Cymbopogon schoenanthus (L) extract ameliorates high fat diet-induced obesity and dyslipidemia via reducing expression of lipogenic and thermogenic proteins

Globally, obesity has become one of the major health problems. This study was conducted to evaluate the anti-obesity potential of Cymbopogon schoenanthus methanolic extract (CS) in rats. Fifty male Wistar rats of six to eight weeks old, 100-120 g body weight (BW) were randomly assigned into 5 groups (n = 10): The control group was fed a basal diet. CS-group was supplied with basal diet and orally given CS (200 mg/kg BW) for 12 weeks. HFD-group was fed a high-fat diet (HFD) for 18 weeks. HFD + CS-group was fed on HFD and CS HFD then CS-group was fed HFD for 12 weeks then shifted to basal diet and CS for another 6 weeks. Phytochemical analysis of CS indicated the presence of various terpenes and flavonoid compounds. Among the compounds characterized are quercetin, apigenin, luteolin, orientin, eudesmene, cymbopogonol, caffeic acid, coumaric acid, and linolenic acid. Supplementation of HFD significantly increased the body weight, levels of serum triacylglycerol, total cholesterol, very low-density lipoprotein, low-density lipo-protein (HDL), glucose, serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities. In addition, HFD up-regulated the protein expression of uncoupling protein (UCP)-1 in both brown and white adipose tissue; and the expression of hepatic mRNA of sterol regulatory element-binding protein (SREBP)-1c and SREBP-2. However, it decreased the serum level of HDL, and protein expression level of UCP-1 in both brown and white adipose tissue. Treatment of HFD-fed animals with CS extract either concurrently (HFD + CS-group), or after obesity induction (HFD then CS-group) significantly reversed all HFD-induced alterations in body weight; food intake; serum biochemical profile (including hyperglycemia, dyslipidemia); and tissue gene expressions. These results indicate that CS methanolic extract ameliorated HFD-induced obesity, serum biochemical, hepatic, and adipose tissue gene expression alterations. CS extract accomplished these effects mostly through its various identified bioactive compounds which have been proven to have anti-obesity and anti-diabetic activities.

Untargeted NMR-based metabolomics analysis of kidney allograft perfusates identifies a signature of delayed graft function

INTRODUCTION

Kidney transplantation (KTx) necessarily conveys an ischemia/reperfusion (I/R) process, which impacts on allograft outcomes. Delayed graft function (DGF) is defined as a non-decrease of serum creatinine by at least 10% daily on 3 consecutive days during the first 7 days post-KTx. DGF significantly conditions both short- and long-term graft outcomes. Still there is a lack of DGF predictive biomarkers.

OBJECTIVES

This study aimed to explore the potential of kidney graft perfusate metabolomics to predict DGF occurrence.

METHODS

49 human perfusates from grafts categorized upon donor type [donation after brain death (DBD)/donation after circulatory death (DCD)] and DGF occurrence and 19 perfusates from a murine model classified upon death type (DBD/DCD) were collected and analyzed by NMR-based metabolomics.

RESULTS

The multivariate analysis of the murine data highlighted significant differences between perfusate metabolomes of DBD versus DCD. These differences were similarly observed in the human perfusates. After correcting for the type of donor, multivariate analysis of human data demonstrated a metabolomics signature that could be correlated with DGF occurrence.

CONCLUSIONS

The metabolome of kidney grafts is influenced by the donor's type in both human and pre-clinical studies and could be correlated with DGF in the human DBD cohort. Thus, metabolomic analysis of perfusate applied prior to KTx may represent a new predictive tool for clinicians in a more personalized management of DGF. Moreover, our data paves the way to better understand the impact of donor's types on the biochemical events occurring between death and the hypothermic storage.

