Artificial receptors for the recognition of phosphorylated molecules

Cu2Cl(OH)3 nanozyme-based colorimetric sensor array for phosphates discrimination and disease identification

The identification of phosphates holds significant importance in many physiological processes and disease diagnosis, and traditional detection techniques struggle to simultaneously detect and distinguish phosphates. The complexity of synthesizing sensing units restricts the construction of sensor arrays as well. In this study, a bifunctional dicopper chloride trihydroxide (Cu2Cl(OH)3) nanozyme with conspicuous laccase- and peroxidase-like activities has been synthesized in basic deep eutectic solvents (DES). Exploiting the various regulatory impacts of multiple phosphates on the dual-enzyme mimicking activities, the sensor array based on the laccase mimic and peroxidase mimic properties of Cu2Cl(OH)3 was designed, which has been successfully harnessed for the identification of eight phosphates (ATP, ADP, AMP, PPi, Pi, GTP, GDP, and GMP). This approach streamlines the creation of sensor arrays. Besides, the three simulated actual samples (healthy individuals, moderately ill patients, and severely ill patients) have been accurately distinguished. This work makes a substantial contribution to enhancing the highly effective construction of array channels and promoting discrimination of phosphates in intricate samples.

Cellular Phosphate Sensing and Anion Binding by an Azacrown-Calixpyrrole Hybrid

A hybrid receptor-sensor for anions originating from the merging of positively charged ammonium moieties for electrostatic attraction/stronger binding of azacrowns with directionality of calixpyrrole hydrogen bond donors for selectivity is investigated. As demonstrated this hybrid receptor-sensor shows a remarkable selectivity for orthophosphate even in the presence of other phosphates and anions found in cellular materials (Kassoc H2PO4 ->H2P2O7 2->AMP-≫ADP2- or ATP3- over halides, nitrate, or hydrogen sulfate; all Na+ salts in water) but also cellular polyphosphate or phospholipids. This selectivity is harnessed in a real-time monitoring of cell lysis by lysozyme, which releases orthophosphate and other phosphates and anions from the cells. This sensitive (LOD 0.4 μM) fluorescence-based microscale method compares favorably with the state-of-the-art techniques but can easily be practiced in a high-throughput screening (HTS) manner. The anion binding and selectivity in aqueous solutions were investigated by NMR and put in context with phosphate binding of the parent calix[4]pyrrole. The microscopic understanding of anion binding by the hybrid receptor was then obtained from a combination of density functional theory (DFT), classical molecular dynamics (MD) with explicit water solvation, and ab initio MD (AIMD) simulations. Correlating the NMR and fluorescence binding data with studies of solvation of the receptor, phosphate anion, and the resulting complex confirms the binding is largely driven by entropic component (TΔS) associated with receptor and anion desolvation.

Cone Angles Quantify and Predict the Affinity and Reactivity of Anion Complexes between Trifluoroborates and Rigid Macrocycles

Steric manipulation is a known concept in molecular recognition but there is currently no linear free energy relationship correlating sterics to the stability of receptor-anion complexes nor to the reactivity of the bound anion. By analogy to Tolman cone angles in cation coordination chemistry, we explore how to define and correlate cone angles of organo-trifluoroborates (R-BF3 -) to the affinities observed for cyanostar-anion binding. We extend the analogy to a rare investigation of the anion's reactivity and how it changes upon binding. The substituent on the anion is used to define the cone angle, θ. A series of 10 anions were studied including versions with ethynyl, ethylene, and ethyl substituents to tune steric bulk across the sp, sp2 and sp3 hybridized α-carbons bearing 0, 1 and 2 hydrogen atoms. A linear relationship between affinity and cone angle is observed for anions bearing substituents larger than the -BF3 - headgroup. This correlation predicted affinities of two new anions to within ±5 %. We explored how complexation affects the reactivity of fluoride exchange. The yield of fluoride transfer from R-BF3 - to Lewis acid triphenylborane is correlated with cone angle. We predict that other rigid macrocycles, like commercially available bambusuril, could follow these trends.

Transition Metal Complexes with Appended Benzimidazole Groups for Sensing Dihydrogenphosphate

Four new complexes [Ru(bpy)2(bbib)](PF6)2, [Ru(phen)2(bbib)](PF6)2, [Re(CO)3(bbib)(py)](PF6) and [Ir(ppy)2(bbib)](PF6) [where bbib=4,4'-bis(benzimidazol-2-yl)-2,2'-bipyridine] have been prepared and their photophysical properties determined. Their behaviour has been studied with a variety of anions in acetonitrile, DMSO and 10 % aquated DMSO. Acetate and dihydrogenphosphate demonstrate a redshift in the bbib ligand associated absorptions suggesting that the ligand is strongly interacting with these anions. The 3MLCT emissive state is sensitive to the introduction of small quantities of anion (sub-stoichiometric quantities) and significant quenching is typically observed with acetate, although this is less pronounced in the presence of water. The emissive behaviour with dihydrogenphosphate is variable, showing systematic changes as anion concentration increases with several distinct interactions evident. 1H- and 31P-NMR titrations in a 10 % D2O-DMSO-D6 mixture suggest that with dihydrogenphosphate, the imidazole group is able to act as both a proton acceptor and donor. It appears that all four complexes can form a {[complex]2-H2PO4} "dimer", a one-to-one species (which the X-ray crystallography study suggests is dimeric in the solid-state), and a complex with a combined bis(dihydrogenphosphate) complex anion. The speciation relies on complex equilibria dependent on several factors including the complex charge, the hydrophobicity of the associated ligands, and the solvent.

