BODIPY-Based Fluorescent Probes for Sensing Protein Surface-Hydrophobicity

Small molecular fluorescent probes featuring protein-assisted functional amplification for improved biosensing and cancer therapeutics

In recent years, small molecular fluorescent probes have significantly advanced biosensing and cancer therapy, enabling applications such as target detection, cellular imaging, fluorescence-guided surgery, and phototherapy. However, conventional small molecular probes face limitations, including low biocompatibility, poor stability, and weak signal intensity. Protein-coordinated fluorescent probes have emerged as a promising solution, leveraging protein-assisted functional amplification to address these challenges. Mechanisms such as environmental shielding, conformational restriction, charge stabilization, and increased local concentration collectively enhance fluorescence emission and phototherapeutic efficacy. This article reviews recent progress (primarily within the last five years) in protein-coordinated fluorescent probes for biosensing and cancer therapy. It begins with a systematic summary of the interaction strategies between proteins and fluorescent probes and details key mechanisms behind protein-assisted functional amplification. Subsequently, the applications of these probes in biosensing and cancer therapy are comprehensively concluded. Finally, current challenges and future prospects are discussed in depth. This review aims to refine design strategies for protein-coordinated fluorescent probes and inspire innovative approaches in biosensing and cancer therapy.

Mechanistic investigation on cellular internalization triggering structure-induced conformational modulation of boron-nitrogen luminogens

Exploring the effects of electron donor (D) and acceptor (A) functional groups in tuning the condensed state properties has been a challenging yet efficient approach to reveal promising materials for cutting-edge applications. Herein, a series of boron-nitrogen (BN) incorporated organic congeners (NBNMe2, NBOMe, NBF, NBCl, NBBr, NBCN, NBPy) appended with functional groups having various degrees of D/A characteristics were developed and their potential in controlling supramolecular assembly and condensed state luminescence features (>90 nm redshift in λ em,max) was explored. Despite the minor structural engineering in BN-based small molecules, they effectively modulated conformational orientation and molecular packing, leading to the directed growth of distinct and highly ordered self-assembly patterns, i.e., nanosheets, nanospheres, nanowires, and nanorods. The structure-property correlation investigation also highlighted the time-dependent fluorescence enhancement for NBPy owing to morphological growth via the fusion of nanospheres into nanowire conformation. Further, these nano-architectures with distinct conformations were employed to examine the mechanistic aspects as well as the influence of morphologies in cellular uptake and imaging, where all the nano-aggregates exhibited lysosomal localization following multiple endocytosis pathways and the nanorods possessed the highest uptakes (CTCF4h/0.5h = 3.11) with respect to other conformations. The in-depth inspection of the structural impact in single crystal X-ray diffraction (SCXRD) analysis disclosed the decisive role of boron atoms and functional group tuning that built a conceptual correlation between the molecular architecture and their photophysical characteristics, supramolecular assembly, and cellular internalization process, offering key insights on the development of rapid and effective drug delivery techniques.

A BODIPY-Containing Covalent Organic Framework as a Highly Porous Photosensitizer for Environmental Remediation and Pollutants Adsorption

The direct incorporation of borondipyrromethene (BODIPY) subunits into the structural backbone of covalent organic frameworks (COFs) gives facile access to porous photosensitizers but is still a challenging task. Here, we introduce β-ketoenamine-linked BDP-TFP-COF, which crystallizes in AA-stacking mode with hcb topology. A comprehensive characterization reveals high crystallinity and enhanced stability in a variety of solvents, excellent mesoporosity (SABET=1042 m2 g-1), broad light absorption in the visible region, and red emission upon the exfoliation of few-layer COF nanosheets. The versatility of multifunctional BODIPY-COFs is highlighted in various applications. Pollutants Bisphenol A (BPA, qmax=426 mg g-1) and Methylene Blue (MB, qmax=96 mg g-1) have been efficiently removed from H2O. Fluorescence quenching or enhancement of exfoliated BDP-TFP-COF nanosheets have been utilized for dual-mode sensing of MB or NEt3, respectively. Ultimately, the photosensitizing effect of the BODIPY units is retained in the COF. Thus, BPD-TFP-COF was established as a metal-free triplet photosensitizer, which efficiently oxidized a mustard gas simulant under visible light irradiation.

Poly(p-Phenyleneethynylene)s-Based Sensor Array for Diagnosis of Clinical Diseases

Inspired by the mammalian taste and olfactory systems, array-based pattern recognition technology has demonstrated significant potential in discerning subtle differences between highly similar compounds and complex mixtures, owing to their unique parallel detection mechanism based on cross-reactive signals. While optical sensor array has been extensively employed in the field of chemical sensing, they encounter significant challenges in non-specific recognition of multiple analytes at low concentrations, particularly in rife environments with complex interferences. Poly(p-phenylene ethynylene)s (PPEs) offer substantial advantages in detecting multi-analytes at low concentrations, owing to its distinctive optical properties, including the "molecular wire" effect, fluorescence super-amplification and super-quenching. This is particularly promising for the parallel detection of ultra-low concentration multi-biomarkers in clinical diseases. As the continuous development of PPEs sensor array, more sensitive methods for rapid detection of clinical disease will be further developed. It will promote the further development of the field of early diagnosis of clinical diseases.

Targeted Adherence and Enhanced Degradation of Feather Keratins by a Novel Prepeptidase C-Terminal Domain-Fused Keratinase

Keratinases are valuable enzymes for converting feather keratin waste into bioactive products but often suffer from poor substrate specificity and low catalytic efficiency. This study reported the creating of a novel keratinase with targeted adherence and specific degradation on feather keratins by fusing prepeptidase C-Terminal (PPC) domain. A PPC domain of metalloprotease E423 specifically adsorbed feather keratins by hydrogen bonds and hydrophobic interactions in a time- and temperature-dependent manner. Stepwise N-/C-terminal truncations disclosed the essential core sequence composed of 21 amino acid residues determining the keratin-targeted adherence. Fusion of the core fragment with a flexible linker (GGGGS)1 achieved the optimal secretion, and improved the catalytic efficiency of a representative keratinase 4-3Ker-MAV by 0.97-fold. Moreover, the feather degradation rate increased from 65 to 82%, representing the highest reported performance for a keratinase. This PPC-fusion strategy opens new horizons in enzyme engineering, promising not only to revolutionize keratin waste valorization but also to inspire the design of substrate-specific biocatalysts across diverse industrial applications.

