Rational design of small molecule fluorescent probes for biological applications

A novel dual-release scaffold for fluorescent labels improves cyclic immunofluorescence

Cyclic immunofluorescence is a powerful method to generate high-content imaging datasets for investigating cell biology and developing therapies. This method relies on fluorescent labels that determine the quality of immunofluorescence and the maximum number of staining cycles that can be performed. Here we present a novel fluorescent labelling strategy, based on antibodies conjugated to a scaffold containing two distinct sites for enzymatic cleavage of fluorophores. The scaffold is composed of a dextran decorated with short ssDNA that upon hybridization with complementary dye-modified oligos result in fluorescent molecules. The developed fluorescent labels exhibit specific staining and remarkable brightness in flow cytometry and fluorescence microscopy. We showed that the combination of DNase-mediated degradation of DNA and dextranse-mediated degradation of the dextran as two complementary enzymatic release mechanisms in one molecule, improves signal erasure from labelled epitopes. We envision that such dual-release labels with high brightness and efficient and specific erasure will advance multiplexed cyclic immunofluorescence approaches and thereby will contribute to gaining new insights in cell biology.

Chemical Control of Fluorescence Lifetime towards Multiplexing Imaging

Fluorescence lifetime imaging has been a powerful tool for biomedical research. Recently, fluorescence lifetime-based multiplexing imaging has expanded imaging channels by using probes that harbor the same spectral channels and distinct excited state lifetime. While it is desirable to control the excited state lifetime of any given fluorescent probes, the rational control of fluorescence lifetimes remains a challenge. Herein, we chose boron dipyrromethene (BODIPY) as a model system and provided chemical strategies to regulate the fluorescence lifetime of its derivatives with varying spectral features. We find electronegativity of structural substituents at the 8' and 5' positions is important to control the lifetime for the green-emitting and red-emitting BODIPY scaffolds. Mechanistically, such influences are exerted via the photo-induced electron transfer and the intramolecular charge transfer processes for the 8' and 5' positions of BODIPY, respectively. Based on these principles, we have generated a group of BODIPY probes that enable imaging experiments to separate multiple targets using fluorescence lifetime as a signal. In addition to BODIPY, we envision modulation of electronegativity of chemical substituents could serve as a feasible strategy to achieve rational control of fluorescence lifetime for a variety of small molecule fluorophores.

Probing Alzheimer's pathology: Exploring the next generation of FDDNP analogues for amyloid β detection

Fluorescent probes are a powerful tool for imaging amyloid β (Aβ) plaques, the hallmark of Alzheimer's disease (AD). Herein, we report the synthesis and comprehensive characterization of 21 novel probes as well as their optical properties and binding affinities to Aβ fibrils. One of these dyes, 1Ae, exhibited several improvements over FDDNP, an established biomarker for Aβ- and Tau-aggregates. First, 1Ae had large Stokes shifts (138-213 nm) in various solvents, thereby reducing self-absorption. With a high quantum yield ratio (φ(dichloromethane/methanol) = 104), 1Ae also ensures minimal background emission in aqueous environments and high sensitivity. In addition, compound 1Ae exhibited low micromolar binding affinity to Aβ fibrils in vitro (Kd = 1.603 µM), while increasing fluorescence emission (106-fold) compared to emission in buffer alone. Importantly, the selective binding of 1Ae to Aβ1-42 fibrils was confirmed by an in cellulo assay, supported by ex vivo fluorescence microscopy of 1Ae on postmortem AD brain sections, allowing unequivocal identification of Aβ plaques. The intermolecular interactions of fluorophores with Aβ were elucidated by docking studies and molecular dynamics simulations. Density functional theory calculations revealed the unique photophysics of these rod-shaped fluorophores, with a twisted intramolecular charge transfer (TICT) excited state. These results provide valuable insights into the future application of such probes as potential diagnostic tools for AD in vitro and ex vivo such as determination of Aβ1-42 in cerebrospinal fluid or blood.

PyrAtes: Modular Organic Salts with Large Stokes Shifts for Fluo-rescence Microscopy

The deployment of small-molecule fluorescent agents plays an ever-growing role in medicine and drug development. Herein, we complement the portfolio of powerful fluorophores, reporting the serendipitous discovery and development of a novel class with an imidazo[1,2-a]pyridinium triflate core, which we term PyrAtes. These fluorophores are synthesized in a single step from readily available materials (>60 examples) and display Stokes shifts as large as 240 nm, while also reaching NIR-I emissions at λmax as long as 720 nm. Computational studies allow the development of a platform for the prediction of λmax and λEm. Furthermore, we demonstrate the compatibility of these novel fluorophores with live cell imaging in HEK293 cells, suggesting PyrAtes as potent intracellular markers.

A novel dual-responsive colorimetric/fluorescent probe for the detection of N2H4 and ClO- and its application in environmental analysis and bioimaging

Hydrazine (N2H4) and hypochlorite (ClO-) are both reactive chemical substances extensively utilized across various industrial domains. Excessive hydrazine (N2H4) and hypochlorite (ClO-) can pose significant risks to the environment, ecosystems, and human health. In order to assess and control the environmental hazard caused by N2H4 and ClO-, there is an imperative need for efficient methods capable of rapid and precise detection of these contaminants. This paper introduces a novel dual-responsive colorimetric/fluorescent probe (MDT) for the detection of N2H4 and ClO- in environmental and biological samples. The probe exhibits turn-on fluorescent responses to N2H4 or ClO- with low detection limits (N2H4: 8 nM; ClO-: 15 nM), large Stokes shifts (N2H4: 175 nm; ClO-: 203 nm), short response time (N2H4: 4 min; ClO-: 5 s) and broad pH range (5-10). In practical applications, MDT has been successfully employed in detecting N2H4 and ClO- in water and soil samples from diverse locations. Test strips loaded with MDT offer a visual and convenient means to track N2H4 vapor and quantify N2H4 and ClO- concentrations in solutions. Finally, MDT has been utilized for sensing N2H4 and ClO- in Arabidopsis thaliana roots and living zebrafish. This study presents a promising tool for monitoring N2H4 and ClO- in the environment and living organisms.

CdSe/ZnS Quantum Rods (QRs) and Phenyl Boronic Acid BODIPY as Efficient Förster Resonance Energy Transfer (FRET) Donor-Acceptor Pair

The reversibility of the covalent interaction between boronic acids and 1,2- or 1,3-diols has put the spotlight on this reaction for its potential in the development of sensors and for the fishing of bioactive glycoconjugates. In this work, we describe the investigation of this reaction for the reversible functionalization of the surface of CdSe/ZnS Quantum Rods (QRs). With this in mind, we have designed a turn-off Förster resonance energy transfer (FRET) system that ensures monitoring the extent of the reaction between the phenyl boronic residue at the meso position of a BODIPY probe and the solvent-exposed 1,2-diols on QRs' surface. The reversibility of the corresponding boronate ester under oxidant conditions has also been assessed, thus envisioning the potential sensing ability of this system.

N-Aryl-DABCO Salts as an Unprecedented Sensing Platform for the Detection of Thiols and Selenols

Quaternary N-aryl-DABCO salts were introduced for the first time as a highly selective sensing platform for thiols and selenols. By employing this platform, a highly sensitive coumarin based "off-on" fluorescent probe was designed and synthesized. The probe possesses a good solubility in water, low background fluorescence, and, most importantly, demonstrates high selectivity to aryl thiols and selenols over their aliphatic counterparts and other common nucleophiles. A dramatic increase in fluorescence intensity is achieved through the selective cleavage of the quaternized DABCO-ring, yielding a piperazine derivatives with a high fluorescence quantum yield (~72 %). Moreover, stability of the probe to the most used reducing agents DTT and TCEP was demonstrated. The limits of detection for p-thiocresol and phenyl selenide were evaluated to be 22 nM and 6 nM, respectively.