Bis-Squaramide-Based [2]Rotaxane Hosts for Anion Recognition

The first examples of bis-squaramide axle containing [2]rotaxanes linked via rigid aryl and flexible alkyl spacers synthesised using copper(I) catalysed active metal template methodology are reported. The halide and oxoanion binding properties of the [2]rotaxanes in aqueous-organic solvent media are examined through extensive 1H-NMR titration experiments to investigate the impact of integrating multiple squaramide motifs on the anion binding capabilities of the interlocked receptors. These studies reveal that the bis-squaramide rotaxane host systems exhibit enhanced halide anion binding capabilities relative to a mono-squaramide axle functionalised rotaxane, demonstrating a rare anti-Hofmeister bias halide anion selectivity trend in aqueous-organic mixtures and highlighting the efficacy of the potent solvent shielded hydrophobic interlocked binding pocket created upon mechanical bond formation. Notably, employing a rigid aryl linker between the two squaramide motifs in the axle component enables the rotaxane host to exhibit strong and selective binding of tetrahedral oxoanions. Conversely, a flexible alkyl spacer facilitates trigonal oxoanion selective recognition by the bis-squaramide [2]rotaxane.

Multi-Hydrogen Bonding on Quaternized-Oligourea Receptor Facilitated Its Interaction with Bacterial Cell Membranes and DNA for Broad-Spectrum Bacteria Killing

Herein, we report a new strategy for the design of antibiotic agents based on the electrostatic interaction and hydrogen bonding, highlighting the significance of hydrogen bonding and the increased recognition sites in facilitating the interaction with bacterial cell membranes and DNA. A series of quaternary ammonium functionalized urea-based anion receptors were studied. While the monodentate mono-urea M1, bisurea M2, and trisurea M3 failed to break through the cell membrane barrier and thus could not kill bacteria, the extended bidentate dimers D1-D3 presented gradually increased membrane penetrating capabilities, DNA conformation perturbation abilities, and broad-spectrum antibacterial activities against E. coli, P. aeruginosa, S. aureus, E. faecalis, and S. epidermidis.

Post-Assembly Polymerization of Discrete Anion-Coordinated Triple Helicate

Hierarchical self-assembly has been recently employed in the construction of anion-coordination-driven gel materials. However, the post-assembly modification strategy, which may be a highly efficient strategy to realize the functionalization of discrete 'aniono' supramolecular architectures, has not been employed yet. Herein we report the first example of anion-coordination-driven gel material cross-linked by well-defined 'aniono' triple helicate through post-assembly polymerization. The obtained gel shows self-healing property and excellent compatibility with various surfaces, including glass, rubber, leaf, PP, and metal. The viscoelastic gel constructed through the post-assembly modification strategy enriches the method to construct the anion-coordination-driven smart materials.

Phosphate selective binding and sensing by halogen bonding tripodal copper(II) metallo-receptors in aqueous media

Combining the potency of non-covalent halogen bonding (XB) with metal ion coordination, the synthesis and characterisation of a series of hydrophilic XB tripodal Cu(II) metallo-receptors, strategically designed for tetrahedral anion guest binding and sensing in aqueous media is described. The reported metallo-hosts contain a tripodal C3-symmetric tris-iodotriazole XB donor anion recognition motif terminally functionalised with tri(ethylene glycol) and permethylated β-cyclodextrin functionalities to impart aqueous solubility. Optical UV-vis anion binding studies in combination with unprecedented quantitative EPR anion titration investigations reveal the XB Cu(II) metallo-receptors exhibit strong and selective phosphate recognition over a range of other monocharged anionic species in competitive aqueous solution containing 40% water, notably outperforming a hydrogen bonding (HB) Cu(II) metallo-receptor counterpart. Electrochemical studies demonstrate further the capability of the metallo-receptors to sense anions via significant cathodic perturbations of the respective Cu(II)/Cu(I) redox couple.

Anion-Carbonyl Interactions

Presented herein is the exploration of a novel non-covalent anion-carbonyl (X-···C═O) interaction using aromatic imides as receptors and halides as lone pair donors. Combined theoretical calculations and experimental methods including 13C NMR, IR, and crystallographic analyses were performed to provide the physical origin and experimental evidence of anion-carbonyl interactions. The EDA analysis (energy decomposition analysis) based on DFT calculation indicates that electrostatic terms are the dominant contributions for the binding energy while electron delocalization also significantly contributes alongside the electrostatic attraction. Orbital interaction (n → π*) involving the delocalization of halide lone pairs on the carbonyl antibonding orbitals was visualized with NBO (Natural Bond Orbital) analysis. 13C NMR and IR spectra demonstrated upfield chemical shifts and red-shift frequency of hosts upon the addition of halides, reflecting the effect of orbital overlap between the halide lone pairs and π* of carbonyl (n → π* contribution). The anion-carbonyl interactions were directly revealed by X-ray structural analysis of anion and benzene triimide complexes.

Applying a Tripodal Hexaurea Receptor for Binding to an Antitumor Drug, Combretastatin-A4 Phosphate

Phosphates play a crucial role in drug design, but their negative charge and high polarity make the transmembrane transport of phosphate species challenging. This leads to poor bioavailability of phosphate drugs. Combretastatin-A4 phosphate (CA4P) is such an anticancer monoester phosphate compound, but its absorption and clinical applicability are greatly limited. Therefore, developing carrier systems to effectively deliver phosphate drugs like CA4P is essential. Anion receptors have been found to facilitate the transmembrane transport of anions through hydrogen bonding. In this study, we developed a tripodal hexaurea anion receptor (L1) capable of binding anionic CA4P through hydrogen bonding, with a binding constant larger than 104 M-1 in a DMSO/water mixed solvent. L1 demonstrated superior binding ability compared to other common anions, and exhibited negligible cell cytotoxicity, making it a promising candidate for future use as a carrier for drug delivery.