Pitfalls of Using ANS Dye Under Molecular Crowding Conditions

The 1-anilino-8-naphthalenesulfonate (ANS) fluorescent dye is widely used in protein folding studies due to the significant increase in its fluorescence quantum yield upon binding to protein hydrophobic regions that become accessible during protein unfolding. However, when modeling cellular macromolecular crowding conditions in protein folding experiments in vitro using crowding agents with guanidine hydrochloride (GdnHCl) as the denaturant, the observed changes in ANS spectral characteristics require careful consideration. This study demonstrates that crowding agents can form clusters that interact differently with ANS. Furthermore, GdnHCl can disrupt these clusters and directly affect the ANS spectral characteristics. A model for the interaction between GdnHCl, crowders, and ANS is proposed. Using bovine serum albumin (BSA) as a model protein, the limitations of using ANS for studying conformational transitions induced by GdnHCl in the presence of crowding agents are demonstrated.

Allergenicity Reduction of Bovine β-Lactoglobulin Binding to Lactic Acid by Masking Epitopes with Lactylation

Lactic acid, an important organic acid, commonly exists in a variety of foods. During food processing, lactic acid may undergo dehydration and condensation with proteins. This study investigated the effect of lactylation on the sensitization of bovine β-lactoglobulin during food processing. First, we screened 19 lactylation sites on β-lactoglobulin through mass spectrometry. Comparing the specific IgE/IgG epitopes of β-lactoglobulin, we found that lactylation masks it. At the same time, the structure of β-lactoglobulin is destroyed after binding to lactic acid. Animal experiment results show that the levels of antibodies (IgE and IgG1) and Th2-type cytokines (IL-4 and IL-13) in vivo induced by lactated β-lactoglobulin are significantly reduced. All results indicate that the allergenicity of β-lactoglobulin is reduced after lactylation. In conclusion, this study provides valuable insights into the molecular mechanisms underlying the reduction of β-lactoglobulin allergenicity by lactylation and lays a solid foundation for the application of lactylation in hypoallergenic foods.

Computational investigation of the effect of BODIPY labelling on peptide-membrane interaction

Optical monitoring of peptide binding to live cells is hampered by the abundance of naturally occurring fluorophores such as tryptophan. Unnatural amino acids incorporating synthetic fluorophores such as BODIPY overcome these optical limitations. A drawback to using fluorophores in lipid binding peptide design is their propensity to override other interactions, potentially causing the peptides to lose their binding selectivity. Here, the binding strength of a selection of peptides incorporating a variety of BODIPY derivatized amino acids has been studied via molecular dynamics simulations to quantify the impact of BODIPY incorporation on peptide-membrane binding behaviour.

Flaring Inflammation and ER Stress by an Organelle-Specific Fluorescent Cage

The endoplasmic reticulum (ER) plays an important role in protein synthesis and its disruption can cause protein unfolding and misfolding. Accumulation of such proteins leads to ER stress, which ultimately promotes many diseases. Routine screening of ER activity in immune cells can flag serious conditions at early stages, but the current clinically used bio-probes have limitations. Herein, an ER-specific fluorophore based on a biocompatible benzothiadiazole-imine cage (BTD-cage) with excellent photophysical properties is developed. The cage outperforms commercially available ER stains in long-term live cell imaging with no fading or photobleaching over time. The cage is responsive to different levels of ER stress where its fluorescence increases accordingly. Incorporating the bio-probe into an immune disorder model, a 6-, 21-, and 48-fold increase in intensity is shown in THP-1, Raw 246.7, and Jurkat cells, respectively (within 15 min). These results strongly support that this system can be used for rapid visual and selective detection of ER stress. It is envisaged that tailoring molecular interactions and molecular recognition using supramolecular improved fluorophores can expand the library of biological probes for enhanced selectivity and targetability toward cellular organelles.

Design and synthesis of a TICT-based red-emissive fluorescent probe for the rapid and selective detection of HSA in human biofluids and live cell imaging

Here, we report the design and synthesis of a D⋯π⋯A-based fluorescent probe, (E)-4-(4-(dibutylamine)-2-hydroxystyryl)-1-methylquinolin-1-ium (DHMQ), which is nonfluorescent in ∼100% PBS buffer medium due to a twisted intra molecular charge transfer (TICT) phenomenon and it becomes highly fluorescent (∼149 fold) in the presence of human serum albumin (HSA), owing to the restriction of its intramolecular free rotation inside the hydrophobic binding cavity of HSA. The site-selective fluorescence displacement assay and molecular docking studies clearly reveal that DHMQ selectively binds at subdomain IB of HSA. The 3σ/slope method was adopted to determine the limit of detection (LOD) value, which was as low as 2.39 nM in ∼100% PBS medium, indicating its high sensitivity towards HSA. The low dissociation constant value [Kd = (1.066 ± 0.017) μM] suggests a strong complexation between the DHMQ and HSA. Importantly, it has been demonstrated that DHMQ is capable of detecting HSA in real human serum and urine samples and was found to be suitable for live cell imaging of HSA.

Protein aggregation monitoring in cells under oxidative stress: a novel fluorescent probe based on a 7-azaindole-BODIPY derivative

The development of new fluorescent probes as molecular sensors is a critical step for the understanding of molecular mechanisms. BODIPY-based probes offer versatility due to their high fluorescence quantum yields, photostability, and tunable absorption/emission wavelengths. Here, we report the synthesis and evaluation of a novel 7-azaindole-BODIPY derivative to probe hydrophobic proteins as well as protein misfolding and aggregation. In organic solvents, this compound shows two efficiently interconverting emissive excited states. In aqueous environments, it forms molecular aggregates with unique photophysical properties. The complex photophysics of the 7-azaindole-BODIPY derivative was explored for sensing applications. In the presence of albumin, the compound is stabilized in hydrophobic protein regions, significantly increasing its fluorescence emission intensity and lifetime. Similar effects occur in the presence of protein aggregates but not with other macromolecules like pepsin, DNA, Ficoll 40, and coconut oil. Fluorescence lifetime imaging microscopy (FLIM) and two-photon fluorescence microscopy on breast (MCF-7) and lung (A549) cancer cells incubated with this compound display longer fluorescence lifetimes and higher emission intensity under oxidative stress. Synchrotron FTIR micro spectroscopy confirmed that the photophysical changes observed were due to protein misfolding and aggregation caused by the oxidative stress. These findings demonstrate that this compound can serve as a fluorescent probe to monitor protein misfolding and aggregation triggered by oxidative stress.

