Tailoring the nuclear Overhauser effect for the study of small and medium-sized molecules by solvent viscosity manipulation

Probing Macromolecular Conformation in Restricted Geometry by PEF: Application to Hydrophobically Modified PAMAM Dendrimers Isolated Inside Surfactant Micelles

The conformation of a series of zero-generation polyamidoamine dendrimers end-labeled with four 1-pyrene-butyroyl, -hexanoyl, -octanoyl, -decanoyl, and -dodecanoyl derivatives, referred to as the PyCX-PAMAM-G0 samples with X = 4, 6, 8, 10, and 12, respectively, was characterized in N,N-dimethylformamide (DMF), dimethyl sulfoxide (DMSO), and aqueous solutions of 50 mM sodium dodecyl sulfate (SDS) or 50 mM dodecyltrimethylammonium bromide (DTAB). The conformation of the PyCX-PAMAM-G0 samples was determined from the global model-free analysis (MFA) of the fluorescence decays, which yielded the average rate constant (⟨k⟩) for pyrene excimer formation (PEF) between an excited and a ground-state pyrenyl labels, with ⟨k⟩ being proportional to the local concentration ([Py]loc) of the pyrenyl labels within the macromolecular volume; ⟨k⟩-vs-[Py]loc plots yielded straight lines passing through the origin in DMF and DMSO, demonstrating that the internal segments of the dendrimers obeyed Gaussian statistics in these two solvents. In aqueous surfactant solutions, the hydrophobic pyrenyl labels induced the interactions of the PyCX-PAMAM-G0 dendrimers with the SDS and DTAB micelles. Plots of ⟨k⟩ as a function of [Py]loc yielded straight lines passing through the origin for the PyCX-PAMAM-G0 samples with X equal to 4, 6, and 8, indicating that the internal segments of these three dendrimers obeyed Gaussian statistics within the surfactant micelles. However, ⟨k⟩ departed from the straight lines for the PyCX-PAMAM-G0 samples with X = 10 and 12 associated with the SDS and DTAB micelles. This behavior indicated that [Py]loc was much larger than expected for the dendrimers prepared with longer alkanoyl linkers. This behavior was attributed to strong hydrophobic interactions between the longer linkers and the dodecyl tails of the surfactants in the hydrophobic core of the micelles, which induced a conformational change for the dendrimers inside the micelles, that could be probed at the molecular level by PEF.

Fluorine Labeling and 19F NMR Spectroscopy to Study Biological Molecules and Molecular Complexes

High-resolution nuclear magnetic resonance (NMR) spectroscopy represents a key methodology for studying biomolecules and their interplay with other molecules. Recent developments in labeling strategies have made it possible to incorporate fluorine into proteins and peptides reliably, with manageable efforts and, importantly, in a highly site-specific manner. Paired with its excellent NMR spectroscopic properties and absence in most biological systems, fluorine has enabled scientists to investigate a rather wide range of scientific objectives, including protein folding, protein dynamics and drug discovery. Furthermore, NMR spectroscopic experiments can be conducted in complex environments, such as cell lysate or directly inside living cells. This review presents selected studies demonstrating how 19F NMR spectroscopic approaches enable to contribute to the understanding of biomolecular processes. Thereby the focus has been set to labeling strategies available and specific NMR experiments performed to answer the underlying scientific objective.

CEST effect of dimethyl sulfoxide at negative offset frequency

Dimethyl sulfoxide (DMSO) has wide biomedical applications such as cryoprotectant and hydrophobic drug carrier. Here, we report for the first time that DMSO can generate a distinctive chemical exchange saturation transfer (CEST) signal at around -2 ppm. Structural analogs of DMSO, including aprotic and protic solvents, also demonstrated CEST signals from -1.4 to -3.8 ppm. When CEST detectable barbituric acid (BA) was dissolved in DMSO solution and was co-loaded to liposome, two obvious peaks at 5 and -2 ppm were observed, indicating that DMSO and related solvent system can be monitored in a label-free manner via CEST, which can be further applied to imaging drug nanocarriers. With reference to previous studies, there could be molecular interactions or magnetization transfer pathways, such as the relayed nuclear Overhauser enhancement (rNOE), that lead to this detectable CEST contrast at negative offset frequencies of the Z-spectrum. Our findings suggest that small molecules of organic solvents could be involved in magnetization transfer processes with water and readily detected by CEST magnetic resonance imaging (MRI), providing a new avenue for detecting solvent-water and solvent-drug interactions.