Blood compatibility of poly(propylene glycol diester) and its water structure observed by differential scanning calorimetry and 2H-nuclear magnetic resonance spectroscopy

Recently, we applied solution 2H-nuclear magnetic resonance spectroscopy (2H NMR) to analyze the water (deuterium oxide, D2O) structure in several biopolymers at ambient temperature. We established that polymers with good blood compatibility (i.e. poly(2-methoxyethyl acrylate) (PMEA)) have water observed at high magnetic fields (upfield) compared with bulk water. Polymers containing poly(propylene glycol) (PPG) or poly(propylene oxide) (PPO) exhibit good compatibility; however, the reason for this remains unclear. In addition, reports on the blood compatibility of PPO/PPG are limited. Therefore, PPG diester (PPGest) was prepared as a model polymer, and its blood compatibility and water structure were investigated. PPGest exhibited excellent blood compatibility. The water in PPGest was observed upfield by 2H NMR, and it was defined as non-freezing water via differential scanning calorimetry. Based on these observations, the relationship between the blood compatibility and water structure of PPGest is discussed by comparing with those of PMEA, and the reason for the good performance of PPG/PPO-based polymers is discussed.

Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank

Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing the establishment of uniform methods of model-vs-data structure validation against restraints and limiting interoperability between restraint-based structure modeling programs. The NEF and NMR-STAR formats provide a standardized approach for representing commonly used NMR restraints. Using these restraint formats, a standardized validation system for assessing structural models of biopolymers against restraints has been developed and implemented in the wwPDB OneDep data deposition-validation-biocuration system. The resulting wwPDB restraint violation report provides a model vs. data assessment of biomolecule structures determined using distance and dihedral restraints, with extensions to other restraint types currently being implemented. These tools are useful for assessing NMR models, as well as for assessing biomolecular structure predictions based on distance restraints.

The structural properties of full-length annexin A11

Annexin A11 (ANXA11) is a calcium-dependent phospholipid-binding protein belonging to the annexin protein family and implicated in the neurodegenerative amyotrophic lateral sclerosis. Structurally, ANXA11 contains a conserved calcium-binding C-terminal domain common to all annexins and a putative intrinsically unfolded N-terminus specific for ANXA11. Little is known about the structure and functions of this region of the protein. By analogy with annexin A1, it was suggested that residues 38 to 59 within the ANXA11 N-terminus could form a helical region that would be involved in interactions. Interestingly, this region contains residues that, when mutated, may lead to clinical manifestations. In the present study, we have studied the structural features of the full-length protein with special attention to the N-terminal region using a combination of biophysical techniques which include nuclear magnetic resonance and small angle X-ray scattering. We show that the N-terminus is intrinsically disordered and that the overall features of the protein are not markedly affected by the presence of calcium. We also analyzed the 38-59 helix hypothesis using synthetic peptides spanning both the wild-type sequence and clinically relevant mutations. We show that the peptides have a remarkable character typical of a native helix and that mutations do not alter the behaviour suggesting that they are required for interactions rather than being structurally important. Our work paves the way to a more thorough understanding of the ANXA11 functions.

Cellular Applications of DNP Solid-State NMR -State of the Art and a Look to the Future

Sensitivity enhanced dynamic nuclear polarization solid-state NMR is emerging as a powerful technique for probing the structural properties of conformationally homogenous and heterogenous biomolecular species irrespective of size at atomic resolution within native environments. Herein we detail advancements that have made acquiring such data, specifically within the confines of intact bacterial and eukaryotic cell a reality, and further discuss the type of structural information that can be presently garnered by the technique's exploitation. Subsequently, we discuss bottlenecks that have thus far curbed cellular DNP-ssNMR's broad adoption, namely a lack of sensitivity and spectral resolution, and explore possible solutions ranging from utilization of new pulse sequences, design of better performing polarizing agents, and application of additional biochemical/ cell biological methodologies.

SimpleNMR: An interactive graph network approach to aid constitutional isomer verification using standard 1D and 2D NMR experiments

Despite progress in computer automated solutions, constitutional isomer verification by NMR using one- and two-dimensional data sets is still, in the main, a manual, user-intensive activity that is challenging for a number of reasons. These include the problem of simultaneously keeping track of the information from a number of separate NMR experiments and the difficulty of another researcher subsequently verifying the assignments made without having to independently repeat the whole analysis. This paper describes a graphical interactive approach that overcomes some of these problems. By using concepts used to visualise graph networks, we have been able to represent the NMR data in a manner that highlights directly the link between the different NMR experiments and the molecule of interest. Furthermore, by making the graph networks interactive, a user can easily validate and correct the assignment and understand the decisions made in arriving at the solution. We have developed a usable proof-of-concept computer program, 'simpleNMR', written in Python to illustrate the ideas and approach.