Metal Ion-Regulated Fluorescent Sensor Array Based on Gold Nanoclusters for Physiological Phosphate Sensing

The detection of physiological phosphates (PPs) is of great importance due to their essential roles in numerous biological processes, but the efficient detection of different PPs simultaneously remains challenging. In this work, we propose a fluorescence sensor array for detecting PPs based on metal-ion-regulated gold nanoclusters (AuNCs) via an indicator-displacement assay. Zn2+ and Eu3+ are selected to assemble with two different AuNCs, resulting in quenching or enhancing their fluorescence. Based on the competitive interaction of metal ions with AuNCs and PPs, the fluorescence of AuNCs will be recovered owing to the disassembly of AuNC-metal ion ensembles. Depending on different PPs' distinct fluorescence responses, a four-channel sensor array was established. The array not only exhibits good discrimination capability for eight kinds of PPs (i.e., ATP, ADP, AMP, GTP, CTP, UTP, PPi, and Pi) via linear discriminant analysis but also enables quantitative detection of single phosphate (e.g., ATP) in the presence of interfering PPs mixtures. Moreover, potential application of the present sensor array for the discrimination of different PPs in real samples (e.g., cell lysates and serum) was successfully demonstrated with a good performance. This work illustrates the great potential of a metal ion-regulated sensor array as a new and efficient sensing platform for differential sensing of phosphates as well as other disease-related biomolecules.

Dynamic mechanostereochemical switching of a co-conformationally flexible [2]catenane controlled by specific ionic guests

Responsive synthetic receptors for adaptive recognition of different ionic guests in a competitive environment are valuable molecular tools for not only ion sensing and transport, but also the development of ion-responsive smart materials and related technologies. By virtue of the mechanical chelation and ability to undergo large-amplitude co-conformational changes, described herein is the discovery of a chameleon-like [2]catenane that selectively binds copper(I) or sulfate ions and its associated co-conformational mechanostereochemical switching. This work highlights not only the advantages and versatility of catenane as a molecular skeleton in receptor design, but also its potential in constructing complex responsive systems with multiple inputs and outputs.

Metal element-based adsorbents for phosphorus capture: Chaperone effect, performance and mechanism

Excessive phosphorus (P) enters the water bodies via wastewater discharges or agricultural runoff, triggering serious environmental problems such as eutrophication. In contrast, P as an irreplaceable key resource, presents notable supply-demand contradictions due to ineffective recovery mechanisms. Hence, constructing a system that simultaneously reduce P contaminants and effective recycling has profound theoretical and practical implications. Metal element-based adsorbents, including metal (hydro) oxides, layered double hydroxides (LDHs) and metal-organic frameworks (MOFs), exhibit a significant chaperone effect stemming from strong orbital hybridization between their intrinsic Lewis acid sites and P (Lewis base). This review aims to parse the structure-effect relationship between metal element-based adsorbents and P, and explores how to optimize the P removal properties. Special emphasis is given to the formation of the metal-P chemical bond, which not only depends on the type of metal in the adsorbent but also closely relates to its surface activity and pore structure. Then, we delve into the intrinsic mechanisms behind these adsorbents' remarkable adsorption capacity and precise targeting. Finally, we offer an insightful discussion of the prospects and challenges of metal element-based adsorbents in terms of precise material control, large-scale production, P-directed adsorption and effective utilization.

Chemical Information Processing by a Responsive Chemical System

Nature has an extraordinary capacity to precisely regulate the chemical reactivity in a highly complex mixture of molecules that is present in the cell. External stimuli lead to transient up- and downregulation of chemical reactions and provide a means for a cell to process information arriving from the environment. The development of synthetic chemical systems with life-like properties requires strategies that allow likewise control over chemical reactivity in a complex environment. Here, we show a synthetic system that mimics the initial steps that take place when a natural signal transduction pathway is activated. Monophosphate nucleosides act as chemical triggers for the self-assembly of nanoreactors that upregulate chemical reactions between reagents present at low micromolar concentrations. Different nucleotides template different assemblies and hence activate different pathways, thus establishing a distinct connection between input and output molecules. Trigger-induced upregulation of chemical reactivity occurs for only a limited amount of time because the chemical triggers are gradually removed from the system by enzymes. It is shown that the same system transiently produces different output molecules depending on the chemical input that is provided.

An Insight into Anion Extraction by Amphiphiles: Hydrophobic Microenvironments as a Requirement for the Extractant Selectivity

Coupling of electron-deficient urea units with aliphatic chains gives rise to amphiphilic compounds that bind to phosphate and benzoate anions in the hydrogen bonding competitive solvent (DMSO) with KAss = 6 580 M-1 and KAss = 4 100 M-1, respectively. The anchoring of these receptor moieties to the dendritic support does not result in a loss of anion binding and enables new applications. Due to the formation of a microenvironment in the dendrimer, the high selectivity of the prepared compound toward benzoate is maintained even in the presence of aqueous media during extraction experiments. In the presence of binding sites at 5 mM concentration, the amount of benzoate corresponding to the full binding site occupancy is transferred into the chloroform phase from its 10 mM aqueous solution. A thorough investigation of the extraction behavior of the dendrimer reported here, supported by a series of molecular dynamics simulations, provides new insight into the fundamental principles of extraction of inorganic anions by amphiphiles.

pH-Dependent phosphate separation using a tripodal hexaurea receptor

We demonstrate that a tripodal hexaurea receptor can selectively bind PO43- anions via 12 hydrogen bonds with up to 3.8 × 106 M-1 binding affinity in DMSO, which is 38-fold stronger than SO42-. This receptor facilitates the extraction of PO43- from strongly basic aqueous solutions into chloroform using liquid-liquid extraction, followed by its release as the H2PO4- anion into an acidic solution. This pH-dependent phosphate extraction successfully enables selective separation of phosphate and sulfate anions.

