of endogenous FA levels in the nucleus of live mammalian cells. Overall, these probes should represent new imaging tools for studying the biology and pathology associated with FA in different intracellular compartments.

A mitochondrial-targeted activity-based sensing probe for ratiometric imaging of formaldehyde reveals key regulators of the mitochondrial one-carbon pool

Formaldehyde (FA) is both a highly reactive environmental genotoxin and an endogenously produced metabolite that functions as a signaling molecule and one-carbon (1C) store to regulate 1C metabolism and epigenetics in the cell. Owing to its signal-stress duality, cells have evolved multiple clearance mechanisms to maintain FA homeostasis, acting to avoid the established genotoxicity of FA while also redirecting FA-derived carbon units into the biosynthesis of essential nucleobases and amino acids. The highly compartmentalized nature of FA exposure, production, and regulation motivates the development of chemical tools that enable monitoring of transient FA fluxes with subcellular resolution. Here we report a mitochondrial-targeted, activity-based sensing probe for ratiometric FA detection, MitoRFAP-2, and apply this reagent to monitor endogenous mitochondrial sources and sinks of this 1C unit. We establish the utility of subcellular localization by showing that MitoRFAP-2 is sensitive enough to detect changes in mitochondrial FA pools with genetic and pharmacological modulation of enzymes involved in 1C and amino acid metabolism, including the pervasive, less active genetic mutant aldehyde dehydrogenase 2*2 (ALDH2*2), where previous, non-targeted versions of FA sensors are not. Finally, we used MitoRFAP-2 to comparatively profile basal levels of FA across a panel of breast cancer cell lines, finding that FA-dependent fluorescence correlates with expression levels of enzymes involved in 1C metabolism. By showcasing the ability of MitoRFAP-2 to identify new information on mitochondrial FA homeostasis, this work provides a starting point for the design of a broader range of chemical probes for detecting physiologically important aldehydes with subcellular resolution and a useful reagent for further studies of 1C biology.

Recent Advances in Electrochemical Sensors for Formaldehyde

Formaldehyde, a ubiquitous indoor air pollutant, plays a significant role in various biological processes, posing both environmental and health challenges. This comprehensive review delves into the latest advancements in electrochemical methods for detecting formaldehyde, a compound of growing concern due to its widespread use and potential health hazards. This review underscores the inherent advantages of electrochemical techniques, such as high sensitivity, selectivity, and capability for real-time analysis, making them highly effective for formaldehyde monitoring. We explore the fundamental principles, mechanisms, and diverse methodologies employed in electrochemical formaldehyde detection, highlighting the role of innovative sensing materials and electrodes. Special attention is given to recent developments in nanotechnology and sensor design, which significantly enhance the sensitivity and selectivity of these detection systems. Moreover, this review identifies current challenges and discusses future research directions. Our aim is to encourage ongoing research and innovation in this field, ultimately leading to the development of advanced, practical solutions for formaldehyde detection in various environmental and biological contexts.

Ratiometric Lysosome-targeting Luminescent Probe Based on a Coumarin-Ruthenium(II) Complex for Formaldehyde Detection and Imaging in Living Cells and Mouse Brain Tissues

Ratiometric luminescence probes have attracted widespread attention because of their self-calibration capability. However, some defects, such as small emission shift, severe spectral overlap and poor water solubility, limit their application in the field of biological imaging. In this study, a unique luminescence probe, Ru-COU, has been developed by combining tris(bipyridine)ruthenium(II) complex with coumarin derivative through a formaldehyde-responsive linker. The probe exhibited a large emission shift (Δλ>100 nm) and good water solubility, achieving ratiometric emission responses at 505 nm and 610 nm toward formaldehyde under acidic conditions. Besides, ratiometric luminescence imaging of formaldehyde in living cells and Alzheimer disease mouse's brain slices demonstrates the potential value of Ru-COU for the diagnosis and treatment of formaldehyde related diseases.

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.

Tunable Electrochemical Peptide Modifications: Unlocking New Levels of Orthogonality for Side-Chain Functionalization

Electrochemical transformations provide enticing opportunities for programmable, residue-specific peptide modifications. Herein, we harness the potential of amidic side-chains as underutilized handles for late-stage modification through the development of an electroauxiliary-assisted oxidation of glutamine residues within unprotected peptides. Glutamine building blocks bearing electroactive side-chain N,S-acetals are incorporated into peptides using standard Fmoc-SPPS. Anodic oxidation of the electroauxiliary in the presence of diverse alcohol nucleophiles enables the installation of high-value N,O-acetal functionalities. Proof-of-principle for an electrochemical peptide stapling protocol, as well as the functionalization of dynorphin B, an endogenous opioid peptide, demonstrates the applicability of the method to intricate peptide systems. Finally, the site-selective and tunable electrochemical modification of a peptide bearing two discretely oxidizable sites is achieved.

