A supramolecular fluorescence probe that simultaneously responds to viscosity and G-quadruplex for autophagy detection.

BACKGROUND: Autophagy, as an essential physiological process in eukaryotes, has been revealed to be closely related to aging and many major diseases. Real-time in situ imaging of autophagy processes in living cells is necessary for timely detection of autophagy defects and the development of treatment methods. Currently, many studies are dedicated to the design of autophagy probes, and various types of fluorescent probes for autophagy detection have been reported. However, most of them are single fluorescence signal outputs, which may lead to non-specific signals. Nowadays a reliable and sensitive autophagy monitoring probe is still essential. RESULTS: A supramolecular fluorescent probe was prepared via the controllable self-assembly of a thiacyanine dye named PTC for tracking autophagy in living cells. PTC was very sensitive to viscosity, and its aggregates were completely converted into monomers as viscosity increased. This process led to a significant increase of over 2000 times in the fluorescence intensity ratio between monomers and aggregates. PTC also exhibited selective affinity for G-quadruplex (G4) structure, which decomposed PTC aggregates into monomers, resulting in a fluorescence ratio increase of up to tens of folds. In living cells, PTC existed as aggregates in lysosomes, maintaining sensitivity to viscosity and G4s. In confocal imaging experiments, PTC sensitively responded to the induction and inhibition of cellular autophagy, displaying opposite changes in the monomer and aggregate fluorescent channels. SIGNIFICANCE: This work provides a reliable fluorescent probe for autophagy detection in live cells, which has the advantages of high sensitivity, low cost, and ease of use, making it have the potential for widespread application. This study also offers a new strategy for designing autophagy probes with both high sensitivity and high specificity.

Harnessing Competitive Interactions to Regulate Supramolecular "Micelle-Droplet-Fiber" Transition and Reversibility in Water.

The supramolecular assembly of proteins into irreversible fibrils is often associated with diseases in which aberrant phase transitions occur. Due to the complexity of biological systems and their surrounding environments, the mechanism underlying phase separation-mediated supramolecular assembly is poorly understood, making the reversal of so-called irreversible fibrillization a significant challenge. Therefore, it is crucial to develop simple model systems that provide insights into the mechanistic process of monomers to phase-separated droplets and ordered supramolecular assemblies. Such models can help in investigating strategies to either reverse or modulate these states. Herein, we present a simple synthetic model system composed of three components, including a benzene-1,3,5-tricarboxamide-based supramolecular monomer, a surfactant, and water, to mimic the condensate pathway observed in biological systems. This highly dynamic system can undergo "micelle-droplet-fiber" transition over time and space with a concentration gradient field, regulated by competitive interactions. Importantly, manipulating these competitive interactions through guest molecules, temperature changes, and cosolvents can reverse ordered fibers into a disordered liquid or micellar state. Our model system provides new insights into the critical balance between various interactions among the three components that determine the pathway and reversibility of the process. Extending this "competitive interaction" approach from a simple model system to complex macromolecules, e.g., proteins, could open new avenues for biomedical applications, such as condensate-modifying therapeutics.

Exceptional longevity of mammalian ovarian and oocyte macromolecules throughout the reproductive lifespan.

The mechanisms contributing to age-related deterioration of the female reproductive system are complex, however aberrant protein homeostasis is a major contributor. We elucidated exceptionally stable proteins, structures, and macromolecules that persist in mammalian ovaries and gametes across the reproductive lifespan. Ovaries exhibit localized structural and cell-type-specific enrichment of stable macromolecules in both the follicular and extrafollicular environments. Moreover, ovaries and oocytes both harbor a panel of exceptionally long-lived proteins, including cytoskeletal, mitochondrial, and oocyte-derived proteins. The exceptional persistence of these long-lived molecules suggest a critical role in lifelong maintenance and age-dependent deterioration of reproductive tissues.

Hydrogen-bonded supramolecular biohybrid frameworks for protein biomineralization constructed from natural phenolic building blocks.

