Elucidating dissociation activation energies in host-guest assemblies featuring fast exchange dynamics

Spectroscopic, biochemical and computational studies of bioactive DNA minor groove binders targeting 5'-WGWWCW-3' motif

Spectroscopic, biochemical, and computational modelling studies have been used to assess the binding capability of a set of minor groove binding (MGB) ligands against the self-complementary DNA sequences 5'-d(CGCACTAGTGCG)-3' and 5'-d(CGCAGTACTGCG)-3'. The ligands were carefully designed to target the DNA response element, 5'-WGWWCW-3', the binding site for several nuclear receptors. Basic 1D 1H NMR spectra of the DNA samples prepared with three MGB ligands show subtle variations suggestive of how each ligand associates with the double helical structure of both DNA sequences. The variations among the investigated ligands were reflected in the line shape and intensity of 1D 1H and 31P-{1H} NMR spectra. Rapid visual inspection of these 1D NMR spectra proves to be beneficial in providing valuable insights on MGB binding molecules. The NMR results were consistent with the findings from both UV DNA denaturation and molecular modelling studies. Both the NMR spectroscopic and computational analyses indicate that the investigated ligands bind to the minor grooves as antiparallel side-by-side dimers in a head-to-tail fashion. Moreover, comparisons with results from biochemical studies offered valuable insights into the mechanism of action, and antitumor activity of MGBs in relation to their structures, essential pre-requisites for future optimization of MGBs as therapeutic agents.

Stabilization of Guest Molecules inside Cation-Lidded Cucurbiturils Reveals that Hydration of Receptor Sites Can Impede Binding

Docking of alkali metal ions to water-soluble macrocyclic receptors generally reduces the affinity of guest molecules due to competitive binding. The idea that solvation water molecules could display a larger steric hindrance towards guest binding than cations has not been considered to date. We show that the docking of large cations to cucurbit[5]uril (CB5) unexpectedly increases (by a factor of 5-8) the binding of hydrophobic guests, methane and ethane. This is due to the removal of water molecules from the carbonyl portals of CB5 during cation binding, which frees up space for hydrophobe encapsulation. In contrast, smaller cations like sodium protrude deeply into the cavity of CB5 and cause the expected decrease in binding, such that the rational selection of alkali cations allows for a variation of up to a factor of 20 in binding of methane and ethane. The statistical analysis of crystallographic data shows that the cavity volume of CB5 can be enlarged by placing large alkali ions (Rb+ and Cs+ ) centro-symmetrically at the portals. The results reveal a hitherto elusive steric hindrance of solvation water molecules near receptor binding sites, which is pertinent for the design of supramolecular catalysts and the understanding of biological receptors.

NMR exchange dynamics studies of metal-capped cyclodextrins reveal multiple populations of host-guest complexes in solution

Metal-capped molecular hosts are unique in supramolecular chemistry, benefitting from the inner cavity's hydrophobic nature and the metal center's electrochemical properties. It is shown here that the paramagnetic properties of the metals in lanthanide-capped cyclodextrins (Ln-α-CDs and Ln-β-CDs) are a convenient NMR indicator for different populations of host-guest complexes in a given solution. The paramagnetic guest exchange saturation transfer (paraGEST) method was used to study the exchange dynamics in systems composed of Ln-α-CDs or Ln-β-CDs with fluorinated guests, revealing multiple co-existing populations of host-guest complexes exclusively in solutions containing Ln-β-CDs. The enhanced spectral resolution of paraGEST, achieved by a strong pseudo contact shift induction, revealed that different molecular guests can adopt multiple orientations within Ln-β-CDs' cavities and, in contrast, only a single orientation inside Ln-α-CDs. Thus, paraGEST, which can significantly improve NMR detectability and spectral resolution of host-guest systems that experience fast exchange dynamics, is a convenient tool for studying supramolecular systems of metal-capped molecular hosts.

Harnessing Pillar[5]arene Host-Guest Complexation To Improve pH Stability and Affect Enzymatic Degradation of the Anticancer Prodrug Capecitabine: A 19 F NMR Study

Cancer is a global health problem, and supramolecular chemotherapy is emerging as a novel strategy to battle the disease. Here, we first evaluated the thermodynamic and kinetic stability of the complexes formed between several water-soluble per-substituted pillar[5]arene derivatives and capecitabine (1), a widely used oral chemotherapeutic prodrug. The exchange rate was studied, for the first time in pillararene chemistry, by the 19 F guest exchange saturation transfer (GEST) NMR technique. Importantly, when we evaluated the effect of complexation on the characteristics of 1, we found that the complexation of 1 with such pillar[5]arene hosts increased capecitabine stability at acidic pH very significantly and slowed its enzymatic degradation by the carboxylesterase enzyme in a manner that depended on the host. These interesting findings could have implications on the clinical use of this heavily used prodrug and might affect the management of cancer patients.