Highly tunable bimane-based fluorescent probes: design, synthesis, and application as a selective amyloid binding dye

Small molecule fluorescent probes are indispensable tools for a broad range of biological applications. Despite many probes being available, there is still a need for probes where photophysical properties and biological selectivity can be tuned as desired. Here, we report the rational design and synthesis of a palette of fluorescent probes based on the underexplored bimane scaffold. The newly developed probes with varied electronic properties show tunable absorption and emission in the visible region with large Stokes shifts. Probes featuring electron-donating groups exhibit rotor effects that are sensitive to polarity and viscosity by "intramolecular charge transfer" (ICT) and twisted intramolecular charge transfer (TICT) mechanisms, respectively. These properties enable their application as "turn-on" fluorescent probes to detect fibrillar aggregates of the α-synuclein (αS) protein that are a hallmark of Parkinson's disease (PD). One probe shows selective binding to αS fibrils relative to soluble proteins in cell lysates and amyloid fibrils of tau and amyloid-β. Finally, we demonstrate the diagnostic potential of the probe in selectively detecting αS fibrils amplified from PD with dementia (PDD) patient samples.

Organic Fluorophores with Large Stokes Shift for the Visualization of Rapid Protein and Nucleic Acid Assays

Organic small-molecule fluorophores, characterized by flexible chemical structure and adjustable optical performance, have shown tremendous potential in biosensing. However, classical organic fluorophore motifs feature large overlap between excitation and emission spectra, leading to the requirement of advanced optical set up to filter desired signal, which limits their application in scenarios with simple settings. Here, a series of wavelength-tunable small-molecule fluorescent dyes (PTs) bearing simple organic moieties have been developed, which exhibit Stokes shift up to 262 nm, molar extinction coefficients ranged 30,000-100,000 M-1 cm-1, with quantum yields up to 54.8 %. Furthermore, these dyes were formulated into fluorescent nanoparticles (PT-NPs), and applied in lateral flow assay (LFA). Consequently, limit of detection for SARS-CoV-2 nucleocapsid protein reached 20 fM with naked eye, a 100-fold improvement in sensitivity compared to the pM detection level for colloidal gold-based LFA. Besides, combined with loop-mediated isothermal amplification (LAMP), the LFA system achieved the visualization of single copy level nucleic acid detection for monkeypox (Mpox).

Novel Peptide-Based Fluorescent Probe for Simultaneous Sensing of Chymotrypsin and Hydrogen Peroxide

The developed multifunctional fluorescent probe enables the simultaneous detection of chymotrypsin as a model protease and hydrogen peroxide as a representative of reactive oxygen species (ROS) in biologically relevant concentration ranges. The chymotrypsin sensing is based on the cleavage of its selectively recognizable peptide sequence and the consequent disruption of FRET between coumarin (DEAC) and fluorescein (FL). Analogously, the presence of hydrogen peroxide causes the gradual degradation of the H2O2-labile benzopyrylium-coumarin (BC) dye. Considering the fluorescence emission responses of individual chymotrypsin-peroxide probe-attached fluorophores after their excitation at 425 nm, the sole presence of either chymotrypsin (50-1000 ng/mL) or hydrogen peroxide (10-200 μM) in a sample could be unambiguously confirmed or refuted. In addition, reliable simultaneous detection and approximate quantification of both studied species in the concentration ranges of 100-1000 ng/mL and 20-200 μM for chymotrypsin and H2O2, respectively, could be performed as well. The obtained results are summarized and visualized in the graphical models.

Stereochemistry-Dependent Labeling of Organelles with a Near-Infrared-Emissive Phosphorus-Bridged Rhodamine Dye in Live-Cell Imaging

The development of near-infrared (NIR) fluorophores that have both excellent chemical stability and photostability, as well as efficient cell permeability, is highly demanded. In this study, we present phospha-rhodamine (POR) dyes which display significantly improved performance for protein labeling. This is achieved by incorporating a 2-carboxy-3-benzothiophenyl group at the 9-position of the xanthene scaffold. The resulting cis and trans isomers were successfully isolated and structurally characterized using X-ray diffraction. The HaloTag ligand conjugates of the two isomers exhibited different staining abilities in live cells. While the cis isomer showed non-specific accumulation on the organelle membranes, the trans isomer selectively labeled the HaloTag-fused proteins, enabling the long-term imaging of cell division and the 5-color imaging of cell organelles. Molecular dynamics simulations of the HaloTag ligand conjugates within the lipid membrane suggested that the cis isomer is more prone to forming oligomers in the membrane. In contrast, the oligomerization of the trans isomer is effectively suppressed by its interaction with the lipid molecules. By taking advantage of the superior labeling performance of the trans isomer and its NIR-emissive properties, multi-color time-lapse super-resolution 3D imaging, namely super-resolution 5D-imaging, of the interconnected network between the endoplasmic reticulum and microtubules was achieved in living cells.

Central Ring Puckering Enhances the Stokes Shift of Xanthene Dyes

Small-molecule dyes are generally designed based on well-understood electronic effects. However, steric hindrance can promote excited-state geometric relaxation, increasing the difference between the positions of absorption and emission bands (the Stokes shift). Accordingly, we hypothesized that sterically induced central ring puckering in xanthene dyes could be used to systematically increase their Stokes shift. Through a combined experimental/quantum-chemical approach, we screened a group of (9-acylimino)-pyronin dyes with a perturbed central ring geometry. Our results showed that an atom with sp3 hybridization in position 10 of (9-acylimino)-pyronins induces central ring puckering and facilitates excited-state geometric relaxation, thereby markedly enhancing their Stokes shifts (by up to ~2000 cm-1). Thus, we prepared fluorescent (9-acylimino)-pyronin pH sensors, which showed a Stokes shift disparity between acid and base forms of up to ~8700 cm-1. Moreover, the concept of ring puckering-enhanced Stokes shift can be applied to a wide range of xanthene analogues found in the literature. Therefore, central ring puckering may be reliably used as a strategy for enhancing Stokes shifts in the rational design of dyes.

Synthetic, biological and optoelectronic properties of phenoxazine and its derivatives: a state of the art review

Phenoxazines have sparked a lot of interest owing to their numerous applications in material science, organic light-emitting diodes, photoredox catalyst, dye-sensitized solar cells and chemotherapy. Among other things, they have antioxidant, antidiabetic, antimalarial, anti-alzheimer, antiviral, anti-inflammatory and antibiotic properties. Actinomycin D, which contains a phenoxazine moiety, functions both as an antibiotic and anticancer agent. Several research groups have worked on various structural modifications over the years in order to develop new phenoxazines with improved properties. Both phenothiazines and phenoxazines have gained prominence in medicine as pharmacological lead structures from their traditional uses as dyes and pigments. Organoelectronics and material sciences have recently found these compounds and their derivatives to be quite useful. Due to this, organic synthesis has been used in an unprecedented amount of exploratory alteration of the parent structures in an effort to create novel derivatives with enhanced biological and material capabilities. As a result, it is critical to conduct more frequent reviews of the work done in this area. Various stages of the synthetic transformation of phenoxazine scaffolds have been depicted in this article. This article aims to provide a state of the art review for the better understanding of the phenoxazine derivatives highlighting the progress and prospects of the same in medicinal and material applications.