Hydrogen bond-mediated supramolecular crystalline materials, such as hydrogen-bonded organic frameworks, offer a promising strategy for protein biomineralization, yet the intricate design and multi-step synthesis of specific orthogonal units in molecular building blocks pose a significant synthetic challenge. Identifying new classes of natural building blocks capable of facilitating supramolecular framework construction while enabling stable protein binding has remained an elusive goal. Here, we introduce a versatile assembly strategy enabling the organization of diverse proteins and phenolic building blocks into highly crystalline hydrogen-bonded supramolecular phenolic frameworks (ProteinX@SPF). The natural ellagic acid (EA) exhibits a centrosymmetric structure with catechol groups on each molecular side, facilitating hydrogen bonding with protein amino acid residues for primary nucleation. Subsequently, EA self-assembles into ProteinX@SPF through hydrogen bonding and π-π interactions. The multiple hydrogen-bonding interactions impart structural rigidity and directional integrity, conferring ProteinX@SPF biohybrids with remarkable resistance to harsh conditions while preserving protein bioactivity. Additionally, the supramolecular stacking induced by π-π interactions endows ProteinX@SPF with long-range ordered nanochannels, which can serve as the gating to sieve the catalytic substrate and thus enhance the biocatalytic specificity. This work sheds light on biomineralization with natural building blocks for functional biohybrids, showing enormous potential in biocatalysis, sensing, and nanomedicine.

Excipient-free nanotransformation of hydrophilic macromolecules using aqueous counter collision for enhanced bioavailability.

The demand for sustainable, eco-friendly biopolymer transdermal delivery systems has increased owing to growing environmental awareness. In this study, we used aqueous counter collision (ACC), a nontoxic nanotransformation method, to convert high- and ultrahigh-molecular-weight hydrophilic macromolecules into their corresponding nanoparticles (NPs). Hyaluronic acid (HA) and crosslinked HA (CLHA) were chosen as the model compounds. Their NPs exhibited particle sizes in the range of 10-100 nm and negative zeta potentials (-20 to -30 mV). Transmission electron microscopy revealed that the NPs were nearly spherical with smooth surfaces. Fourier-transform infrared and proton nuclear magnetic resonance spectroscopy and agarose gel electrophoresis confirmed that the structures and molecular weights of HA and CLHA remained unaltered after ACC. However, the storage and loss moduli of HANPs and CLHANPs were significantly lower than those of HA and CLHA, respectively. Furthermore, the permeation of HANPs and CLHANPs in reconstructed human skin and human cadaver skin was visualized and quantified. HANPs and CLHANPs penetrated deeper into the skin, whereas HA and CLHA were mainly found in the stratum corneum. The total skin absorption (permeation and deposition) of HANPs and CLHANPs was approximately 2.952 and 5.572 times those of HA and CLHA, respectively. Furthermore, HANPs and CLHANPs exhibited resistance to enzyme and free radical degradation. Our findings reveal ACC as a promising, sustainable hydrophilic macromolecule delivery system compared with the chemical hydrolysis of HA.

Recent advance of physicochemical, structural properties, potential health benefits and application of bioactive macromolecules from Porphyra haitanensis: A review.

Porphyra haitanensis (P. haitanensis) belongs to the class Rhodophyta and the family Bangiaceae, which is a unique artificially cultivated seaweed in China, especially in the coastal areas of Fujian and Zhejiang province. P. haitanensis is rich in amino acids, mineral elements, proteins, polysaccharides, and trace elements, with proteins and polysaccharides being the main components. P. haitanensis proteins and polysaccharides have variety of biological activities, including antioxidant, anticancer, immunomodulatory, anti-allergic and anti-aging activities, among others. This review introduced and summarized the preparation, isolation and purification, phytochemistry and structural properties, and biological activities of P. haitanensis proteins and polysaccharide, as well as their biomedical and food applications. Furthermore, a thorough analysis of the current trends and perspectives on P. haitanensis bioactive macromolecules were highlighted and prospected. Hopefully, this review can provide a useful reference value for the development and application of P. haitanensis bioactive macromolecules in the field of biomedical and food in the future.

Utilizing anomalous signals for element identification in macromolecular crystallography.