Comparative Studies of the Structural and Physicochemical Properties of the First Fullerene Derivative FD-C60 (Fullerenol) and Second Fullerene Derivate SD-C60 (3HFWC)

In order to maximally reduce the toxicity of fullerenol (the first derivative of C60, FD-C60), and increase its biomedical efficiency, the second derivative SD-C60 (3HFWC, Hyper-Harmonized Hydroxylated Fullerene Water Complex) was created. Several different methods were applied in the comparative characterization of FD-C60 and SD-C60 with the same OH groups in their core. FD-C60 as an individual structure was about 1.3 nm in size, while SD-C60 as an individual structure was 10-30 nm in size. Based on ten physicochemical methods and techniques, FD-C60 and SD-C60 were found to be two different substances in terms of size, structure, and physicochemical properties; FD-C60, at 100 °C, had endothermic characteristics, while SD-C60, at 133 °C, had exothermic characteristics; FD-C60 did not have water layers, while SD-C60 had water layers; the zeta potential of FD-C60 was -25.85 mV, while it was -43.29 mV for SD-C60. SD-C60 is a promising substance for use in cosmetics and pharmaceuticals.

Diverse diterpenoids and a triterpenoid from Euphorbia spinidens Bornm. ex Prokh

Four previously unreported diterpenoids including three ent-atisanes (1-3) and one ent-abietane (4), along with one known linear triterpenoid (5) and five known diterpenoids including four myrsinanes (6-9), and one abietane (10) have been isolated from the roots of Euphorbia spinidens Bornm. ex Prokh. The structures were determined on the basis of extensive spectroscopic analyses including HR-ESI-MS, 1D and 2D NMR and comparison of the data with those reported in the literature. Antimicrobial potential of isolated compounds were also evaluated. Guionianol B (10) showed good antibacterial activity against Staphylococcus aureus and Bacillus subtilis with MIC value of 6.25 μg/mL.

The catalytic domain of free or ligand bound histone deacetylase 4 occurs in solution predominantly in closed conformation

Human histone deacetylase 4 (HDAC4) is a key epigenetic regulator involved in a number of important cellular processes. This makes HDAC4 a promising target for the treatment of several cancers and neurodegenerative diseases, in particular Huntington's disease. HDAC4 is highly regulated by phosphorylation and oxidation, which determine its nuclear or cytosolic localization, and exerts its function through multiple interactions with other proteins, forming multiprotein complexes of varying composition. The catalytic domain of HDAC4 is known to interact with the SMRT/NCOR corepressor complex when the structural zinc-binding domain (sZBD) is intact and forms a closed conformation. Crystal structures of the HDAC4 catalytic domain have been reported showing an open conformation of HDAC4 when bound to certain ligands. Here, we investigated the relevance of this HDAC4 conformation under physiological conditions in solution. We show that proper zinc chelation in the sZBD is essential for enzyme function. Loss of the structural zinc ion not only leads to a massive decrease in enzyme activity, but it also has serious consequences for the overall structural integrity and stability of the protein. However, the Zn2+ free HDAC4 structure in solution is incompatible with the open conformation. In solution, the open conformation of HDAC4 was also not observed in the presence of a variety of structurally divergent ligands. This suggests that the open conformation of HDAC4 cannot be induced in solution, and therefore cannot be exploited for the development of HDAC4-specific inhibitors.

Dendrobium officinale polysaccharides-chemical properties and pharmacodynamic effects on the airways in experimental conditions

The study aimed to analyze the effects of Dendrobium polysaccharides on the cough and airway reactivity and compare them with the effects of clinically used antitussives (codeine phosphate and butamirate citrate) and bronchodilators (salbutamol), using the guinea pig test system. Dendrobium officinale polysaccharides contained proteins (4.0 wt%) and phenolic compounds (1.7 wt%) with a molecular weight of 25,000 g/mol. The sugar analysis revealed a dominance of glucose (93.7 wt%) and a lesser amount of mannose (5.1 wt%) while other sugar quantities were negligible. Methylation analysis indicated the presence of highly branched polysaccharides. Glucose was found mainly as terminal, 1,4- and 1,6-linked. Furthermore, some 1,4- and 1,6-linked glucose units were found branched at O2, O3, and O6/O4. Mannose was terminal and 1,4-linked. NMR spectra signals indicate the presence of the (1→4)-linked α-d-glucan, (1→4)-linked β-d-glucan branched at position O6, (1→6)-linked β-d-glucan branched at position O3 and (1→4)-linked glucomannan. Pharmacological studies showed statistically significant antitussive activity of Dendrobium polysaccharides, exceeding the effect of clinically used antitussives, which may be partially associated with confirmed bronchodilation and the ability of polysaccharides to increase the threshold of cough receptor activation. Dendrobium polysaccharides may increase the possibility of symptomatic treatment of cough, especially in asthmatics.

