Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial arrangements of cyclodextrin host-guest complexes in solution studied by ¹³C NMR and molecular modelling.

ABSTRACT: ¹³C NMR spectroscopic analyses of C_s symmetric guest molecules in the cyclodextrin host cavity, combined with molecular modelling and solid-state X-ray analysis, provides a detailed description of the spatial arrangement of cyclodextrin host-guest complexes in solution. The chiral cavity of the cyclodextrin molecule creates an anisotropic environment for the guest molecule resulting in a splitting of its prochiral carbon signals in ¹³C NMR spectra. This signal split can be correlated to the distance of the guest atoms from the wall of the host cavity and to the spatial separation of binding sites preferred by pairs of prochiral carbon atoms. These measurements complement traditional solid-state analyses, which rely on the crystallization of host-guest complexes and their crystallographic analysis.

SUBMITTER: Lebedinskiy K

PROVIDER: S-EPMC10896224 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Spatial arrangements of cyclodextrin host-guest complexes in solution studied by 13C NMR and molecular modelling.

Lebedinskiy Konstantin K Barvík Ivan I Tošner Zdeněk Z Císařová Ivana I Jindřich Jindřich J Hrdina Radim R

Beilstein journal of organic chemistry 20240220

13C NMR spectroscopic analyses of Cs symmetric guest molecules in the cyclodextrin host cavity, combined with molecular modelling and solid-state X-ray analysis, provides a detailed description of the spatial arrangement of cyclodextrin host-guest complexes in solution. The chiral cavity of the cyclodextrin molecule creates an anisotropic environment for the guest molecule resulting in a splitting of its prochiral carbon signals in 13C NMR spectra. ...[more]

PMID: 38410781

Similar Datasets

Advantages of Induced Circular Dichroism Spectroscopy for Qualitative and Quantitative Analysis of Solution-Phase Cyclodextrin Host-Guest Complexes.

Project description:The presence of a chiral or chirally perturbed chromophore in the molecule under investigation is a fundamental requirement for the appearance of a circular dichroism (CD) spectrum. For native and for most of the substituted cyclodextrins, this condition is not applicable, because although chiral, cyclodextrins lack a chromophore group and therefore have no characteristic CD spectra over 220 nm. The reason this method can be used is that if the guest molecule has a chromophore group and this is in the right proximity to the cyclodextrin, it becomes chirally perturbed. As a result, the complex will now provide a CD signal, and this phenomenon is called induced circular dichroism (ICD). The appearance of the ICD spectrum is clear evidence of the formation of the complex, and the spectral sign and intensity is a good predictor of the structure of the complex. By varying the concentration of cyclodextrin, the ICD signal changes, resulting in a saturation curve, and from these data, the stability constant can be calculated for a 1:1 complex. This article compares ICD and NMR spectroscopic and molecular modeling results of cyclodextrin complexes of four model compounds: nimesulide, fenbufen, fenoprofen, and bifonazole. The results obtained by the different methods show good agreement, and the structures estimated from the ICD spectra are supported by NMR data and molecular modeling.

| S-EPMC10779089 | biostudies-literature

Platinum(IV)-Ferrocene Conjugates and Their Cyclodextrin Host-Guest Complexes.

Project description:Reported here are new platinum(IV) (Pt(IV)) complexes bearing ferrocene (Fc) moieties. These systems differ from one another only by the nature of the functional group (ester vs amide) connecting the linker to the Fc subunits. This minor structural variation (one atom difference) leads to major differences in solubility, stability, and antiproliferative activity against lung (A549) cancer cells. The host-guest chemistry of these complexes was investigated in an aqueous medium in the presence of β-cyclodextrins (β-CD), either free or in the form of a covalently linked Fc-Pt-β-CD hybrid. An inclusion complex between Fc and β-CD is formed in aqueous media, presumably as a result of hydrophobic interactions involving the Fc and the inner β-CD cavity. Consequently, it proved possible to use a β-CD-based strategy to purify the Pt-Fc conjugates in this study under aqueous conditions (by means of C18 silica gel columns). The use of a β-CD adjuvant also allowed dimethyl sulfoxide (DMSO) to be avoided as an organic cosolvent in cell studies. The amide version reported here (2) proved to be more soluble, more stable, and more active than the ester analogue (11) in A549 cells. The use of a β-CD functionalized with a fluorescent probe allowed intracellular Pt-Fc localization to be visualized by confocal fluorescence microscopy.

| S-EPMC6953482 | biostudies-literature

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

Project description: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.

| S-EPMC10599603 | biostudies-literature

113Cd as a Probe in NMR Studies of Allosteric Host-Guest-Ligand Complexes of Porphyrin Cage Compounds.

