Small-molecule fluorescent probes: big future for specific bacterial labeling and infection detection

Illuminating antifungal mode of action and resistance with fluorescent probes

The rise in fungal infections, driven by pathogens resistant to the limited scope of antifungal agents available, poses an increasing threat to global health and the economy. Addressing this challenge requires a thorough understanding of the mechanisms of antifungal agents and the development of advanced resistance diagnostic methods. This opinion manuscript highlights recent advancements in antifungal research, with a focus on chemical biology approaches, particularly the development of fluorescent probes derived from various antifungal agents. These probes reveal new aspects of antifungal activity and provide deeper insights into modes of action and resistance mechanisms. Live cell imaging of fungal pathogens labeled with these probes has uncovered novel strategies to enhance antifungal efficacy, understand virulence factors, and detect resistance. These unique small-molecule tools offer powerful new avenues for addressing the fungal infections crisis, harnessing chemical biology approaches to develop innovative solutions to the global challenges posed by fungi.

Harnessing from Nature - Evolving Potential of Antimicrobial Peptide

Antimicrobial peptides (AMPs) are recognized as one of the most ancient components of innate immunity, playing a pivotal role as the first line of host defense systems. These evolutionarily conserved molecules have been identified in various organisms, from prokaryotes to humans. AMPs establish a delicate balanced relationship between host and microbes, by simultaneously regulating the biological activities of pathogens and commensal microbes. Given the escalating global concern over antibiotic resistance, there is an urgent need to explore alternative strategies to combat challenging infectious diseases. AMPs have emerged as promising candidates employed in clinical practice due to their sustainable bactericidal properties. Witnessed by deep understanding of AMPs actions toward host and bacteria, the potential applications of AMPs extend far beyond infection control. Emerging developments harnessed natural capabilities of AMPs to optimize their roles in modulating host signaling, treating diverse diseases, advancing biosensing and bioimaging technologies. In this Concept paper, we provide a comprehensive overview of the diversity and properties of AMPs. Additionally, we elaborate on the mechanisms underlying AMP activity and bacterial responses counteracting AMPs' functions. Most importantly, we discuss potential biomedical applications of AMPs and offer perspectives on their future development.

A multi-valent polymyxin-based fluorescent probe for the detection of Gram-negative infections

A multi-branched fluorogenic probe for the rapid and specific detection of Gram-negative bacteria is reported. Three Gram-negative-targeting azido-modified polymyxins were clicked onto a trivalent scaffold functionalised with the environmental green-emitting fluorophore 7-nitrobenz-2-oxa-1,3-diazole. The probe allowed wash-free detection of target bacteria with increased sensitivity and lower limits of detection compared to monovalent probes.

Imaging of Gut Bacterial Macroscopic Changes in Simulated Microgravity-Exposed Rats via In Vivo Metabolic Labeling

The impact of the microgravity environment on gut bacteria has been widely recognized to induce notable gastrointestinal pathology during extended spaceflight. However, most current studies for gut microbiome homeostasis profiling are based on the 16S rRNA gene sequencing of fecal samples; this technology faces challenges in analyzing gut bacterial alterations in situ, dynamically, and with high spatiotemporal resolution. Herein, we present the utilization of bioorthogonal metabolic labeling for noninvasive imaging of gut bacterial macroscopic changes in simulated microgravity (SMG) rats. After being subsequently labeled with the metabolic reporters d-Ala-N3 and ICG-DBCO through click chemistry, it was shown that SMG can trigger obvious perturbation of gut bacteria, evidenced by the significant increase in the total bacterial content and spatial distribution variations. Such a difference was accompanied by the occurrence of intestinal inflammation and tissue damage. Compared with 16S rRNA genome analysis focusing on composition and diversity, the metabolic labeling strategy provides unprecedented insights into the macroscopic changes of the gut bacterial content and distribution under SMG. Our study will be helpful for investigating the biological implication of SMG-induced imbalance in gut bacteria, potentially promoting the deep investigation of the complex gastrointestinal pathology in space biomedicine.

