Autophagy Caught in the Act: A Supramolecular FRET Pair Based on an Ultrastable Synthetic Host-Guest Complex Visualizes Autophagosome-Lysosome Fusion

ESIPT Nano-Emitter to Probe Lysosome Biogenesis in Live Cells

Endosome-lysosome fusion and endo-lysosome fission-mediated lysosome biogenesis are crucial in regulating cellular health, and their dysregulation signifies disease. Tracking such intricate events with minimal disturbance remains elusive due to the scarcity of single-component synthetic probes capable of distinctly and simultaneously labeling both endosomes and lysosomes. Here, an amphiphilic π-conjugated imine probe is designed that forms micellar self-assemblies in water, called Nano-emitter, which distinctly and simultaneously labels endosomes and lysosomes upon monochromatic-wavelength excitation. ESIPT (Excited State Intramolecular Proton Transfer) active Nano-emitter shows red fluorescence at endosomal pH. Its hydrolysis to fluorescent amine, PEG-Naph at lysosomal pH illuminated lysosomes fluorescent green, with both imine and amine forms excitable using a 405 nm confocal laser. The two-color labeling of endosomes and lysosomes enabled tracking of their fusion and lysosome-biogenesis processes in living cells. Using multiplexed time-lapse imaging with Nano-emitter and anti-cancer drug doxorubicin, the role of these processes is investigated in lysosome-mediated doxorubicin sequestration in MCF-7 cells. The results show that endosomes as well as endo-lysosomes also sequestered doxorubicin apart from lysosomes. Interestingly, doxorubicin-sequestered endo-lysosomes underwent fission and generated more doxorubicin-sequestered lysosomes, preventing the drug's nuclear localization. Such versatile probes can enhance the understanding of drug sequestration and foster therapeutic strategies.

A FRET Autophagy Imaging Platform by Macrocyclic Amphiphile

Autophagy is a ubiquitous process of organelle interaction in eukaryotic cells, in which various organelles or proteins are recycled and operated through the autophagy pathway to ensure nutrient and energy homeostasis. Although numerous fluorescent probes have been developed to image autophagy, these environment-responsive probes suffer from inherent deficiencies such as inaccuracy and limited versatility. Here, we present a modular macrocyclic amphiphile Förster Resonance Energy Transfer (FRET) platform (SC6A12C/NCM, SN), constructed through the amphiphilic assembly of sulfonatocalix[6]arene (SC6A12C) with N-cetylmorpholine (NCM) for lysosome targeting. The hydrophobic fluorophore BPEA (FRET donor) was entrapped within the inner hydrophobic phase and showed strong fluorescence emission. Attributed to the broad-spectrum encapsulation of SC6A12C, three commercially available organelle probes (Mito-Tracker Red, ER Tracker Red, and RhoNox-1) were selected as SC6A12C guests (FRET acceptors). During autophagy process, the formation of intracellular host-guest complexes leads to strong FRET signal, allowing us to visualize the fusion of mitochondria, endoplasmic reticulum, and Golgi apparatus with lysosomes, respectively. This study provides a versatile and accessible platform for imaging organelle autophagy.

Efficient anticancer drug delivery using nano-colloids self-assembled with an unconventional amphiphile bearing pumpkin-shaped host molecule

A new type of amphiphiles bearing macrocycle such as cucurbit[7]uril (CB[7]) spontaneously forms a nanomaterial in water, specifically vesicles (tACB[7] vesicles) with a positive surface charge, verified through various analytical techniques including TIRF, DLS and TEM. Functional validation not only reveals the accessibility of the CB[7] portal on these vesicles allowing CB[7]-based host-guest interactions with various functional guest molecules such as fluorescein isothiocyanate conjugated adamantylammonium and spermine (FITC-AdA and FITC-SPM, respectively) using confocal laser scanning microscopy, but also showcases the effective internalization of tACB[7] vesicles into cancer cells with the anticancer drug oxaliplatin (OxPt), as a guest to CB[7], through in vitro cell experiments. Hence, this study provides a blueprint to impart amphiphilic properties to CB[7] through synthetic design and highlights the potential of CB[7] derivatives as a new class of unconventional amphiphiles self-assembling into functional nanomaterials for advanced drug delivery.

Supramolecular Guest Exchange in Cucurbit[7]uril for Bioorthogonal Fluorogenic Imaging across the Visible Spectrum

Fluorogenic probes that unmask fluorescence signals in response to bioorthogonal reactions are a powerful new addition to biological imaging. They can significantly reduce background fluorescence and minimize nonspecific signals, potentially enabling real-time, high-contrast imaging without the need to wash out excess fluorophores. While diverse classes of highly refined synthetic fluorophores are now readily available, integrating them into a bioorthogonal fluorogenic scheme still requires extensive design efforts and customized structural alterations to optimize quenching mechanisms for each specific fluorophore scaffold. Herein, we present a highly generalizable strategy that can produce an efficient bioorthogonal fluorogenic response from essentially any readily available fluorophore without further structural alterations. We designed this strategy based on the macrocyclic cucurbit[7]uril (CB7) host, where a fluorogenic response is achieved by programming a guest exchange reaction within the macrocyclic cavity. We employed this strategy to rapidly create fluorogenic probes across the visible spectrum from diverse fluorophore scaffolds, which enabled no-wash imaging in live cells and tissues with minimal background signal. Finally, we demonstrated that this strategy can be combined with metabolic labeling for fluorogenic detection of metabolically tagged mycobacteria under no-wash conditions and paired with covalently clickable probes for high-contrast super-resolution and multiplexed imaging in cells and tissues.

