Design of Fluorescent Probes for Bioorthogonal Labeling of Carbonylation in Live Cells

Small-Molecule Probe for Imaging Oxidative Stress-Induced Carbonylation in Live Cells

Protein carbonylation has been known as the major form of irreversible protein modifications and is also widely used as an indicator of oxidative stress in the biological environment. In the presence of oxidative stress, biological systems tend to produce large amounts of carbonyl moieties; these carbonyl groups do not have particular UV-Vis and fluorescence spectroscopic characteristics that we can differentiate, observe, and detect. Thus, their detection and quantification can only be performed using specific chemical probes. Commercially available fluorescent probes to detect specific carbonylation in biological systems have been used, but their chemical portfolio is still very limited. This protocol outlines the methods and procedures employed to synthesize a probe, (E,Z)-2-(2-(2-hydroxybenzylidene)hydrazonyl)-5-nitrophenol (2Hzin5NP), and assess its impact on carbonylation in human cells. The synthesis involves several steps, including the preparation of its hydrazone compounds mimicking cell carbonyls, 2-Hydrazinyl 5-nitrophenol, (E,Z)-2-(2-ethylidenehydrazonyl)-5-nitrophenol, and the final product (E,Z)-2-(2-(2-hydroxybenzylidene)hydrazonyl)-5-nitrophenol. The evaluation of fluorescence quantum yield and subsequent cell culture experiments are detailed for the investigation of 2Hzin5NP effects on cell proliferation and carbonylation. Key features • This protocol builds upon probe development using click chemistry method by Dilek et al. [1], and its biolabeling application in renal cancer cell lines. • The non-fluorescent probe has a fast reaction with carbonyl moieties at neutral pH to form a stable fluorescent product leading to a spectroscopic alteration. • Microscopic and fluorometric analyses can distinguish the exogenous and endogenous ROS-induced carbonylation profile in human dermal fibroblasts along with renal cell carcinoma. • Carbonylation level that differs in response to exogenous and endogenous stress in healthy and cancer cells can be detected by the newly synthesized fluorescent probe.

Current Probes for Imaging Carbonylation in Cellular Systems and Their Relevance to Progression of Diseases

Oxidative stress resulted from reactive oxygen or nitrogen species in biological systems has a significant role in the diagnosis/progression of several human diseases. Human diseases associated with oxidative stress include Alzheimer's disease, chronic lung disease, chronic renal failure, cancer, diabetes, and fibrosis. In oxidative stress conditions, carbonylation process can be described as one of the most common modifications in biomolecules that takes place in the presence of carbonyl (C = O) groups which are introduced into molecules by direct metal-catalyzed oxidation of certain amino acids or indirectly by reaction with the oxidation of lipids and sugars. At a molecular cellular level, carbonylation can cause some defective biological consequences or chemical transformations in cells. During this process, specifically, carbonylated proteins can be accumulated in cells and trigger to develop some diseases in human body. The role of the accumulation of carbonylated proteins in the progression of several diseases has also been reported in the literature, such as neurodegenerative diseases, diabetes, obesity, aging, and cancer. Early detection of carbonylation process is, therefore, very critical to monitor these diseases at an early stage. Finding a suitable biomarker or probe is very challenging due to the need for multiple criteria: high fluorescence efficiency, stability, toxicity, and permeability. If they are designed with a good strategy, these probes are highly effective in cell biology applications and they can be used as good diagnostic tools for monitoring oxidative stress-induced carbonylation in relevant diseases. This review highlights the design and use of recent fluorescent probes for visualization of carbonylation in cellular systems and the relationship between oxidative stress and carbonyl species for causing long-term disease complications.

Research Progress and Application of Bioorthogonal Reactions in Biomolecular Analysis and Disease Diagnosis

Bioorthogonal reactions are rapid, specific and high yield reactions that can be performed in in vivo microenvironments or simulated microenvironments. At present, the main biorthogonal reactions include Staudinger ligation, copper-catalyzed azide alkyne cycloaddition, strain-promoted [3 + 2] reaction, tetrazine ligation, metal-catalyzed coupling reaction and photo-induced biorthogonal reactions. To date, many reviews have reported that bioorthogonal reactions have been used widely as a powerful tool in the field of life sciences, such as in target recognition, drug discovery, drug activation, omics research, visualization of life processes or exogenous bacterial infection processes, signal transduction pathway research, chemical reaction dynamics analysis, disease diagnosis and treatment. In contrast, to date, few studies have investigated the application of bioorthogonal reactions in the analysis of biomacromolecules in vivo. Therefore, the application of bioorthogonal reactions in the analysis of proteins, nucleic acids, metabolites, enzyme activities and other endogenous molecules, and the determination of disease-related targets is reviewed. In addition, this review discusses the future development opportunities and challenges of biorthogonal reactions. This review presents an overview of recent advances for application in biomolecular analysis and disease diagnosis, with a focus on proteins, metabolites and RNA detection.

Retro Diels-Alder Fragmentation of Fulvene-Maleimide Bioconjugates for Mass Spectrometric Detection of Biomolecules

Diels-Alder chemistry is a well-explored avenue for the synthesis of bioactive materials; however, its potential applications have recently expanded following the development of reactions that can be performed in buffered aqueous environments at low temperatures, including fulvene-maleimide [4 + 2] cycloadditions. In this study, we synthesized two novel amine-reactive fulvene linkers to demonstrate the application of this chemistry for generating mass spectrometry-cleavable labels ("mass tags"), which can be used for the labeling and detection of proteins. Successful conjugation of these linkers to maleimide-labeled peptides was observed at low temperatures in phosphate-buffered saline, allowing the non-destructive modification of proteins with such mass tags. The labile nature of fulvene-maleimide adducts in the gas phase also makes them suitable for both matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrometric analysis. Unlike previous examples of MALDI mass tags, we show that fulvene-maleimide cycloaddition adducts fragment predictably upon gas-phase activation without the need for bulky photocleavable groups. Further exploration of this chemistry could therefore lead to new approaches for mass spectrometry-based bioassays.

A Novel Fluorogenic Assay for the Detection of Nephrotoxin-Induced Oxidative Stress in Live Cells and Renal Tissue

Drug-induced kidney injury frequently leads to aborted clinical trials and drug withdrawals. Sufficiently sensitive sensors capable of detecting mild signs of chemical insult in cell-based screening assays are critical to identifying and eliminating potential toxins in the preclinical stage. Oxidative stress is a common early manifestation of chemical toxicity, and biomolecule carbonylation is an irreversible repercussion of oxidative stress. Here, we present a novel fluorogenic assay using a sensor, TFCH, that responds to biomolecule carbonylation and efficiently detects modest forms of renal injury with much greater sensitivity than standard assays for nephrotoxins. We demonstrate that this sensor can be deployed in live kidney cells and in renal tissue. Our robust assay may help inform preclinical decisions to recall unsafe drug candidates. The application of this sensor in identifying and analyzing diverse pathologies is envisioned.