Fluorescent Antimicrobial Peptides Based on Nile Red: Effect of Conjugation Site and Chemistry on Wash-Free Staining of Bacteria

Fluorescent probes for bacterial detection can be obtained by conjugating antimicrobial peptides with fluorescent dyes. However, little is known about the effect of the conjugation site and linker chemistry on staining efficiency. We synthesized three conjugates of the antimicrobial peptide ubiquicidin with the environmentally sensitive fluorophore Nile Red that differed by the attachment site and the chemical composition of the linker. We showed that incorporating fluorophore as a minimalistic non-natural amino acid resulted in a superior probe compared with the typically used bioconjugation approaches. The new peptide-based probe named UNR-1 displayed red fluorescence and enabled robust wash-free staining of Gram-positive and Gram-negative bacteria. The probe exhibited selectivity over mammalian cells and enabled rapid fluorescence detection of bacteria by fluorescence microscopy and flow cytometry in an add-and-read format. Our results may foster the development of next-generation fluorescent AMPs for clinical laboratory diagnostics and medical imaging.

Real time monitoring of nerve agent mimics: Novel solid state emitter for enhanced precision and reliability

Chemical nerve agents are hazardous compounds that terrorists can exploit to pose a significant threat to public safety and national security. The nucleophilic behaviour of these agents enables their interaction with acetyl cholinesterase in the body, leading to paralysis and potentially fatal consequences. Therefore, developing robust and efficient detection methods for these agents is crucial for preventing their misuse. In this manuscript, (E)-12-(1-hydrazineylideneethyl)benzo[f]pyrido[1,2-a]indole-6,11-dione (HBID) is developed as a novel colorimetric and fluorometric probe for the detection of specific chemical nerve agent simulants in both liquid and vapor phase. HBID reacts rapidly with diethyl chlorophosphate (DCP), a common nerve agent simulant, leading to a significant increase in the fluorescence intensity. Under optimized conditions, HBID exhibits high sensitivity, good recyclability, fast response and low limit of detection (0.092 µM). NMR and mass spectral studies suggest that the reaction involves the nucleophilic addition of HBID to DCP, forming a phosphate ester. Additionally, the developed sensor demonstrates viscosity-sensitive AIE phenomena thus greatly expanding its potential applications in biological systems. This sensitivity enables precise detection and visualization of viscosity changes within cellular environments, making the sensor an invaluable tool for studying complex biological processes. The developed probe also detects pH within biologically relevant range (4-6). In practical applications, the probe-treated strips efficiently detected DCP vapor in real time, showing a noticeable fluorescence response. Further, the probe has a strong potential to detect the presence of DCP in the soil samples.

Chiral Fluorescent Antifungal Azole Probes Detect Resistance, Uptake Dynamics, and Subcellular Distribution in Candida Species

Azoles are essential for fungal infection treatment, yet the increasing resistance highlights the need for innovative diagnostic tools and strategies to revitalize this class of antifungals. We developed two enantiomers of a fluorescent antifungal azole probe (1 S and 1 R ), analyzing 60 Candida strains via live-cell microscopy. A database of azole distribution images in strains of Candida albicans, Candida glabrata, and Candida parapsilosis, among the most important pathogenic Candida species, was established and analyzed. This analysis revealed distinct populations of yeast cells based on the correlation between fluorescent probe uptake and cell diameter. Varied uptake levels and subcellular distribution patterns were observed in C. albicans, C. glabrata, and C. parapsilosis, with the latter displaying increased localization to lipid droplets. Comparison of the more potent fluorescent antifungal azole probe enantiomer 1 S with the moderately potent enantiomer 1 R highlighted time-dependent differences in the uptake profiles. The former displayed a marked elevation in uptake after approximately 150 min, indicating the time required for significant cell permeabilization to occur and its association with the azole's antifungal activity potency. Divergent uptake levels between susceptible and high efflux-based azole-resistant strains were detected, offering a rapid diagnostic approach for identifying azole resistance. This study highlights unique insights achievable through fluorescent antifungal azole probes, unraveling the complexities of azole resistance, subcellular dynamics, and uptake within fungal pathogens.

