A Photocrosslinking Probe to Capture the Substrates of Caseinolytic Protease P

Protein homeostasis in bacteria is regulated by proteases such as the tetradecameric caseinolytic protease P (ClpP). Although substrates of ClpP have been successfully deciphered in genetically engineered cells, methods which directly trap processed proteins within native cells remain elusive. Here, we introduce an in situ trapping strategy which utilizes trifunctional probes that bind to the active site serine of ClpP and capture adjacent substrates with an attached photocrosslinking moiety. After enrichment using an alkyne handle, substrate deconvolution by mass spectrometry (MS) is performed. We show that our two traps bind substoichiometrically to ClpP, retain protease activity, exhibit unprecedented selectivity for Staphylococcus aureus ClpP in living cells and capture numerous known and novel substrates. The exemplary validation of trapped hits using a targeted proteomics approach confirmed the fidelity of this technology. In conclusion, we provide a novel chemical platform suited for the discovery of serine protease substrates beyond genetic engineering.

Activity-Based Fluorescent Probes for Hydrogen Sulfide and Related Reactive Sulfur Species

Hydrogen sulfide (H2S) is not only a well-established toxic gas but also an important small molecule bioregulator in all kingdoms of life. In contemporary biology, H2S is often classified as a "gasotransmitter," meaning that it is an endogenously produced membrane permeable gas that carries out essential cellular processes. Fluorescent probes for H2S and related reactive sulfur species (RSS) detection provide an important cornerstone for investigating the multifaceted roles of these important small molecules in complex biological systems. A now common approach to develop such tools is to develop "activity-based probes" that couple a specific H2S-mediated chemical reaction to a fluorescent output. This Review covers the different types of such probes and also highlights the chemical mechanisms by which each probe type is activated by specific RSS. Common examples include reduction of oxidized nitrogen motifs, disulfide exchange, electrophilic reactions, metal precipitation, and metal coordination. In addition, we also outline complementary activity-based probes for imaging reductant-labile and sulfane sulfur species, including persulfides and polysulfides. For probes highlighted in this Review, we focus on small molecule systems with demonstrated compatibility in cellular systems or related applications. Building from breadth of reported activity-based strategies and application, we also highlight key unmet challenges and future opportunities for advancing activity-based probes for H2S and related RSS.

A photo-responsive fluorescent amphiphile for target-specific and image-guided drug delivery applications

Multifunctional drug delivery systems are the centerpiece of effective chemotherapeutic strategies. Herein, we report the synthesis of an acetazolamide-linked cyanine-3-based NIR-responsive fluorescent macrocyclic amphiphile that self-assembled into spherical nanostructures in the aqueous medium via a J-aggregation pattern. The amphiphile shows various favorable properties of lipids. The photocleavage of the strained dioxacycloundecine ring induces spherical to nanotubular self-assembly with concomitant release of an encapsulated anticancer drug, doxorubicin (Dox), in a controlled manner. The CA-IX targeted amphiphile also showed lower cytotoxicity, effective cellular uptake, and Dox delivery to the model carcinoma cells.

Molecular isomerization triggered by H2S to an NIR accessible first direct visualization of Ca2+-dependent production in living HeLa cells

Few studies determined the role of intracellular labile Ca²⁺ in H₂S homeostasis. Undoubtedly, fluorescent probes are powerful tools for exploring the question because of their unique advantages: non-destruction, visualization, and multi-levels imaging. Herein, a near-infrared (λ_em = 687 nm) and methylene blue chromophore-based fluorescent probe (MB1) for H₂S was rationally developed. Based on its high sensitivity and selectivity, MB1 was employed to image the concentration change of H₂S, upon stimulating it with ionomycin (a specific calcium ionophore). We found that the intracellular labile Ca²⁺ acted as a promotor for H₂S production in living cells. Furthermore, cystathionine γ-lyase (CSE) might have functioned as a positive mediator of Ca²⁺-dependent H₂S production. These direct and visible links for H₂S/Ca²⁺ will help us to understand the complex signaling in a better way.

A hydrogen sulfide triggered self-immolative fluorescent probe for lysosome labeling in live cells

We developed a naphthalimide-based, lysosome-targeting, and self-immolative fluorescent probe for H₂S detection.

Fast-Response Turn-on Fluorescent Probes Based on Thiolysis of NBD Amine for H2 S Bioimaging

Hydrogen sulfide (H2 S) is an important endogenous signaling molecule with multiple biological functions. New selective fluorescent turn-on probes based on fast thiolyling of NBD (7-nitro-1,2,3-benzoxadiazole) amine were explored for sensing H2 S in aqueous buffer and in living cells. The syntheses of both probes are simple and quite straightforward. The probes are highly sensitive and selective toward H2 S over other biologically relevant species. The fluorescein-NBD-based probe showed 65-fold green fluorescent increase upon H2 S activation. The rhodamine-NBD-based probe reacted rapidly with H2 S (t1/2 ≈1 min) to give a 4.5-fold increase in red fluorescence. Moreover, both probes were successfully used for monitoring H2 S in living cells and in mice. Based on such probe-based tools, we could observe H2 O2 -induced H2 S biogenesis in a concentration-dependent and time-dependent fashion in living cells.