Sensitivity-enhanced NMR 15N R1 and R1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields

NMR relaxation experiments provide residue-specific insights into the structural dynamics of proteins. Here, we present an optimized set of sensitivity-enhanced 15N R1 and R1ρ relaxation experiments applicable to fully protonated proteins. The NMR pulse sequences are conceptually similar to the set of TROSY-based sequences and their HSQC counterpart (Lakomek et al., J. Biomol. NMR 2012). Instead of the TROSY read-out scheme, a sensitivity-enhanced HSQC read-out scheme is used, with improved and easier optimized water suppression. The presented pulse sequences are applied on the cytoplasmic domain of the SNARE protein Synpatobrevin-2 (Syb-2), which is intrinsically disordered in its monomeric pre-fusion state. A two-fold increase in the obtained signal-to-noise ratio is observed for this intrinsically disordered protein, therefore offering a four-fold reduction of measurement time compared to the TROSY-detected version. The inter-scan recovery delay can be shortened to two seconds. Pulse sequences were tested at 600 MHz and 1200 MHz 1H Larmor frequency, thus applicable over a wide magnetic field range. A comparison between protonated and deuterated protein samples reveals high agreement, indicating that reliable 15N R1 and R1ρ rate constants can be extracted for fully protonated and deuterated samples. The presented pulse sequences will benefit not only for IDPs but also for an entire range of low and medium-sized proteins.

Molecular mechanism of NAD+ and NMN binding to the Nudix homology domains of DBC1

Deleted in breast cancer 1 (DBC1) is a human nuclear protein that modulates the activities of various proteins involved in cell survival and cancer progression. Oxidized form of nicotinamide adenine dinucleotide (NAD+) is suggested to bind to the Nudix homology domains (NHDs) of DBC1, thereby regulating DBC1-Poly (ADP-ribose) polymerase 1 (PARP1) interactions, resulting in the restoration of DNA repair. Using Nuclear Magnetic Resonance (NMR) and Isothermal Titration Calorimetry (ITC), we confirmed NAD+ and its precursor nicotinamide mononucleotide (NMN) both bind the NHD domain of DBC1 (DBC1354-396). NAD+ likely interacts with DBC1354-396 through hydrogen bonding, with a binding affinity (8.99 μM) nearly twice that of NMN (17.0 μM), and the key binding sites are primarily residues E363 and D372, in the agreement with Molecular Docking experiments. Molecular Dynamics (MD) simulation further demonstrated E363 and D372's anchoring role in the binding process. Additional mutagenesis experiments of E363 and D372 confirmed their critical involvement of ligand-protein interactions. These findings lead to a better understanding of how NAD+ and NMN regulate DBC1, thereby offering insights for the development of targeted therapies and drug research focused on DBC1-associated tumors.

Carbon-13 chemical shift tensor measurements for nitrogen-dense compounds

This paper reports the principal values of the 13 C chemical shift tensors for five nitrogen-dense compounds (i.e., cytosine, uracil, imidazole, guanidine hydrochloride, and aminoguanidine hydrochloride). Although these are all fundamentally important compounds, the majority do not have 13 C chemical shift tensors reported in the literature. The chemical shift tensors are obtained from 1 H→13 C cross-polarization magic-angle spinning (CP/MAS) experiments that were conducted at a high field of 18.8 T to suppress the effects of 14 N-13 C residual dipolar coupling. Quantum chemical calculations using density functional theory are used to obtain the 13 C magnetic shielding tensors for these compounds. The best agreement with experiment arises from calculations using the hybrid functional PBE0 or the double-hybrid functional PBE0-DH, along with the triple-zeta basis sets TZ2P or pc-3, respectively, and intermolecular effects modeled using large clusters of molecules with electrostatic embedding through the COSMO approach. These measurements are part of an ongoing effort to expand the catalog of accurate 13 C chemical shift tensor measurements, with the aim of creating a database that may be useful for benchmarking the accuracy of quantum chemical calculations, developing nuclear magnetic resonance (NMR) crystallography protocols, or aiding in applications involving machine learning or data mining. This work was conducted at the National High Magnetic Field Laboratory as part of a 2-week school for introducing undergraduate students to practical laboratory experience that will prepare them for scientific careers or postgraduate studies.