Nonperturbative Fluorogenic Labeling of Immunophilins Enables the Wash-free Detection of Immunosuppressants

Immunosuppressants are clinically approved drugs to treat the potential rejection of transplanted organs and require frequent monitoring due to their narrow therapeutic window. Immunophilins are small proteins that bind immunosuppressants with high affinity, yet there are no examples of fluorogenic immunophilins and their potential application as optical biosensors for immunosuppressive drugs in clinical biosamples. In the present work, we designed novel diazonium BODIPY salts for the site-specific labeling of tyrosine residues in peptides via solid-phase synthesis as well as for late-stage functionalization of whole recombinant proteins. After the optimization of a straightforward one-step labeling procedure for immunophilins PPIA and FKBP12, we demonstrated the application of a fluorogenic analogue of FKBP12 for the selective detection of the immunosuppressant drug tacrolimus, including experiments in urine samples from patients with functioning renal transplants. This chemical methodology opens new avenues to rationally design wash-free immunophilin-based biosensors for rapid therapeutic drug monitoring.

BODIPY(aryl)iodonium salts in the efficient synthesis of diversely functionalized BODIPYs and selective detection of serum albumin

BODIPY(aryl)iodonium salts were readily accessible from the high-yielding reaction of BODIPY with iodoarenes or hydroxyl(tosyloxy)iodoarenes in the presence of m-CPBA. The prepared BODIPY(aryl)iodonium salts bearing substituents of varied electronic nature were utilized for the direct syntheses of thiocyanate, azide, amine and acrylate functionalized BODIPYs and β,β'-bis-BODIPYs. The regioselective syntheses of α-piperidinyl and β-piperidinyl substituted BODIPYs were achieved through the reaction of BODIPY(aryl)iodonium salts with piperidine in the absence and presence of copper(I). Expeditious and high yielding (79-82%) synthesis of β,β'-bis-BODIPYs was also developed through the palladium-catalyzed reductive coupling of the easily accessible BODIPY(aryl)iodonium salts. Some of the indole-appended BODIPYs and bis-BODIPYs displayed strong absorption in the visible region (∼610 nm). The BODIPY(aryl)iodonium salts also showed significant binding with serum albumin and were observed to be selective serum protein sensors with estimated limits of detection as low as 7 μg mL-1 in some cases.

Comparative Analysis of Protein Surface Hydrophobicity Maps Determined by Sparse Sampling INDUS and Spatial Aggregation Propensity

Protein surface hydrophobicity plays a central role in various biological processes such as protein folding and aggregation, as well as in the design and manufacturing of biotherapeutics. While the hydrophobicity of protein surface patches has been linked to their constituent residue hydropathies, recent research has shown that protein surface hydrophobicity is more complex and characterized by the response of water to these surfaces. In this work, we employ water density perturbations to map the surface hydrophobicity of a set of model proteins using sparse indirect umbrella sampling simulations (SSI). This technique is used to identify hydrophobic surface patches for the set of model proteins, and the results are compared to those obtained from the widely adopted spatial aggregation propensity (SAP) technique. While SAP-based calculations show agreement with SSI in some cases, there are several examples of disagreement. We identify four general classes of difference in behavior and study factors that contribute to these differences. We find that the SAP method can sometimes mask the effect of weakly nonpolar or isolated nonpolar residues that can lead to strong hydrophobic patches on the protein surface. In addition, hydrophobic patches identified by SAP can exhibit shifts in both position and strength on the SSI map. Our results demonstrate that the combination of topography and chemical context controls the hydrophobicity of a given patch above and beyond the intrinsic polarity of the residues present on the patch surface. The availability of more accurate protein hydrophobicity maps in concert with new classes of hydrophobic molecular descriptors may create significant opportunities for in silico prediction of protein behavior for a range of applications, such as protein design, biomanufacturability, and downstream bioprocessing.

Synthesis, Structural, and Optical Properties of Azuleno[1,2-c]pyran-1-ones: Bro̷nsted Acid-Mediated Cyclization of 2-Azulenylalkynes

Pyrones and their aromatic ring-fused derivatives have gained significant attention due to their diverse biological activities and potential as foundational frameworks for advanced materials. In this paper, we describe a proficient approach for the preparation of azuleno[1,2-c]pyran-1-ones, which are difficult to produce by using conventional methods. The synthesis was achieved through Bro̷nsted acid-mediated cyclization of 2-azulenylalkynes. The structural and optical properties of azuleno[1,2-c]pyran-1-ones were characterized by single-crystal X-ray analysis, NMR, UV/vis, and fluorescence spectroscopies. Under acidic conditions, these compounds displayed notable spectral alterations and emission, distinct from their spectra in neutral medium. These results suggest that azuleno[1,2-c]pyran-1-ones hold great potential for applications in organic electronic materials and fluorescent pH sensors.

Ultrafast fluorescence depolarisation in green fluorescence protein tandem dimers as hydrophobic environment sensitive probes

Advances in ultra-fast photonics have enabled monitoring of biochemical interactions on a sub nano-second time scale. In addition, picosecond dynamics of intermolecular energy transfer in fluorescent proteins has been observed. Here, we present the development of a genetically encoded fluorescent sensor that can detect changes in hydrophobicity by monitoring ultrafast fluorescence depolarisation. Our sensor is composed of a pair of dimeric enhanced green fluorescent proteins (dEGFPs) linked by a flexible amino-acid linker. We show dimerisation is perturbed by the addition of glycerol which interferes with the hydrophobic interaction of the two proteins. Time-resolved fluorescence anisotropy revealed a systematic attenuation of ultrafast fluorescence depolarisation when the sensor was exposed to increasing glycerol concentrations. This suggests that as hydrophobicity increases, dEGFP pairing decreases within a tandem dimer. Un-pairing of the protein fluorophores dramatically alters the rate of energy transfer between the proteins, resulting in an increase in the limiting anisotropy of the sensor.