Synthesis, Spectral Characterization and Photoluminescence of 3-chloro-6-methoxy-2-(methylsulfanyl)quinoxaline in Different Solvents: An Experimental and Theoretical Investigation Using DFT

In the present work, we synthesized 3-chloro-6-methoxy-2-(methyl sulfanyl) quinoxaline (3MSQ) using a microwave-assisted synthesis method. The physicochemical structural analysis of the synthesized compound utilizing 1H-NMR, 13C-NMR, and FT-IR spectroscopy techniques. The photophysical properties of 3MSQ was examined through absorption and fluorescence spectroscopy. Spectroscopic analyses revealed a bathochromic shift in both absorption and fluorescence spectra, attributed to the π → π* transition. Ground and excited state dipole moments was experimentally determined using the solvatochromic shift method, employing various correlations such as Lippert's, Bakhshiev's, Kawski-Chamma-Viallet's equations, and solvent polarity parameters. Our findings indicate that the excited state dipole moments exceed those of the ground state, suggesting increased polarity in the excited state. Further, the while detailed bond length, bond angles, dihedral angles, Mulliken charge distribution, ground state dipole moments and HOMO-LUMO energy gap estimated through ab initio computations using Gaussian-09W. The value of energy band gap obtained from both the methods are in good agreement. Furthermore, employing DFT computational analysis, we identified reactive centers such as electrophilic and nucleophilic sites using molecular electrostatic potential (MESP) 3D plots. Additionally, CIE chromaticity analysis was performed to understand the photoluminescent properties of 3MSQ. The insights derived from these analyses contribute to a better understanding of the molecule's electronic structure, photophysical properties, and solute-solvent interactions, thus providing valuable information regarding its behaviour and characteristics under diverse conditions. These results contribute to a comprehensive understanding of the molecular structure and properties of 3-chloro-6-methoxy-2-(methyl sulfanyl) quinoxaline (3MSQ).

Novel mono substituted pyridoimidazoisoquinoliniums via a silver-catalyzed intramolecular cyclization and their applications in cellular imaging

Cationic heterocycles, an important class of organic compounds soluble in polar solvents, have been gaining attention in the construction of fluorescent probes. This paper reports the quick synthesis of novel pyrido[1',2';2,3]imidazo[5,1-a]isoquinoliniums starting from 2-(2-ethynylphenyl)imidazo[1,2-a]pyridines at room temperature via intramolecular cyclization by employing a catalytic amount of silver trifluoromethanesulfonate in addition to lithium trifluoromethanesulfonate and silica gel as the counter anion source and additive, respectively. The designed pyridoimidazoisoquinoliniums consisted of an imidazo[1,2-a]pyridine fused isoquinolinium. The X-ray diffraction results revealed that pyrido[1',2';2,3]imidazo[5,1-a]isoquinolinium trifluoromethanesulfonate contained considerable planar parent skeletons and interacted by π-π stacking with neighbouring molecules. Furthermore, in a methanol solution the designed 6-phenyl derivative exhibited strong fluorescence in the 420-450 nm region in addition to strong mitochondrial specificity in a cell staining assay.

Magnetic-responsive upconversion luminescence resonance energy transfer (LRET) biosensor for ultrasensitive detection of SARS-CoV-2 spike protein

Upconversion nanoparticles (UCNPs) are ideal donors for luminescence resonance energy transfer (LRET)-based biosensors due to their excellent upconversion luminescence properties. However, the relatively large size of antibodies and proteins limits the application of UCNPs-based LRET biosensors in protein detection because the large steric hindrance of proteins leads to low energy transfer efficiency between UCNPs and receptors. Herein, we developed a magnetic responsive UCNPs-based LRET biosensor to control the coupling distance between antibody-functionalized UCNPs (Ab-UCNPs) as donors and antibody-PEG linker-magnetic gold nanoparticles (Ab-PEG-MGNs) as acceptors for ultrasensitive and highly selective detection of SARS-CoV-2 spike proteins. Our results showed that this platform reversibly shortened the coupling distance between UCNPs and MGNs and enhanced the LRET signal with a 10-fold increase in the limit of detection (LOD) from 20.6 pg/mL without magnetic modulation to 2.1 pg/mL with magnetic modulation within 1 h. The finite-difference time-domain (FDTD) simulation with cyclic distance change confirmed the distance-dependent LRET efficiency under magnetic modulation, which supported the experimental results. Moreover, the applications of this magnetic-responsive UCNP-based LRET biosensor could be extended to other large-size biomolecule detection.

Development of an environmentally sensitive fluorescent peptide probe for MrgX2 and application in ligand screening of peptide antibiotics

Mast cells (MCs) are primary effector cells involved in immediate allergic reactions. Mas-related G protein-coupled receptor-X2 (MrgX2), which is highly expressed on MCs, is involved in receptor-mediated drug-induced pseudo-anaphylaxis. Many small-molecule drugs and peptides activate MrgX2, resulting in MC activation and allergic reactions. Although small-molecule drugs can be identified using existing MrgX2 ligand-screening systems, there is still a lack of effective means to screen peptide ligands. In this study, to screen for peptide drugs, the MrgX2 high-affinity endogenous peptide ligand substance P (SP) was used as a recognition group to design a fluorescent peptide probe. Spectroscopic properties and fluorescence imaging of the probe were assessed. The probe was then used to screen for MrgX2 agonists among peptide antibiotics. In addition, the effects of peptide antibiotics on MrgX2 activation were investigated in vivo and in vitro. The environment-sensitive property of the probe was revealed by the dramatic increase in fluorescence intensity after binding to the hydrophobic ligand-binding domain of MrgX2. Based on these characteristics, it can be used for in situ selective visualization of MrgX2 in live cells. The probe was used to screen ten types of peptide antibiotics, and we found that caspofungin and bacitracin could compete with the probe and are hence potential ligands of MrgX2. Pharmacological experiments confirmed this hypothesis; caspofungin and bacitracin activated MCs via MrgX2 in vitro and induced local anaphylaxis in mice. Our research can be expected to provide new ideas for screening MrgX2 peptide ligands and reveal the mechanisms of adverse reactions caused by peptide drugs, thereby laying the foundation for improving their clinical safety.

Next-Generation Tags for Fluorine Nuclear Magnetic Resonance: Designing Amplification of Chemical Shift Sensitivity

Fluorine NMR is a highly sensitive technique for delineating the conformational states of biomolecules and has shown great utility in drug screening and in understanding protein function. Current fluorinated protein tags leverage the intrinsic chemical shift sensitivity of the 19F nucleus to detect subtle changes in protein conformation and topology. This chemical shift sensitivity can be amplified by embedding the fluorine or trifluoromethyl reporter within a pyridone. Due to their polarizability and rapid tautomerization, pyridones exhibit a greater range of electron delocalization and correspondingly greater 19F NMR chemical shift dispersion. To assess the chemical shift sensitivity of these tautomeric probes to the local environment, 19F NMR spectra of all possible monofluorinated and trifluoromethyl-tagged versions of 2-pyridone were recorded in methanol/water mixtures ranging from 100% methanol to 100% water. 4-Fluoro-2-pyridone and 6-(trifluoromethyl)-2-pyridone (6-TFP) displayed the greatest sensitivity of the monofluorinated and trifluoromethylated pyridones, exceeding that of known conventional CF3 reporters. To evaluate the utility of tautomeric pyridone tags for 19F NMR of biomolecules, the alpha subunit of the stimulatory G protein (Gsα) and human serum albumin (HSA) were each labeled with a thiol-reactive derivative of 6-TFP and the spectra were recorded as a function of various adjuvants and drugs. The tautomeric tag outperformed the conventional tag, 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide through the improved resolution of several functional states.