Project description:Cadmium porphyrin cage compounds Cd1 and 113 Cd1 have been synthesized from the free base porphyrin cage derivative H21 and Cd(OAc)2 ⋅ 2 H2O or 113Cd(OAc)2 ⋅ 2 H2O, respectively. The compounds form allosteric complexes with the positively charged guests N,N'-dimethylimidazolium hexafluorophosphate (DMI) and N,N'-dimethylviologen dihexafluorophosphate (Me2V), which bind in the cavity of the cage, and tbupy, which coordinates as an axial ligand to the outside of the cage. In the presence of tbupy, the binding of DMI in Cd1 is enhanced by a factor of ∼31, while the presence of DMI or Me2V in the cavity of Cd1 enhances the binding of tbupy by factors of 55 and 85, respectively. The X-ray structures of the coordination complexes of Cd1 with acetone, acetonitrile, and pyridine, the host-guest complex of Cd1 with a bound viologen guest, and the ternary allosteric complex of Cd1 with a bound DMI guest and a coordinated tbupy ligand, were solved. These structures revealed relocations of the cadmium center in and out of the porphyrin plane, depending on whether a guest or a ligand is present. 113Cd NMR could be employed as a tool to quantify the binding of guests and ligands to 113 Cd1. 1D EXSY experiments on the ternary allosteric system Cd1-tbupy-Me2V revealed that the coordination of tbupy significantly slowed down the dissociation of the Me2V guest. Eyring plots of the dissociation process revealed that this kinetic allosteric effect is entropic in nature.

| S-EPMC9324901 | biostudies-literature

Measurement of Single-Molecule Forces in Cholesterol and Cyclodextrin Host-Guest Complexes.

Project description:Biological host molecules such as β-cyclodextrins (β-CDs) have been used to remove cholesterol guests from membranes and artery plaques. In this work, we calibrated the host-guest intermolecular mechanical forces (IMMFs) between cholesterol and cyclodextrin complexes by combining single-molecule force spectroscopy in optical tweezers and computational molecular simulations for the first time. Compared to native β-CD, methylated beta cyclodextrins complexed with cholesterols demonstrated higher mechanical stabilities due to the loss of more high-energy water molecules inside the methylated β-CD cavities. This result is consistent with the finding that methylated β-CD is more potent at solubilizing cholesterols than β-CD, suggesting that the IMMF can serve as a novel indicator to evaluate the solubility of small molecules such as cholesterols. Importantly, we found that the force spectroscopy measured in such biological host-guest complexes is direction-dependent: pulling from the alkyl end of the cholesterol molecule resulted in a larger IMMF than that from the hydroxyl end of the cholesterol molecule. Molecular dynamics coupled with umbrella sampling simulations further revealed that cholesterol molecules tend to enter or leave from the wide opening of cyclodextrins. Such an orientation rationalizes that cyclodextrins are rather efficient at extracting cholesterols from the phospholipid bilayer in which hydroxyl groups of cholesterols are readily exposed to the hydrophobic cavities of cyclodextrins. We anticipate that the IMMF measured by both experimental and computational force spectroscopy measurements help elucidate solubility mechanisms not only for cholesterols in different environments but also to host-guest systems in general, which have been widely exploited for their solubilization properties in drug delivery, for example.

| S-EPMC8788999 | biostudies-literature

Cyclodextrin-based host-guest complexes loaded with regorafenib for colorectal cancer treatment.

Project description:The malignancy of colorectal cancer (CRC) is connected with inflammation and tumor-associated macrophages (TAMs), but effective therapeutics for CRC are limited. To integrate therapeutic targeting with tumor microenvironment (TME) reprogramming, here we develop biocompatible, non-covalent channel-type nanoparticles (CNPs) that are fabricated through host-guest complexation and self-assemble of mannose-modified γ-cyclodextrin (M-γ-CD) with Regorafenib (RG), RG@M-γ-CD CNPs. In addition to its carrier role, M-γ-CD serves as a targeting device and participates in TME regulation. RG@M-γ-CD CNPs attenuate inflammation and inhibit TAM activation by targeting macrophages. They also improve RG's anti-tumor effect by potentiating kinase suppression. In vivo application shows that the channel-type formulation optimizes the pharmacokinetics and bio-distribution of RG. In colitis-associated cancer and CT26 mouse models, RG@M-γ-CD is proven to be a targeted, safe and effective anti-tumor nanomedicine that suppresses tumor cell proliferation, lesions neovascularization, and remodels TME. These findings indicate RG@M-γ-CD CNPs as a potential strategy for CRC treatment.

| S-EPMC7858623 | biostudies-literature

Solution phase refinement of active site structure using 2D NMR and judiciously 13C-labeled cytochrome P450.

