Aqueous recognition of purine and pyrimidine bases by an anthracene-based macrocyclic receptor

Amide cyclodextrin that recognises monophosphate anions in harmony with water molecules

Anion recognition in water by synthetic host molecules is a popular and challenging topic. It has been considered difficult because the water molecules compete for the recognition units. In this study, we have successfully created a novel macrocycle that achieves precise recognition through multipoint hydrogen bonding in harmony with water molecules. Specifically, an N-methylpyridinium amide β-cyclodextrin (β-CD) derivative 1(OTf)7 was synthesized, whose amide groups are directly attached to each pyranose ring. The pyridinium amide CD encapsulated a monophosphate anion in water, but it did not show interactions with sulfonates or carboxylates, thus a remarkable selectivity was demonstrated. Two monophosphates with different substituents, phenyl phosphate (PhOPO3 2-) and adamantyl phosphate (AdOPO3 2-), exhibited interesting contrasting pictures in the inclusion process, which were revealed by a combination of NOESY experiments, ITC measurements, and MD simulations. PhOPO3 2- was positioned slightly "upper" (closer to the pyridinium amide side) in 17+ with the oxygen atom of the phosphate ester R-O-P involved in the hydrogen bonds with the amide N-H, and configurational entropy plays a key role in the inclusion. Meanwhile, AdOPO3 2- was positioned "lower" (closer to the methoxy rim of CD) with the terminal -PO3 2- forming hydrogen bonds with the amides, and the hydrophobic effect is a major contributing driving force of the inclusion. The molecular design presented herein to achieve the precise recognition in water and clarification of the detailed mechanisms including the hydration phenomenon greatly contribute to the development of functional molecules that work in aqueous environments.

Supramolecular chemical biology: designed receptors and dynamic chemical systems

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

Biomimetic Hydrogen-Bonded G ⋅ C ⋅ G ⋅ C Quadruplex within a Tetraphenylethene-Based Octacationic Spirobicycle in Water

In biological systems, nucleotide quadruplexes (such as G-quadruplexes) in DNA and RNA that are held together by multiple hydrogen bonds play a crucial functional role. The biomimetic formation of these hydrogen-bonded quadruplexes captured by artificial systems in water poses a significant challenge but can offer valuable insights into these complex functional structures. Herein, we report the formation of biomimetic hydrogen-bonded G ⋅ C ⋅ G ⋅ C quadruplex captured by a tetraphenylethene (TPE) based octacationic spirobicycle (1). The spirobicyclic compound possesses a three-dimensional (3D) crossing dual-cavity structure, which enables the encapsulation of four d(GpC) dinucleotide molecules, thereby realizing 1 : 4 host-guest complexation in water. The X-ray structure reveals that four d(GpC) molecules further form a two-layer G ⋅ C ⋅ G ⋅ C quadruplex with Watson-Crick hydrogen bonds, which are stabilized within the dual hydrophobic cavities of 1 through the cooperative non-covalent interactions of hydrogen bonds, CH⋅⋅⋅π interactions, and hydrophobic effect. Due to the dynamically-rotational propeller chirality of TPE units, 1 with adaptive chirality can further serve as a chiroptical sensor to exhibit opposite Cotton effects with mirror-image CD spectra for the pH-dependent hydrogen-bonded assemblies of d(GpC) including the Watson-Crick G ⋅ C ⋅ G ⋅ C (pH 9.22) and Hoogsteen G ⋅ C+ ⋅ G ⋅ C+ (pH 5.74) quartets through the host-guest chirality transfer in water.