A multi-signal mitochondria-targeted fluorescent probe for simultaneously distinguishing biothiols and realtime visualizing its metabolism in cancer cells and tumor models

Biothiols and its metabolite SO2 derivatives play vital roles in various physiological processes. Although a few probes have been designed for monitoring the metabolism of biothiols, developing multi-signal fluorescent probes with practicability for simultaneously distinguishing biothiols (GSH, Cys and Hcy) and real-time visualizing SO2 derivatives is an enormous challenge. To better visualize biothiols metabolism in vitro and vivo, we developed a novel multi-signal NIR fluorescent probe (probe 2) with mitochondria-targeted for distinguishing biothiols and its metabolism, based on an ICT-PET synergetic mechanism. Probe 2 with dual recognition sites distinguishing detected Cys/Hcy (Red-Green), GSH (Green) and SO32- (Blue) via three channels. First probe 2 distinguished Cys and GSH to estimate main biothiols in living cells through the ratio changes of two well-defined emission bands (Red-Green), and then imaged its metabolite SO2 with ratiometric fluorescence (Red-Blue), eliminating the interference by different biothiols. Notably, probe 2 exhibits satisfactory sensitivity (detection limit: 0.21, 0.13, 0.14 and 3.06 μM for Cys, Hcy, GSH and SO32-, respectively), high selectivity, reliability at physiological pH, and rapid fluorescence response (within 10 min). Given these advantages, probe 2 has been successfully applied to the real-time monitor GSH metabolic process in MCF-7 cells and biothiols metabolism in breast cancer, suggesting biothiols metabolic changes might be a diagnostic indicator during cancer treatment. So probe 2 is a convenient and efficient tool for understanding the physiological functions of biothiols and its metabolism.

Chronological development of functional fluorophores for bio-imaging

Functional fluorophores represent an emerging research field, distinguished by their diverse applications, especially in sensing and cellular imaging. After the discovery of quinine sulfate and subsequent elucidation of the fluorescence mechanism by Sir George Stokes, research in the field of fluorescence gained momentum. Over the past few decades, advancements in sophisticated instruments, including super-resolution microscopy, have further promoted cellular imaging using traditional fluorophores. These advancements include deciphering sensing mechanisms via photochemical reactions and scrutinizing the applications of fluorescent probes that specifically target organelles. This approach elucidates molecular interactions with biomolecules. Despite the abundance of literature illustrating different classes of probe development, a concise summary of newly developed fluorophores remains inadequate. In this review, we systematically summarize the chronological discovery of traditional fluorophores along with new fluorophores. We briefly discuss traditional fluorophores ranging from visible to near-infrared (NIR) in the context of cellular imaging and in vivo imaging. Furthermore, we explore ten new core fluorophores developed between 2007 and 2022, which exhibit advanced optical properties, providing new insights into bioimaging. We illustrate the utilization of new fluorophores in cellular imaging of biomolecules, such as reactive oxygen species (ROS), reactive nitrogen species (RNS), and proteins and microenvironments, especially pH and viscosity. Few of the fluorescent probes provided new insights into disease progression. Furthermore, we speculate on the potential prospects and significant challenges of existing fluorophores and their potential biomedical research applications. By addressing these aspects, we intend to illuminate the compelling advancements in fluorescent probe development and their potential influence across various fields.

Synthesis of Di(thiophen-2-yl) Substituted Pyrene-Pyridine Conjugated Scaffold and DFT Insights: A Selective and Sensitive Colorimetric, and Ratiometric Fluorescent Sensor for Fe(III) Ions

In this context, we used the multicomponent Chichibabin pyridine synthesis reaction to synthesize a novel di(thiophen-2-yl) substituted and pyrene-pyridine fluorescent molecular hybrid. The computational (DFT and TD-DFT) and experimental investigations were performed to understand the photophysical properties of the synthesized new structural scaffold. The synthesized ligand displays highly selective fluorescent sensing properties towards Fe3+ ions when compared to other competitive metal ions (Al3+, Ba2+, Ca2+, Cd2+, Co2+, Cr3+, Cu2+, Fe2+, Hg2+, Na+, Ni2+, Pb2+, Sr2+, Sn2+ and Zn2+). The photophysical properties studies reveal that the synthesized hybrid molecule has a binding constant of 2.30 × 103 M-1 with limit of detection (LOD) of 4.56 × 10-5 M (absorbance mode) and 5.84 × 10-5 M (emission mode) for Fe3+ ions. We believe that the synthesized pyrene-conjugated hybrid ligand can serve as a potential fluorescent chemosensor for the selective and specific detection of Fe3+ ions.

Recent design strategies and applications of organic fluorescent probes for food freshness detection

Food spoilage poses a significant risk to human health, making the assessment of food freshness essential for ensuring food safety and quality. In recent years, there has been rapid progress in the development of fast detection technologies for food freshness. Among them, organic fluorescent probes have garnered significant attention in the field of food safety and sensing due to their easy functionalization, high sensitivity, and user-friendly nature. To comprehensively examine the latest advancements in organic fluorescent probes for food freshness detection, this review summarized their applications within the past five years. Initially, the fundamental detection principles of organic fluorescent probes are outlined. Subsequently, the recent research progress in utilizing organic fluorescent probes to detect various chemical indicators of freshness are discussed. Finally, the challenges and future directions for organic fluorescent probes in food freshness detection are elaborated upon. While, organic fluorescent probes have demonstrated their effectiveness in evaluating food freshness and possess great potential for practical applications, further research is still needed to enable their widespread commercial utilization. With continued advancements in synthesis and functionalization techniques, organic fluorescent probes will contribute to enhancing the efficiency of food safety detection.

Nile Blue: A Red-Emissive Fluorescent Dye That Displays Differential Self-Assembly and Binding to G-Quadruplexes

Nile Blue (NB) is a red-emissive dye that is well-known for imaging and staining applications. In this work, we describe the interaction of NB with various types of G-quadruplexes belonging to different topologies, molecularities, and conformations. Using spectroscopic techniques, we have determined the preferential binding of NB to c-Myc G-quadruplex and the other aspects of its binding. Concentration- and temperature-dependent studies showed that NB exists in a dynamic equilibrium between monomeric and H-aggregated states, which could be modulated by the addition of external agents such as anionic surfactants. NB displayed differential self-assembly with different types of G-quadruplex and duplex DNAs modulating its dynamic equilibrium between the monomeric and H-aggregated states. Fluorescence-based displacement studies revealed a 1:1 binding stoichiometry upon interaction with c-Myc G-quadruplex and an association constant of Kapp = 6.7 × 106 M-1. Circular dichroism studies indicated that NB does not cause changes in the overall conformation of either G-quadruplexes or duplexes; however, it does indicate nucleic acid-dependent self-assembly at higher concentrations. Heat capacity measurement showed a more negative change when compared to that in DNA duplex, indicating more burial of the polar surface area by NB to the G-quadruplex host.