Highly sensitive fluorescent determination of sulfide using BSA-capped CdS quantum dots

Schematic illustration of the BSA-CdS QD-based sensing system for sulfide detection.

FRET-based fluorescence ratiometric and colorimetric sensor to discriminate Fe3+ from Fe2+

A new benzothiazole–quinoline–rhodamine-6G-based probe was synthesised. The probe can exclusively detect Fe³⁺ through a ratiometric manner in a mixed aqueous system with a detection limit in the 10⁻⁸ M range.

A new strategy to construct a FRET platform for ratiometric sensing of hydrogen sulfide

We introduce a new FRET strategy to construct a ratiometric fluorescent H2S sensor. The ratio emission signal of the coumarin-naphthalimide dyad is modulated by the FRET process, which works in coordination with the ICT mechanism. The FRET process on/off is controlled through tuning the overlap level of the donor emission spectrum with the acceptor absorption via modulation of the acceptor fluorophore absorption wavelength. was applied to visualize both the intracellular exogenous and endogenous H2S through blue and green emission channels.

Chemical probes for molecular imaging and detection of hydrogen sulfide and reactive sulfur species in biological systems

Hydrogen sulfide (H2S), a gaseous species produced by both bacteria and higher eukaryotic organisms, including mammalian vertebrates, has attracted attention in recent years for its contributions to human health and disease. H2S has been proposed as a cytoprotectant and gasotransmitter in many tissue types, including mediating vascular tone in blood vessels as well as neuromodulation in the brain. The molecular mechanisms dictating how H2S affects cellular signaling and other physiological events remain insufficiently understood. Furthermore, the involvement of H2S in metal-binding interactions and formation of related RSS such as sulfane sulfur may contribute to other distinct signaling pathways. Owing to its widespread biological roles and unique chemical properties, H2S is an appealing target for chemical biology approaches to elucidate its production, trafficking, and downstream function. In this context, reaction-based fluorescent probes offer a versatile set of screening tools to visualize H2S pools in living systems. Three main strategies used in molecular probe development for H2S detection include azide and nitro group reduction, nucleophilic attack, and CuS precipitation. Each of these approaches exploits the strong nucleophilicity and reducing potency of H2S to achieve selectivity over other biothiols. In addition, a variety of methods have been developed for the detection of other reactive sulfur species (RSS), including sulfite and bisulfite, as well as sulfane sulfur species and related modifications such as S-nitrosothiols. Access to this growing chemical toolbox of new molecular probes for H2S and related RSS sets the stage for applying these developing technologies to probe reactive sulfur biology in living systems.

Cd(2+) Triggered the FRET "ON": A New Molecular Switch for the Ratiometric Detection of Cd(2+) with Live-Cell Imaging and Bound X-ray Structure

On the basis of the Förster resonance energy transfer mechanism between rhodamine and quinoline-benzothiazole conjugated dyad, a new colorimetric as well as fluorescence ratiometric probe was synthesized for the selective detection of Cd(2+). The complex formation of the probe with Cd(2+) was confirmed through Cd(2+)-bound single-crystal structure. Capability of the probe as imaging agent to detect the cellular uptake of Cd(2+) was demonstrated here using living RAW cells.

Fluorescence resonance energy transfer in a binary organic nanoparticle system and its application

Fluorescent organic nanoparticles have a much better photostability than molecule-based probes. Here, we report a simple strategy to detect chemicals and biomolecules by a binary nanoparticle system based on fluorescence resonance energy transfer (FRET). Poly(9,9-di-n-octylfluorenyl-2,7-diyl) (PFO, energy donor) and poly [2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV, energy acceptor) are utilized to prepare the binary nanoparticle system through a reprecipitation method. Since the FRET process is strongly distance-dependent, a change in the interparticle distance between the two kinds of nanoparticles after introduction of analytes will alter the FRET efficiency. The response of the binary nanoparticle system to cationic polyelectrolytes was investigated by monitoring the FRET efficiency from PFO to MEH-PPV nanoparticles and the fluorescence color of the nanoparticle solutions. Furthermore, the cationic polyelectrolyte pretreated binary nanoparticle system can be used to detect DNA by desorption of nanoparticles from the polyelectrolyte's chains and the detection concentration can go down to 10(-14) M. Thus, the binary nanoparticle system shows great promise for applications in chemical sensing or biosensing.

A remarkable ratiometric fluorescent chemodosimeter for very rapid detection of hydrogen sulfide in the vapour phase and living cells

A ratiometric fluorescent probe having a fast response and a large Stokes shift detects SH⁻ both in solid and vapour phases and this probe is used for fluorescence imaging of SH⁻ in living cells.

A FRET–ICT dual-quenching fluorescent probe with large off–on response for H2S: synthesis, spectra and bioimaging

A FRET–ICT dual-quenching fluorescent probe with significant off–on response toward H₂S is rationally designed and prepared for imaging of H₂S in living cells.

A highly selective and fast-response fluorescent probe for visualization of enzymatic H2S production in vitro and in living cells

The o-fluorinated-azido-capped rhodamine probe was developed for visualization of enzymatic H₂S production both in vitro and in living cells.