A High-Affinity "Synthavidin" Receptor for Squaraine Dyes

Strong-binding host-guest pairings in aqueous media have potential as "supramolecular glues" in biomedical techniques, complementing the widely-used (strept)avidin-biotin combination. We have previously found that squaraine dyes are bound very strongly by tetralactam macrocycles possessing anthracenyl units as cavity walls. Here we show that replacing the anthracenes with pentacyclic 5,7,12,14-tetrahydro-5,7,12,14-tetraoxapentacene (TOP) units generates receptors which bind squaraines with increased affinities (around Ka =1010  m-1 ) and improved selectivities. Binding can be followed through changes to squaraine fluorescence and absorbance. The TOP units are easy to prepare and potentially variable, while the TOP-based receptor shows improved photostability, both in itself and in complex with squaraines. The results suggest that this system could prove valuable in the further development of practical "synthavidin" chemistry.

Supramolecular Recognition of Cytidine Phosphate in Nucleotides and RNA Sequences

Supramolecular recognition of nucleotides would enable manipulating crucial biochemical pathways like transcription and translation directly and with high precision. Therefore, it offers great promise in medicinal applications, not least in treating cancer or viral infections. This work presents a universal supramolecular approach to target nucleoside phosphates in nucleotides and RNA. The artificial active site in new receptors simultaneously realizes several binding and sensing mechanisms: encapsulation of a nucleobase via dispersion and hydrogen bonding interactions, recognition of the phosphate residue, and a self-reporting feature-"turn-on" fluorescence. Key to the high selectivity is the conscious separation of phosphate- and nucleobase-binding sites by introducing specific spacers in the receptor structure. We have tuned the spacers to achieve high binding affinity and selectivity for cytidine 5' triphosphate coupled to a record 60-fold fluorescence enhancement. The resulting structures are also the first functional models of poly(rC)-binding protein coordinating specifically to C-rich RNA oligomers, e.g., the 5'-AUCCC(C/U) sequence present in poliovirus type 1 and the human transcriptome. The receptors bind to RNA in human ovarian cells A2780, causing strong cytotoxicity at 800 nM. The performance, self-reporting property, and tunability of our approach open up a promising and unique avenue for sequence-specific RNA binding in cells by using low-molecular-weight artificial receptors.

Recognition Site Modifiable Macrocycle: Synthesis, Functional Group Variation and Structural Inspection

Traditional macrocyclic molecules encode recognition sites in their structural backbones, which limits the variation of the recognition sites and thus, would restrict the adjustment of recognition properties. Here, we report a new oligoamide-based macrocycle capable of varying the recognition functional groups by post-synthesis modification on its structural backbone. Through six steps of common reactions, the parent macrocycle (9) can be produced in gram scale with an overall yield of 31%. The post-synthesis modification of 9 to vary the recognition sites are demonstrated by producing four different macrocycles (10-13) with distinct functional groups, 2-methoxyethoxyl (10), hydroxyl (11), carboxyl (12) and amide (13), respectively. The ¹H NMR study suggests that the structure of these macrocycles is consistent with our design, i.e., forming hydrogen bonding network at both rims of the macrocyclic backbone. The ¹H-¹H NOESY NMR study indicates the recognition functional groups are located inside the cavity of macrocycles. At last, a preliminary molecular recognition study shows 10 can recognize n-octyl-β-D-glucopyranoside (14) in chloroform.

Tricyclic octaurea "Temples" for the recognition of polar molecules in water

Two water-soluble tricyclic "Temple" macrocycles featuring pyrene roof/floor units and bis-urea spacers have been synthesised and studied as receptors for aromatic compounds in aqueous media. The tricycles show good selectivity for methylated purine alkaloids such as caffeine versus unsubstituted heterocycles such as adenine and indole. Binding is signalled by major changes in fluorescence, apparently due to the break-up of intramolecular excimers. The formation of excimers implies cavity collapse in the absence of guests explaining why, unlike an earlier relative, these receptors do not bind carbohydrates. Naphthalenediimides (NDIs) have also been studied as geometrically complementary guests, and indeed bind especially strongly (K_a > 10⁷ M^-1); this powerful and selective association suggests potential applications in supramolecular self-assembly.