AutoParams: An Automated Web-Based Tool To Generate Force Field Parameters for Molecular Dynamics Simulations

Many research questions benefit from molecular dynamics simulations to observe the motions and conformations of molecules over time, which rely on force fields that describe sets of common molecules by category. With the increase of importance for large data sets used in machine learning and growing computational efficiency, the ability to rapidly create large numbers of force field inputs is of high importance. Unusual molecules, such as nucleotide analogues, functionalized carbohydrates, and modified amino acids, are difficult to describe consistently using standard force fields, requiring the development of custom parameters for each unique molecule. While these parameters may be created by individual users, the process can become time-consuming or may introduce errors that may not be immediately apparent. We present an open-source automated parameter generation service, AutoParams, which requires minimal input from the user and creates useful Amber force field parameter sets for most molecules, particularly those that combine molecular types (e.g., a carbohydrate functionalized with a benzene). We include hierarchical atom-typing logic that makes it straightforward to expand with additional force fields and settings, and options for creating monomers in polymers, such as functionalized amino acids. It can be straightforwardly linked to any charge generation program and currently has interfaces to Psi4, PsiRESP, and TeraChem. It is open source and is available via GitHub. It includes error checking and testing protocols to ensure the parameters will be sufficient for subsequent molecular dynamics simulations and streamlines the creation of force field databases.

Spectroscopic techniques for monitoring stem cell and organoid proliferation in 3D environments for therapeutic development

Spectroscopic techniques for monitoring stem cell and organoid proliferation have gained significant attention in therapeutic development. Spectroscopic techniques such as fluorescence, Raman spectroscopy, and infrared spectroscopy offer noninvasive and real-time monitoring of biochemical and biophysical changes that occur during stem cell and organoid proliferation. These techniques provide valuable insight into the underlying mechanisms of action of potential therapeutic agents, allowing for improved drug discovery and screening. This review highlights the importance of spectroscopic monitoring of stem cell and organoid proliferation and its potential impact on therapeutic development. Furthermore, this review discusses recent advances in spectroscopic techniques and their applications in stem cell and organoid research. Overall, this review emphasizes the importance of spectroscopic techniques as valuable tools for studying stem cell and organoid proliferation and their potential to revolutionize therapeutic development in the future.

Rational Design of Cost-Effective 4-Styrylcoumarin Fluorescent Derivatives for Biomolecule Labeling

Fluorescent labels are key tools in a wide range of modern scientific applications, such as fluorescence microscopy, flow cytometry, histochemistry, direct and indirect immunochemistry, and fluorescence in situ hybridization (FISH). Small fluorescent labels have important practical advantages as they allow maximizing the fluorescence signal by binding multiple fluorophores to a single biomolecule. At present, the most widely used fluorescent labels available present small Stokes shifts and are too costly to be used in routine applications. In this work we present four new coumarin derivatives, as promising and inexpensive fluorescent labels for biomolecules, obtained through a cost-effective, efficient, and straightforward synthetic strategy. Density functional theory and time-dependent density functional theory calculations of the electronic ground and lowest-lying singlet excited states were carried out in order to gain insights into the observed photophysical properties.

Amphiphilic Fluorinated Unimer Micelles as Nanocarriers of Fluorescent Probes for Bioimaging

The unique self-assembly properties of unimer micelles are exploited for the preparation of fluorescent nanocarriers embedding hydrophobic fluorophores. Unimer micelles are constituted by a (meth)acrylate copolymer with oligoethyleneglycol and perflurohexylethyl side chains (PEGMA90-co-FA10) in which the hydrophilic and hydrophobic comonomers are statistically distributed along the polymeric backbone. Thanks to hydrophobic interactions in water, the amphiphilic copolymer forms small nanoparticles (<10 nm), with tunable properties and functionality. An easy procedure for the encapsulation of a small hydrophobic molecule (C153 fluorophore) within unimer micelles is presented. UV-vis, fluorescence, and fluorescence anisotropy spectroscopic experimental data demonstrate that the fluorophore is effectively embedded in the nanocarriers. Moreover, the nanocarrier positively contributes to preserve the good emissive properties of the fluorophore in water. The efficacy of the dye-loaded nanocarrier as a fluorescent probe is tested in two-photon imaging of thick ex vivo porcine scleral tissue.

Chemical biology fluorescent tools for in vitro investigation of the multidrug resistant P-glycoprotein (P-gp) expression in tumor cells

Selective P-glycoprotein (P-gp)-targeted fluorescent conjugates are desirable tools to investigate the role of P-gp, a protein strongly implicated in mediating multidrug resistance and a major cause of chemotherapy failure. Herein, we report the development of 25 novel fluorescent small-molecule conjugates with varying physicochemical and optical properties, and their biological evaluation in a cell model as P-gp targeted constructs. This investigation revealed relationships between molecular structure and cell behavior and uncovered the capacity of conjugates with varying fluorophores to selectively target P-gp. Sulfocyanine 3 labeled conjugates (5, 10, 24, 29, 34) showed a particular intracellular staining pattern. Other conjugates bearing a boron dipyrromethene (BODIPY) core (3, 8, 13, 22, 27 (BODIPY FL), 12 (BODIPY 564/570) and 4, 9 (BODIPY 650/665)) or a 7-nitrobenz-2-oxa-1,3-diazole (NBD) core (11, 30) showed potential for global P-gp direct detection and quantification. These fluorescent conjugates holds key advantages over existing methods for drug resistance evaluation with regards to P-gp expression and could be used as innovative tools in preclinical assays and clinical diagnosis.

Vascularized tumor on a microfluidic chip to study mechanisms promoting tumor neovascularization and vascular targeted therapies

The cascade of events leading to tumor formation includes induction of a tumor supporting neovasculature as a primary hallmark of cancer. Developing vasculature is difficult to evaluate in vivo but can be captured using microfluidic chip technology and patient derived cells. Herein, we established an on chip approach to investigate the mechanisms promoting tumor vascularization and vascular targeted therapies via co-culture of metastatic renal cell carcinoma spheroids and endothelial cells in a 3D environment. Our model permitted real-time, high-resolution observation and assessment of tumor-induced angiogenesis, where endothelial cells sprout towards the tumor and mimic a vascular network. Bevacizumab, an angiogenic inhibitor, disrupted interactions between vessels and tumors, destroying the vascular network. The on chip approach enabled assessment of endothelial cell biology, vessel's functionality, drug delivery, and molecular expression of PSMA. Finally, observations in the vascularized tumor on chip permitted direct and conclusive quantification of this therapy in weeks as opposed to months in a comparable animal model.

Teaser

Vascularized tumor on microfluidic chip provides opportunity to study targeted therapies and improves preclinical drug discovery.

Plasmonic Fluorescence Enhancement in Diagnostics for Clinical Tests at Point-of-Care: A Review of Recent Technologies

Fluorescence-based biosensors have widely been used in the life-sciences and biomedical applications due to their low limit of detection and a diverse selection of fluorophores that enable simultaneous measurements of multiple biomarkers. Recent research effort has been made to implement fluorescent biosensors into the exploding field of point-of-care testing (POCT), which uses cost-effective strategies for rapid and affordable diagnostic testing. However, fluorescence-based assays often suffer from their feeble signal at low analyte concentrations, which often requires sophisticated, costly, and bulky instrumentation to maintain high detection sensitivity. Metal- and metal oxide-based nanostructures offer a simple solution to increase the output signal from fluorescent biosensors due to the generation of high field enhancements close to a metal or metal oxide surface, which has been shown to improve the excitation rate, quantum yield, photostability, and radiation pattern of fluorophores. This article provides an overview of existing biosensors that employ various strategies for fluorescence enhancement via nanostructures and have demonstrated the potential for use as POCT. Biosensors using nanostructures such as planar substrates, freestanding nanoparticles, and metal-dielectric-metal nanocavities are discussed with an emphasis placed on technologies that have shown promise towards POCT applications without the need for centralized laboratories.