Comparative Analysis of Bare and Quercetin-Loaded Nonionic Block Copolymer Micelles in an Artificial Gastrointestinal Medium

Block copolymer micelles have been increasingly used for the solubilization and delivery of hydrophobic drugs. There exists a possibility of dissociation of micelles and formation of other association structures in contact with the gastrointestinal fluid. In this study, we demonstrated the effect of the fed-state intestinal fluid (FeSSIF) upon characteristics of bare and quercetin (QCT)-loaded pluronic 123 (P123) micelles. Characterizations were performed using dynamic light scattering (DLS), 1H NMR, heteronuclear single-quantum coherence (HSQC), two-dimensional 1H-1H nuclear Overhauser effect spectroscopy (2D-NOESY), and diffusion-ordered spectroscopy (DOSY). In the case of bare micelles, we found copolymer-bile salt mixed aggregates without any noticeable change in size. DOSY data revealed that lecithin formed a separate aggregate in the FeSSIF. Complete micellar solubilization of QCT could be verified by the disappearance of its proton signals. At higher dose levels, the diffusion coefficient of micelles increased in the FeSSIF. We speculate that QCT-induced hydrophobicity and availability of FeSSIF components would have driven the formation of small-sized mixed assemblies. On the contrary, the diffusion coefficient of micelles decreased with an increase in the QCT load in the medium devoid of FeSSIF components. We deduce that lack of lecithin and bile salts precluded the formation of mixed assemblies in this case, and therefore, micelles turned heavier at higher QCT loads. Such insights on self-assembled formulations can be valuable in improving their biological performance.

Structural and sorption characteristics of an aerogel composite material loaded with flufenamic acid: insights from MAS NMR and high-pressure NOESY studies

The structural and sorption characteristics of a composite material consisting of a silica aerogel loaded with flufenamic acid were investigated using a variety of nuclear magnetic resonance techniques. The composite structure was analyzed using magic angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy, which revealed significant interactions between the aerogel matrix and the FFA molecules. Solid-state 29Si NMR provided insights into the aerogel's stability, while 1H and 13C NMR confirmed the presence of FFA in the matrix, with signals from FFA molecules observed alongside tetraethoxysilane (TEOS) groups. Ethanol-induced desorption of FFA led to narrowed spectral lines, suggesting the breaking of intermolecular hydrogen bonds. 19F MAS NMR spectra indicated changes in FFA local environments upon loading into AG pores. Evaluation of CO2 sorption characteristics using 13C NMR demonstrated a slower sorption rate for AG + FFA than that for pure AG, attributed to decreased pore volume. Furthermore, nuclear Overhauser effect spectroscopy (NOESY) was employed to explore the conformational behavior of FFA within the aerogel matrix. The results indicated a shift in conformer populations, particularly those related to the rotation of one cyclic fragment relative to the other. These findings provide insights into the structural and sorption characteristics of the AG + FFA composite, which are valuable for developing novel drug solid forms.

Influence of Solvent Polarity on the Conformer Ratio of Bicalutamide in Saturated Solutions: Insights from NOESY NMR Analysis and Quantum-Chemical Calculations

The study presents a thorough and detailed analysis of bicalutamide's structural and conformational properties. Quantum chemical calculations were employed to explore the conformational properties of the molecule, identifying significant energy differences between conformers. Analysis revealed that hydrogen bonds stabilise the conformers, with notable variations in torsion angles. Conformers were classified into 'closed' and 'open' types based on the relative orientation of the cyclic fragments. NOE spectroscopy in different solvents (CDCl3 and DMSO-d6) was used to study the conformational preferences of the molecule. NOESY experiments provided the predominance of 'closed' conformers in non-polar solvents and a significant presence of 'open' conformers in polar solvents. The proportions of open conformers were 22.7 ± 3.7% in CDCl3 and 59.8 ± 6.2% in DMSO-d6, while closed conformers accounted for 77.3 ± 3.7% and 40.2 ± 6.2%, respectively. This comprehensive study underscores the solvent environment's impact on its structural behaviour. The findings significantly contribute to a deeper understanding of conformational dynamics, stimulating further exploration in drug development.