Fluorescent Guanidinium-Azacarbazole for Oxoanion Binding in Water

Oxoanions such as carboxylates, phosphates, and sulfates play important roles in both chemistry and biology and are abundant on the cell surface. We report on the synthesis and properties of a rationally designed guanidinium-containing oxoanion binder, 1-guanidino-8-amino-2,7-diazacarbazole (GADAC). GADAC binds to a carboxylate, phosphate, and sulfate in pure water with affinities of 3.6 × 104, 1.1 × 103, and 4.2 × 103 M-1, respectively. Like 2-azacarbazole, which is a natural product that enables scorpions to fluoresce, GADAC is fluorescent in water (λabs = 356 nm, λem = 403 nm, ε = 13,400 M-1 cm-1). The quantum yield of GADAC is pH-sensitive, increasing from Φ = 0.12 at pH 7.4 to Φ = 0.53 at pH 4.0 as a result of the protonation of the aminopyridine moiety. The uptake of GADAC into live human melanoma cells is detectable in the DAPI channel at low micromolar concentrations. Its properties make GADAC a promising candidate for applications in oxoanion binding and fluorescence labeling in biological (e.g., the delivery of cargo into cells) and other contexts.

A squaramide cage capable of binding and extracting H2PO4- and HP2O73- in highly polar protic media

A novel squaramide cage (2) binds H2PO4- and HP2O73- with high selectivity and affinity in a highly polar protic solvent system. Receptor 2 is also able to extract these hydrophilic anions into a chloroform phase from water. The X-ray crystal structure demonstrated that compound 2 forms a complex with H2PO4- with 1 : 1 stoichiometry in the solid state.

Steric Control over the Threading of Pyrophosphonates with One or Two Cyanostar Macrocycles during Pseudorotaxane Formation

The supramolecular recognition of anions is increasingly harnessed to achieve the self-assembly of supramolecular architectures, ranging from cages and polymers to (pseudo)rotaxanes. The cyanostar (CS) macrocycle has previously been shown to form 2 : 1 complexes with organophosphate anions that can be turned into [3]rotaxanes by stoppering. Here we achieved steric control over the assembly of pseudorotaxanes comprising the cyanostar macrocycle and a thread that is based, for the first time, on organo-pyrophosphonates. Subtle differences in steric bulk on the threads allowed formation of either [3]pseudorotaxanes or [2]pseudorotaxanes. We demonstrate that the threading kinetics are governed by the steric demand of the organo-pyrophosphonates and in one case, slows down to the timescale of minutes. Calculations show that the dianions are sterically offset inside the macrocycles. Our findings broaden the scope of cyanostar-anion assemblies and may have relevance for the design of molecular machines whose directionality is a result of relatively slow slipping.

Azacrown-calixpyrrole isosteres: receptors and sensors for anions

Calix[4]pyrroles (CPs) and polyammonium azacrowns (ACs) are well-known receptors for anions. CPs bind anions by directional hydrogen bonds that do not always work well for aqueous analytes. The positive charge in polyammonium ACs allows for a stronger but non-directional anion-ammonium electrostatic attraction but lack selectivity. Bridging the gap between CPs and ACs could increase affinity and potentially preserve the selectivity of anion binding. We have synthesized a flexible calixpyrrole-azacrown near isosteric receptor and incorporated an environmentally sensitive dansyl fluorophore to enable fluorescence measurements. Anion binding was evaluated using NMR and fluorescence titrations. The isosteric receptor shows a strong affinity for aqueous phosphates and phosphonates (Na⁺ salts) in the order HAsO₄^2- > H₂PO₄^- > H₂P₂O₇^2- > glyphosate^2- > AMP^- > methylphosphonate^- ≫ ADP^2- or ATP^3- but does not bind halides. This is in stark contrast to CP which shows a strong preference for halides over oxyanions. The anion binding by the new receptor was accompanied by analyte-specific changes in fluorescence intensity and spectral width and by a wavelength shift. These parameters were used in qualitative and quantitative sensing of aqueous anions. By applying machine-learning algorithms, such as linear discriminant analysis and support vector machine linear regression, this one sensor can differentiate between 10 different analytes and accurately quantify herbicide glyphosate and methylphosphonate, a product of sarin, soman or cyclosarin hydrolysis. In fact, glyphosate can be quantified even in the presence of competing anions such as orthophosphate (LODs were ≤ 1 μM).

Pyrene-Containing Polyamines as Fluorescent Receptors for Recognition of PFOA in Aqueous Media

The globally widespread perfluorooctanoic acid (PFOA) is a concerning environmental contaminant, with a possible toxic long-term effects on the environment and human health The development of sensible, rapid, and low-cost detection systems is a current change in modern environmental chemistry. In this context, two triamine-based chemosensors, L1 and L2, containing a fluorescent pyrene unit, and their Zn(II) complexes are proposed as fluorescent probes for the detection of PFOA in aqueous media. Binding studies carried out by means of fluorescence and NMR titrations highlight that protonated forms of the receptors can interact with the carboxylate group of PFOA, thanks to salt bridge formation with the ammonium groups of the aliphatic chain. This interaction induces a decrease in the fluorescence emission of pyrene at neutral and slightly acidic pH values. Similarly, emission quenching has also been observed upon coordination of PFOA by the Zn(II) complexes of the receptors. These results evidence that simple polyamine-based molecular receptors can be employed for the optical recognition of harmful pollutant molecules, such as PFOA, in aqueous media.