Host-guest binding between cucurbit[8]uril and amphiphilic peptides achieved tunable supramolecular aggregates for cancer diagnosis

The manipulation of biocompatible supramolecular nanostructures at subcellular and cellular levels has become one of the increasingly significant topics but remains a formidable challenge in chemical and biological science. In this work, a controllable supramolecular aggregate based on host-guest competitive binding is elaborately constructed using cucurbit[8]uril, methionine-containing amphiphilic peptide, and perylene diimide, displaying in situ oxidation-driven macrocycle-confined fluorescence enhancement for cell imaging and morphological reconstruction for cancer cell death. The experimental results demonstrate that cucurbit[8]uril possesses a high binding affinity with the methionine peptide, while this value sharply decreases after the methionine residue is oxidized to sulfoxide or sulfone. Therefore, perylene diimide can be competitively included by cucurbit[8]uril in the co-assemblies, eventually resulting in a 10-fold fluorescence enhancement and the conversion of topological morphology from nano-sized particles to micron-sized sheets. Moreover, the obtained ternary assemblies can be oxidized by endogenous reactive oxygen species in cancer cells, thus not only providing enhanced fluorescence for cell imaging, but also leading to endoplasmic reticulum dysfunction and significant cell death. Therefore, the controllable and oxidation-responsive morphological transformation based on the host-guest competitive binding in biological media can be viewed as a feasible means for efficient disease theragnosis.

Supramolecular delivery of dinuclear ruthenium and osmium MCU inhibitors

The transmembrane protein known as the mitochondrial calcium uniporter (MCU) mediates the influx of calcium ions (Ca2+) into the mitochondrial matrix. An overload of mitochondrial Ca2+ ( m Ca2+) is directly linked to damaging effects in pathological conditions. Therefore, inhibitors of the MCU are important chemical biology tools and therapeutic agents. Here, two new analogues of previously reported Ru- and Os-based MCU inhibitors Ru265 and Os245, of the general formula [(C10H15CO2)M(NH3)4(μ-N)M(NH3)4(O2CC10H15)](CF3SO3)3, where M = Ru (1) or Os (2), are reported. These analogues bear adamantane functional groups, which were installed to act as guests for the host molecule cucurbit-[7]-uril (CB[7]). These complexes were characterized and analyzed for their efficiency as guests for CB[7]. As shown through a variety of spectroscopic techniques, each adamantane ligand is encapsulated into one CB[7], affording a supramolecular complex of 1 : 2 stoichiometry. The biological effects of these compounds in the presence and absence of two equiv. CB[7] were assessed. Both complexes 1 and 2 exhibit enhanced cellular uptake compared to the parent compounds Ru265 and Os245, and their uptake is increased further in the presence of CB[7]. Compared to Ru265 and Os245, 1 and 2 are less potent as m Ca2+ uptake inhibitors in permeabilized cell models. However, in intact cell systems, 1 and 2 inhibit the MCU at concentrations as low as 1 μM, marking an advantage over Ru265 and Os245 which require an order of magnitude higher doses for similar biological effects. The presence of CB[7] did not affect the inhibitory properties of 1 and 2. Experiments in primary cortical neurons showed that 1 and 2 can elicit protective effects against oxygen-glucose deprivation at lower doses than those required for Ru265 or Os245. At low concentrations, the protective effects of 1 were modulated by CB[7], suggesting that supramolecular complex formation can play a role in these biological conditions. The in vivo biocompatibility of 1 was investigated in mice. The intraperitoneal administration of these compounds and their CB[7] complexes led to time-dependent induction of seizures with no protective effects elicited by CB[7]. This work demonstrates the potential for supramolecular interactions in the development of MCU inhibitors.

OrthoID: profiling dynamic proteomes through time and space using mutually orthogonal chemical tools

Identifying proteins at organelle contact sites, such as mitochondria-associated endoplasmic reticulum membranes (MAM), is essential for understanding vital cellular processes, yet challenging due to their dynamic nature. Here we report "OrthoID", a proteomic method utilizing engineered enzymes, TurboID and APEX2, for the biotinylation (Bt) and adamantylation (Ad) of proteins close to the mitochondria and endoplasmic reticulum (ER), respectively, in conjunction with high-affinity binding pairs, streptavidin-biotin (SA-Bt) and cucurbit[7]uril-adamantane (CB[7]-Ad), for selective orthogonal enrichment of Bt- and Ad-labeled proteins. This approach effectively identifies protein candidates associated with the ER-mitochondria contact, including LRC59, whose roles at the contact site were-to the best of our knowledge-previously unknown, and tracks multiple protein sets undergoing structural and locational changes at MAM during mitophagy. These findings demonstrate that OrthoID could be a powerful proteomics tool for the identification and analysis of spatiotemporal proteins at organelle contact sites and revealing their dynamic behaviors in vital cellular processes.