Can simple 'molecular' corrections outperform projector augmented-wave density functional theory in the prediction of 35 Cl electric field gradient tensor parameters for chlorine-containing crystalline systems?

Many-body expansion (MBE) fragment approaches have been applied to accurately compute nuclear magnetic resonance (NMR) parameters in crystalline systems. Recent examples demonstrate that electric field gradient (EFG) tensor parameters can be accurately calculated for 14 N and 17 O. A key additional development is the simple molecular correction (SMC) approach, which uses two one-body fragment (i.e., isolated molecule) calculations to adjust NMR parameter values established using 'benchmark' projector augmented-wave (PAW) density functional theory (DFT) values. Here, we apply a SMC using the hybrid PBE0 exchange-correlation (XC) functional to see if this can improve the accuracy of calculated 35 Cl EFG tensor parameters. We selected eight organic and two inorganic crystal structures and considered 15 chlorine sites. We find that this SMC improves the accuracy of computed values for both the 35 Cl quadrupolar coupling constant (CQ ) and the asymmetry parameter ( η Q ) by approximately 30% compared with benchmark PAW DFT values. We also assessed a SMC that offers local improvements not only in terms of the quality of the XC functional but simultaneously in the quality of the description of relativistic effects via the inclusion of spin-orbit effects. As the inorganic systems considered contain heavy atoms bonded to the chlorine atoms, we find further improvements in the accuracy of calculated 35 Cl EFG tensor parameters when both a hybrid functional and spin-orbit effects are included in the SMC. On the contrary, for chlorine-containing organics, the inclusion of spin-orbit relativistic effects using a SMC does not improve the accuracy of computed 35 Cl EFG tensor parameters.

Biophysical and Structural Characterization of the Interaction between Human Galectin-3 and the Lipopolysaccharide from Pseudomonas aeruginosa

Given the significant involvement of galectins in the development of numerous diseases, the aim of the following work is to further study the interaction between galectin-3 (Gal3) and the LPS from Pseudomonas aeruginosa. This manuscript focused on the study of the interaction of the carbohydrate recognition domain of Gal3 with the LPS from Pseudomonas aeruginosa by means of different complementary methodologies, such as circular dichroism; spectrofluorimetry; dynamic and static light scattering and evaluation of the impact of Gal3 on the redox potential membranes of Escherichia coli and P. aeruginosa cells, as well as ITC and NMR studies. This thorough investigation reinforces the hypothesis of an interaction between Gal3 and LPS, unraveling the structural details and providing valuable insights into the formation of these intricate molecular complexes. Taken together, these achievements could potentially prompt the design of therapeutic drugs useful for the development of agonists and/or antagonists for LPS receptors such as galectins as adjunctive therapy for P. aeruginosa.

Biochemical and cellular characterization of the CISD3 protein: Molecular bases of cluster release and destabilizing effects of nitric oxide

The NEET proteins, an important family of iron-sulfur (Fe-S) proteins, have generated a strong interest due to their involvement in diverse diseases such as cancer, diabetes, and neurodegenerative disorders. Among the human NEET proteins, CISD3 has been the least studied, and its functional role is still largely unknown. We have investigated the biochemical features of CISD3 at the atomic and in cellulo levels upon challenge with different stress conditions i.e., iron deficiency, exposure to hydrogen peroxide, and nitric oxide. The redox and cellular stability properties of the protein agree on a predominance of reduced form of CISD3 in the cells. Upon the addition of iron chelators, CISD3 loses its Fe-S clusters and becomes unstructured, and its cellular level drastically decreases. Chemical shift perturbation measurements suggest that, upon cluster oxidation, the protein undergoes a conformational change at the C-terminal CDGSH domain, which determines the instability of the oxidized state. This redox-associated conformational change may be the source of cooperative electron transfer via the two [Fe2S2] clusters in CISD3, which displays a single sharp voltammetric signal at -31 mV versus SHE. Oxidized CISD3 is particularly sensitive to the presence of hydrogen peroxide in vitro, whereas only the reduced form is able to bind nitric oxide. Paramagnetic NMR provides clear evidence that, upon NO binding, the cluster is disassembled but iron ions are still bound to the protein. Accordingly, in cellulo CISD3 is unaffected by oxidative stress induced by hydrogen peroxide but it becomes highly unstable in response to nitric oxide treatment.