An aggregation induced emission active bis-heteroleptic ruthenium(II) complex for luminescence light-up detection of pyrophosphate ions

A red emissive ruthenium(II) complex 1[PF6]2 of an amino ethanol substituted 1,10-phenanthroline-based ligand (L1) has been developed and characterized by spectroscopic analysis and single-crystal X-ray diffraction. Complex 1 shows an aggregation-induced emission (AIE) enhancement and forms nano-aggregates in the poor solvent water and highly dense polyethylene glycol (PEG) media. The possible reason behind the AIE properties may be the rigidity gained through weak supramolecular interactions between neighbouring phenanthroline ligands and PF₆^- counterions. The AIE properties were supported by UV-vis and photoluminescence (PL) spectroscopy and dynamic light scattering (DLS) studies to substantiate the formation of nano-aggregates and to understand the morphology of the aggregated particles, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) studies were performed. Compound 1[PF6]2 was highly selective towards pyrophosphate ions (PPi) over other phosphates such as ATP, ADP, AMP and H₂PO₄^- ions and other competitive anions in the PL spectroscopic channel in acetonitrile. The PL titrations of 1[PF6]2 with PPi in CH₃CN furnished the association constant K_a = 1.08 × 10⁴ M^-1 and the detection limit was calculated as low as 1.54 μM. The PPi detection has been established through the unique H-bonding interaction, supported by ¹H NMR titration. Finally, the cytotoxicity study and bioimaging were carried out for biological application. The complex shows very low cytotoxicity and good biocompatibility and is suitable for intracellular PPi imaging.

Multiplex Identification of Post-Translational Modifications at Point-of-Care by Deep Learning-Assisted Hydrogel Sensors

Multiplex detection of protein post-translational modifications (PTMs), especially at point-of-care, is of great significance in cancer diagnosis. Herein, we report a machine learning-assisted photonic crystal hydrogel (PCH) sensor for multiplex detection of PTMs. With closely-related PCH sensors microfabricated on a single chip, our design achieved not only rapid screening of PTMs at specific protein sites by using only naked eyes/cellphone, but also the feasibility of real-time monitoring of phosphorylation reactions. By taking advantage of multiplex sensor chips and a neural network algorithm, accurate prediction of PTMs by both their types and concentrations was enabled. This approach was ultimately used to detect and differentiate up/down regulation of different phosphorylation sites within the same protein in live mammalian cells. Our developed method thus holds potential for POC identification of various PTMs in early-stage diagnosis of protein-related diseases.

Modeling of minimal systems based on ATP-Zn coordination for chemically fueled self-assembly

Following nature's example, there is currently strong interest in using adenosine 5'-triphosphate (ATP) as a fuel for the self-assembly of functional materials with transient/non-equilibrium behaviours. These hold great promise for applications, e.g. in catalysis and drug delivery. In a recent seminal work [Maiti et al., Nat. Chem., 2016, 8, 725], binding of ATP to the metallosurfactant zinc hexadecyl-1,4,7-triazacyclononane ([ZnC₁₆ TACN]²⁺) was exploited to produce ATP-fueled transient vesicles. Crucial to the complex formation is the ability of ATP to bind to the metal ion. As a first step to unveil the key elements underlying this process, we investigate the interaction of ATP with Zn²⁺ and with methyl-1,4,7-triazacyclononane ([ZnCH₃ TACN]²⁺), using all-atom molecular dynamics simulations. The free energy landscape of the complex formation is sampled using well-tempered metadynamics with three collective variables, corresponding to the coordination numbers of Zn²⁺ with the oxygen atoms of the three phosphate groups. We find that the structure of the ternary complex is controlled by direct triphosphate coordination to zinc, with a minor role played by the interactions between ATP and CH₃ TACN which, however, may be important for the build-up of supramolecular assemblies.

A naphthalimide-tyrosine-based dicationic amphiphile for intracellular 'turn-on' simultaneous detection of ATP and CTP

We have developed a new naphthalimide-based amphiphile (YN-1) for the simultaneous detection of ATP and CTP. In YN-1, the cationic tyrosine-linked polyamine (+2 charge, hydrophilic unit) is appended at the -peri position of naphthalimide (hydrophobic unit). YN-1 and its Boc-protected compound 4 were characterized using state-of-the-art spectroscopic and optical techniques such as NMR, IR, UV-vis and fluorescence. The fluorescence data revealed that YN-1 showed a 'turn-on' (λ_em = 440 nm) fluorescence response for nanomolar detection of nucleoside triphosphates such as ATP and CTP in 20% HEPES buffer-DMSO solution. YN-1 also showed a concentration-based discrimination between ATP and CTP. YN-1 has been successfully applied for bioimaging of nucleoside triphosphates in MCF-7 live cancer cells with good compatibility. Therefore, the important findings from the present work will provide insight for future development of fluorescent probes to detect various kinds of essential nucleoside triphosphates.

Ensemble Modified Aptamer Based Pattern Recognition for Adaptive Target Identification

The difficulty of the molecular design and chemical synthesis of artificial sensing receptors restricts their diagnostic and proteomic applications. Herein, we report a concept of "ensemble modified aptamers" (EMAmers) that exploits the collective recognition abilities of a small set of protein-like side-chain-modified nucleic acid ligands for discriminative identification of molecular or cellular targets. Different types and numbers of hydrophobic functional groups were incorporated at designated positions on nucleic acid scaffolds to mimic amino acid side chains. We successfully assayed 18 EMAmer probes with differential binding affinities to seven proteins. We constructed an EMAmer-based chemical nose sensor and demonstrated its application in blinded unknown protein identification, giving a 92.9% accuracy. Additionally, the sensor is generalizable to the detection of blinded unknown bacterial and cellular samples, which enabled identification accuracies of 96.3% and 94.8%, respectively. This sensing platform offers a discriminative means for adaptive target identification and holds great potential for diverse applications.