Project description:The Cytochrome P450 (CYP450) superfamily has been the subject of intense research for over six decades. Here the HU227 strain of E. coli, lacking the δ-aminolevulinic acid (δ-ALA) synthase gene, was employed, along with [5-13C] δ-ALA, in the heterologous expression of P450cam harboring a prosthetic group labeled with 13C at the four methine carbons (Cm) and pyrrole Cα positions. The product was utilized as a proof of principle strategy for defining and refining solution phase active site structure in cytochrome P450cam, providing proton-to-proton distances from 13CmH to protons on bound substrate or nearby amino acid residues, using short mixing time 2D or 3D NOESY-HMQC methods. The results reveal the interesting finding that 2D 13C-filtered NOESY-HMQC can be used to obtain distances between protons on labeled 13C to positions of protons nearby in the active site, confirming the utility of this NMR-based approach to probing active site structure under physiological conditions. Such 13C-heme-filtered NOE data complement X-ray crystallographic and T1-based NMR measurements; and, may also be of potentially significant utility in furnishing experimental distance constraints in validations of docking routines commonly employed for determining the relative affinities and binding orientations of drug candidates with CYP450s.

| S-EPMC10725731 | biostudies-literature

Proliferating cell nuclear antigen (PCNA) interactions in solution studied by NMR.

Project description:PCNA is an essential factor for DNA replication and repair. It forms a ring shaped structure of 86 kDa by the symmetric association of three identical protomers. The ring encircles the DNA and acts as a docking platform for other proteins, most of them containing the PCNA Interaction Protein sequence (PIP-box). We have used NMR to characterize the interactions of PCNA with several other proteins and fragments in solution. The binding of the PIP-box peptide of the cell cycle inhibitor p21 to PCNA is consistent with the crystal structure of the complex. A shorter p21 peptide binds with reduced affinity but retains most of the molecular recognition determinants. However the binding of the corresponding peptide of the tumor suppressor ING1 is extremely weak, indicating that slight deviations from the consensus PIP-box sequence dramatically reduce the affinity for PCNA, in contrast with a proposed less stringent PIP-box sequence requirement. We could not detect any binding between PCNA and the MCL-1 or the CDK2 protein, reported to interact with PCNA in biochemical assays. This suggests that they do not bind directly to PCNA, or they do but very weakly, with additional unidentified factors stabilizing the interactions in the cell. Backbone dynamics measurements show three PCNA regions with high relative flexibility, including the interdomain connector loop (IDCL) and the C-terminus, both of them involved in the interaction with the PIP-box. Our work provides the basis for high resolution studies of direct ligand binding to PCNA in solution.

| S-EPMC3491057 | biostudies-literature

Adamantane-Substituted Purine Nucleosides: Synthesis, Host–Guest Complexes with β-Cyclodextrin and Biological Activity

Project description:Purine nucleosides represent an interesting group of nitrogen heterocycles, showing a wide range of biological effects. In this study, we designed and synthesized a series of 6,9-disubstituted and 2,6,9-trisubstituted purine ribonucleosides via consecutive nucleophilic aromatic substitution, glycosylation, and deprotection of the ribofuranose unit. We prepared eight new purine nucleosides bearing unique adamantylated aromatic amines at position 6. Additionally, the ability of the synthesized purine nucleosides to form stable host–guest complexes with β-cyclodextrin (β-CD) was confirmed using nuclear magnetic resonance (NMR) and mass spectrometry (ESI-MS) experiments. The in vitro antiproliferative activity of purine nucleosides and their equimolar mixtures with β-CD was tested against two types of human tumor cell line. Six adamantane-based purine nucleosides showed an antiproliferative activity in the micromolar range. Moreover, their effect was only slightly suppressed by the presence of β-CD, which was probably due to the competitive binding of the corresponding purine nucleoside inside the β-CD cavity.

| S-EPMC9739181 | biostudies-literature

Complexity of protein energy landscapes studied by solution NMR relaxation dispersion experiments.

Project description:The millisecond time scale motions in ribonuclease A (RNase A) were studied by solution NMR CPMG and off-resonance R1? relaxation dispersion experiments over a wide pH and temperature range. These experiments identify three separate protein regions termed Cluster 1, Cluster 2, and R33, whose motions are governed by distinct thermodynamic parameters. Moreover, each of these regions has motions with different pH dependencies. Cluster 1 shows an increase in activation enthalpy and activation entropy as the pH is lowered, whereas Cluster 2 exhibits the opposite behavior. In contrast, the activation enthalpy and entropy of R33 show no pH dependence. Compounding the differences, ?? values for Cluster 2 are characteristic of two-site conformational exchange, yet similar analysis for Cluster 1 indicates that this region of the enzyme exhibits conformational fluctuations between a major conformer and a pH-dependent average of protonated and deprotonated minor conformers.

| S-EPMC4710144 | biostudies-literature