Shifting the Triangle-Square Equilibrium of Self-Assembled Metallocycles by Guest Binding with Enhanced Photosensitization

Shifting a triangle-square equilibrium in one direction is an important problem in supramolecular self-assembly. Reaction of a benzothiadiazole-based diimidazole donor with a cis-Pt(II) acceptor yielded an equilibrium mixture of a triangle ([C₁₈H₂₄N₁₀O₆S₁Pt₁]₃≡ PtMC^T) and a square ([C₁₈H₂₄N₁₀O₆S₁Pt₁]₄≡ PtMC^S). We report here the shifting of such equilibrium toward a triangle using a guest (pyrene aldehyde, G1). While both benzothiadiazole and pyrene aldehyde can form reactive oxygen species (ROS) in organic solvents, their therapeutic use in water is restricted due to aqueous insolubility. The enhanced water solubility of the benzothiadiazole unit and G1 by macrocycle formation and host-guest complexation, respectively, enabled enhanced ROS generation by the host-guest complex (G1' ⊂ PtMC^T) in water (G1' = hydrated form of G1). The guest-encapsulated metallacycle (G1' ⊂ PtMC^T) has shown synergistic antibacterial activity compared to the mixture of macrocycles upon white-light irradiation due to enhanced ROS generation. The mechanism for such enhanced activity was established by measuring the oxidative stress and relative internalization of PtMCs and G1' ⊂ PtMC^T.

A fluorescent, chirality-responsive, and water-soluble cage as a multifunctional molecular container for drug delivery

In recent years, the rational design and construction of drug delivery systems (DDSs) via a supramolecular approach for improving chemical therapeutics have gained significant attention. Here, we report a host-guest DDS formed from a fluorescent, chirality-responsive, and water-soluble tetraphenylethene-based octacationic cage as a fluorescent/chiral probe, solubilizer, and molecular cargo, which can recognize chiral nucleoside drugs, enhance the solubility of insoluble drugs, and protect drugs from the outside environment by forming host-guest complexes in aqueous solution. Given the fluorescence properties and dynamically rotational conformation of tetraphenylethene (TPE) units, this fluorescent and chirality-responsive cage exhibits different responses including turn-on/turn-off fluorescence and negative/positive circular dichroism (CD) when binding with different chiral nucleoside drugs in water, resulting in multiple-responsive photophysical behaviors for these chiral drugs. Furthermore, this water-soluble cationic cage with a hydrophobic cavity can improve the water solubility of insoluble drugs (e.g., CPT) by forming host-guest complexes in water. More importantly, this multifunctional cage exhibits a low toxicity to both human colon and breast cancer cell lines in vitro, and drugs encapsulated by the cage are more effective in killing cancer cells than drugs alone. Finally, the on-off-on fluorescence responses in the formation and dissociation processes of the cage⊃drug complexes have been successfully used to monitor drug release and track drug delivery by fluorescence microscopy in vitro. Therefore, this fluorescent, chirality-responsive, and water-soluble cage as a multifunctional molecular container can be used to construct a smart drug delivery system with several functions of fluorescence and CD detection, water solubilization, real-time monitoring, and chemotherapy.

When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water

Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water-mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor-substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.

Enhanced Biological Imaging via Aggregation-Induced Emission Active Porous Organic Cages

Porous organic cages (POCs) have many advantages, including superior microenvironments, good monodispersity, and shape homogeneity, excellent molecular solubility, high chemical stability, and intriguing host-guest chemistry. These properties enable POCs to overcome the limitations of extended porous networks such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs). However, the applications of POCs in bioimaging remain limited due to the problems associated with their rigid and hydrophobic structures, thus leading to strong aggregation-caused quenching (ACQ) in aqueous biological media. To address this challenge, we report the preparation of aggregation-induced emission (AIE)-active POCs capable of stimuli responsiveness for enhanced bioimaging. We rationally design a hydrophilic, structurally flexible tetraphenylethylene (TPE)-based POC that is almost entirely soluble in aqueous solutions. This POC's conformationally flexible superstructure allows the dynamic rotation of the TPE-based phenyl rings, thus endowing impressive AIE characteristics for responses to environmental changes such as temperature and viscosity. We employ these notable features in the bioimaging of living cells and obtain good performance, demonstrating that the present AIE-active POCs are suitable candidates for further biological applications.