Highly Efficient Photodynamic Hydrogel with AIE-Active Photosensitizers toward Methicillin-Resistant Staphylococcus aureus Ultrafast Imaging and Killing

Methicillin-resistant Staphylococcus aureus (MRSA) causes great health hazards to society because most antibiotics are ineffective. Photodynamic treatment (PDT) has been proposed to combat MRSA due to the advantage of imaging-guided no-drug resistance therapy. However, the traditional photosensitizers for PDT are limited by aggregation-caused quenching for imaging and low photodynamic antibacterial efficiency. In this work, we synthesize a new aggregation-induced emission (AIE) photosensitizer (APNO), which can ultrafast distinguish between Gram-positive and Gram-negative bacteria within 3 s by AIE-active photosensitizer imaging. Meanwhile, APNO can generate antibacterial reactive oxygen species under light irradiation, which holds potential for antibacterial PDT. Then, APNO is loaded by PHEAA hydrogel to obtain a highly efficient photodynamic hydrogel (APNO@gel). In vitro results show complete inhibition of MRSA by APNO@gel under lower-power light irradiation. Transcriptome analysis is performed to investigate antibacterial mechanism of APNO@gel. Most importantly, APNO@gel also exhibits significant inhibition and killing ability of MRSA in the MRSA wound infection model, which will further promote rapid wound healing. Therefore, the photodynamic hydrogel provides a promising strategy toward MRSA ultrafast imaging and killing.

Enzymatic Activity Profiling Using an Ultrasensitive Array of Chemiluminescent Probes for Bacterial Classification and Characterization

Identification and characterization of bacterial species in clinical and industrial settings necessitate the use of diverse, labor-intensive, and time-consuming protocols as well as the utilization of expensive and high-maintenance equipment. Furthermore, while cutting-edge identification technologies such as mass spectrometry and PCR are highly effective in identifying bacterial pathogens, they fall short in providing additional information for identifying bacteria not present in the databases upon which these methods rely. In response to these challenges, we present a robust and general approach to bacterial identification based on their unique enzymatic activity profiles. This method delivers results within 90 min, utilizing an array of highly sensitive and enzyme-selective chemiluminescent probes. Leveraging our recently developed technology of chemiluminescent luminophores, which emit light under physiological conditions, we have crafted an array of probes designed to rapidly detect various bacterial enzymatic activities. The array includes probes for detecting resistance to the important and large class of β-lactam antibiotics. The analysis of chemiluminescent fingerprints from a diverse range of prominent bacterial pathogens unveiled distinct enzymatic activity profiles for each strain. The reported universally applicable identification procedure offers a highly sensitive and expeditious means to delineate bacterial enzymatic activity fingerprints. This opens new avenues for characterizing and identifying pathogens in research, clinical, and industrial applications.

CellT-Net: A Composite Transformer Method for 2-D Cell Instance Segmentation

Cell instance segmentation (CIS) via light microscopy and artificial intelligence (AI) is essential to cell and gene therapy-based health care management, which offers the hope of revolutionary health care. An effective CIS method can help clinicians to diagnose neurological disorders and quantify how well these deadly disorders respond to treatment. To address the CIS task challenged by dataset characteristics such as irregular morphology, variation in sizes, cell adhesion, and obscure contours, we propose a novel deep learning model named CellT-Net to actualize effective cell instance segmentation. In particular, the Swin transformer (Swin-T) is used as the basic model to construct the CellT-Net backbone, as the self-attention mechanism can adaptively focus on useful image regions while suppressing irrelevant background information. Moreover, CellT-Net incorporating Swin-T constructs a hierarchical representation and generates multi-scale feature maps that are suitable for detecting and segmenting cells at different scales. A novel composite style named cross-level composition (CLC) is proposed to build composite connections between identical Swin-T models in the CellT-Net backbone and generate more representational features. The earth mover's distance (EMD) loss and binary cross entropy loss are used to train CellT-Net and actualize the precise segmentation of overlapped cells. The LiveCELL and Sartorius datasets are utilized to validate the model effectiveness, and the results demonstrate that CellT-Net can achieve better model performance for dealing with the challenges arising from the characteristics of cell datasets than state-of-the-art models.

