NMR Tools Research Articles

Molecular modeling and antimicrobial activity of newly synthesized benzothiazole-thiazole conjugates

The benzothiazole-thiazole conjugates 4, 5, 6, 7a-c, and 8 were synthesized by introducing a thiazole moiety into the precursor 2-acetamido-6-(2-cyanoacetyl)benzothiazole (3), using a different synthetic method. The structures of these conjugates were determined using FT-IR, 1H/13C NMR, and mass spectral tools. The density functional theory (DFT) modeling of the synthesized hybrids disclosed that all have an angular configuration except for parent 3, who was flat. They presented low frontier molecular orbitals (FMO’s) gap (ΔEH-L), 3.23–4.60 eV, wherein the hybrids 7b and 3 have the least and most values. Meanwhile, the novel conjugates’ antibacterial effectiveness was tested against several pathogenic microorganisms, as well as Gram (+ve), Gram (−ve), and fungal strains. Conjugates 7a-c presented significant antimicrobial effectiveness against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). However, the synthesized conjugates were evaluated as inhibitors of DNA gyrase, an enzyme critical for bacterial DNA replication. Also, molecular docking simulations were performed for the synthesized conjugates towards PDB: 2XCT, PDB: 1 s14, and PDB: 5tz1 proteins. Both conjugates (7a and 7b) displayed higher binding scores and stable molecular interactions. Moreover, the physicochemical profiles and predicted bioavailability of the newly synthesized benzothiazole-thiazole conjugates were predicted by the SwissADME tools. The study revealed that conjugates 5 and 8 demonstrate the most favorable pharmacokinetic properties and bioavailability scores, making them prime candidates for further pharmaceutical development.

Solvent solute interaction (IEFPCM model), Michael addition-based anticancer drug synthesis, FTIR, NMR, and UV–visible investigations of spirooxindole-pyranoindole (2AIPC) − in vitro and in silico anti-cancer activity

Herein, click chemistry was chosen to synthesize 2AIPC using Knoevenegel and Michael addition reactions. In this synthesis, Lewis base was attracted by the generation of sp3 hybridized carbanion at active methylene group in the reactants for propagation reaction proceeding towards conducting the Michael addition product. The synthesized 2AIPC was characterized by NMR(13C and 1H), UV, FTR and FT-IR analytical tools; it was also evaluated utilizing density functional theory. According to DFT analyses, the comparative study of the functional groups of 2AIPC molecule was successfully described using Raman and FT-IR spectra with simulated spectra. NLO behaviour and charge exchange utilizing the hyperpolarizability and FMO band gap characteristics were also investigated. Through computational studies using MEP, FUKUI, RDG, and NBO, intermolecular interaction and the reactive area of the synthesized molecule were demonstrated.Moreover, the anticancer activity under the in-vitro analysis was tested, and the molecule showed 61.04 % GI against the K-562 leukemia cells at 10-5 M. Molecular docking also evaluated cytotoxicity by in silico study against leukemia-related proteins (60QN, 6OQC, 1EMR, and 606F). The docked complexes showed binding affinities of −7.82, −7.1, −6.9, and −6.71 kcal/mol. A nucleophile elimination process at 2AIPC’s main amino group may also increase the molecule’s potential to be a more effective lead medication.

Speeding-up the Determination of Protein-Ligand Affinities by STD NMR: The Reduced Data Set STD NMR Approach (rd-STD NMR).

STD NMR spectroscopy is a powerful ligand-observed NMR tool for screening and characterizing the interactions of small molecules and low molecular weight fragments with a given macromolecule, identifying the main intermolecular contacts in the bound state. It is also a powerful analytical technique for the accurate determination of protein-ligand dissociation constants (KD) of medium-to-weak affinity, of interest in the pharmaceutical industry. However, accurate KD determination and epitope mapping requires a long series of experiments at increasing saturation times to carry out a full analysis using the so-called STD NMR build-up curve approach and apply the "initial slopes approximation". Here, we have developed a new protocol to bypass this important limitation, which allows us to obtain initial slopes by using just two saturation times and, hence, to very quickly determine precise protein-ligand dissociation constants by STD NMR.