Surfactant Micellar and Vesicle Microenvironments and Structures under Synthetic Organic Conditions

Fluorescence lifetime imaging microscopy (FLIM) reveals vesicle sizes, structures, microenvironments, reagent partitioning, and system evolution with two chemical reactions for widely used surfactant-water systems under conditions relevant to organic synthesis, including during steps of Negishi cross-coupling reactions. In contrast to previous investigations, the present experiments characterize surfactant systems with representative organohalide substrates at high concentrations (0.5 M) that are reflective of the preparative-scale organic reactions performed and reported in water. In the presence of representative organic substrates, 2-iodoethylbenzene and 2-bromo-6-methoxypyridine, micelles swell into emulsion droplets that are up to 20 μm in diameter, which is 3-4 orders of magnitude larger than previously measured in the absence of an organic substrate (5-200 nm). The partitioning of reagents in these systems is imaged through FLIM─demonstrated here with nonpolar, amphiphilic, organic, basic, and oxidative-addition reactive compounds, a reactive zinc metal powder, and a palladium catalyst. FLIM characterizes the chemical species and/or provides microenvironment information inside micelles and vesicles. These data show that surfactants cause surfactant-dictated microenvironments inside smaller micelles (<200 nm) but that addition of a representative organic substrate produces internal microenvironments dictated primarily by the substrate rather than by the surfactant, concurrent with swelling. Addition of a palladium catalyst causes the internal environments to differ between vesicles─information that is not available through nor predicted from prior analytical techniques. Together, these data provide immediately actionable information for revising reaction models of surfactant-water systems that underpin the development of sustainable organic chemistry in water.

Switchable Hydrophobic Pockets in DNA Protocells Enhance Chemical Conversion

Synthetic cell models help us understand living cells and the origin of life. Key aspects of living cells are crowded interiors where secondary structures, such as the cytoskeleton and membraneless organelles/condensates, can form. These can form dynamically and serve structural or functional purposes, such as protection from heat shock or as crucibles for various biochemical reactions. Inspired by these phenomena, we introduce a crowded all-DNA protocell and encapsulate a temperature-switchable DNA-b-polymer block copolymer, in which the synthetic polymer phase-segregates at elevated temperatures. We find that thermoreversible phase segregation of the synthetic polymer occurs via bicontinuous phase separation, resulting in artificial organelle structures that can reorient into larger domains depending on the viscoelastic properties of the protocell interior. Fluorescent sensors confirm the formation of hydrophobic compartments, which enhance the reactivity of bimolecular reactions. This study leverages the strengths of biological and synthetic polymers to construct advanced biohybrid artificial cells that provide insights into phase segregation under crowded conditions and the formation of organelles and microreactors in response to environmental stress.

Turning Food Protein Waste into Sustainable Technologies

For each kilogram of food protein wasted, between 15 and 750 kg of CO2 end up in the atmosphere. With this alarming carbon footprint, food protein waste not only contributes to climate change but also significantly impacts other environmental boundaries, such as nitrogen and phosphorus cycles, global freshwater use, change in land composition, chemical pollution, and biodiversity loss. This contrasts sharply with both the high nutritional value of proteins, as well as their unique chemical and physical versatility, which enable their use in new materials and innovative technologies. In this review, we discuss how food protein waste can be efficiently valorized not only by reintroduction into the food chain supply but also as a template for the development of sustainable technologies by allowing it to exit the food-value chain, thus alleviating some of the most urgent global challenges. We showcase three technologies of immediate significance and environmental impact: biodegradable plastics, water purification, and renewable energy. We discuss, by carefully reviewing the current state of the art, how proteins extracted from food waste can be valorized into key players to facilitate these technologies. We furthermore support analysis of the extant literature by original life cycle assessment (LCA) examples run ad hoc on both plant and animal waste proteins in the context of the technologies considered, and against realistic benchmarks, to quantitatively demonstrate their efficacy and potential. We finally conclude the review with an outlook on how such a comprehensive management of food protein waste is anticipated to transform its carbon footprint from positive to negative and, more generally, have a favorable impact on several other important planetary boundaries.

Near-Infrared Probes for Biothiols (Cysteine, Homocysteine, and Glutathione): A Comprehensive Review

Biothiols (cysteine, homocysteine, and glutathione) are an important class of compounds with a free thiol group. These biothiols plays an important role in several metabolic processes in living bodies when present in optimum concentration. Researchers have developed several probes for the detection and quantification of biothiols that can absorb in UV, visible, and near-infrared (NIR) regions of the electromagnetic spectrum. Among them, NIR organic probes have attracted significant attention due to their application in in vivo and in vitro imaging. In this review, we have summarized probes for these biothiols, which could work in the NIR region, and discussed their sensing mechanism and potential applications. Along with focusing on the pros and cons of the reported probes we have classified them according to the fluorophore used and summarized their photophysical and sensing properties (emission, response time, limit of detection).

Progress in the Development of Imidazopyridine-Based Fluorescent Probes for Diverse Applications

Different classes of Imidazopyridine i.e., Imidazo[1,2-a]pyridine, Imidazo[1,5-a] pyridine, Imidazo[4,5-b]pyridine, have shown versatile applications in various fields. In this review, we have concisely presented the usefulness of the fluorescent property of imidazopyridine in different fields such as imaging tools, optoelectronics, metal ion detection, etc. Fluorescence mechanisms such as excited state intramolecular proton transfer, photoinduced electron transfer, fluorescence resonance energy transfer, intramolecular charge transfer, etc. are incorporated in the designed fluorophore to make it for fluorescent applications. It has been widely employed for metal ion detection, where selective metal ion detection is possible with triazole-attached imidazopyridine, β-carboline imidazopyridine hybrid, quinoline conjugated imidazopyridine, and many more. Also, other popular applications involve organic light emitting diodes and cell imaging. This review shed a light on recent development in this area especially focusing on the optical properties of the molecules with their usage which would be helpful in designing application-based new imidazopyridine derivatives.