Systematic Screening of Trigger Moieties for Designing Formaldehyde Fluorescent Probes and Application in Live Cell Imaging

Formaldehyde (FA) is involved in multiple physiological regulatory processes and plays a crucial role in memory storage. Meanwhile, FA has a notorious reputation as a toxic compound, and it will cause a variety of diseases if its level is unbalanced in the human body. To date, there have been numerous fluorescent probes for FA imaging reported. Among them, the probes based on the 2-aza-Cope rearrangement have attracted the most attention, and their applications in cell imaging have been greatly expanded. Herein, we screened the various trigger moieties of FA fluorescent probes based on the mechanism of 2-aza-Cope rearrangement. FA-2, in which a fluorophore is connected to a 4-nitrobenzylamine group and an allyl group, demonstrated the highest sensitivity, selectivity, and reaction kinetics. Furthermore, FA-Lyso, derived from FA-2, has been successfully designed and applied to monitor exogenous and endogenous FA fluctuations in lysosomes of living cells.

Rhodamine-based cyclic hydrazide derivatives as fluorescent probes for selective and rapid detection of formaldehyde

We describe fluorescent probes to detect formaldehyde (FA) in aqueous solutions and cells. The probes rapidly respond to FA in aqueous solutions and have great selectivity toward FA over other biologically relevant analytes. The results of cell studies reveal that probe 1 can be utilized to monitor endogenous and exogenous FA in live cells.

Photo-Responsive Micelles with Controllable and Co-Release of Carbon Monoxide, Formaldehyde and Doxorubicin

Endogenous gases have attracted much attention due to their potent applications in disease therapies. The combined therapy, including gaseous molecules and other medicines that can create synergistic effects, is a new way for future treatment. However, due to the gaseous state, gas utilization in medical service is still limited. To pave the way for future usage, in this work, an amphiphilic block copolymer containing nitrobenzyl ether, 3-hydroxyflavone (3-HF) derivatives and ether linker was constructed. The nitrobenzyl ether group endows the polymer with a photo-responsive character. Upon light illumination, 3-HF derivatives can be triggered for carbon monoxide (CO) release. The ether linker can also be released emitting formaldehyde (FA). The self-assembly induced micelle can encompass medicine, e.g., doxorubicin (DOX), into it and a controlled release of DOX can be realized upon light illumination. As far as we know, there is no report on the combination donor of CO and DOX and this is the first attempt on the co-release of CO, FA and DOX.

Approaches to Formaldehyde Measurement: From Liquid Biological Samples to Cells and Organisms

Formaldehyde (FA) is the simplest aldehyde present both in the environment and in living organisms. FA is an extremely reactive compound capable of protein crosslinking and DNA damage. For a long time, FA was considered a "biochemical waste" and a by-product of normal cellular metabolism, but in recent decades the picture has changed. As a result, the need arose for novel instruments and approaches to monitor and measure not only environmental FA in water, cosmetics, and household products, but also in food, beverages and biological samples including cells and even organisms. Despite numerous protocols being developed for in vitro and in cellulo FA assessment, many of them have remained at the "proof-of-concept" stage. We analyze the suitability of different methods developed for non-biological objects, and present an overview of the recently developed approaches, including chemically-synthesized probes and genetically encoded FA-sensors for in cellulo and in vivo FA monitoring. We also discuss the prospects of classical methods such as chromatography and spectrophotometry, and how they have been adapted in response to the demand for precise, selective and highly sensitive evaluation of FA concentration fluctuations in biological samples. The main objectives of this review is to summarize data on the main approaches for FA content measurement in liquid biological samples, pointing out the advantages and disadvantages of each method; to report the progress in development of novel molecules suitable for application in living systems; and, finally, to discuss genetically encoded FA-sensors based on existing natural biological FA-responsive elements.

Quinolizinium-based fluorescent probes for formaldehyde detection in aqueous solution, serum, and test strip via 2-aza-Cope rearrangement

Formaldehyde is an abundant contaminant in food and environments causing various diseases. Thus, the development of fast, simple, and selective formaldehyde detection is of great interest. Herein, novel quinolizinium-based fluorescent probes were designed based on a 2-aza-Cope rearrangement reaction and showed high selectivity to formaldehyde by fluorescence emission shift. We successfully reduced the detection time by increasing the bulkiness of the homoallylic moiety. The probes were applied to detect formaldehyde in aqueous solution, serum, and paper format.

Reaction-based fluorescent and chemiluminescent probes for formaldehyde detection and imaging

Formaldehyde (FA), a reactive carbonyl species, is classified as Group 1 carcinogen by International Agency for Research on Cancer (IARC) in 2004. In addition, clinical studies have implicated that elevated levels of FA have been associated with different kinds of diseases, such as neurodegenerative diseases, diabetes, and chronic liver and heart disorders. However, in addition to the direct inhalation of FA in the environment, most organisms can also produce FA endogenously by demethylases and oxidases during the metabolism of amino acids and xenobiotics. Since FA plays an important role in physiological and pathological processes, developing reliable and efficient methods to monitor FA levels in biological samples is crucial. Reaction-based fluorescent/chemiluminescent probes have provided robust methods for FA detection and real-time visualization in living organisms. In this highlight, we will summarize the major developments in the structure design and applications of FA probes in recent years. Three main strategies for designing FA probes have been discussed and grouped by different reaction mechanisms. In addition, some miscellaneous reaction mechanisms have also been discussed. We also highlight novel applications of these probes in biological systems, which offer powerful tools to discover the diverse functions of FA in physiology and pathology processes.