Overcoming barriers with non-covalent interactions: supramolecular recognition of adamantyl cucurbit[n]uril assemblies for medical applications

Adamantane, a staple in medicinal chemistry, recently became a cornerstone of a supramolecular host-guest drug delivery system, ADA/CB[n]. Owing to a good fit between the adamantane cage and the host cavity of the cucurbit[n]uril macrocycle, formed strong inclusion complexes find applications in drug delivery and controlled drug release. Note that the cucurbit[n]uril host is not solely a delivery vehicle of the ADA/CB[n] system but rather influences the bioactivity and bioavailability of drug molecules and can tune drug properties. Namely, as host-guest interactions are capable of changing the intrinsic properties of the guest molecule, inclusion complexes can become more soluble, bioavailable and more resistant to metabolic conditions compared to individual non-complexed molecules. Such synergistic effects have implications for practical bioapplicability of this complex system and provide a new viewpoint to therapy, beyond the traditional single drug molecule approach. By achieving a balance between guest encapsulation and release, the ADA/CB[n] system has also found use beyond just drug delivery, in fields like bioanalytics, sensing assays, bioimaging, etc. Thus, chemosensing in physiological conditions, indicator displacement assays, in vivo diagnostics and hybrid nanostructures are just some recent examples of the ADA/CB[n] applicability, be it for displacements purposes or as cargo vehicles.

Development of self-cooperative nanochaperones with enhanced activity to facilitate protein refolding

Regulating protein folding including assisting de novo folding, preventing misfolding and aggregation, and facilitating refolding of proteins are of significant importance for retaining protein's biological activities. Here, we report a mixed shell polymeric micelle (MSPM)-based self-cooperative nanochaperone (self-CO-nChap) with enhanced activity to facilitate protein refolding. This self-CO-nChap was fabricated by introducing Hsp40-mimetic artificial carriers into the traditional nanochaperone to cooperate with the Hsp70-mimetic confined hydrophobic microdomains. The artificial carrier facilitates transfer and immobilization of client proteins into confined hydrophobic microdomains, by which significantly improving self-CO-nChap's capability to inhibit unfolding and aggregation of client proteins, and finally facilitating refolding. Compared to traditional nanochaperones, the self-CO-nChap significantly enhances the thermal stability of horseradish peroxidase (HRP) epicyclically under harsher conditions. Moreover, the self-CO-nChap efficiently protects misfolding-prone proteins, such as immunoglobulin G (IgG) antibody from thermal denaturation, which is hardly achieved using traditional nanochaperones. In addition, a kinetic partitioning mechanism was devised to explain how self-CO-nChap facilitates refolding by regulating the cooperative effect of kinetics between the nanochaperone and client proteins. This work provides a novel strategy for the design of protein folding regulatory materials, including nanochaperones.

Challenges and Opportunities of Functionalized Cucurbiturils for Biomedical Applications

Cucurbit[n]uril (CB[n]) macrocycles (especially CB[5] to CB[8]) have shown exceptional attributes since their discovery in 2000. Their stability, water solubility, responsiveness to several stimuli, and remarkable binding properties have enabled a growing number of biological applications. Yet, soon after their discovery, the challenge of their functionalization was set. Nevertheless, after more than two decades, a myriad of CB[n] derivatives has been described, many of them used in cells or in vivo for advanced applications. This perspective summarizes key advances of this burgeoning field and points to the next opportunities and remaining challenges to fully express the potential of these fascinating macrocycles in biology and biomedical sciences.

A Combination of Bio-Orthogonal Supramolecular Clicking and Proximity Chemical Tagging as a Supramolecular Tool for Discovery of Putative Proteins Associated with Laminopathic Disease

Protein mutations alter protein-protein interactions that can lead to a number of illnesses. Mutations in lamin A (LMNA) have been reported to cause laminopathies. However, the proteins associated with the LMNA mutation have mostly remained unexplored. Herein, a new chemical tool for proximal proteomics is reported, developed by a combination of proximity chemical tagging and a bio-orthogonal supramolecular latching based on cucurbit[7]uril (CB[7])-based host-guest interactions. As this host-guest interaction acts as a noncovalent clickable motif that can be unclicked on-demand, this new chemical tool is exploited for reliable detection of the proximal proteins of LMNA and its mutant that causes laminopathic dilated cardiomyopathy (DCM). Most importantly, a comparison study reveals, for the first time, mutant-dependent alteration in LMNA proteomic environments, which allows to identify putative laminopathic DCM-linked proteins including FOXJ3 and CELF2. This study demonstrates the feasibility of this chemical tool for reliable proximal proteomics, and its immense potential as a new research platform for discovering biomarkers associated with protein mutation-linked diseases.