Rapid and visual identification of β-lactamase subtypes for precision antibiotic therapy

The abuse of antibiotics urgently requires rapid identification of drug-resistant bacteria at the point of care (POC). Here we report a visual paper sensor that allows rapid (0.25-3 h) discrimination of the subtypes of β-lactamase (the major cause of bacterial resistance) for precision antibiotic therapy. The sensor exhibits high performance in identifying antibiotic-resistant bacteria with 100 real samples from patients with diverse bacterial infections, demonstrating 100% clinical sensitivity and specificity. Further, this sensor can enhance the accuracy of antibiotic use from 48% empirically to 83%, and further from 50.6% to 97.6% after eliminating fungal infection cases. Our work provides a POC testing platform for guiding effective management of bacterial infections in both hospital and community settings.

Illuminating Bacterial Contamination in Water Sources: The Power of Fluorescence-Based Methods

Bacterial contamination of water sources is a significant public health concern, and therefore, it is important to have accurate and efficient methods for monitoring bacterial concentration in water samples. Fluorescence-based methods, such as SYTO 9 and PI staining, have emerged as a promising approach for real-time bacterial quantification. In this review, we discuss the advantages of fluorescence-based methods over other bacterial quantification methods, including the plate count method and the most probable number (MPN) method. We also examine the utility of fluorescence arrays and linear regression models in improving the accuracy and reliability of fluorescence-based methods. Overall, fluorescence-based methods offer a faster, more sensitive, and more specific option for real-time bacterial quantification in water samples.

RNA-Selective Small-Molecule Ligands: Recent Advances in Live-Cell Imaging and Drug Discovery

RNA structures, including those formed from coding and noncoding RNAs, alternative to protein-based drug targets, could be a promising target of small molecules for drug discovery against various human diseases, particularly in anticancer, antibacterial and antivirus development. The normal cellular activity of cells is critically dependent on the function of various RNA molecules generated from DNA transcription. Moreover, many studies support that mRNA-targeting small molecules may regulate the synthesis of disease-related proteins via the non-covalent mRNA-ligand interactions that do not involve gene modification. RNA-ligand interaction is thus an attractive approach to address the challenge of "undruggable" proteins in drug discovery because the intracellular activity of these proteins is hard to be suppressed with small molecule ligands. We selectively surveyed a specific area of RNA structure-selective small molecule ligands in fluorescence live cell imaging and drug discovery because the area was currently underexplored. This state-of-the-art review thus mainly focuses on the research published within the past three years and aims to provide the most recent information on this research area; hopefully, it could be complementary to the previously reported reviews and give new insights into the future development on RNA-specific small molecule ligands for live cell imaging and drug discovery.

Boron Applications in Prevention, Diagnosis and Therapy for High Global Burden Diseases

The role of boron-containing compounds (BCCs) in medicine is growing [...]

FluoroPi Device With SmartProbes: A Frugal Point-of-Care System for Fluorescent Detection of Bacteria From a Pre-Clinical Model of Microbial Keratitis

Purpose

Rapid and accurate diagnosis of microbial keratitis (MK) could greatly improve patient outcomes. Here, we present the development of a rapid, accessible multicolour fluorescence imaging device (FluoroPi) and evaluate its performance in combination with fluorescent optical reporters (SmartProbes) to distinguish bacterial Gram status. Furthermore, we show feasibility by imaging samples obtained by corneal scrape and minimally invasive corneal impression membrane (CIM) from ex vivo porcine corneal MK models.

Methods

FluoroPi was built using a Raspberry Pi single-board computer and camera, light-emitting-diodes (LEDs), and filters for white-light and fluorescent imaging, with excitation and detection of bacterial optical SmartProbes: Gram-negative, NBD-PMX (exmax 488 nm); Gram positive, Merocy-Van (exmax 590 nm). We evaluated FluoroPi with bacteria (Pseudomonas aeruginosa and Staphylococcus aureus) isolated from ex vivo porcine corneal models of MK by scrape (needle) and CIM with the SmartProbes.