Fluorogenic gemcitabine based light up sensor for serum albumin detection in complex biological matrices

Herein we report fluorogenic derivative of gemcitabine (GEM-DNS), synthesized from gemcitabine hydrochloride and dansyl chloride in a single step. Owing to its large stoke shift of ∼200 nm and intriguing photophysical properties, the said dye has been utilized to estimate albumin concentration in complex bio-media such as human urine and blood serum. High sensitivity and selectivity towards albumin make the aforementioned dye a powerful diagnostic tool to detect ailments such as liver cirrhosis, diabetes, hypertension etc.

Nonbenzenoid BODIPY Analogues: Synthesis, Structural Organization, Photophysical Studies, and Cell Internalization of Biocompatible N-Alkyl-Aminotroponyl Difluoroboron (Alkyl-ATB) Complexes

The alkyl-BODIPY derivatives are lipid types of fluorescent molecules that exhibit a unique structure and functions including sensing of hydrophobic microenvironments in living cells. Their synthesis involves multisteps from the core structure dipyrromethene scaffold. The alkyl-BODIPY analogues are sought to derivatize with minimal synthetic steps even by altering the core structures derived from benzenoid aromatic moiety. Recently, the nonbenzenoid scaffold (aminotropone) has been explored to synthesize troponyl-BODIPY analogues, which are fluorescent. In the repertoire of nonbenzenoid analogue, N-alkyl-aminotroponyl difluoroboron (alkyl-ATB) is rationally designed comprising long-chain hydrocarbons to explore the lipid type of fluorescent molecules. This report describes the synthesis, photophysical studies, structural organization, and biocompatibilities of ATB derivatives containing different lengths of alkyl chain at 2-aminotropone scaffold. The photophysical studies of ATB derivatives reveal their fluorescence behaviors in organic solvents (CH₃OH/CH₃CN) with a quantum yield of ∼10 to 15%. These ATB derivatives also exhibit fluorescence characters in the solid state though their quantum yield is relatively low. Cell permeability and cytotoxicity studies reveal that alkyl-ATB derivatives are permeable to HeLa/HEK293T cell lines and show negligible cytotoxicity. The biocompatibility of alkyl-ATB derivatives is studied and confirmed by cell viability (MTT) assay to the HeLa/HEK293T cell lines. Importantly, the cell internalization studies of the representative alkyl-ATB molecule by fluorescence microscopy show that octyl-ATB is efficiently detectable at the cytoplasmic membrane and cellular nucleus in HeLa cells. Hence, alkyl-ATB derivatives are potential fluorescent molecules for developing probes to visualize cellular components under a fluorescence microscope.

Application of meso-CF3-Fluorophore BODIPY with Phenyl and Pyrazolyl Substituents for Lifetime Visualization of Lysosomes

A bright far-red emitting unsymmetrical meso-CF₃-BODIPY fluorescent dye with phenyl and pyrazolyl substituents was synthesized by condensation of trifluoropyrrolylethanol with pyrazolyl-pyrrole, with subsequent oxidation and complexation of the formed dipyrromethane. This BODIPY dye exhibits optical absorption at λ_ab ≈ 610-620 nm and emission at λ_em ≈ 640-650 nm. The BODIPY was studied on Ehrlich carcinoma cells as a lysosome-specific fluorescent dye that allows intravital staining of cell structures with subsequent real-time monitoring of changes occurring in the cells. It was also shown that the rate of uptake by cells, the rate of intracellular transport into lysosomes, and the rate of saturation of cells with the dye depend on its concentration in the culture medium. A concentration of 5 μM was chosen as the most suitable BODIPY concentration for fluorescent staining of living cell lysosomes, while a concentration of 100 μM was found to be toxic to Ehrlich carcinoma cells.

Spanning BODIPY fluorescence with self-assembled micellar clusters

BODIPY dyes possess favorable optical properties for a variety of applications including in vivo and in vitro diagnostics. However, their utilization might be limited by their water insolubility and incompatibility with chemical modifications, resulting in low aggregation stability. Here, we outline the route for addressing this issue. We have demonstrated two approaches, based on dye entrapment in micellar coordination clusters (MCCs); this provides a general solution for water solubility as well as aggregation stability of the seven BODIPY derivatives. These derivatives have various bulky aromatic substituents in the 2,3,5,6- and meso-positions and can rotate relative to a dipyrrin core, which also provides molecular rotor properties. The molecular structural features and the presence of aromatic groups allows BODIPY dyes to be used as "supporting molecules", thus promoting micelle-micelle interaction and micellar network stabilization. In the second approach, self-micellization, following BODIPY use, leads to MCC formation without the use of any mediators, including chelators and/or metal ions. In both approaches, BODIPY exhibits an excellent optical response, at a concentration beyond its solubilization limit in aqueous media and without undesired crystallization. The suggested approaches represent systems used to encapsulate BODIPY in a capsule-based surfactant environment, enabling one to track the aggregation of BODIPY; these approaches represent an alternative system to study and apply BODIPY's molecular rotor properties. The stabilized compounds, i.e., the BODIPY-loaded MCCs, provide a unique feature of permeability to hydrophilic ligand-switching proteins such as BSA; they exhibit a bright "turn-on" fluorescence signal within the clusters via macromolecular complexation, thus expanding the possibilities of water-soluble BODIPY-loaded MCCs utilization for functional indicators.

Intra-micellar and extra-micellar oxidation in phosphate and histidine buffers containing polysorbate 80

Polysorbate is a key excipient included in formulations of therapeutic proteins to help prevent aggregation and surface adsorption. The stability of both polysorbate and therapeutic proteins can be compromised by oxidative degradation. In general, polysorbate is added to formulations at concentrations above the critical micelle concentration (cmc). To date, however, few experiments have quantitatively addressed the extent of extra- and intra-micellar oxidation of polysorbate in pharmaceutically relevant buffers. This study utilizes 2,2'-azobis(2-methylpropionamidine)dihydrochloride (AAPH), a peroxyl radical-generating initiator, C11-BODIPY(581/591), a lipid peroxidation probe, and fluorescence spectroscopy to reveal that both intra- and extra-micellar oxidation proceed in pharmaceutically relevant phosphate and histidine buffers. It is further demonstrated that the relative extent of oxidation observed in the intra- and extra-micellar compartments is similar irrespective of the buffer system.