Fluorophore-based host-guest assembly complexes for imaging and therapy

Recently, supramolecular chemistry with its unique properties has received considerable attention in many fields. Supramolecular fluorescent systems constructed on the basis of macrocyclic hosts are not only effective in overcoming the limitations of imaging and diagnostic reagents, but also in enhancing their performances. This paper summarizes the recent advances in supramolecular fluorescent systems based on host-guest interactions and their application in bioimaging and therapy as well as the challenges and prospects in developing novel supramolecular fluorescent systems.

Construction of Artificial Light-Harvesting Systems Based on Aggregation-Induced Emission Type Supramolecular Self-Assembly Metallogels

A method for preparing new artificial light-harvesting systems (ALHSs) based on supramolecular metallogels was proposed. Various metal ions were introduced into a solution of a bi-benzimidazole compound (P) in ethylene glycol, and P exhibited high selectivity toward Al3+, as indicated by the noticeable red shift (49 nm) observed in the fluorescence spectra of P after the addition of Al3+. Interestingly, the gelator, P, could self-assemble into a stable supramolecular gel (P-gel) that exhibits strong aggregation-induced emission in ethylene glycol. Thus, two ALHSs were successfully prepared in a gel environment. The P-Al3+ assembly acts as the donor in the ALHSs, while BODIPY 505/515 (BDP) and rhodamine 6G (Rh6G), which are loaded onto the P-Al3+ assembly, act as acceptors. In these two diverse systems, the occurrence of an energy transfer process is confirmed from the P-Al3+ assembly to BDP and Rh6G. The findings of this study will enable the design and fabrication of ALHSs.

Artificial light-harvesting systems based on supramolecular self-assembly multi-component metallogels

This paper proposes a strategy for fabricating new artificial light-harvesting systems (ALHSs) based on supramolecular multi-component metallogels. Al³⁺ was introduced into a solution of an acylhydrazone compound (L) in DMSO or DMF to form the L-Al³⁺ assembly. After adding Al³⁺ to the L solution, a noticeable blue shift appeared in the fluorescence spectra of L. Moreover, L could form a gel (L-B-gel) with 1,3:2,4-dibenzylidene sorbitol (B) in a DMSO-H₂O binary solution. Finally, we obtained a multi-component metallogel (L-Al³⁺-B-gel) and successfully fabricated two ALHSs (L-Al³⁺/rhodamine 6G (Rh6G) and L-Al³⁺/rhodamine B (RhB)). In these systems, the L-Al³⁺ supramolecular assembly acts as the donor, while Rh6G and RhB act as acceptors. Additionally, we confirmed an energy-transfer process from the L-Al³⁺ component to Rh6G and RhB separately. The proposed fabrication strategy will facilitate the development of ALHSs.

Supramolecular Self-Assembly in Living Cells

Supramolecular interactions rely on non-covalent forces, such as hydrophobic effects, hydrogen-bonding, and electrostatic interactions, which govern many intracellular biological pathways. In cellulo supramolecular self-assembly is mainly based on host-guest interactions, changes in pH, enzymes, and polymerization-induced self-assembly to accurately induce various unnatural reactions without disturbing natural biological processes. This process can produce synthetic biocompatible macromolecules to control cell properties and regulate biological functions, such as cell proliferation and differentiation. This Minireview focuses on the latest reports in the field of in cellulo supramolecular self-assembly and anticipates future advances regarding its activation in response to internal and external stimuli, such as pH changes, reactive oxygen species, and enzymes, as well as external light illumination.

Encapsulation of Trimethine Cyanine in Cucurbit[8]uril: Solution versus Solid‐State Inclusion Behavior

Inclusion of polymethine cyanine dyes in the cavity of macrocyclic receptors is an effective strategy to alter their absorption and emission behavior in aqueous solution. In this paper, the effect of the host‐guest interaction between cucurbit[8]uril (CB[8]) and a model trimethine indocyanine (Cy3) on dye spectral properties and aggregation in water is investigated. Solution studies, performed by a combination of spectroscopic and calorimetric techniques, indicate that the addition of CB[8] disrupts Cy3 aggregates, leading to the formation of a 1 : 1 host‐guest complex with an association constant of 1.5×10⁶ M⁻¹. At concentrations suitable for NMR experiments, the slow formation of a supramolecular polymer was observed, followed by precipitation. Single crystals X‐ray structure elucidation confirmed the formation of a polymer with 1 : 1 stoichiometry in the solid state.