Results

FluoroPi provides <1 µm resolution and was able to readily distinguish bacteria isolated from ex vivo models of MK from tissue debris when combined with SmartProbes, retrieved by both scrape and CIM. Single bacteria could be resolved within the field of view, with limits of detection demonstrated as 103 to 104 CFU/mL. Sample preparation prior to imaging was minimal (wash-free), and imaging and postprocessing with FluoroPi were straightforward, confirming ease of use.

Conclusions

FluoroPi coupled with SmartProbes provides effective, low-cost bacterial imaging, delineating Gram-negative and Gram-positive bacteria directly sampled from a preclinical model of MK.

Translational Relevance

This study provides a crucial stepping stone toward clinical translation of a rapid, minimally invasive diagnostic approach for MK.

Molecular probes for fluorescent sensing of metal ions in non-mammalian organisms

While metal ions play an important role in the proper functioning of all life, many questions remain unanswered about exactly how different metals contribute to health and disease. The development of fluorescent probes, which respond to metals, has allowed greater understanding of the cellular location, concentration and speciation of metals in living systems, giving a new appreciation of their function. While the focus of studies using these fluorescent tools has largely been on mammalian organisms, there has been relatively little application of these powerful tools to other organisms. In this review, we highlight recent examples of molecular fluorophores, which have been applied to sensing metals in non-mammalian organisms.

Polymyxin-based fluorescent probes to combat Gram-negative antimicrobial resistance

Reliable diagnostic approaches especially those targeting critical Gram-negative bacteria are urgently needed for the prevention of antimicrobial resistance. Polymyxin B (PMB) which specifically targets the outer membrane of Gram-negative bacteria is the last-line antibiotic against life-threatening multidrug-resistant Gram-negative bacteria. However, increasing number of studies have reported the spread of PMB-resistant strains. With the aim to specifically detect Gram-negative bacteria and potentially reduce the irrational use of antibiotics, we herein rationally designed two Gram-negative bacteria specific fluorescent probes based on our previous activity-toxicity optimization of PMB. The in vitro probe PMS-Dns showed fast and selective labeling of Gram-negative pathogens in complex biological cultures. Subsequently, we constructed the caged in vivo fluorescent probe PMS-Cy-NO₂ by conjugating bacterial nitroreductase (NTR)-activatable positive charged hydrophobic near-infrared (NIR) fluorophore with polymyxin scaffold. Significantly, PMS-Cy-NO₂ exhibited excellent Gram-negative bacterial detection capability with the differentiation between Gram-positive and Gram-negative in a mouse skin infection model.

Click Triazole as a Linker for Pretargeting Strategies: Synthesis, Docking Investigations, Fluorescence Diagnosis, and Antibacterial Action Studies

In this study, three compounds A1, A2, and A3 and fluorescent probes T1, T2, T3, and T4 were designed and synthesized. ¹H NMR, ¹³C NMR, and MS characterization and elemental analysis were used to confirm A1-A3 and T1-T4. A1-A3 and T1-T4 formed diagnostic molecules by "click" reactions. A1-A3 and T1-T4 did not significantly increase cell death at concentrations of 80 μmol/L. Preliminary screening of the compounds for antibacterial activity revealed that A2 has better antibacterial activity against Agrobacterium tumefaciens. The synthesized compounds and fluorescent probes can be targeted and combined in the physiological condition to form diagnostic molecules for fluorescence detection of Agrobacterium tumefaciens. The binding sites of A1-A3 were deduced theoretically using the AutoDock Vina software docking tool. Further study of the mechanism of the antibacterial action of these compounds is likely to identify new agents against resistant bacterial strains.

A fluorescent probe for alkylating agents and its quantification of triflate as a genotoxic impurity

The responses of a reaction-based fluorescent probe BI-Py towards alkyl halide, epoxide, carbonate, sulfate, sulphonate and triflate were evaluated and the probe achieved selective detection of ethyl triflate in acetonitrile with a LOD of 1.08 μM. BI-Py exhibited great potential for detecting triflate as a genotoxic impurity in drug substances.