Synthesis, characterization and biological investigations of some new Oxadiazoles: In-vitro and In-Silico approach

A series of new oxadiazole derivatives, namely 1-{2-substituted phenyl −5-[2-tifluoromethyl)-1H-indol-3-yl]-3-(2H)-ylethanone 1,3,4-oxadiazoles were synthesized and investigated in this research. Using AutoDockVina 4.2, the new compounds VIb and VIc were extensively investigated for their ADMET characteristics and in-silico drug receptor interactions with the target enzyme, GlcN-6-P synthase (PDB ID: 2FV5). The existence of an electron-withdrawing group and a lipophilic functional group substituted at the phenyl ring was observed to be more active than in other molecules. The new molecules drug ability was investigated using ADMET experiments performed by Swiss ADME software, and the newly synthesized compounds qualified for ADME characteristics and followed Lipinski’s rule of five. FTIR, 1H NMR, 13CNMR, and mass spectrometry tools were used to characterize the prepared substances. The prepared substances were screened for antibacterial activity against gram-positive (Bacillus subtilis, Staphylococcus aureus) and gram-negative microbes (Pseudomonas aeruginosa and Escherichia coli) using cup plate and MIC techniques. These substances were also screened for antifungal activity against Aspergillus niger and Candida albicans, with Ampicillin and Amphotericin B serving as standard references. The compounds VIb and VIc have more antibacterial action than antifungal activity among the synthesized substances. Compounds VIa to VIf were examined for in vitro antioxidant activity and compounds VIb and VIc has displayed significant antioxidant potentials with IC50 values 45.16 and 38.14 in DPPH assay. The compounds VIa–f were tested for anticancer activity using MDA-MB 361 cell lines using MTT assays, and the IC50 values were recorded, out of which VIb and VIc displayed the lowest IC50 values. In-silico drug receptor interactions with the target enzyme, phosphoinositide-3-kinase (PI3K), with PDB ID: 3MJW were predicted as supportive evidence for the anticancer properties of the synthesized scaffolds.

Synthesis and characterization of a pyridinium IL-tagged Schiff base Pd(II)-complex: An efficient catalyst for the Suzuki reaction at room temperature under aerobic conditions

To address some drawbacks associated with the Suzuki reaction herein we report a new pyridinium IL-tagged Schiff base Pd(II)-complex. First pyridinium IL was synthesized and condensed with salicylaldehyde to prepare a new IL-tagged Schiff base which on metalation with Pd(OAc)2 gives pyridinium IL-tagged Schiff base Pd(II)-complex. The synthesized compounds were then well characterized by Elemental analysis, UV–Visible, Magnetic Moment, IR, NMR, HRMS, MALDI, and PXRD tools. A square planar geometry was assigned for the Pd(II)-complex based on the spectroscopic and other data obtained. The catalytic activity of the Pd(II)-complex was then appraised for the Suzuki reactions in EtOH under aerobic conditions at room temperature with a time frame of 1 h. The results show that the Pd-complex facilitates the reaction under the given condition efficiently to produce a high yield of the products with low catalyst loading. And more importantly, the Pd-complex could be recovered easily and recycled up to six runs with minimum loss in its catalytic activity.

Pure shift FESTA: An ultra-high resolution NMR tool for the analysis of complex fluorine-containing spin systems.

NMR measurements of molecules containing sparse fluorine atoms are becoming increasingly common due to their prevalence in medicinal chemistry. However, the presence of both homonuclear and heteronuclear scalar couplings severely complicates their analysis by NMR. In complex systems, FESTA, a heteronuclear spectral editing method, allows simplified 1 H NMR spectra to be obtained containing only 1 H signals from the same spin system as a chosen 19 F. Despite spectral simplification, signal overlap due to the presence of scalar couplings is often a problem in FESTA spectra. Here, we report a new experiment that combines FESTA and pure shift methods to provide fully decoupled ultra-high resolution FESTA spectra showing a single signal for each 1 H chemical environment. The utility of the method is demonstrated for the analysis of two complex fluorine-containing mixtures of pharmaceutical and biochemical interest.

Introducing NMR strategies to define water molecules that drive metal binding in a transcriptional regulator