Highly sensitive fluorescent probes for selective detection of hypochlorite: Applications in blood serum and cell imaging

Being one of the vital reactive oxygen species (ROS), abnormal level of hypochlorite ion (ClO^-) may pose detrimental threats to living organisms. Therefore, highly selective, and rapid monitoring of ClO^- in living system is of prime importance to protect living organisms from its harmful effects. In this regard, design of synthetic fluorescent probes for ClO^- has garnered considerable attention. However less fluorescence emission in aggregated state and less photostability of several existing probes for ClO^- inspired us to design aggregation induced emission (AIE) active fluorescent probes SH1 and SH2. Probes were rationally designed by introducing thiourea moiety that selectively reacted through desulfurization reaction and resulted in highly selective detection of ClO^-. Hypochlorite induced desulfurization reaction was validated through ¹H NMR titration and DFT studies. Fine tuning of probes SH1 and SH2 prompted highly sensitive nanoscale (55 nM and 77 nM) and rapid (15 and 35 sec) detection of ClO^-. Probe SH1 displayed less cytotoxic effect to live cells before it was successfully applied for bioimaging of ClO^- in live MCF-7 cells. Moreover, probes displayed excellent sensing potential for ClO^- in blood serum and real water samples. Advantageously, probe coated portable fluorescent films were fabricated for the easy and fast monitoring of ClO^-. Of note, this work offers excellent design strategy for highly selective detection of ClO^- that may lead to clinical trials.

In Vivo Fluorescence Molecular Imaging Using Covalent Organic Nanosheets Without Labeling

Organic nanomaterials, as nanocarrier platforms, have tremendous potential for biomedical applications. The authors successfully prepared novel two-dimensional covalent organic nanosheets (CONs) that can be used as efficient in vivo bioimaging probes by condensing 1,3,5-triformylglucinol (Tp) and 2,7-diaminopyrene (Py) to produce TpPy covalent organic frameworks (COFs). TpPy COFs are then subjected to a liquid exfoliation process to obtain TpPy CONs (< 200 nm in size and < 1.7 nm in thickness). TpPy CONs disperse well in water to provide a stable, homogeneous colloidal suspension, which shows favorable photoluminescence properties. Cell viability tests using MDA-MB-231 and RAW 264.7 cells reveal that TpPy CONs are low in cytotoxicity. Confocal microscopy reveals clear fluorescent cell images after incubation with TpPy CONs for 24 h, without reduction in cell activity or cytosolic aggregation. To investigate the biological behavior of the TpPy CONs, the authors perform an in vivo fluorescence imaging study using MDA-MB-231 tumor-bearing mice. After intravenous injection of TpPy CONs disperse in phosphate-buffered saline (PBS), persistent and strong fluorescence signals are observed in the tumor region, with low background signals from normal tissues at 1, 3, 12, and 24 h after injection. Furthermore, these in vivo imaging results concurred with ex vivo biodistribution and histological results.

Recent Progress in the Rational Design of Biothiol-Responsive Fluorescent Probes

Biothiols such as cysteine, homocysteine, and glutathione play significant roles in important biological activities, and their abnormal concentrations have been found to be closely associated with certain diseases, making their detection a critical task. To this end, fluorescent probes have become increasingly popular due to their numerous advantages, including easy handling, desirable spatiotemporal resolution, high sensitivity, fast response, and favorable biocompatibility. As a result, intensive research has been conducted to create fluorescent probes for the detection and imaging of biothiols. This brief review summarizes recent advances in the field of biothiol-responsive fluorescent probes, with an emphasis on rational probe design, including the reaction mechanism, discriminating detection, reversible detection, and specific detection. Furthermore, the challenges and prospects of fluorescence probes for biothiols are also outlined.

A modular aldol approach for internal fluorescent molecular rotor chalcone surrogates for DNA biosensing applications

Fluorescent molecular rotors (FMRs) are critical tools for probing nucleic acid structure and function. Many valuable FMRs have been incorporated into oligonucleotides, although the methods of doing so can be cumbersome. Development of synthetically simple, high yielding modular methods to fine-tune dye performance is crucial to expand the biotechnological applications of oligonucleotides. Herein, we report the utility of 6-hydroxy-indanone (6HI) with a glycol backbone to serve as a handle for on-strand aldehyde capture as a modular aldol approach for site-specific insertion of internal FMR chalcones. Aldol reactions with aromatic aldehydes containing N-donors proceed in high yield to create modified DNA oligonucleotides, which in the duplex match the stability of the fully paired canonical B-form with strong stacking interactions between the planar probe and the flanking base pairs, as evidenced by molecular dynamics (MD) simulations. The FMR chalcones possess remarkable quantum yields (Φ_fl up to 76%) in duplex DNA, coupled with large Stokes shifts (Δν up to 155 nm), light-up emissions (I_rel up to 60-fold) that span the visible region (λ_em 518-680 nm) with brightness up to 17 480 cm^-1 M^-1. The library also contains a FRET pair and dual emission probes, suitable for ratiometric sensing. The ease of aldol insertion coupled with the excellent performance of the FMR chalcones permits their future wide-spread use.

PET radiotracers and fluorescent probes for imaging human carbonic anhydrase IX and XII in hypoxic tumors

Positron emission tomography (PET) and fluorescent imaging play a pivotal role in medical diagnosis, biomedical oncologic research, and drug development process, which include identification of target location, target engagement, but also prove on mechanism of action or pharmacokinetics of new drug candidates. PET estimates physiological changes at the molecular level using specific radiotracers containing a short-lived positron emitting radionuclide such as fluorine-18 or carbon-11, whereas fluorescent imaging techniques use fluorescent probes labeled with suitable drug candidates for detection at the molecular level. The human carbonic anhydrase (hCA) isoforms IX and XII are overexpressed in hypoxic cancer cells, promoting tumor growth by regulating extra/intracellular pH, ferroptosis, and metabolism, being recognized as promising targets for anticancer theranostic agents. In this review, we have focused on PET radiotracers as well as fluorescent probes for diagnosis and treatment of tumors expressing hCA IX and hCA XII.

Luminescence and Palladium: The Odd Couple

The synthesis, photophysical properties, and applications of highly fluorescent and phosphorescent palladium complexes are reviewed, covering the period 2018–2022. Despite the fact that the Pd atom appears closely related with an efficient quenching of the fluorescence of different molecules, different synthetic strategies have been recently optimized to achieve the preservation and even the amplification of the luminescent properties of several fluorophores after Pd incorporation. Beyond classical methodologies such as orthopalladation or the use of highly emissive ligands as porphyrins and related systems (for instance, biladiene), new concepts such as AIE (Aggregation Induced Emission) in metallacages or in coordination-driven supramolecular compounds (CDS) by restriction of intramolecular motions (RIM), or complexes showing TADF (Thermally Activated Delayed Fluorescence), are here described and analysed. Without pretending to be comprehensive, selected examples of applications in areas such as the fabrication of lighting devices, biological markers, photodynamic therapy, or oxygen sensing are also here reported.