Multi-stimuli programmable FRET based RGB absorbing antennae towards ratiometric temperature, pH and multiple metal ion sensing

A red-green-blue (RGB) multichromophoric antenna 1 consisting of energy donors naphthalimides and perylenediimides and a central aza-BODIPY energy acceptor along with two subchromophoric red-blue (RB 6) and green-blue (GB 12) antennae was designed that showed efficient cascade Förster resonance energy transfer (FRET). RGB antenna 1 showed pronounced temperature-dependent emission behaviour where emission intensities in green and red channels could be tuned in opposite directions by temperature giving rise to unique ratiometric sensing with a temperature sensitivity of 0.4% °C. RGB antenna 1 showed reversible absorption modulation selectively in the blue region (RGB ↔ RG) upon acid/base addition giving rise to pH sensing behaviour. Furthermore, RGB antenna 1 was utilized to selectively sense metal ions such as Co2+ and Fe3+ through a FRET turn-off mechanism induced by a redox process at the aza-BODIPY site that resulted in the selective spectral modulation of the red band (i.e., RGB → GB). Model antenna RB 6 showed white light emission with chromaticity coordinates (0.32, 0.33) on acid addition. Antennae 1, 6 and 12 also exhibited solution state electrochromic switching characterized by distinct colour changes upon changing the potential. Finally, antennae 1, 6 and 12 served as reversible fluorescent inks in PMMA/antenna blends whereby the emission colours could be switched or tuned using different stimuli such as acid vapour, temperature and metal ions.

Visualization of lipophagy using a supramolecular FRET pair

A rationally designed supramolecular FRET pair consisting of cyanine3-cucurbit[7]uril (Cy3-CB[7]) and boron-dipyrromethene 630/650-adamantylammonium (BDP-AdA) can be used to visualize organelle-specific autophagy events. The intracellular accumulations of Cy3-CB[7] in lysosomes and BDP-AdA in lipid droplets (LDs) and the formation of an intracellular host-guest complex between Cy3-CB[7] and BDP-AdA resulting in FRET signals allow us to visualize the fusion of LDs with lysosomes, namely, lipophagy. This study demonstrates the potential of supramolecular imaging based on bio-orthogonal host-guest interactions in the investigation of selective autophagy events.

A hybrid aggregate FRET probe from the mixed assembly of cyanine dyes for highly specific monitoring of mitochondria autophagy

Mitochondria autophagy, also known as mitophagy, is a process in which mitochondria are wrapped by autophagosomes and fused with lysosomes for degradation. This process is essential for mitochondrial quality control. Here, we developed a hybrid aggregate FRET probe through mixed assembly of two cyanine dyes FMOTY and AMTC. In live cells, FMOTY and AMTC exist independently in lysosomes and mitochondria and will not produce interfering FRET background signals. The FRET signal is only generated when mitochondria is transported to lysosomes during mitophagy. This allows the hybridized aggregate to be used as a highly specific probe for monitoring mitophagy.

Synthesis of an AIEgen functionalized cucurbit[7]uril for subcellular bioimaging and synergistic photodynamic therapy and supramolecular chemotherapy

Aggregation-induced emission (AIE) based fluorophores (AIEgens) have attracted increasing attention for biomedical applications due to their unique optical properties. Here we report an AIE photosensitizer functionalized CB[7], namely AIECB[7], which could spontaneously self-assemble into nanoaggregates in aqueous solutions. Interestingly, the carbonyl-lace of CB[7] may potentially act as a proton acceptor in an acidic environment to fine-tune the fluorescence and singlet oxygen generation of AIECB[7] nanoaggregates by regulating the inner stacking of AIEgens. Additionally, benefiting from the guest-binding properties of CB[7], oxaliplatin was included into AIECB[7] nanoaggregates for combined photodynamic therapy and supramolecular chemotherapy. To show the modular versatility of this supramolecular system, a hypoxia-activatable prodrug banoxantrone (AQ4N) was loaded into AIECB[7] nanoaggregates, which exhibited synergistic antitumor effects on a multicellular tumor spheroid model (MCTS). This work not only provides AIECB[7] for versatile theranostic applications, but also offers important new insights into the design and development of macrocycle-conjugated AIE materials for diverse biomedical applications.

Clicking of organelle-enriched probes for fluorogenic imaging of autophagic and endocytic fluxes

Autophagy and endocytosis are essential in regulating cellular homeostasis and cancer immunotherapeutic responses. Existing methods for autophagy and endocytosis imaging are susceptible to cellular micro-environmental changes, and direct fluorogenic visualization of their fluxes remains challenging. We develop a novel strategy via clicking of organelle-enriched probes (COP), which comprises a pair of trans-cyclooctenol (TCO) and tetrazine probes separately enriched in lysosomes and mitochondria (in autophagy) or plasma membrane (in endocytosis). These paired probes are merged and boost a fluorogenic click reaction in response to autophagic or endocytic flux that ultimately fuses mitochondria or plasma membrane into lysosomes. We demonstrate that this strategy enables direct visualization of autophagic and endocytic fluxes, and confer insight into correlation of autophagic or endocytic flux to cell surface expression of immunotherapeutic targets such as MHC-I and PD-L1. The COP strategy provides a new paradigm for imaging autophagic and endocytic fluxes, and affords potential for improved cancer immunotherapy using autophagy or endocytosis inhibitors.