pH- and temperature-responsive supramolecular assemblies with highly adjustable viscoelasticity: a multi-stimuli binary system

Stimuli-responsive materials are increasingly needed for the development of smart electronic, mechanical, and biological devices and systems relying on switchable, tunable, and adaptable properties. Herein, we report a novel pH- and temperature-responsive binary supramolecular assembly involving a long-chain hydroxyamino amide (HAA) and an inorganic hydrotrope, boric acid, with highly tunable viscous and viscoelastic properties. The system under investigation demonstrates a high degree of control over its viscosity, with the capacity to achieve over four orders of magnitude of control through the concomitant manipulation of pH and temperature. In addition, the transformation from non-Maxwellian to Maxwellian fluid behavior could also be induced by changing the pH and temperature. Switchable rheological properties were ascribed to the morphological transformation between spherical vesicles, aggregated/fused spherical vesicles, and bicontinuous gyroid structures revealed by cryo-TEM studies. The observed transitions are attributed to the modulation of the head group spacing between HAA molecules under different pH conditions. Specifically, acidic conditions induce electrostatic repulsion between the protonated amino head groups, leading to an increased spacing. Conversely, under basic conditions, the HAA head group spacing is reduced due to the intercalation of tetrahydroxyborate, facilitated by hydrogen bonding.

The Contributions of Supramolecular Kinetics to Dynamics of Supramolecular Polymers

Supramolecular polymers exhibit well-controlled dynamics with fascinating capacity for remodeling, self-healing, and stimuli-responsiveness. Supramolecular kinetics of non-covalent bonds is a dominant control handle among the relevant factors to tailor dynamics of supramolecular polymers. This Review focuses on elucidating how supramolecular kinetics dictates the polymer dynamics in supramolecular polymer systems. The ways to tailor supramolecular kinetics are firstly examined as prerequisites for structure-activity study of supramolecular polymers. We next discuss the role of supramolecular kinetics in supramolecular polymers under different polymer architectures by the combination of both of theoretical and experimental studies. Finally, we conclude by discussing the existing challenges and opportunities in the current studies.

Rapid analytical CEST spectroscopy of competitive host-guest interactions using spatial parallelization with a combined approach of variable flip angle, keyhole and averaging (CAVKA)

A serious limitation of high resolution ¹²⁹Xe chemical exchange saturation transfer (CEST) NMR spectroscopy for comparing competitive host-guest interactions from different samples is the long acquisition time due to step-wise encoding of the chemical shift dimension. A method of optimized use of ¹²⁹Xe spin magnetization to enable the accelerated and simultaneous acquisition of CEST spectra from multiple samples or regions in a setup is described. The method is applied to investigate the host-guest system of commercially available cucurbit[7]uril (CB7) and xenon with competing guests: cis-1,4-bis(aminomethyl)cyclohexane, cadaverine, and putrescine. Interactions with the different guests prove that the observed CEST signal is from a CB6 impurity and that CB7 itself does not produce a CEST signal. Instead, rapid interactions between xenon and CB7 manifest in the spectrum as a broad saturation response that could be suppressed by cis-1,4-bis(aminomethyl)cyclohexane. This guest prevents interactions at the CB7 portals. The suggested method represents a type of spectroscopic imaging that is capable of capturing the exchange kinetics information of systems that otherwise suffer from shortened T₂ times and yields multiple spectra for comparing exchange conditions with a reduction of >95% in acquisition time. The spectral quality is sufficient to perform quantitative analysis and quantifications relative to a CB6 standard as well as relative to a known blocker concentration (putrescine) that both reveal an unexpectedly high CB6 impurity of ca. 8%.

Simultaneous analyte indicator binding assay (SBA) for the monitoring of reversible host-guest complexation kinetics

Very little information is available on the kinetics of the self-assembly and dissociation of optically silent building blocks despite the importance of such data in the rational design of tailor-made host-guest systems. We introduce here a novel time-resolved method that enables the simultaneous determination of complex formation and complex dissociation rate constants for inclusion-type host-guest complexes. The simultaneous analyte indicator binding assay (SBA) gives also direct access to binding affinities, thus largely simplifying the experimental procedure for a full kinetic and thermodynamic characterisation of host-guest systems.

Solution NMR of synthetic cavity containing supramolecular systems: what have we learned on and from?