Applications of Synthetic Receptors in Bioanalysis and Drug Transport

Synthetic receptors are powerful tools for molecular recognition. They can bind to guests with high selectivity and affinity, and their structures are tunable and diversified. These features, plus the relatively low cost and high simplicity in synthesis and modification, support the feasibility of array-based molecular analysis with synthetic receptors for improved selectivity in the recognition of a wide range of targets. More attractively, host-guest interaction is reversible and guest displacement allows biocompatible and gentle release of the host-bound molecules, simplifying the stimulation designs needed to control analyte sensing, enrichment, and transportation. Here, we highlight a few recent advancements in using synthetic receptors for molecular analysis and manipulation, with the focus on macrocyclic receptors and their applications in displacement sensing, separation, imaging, and drug transport.

Anion-Controlled Synthesis of Novel Guanidine-Substituted Oxanorbornanes

The cycloaddition of simple alkyl-substituted guanidine derivatives is an interesting approach toward polycyclic superbases and guanidine-based organocatalysts. Due to the high nucleophilicity of guanidines, an aza-Michael reaction with dienophiles is more common and presents a huge obstacle in achieving the desired synthetic goal. Our preliminary investigations indicated that the proton could act as a suitable protecting group to regulate the directionality of the reaction. To investigate the role of the protonation state and type of anion, the reactivity of furfuryl guanidines with dimethyl acetylenedicarboxylate was explored. Furfuryl guanidines showed a strong reaction dependence on the nucleophilicity of the counterion and the structure of guanidine. While the reaction of DMAD with the guanidinium halides provided products of an aza-Michael addition, Diels-Alder cycloaddition occurred if non-nucleophilic hexafluorophosphate salts were used. Depending on the structure and the reaction conditions, oxanorbornadiene products underwent subsequent intramolecular cyclization. A tendency toward intramolecular cyclization was interpreted in terms of the pK_a of different positions of the guanidine functionality in oxanorbornadienes. New polycyclic guanidines had a slightly decreased pK_a in acetonitrile and well-defined geometry suitable for the buildup of selective sensors.

Endohedrally Functionalized Heteroleptic Coordination Cages for Phosphate Ester Binding

Metallosupramolecular hosts of nanoscopic dimensions, which are able to serve as selective receptors and catalysts, are usually composed of only one type of organic ligand, restricting diversity in terms of cavity shape and functional group decoration. We report a series of heteroleptic [Pd2 A2 B2 ] coordination cages that self-assemble from a library of shape complementary bis-monodentate ligands in a non-statistical fashion. Ligands A feature an inward pointing NH function, able to engage in hydrogen bonding and amenable to being functionalized with amide and alkyl substituents. Ligands B comprise tricyclic aromatic backbones of different shape and electronic situation. The obtained heteroleptic coordination cages were investigated for their ability to bind phosphate diesters as guests. All-atom molecular dynamics (MD) simulations in explicit solvent were conducted to understand the mechanistic relationships behind the experimentally determined guest affinities.

Anion-Coordination-Driven Assembly: From Discrete Supramolecular Self-Assemblies to Functional Soft Materials

Anion templated assembly of supramolecular systems has been extensively explored in previous reports, whereas anions serve only as an auxiliary and spectator role. With the development of anion coordination chemistry in recent years, anion coordination-driven assembly (ACDA) has emerged as a new strategy for the construction of supramolecular self-assemblies. Anions are proved to exist as the main actors in the construction of supramolecular architectures, i. e., serve as the coordination center. This Review will focus on the recent progress in anion-coordination-driven assembly of discrete supramolecular architectures, such as helicates, polyhedrons and polygons, and the various applications of 'aniono'-systems. At the end of this Review, we highlight current challenges and opportunities for future research of anion-coordination-driven self-assembly.

Triazol-Methanaminium-Pillar[5]arene-Functionalized Single Nanochannel for Quantitative Analysis of Pyrophosphate in Water

Inorganic pyrophosphate (PPi) is an important biological functional anion and plays crucial roles in life science, environmental science, medicine, and chemical process. Quantification of PPi in water has far-reaching significance for life exploration, disease diagnosis, and water pollution control. The label-free quantitative detection of PPi anions with a nanofluidic sensing device based on a conical single nanochannel is demonstrated. The channel surface is functionalized with a synthetic PPi receptor, triazol-methanaminium-functionalized pillar[5]arene (TAMAP5), using carbodiimide coupling chemistry. Due to the specific binding between TAMAP5 and PPi, the functionalized nanochannel can discriminate PPi from other inorganic anions with high selectivity through ionic current recording, even in the presence of various interfering anions. The current response exhibits a linear correlation with PPi concentration in the range from 1 × 10^-7 to 1 × 10^-4 M with a limit of detection of 6.8 × 10^-7 M. A spike-and-recovery analysis of PPi in East Lake water samples indicates that the proposed nanofluidic sensor has the ability to quantitate micromolar concentrations of PPi in environmental water samples.