Covalent cucurbit[7]uril-dye conjugates for sensing in aqueous saline media and biofluids

Non-covalent chemosensing ensembles of cucurbit[n]urils (CBn) have been widely used in proof-of-concept sensing applications, but they are prone to disintegrate in saline media, e.g. biological fluids. We show here that covalent cucurbit[7]uril-indicator dye conjugates are buffer- (10× PBS buffer) and saline-stable (up to 1.4 M NaCl) and allow for selective sensing of Parkinson's drug amantadine in human urine and saliva, where the analogous non-covalent CB7⊃dye complex is dysfunctional. The in-depth analysis of the covalent host-dye conjugates in the gas-phase, and deionized versus saline aqueous media revealed interesting structural, thermodynamic and kinetic effects that are of general interest for the design of CBn-based supramolecular chemosensors and systems. This work also introduces a novel high-affinity indicator dye for CB7 through which fundamental limitations of indicator displacement assays (IDA) were exposed, namely an impractical slow equilibration time. Unlike non-covalent CBn⊃dye reporter pairs, the conjugate chemosensors can also operate through a SN2-type guest-dye exchange mechanism, which shortens assay times and opens new avenues for tailoring analyte-selectivity.

Purification of protein therapeutics via high-affinity supramolecular host-guest interactions

Efficient purification is crucial to providing large quantities of recombinant therapeutic proteins, such as monoclonal antibodies and cytokines. However, affinity techniques for manufacturing protein therapeutics that use biomolecule-conjugated agarose beads that harness specific biomolecular interactions suffer from issues related to protein denaturation, contamination and the need to maintain biomolecule-specific conditions for efficient protein capture. Here, we report a versatile and scalable method for the purification of recombinant protein therapeutics. The method exploits the high-affinity and controllable host-guest interactions between cucurbit[7]uril (CB[7]) and selected guests such as adamantylammonium. We show that the Herceptin (the brand name of trastuzumab, a monoclonal antibody drug used to treat breast cancer) and the much smaller cytokine interferon α-2a can be purified by site-specifically tagging them with adamantylammonium using the enzyme sortase A, followed by high-affinity binding with CB[7]-conjugated agarose beads and the recovery of the protein using a guest with a stronger affinity for CB[7]. The thermal and chemical stability of CB[7] beads and their scalability, recyclability and low cost may also make them advantageous for the manufacturing of biosimilars.

Multifunctional Supramolecular Assemblies with Aggregation-Induced Emission (AIE) for Cell Line Identification, Cell Contamination Evaluation, and Cancer Cell Discrimination

It is undoubted the important role of cells in biology and medicine, but worldwide misidentified and cross-contaminated cell lines have caused much trouble in related fields. Herein, three kinds of supramolecular AIE (aggregation-induced emission) nanoassemblies were constructed by the host-guest interaction between tetraphenylethene (TPE) derivatives and cucurbit[8]uril (CB[8]). Based on the recognized mechanism of AIE, the TPE derivatives could achieve stronger fluorescence emission and higher fluorescence quantum yield after assembling with CB[8]. Moreover, the constructed supramolecular AIE complexes obtained well-confirmed nanostructures and exhibited different sizes and shapes. Correspondingly, they generated characteristic biological properties and fluorescence enhancement of cells. Inspired by the concept of Big Data Analysis, these fluorescence signals were further transformed into a unique fingerprint of cells via linear discriminant analysis. Immediately, we realized the veracious identification between a normal cell line, two cancer cell lines, and two metastasized cancer cell lines in a qualitative analysis. More importantly, it was well used to monitor the evaluation of cross-contaminated cells and the discrimination of cancer cells. As a proper bioapplication of ideal supramolecular nanomaterials, this system was easy to learn and apply, and the whole procedure was kept to 20 min, without cell disruption, centrifugation, or washing steps.

MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions

Microbiome–host interactions play significant roles in health and in various diseases including autoimmune disorders. Uncovering these inter-kingdom cross-talks propels our understanding of disease pathogenesis and provides useful leads on potential therapeutic targets. Despite the biological significance of microbe–host interactions, there is a big gap in understanding the downstream effects of these interactions on host processes. Computational methods are expected to fill this gap by generating, integrating, and prioritizing predictions—as experimental detection remains challenging due to feasibility issues. Here, we present MicrobioLink, a computational pipeline to integrate predicted interactions between microbial and host proteins together with host molecular networks. Using the concept of network diffusion, MicrobioLink can analyse how microbial proteins in a certain context are influencing cellular processes by modulating gene or protein expression. We demonstrated the applicability of the pipeline using a case study. We used gut metaproteomic data from Crohn’s disease patients and healthy controls to uncover the mechanisms by which the microbial proteins can modulate host genes which belong to biological processes implicated in disease pathogenesis. MicrobioLink, which is agnostic of the microbial protein sources (bacterial, viral, etc.), is freely available on GitHub.