Staphylococcus aureus CzrA is a paradigmatic member of the ArsR family of transcriptional metalloregulators, which are critical for the bacterial response to stress. Zinc binding to CzrA, which induces DNA derepression, is entropically driven, as shown by calorimetry. A detailed equilibrium dynamics study of different allosteric states of CzrA revealed that zinc induces an entropy redistribution that controls for DNA binding regulation; however, this change in conformational entropy only accounts for a small net contribution to the total entropy. This difference between the change in conformational entropy vs. total entropy of zinc binding implies a significant contribution of solvent molecule rearrangements to this equilibrium. However, the absence of major structural changes suggests that solvent rearrangements occur mainly on the protein surface and/or from zinc desolvation, concomitant with a dynamical redistribution of conformational entropy. Previous results also suggest that zinc binding not only leads to a redistribution of protein internal dynamics, but also release of water molecules from the protein surface. In turn, these water molecules may make a significant contribution to the allosteric response that results in dissociation from the DNA.Quantifying the differential hydration of two conformational states that share very similar crystal structures and then correlating this with the protein's solvent entropy change constitutes an unresolved problem, even when thermodynamics suggest a significant contribution of solvent entropy. Here, we present different avenues to dissect hydration dynamics in a metal-binding transcriptional regulator that provide different insights into this complex problem. We explore primary solution NMR tools for probing protein–water interactions: the laboratory frame nuclear Overhauser effect (NOE) and its rotating frame counterpart (ROE) between long-lived water molecules and the protein residues. The wNOE/wROE ratio is a promising tool for the detection of hydration dynamics near the surface of a protein in a site-specific manner, minimizing contamination from bulk solvent. Molecular dynamics simulations and computational methods designed to provide a spatially resolved picture of solvent thermodynamics were also employed to provide a more complete panorama of solvent redistribution.

Buchwald coupling promoted benign synthesis of benzoxazine derivatives supported Cu complexes with their multipurpose potential in antimicrobial and catalytical fields

A novel series of benzoxazine derivatives have been synthesized via microwave assistance and used as ligands for the synthesis of their Cu(II) complexes using the same benign method. Synthesized ligands as well as complexes were characterized using NMR, LCMS, and FT-IR analytical tools. The crystalline nature of complexes has been analyzed by powder XRD. These complexes have been tested against six bacterial and three fungal species for their antimicrobial evaluation. Complexes have shown good antimicrobial activity against human pathogens as compared with their ligands, and varied with different pathogens. The molecular docking study against 4GQQ and 5cdp proteins with synthesized complexes was performed to see the necessary interactions responsible for anti-bacterial activity. The docking analysis of the Vid and Via complexes have supported the antibacterial activity exhibiting high GSC score and area obtained through PatchDoc server. The reduction activity shown by the Vib, Vic and Vid complexes inferred about their utility in catalytically process in industries.

Hard Carbons Derived from Phenyl Hyper-Crosslinked Polymers for Lithium-Ion Batteries

Hyper-crosslinked polymers are attracting extensive attention owing to their ease of design and synthesis. Based on the flexibility of its molecular design, a hyper-crosslinked polymer with a π-conjugated structure and its derived carbon were synthesized by the Friedel–Crafts reaction. The polymer and its derived hard carbon material were characterized by FTIR, 13C NMR, Raman, BET, and other characterization tools. The electrochemical properties of both materials as anode electrodes of lithium-ion batteries were investigated. Benefiting from the highly cross-linked skeleton and conjugated structure, the as-prepared carbon materials still had high specific surface area (583 m2 g−1) and porosity (0.378 cm3 g−1) values. The hard carbon (CHCPB) anode possessed the powerful reversible capacity of 699 mAh g−1 at 0.1A g−1, and it had an excellent rate of performance of 165 mAh g−1 at the large current density of 5.0 A g−1. Long-cycle performance for 2000 charge/discharge cycles displayed that the capacity was kept at 148 mAh g−1 under 2 A g−1. This work contributes to a better understanding of the properties of hard carbon materials derived from hyper-crosslinked polymers and how this class of materials can be further exploited in various applications.

Parahydrogen hyperpolarized NMR detection of underivatized short oligopeptides.

Parahydrogen hyperpolarization has evolved into a versatile tool in NMR, allowing substantial sensitivity enhancements in analysis of biological samples. Herein we show how its application scope can be extended from small metabolites to underivatized oligopeptides in solution. Based on a homologous series of alanine oligomers, we report on an experimental and DFT study on the structure of the oligopeptide and hyperpolarization catalyst complexes formed in the process. We demonstrate that alanine oligomers coordinate to the iridium carbene-based catalyst in three different ways, each giving rise to distinctive hydride signals. Moreover, the exact structures of the transient oligopeptide-catalyst complexes are oligomer-specific. This work gives a first insight into how the organometallic iridium-N-heterocyclic carbene-based parahydrogen hyperpolarization catalyst interacts with biopolymers that have multiple catalyst binding sites. A preliminary application example is demonstrated for oligopeptide detection in urine, a complex biological mixture.

