Host-guest binding in water, salty water, and biofluids: general lessons for synthetic, bio-targeted molecular recognition

Supramolecular Mitigation of the Cyanine Limit Problem

Currently, there is a substantial research effort to develop near-infrared fluorescent polymethine cyanine dyes for biological imaging and sensing. In water, cyanine dyes with extended conjugation are known to cross over the "cyanine limit" and undergo a symmetry breaking Peierls transition that favors an unsymmetric distribution of π-electron density and produces a broad absorption profile and low fluorescence brightness. This study shows how supramolecular encapsulation of a newly designed series of cationic, cyanine dyes by cucurbit[7]uril (CB7) can be used to alter the π-electron distribution within the cyanine chromophore. For two sets of dyes, supramolecular location of the surrounding CB7 over the center of the dye favors a nonpolar ground state, with a symmetric π-electron distribution that produces a sharpened absorption band with enhanced fluorescence brightness. The opposite supramolecular effect (i.e., broadened absorption and partially quenched fluorescence) is observed with a third set of dyes because the surrounding CB7 is located at one end of the encapsulated cyanine chromophore. From the perspective of enhanced near-infrared bioimaging and sensing in water, the results show how that the principles of host/guest chemistry can be employed to mitigate the "cyanine limit" problem.

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.

An Optical Probe for Real-Time Monitoring of Self-Replicator Emergence and Distinguishing between Replicators

Self-replicating systems play an important role in research on the synthesis and origin of life. Monitoring of these systems has mostly relied on techniques such as NMR or chromatography, which are limited in throughput and demanding when monitoring replication in real time. To circumvent these problems, we now developed a pattern-generating fluorescent molecular probe (an ID-probe) capable of discriminating replicators of different chemical composition and monitoring the process of replicator formation in real time, giving distinct signatures for starting materials, intermediates, and final products. Optical monitoring of replicators dramatically reduces the analysis time and sample quantities compared to most currently used methods and opens the door for future high-throughput experimentation in protocell environments.

Analyte sensing with unselectively binding synthetic receptors: virtues of time-resolved supramolecular assays

Time-resolved supramolecular assays probe analyte-characteristic complexation and decomplexation rates. Consequently, even unselectively binding synthetic receptors can be used for analyte identification and quantification.

Modular and hierarchical self-assembly of siRNAs into supramolecular nanomaterials for soft and homogeneous siRNA loading and precise and visualized intracellular delivery

siRNA therapeutics are challenged by homogeneous and efficient loading, maintenance of biological activities, and precise, dynamic and monitorable site-release. Herein, supramolecular nanomaterials of WP5⊃G–siRNA were constructed by modular and hierarchical self-assembly of siRNA with guest (3,6-di(thiophen-2-yl)pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione derivative, G) and host (pillar[5]arene, WP5) molecules in the same system. Demonstrated by experiments and theoretical calculations, WP5⊃G–siRNA was constructed via comprehensive weak interactions including electrostatic, hydrophobic–hydrophilic, host–guest and π–π interactions. Therefore, siRNAs were efficiently loaded, maintaining good stability, bioactivities and biocompatibilities. At pH 6.8, G was protonated to give weak acidic-responsive “turn-on” fluorescent signals, which realized the precise location of cancer sites. This triggered a subsequent delivery and a dynamic release of siRNA in cancer cells under acidic conditions for the entire collapse of WP5⊃G–siRNA by the protonation of both WP5 and G. By both in vitro and in vivo experiments, precise and visualized delivery to cancer sites was achieved to exhibit effective tumour inhibition. This provided an efficient and soft strategy of siRNA therapies and expanded the application of supramolecular nanomaterials in diagnosis and treatment.

Supramolecular nanomaterials of WP5⊃G–siRNA were constructed by modular and hierarchical self-assembly of siRNA with guest and host molecules, initiating weak acidic-responsive, precise and visualized intracellular delivery for efficient therapies.

Molecular recognition of catechol on crystal-like surface of periodic mesoporous organosilica containing pyridinylethynylpyridine

A new periodic mesoporous organosilica (PMO) containing pyridinylethynylpyridine (PEPy) was successfully synthesized under basic conditions in the presence of a cationic surfactant. The PEPy-PMO had a unique mesoporous structure with...

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.