Combined NMR and MS-based metabonomics and real-time PCR analyses reveal dynamic metabolic changes of Ganoderma lucidum during fruiting body growing

Ganoderma lucidum (G. lucidum) is a rare medicinal fungus with various beneficial properties. One of its main components, ganoderic acids (GAs), are important triterpenoids known for their sedative and analgesic, hepatoprotective, and anti-tumor activities. Understanding the growth and development of the G. lucidum fruiting body is crucial for determining the optimal time to harvest them. In this study, we used nuclear magnetic resonance (NMR) spectroscopy to systematically characterize the metabolites of G. lucidum at seven distinct developmental stages. We also measured the contents of seven kinds of GAs using LC-MS/MS. A total of 49 metabolites were detected in G. lucidum, including amino acids, sugars, organic acids and GAs. During the transition from the bud development period (I) to the budding period (II), we observed a rapid accumulation of glucose, tyrosine, nicotinamide ribotide, inosine and GAs. After the budding period, the contents of most metabolites decreased until the mature period (VII). In addition, the contents of GAs showed an initial raising, followed by a decline during the elongation period, except for GAF, which exhibited a rapid raise during the mature stage. We also detected the expression of several genes involved in GA synthesis, finding that most genes including 16 cytochrome P450 monooxygenase were all down-regulated during periods IV and VII compared to period I. These findings provide valuable insights into the dynamic metabolic profiles of G. lucidum throughout its growth stage, and it is recommended to harvest G. lucidum at period IV.

A combined approach of structure-based virtual screening and NMR to interrupt the PD-1/PD-L1 axis: Biphenyl-benzimidazole containing compounds as novel PD-L1 inhibitors

Immunotherapy has emerged as a game-changing approach for cancer treatment. Although monoclonal antibodies (mAbs) targeting the programmed cell death protein 1/programmed cell death protein 1 ligand 1 (PD-1/PD-L1) axis have entered the market revolutionizing the treatment landscape of many cancer types, small molecules, although presenting several advantages including the possibility of oral administration and/or reduced costs, struggled to enter in clinical trials, suffering of water insolubility and/or inadequate potency compared with mAbs. Thus, the search for novel scaffolds for both the design of effective small molecules and possible synergistic strategies is an ongoing field of interest. In an attempt to find novel chemotypes, a virtual screening approach was employed, resulting in the identification of new chemical entities with a certain binding capability, the most versatile of which was the benzimidazole-containing compound 10. Through rational design, a small library of its derivatives was synthesized and evaluated. The homogeneous time-resolved fluorescence (HTRF) assay revealed that compound 17 shows the most potent inhibitory activity (IC50 ) in the submicromolar range and notably, differently from the major part of PD-L1 inhibitors, exhibits satisfactory water solubility properties. These findings highlight the potential of benzimidazole-based compounds as novel promising candidates for PD-L1 inhibition.

XFEL structure of carbonic anhydrase II: a comparative study of XFEL, NMR, X-ray and neutron structures

The combination of X-ray free-electron lasers (XFELs) with serial femtosecond crystallography represents cutting-edge technology in structural biology, allowing the study of enzyme reactions and dynamics in real time through the generation of `molecular movies'. This technology combines short and precise high-energy X-ray exposure to a stream of protein microcrystals. Here, the XFEL structure of carbonic anhydrase II, a ubiquitous enzyme responsible for the interconversion of CO2 and bicarbonate, is reported, and is compared with previously reported NMR and synchrotron X-ray and neutron single-crystal structures.