Reduction/Oxidation-Responsive Hierarchical Nanoparticles with Self-Driven Degradability for Enhanced Tumor Penetration and Precise Chemotherapy

Deep tumor penetration, long blood circulation, rapid drug release, and sufficient stability are the most concerning dilemmas of nano-drug-delivery systems for efficient chemotherapy. Herein, we develop reduction/oxidation-responsive hierarchical nanoparticles co-encapsulating paclitaxel (PTX) and pH-stimulated hyaluronidase (pSH) to surmount the sequential biological barriers for precise cancer therapy. Poly(ethylene glycol) diamine (PEG-dia) is applied to collaboratively cross-link the shell of nanoparticles self-assembled by a hyaluronic acid-stearic acid conjugate linked via a disulfide bond (HA-SS-SA, HSS) to fabricate the hierarchical nanoparticles (PHSS). The PTX and pSH coloaded hierarchical nanoparticles (PTX/pSH-PHSS) enhance the stability in normal physiological conditions and accelerate drug release at tumorous pH, and highly reductive or oxidative environments. Functionalized with PEG and HA, the hierarchical nanoparticles preferentially prolong the circulation time, accumulate at the tumor site, and enter MDA-MB-231 cells via CD44-mediated endocytosis. Within the acidic tumor micro-environment, pSH would be partially reactivated to decompose the dense tumor extracellular matrix for deep tumor penetration. Interestingly, PTX/pSH-PHSS could be degraded apace by the completely activated pSH within endo/lysosomes and the intracellular redox micro-environment to facilitate drug release to produce the highest tumor inhibition (93.71%) in breast cancer models.

Alkyl-Substituted Cucurbit[6]uril Bridged β-Cyclodextrin Dimer Mediated Intramolecular FRET Behavior

A novel triazolyl bridged cucurbituril (CB)-cyclodextrin (CD) dimer was synthesized via click reaction of monopropargyl modified octamethylcucurbit[6]uril and mono-6-azido-β-cyclodextrin. Moreover, it could form stable supramolecular inclusion complexes possessing efficient fluorescence resonance energy transfer, which benefited from the fact that CD and CB can bind amantadine- and pyridinium-containing fluorophores simultaneously. The supramolecular inclusion complex behaviors were investigated by NMR spectroscopy, UV-vis absorption, and fluorescence spectroscopy.

Visual monitoring of the lysosomal pH changes during autophagy with a red-emission fluorescent probe

Autophagy plays crucial roles in maintaining normal intracellular homeostasis. Molecular probes capable of monitoring lysosomal pH changes during autophagy are still highly required yet challenging to develop. Here, a lysosome-targeting fluorescent pH probe, RML, is presented by introducing a methylcarbitol unit as the lysosome-targeting group to rhodamine B, which is highly sensitive to pH changes. RML exhibits remarkable pH-dependent behavior at 583 nm with a fluorescent enhancement of more than 148-fold. The pK_a value is determined as 4.96, and the linear response with pH changes from 4.50-5.70, which is favorable for lysosomal pH imaging. We also confirm that RML diffuses selectively into lysosomes using confocal fluorescence microscopy. Using RML, we have successfully visualized autophagy by monitoring the lysosomal pH changes.

Cucurbit[7]uril-conjugated dyes as live cell imaging probes: investigation on their cellular uptake and excretion pathways

Here we report the endocytosis and excretion pathways of two different dye-conjugated cucurbit[7]urils, (cyanine 3-conjugated CB[7] and rhodamine X-conjugated CB[7]), which have great potential as molecular probes for live cell imaging. The dye-CB[7]s are translocated into live cells (human breast carcinoma cells, MCF-7) via multiple pathways, predominantly by clathrin-mediated endocytosis, and excreted from cells via lysosome-associated exocytosis. Interestingly, the CB[7] moiety has a substantial influence on the uptake and excretion pathways. These findings may widen the applications of the dyes conjugated to CB[7] and assist in the design of new molecular probes for live cell imaging.

Supra-blot: an accurate and reliable assay for detecting target proteins with a synthetic host molecule–enzyme hybrid

A new way to detect target proteins is developed using a high-affinity host–guest interaction for a wide variety of biological samples including bacteria and mammalian cells.

A highly efficient light-harvesting system with sequential energy transfer based on a multicharged supramolecular assembly

A highly efficient light-harvesting system with two-step sequential energy transfer was designed by the nonconvalent interaction of pillar[5]arene with pyridinium modified tetraphenylethene, sulforhodamine 101 and sulfonated aluminum phthalocyanine.

Modelling haemoproteins: porphyrins and cyclodextrins as sources of inspiration

The association of hydrophobic cavities with porphyrin derivatives has been used to mimic haemoprotein structures. The most employed cavity in this field is β-cyclodextrin (β-CD), and scaffolds combining β-CDs and porphyrins are expected to inspire the combination of porphyrins and cucurbiturils in the near future. Aside from providing water solubility to various porphyrinic structures, the β-CD framework can also modulate and control the reactivity of the metal core of the porphyrin. After a general introduction of the challenges faced in the field of haemoprotein models and the binding behavior of β-CDs, this article will discuss covalent and non-covalent association of porphyrins with β-CDs. In each approach, the role of the CD differs according to the relative position of the concave CD host, either directly controlling the binding and transformation of a substrate on the metalloporphyrin or playing a dual role of controlling the water solubility and selecting the axial ligand of the metal core. The discussion will be of interest to the cucurbituril community as well as to the cavitand community, as the information provided should be useful for the design of haemoprotein mimics using cucurbiturils.