AlphaFold2 has revolutionized structural biology by offering unparalleled accuracy in predicting protein structures. Traditional methods for determining protein structures, such as X-ray crystallography and cryo-electron microscopy, are often time-consuming and resource-intensive. AlphaFold2 provides models that are valuable for molecular replacement, aiding in model building and docking into electron density or potential maps. However, despite its capabilities, models from AlphaFold2 do not consistently match the accuracy of experimentally determined structures, need to be validated experimentally and currently miss some crucial information, such as post-translational modifications, ligands and bound ions. In this paper, the advantages are explored of collecting X-ray anomalous data to identify chemical elements, such as metal ions, which are key to understanding certain structures and functions of proteins. This is achieved through methods such as calculating anomalous difference Fourier maps or refining the imaginary component of the anomalous scattering factor f''. Anomalous data can serve as a valuable complement to the information provided by AlphaFold2 models and this is particularly significant in elucidating the roles of metal ions.

Small-molecule properties define partitioning into biomolecular condensates.

Biomolecular condensates regulate cellular function by compartmentalizing molecules without a surrounding membrane. Condensate function arises from the specific exclusion or enrichment of molecules. Thus, understanding condensate composition is critical to characterizing condensate function. Whereas principles defining macromolecular composition have been described, understanding of small-molecule composition remains limited. Here we quantified the partitioning of ~1,700 biologically relevant small molecules into condensates composed of different macromolecules. Partitioning varied nearly a million-fold across compounds but was correlated among condensates, indicating that disparate condensates are physically similar. For one system, the enriched compounds did not generally bind macromolecules with high affinity under conditions where condensates do not form, suggesting that partitioning is not governed by site-specific interactions. Correspondingly, a machine learning model accurately predicts partitioning using only computed physicochemical features of the compounds, chiefly those related to solubility and hydrophobicity. These results suggest that a hydrophobic environment emerges upon condensate formation, driving the enrichment and exclusion of small molecules.

Remarkable Stability of Glutathione-Based Supramolecular Gel in the Presence of Oxidative Stress from Hydrogen Peroxide.

Low molecular weight 7-methoxy-3-(p-nitrophenyl)iminocoumarin (MNI) with donor and acceptor groups has been synthesized. The molecule shows typical π-stacking geometry in the crystal structure. In this study, MNI, an achiral small organic molecule, forms a nanostructured supramolecular gel along with a short peptide sequence glutathione (GSH). The self-assembly of the achiral organic coumarin component and chiral biomolecule produces a chiral gel with helical fiber structures. Interestingly, the helicities of chiral gels are controlled by the solvent ratio, where MNI in DMSO and GSH in water has been used. Variation of the solvent ratio from 6:4 to 1:9 for DMSO:H2O results in six gels (4, 5, 6, 7, 8 and 9), where the gel numbers signify the water content ratio. FE-SEM analysis shows gel fibers with right-handed helical structures, which have been further confirmed by circular dichroism (CD) with notable helicity in 4 to 6. This is the first report of controlled chiral helical nanostructured supramolecular gel formation by a solvent mixture with an organic small molecule and biomolecule. Interestingly, storage modulus (G') initially decreases from 4 to 6 and further increases up to 9. An opposite strain (%) trend was observed among these six gels. These unusual solvent-dependent gel properties have been further applied to monitor the stability of the gels in the presence of hydrogen peroxide (H2O2), which converts GSH to oxidized glutathione (GSSG) in general. The oxidative stress from H2O2 disrupts 4 to 6 gels, and precipitation occurs. It is noteworthy to mention that GSSG alone cannot form a gel with the MNI molecule and forms a precipitate. Remarkably, on the other hand, 7 to 9 remain as strong gels even after H2O2 treatment. Among all six gels, 9 shows extraordinary stability of gels even after H2O2 treatment.

Hydration effect and molecular geometry conformation as critical factors affecting the longevity stability of G4-structure-based supramolecular hydrogels.