Tunable Photoinduced Charge Transfer at the Interface between Benzoselenadiazole-Based MOF Linkers and Thermally Activated Delayed Fluorescence Chromophore

Structural modifications to molecular systems that lead to the control of photon emission processes at the interfaces between photoactive materials play a key role in the development of fluorescence sensors, X-ray imaging scintillators, and organic light-emitting diodes (OLEDs). In this work, two donor-acceptor systems were used to explore and reveal the effects of slight changes in chemical structure on interfacial excited-state transfer processes. A thermally activated delayed fluorescence (TADF) molecule was chosen as the molecular acceptor. Meanwhile, two benzoselenadiazole-core MOF linker precursors, Ac-SDZ and SDZ, with the presence and absence of a C≡C bridge, respectively, were carefully chosen as energy and/or electron-donor moieties. We found that the SDZ -TADF donor-acceptor system exhibited efficient energy transfer, as evidenced by steady-state and time-resolved laser spectroscopy. Furthermore, our results demonstrated that the Ac-SDZ-TADF system exhibited both interfacial energy and electron transfer processes. Femtosecond-mid-IR (fs-mid-IR) transient absorption measurements revealed that the electron transfer process takes place on the picosecond timescale. Time-dependent density functional theory (TD-DFT) calculations confirmed that photoinduced electron transfer occurred in this system and demonstrated that it takes place from C≡C in Ac-SDZ to the central unit of the TADF molecule. This work provides a straightforward way to modulate and tune excited-state energy/charge transfer processes at donor-acceptor interfaces.

Development of a push-π-pull phenothiazine-vinyl-isophorone fluorophore: a novel solvatochromic and pH indicator

Knoevenagel condensation of phenothiazine-3,7-dicarbaldehyde with an isophorone yielded a new phenothiazine derivative (PTZ-c) fluorophore. The solvatochromic and pH-sensing abilities of PTZ-c, an asymmetric fluorophore with a single isophorone molecule, were shown to be exceptional. PTZ-c produced very delicate absorbance and emission spectra. When the polarity of the solvent was increased, the PTZ-c emission spectra showed greater sensitivity than the absorption spectra. Multiple spectroscopic techniques, including Fourier transform infrared spectroscopy, nuclear magnetic resonance, and mass spectrometry, were used to characterize the manufactured PTZ-c sensor. To demonstrate the beneficial solvatochromic behaviour associated with intramolecular charge transfer, the absorption spectra of the synthesized DA PTZ-c dye were analyzed in different solvents of varying polarity. Band intensity and the wavelength of PTZ-c emission were also found to be highly solvent dependent. It was observed that when solvent polarity was increased to a maximum of 4122 cm^-1 , Stokes' shift also increased. To analyze the Stokes' shift that depended on the solvent, a linear correlation between solvation and energy was used. An investigation of PTZ-c quantum yield (ф) was also conducted. Both the absorbance and fluorescence spectra of the sensor in dimethylformamide as a function of pH were studied. A fluorescence peak was seen at 562 nm, whereas the greatest absorption wavelengths were found at 403 and 317 nm. It was shown that the pH-sensing mechanism depended on protons removed from the PTZ-c chromophore, which caused a colour shift and variation in both emission and colorimetric properties.

Synthesis, Optical Properties, and Antiproliferative Evaluation of NBD-Triterpene Fluorescent Probes

A fluorescent labeling protocol for hydroxylated natural compounds with promising antitumor properties has been used to synthesize, in yields of 72-86%, 12 derivatives having fluorescent properties and biological activity. The reagent used for the synthesis of these fluorescent derivatives was 7-nitrobenzo-2-oxa-1,3-diazole chloride (NBD-Cl). The linkers employed to bind the NBD-Cl reagent to the natural compounds were ω-amino acids (Aa) of different chain lengths. The natural triterpene compounds chosen were oleanolic and maslinic acid, as their corresponding 28-benzylated derivatives. Thus, 12 NBD-Aa-triterpene conjugates have been studied for their optical fluorescence properties and their biological activities against cell proliferation in three cancer cell lines (B16-F10, HT-29, and HepG2), compared with three nontumor cell lines (HPF, IEC-18, and WRL68) from different tissues. The results of the fluorescence study have shown that the best fluorescent labels are those in which the ω-amino acid chain is shorter, and the carboxylic group is not benzylated. Analysis by confocal microscopy showed that these compounds were rapidly incorporated into cells in all three cancer cell lines, with these same derivatives showing the highest toxicity against the cancer cell lines tested. Then, the fluorescent labeling of these NBD-Aa-triterpene conjugates enabled their uptake and subcellular distribution to be followed in order to probe in detail their biological properties at the cellular and molecular level.

Strong Coupling between Surface Plasmon Resonance and Exciton of Labeled Protein-Dye Complex for Immunosensing Applications

In this study, we present an analysis of the optical response of strong coupling between SPR and labeled proteins. We demonstrate a sensing methodology that allows to evaluate the protein mass adsorbed to the gold's surface from the Rabi gap, which is a direct consequence of the strong light-matter interaction between surface plasmon polariton and dye exciton of labeled protein. The total internal reflection ellipsometry optical configuration was used for simulation of the optical response for adsorption of HSA-Alexa633 dye-labeled protein to a thin gold layer onto the glass prism. It was shown that Rabi oscillations had parabolic dependence on the number of labeled proteins attached to the sensor surface; however, for photonic-plasmonic systems in real experimental conditions, the range of the Rabi energy is rather narrow, thus it can be linearly approximated. This approach based on the strong coupling effect paves the alternative way for detection and monitoring of the interaction of the proteins on the transducer surface through the change of coupling strengths between plasmonic resonance and the protein-dye complex.

Solvatochromic Sensitivity of BODIPY Probes: A New Tool for Selecting Fluorophores and Polarity Mapping

This research work is devoted to collecting a high-quality dataset of BODIPYs in a series of 10-30 solvents. In total, 115 individual compounds in 71 solvents are represented by 1698 arrays of the spectral and photophysical properties of the fluorophore. Each dye for a series of solvents is characterized by a calculated value of solvatochromic sensitivity according to a semiempirical approach applied to a series of solvents. The whole dataset is classified into 6 and 24 clusters of solvatochromic sensitivity, from high negative to high positive solvatochromism. The results of the analysis are visualized by the polarity mapping plots depicting, in terms of wavenumbers, the absorption versus emission, stokes shift versus - (absorption maxima + emission maxima), and quantum yield versus stokes shift. An analysis of the clusters combining several dyes in an individual series of solvents shows that dyes of a high solvatochromic sensitivity demonstrate regular behaviour of the corresponding plots suitable for polarity and viscosity mapping. The fluorophores collected in this study represent a high quality dataset of pattern dyes for analytical and bioanalytical applications. The developed tools could be applied for the analysis of the applicability domain of the fluorescent sensors.