Jacob Schaefer III

Jacob Schaefer III, 83, died June 27 in Saint Louis, Missouri. “Jake published the first 13 C NMR spectra of synthetic copolymers, the first magic-angle spinning 13 C NMR spectrum of a solid polymer, and the first cross-polarization magic angle spinning (CPMAS) 13 C NMR spectra of polymers. His laboratory produced monumental NMR tools including CPMAS, rotational-echo, double-resonance (REDOR), and multichannel transmission line probes. Today, these tools are so widely used that they are simply referenced by their acronyms, and their impact on medicine, biochemistry, and materials science has been profound. Jake himself applied these techniques to important studies that led to advanced understanding of proteins, living cell metabolism, and polymers.”—Lee G. Sobotka, Lynette Cegelski, Richard Loomis, and Karen Wooley, colleagues Most recent title: Charles Allen Thomas Emeritus Professor of Chemistry, Washington University in St. Louis Education: BS, chemistry, Carnegie Institute of Technology, 1960; PhD, chemistry, University of Minnesota, 1964

Towards autonomous analysis of chemical exchange saturation transfer experiments using deep neural networks

Macromolecules often exchange between functional states on timescales that can be accessed with NMR spectroscopy and many NMR tools have been developed to characterise the kinetics and thermodynamics of the exchange processes, as well as the structure of the conformers that are involved. However, analysis of the NMR data that report on exchanging macromolecules often hinges on complex least-squares fitting procedures as well as human experience and intuition, which, in some cases, limits the widespread use of the methods. The applications of deep neural networks (DNNs) and artificial intelligence have increased significantly in the sciences, and recently, specifically, within the field of biomolecular NMR, where DNNs are now available for tasks such as the reconstruction of sparsely sampled spectra, peak picking, and virtual decoupling. Here we present a DNN for the analysis of chemical exchange saturation transfer (CEST) data reporting on two- or three-site chemical exchange involving sparse state lifetimes of between approximately 3–60 ms, the range most frequently observed via experiment. The work presented here focuses on the 1H CEST class of methods that are further complicated, in relation to applications to other nuclei, by anti-phase features. The developed DNNs accurately predict the chemical shifts of nuclei in the exchanging species directly from anti-phase 1HN CEST profiles, along with an uncertainty associated with the predictions. The performance of the DNN was quantitatively assessed using both synthetic and experimental anti-phase CEST profiles. The assessments show that the DNN accurately determines chemical shifts and their associated uncertainties. The DNNs developed here do not contain any parameters for the end-user to adjust and the method therefore allows for autonomous analysis of complex NMR data that report on conformational exchange.

A machine learning framework for low-field NMR data processing

Low-field (nuclear magnetic resonance) NMR has been widely used in petroleum industry, such as well logging and laboratory rock core analysis. However, the signal-to-noise ratio is low due to the low magnetic field strength of NMR tools and the complex petrophysical properties of detected samples. Suppressing the noise and highlighting the available NMR signals is very important for subsequent data processing. Most denoising methods are normally based on fixed mathematical transformation or hand-design feature selectors to suppress noise characteristics, which may not perform well because of their non-adaptive performance to different noisy signals. In this paper, we proposed a “data processing framework” to improve the quality of low field NMR echo data based on dictionary learning. Dictionary learning is a machine learning method based on redundancy and sparse representation theory. Available information in noisy NMR echo data can be adaptively extracted and reconstructed by dictionary learning. The advantages and application effectiveness of the proposed method were verified with a number of numerical simulations, NMR core data analyses, and NMR logging data processing. The results show that dictionary learning can significantly improve the quality of NMR echo data with high noise level and effectively improve the accuracy and reliability of inversion results. • A “data processing framework” is proposed to improve the quality of low-field NMR echo data. • Dictionary learning is employed for adaptive dictionary construction and available signal characteristics extraction for denoising noisy NMR echo data. • Simulations and practical applications have verified the performance of improving quality of NMR echo data and enhancing the accuracy and reliability of inversion results with dictionary learning.

Surface NMR using quantum sensors in diamond

NMR is a noninvasive, molecular-level spectroscopic technique widely used for chemical characterization. However, it lacks the sensitivity to probe the small number of spins at surfaces and interfaces. Here, we use nitrogen vacancy (NV) centers in diamond as quantum sensors to optically detect NMR signals from chemically modified thin films. To demonstrate the method's capabilities, aluminum oxide layers, common supports in catalysis and materials science, are prepared by atomic layer deposition and are subsequently functionalized by phosphonate chemistry to form self-assembled monolayers. The surface NV-NMR technique detects spatially resolved NMR signals from the monolayer, indicates chemical binding, and quantifies molecular coverage. In addition, it can monitor in real time the formation kinetics at the solid-liquid interface. With our approach, we show that NV quantum sensors are a surface-sensitive NMR tool with femtomole sensitivity for in situ analysis in catalysis, materials, and biological research.