NMR has been instrumental in studies of both the structure and dynamics of molecular systems for decades, so it is not surprising that NMR has played a pivotal role in the study of host-guest complexes and supramolecular systems. In this mini-review, selected examples will be used to demonstrate the added value of using (multiparametric) NMR for studying macrocycle-based host-guest and supramolecular systems. We will restrict the discussion to synthetic host systems having a cavity that can engulf their guests thus restricting them into confined spaces. So discussion of selected examples of cavitands, cages, capsules and their complexes, aggregates and polymers as well as organic cages and porous liquids and other porous materials will be used to demonstrate the insights that have been gathered from the extracted NMR parameters when studying such systems emphasizing the information obtained from somewhat less routine NMR methods such as diffusion NMR, diffusion ordered spectroscopy (DOSY) and chemical exchange saturation transfer (CEST) and their variants. These selected examples demonstrate the impact that the results and findings from these NMR studies have had on our understanding of such systems and on the developments in various research fields.

Fast Ion-Chelate Dissociation Rate for In Vivo MRI of Labile Zinc with Frequency-Specific Encodability

Fast ion-chelate dissociation rates and weak ion-chelate affinities are desired kinetic and thermodynamic features for imaging probes to allow reversible binding and to prevent deviation from basal ionic levels. Nevertheless, such properties often result in poor readouts upon ion binding, frequently result in low ion specificity, and do not allow the detection of a wide range of concentrations. Herein, we show the design, synthesis, characterization, and implementation of a Zn²⁺-probe developed for MRI that possesses reversible Zn²⁺-binding properties with a rapid dissociation rate (k_off = 845 ± 35 s^–1) for the detection of a wide range of biologically relevant concentrations. Benefiting from the implementation of chemical exchange saturation transfer (CEST), which is here applied in the ¹⁹F-MRI framework in an approach termed ion CEST (iCEST), we demonstrate the ability to map labile Zn²⁺ with spectrally resolved specificity and with no interference from competitive cations. Relying on fast k_off rates for enhanced signal amplification, the use of iCEST allowed the designed fluorinated chelate to experience weak Zn²⁺-binding affinity (K_d at the mM range), but without compromising high cationic specificity, which is demonstrated here for mapping the distribution of labile Zn²⁺ in the hippocampal tissue of a live mouse. This strategy for accelerating ion-chelate k_off rates for the enhancement of MRI signal amplifications without affecting ion specificity could open new avenues for the design of additional probes for other metal ions beyond zinc.

From Selection to Instruction and Back: Competing Conformational Selection and Induced Fit Pathways in Abiotic Hosts

Two limiting cases of molecular recognition, induced fit (IF) and conformational selection (CS), play a central role in allosteric regulation of natural systems. The IF paradigm states that a substrate "instructs" the host to change its shape after complexation, while CS asserts that a guest "selects" the optimal fit from an ensemble of preexisting host conformations. With no studies that quantitatively address the interplay of two limiting pathways in abiotic systems, we herein and for the first time describe the way by which twisted capsule M-1, encompassing two conformers M-1(+) and M-1(-), trap CX₄ (X=Cl, Br) to give CX₄ ⊂M-1(+) and CX₄ ⊂M-1(-), with all four states being in thermal equilibrium. With the assistance of 2D EXSY, we found that CBr₄ would, at its lower concentrations, bind M-1 via a M-1(+)→M-1(-)→CBr₄ ⊂M-1(-) pathway corresponding to conformational selection. For M-1 complexing CCl₄ though, data from 2D EXSY measurements and 1D NMR line-shape analysis suggested that lower CCl₄ concentrations would favor CS while the IF pathway prevailed at higher proportions of the guest. Since CS and IF are not mutually exclusive, we reason that our work sets the stage for characterizing the dynamics of a wide range of already existing hosts to broaden our fundamental understanding of their action. The objective is to master the way in which encapsulation takes place for designing novel and allosteric sequestering agents, catalysts and chemosensors akin to those found in nature.

Single Fluorinated Agent for Multiplexed 19 F-MRI with Micromolar Detectability Based on Dynamic Exchange

The weak thermal polarization of nuclear spins limits the sensitivity of MRI, even for MR-sensitive nuclei as fluorine-19. Therefore, despite being the source of inspiration for the development of background-free MRI for various applications, including for multiplexed imaging, the inability to map very low concentrations of targets using ¹⁹ F-MRI raises the need to further enhance this platform's capabilities. Here, we employ the principles of CEST-MRI in ¹⁹ F-MRI to obtain a 900-fold signal amplification of a biocompatible fluorinated agent, which can be presented in a "multicolor" fashion. Capitalizing on the dynamic interactions in host-guest supramolecular assemblies in an approach termed GEST, we demonstrate that an inhalable fluorinated anesthetic can be used as a single ¹⁹ F-probe for the concurrent detection of micromolar levels of two targets, with potential in vivo translatability. Further extending GEST with new designs could expand the applicability of ¹⁹ F-MRI to the mapping of targets that have so-far remained non-detectable.