Polymeric dual-modal imaging nanoprobe with two-photon aggregation-induced emission for fluorescence imaging and gadolinium-chelation for magnetic resonance imaging

Nanoprobes that offer both fluorescence imaging (FI) and magnetic resonance imaging (MRI) can provide supplementary information and hold synergistic advantages. However, synthesis of such dual-modality imaging probes that simultaneously exhibit tunability of functional groups, high stability, great biocompatibility and desired dual-modality imaging results remains challenging. In this study, we used an amphiphilic block polymer from (ethylene glycol) methyl ether methacrylate (OEGMA) and N-(2-hydroxypropyl) methacrylamide (HPMA) derivatives as a carrier to conjugate a MR contrast agent, Gd-DOTA, and a two-photon fluorophore with an aggregation-induced emission (AIE) effect, TPBP, to construct a MR/two-photon fluorescence dual-modality contrast agent, Gd-DOTA-TPBP. Incorporation of gadolinium in the hydrophilic chain segment of the OEGMA-based carrier resulted in a high r₁ value for Gd-DOTA-TPBP, revealing a great MR imaging resolution. The contrast agent specifically accumulated in the tumor region, allowing a long enhancement duration for vascular and tumor contrast-enhanced MR imaging. Meanwhile, coupling TPBP with AIE properties to the hydrophobic chain segment of the carrier not only improved its water solubility and reduced its cytotoxicity, but also significantly enhanced its imaging performance in an aqueous phase. Gd-DOTA-TPBP was also demonstrated to act as an excellent fluorescence probe for two-photon-excited bioimaging with higher resolution and greater sensitivity than MRI. Since high-resolution, complementary MRI/FI dual-modal images were acquired at both cellular and tissue levels in tumor-bearing mice after application of Gd-DOTA-TPBP, it has great potential in the early phase of disease diagnosis.

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A highly stable and biocompatibility MR/two-photon AIE fluorescent dual-modality imaging probe Gd-DOTA-TPBP is prepared.

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Gd-DOTA and TPBP are conjugated to the hydrophilic and hydrophobic chain of the amphiphilic block polymer, respectively.

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The different coupling sites of Gd-DOTA and TPBP promote dual-modality imaging effects of Gd-DOTA-TPBP after self-assembly.

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The dual-modality images with Gd-DOTA-TPBP have obtained complementary information at the cellular and tissue level in vivo.

Synthesis of nitrogen mustard-based fluorophores for cell imaging and cytotoxicity studies

Nitrogen mustards are important alkylating anticancer drugs used for neoplasms treatment. However, little research about the integration of luminophore into nitrogen mustard-based compounds for both imaging and therapeutic application was reported. In this study, we report a series of novel nitrogen mustard-containing 1-furyl-2-en-1-one and 1-thienyl-2-en-1-one derivatives as intramolecular charge transfer-based luminophore for research in both imaging subcellular localization and antiproliferation toward lung cancer cells. The target products were prepared by Knoevenagel condensation and characterized by nuclear magnetic resonance and high-resolution mass spectrometer. The absorption and fluorescence studies were carried out by ultraviolet-visible and fluorescence spectrophotometers, respectively. Cell morphology was observed under an inverted microscope. Cytotoxicity test was detected by MTT assay. Cellular localization was observed by a confocal laser scanning microscope. Colony formation ability was carried out by colony formation assay. Cell migration ability was detected by transwell migration assay. Differences between the two groups were analyzed by two-tailed Student's t-test. The difference with P < 0.05 (*) was considered statistically significant. The compounds were synthesized in high yield. The λmax and Stokes shift of these compounds reach up to 567 and 150 nm, respectively. These compounds exhibited good antiproliferative activity against lung cancer cells, with compound 3h exhibiting the best IC50 of 13.1 ± 2.7 μM. Furthermore, the selected compound 3h is located preferentially in lysosomes and a small amount in nuclei, effectively inhibiting cell colony formation and migration abilities toward A549 cells. These findings suggested that nitrogen mustard-based fluorophores might be a potential effective chemotherapeutic agent in lung cancer therapy.

In vivo protein-based biosensors: seeing metabolism in real time

Biological homeostasis is a dynamic and elastic equilibrium of countless interlinked biochemical reactions. A key goal of life sciences is to understand these dynamics; bioengineers seek to reconfigure such networks. Both goals require the ability to monitor the concentration of individual intracellular metabolites with sufficient spatiotemporal resolution. To achieve this, a range of protein or protein/DNA signalling circuits with optical readouts have been constructed. Protein biosensors can provide quantitative information at subsecond temporal and suborganelle spatial resolution. However, their construction is fraught with difficulties related to integrating the affinity- and selectivity-endowing components with the signal reporters. We argue that development of efficient approaches for construction of chemically induced dimerisation systems and reporter domains with large dynamic ranges will solve these problems.

Near-Infrared Dyes: Towards Broad-Spectrum Antivirals

Broad antiviral activity in vitro is known for many organic photosensitizers generating reactive oxygen species under irradiation with visible light. Low tissue penetration of visible light prevents further development of antiviral therapeutics based on these compounds. One possible solution to this problem is the development of photosensitizers with near-infrared absorption (NIR dyes). These compounds found diverse applications in the photodynamic therapy of tumors and bacterial infections, but they are scarcely mentioned as antivirals. In this account, we aimed to evaluate the therapeutic prospects of various NIR-absorbing and singlet oxygen-generating chromophores for the development of broad-spectrum photosensitizing antivirals.

In Vitro and In Vivo Evaluation of Targeted Fluorescent Imaging Agents for Diagnosis and Resection of Cancer

Local re-occurrence of cancer in patients with solid tumors is currently the most common reason for failure of treatment strategies. This fact indicates that prevailing approaches for tumor resection can cure only 50% of patients. A major cause of failure in tumor resection is off-target drug cytotoxicity and lack of sensitivity in tumor detection methods. These disadvantages are addressed with the development of targeted therapy and diagnostics, which significantly aid treatment strategies. Targeted diagnostics exploit properties of tumor cells that show significant up-regulation of tumor biomarkers. These biomarkers are targeted by a homing ligand attached to a fluorophore for visual inspection during surgery. However, these approaches suffer from disadvantages like high autofluorescence from background tissues, tissue absorption, and scattering, resulting in decreased image sensitivity and resolution. The use of near-infrared (NIR) fluorophores to overcome these drawbacks has generated unprecedented interest among researchers. The NIR window lies within the range of 650 to 1,700 nm, which results in reduced absorption and scattering by the tissues, thereby providing deeper tissue penetration and reduced autofluorescence. NIR fluorophores can be designed to target tumor biomarkers such as prostate specific membrane antigen (PSMA) or folate receptors found over-expressed on cancer tissues. These targeted fluorophores consist of small-molecule ligands conjugated with NIR dyes that bind with high specificity to PSMA and folic acid receptors. In this protocol, we have extensively described the methodology for the synthesis of targeted NIR agents for PSMA (DUPA-NIR bioconjugate) and folic acid (folate-NIR bioconjugate), along with detailed steps for preclinical evaluation. Procedures to calculate the binding affinity to cancer cells in vitro are described, along with uptake and biodistribution in different mice models in vivo. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Synthesis and purification of DUPA and folate-peptide linkers via a SPPS strategy Basic Protocol 2: Conjugation, purification, and characterization of targeted bioconjugates with NIR probe for deep-tissue imaging applications Basic Protocol 3: In vitro evaluation of binding affinity of targeted DUPA-NIR and folate-NIR bioconjugates using a spectrophotometer Basic Protocol 4: Induction of tumor in mice to develop CDX or metastatic tumor models Basic Protocol 5: Intravenous administration of targeted DUPA-NIR and folate-NIR bioconjugates in mouse CDX or metastatic tumor models for deep-tissue NIR imaging and tumor resection.