On-Cell NMR Contributions to Membrane Receptor Binding Characterization.

NMR spectroscopy has matured into a powerful tool to characterize interactions between biological molecules at atomic resolution, most importantly even under near to native (physiological) conditions. The field of in-cell NMR aims to study proteins and nucleic acids inside living cells. However, cells interrogate their environment and are continuously modulated by external stimuli. Cell signaling processes are often initialized by membrane receptors on the cell surface; therefore, characterizing their interactions at atomic resolution by NMR, hereafter referred as on-cell NMR, can provide valuable mechanistic information. This review aims to summarize recent on-cell NMR tools that give information about the binding site and the affinity of membrane receptors to their ligands together with potential applications to in vivo drug screening systems.

When the MOUSE leaves the house.

Change is inherent to time being transient. With the NMR-MOUSE (MObile Universal Surface Explorer) having matured into an established NMR tool for nondestructive testing of materials, this forward-looking retrospective assesses the challenges the NMR-MOUSE faced when deployed outside a protected laboratory and how its performance quality can be maintained and improved when operated under adverse conditions in foreign environments. This work is dedicated to my dear colleague and friend Geoffrey Bodenhausen on the occasion of his crossing an honorable timeline in appreciation of his ever-continuing success of fueling the dynamics of magnetic resonance.

Probing the Interactions of Porphyrins with Macromolecules Using NMR Spectroscopy Techniques.

Porphyrinic compounds are widespread in nature and play key roles in biological processes such as oxygen transport in blood, enzymatic redox reactions or photosynthesis. In addition, both naturally derived as well as synthetic porphyrinic compounds are extensively explored for biomedical and technical applications such as photodynamic therapy (PDT) or photovoltaic systems, respectively. Their unique electronic structures and photophysical properties make this class of compounds so interesting for the multiple functions encountered. It is therefore not surprising that optical methods are typically the prevalent analytical tool applied in characterization and processes involving porphyrinic compounds. However, a wealth of complementary information can be obtained from NMR spectroscopic techniques. Based on the advantage of providing structural and dynamic information with atomic resolution simultaneously, NMR spectroscopy is a powerful method for studying molecular interactions between porphyrinic compounds and macromolecules. Such interactions are of special interest in medical applications of porphyrinic photosensitizers that are mostly combined with macromolecular carrier systems. The macromolecular surrounding typically stabilizes the encapsulated drug and may also modify its physical properties. Moreover, the interaction with macromolecular physiological components needs to be explored to understand and control mechanisms of action and therapeutic efficacy. This review focuses on such non-covalent interactions of porphyrinic drugs with synthetic polymers as well as with biomolecules such as phospholipids or proteins. A brief introduction into various NMR spectroscopic techniques is given including chemical shift perturbation methods, NOE enhancement spectroscopy, relaxation time measurements and diffusion-ordered spectroscopy. How these NMR tools are used to address porphyrin–macromolecule interactions with respect to their function in biomedical applications is the central point of the current review.

NMR Spectroscopy in the Conformational Analysis of Peptides: An Overview.

NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. This review provides a toolkit to investigate peptide conformational properties by NMR. Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through PubMed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.

NMR techniques in studying water in biotechnological systems.

Different NMR methodologies have been considered in studying water as a part of the structure of heterogeneous biosystems. The current work mostly describes NMR techniques to investigate slow translational dynamics of molecules affecting anisotropic properties of polymers and biomaterials. With these approaches, information about organized structures and their stability could be obtained in conditions when external factors affect biomolecules. Such changes might include rearrangement of macromolecular conformations at fabrication of nano-scaffolds for tissue engineering applications. The changes in water-fiber interactions could be mirrored by the magnetic resonance methods in various relaxations, double-quantum filtered (DQF), 1D and 2D translational diffusion experiments. These findings effectively demonstrate the current state of NMR studies in applying these experiments to the various systems with the anisotropic properties. For fibrous materials, it is shown how NMR correlation experiments with two gradients (orthogonal or collinear) encode diffusion coefficients in anisotropic materials and how to estimate the permeability of cell walls. It is considered how the DQF NMR technique discovers anisotropic water in natural polymers with various cross-links. The findings clarify hydration sites, dynamic properties, and binding of macromolecules discovering the role of specific states in improving scaffold characteristics in tissue engineering processes. Showing the results in developing these NMR tools, this review focuses on the ways of extracting information about biophysical properties of biomaterials from the NMR data obtained.

Zebrafish Oocytes as a Tool for Eukaryotic In-Cell NMR

Zebrafish Oocytes as a Tool for Eukaryotic In-Cell NMR