Bio-orthogonal Supramolecular Latching inside Live Animals and Its Application for in Vivo Cancer Imaging

Here, we demonstrate a supramolecular latching tool for bio-orthogonal noncovalent anchoring of small synthetic molecules in live animal models using a fully synthetic high-affinity binding pair between cucurbit[7]uril (CB[7]) and adamantylammonium (AdA). This supramolecular latching system is small (∼1 kDa), ensuring efficient uptake into cells, tissues, and whole organisms. It is also chemically robust and resistant to enzymatic degradation and analogous to well-characterized biological systems in terms of noncovalent binding. Occurrence of fluorescence resonance energy transfer (FRET) between cyanine 3-CB[7] (Cy3-CB[7]) and boron-dipyrromethene 630/650X-AdA (BDP630/650-AdA) inside a live worm (Caenorhabditis elegans) indicates efficient in situ high-affinity association between AdA and CB[7] inside live animals. In addition, selective visualization of a cancer site of a live mouse upon supramolecular latching of cyanine 5-AdA (Cy5-AdA) on prelocalized CB[7]-conjugating antibody on the cancer site demonstrates the potential of this synthetic system for in vivo cancer imaging. These findings provide a fresh insight into the development of new chemical biology tools and medical therapeutic systems.

Monitoring autophagy in live cells with a fluorescent light-up probe for G-quadruplex structures

Monitoring autophagy in live cells with a fluorescent light-up probe for G-quadruplex structures.

Direct observation of selective autophagy induction in cells and tissues by self-assembled chiral nanodevice

The interactions between chiral nanomaterials and organisms are still challenging and mysterious. Here, a chiral nanodevice made of yolk-shell nanoparticles tetrahedron (UYTe), centralized with upconversion nanoparticles (UCNPs), was fabricated to induce autophagy in vivo. The proposed chiral nanodevice displayed a tunable circular dichroism (CD) signal when modified with different enantiomers of glutathione (GSH). Notably, UYTe showed significant chirality-dependent autophagy-inducing ability after D-GSH-modification because the enhanced oxidative stress and accumulation in living cell. The activation of autophagy resulted in the reduced intracellular CD intensity from the disassembly of the structure. The intracellular ATP concentration was simultaneously enhanced in response to autophagy activity, which was quantitatively bio-imaged with the upconversion luminescence (UCL) signal of the UCNP that escaped from UYTe. The autophagy effect induced in vivo by the chiral UYTe was also visualized with UCL imaging, demonstrating the great potential utility of the chiral nanostructure for cellular biological applications.

Synthetic Host-Guest Assembly in Cells and Tissues: Fast, Stable, and Selective Bioorthogonal Imaging via Molecular Recognition

Bioorthogonal strategies are continuing to pave the way for new analytical tools in biology. Although a significant amount of progress has been made in developing covalent reaction based bioorthogonal strategies, balanced reactivity, and stability are often difficult to achieve from these systems. Alternatively, despite being kinetically beneficial, the development of noncovalent approaches that utilize fully synthetic and stable components remains challenging due to the lack of selectivity in conventional noncovalent interactions in the living cellular environment. Herein, we introduce a bioorthogonal assembly strategy based on a synthetic host-guest system featuring Cucurbit[7]uril (CB[7]) and adamantylamine (ADA). We demonstrate that highly selective and ultrastable host-guest interaction between CB[7] and ADA provides a noncovalent mechanism for assembling labeling agents, such as fluorophores and DNA, in cells and tissues for bioorthogonal imaging of molecular targets. Additionally, by combining with covalent reaction, we show that this CB[7]-ADA based noncovalent interaction enables simultaneous bioorthogonal labeling and multiplexed imaging in cells as well as tissue sections. Finally, we show that interaction between CB[7] and ADA fulfills the demands of specificity and stability that is required for assembling molecules in the complexities of a living cell. We demonstrate this by sensitive detection of metastatic cancer-associated cell surface protein marker as well as by showing the distribution and dynamics of F-actin in living cells.

Supramolecular latching system based on ultrastable synthetic binding pairs as versatile tools for protein imaging

Here we report ultrastable synthetic binding pairs between cucurbit[7]uril (CB[7]) and adamantyl- (AdA) or ferrocenyl-ammonium (FcA) as a supramolecular latching system for protein imaging, overcoming the limitations of protein-based binding pairs. Cyanine 3-conjugated CB[7] (Cy3-CB[7]) can visualize AdA- or FcA-labeled proteins to provide clear fluorescence images for accurate and precise analysis of proteins. Furthermore, controllability of the system is demonstrated by treating with a stronger competitor guest. At low temperature, this allows us to selectively detach Cy3-CB[7] from guest-labeled proteins on the cell surface, while leaving Cy3-CB[7] latched to the cytosolic proteins for spatially conditional visualization of target proteins. This work represents a non-protein-based bioimaging tool which has inherent advantages over the widely used protein-based techniques, thereby demonstrating the great potential of this synthetic system.