Nucleoside-derived supramolecular hydrogels based on G4-structures have been extensively developed in the biomedical sector and recognized for superior excellent biocompatibility and biodegradability. However, limited longevity and stability present a significant challenge. Chemical modifications in the molecular structure have been shown to enhance the longevity stability of G4-structure-based supramolecular hydrogels, but the precise way in which the molecular structure impacts the stability of the G4-structures and consequently affects the properties of the hydrogel remains to be elucidated. This issue represents a notable challenge in the field, which restricts their further applications to some extent. In this study, single crystals of Gd, αGd and αGd* were cultivated and compared with G. Notably, before this study, the single crystal structures of all natural nucleosides, with the exception of Gd, had been determined. The investigation into the molecular structure and supramolecular self-assembly properties of four guanosine analogs at the atomic scale revealed that the formation of G-quartets is critical for their ability to form hydrogels. The stability of the sugar ring geometry conformation (an intrinsic factor) and the disorder and strength of the hydration effect (extrinsic factors) are vital for maintaining the stability of the G4-structures. The rapid cooling changes the molecular geometry conformation, and the organic solvent changes the hydration effect, which can improve the longevity stability of G4-structure-based supramolecular hydrogels instead of chemical modifications. Consequently, the lifespan of the hydrogels was extended from 2 h to over one week. This advancement is expected to offer significant insights for future research in designing and developing G4-structure-based supramolecular hydrogels.

In situ biocatalytic ATP regulated, transient supramolecular polymerization.

Temporal control over self-assembly processes is a highly desirable attribute that is efficiently exhibited by biological systems, such as actin filaments. In nature, various proteins undergo enzymatically catalysed chemical reactions that kinetically govern their structural and functional properties. Consequently, any stimuli that can alter their reaction kinetics can lead to a change in their growth or decay profiles. This underscores the urgent need to investigate bioinspired, adaptable and controllable synthetic materials. Herein we intend to develop a general strategy for controlling the growth and decay of self-assembled systems via enzymatically coupled reactions. We achieve this by the coupling of enzymes phosphokinase/phosphatase with a bolaamphiphilic cationic chromophore (PDI) which selectively self-assembles with ATP and disassembles upon its enzymatic hydrolysis. The aggregation process is efficiently regulated by the controlled in situ generation of ATP, through enzymatic reactions. By carefully managing the ATP generating components, we realize precise control over the self-assembly process. Moreover, we also show self-assembled structures with programmed temporal decay profiles through coupled enzymatic reactions of ATP generation and hydrolysis, essentially rendering the process dissipative. This work introduces a novel strategy to generate a reaction-coupled one-dimensional nanostructure with controlled dimensions inspired by biological systems.

Supramolecular H-Aggregates of Squaraines with Enhanced Type I Photosensitization for Combined Photodynamic and Photothermal Therapy.

Combined photodynamic and photothermal therapy (PDT and PTT) can achieve more superior therapeutic effects than the sole mode by maximizing the photon utilization, but there remains a significant challenge in the development of related single-molecule photosensitizers (PSs), particularly those with type I photosensitization. In this study, self-assembly of squaraine dyes (SQs) is shown to be a promising strategy for designing PSs for combined type I PDT and PTT, and a supramolecular PS (TPE-SQ7) has been successfully developed through subtle molecular design of an indolenine SQ, which can self-assemble into highly ordered H-aggregates in aqueous solution as well as nanoparticles (NPs). In contrast to the typical quenching effect of H-aggregates on reactive oxygen species (ROS) generation, our results encouragingly manifest that H-aggregates can enhance type I ROS (•OH) generation by facilitating the intersystem crossing process while maintaining a high PTT performance. Consequently, TPE-SQ7 NPs with ordered H-aggregates not only exhibit superior combined therapeutic efficacy than the well-known PS (Ce6) under both normoxic and hypoxic conditions but also have excellent biosafety, making them have important application prospects in tumor phototherapy and antibacterial fields. This study not only proves that the supramolecular self-assembly of SQs is an effective strategy toward high-performance PSs for combined type I PDT and PTT but also provides a different understanding of the effect of H-aggregates on the PDT performance.

Streamlining LC-MS Characterization of Pharmaceutical Polymers by Fourier-Transform-Based Deconvolution and Macromolecular Mass Defect Analysis.