A selective hybrid fluorescent sensor for fructose detection based on a phenylboronic acid and BODIPY-based hydrophobicity probe

Fructose is widely used in the food industry. However, it may be involved in diseases by generating harmful advanced glycation end-products. We have designed and synthesized a novel fluorescent probe for fructose detection by combining a phenylboronic acid group with a BODIPY-based hydrophobicity probe. This probe showed a linear fluorescence response to d-fructose concentration in the range of 100-1000 μM, with a detection limit of 32 μM, which is advantageous for the simple and sensitive determination of fructose.

BODIPY nanoparticles functionalized with lactose for cancer-targeted and fluorescence imaging-guided photodynamic therapy

A series of four lactose-modified BODIPY photosensitizers (PSs) with different substituents (-I, -H, -OCH₃, and -NO₂) in the para-phenyl moiety attached to the meso-position of the BODIPY core were synthesized; the photophysical properties and photodynamic anticancer activities of these sensitizers were investigated, focusing on the electronic properties of the different substituent groups. Compared to parent BODIPY H, iodine substitution (BODIPY I) enhanced the intersystem crossing (ISC) to produce singlet oxygen (¹O₂) due to the heavy atom effect, and maintained a high fluorescence quantum yield (Φ_F) of 0.45. Substitution with the electron-donating methoxy group (BODIPY OMe) results in a significant perturbation of occupied frontier molecular orbitals and consequently achieves higher ¹O₂ generation capability with a high Φ_F of 0.49, while substitution with the electron-withdrawing nitro group (BODIPY NO2) led a perturbation of unoccupied frontier molecular orbitals and induces a forbidden dark S₁ state, which is negative for both fluorescence and ¹O₂ generation efficiencies. The BODIPY PSs formed water-soluble nanoparticles (NPs) functionalized with lactose as liver cancer-targeting ligands. BODIPY I and OMe NPs showed good fluorescence imaging and PDT activity against various tumor cells (HeLa and Huh-7 cells). Collectively, the BODIPY NPs demonstrated high ¹O₂ generation capability and Φ_F may create a new opportunity to develop useful imaging-guided PDT agents for tumor cells.

Mitochondrion-Targeting PEGylated BODIPY Dyes for Near-Infrared Cell Imaging and Photodynamic Therapy

A series of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene-based photosensitizers (AmBXI, X = H, M, Br) featuring a cationic mitochondrion-targeting group and near-infrared (NIR) absorption was synthesized. After extending the photosensitizers’ π–π conjugation via Knoevenagel...

Iodine(III)-promoted regioselective and efficient synthesis of β-triazolyl BODIPYs for the selective recognition of nickel ion and bovine serum albumin

Various ꞵ-triazolyl tethered BODIPYs were efficiently prepared in a sequential one-pot protocol involving the initial reaction of BODIPY with iodobenzene diacetate (IBD) and sodium azide to in situ generate BODIPY...

Design, synthesis and mechanistic studies of a TICT based fluorogenic probe for lighting up protein HSA

Human serum albumin (HSA) in blood serves as an important biomarker for clinical diagnosis, and fluorescence sensing method has attracted extensive attention. In this work, a small organic molecule probe, YS8, involving twisted intramolecular charge transfer (TICT) characteristic, was designed and investigated to detect HSA. YS8 kept silent state in fluorescence under physiological conditions, but the encapsulation of YS8 in the hydrophobic subdomain IB region of HSA inhibited the TICT state and produced a clear light-up fluorescent signal. Especially, YS8 was demonstrated to be an efficient fluorogenic probe to discriminate HSA from other proteins including the bovine serum albumin (BSA). Moreover, YS8/HSA complex could be applied in fluorescence imaging in living cells and is also useful in the study of artificial fluorescent protein (AFP).

Hydrophobic Cargo Encapsulation into Virus Protein Cages by Self-Assembly in an Aprotic Organic Solvent

While extensive studies of virus capsid assembly in environments mimicking in vivo conditions have led to an understanding of the thermodynamic driving forces at work, applying this knowledge to virus assembly in other solvents than aqueous buffers has not been attempted yet. In this study, Brome mosaic virus (BMV) capsid proteins were shown to preserve their self-assembly abilities in an aprotic polar solvent, dimethyl sulfoxide (DMSO). This facilitated protein cage encapsulation of nanoparticles and dye molecules that favor organic solvents, such as β-NaYF4-based upconversion nanoparticles and BODIPY dye. Assembly was found to be robust relative to a surprisingly broad range of DMSO concentrations. Cargos with poor initial stability in aqueous solutions were readily encapsulated at high DMSO concentrations and then transferred to aqueous solvents, where they remained stable and preserved their function for months.

Molecular rotors as reporters for viscosity of solutions of collagen like peptides

We have studied the suitability of using a molecular rotor-based steady-state fluorometric assay for evaluating changes in both the conformation and the viscosity of collagen-like peptide solutions. Our results indicate that a positive charge incorporated on the hydrophobic tail of the BODIPY molecular rotor favours the dye specificity as a reporter for viscosity of these solutions.

Cytotoxicity of Amino-BODIPY Modulated via Conjugation with 2-Phenyl-3-Hydroxy-4(1H)-Quinolinones

The combination of cytotoxic amino-BODIPY dye and 2-phenyl-3-hydroxy-4(1H)-quinolinone (3-HQ) derivatives into one molecule gave rise to selective activity against lymphoblastic or myeloid leukemia and the simultaneous disappearance of the cytotoxicity against normal cells. Both species' conjugation can be realized via a disulfide linker cleavable in the presence of glutathione characteristic for cancer cells. The cleavage liberating the free amino-BODIPY dye and 3-HQ derivative can be monitored by ratiometric fluorescence or by the OFF-ON effect of the amino-BODIPY dye. A similar cytotoxic activity is observed when the amino-BODIPY dye and 3-HQ derivative are connected through a non-cleavable maleimide linker. The work reports the synthesis of several conjugates, the study of their cleavage inside cells, and cytotoxic screening.

Preparation of an antigen-responsive fluorogenic immunosensor by tyrosine chemical modification of the antibody complementarity determining region

Full-length pharmaceutical antibodies, trastuzumab and rituximab, were chemically modified into Quenchbody, a fluorescent immunosensor, using a two-step reaction: (1) selective tyrosine residue modification of antibody complementarity determining regions (CDRs), and (2) introduction of fluorescent dye molecules by Cu-free click reaction. Without the need for genetic manipulation and time-consuming examination of protein expression conditions, the antibody-dye combination with good antigen response efficiency was examined in a simple two-hour operation.