Conformations of Macrocyclic Peptides Sampled by Nuclear Magnetic Resonance: Models for Cell-Permeability

The biological activities and pharmacological properties of peptides and peptide mimetics are determined by their conformational states. Therefore, a detailed understanding of the conformational landscape is crucial for rational drug design. Nuclear magnetic resonance (NMR) is the only method for structure determination in solution. However, it remains challenging to determine the structures of peptides using NMR because of very weak nuclear Overhauser effects (NOEs), the semiquantitative nature of the rotating frame Overhauser effect (ROE), and the low number of NOEs/ROEs in N-methylated peptides. In this study, we introduce a new approach to investigating the structures of modified macrocyclic peptides. We utilize exact NOEs (eNOEs) in viscous solvent mixtures to replicate various cellular environments. eNOEs provide detailed structural information for highly dynamic modified peptides. Structures of high precision were obtained for cyclosporin A, with a backbone atom rmsd of 0.10 Å. Distinct conformational states in different environments were identified for omphalotin A (OmphA), a fungal nematotoxic and multiple backbone N-methylated macrocyclic peptides. A model for cell-permeation is presented for OmphA, based on its structures in polar, apolar, and mixed polarity solvents. During the transition from a polar to an apolar environment, OmphA undergoes a rearrangement of its H-bonding network, accompanied by a cis to trans isomerization of the ω torsion angle within a type VIa β-turn. We hypothesize that the kinetics of these conformational transitions play a crucial role in determining the membrane-permeation capabilities of OmphA.

NMR methods for the analysis of mixtures

NMR spectroscopy is a powerful approach for the analysis of mixtures. Its usefulness arises in large part from the vast landscape of methods, and corresponding pulse sequences, that have been and are being designed to tackle the specific properties of mixtures of small molecules. This feature article describes a selection of methods that aim to address the complexity, the low concentrations, and the changing nature that mixtures can display. These notably include pure-shift and diffusion NMR methods, hyperpolarisation methods, and fast 2D NMR methods such as ultrafast 2D NMR and non-uniform sampling. Examples or applications are also described, in fields such as reaction monitoring and metabolomics, to illustrate the relevance and limitations of different methods.

Use of Diethanolamine as a Viscous Solvent for Mixture Analysis by Multidimensional Heteronuclear ViscY NMR Experiments

Diethanolamine/DMSO-d₆ as a viscous binary solvent is first reported for the individualization of low-polarity mixture components by multidimensional heteronuclear ViscY NMR experiments under spin diffusion conditions. Solvent viscosity induces the slowing down of molecular tumbling, hence promoting magnetization transfer by dipolar longitudinal cross-relaxation. As a result, all ¹H nuclei resonances within the same molecule may correlate in a 2D nuclear Overhauser effect spectroscopy (NOESY) spectrum, giving access to mixture analysis. We offer a new way to analyze mixtures by considering 3D heteronuclear heteronuclear single-quantum coherence-NOESY (HSQC-NOESY) experiments under viscous conditions. We state the individualization of four low-polarity chemical compounds dissolved in the diethanolamine/DMSO-d₆ solvent blend using homonuclear selective 1D, 2D ¹H-¹H NOESY experiments and heteronuclear 1D, 2D ¹H-¹⁹F heteronuclear Overhauser effect spectroscopy, 2D ¹H-¹⁹F, ¹H-³¹P HSQC-NOESY, and 3D ¹H-¹⁹F-¹H, ¹H-³¹P-¹H HSQC-NOESY experiments by taking profit from spin diffusion.

Taxonomy-Focused Natural Product Databases for Carbon-13 NMR-Based Dereplication

The recent revival of the study of organic natural products as renewable sources of medicinal drugs, cosmetics, dyes, and materials motivated the creation of general purpose structural databases. Dereplication, the efficient identification of already reported compounds, relies on the grouping of structural, taxonomic and spectroscopic databases that focus on a particular taxon (species, genus, family, order, etc.). A set of freely available python scripts, CNMR_Predict, is proposed for the quick supplementation of taxon oriented search results from the naturaL prOducTs occUrrences database (LOTUS, lotus.naturalproducts.net) with predicted carbon-13 nuclear magnetic resonance data from the ACD/Labs CNMR predictor and DB software (acdlabs.com) to provide easily searchable databases. The database construction process is illustrated using Brassica rapa as a taxon example.