Efficient fluorescent recognition of ATP/GTP by a water-soluble bisquinolinium pyridine-2,6-dicarboxamide compound. Crystal structures, spectroscopic studies and interaction mode with DNA

The new dicationic pyridine-2,6-dicarboxamide-based compound 1 bearing two N-alkylquinolinium units was synthesized, structurally determined by single-crystal X-ray diffraction, and studied in-depth as a fluorescent receptor for nucleotides and inorganic phosphorylated anions in pure water. The addition of nucleotides to 1 at pH = 7.0 quenches its blue emission with a selective affinity towards adenosine 5'-triphosphate (ATP) and guanosine 5'-tripohosphate (GTP) over other nucleotides such CTP, UTP, ADP, AMP, dicarboxylates and inorganic anions. On the basis of the spectroscopic tools (1H, 31P NMR, UV-vis, fluorescence), MS measurements and DFT calculations, receptor 1 binds ATP with high affinity (log K = 5.04) through the simultaneous formation of strong hydrogen bonds and π-π interactions between the adenosine fragment and quinolinium ring with binding energy calculated in 8.7 kcal mol-1. High affinity for ATP/GTP is attributed to the high acidity of amides and preorganized rigid structure of 1. Receptor 1 is an order of magnitude more selective for ATP than GTP. An efficient photoinduced electron transfer quenching mechanism with simultaneous receptor-ATP complexation in both the excited and ground states is proposed. Additionally, multiple spectroscopic studies and molecular dynamics simulations showed that 1 can intercalate into DNA base pairs.

Proton‐Gradient‐Driven Sensitivity Enhancement of Liposome‐Encapsulated Supramolecular Chemosensors

An overarching challenge in the development of supramolecular sensor systems is to enhance their sensitivity, which commonly involves the synthesis of refined receptors with increased affinity to the analyte. We show that a dramatic sensitivity increase by 1–2 orders of magnitude can be achieved by encapsulating supramolecular chemosensors inside liposomes and exposing them to a pH gradient across the lipid bilayer membrane. This causes an imbalance of the influx and efflux rates of basic and acidic analytes leading to a significantly increased concentration of the analyte in the liposome interior. The utility of our liposome‐enhanced sensors was demonstrated with various host–dye reporter pairs and sensing mechanisms, and we could easily increase the sensitivity towards multiple biologically relevant analytes, including the neurotransmitters serotonin and tryptamine.

Luminescent Lanthanide Probes for Inorganic and Organic Phosphates

Inorganic and organic phosphates-including orthophosphate, nucleotides, and DNA-are some of the most fundamental anions in cellular biology, regulating numerous processes of both medical and environmental significance. The characteristic long lifetimes of emitting lanthanides, including the brighter europium(III) and terbium(III), make them ideally suited for the development of molecular probes for the detection of phosphates directly in complex aqueous media. Moreover, given their high oxophilicity and the exquisite sensitivity of their quantum yields to their hydration number, those luminescent lanthanides are perfect for the detection of phosphates. Herein we discuss the principles that have guided the recent developments of molecular probes selective for inorganic or organic phosphates and how these lanthanide complexes facilitate the study of numerous biological processes.

Further Dimensions for Sensing in Biofluids: Distinguishing Bioorganic Analytes by the Salt-Induced Adaptation of a Cucurbit[7]uril-Based Chemosensor

Insufficient binding selectivity of chemosensors often renders biorelevant metabolites indistinguishable by the widely used indicator displacement assay. Array-based chemosensing methods are a common workaround but require additional effort for synthesizing a chemosensor library and setting up a sensing array. Moreover, it can be very challenging to tune the inherent binding preference of macrocyclic systems such as cucurbit[n]urils (CBn) by synthetic means. Using a novel cucurbit[7]uril-dye conjugate that undergoes salt-induced adaptation, we now succeeded in distinguishing 14 bioorganic analytes from each other through the facile stepwise addition of salts. The salt-specific concentration-resolved emission provides additional information about the system at a low synthetic effort. We present a data-driven approach to translate the human-visible curve differences into intuitive pairwise difference measures. Ion mobility experiments combined with density functional theory calculations gave further insights into the binding mechanism and uncovered an unprecedented ternary complex geometry for CB7. TThis work introduces the non-selectively binding, salt-adaptive cucurbit[n]uril system for sensing applications in biofluids such as urine, saliva, and blood serum.

Stable Cd Metal-Organic Framework as a Multiresponsive Luminescent Biosensor for Rapid, Accurate, and Recyclable Detection of Hippuric Acid, Nucleoside Phosphates, and Fe3+ in Urine and Serum

Detecting biomarkers associated with diseases has significant meaning for early prevention, diagnosis, and treatment of diseases. The development of luminescent biosensors for rapid and accurate detection in real urine and serum is urgently desired for human health monitoring. Herein, a luminescent cadmium metal-organic framework, {[Cd(L)(bpbix)]·x(solv)}_n (1), was successfully prepared by using a urea-functionalized dicarboxylate ligand, 5-(3-(pyridin-4-yl)ureido)isophthalic acid (H₂L), 4,4'-bis((1H-imidazol-1-yl)methyl)biphenyl (bpbix), and the Cd²⁺ ion. The structure of 1 presents a 2-fold interpenetrating three-dimensional pillared-layer framework. The complex 1 exhibits good stability in different-pH aqueous solutions and physiological fluids. Strikingly, the complex 1 shows quick response, high sensitivity, good anti-interference performance, and a recyclable ability for simultaneous sensing of hippuric acid (HA), nucleoside phosphates, and Fe³⁺ in water. More significantly, this sensor can realize the sensitive and accurate detection of HA, nucleoside phosphates, and Fe³⁺ in real urine and serum and meet the practical detection needs in clinical diagnosis. These results indicate that the complex 1 as a multiresponsive luminescent biosensor possesses great potential for practical detection of HA, nucleoside phosphates, and Fe³⁺ in biological samples.