Achieving Ultrasensitive Chromogenic Probes for Rapid, Direct Detection of Carbapenemase-Producing Bacteria in Sputum

Carbapenemase-producing bacteria (CPB) stand as the most dangerous "superbugs" in the clinic. Rapid point-of-care (POC) detection of CPB in clinical samples is key to timely and effective infection management. We herein report the first ultrasensitive chromogenic probe that allows direct POC detection of CPB in clinical sputum samples at a sample-to-result time of less than 15 min. This chromogenic probe is modularly designed by conjugating the carbapenem core with a benzene derivative bearing an electronegativity-tunable substituent. Unexpectedly high sensitivity was achieved simply by choosing strong electron-withdrawing substituents, such as -N⁺(CH₃)₃, without resorting to complex molecular design. Through integrating the probes with a portable paper chip, 24 out of 80 clinical sputum samples from sepsis patients with lung infections were quickly diagnosed as CPB-positive, exhibiting 100% clinical sensitivity and specificity. This low-cost paper chip assay can be readily performed on-site, breaking through the dilemma of rapid CPB detection, especially in resource-limited settings.

A Self-Assembling Probe for Imaging the States of Golgi Apparatus in Live Single Cells

Despite the enormous progress in genomics and proteomics, it is still challenging to assess the states of organelles in living cells with high spatiotemporal resolution. Based on our recent finding of enzyme-instructed self-assembly of a thiophosphopeptide that targets the Golgi Apparatus (GA) instantly, we use the thiophosphopeptide, which is enzymatically responsive and redox active, as an integrative probe for revealing the state of the GA of live cells at the single cell level. By imaging the probe in the GA of live cells over time, our results show that the accumulation of the probe at the GA depends on cell types. By comparison to a conventional Golgi probe, this self-assembling probe accumulates at the GA much faster and are sensitive to the expression of alkaline phosphatases. In addition, subtle changes of the fluorophore results in slightly different GA responses. This work illustrates a novel class of active molecular probes that combine enzyme-instructed self-assembly and redox reaction for high-resolution imaging of the states of subcellular organelles over a large area and extended times.

Metabolically Specific In Situ Fluorescent Visualization of Bacterial Infection on Wound Tissues

The ability to effectively detect bacterial infection in human tissues is important for the timely treatment of the infection. However, traditional techniques fail to visualize bacterial species adhered to host cells in situ in a target-specific manner. Dihydropteroate synthase (DHPS) exclusively exists in bacterial species and metabolically converts p-aminobenzoic acid (PABA) to folic acid (FA). By targeting this bacterium-specific metabolism, we have developed a fluorescent imaging probe, PABA-DCM, based on the conjugation of PABA with a long-wavelength fluorophore, dicyanomethylene 4H-pyran (DCM). We confirmed that the probe can be used in the synthetic pathway of a broad spectrum of Gram-positive and negative bacteria, resulting in a significantly extended retention time in bacterial over mammalian cells. We validated that DHPS catalytically introduces a dihydropteridine group to the amino end of the PABA motif of PABA-DCM, and the resulting adduct leads to an increase in the FA levels of bacteria. We also constructed a hydrogel dressing containing PABA-DCM and graphene oxide (GO), termed PABA-DCM@GO, that achieves target-specific fluorescence visualization of bacterial infection on the wounded tissues of mice. Our research paves the way for the development of fluorescent imaging agents that target species-conserved metabolic pathways of microorganisms for the in situ monitoring of infections in human tissues.

A colorimetric and fluorometric probe for phenylhydrazine and its application in real samples

A fluorescent probe for phenylhydrazine detection was developed with aldehyde as the recognition group and good selectivity towards phenylhydrazine over hydrazine, hydroxylamine and other amines was observed. Its application in real water samples and fast visualization of phenylhydrazine using a probe-loaded paper strip were demonstrated.

Single bacteria detection by droplet DNAzyme-coupled rolling circle amplification

We described a new system termed droplet DNAzyme-coupled rolling circle amplification (dDRCA) that can selectively detect bacteria from clinical urine samples with single-cell sensitivity within 1.5 h compared with the several hours needed for traditionally used culture-based methods.