Synthesis of a large-cavity carbazole macrocycle for size-dependent recognition

A large-cavity carbazole macrocycle (1) is reported through condensation of a long and rigid monomer and paraformaldehyde. 1 exhibits highly selective binding of large-sized tetra(n-propyl) ammonium cation 3⁺. The complexation of 3⁺ by 1 is counter anion-dependent, where Cl^- gives the highest association constant of 3010 ± 230 M^-1.

A Sulfonated Tweezer-Shaped Receptor Selectively Recognizes Caffeine in Water

The selective recognition of caffeine in water among structurally related xanthines and purine or pyrimidine bases was achieved by a simple tweezer-shaped receptor featuring sulfonate hydrosolubilizing groups. The remarkable affinity for caffeine, among the highest reported thus far in the literature and larger than that shown by adenosine receptors of all subtypes, stems from a synergistic combination of hydrogen bonding, CH−π, and π-stacking interactions.

Breathing Room: Restoring Free Rotation in a Schiff-Base Macrocycle through Endoperoxide Formation

Macrocyclization is a popular method for preparing hosts, but it can have unintended effects, like limiting molecular free rotation to yield mixtures of inseparable isomers. We report a [3 + 3] Schiff-base macrocycle (1) with anthracene bridges. Restricted rotation about the phenyl-anthracene bonds leads 1 to exist as a mixture of conformations (1^C_s and 1^C_3v). Macrocycle 1 was photooxidized to tris(endoperoxide) adduct 4, alleviating restricted rotation. These results were supported by spectroscopic, structural, and computational analyses.

Molecular recognition and photoprotection of riboflavin in water by a biomimetic host

A water-soluble tetralactam macrocycle with 2,6-diethoxynaphthalene groups as side walls is able to strongly bind riboflavin (K_a >10⁷ M^-1) in water through hydrogen bonding and the hydrophobic effect. The encapsulated riboflavin can be stabilized by the host against photo-degradation under UV-vis irradiation, which may be harnessed to extend the shelf life of riboflavin.

Supramolecular capture of highly polar amidosquaraine dye in water with nanomolar affinity and large turn-on fluorescence

A supramolecular dye-capture system comprising anionic amidosquaraine guest and macrocyclic tetralactam host exhibits nanomolar affinity and "turn on" visible fluorescence. Utility is demonstrated with a new fluorescent assay for liposome leakage induced by the biomedically important enzyme phospholipase A₂.

Hierarchical Two-Level Supramolecular Chirality of an Achiral Anthracene-Based Tetracationic Nanotube in Water

Herein, we report an achiral anthracene-based tetracationic nanotube (1⋅4Cl^- ) that shows two levels of supramolecular chirality: namely, conformationally adaptive host-guest complexation with nucleoside triphosphates (e.g. ATP, GTP, CTP, and UTP) and twisted packing of the chiral host-guest complexes in water. Interestingly, achiral 1⋅4Cl^- exhibits chiral recognition for ATP/GTP and CTP/UTP through structural transformation of its intramolecular M- and P-twisted conformation as the first level of supramolecular chirality, which leads to adaptive chirality with opposite CD responses. Furthermore, the formation of chiral M-1⋅4Cl^- ⊃ATP can promote an intermolecular P-twisted dimeric packing of anthracene rings as the second level of supramolecular chirality to achieve assembled chirality with strong circularly polarized luminescence arising from the excimer ((+)-CPL, g_lum ≈10^-2 ) in water.