Bioapplication of cyclodextrin-containing montmorillonite

Recent progresses in the integration of CDs and montmorillonite, as well as applications of CD-containing montmorillonite hybrid host systems are summarized in this review. Several efficient synthesis strategies, such as ion exchange, metal coordination, supramolecular strategies, polymerizations and organic synthesis methods, have been discussed during the preparation of CDs/montmorillonite hybrid composites. In particular, diverse instrumental techniques were highly recommended for characterizing the as-obtained hybrid systems, including their chemical composition and structures, crystallinity, surface/self-assembled morphologies, as well as other particular physiochemical properties, providing a direct guide for promoting the desired structures and exploring various applications. It should be noted that the introduction of functional groups, as well as the integration of CDs and montmorillonite granted the thus obtained CD-containing montmorillonite hybrid host systems a lot of unique features, providing great opportunities for expanding the practical applications to a series of biological and environmental areas, such as biosensors, sorption and decontamination of bio/environmental hazardous materials, biostudies about aqueous dispersity, stability and biocompatibility, drug loading and target delivery, controlled and sustained drug release, as well as antibacterial.

Binding Methylarginines and Methyllysines as Free Amino Acids: A Comparative Study of Multiple Host Classes*

Methylated free amino acids are an important class of targets for host‐guest chemistry that have recognition properties distinct from those of methylated peptides and proteins. We present comparative binding studies for three different host classes that are each studied with multiple methylated arginines and lysines to determine fundamental structure‐function relationships. The hosts studied are all anionic and include three calixarenes, two acyclic cucurbiturils, and two other cleft‐like hosts, a clip and a tweezer. We determined the binding association constants for a panel of methylated amino acids using indicator displacement assays. The acyclic cucurbiturils display stronger binding to the methylated amino acids, and some unique patterns of selectivity. The two other cleft‐like hosts follow two different trends, shallow host (clip) following similar trends to the calixarenes, and the other more closed host (tweezer) binding certain less‐methylated amino acids stronger than their methylated counterparts. Molecular modelling sheds some light on the different preferences of the various hosts. The results identify hosts with new selectivities and with affinities in a range that could be useful for biomedical applications. The overall selectivity patterns are explained by a common framework that considers the geometry, depth of binding pockets, and functional group participation across all host classes.

Self-assembly of a water-soluble endohedrally functionalized coordination cage including polar guests

Coordination cages containing endohedrally functionalized aromatic cavities are scarce in the literature. Herein, we report the self-assembly of a tetra-cationic super aryl-extended calix[4]pyrrole tetra-pyridyl ligand into a water-soluble Pd(ii)-cage featuring two endohedral polar binding sites. They are defined by the four pyrrole NHs of the calix[4]pyrrole unit and the four inwardly directed α-protons of the coordinated pyridyl groups. The efficient assembly of the Pd(ii)-cage requires the inclusion of mono- and ditopic pyridyl N-oxide and aliphatic formamide guests. The monotopic guests only partially fill the cage's cavity and require the co-inclusion of a water molecule that is likely hydrogen-bonded to the endohedral α-pyridyl protons. The ditopic guests are able to completely fill the cage's cavity and complement both binding sites. We observed high conformational selectivity in the inclusion of the isomers of α,ω-bis-formamides. We briefly investigate the uptake and release mechanism/kinetics of selected polar guests by the Pd(ii)-cage using pair-wise competition experiments.

A tetra-cationic calix[4]pyrrole tetra-pyridyl ligand self-assembles into a water-soluble Pd(ii)-cage featuring two endohedral polar binding sites. The Pd(ii)-cage encapsulates pyridyl N-oxide and aliphatic formamide guests in water.

A Newly Designed Water Soluble Uranyl-Salophen Complex for Anion Recognition

A novel water-soluble uranyl-salophen (salophen=N,N'-disalicylidene-o-phenylenediaminate) complex was obtained. Solubility was achieved in aqueous methyl-β-cyclodextrin solutions, taking advantage of the host-guest interactions established with the adamantyl moieties present on the ligand skeleton. Such an approach facilitates the synthesis of the receptor and the purification processes and, in perspective, can be definitely applicable to other molecular scaffolds. UV/Vis titration experiments demonstrate that the capacity of the uranyl-salophen core to behave as a receptor for anions is retained in water and appears comparable with that previously reported for other water-soluble uranyl-salophen systems. Hence the presence of cyclodextrins does not interfere with molecular recognition processes.