Polymer conjugation has risen in importance over the past three decades as a means of increasing the in vivo half-life of biotherapeutics, with benefits including better stability, greater drug efficacy, and lower toxicity. However, the intrinsic variability of polymer synthesis results in products with broad distributions in chain length and branching structure, complicating quality control for successful functionalization and downstream conjugation. Frequently, a combination of several analytical techniques is required for comprehensive characterization. While liquid chromatography-mass spectrometry (LC-MS) is a powerful platform that can provide detailed molecular features of polymers, the mass spectra are inherently challenging to interpret due to high mass polydispersity and overlapping charge distributions. Here, by leveraging Fourier transform-based deconvolution and macromolecular mass defect analysis, we demonstrate a new way to streamline pharmaceutical polymer analysis, shedding light on polymer size, composition, branching, and end-group functionalization with the capability for reaction monitoring.

Perspectives on solution-based small angle X-ray scattering for protein and biological macromolecule structural biology.

Small-angle X-ray scattering (SAXS) is used to extract structural information from a wide variety of non-crystalline samples in different fields (e.g., materials science, physics, chemistry, and biology). This review provides an overview of SAXS as applied to structural biology, specifically for proteins and other biomacromolecules in solution with an emphasis on extracting key structural parameters and the interpretation of SAXS data using a diverse array of techniques. These techniques cover aspects of building and assessing models to describe data measured from monodispersed and ideal dilute samples through to more complicated structurally polydisperse systems. Ab initio modelling, rigid body modelling as well as normal-mode analysis, molecular dynamics, mixed component and structural ensemble modelling are discussed. Dealing with polydispersity both physically in terms of component separation as well as approaching the analysis and modelling of data of mixtures and evolving systems are described, including methods for data decomposition such as single value decomposition/principle component analysis and evolving factor analysis. This review aims to highlight that solution SAXS, with the cohort of developments in data analysis and modelling, is well positioned to build upon the traditional 'single particle view' foundation of structural biology to take the field into new areas for interpreting the structures of proteins and biomacromolecules as population-states and dynamic structural systems.

Biological macromolecule-based hydrogels with antibacterial and antioxidant activities for wound dressing: A review.

Because of the complex symptoms resulting from metabolic dysfunction in the wound microenvironment during bacterial infections, along with the necessity to combat free radicals, achieving prompt and thorough wound healing remains a significant medical challenge that has yet to be fully addressed. Moreover, the misuse of common antibiotics has contributed to the emergence of drug-resistant bacteria, underscoring the need for enhancements in the practical and commonly utilized approach to wound treatment. In this context, hydrogel dressings based on biological macromolecules with antibacterial and antioxidant properties present a promising new avenue for skin wound treatment due to their multifunctional characteristics. Despite the considerable potential of this innovative approach to wound care, comprehensive research on these multifunctional dressings is still insufficient. Consequently, the development of advanced biological macromolecule-based hydrogels, such as chitosan, alginate, cellulose, hyaluronic acid, and others, has been the primary focus of this study. These materials have been enriched with various antibacterial and antioxidant agents to confer multifunctional attributes for wound healing purposes. This review article aims to offer a comprehensive overview of the latest progress in this field, providing a critical theoretical basis for future advancements in the utilization of these advanced biological macromolecule-based hydrogels for wound healing.

Supramolecular materials constructed from synthetic glycopeptides via aqueous self-assembly and their bioapplications in immunotherapy.

Synthetic glycopeptides capable of self-assembly in aqueous environments form a range of supramolecular nanostructures, such as nanoparticles and nanofibers, owing to their amphiphilic nature and the diverse structures of the saccharides introduced. These glycopeptide-based supramolecular materials are promising for immunotherapy applications because of their biocompatibility and multivalent saccharide display, which enhances lectin-saccharide interactions. This review highlights recent advances in the molecular design of synthetic glycopeptide-based supramolecular materials and their use as immunomodulatory agents.

Deep eutectic solvent: Synthesis, classification, properties and application in macromolecular substances.