A BODIPY-O-glycoside based near-infrared fluorescent sensor for serum albumin

Highly sensitive and selective near-infrared fluorescent bioprobes for serum albumin detection and quantification are in high demand for biomedical applications. Herein, we report a near-infrared emitting BODIPY-O-glycoside dye as a turn-on emission sensor for serum albumin. To the best of our knowledge, this is the first report of NIR-emitting BODIPY dyes for serum albumin sensing. Despite the various outstanding photophysical properties of the BODIPY dyes, their insolubility in water/biological media restricts their real biomedical applications. To overcome this issue, highly stable unadulterated BODIPY-O-glycoside nanoparticles (BDP-Glu-NPs) were prepared in aqueous solution by self-assembly of amphiphilic BODIPY-O-glycoside dyes. The BDP-Glu-NPs were characterized by spectroscopic, NMR, DLS and TEM studies. The ability of the BDP-Glu-NPs for the detection and quantification of serum albumin was demonstrated. It showed a 150-fold fluorescence enhancement in the presence of serum albumin, with excellent selectivity over other amino acids, porphyrin, proteins and various inorganic salts. Detection of human serum albumin (HSA) in urine samples showed that the bioprobe is applicable to a clinically significant range of the analytes with very low detection limit. These results suggested that the BDP-Glu-NPs can act as potential bioprobe to quantify albumin in biochemical and clinical samples.

A boron dipyrromethene (BODIPY) based probe for selective passive sampling of atmospheric nitrous acid (HONO) indoors

People spend up to 90% of their time indoors, and yet our understanding of indoor air quality and the chemical processes driving it are poorly understood, despite levels of key pollutants typically being higher indoors compared to outdoors. Nitrous acid (HONO) is a species that drives these indoor chemical processes, with potentially detrimental health effects. In this work, a BODIPY-based probe was synthesized with the aim of developing the first selective passive sampler for atmospheric HONO. Our probe and its products are easily detected by UV-Vis spectroscopy with molar extinct coefficients of 37 863 and 33 787 M^-1 cm^-1, respectively, and a detection limit of 14.8 ng mL^-1. When protonated, the probe fluoresces with a quantum yield of 33%, which is turned off upon reaction. The synthesized BODIPY probe was characterized using NMR and UV-Vis spectroscopy. Products were characterized by UV-Vis and ultra high-resolution mass spectrometry. The reaction kinetics of the probe with nitrite was studied using UV-Vis spectroscopy, which had a pseudo-first-order rate of k = 7.7 × 10^-4 s^-1. The rapid reaction makes this probe suitable for targeted ambient sampling of HONO. This was investigated through a proof-of-concept experiment with gaseous HONO produced by a custom high-purity calibration source delivering the sample to the BODIPY probe in an acidic aqueous solution in clean air and a real indoor air matrix. The probe showed quantitative uptake of HONO in both cases to form the same products observed from reaction with nitrite, with no indication of interferences from ambient NO or NO₂. The chemical and physical characteristics of the probe therefore make it ideal for use in passive samplers for selective sampling of HONO from the atmosphere.

Stimuli Responsive Confinement of a Molecular Rotor Based BODIPY Dye inside a Cucurbit[7]uril Nanocavity

Present study reports the interaction of a molecular rotor based BODIPY dye, 8-anilino-BODIPY (ABP), with a versatile macrocyclic molecule, cucurbit[7]uril (CB7), investigated through various techniques such as ground-state absorption, steady-state fluorescence, time-resolve emission, proton NMR, and quantum chemical studies. Although BODIPY dyes have widespread applications due to their intriguing photochemical properties, studies on their noncovalent interactions with different macrocyclic hosts, especially regarding their supramolecularly induced modulations in photophysical properties are very limited. The investigated BODIPY dye, especially its protonated ABPH⁺ form (pH ∼ 1), shows a large fluorescence enhancement on its interaction with the CB7 host, due to large reduction in the structural flexibility for the bound dye, causing a suppression in its nonradiative de-excitation process in the excited state. Unlike ABPH⁺, the neutral ABP form (pH ∼ 7) shows considerably weaker interaction with CB7. For ABPH⁺-CB7 system, observed photophysical results indicate formation of both 1:1 and 1:2 dye-to-host complexes. Plausible geometries of these complexes are obtained from quantum chemical studies which are substantiated nicely from ¹H NMR results. The response of the ABPH⁺-CB7 system toward changing temperature of the solution have also been investigated elaborately to understand the potential of the system in different stimuli-responsive sensor applications.

Electrokinetic Perfusion Through Three-Dimensional Culture Reduces Cell Mortality

Cell proliferation and survival are dependent on mass transfer. In vivo, fluid flow promotes mass transfer through the vasculature and interstitial space, providing a continuous supply of nutrients and removal of cellular waste products. In the absence of sufficient flow, mass transfer is limited by diffusion and poses significant challenges to cell survival during tissue engineering, tissue transplantation, and treatment of degenerative diseases. Artificial perfusion may overcome these challenges. In this work, we compare the efficacy of pressure driven perfusion (PDP) with electrokinetic perfusion (EKP) toward reducing cell mortality in three-dimensional cultures of Matrigel extracellular matrix. We characterize electro-osmotic flow through Matrigel to identify conditions that generate similar interstitial flow rates to those induced by pressure. We also compare changes in cell mortality induced by continuous or pulsed EKP. We report that continuous EKP significantly reduced mortality throughout the perfusion channels more consistently than PDP at similar flow rates, and pulsed EKP decreased mortality just as effectively as continuous EKP. We conclude that EKP has significant advantages over PDP for promoting tissue survival before neovascularization and angiogenesis. Impact statement Interstitial flow helps promote mass transfer and cell survival in tissues and organs. This study generated interstitial flow using pressure driven perfusion (PDP) or electrokinetic perfusion (EKP) to promote cell viability in three-dimensional cultures. EKP through charged extracellular matrices possesses significant advantages over PDP and may promote cell survival during tissue engineering, transplantations, and treatment of degenerative diseases.