Multiple-Aptamer-Integrated DNA-Origami-Based Chemical Nose Sensors for Accurate Identification of Cancer Cells

Developing simple, rapid, and accurate methods for cancer cell identification could facilitate early cancer diagnosis and tumor metastasis research. Herein, we develop a novel chemical nose sensor that employs the collective recognition abilities of a set of multiple-aptamer-integrated DNA origami (MADO) probes for discriminative identification of cancer cells. By controlling the types and/or copies of aptamers assembled on the DNA origami nanostructure, we constructed five MADO probes with differential binding affinities (ranging from 3.08 to 78.92 nM) to five types of cells (HeLa, MDA-MB-468, MCF-7, HepG2, and MCF-10A). We demonstrate the utility of the MADO-based chemical nose sensor in the identification of blinded unknown cell samples with a 95% accuracy. This sensing platform holds great potential for applications in medical diagnostics.

Neuro-Fuzzification Architecture for Modeling of Electrochemical Ion-Sensing Data of Imidazole-Dicarboxylate-Based Ru(II)-Bipyridine Complex

Anion- and pH-sensing behaviors of an imidazole-dicarboxylate-based Ru(II)-bipyridine complex possessing a number of dissociable protons in its secondary coordination sphere are employed here for the creation of multiple Boolean and fuzzy logic systems. The absorption, emission, and electrochemical behaviors of the metalloreceptor were significantly modulated upon the influence of basic anions (such as F^-, AcO^-, and H₂PO₄^-) as well as by altering the pH of the solution. Interestingly, the deprotonation of the metalloreceptor by selected anions or by alkaline pH, followed by its restoration to its original form by acid or acidic pH is reversible and could be repeated many times. The metalloreceptor is capable to demonstrate several advanced Boolean functions, namely, three-input OR gate, set-reset flip-flop logic, and traffic signal, by employing its electrochemical responses through proper use of different inputs. Administering exhaustive sensing experiments by changing the analyte concentration within a wide range is usually tedious as well as exorbitantly costly. To get rid of these difficulties, we employed here several soft computing approaches such as artificial neural networks (ANN), fuzzy logic systems (FLS), or adaptive neuro-fuzzy inference system (ANFIS) to foresee the experimental sensing data and to appropriately model the protonation-deprotonation behaviors of the metalloreceptor. Reasonably good correlation between the experimental and model output data is also reflected in their tested root-mean-square error values (0.115961 and 0.118894 for the ANFIS model).

A double-decker cage for allosteric encapsulation of ATP

In this work, we describe the preparation of double-decker cage [1-H₆]⁶⁺ comprising two binding pockets, each with three ammonium and three amide hydrogen bonding sites. This novel host possesses a high affinity for trapping two molecules of ATP in an allosteric fashion, with both experiments and theory suggesting the synergistic action of charged hydrogen bonds and π-π stacking in the encapsulation.

Combining Excellent Selectivity with Broad Target Scope: Biosensing with Arrayed Deep Cavitand Hosts

Simple macrocyclic water-soluble hosts such as cucurbiturils, cyclophanes, and calixarenes have long been used for biosensing via indicator displacement assays. Using multiple hosts and dyes in an arrayed format allows pattern recognition-based "chemical nose" sensing, which confers exquisite selectivity, even rivaling the abilities of biological recognition tools such as antibodies. However, a challenge in indicator displacement-based biosensing with macrocyclic hosts is that selectivity and scope are often inversely correlated: strong selectivity for a specific target can limit wide application, and broad scope sensing can suffer from a lack of selectivity between similar targets. This problem can be addressed by using water-soluble, self-folding deep cavitands as hosts. These flexible bowl-shaped receptors can be easily functionalized with different motifs at the upper and lower rim, and the large cavities can bind many different fluorescent dyes, causing either fluorescence enhancement or quenching upon binding.Cavity-based affinity is strongest for NMe₃⁺ groups such as trimethyl-lysine, and we have exploited this for the site-selective recognition of post-translational lysine methylations in oligopeptides. The host recognizes the NMe₃⁺ group, and by applying differently functionalized hosts in an arrayed format, discrimination between identical modifications at different positions on the oligopeptide is possible. Multiple recognition elements can be exploited for selectivity, including a defined, yet "breathable" cavity, and variable upper rim functions oriented toward the target.While the performance of the host/guest sensing system is impressive for lysine methylations, the most important advance is the use of multiple different sensing mechanisms that can target a broad range of different biorelevant species. The amphiphilic deep cavitands can both bind fluorescent dyes and interact with charged biomolecules. These non-cavity-based interactions, when paired with additives such as heavy metal ions, modulate fluorescence response in an indirect manner, and these different mechanisms allow selective recognition of serine phosphorylation, lysine acetylation, and arginine citrullination. Other targets include heavy metals, drugs of abuse, and protein isoforms. Furthermore, the hosts can be applied in supramolecular tandem assays of enzyme function: the broad scope allows analysis of such different enzymes as chromatin writers/erasers, kinases, and phosphatases, all from a single host scaffold. Finally, the indirect sensing concept allows application in sensing different oligonucleotide secondary structures, including G-quadruplexes, hairpins, triplexes, and i-motifs. Discrimination between DNA strands with highly similar structures such as G-quadruplex strands with bulges and vacancies can be achieved. Instead of relying on a single highly specific fluorescent probe, the synthetic hosts tune the fluorophore-DNA interaction, introducing multiple recognition equilibria that modulate the fluorescence signal. By applying machine learning algorithms, a classification model can be established that can accurately predict the folding state of unknown sequences. Overall, the unique recognition profile of self-folded deep cavitands provides a powerful, yet simple sensing platform, one that can be easily tuned for a wide scope of biorelevant targets, in complex biological media, without sacrificing selectivity in the recognition.