Deep eutectic solvent (DES) is a kind of solvent prepared by mixing hydrogen bond donors and hydrogen bond acceptors, and have become a hot topic in ecological civilization construction due to its low toxicity and sustainability. Its excellent properties such as low volatility, thermal stability and biodegradability make it stand out among many organic solvents and widely used in fields including medicine, chemical industry and agriculture, with broad development prospects. In recent years, the application of DES in the food field has mostly focused on the extraction of small molecular substances, and there are few summaries on the application of DES in macromolecular substances. In this review, we introduced the synthesis, classification and properties of DES, and summarized the application of DES in the food industry for macromolecular substances, including the extraction of macromolecular substances such as chitosan and pectin, as well as the preparation of related macromolecular substrate films. At the same time, we analyzed the characteristics of DES and its advantages and limitations in application, and provided prospects for future development.

Supramolecular chemical biology: designed receptors and dynamic chemical systems.

Supramolecular chemistry focuses on the study of species joined by non-covalent interactions, and therefore on dynamic and relatively ill-defined structures. Despite being a well-developed field, it has to face important challenges when dealing with the selective recognition of biomolecules in highly competitive biomimetic media. However, supramolecular interactions reside at the core of chemical biology systems, since many processes in nature are governed by weak, non-covalent, strongly dynamic contacts. Therefore, there is a natural connection between these two research fields, which are not frequently related or share interests. In this feature article, I will highlight our most recent results in the molecular recognition of biologically relevant species, following different conceptual approaches from the most conventional design of elaborated receptors to the less popular dynamic combinatorial chemistry methodology. Selected illustrative examples from other groups will be also included. The discussion has been focused mainly on systems with potential biomedical applications.

Supramolecular polyplexes from Janus peptide nucleic acids (bm-PNA-G5): self-assembled bm-PNA G-quadruplex and its tetraduplex with DNA.

Nucleic acids (DNA and RNA) can form diverse secondary structures ranging from hairpins to duplex, triplex, G4-tetraplex and C4-i-motifs. Many of the DNA analogues designed as antisense oligonucleotides (ASO) are also adept at embracing such folded structures, although to different extents with altered stabilities. One such analogue, peptide nucleic acid (PNA), which is uncharged and achiral, forms hybrids with complementary DNA/RNA with greater stability and specificity than DNA:DNA/RNA hybrids. Like DNAs, these single-stranded PNAs can form PNA:DNA/RNA duplexes, PNA:DNA:PNA triplexes, PNA-G4 tetraplexes and PNA-C4-i-motifs. We have recently designed Janus-like bimodal PNAs endowed with two different nucleobase sequences on either side of a single aminoethylglycyl (aeg) PNA backbone and shown that these can simultaneously bind to two complementary DNA sequences from both faces of PNA. This leads to the formation of supramolecular polyplexes such as double duplexes, triple duplexes and triplexes of double duplexes with appropriate complementary DNA/RNA. Herein, we demonstrate that Janus/bimodal PNA with a poly G-sequence on the triazole side of the PNA backbone and mixed bases on the t-amide side, templates the initial formation of a (PNA-G5)4 tetraplex (triazole side), followed by the formation of a PNA:DNA duplex (t-amide side). Such a polyplex shows synergistic overall stabilisation compared to the isolated duplexes/quadruplex. The assembly of polyplexes with a shared backbone for duplexes and tetraplexes is programmable and may have potential applications in the self-assembly of nucleic acid nano- and origami structures. It is also shown that Janus PNAs enter the cells better than the standard aeg-PNA oligomers, and hence have implications for in vivo applications as well.

Macrocycle-Based Supramolecular Drug Delivery Systems: A Concise Review.

Efficient delivery of therapeutic agents to the lesion site or specific cells is an important way to achieve "toxicity reduction and efficacy enhancement". Macrocycles have always provided many novel ideas for drug or gene loading and delivery processes. Specifically, macrocycles represented by crown ethers, cyclodextrins, cucurbit[n]urils, calix[n]arenes, and pillar[n]arenes have unique properties, which are different cavity structures, good biocompatibility, and good stability. Benefited from these diverse properties, a variety of supramolecular drug delivery systems can be designed and constructed to effectively improve the physical and chemical properties of guest molecules as needed. This review provides an outlook on the current application status and main limitations of macrocycles in supramolecular drug delivery systems.