Theoretical predictions of the spectroscopic properties of BODIPY dyes: Effects of the fused aromatic and heteroaromatic rings at the b, g bonds

The fusion of aryl and heteroaryl moieties in the BODIPY skeleton is the important route to design BODIPYs exhibiting absorption and fluorescence in red or near infra-red regions. Despite the importance of this approach, little is known about the influence of aryl and heteroaryl rings on the position of the energy levels of the lower electronic states of such dyes. In this paper, the influence of benzene (B), thiophene (T) and furan (F) rings fused in the BODIPY core (b) at both b and g bonds on the optical properties of the symmetric BbB, TbT and FbF and asymmetric TbF, BbF and BbT dyes have been investigated by TD-CAM-B3LYP and RI-CC2 calculations. We have shown that in contrast to the locally excited (LE0-type) main vertical state, energy of which is nearly the same for all the substituents at the b and g bonds, energy of the next two states of the LE1- and LE2-type for the symmetric dyes or the charge transfer (CT1- and CT2-type) for the asymmetric dyes depends strongly on the nature of the rings at the b and g bonds. The benzene-fused dyes (BbF, BbT, BbB) have the lowest energy of the excited levels of the LE-type (or CT1-type) states, and inversion with LE0-type levels occurs. As a result, the dramatic decrease of the fluorescence quantum yield is expected in these cases. The identification of these effects provides a quality framework for understanding of how fused substituents regulate photophysical processes of BODIPYs.

Dominant entropic binding of perfluoroalkyl substances (PFASs) to albumin protein revealed by 19F NMR

Mechanistic insight into protein binding by poly- and perfluoroalkyl substances (PFASs) is critical to understanding how PFASs distribute and accumulate within the body and to developing predictive models within and across classes of PFASs. Fluorine nuclear magnetic resonance spectroscopy (19F NMR) has proven to be a powerful, yet underutilized tool to study PFAS binding; chemical shifts of each fluorine group reflect the local environment along the length of the PFAS molecule. Using bovine serum albumin (BSA), we report dissociation constants, Kd, for four common PFASs well below reported critical micelle concentrations (CMCs) - perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorohexanesulfonic acid (PFHxS), and perfluorooctanesulfonic acid (PFOS) - as a function of temperature in phosphate buffered saline. Kd values were determined based on the difluoroethyl group adjacent to the anionic headgroups and the terminal trifluoromethyl groups. Our results indicate that the hydrophobic tails exhibit greater binding affinity relative to the headgroup, and that the binding affinities are generally consistent with previous results showing that greater PFAS hydrophobicity leads to greater protein binding. However, the binding mechanism was dominated by entropic hydrophobic interactions attributed to desolvation of the PFAS tails within the hydrophobic cavities of the protein and on the surface of the protein. In addition, PFNA appears to form hemimicelles on the protein surfaces below reported CMC values. This work provides a renewed approach to utilizing 19F NMR for PFAS-protein binding studies and a new perspective on the role of solvent entropy.

Impact of binding to the multidrug resistance regulator protein LmrR on the photo-physics and -chemistry of photosensitizers

Light activated photosensitizers generate reactive oxygen species (ROS) that interfere with cellular components and can induce cell death, e.g., in photodynamic therapy (PDT). The effect of cellular components and especially proteins on the photochemistry and photophysics of the sensitizers is a key aspect in drug design and the correlating cellular response with the generation of specific ROS species. Here, we show the complex range of effects of binding of photosensitizer to a multidrug resistance protein, produced by bacteria, on the formers reactivity. We show that recruitment of drug like molecules by LmrR (Lactococcal multidrug resistance Regulator) modifies their photophysical properties and their capacity to induce oxidative stress especially in 1O2 generation, including rose bengal (RB), protoporphyrin IX (PpIX), bodipy, eosin Y (EY), riboflavin (RBF), and rhodamine 6G (Rh6G). The range of neutral and charged dyes with different exited redox potentials, are broadly representative of the dyes used in PDT.

Probing heat and oxidation induced conformational changes of molecular chaperone artemin by excitation-emission fluorescence spectroscopy

Artemin is a potent molecular chaperone, which protects Artemia embryos undergoing encystment against extreme environmental stresses. In the present work, we have examined the structural changes of artemin from A. urmiana upon exposure to oxidant and heat, by using CD measurements as well as excitation-emission fluorescence spectroscopy as a powerful tool for monitoring the conformational transitions and molecular interactions in proteins. We have also provided here the first document on reporting the three dimensional fluorescence spectra of a protein using ANS. Totally, the fluorescence results indicated that the microenvironments of tyrosine and tryptophan residues and the hydrophobic pockets as well as the polypeptide backbone or secondary structure of the chaperone were influenced in responses to heat and H₂O₂ in different degrees. Moreover, the native state of artemin did not induce a considerable exposure of the internal non-polar groups to the solvent. Besides, the excitation-emission spectra of heated artemin by ANS revealed new emission peaks at 430-450 nm when it was excited at 330 nm, which suggests probable exposure of new binding sites for hydrophobic or electrostatic interactions of the protein with ANS. The protein also showed a greater conformational sensitivity to the temperature fluctuations compared to oxidation. Here, we presented some evidence in support of the relation between artemin and its stress dependent activation in vitro and in vivo. This study can expect that the EEM fluorescence spectroscopy could provide a promising tool to study conformational transitions of proteins.

Resolving Binding Events on the Multifunctional Human Serum Albumin

Physiological processes rely on initial recognition events between cellular components and other molecules or modalities. Biomolecules can have multiple sites or mode of interaction with other molecular entities, so that a resolution of the individual binding events in terms of spatial localization as well as association and dissociation kinetics is required for a meaningful description. Here we describe a trichromatic fluorescent binding- and displacement assay for simultaneous monitoring of three individual binding sites in the important transporter and binding protein human serum albumin. Independent investigations of binding events by X-ray crystallography and time-resolved dynamics measurements (switchSENSE technology) confirm the validity of the assay, the localization of binding sites and furthermore reveal conformational changes associated with ligand binding. The described assay system allows for the detailed characterization of albumin-binding drugs and is therefore well-suited for prediction of drug-drug and drug-food interactions. Moreover, conformational changes, usually associated with binding events, can also be analyzed.