Functioning of Saccharomyces cerevisiae in honey coffee (Coffea canephora) and their effect on metabolites, volatiles and flavor profiles

Post-harvesting and microbial activity of coffee play a critical role in the metabolites and the sensory quality of the brew. The pulped natural/honey coffee process is an improvised semi-dry technique consisting of prolonged fermentation of depulped coffee beans excluding washing steps. The starter culture application in coffee industry plays an important role to enhance the cup quality. This work focuses on the fermentation of pulped natural/honey Robusta coffee with a starter culture (Saccharomyces cerevisiae MTCC 173) and the identification of fermentation patterns through 1H NMR, microbial ecology, volatomics and organoleptics of brew. Fermentation was accelerated by yeast populace (10 cfu log/mL) for 192 h. Principal compound analysis performed on 1H NMR led to the investigation of metabolites such as sugars, alkaloids, alcohols, organic acids and amino acids. Detection of some sugars and organic acids represented that the starter cultures imparted few metabolic changes during the process. A major activity of sugars in fermentation with 83.3 % variance in PC 1 and 16.7 % in PC 2 was observed. The chemical characteristics such as carbohydrates (41.88 ± 0.77 mg/g), polyphenols (34.16 ± 0.79 mg/g), proteins (58.54 ± 0.66 mg/g), caffeine (26.54 ± 0.06 mg/g), and CGA (21.83 ± 0.04 mg/g) were also evaluated. The heatmap-based visualization of GC-MS accorded characterization of additional 5 compounds in treated (T) coffee contributing to sweet, fruity and caramelly odor notes compared to untreated (UT). The sensory outlines 72.5 in T and 70.5 in UT scores. Preparation of honey coffee with Saccharomyces cerevisiae is the first report, which modulated the flavor and quality of coffee.

Phytochemical investigation and antitumor activity of coumarins from Sicilian accession of Ferulago nodosa (L.) Boiss. roots

Ferulago nodosa (L.) Boiss. (Apiaceae) is a species occurring in the Balkan-Tyrrhenian area being present in Crete, Greece, Albania, and probably in Macedonia. From the roots of this accession of species, not previously investigated, four coumarins, grandivittin, aegelinol benzoate, felamidin and aegelinol, and two terpenoids, (2E)-3-methyl-4-[(3-methyl-1-oxo-2-buten-1yl)oxy]-2-butenoic acid and pressafonin-A, were isolated and spectroscopically characterized. The last one was never detected in Ferulago species. The evaluation of the anti-tumor effects of F. nodosa coumarins on colon cancer HCT116 cells showed only a modest effect on reduction of tumor cell viability. For aegelinol, the reduction of colon cancer cell viability already appears with 25 µΜ, while using 50 e 100 µM doses of marmesin the residual viability amounted to 70% and 54%, respectively. This effect resulted more evident at higher doses of compounds (at 200 µM from 80% to 0%). The most effective compounds resulted coumarins lacking ester group.

Optimization and degradation studies of cellulose transesterification to palmitate esters in superbase ionic liquid

Cellulose palmitates (CPs) were synthesized with varying degrees of substitution (DS) via a catalyst-free, homogeneous transesterification of cellulose in a novel superbase ionic liquid (SB-IL) system, specifically 5-methyl-1,5,7-triaza-bicyclo[4.3.0]non-6-enium acetate [mTBNH][OAc], combined with dimethyl sulfoxide (DMSO) as a co-solvent, using vinyl palmitate as the acylating agent. We examined the influence of reaction temperature, reaction time, and the molar ratio of vinyl palmitate to anhydroglucose unit (AGU) on the DS, which ranged from 0.5 to 2.3 under the given conditions. Notably, the reaction order of the three hydroxy groups was C6-OH > C2-OH > C3-OH. To elucidate the chemical structure of CPs and confirm the transesterification process, various spectroscopic techniques including 1H nuclear magnetic resonance (NMR), 13C NMR, heteronuclear single quantum correlation (HSQC), and solid-state NMR were employed. Higher reaction temperatures and extended reaction times led to a decrease in the DS of CPs, potentially due to the degradation of some of the involved chemicals during the transesterification process. We also investigated the stability of the pure ionic liquid (IL) and the IL + DMSO solvent system at elevated temperatures by heating them at 100 °C for 5 h, confirming their chemical integrity through 1H NMR analysis. Additionally, we assessed the compatibility between the solvent system and cellulose by subjecting a mixture of cellulose and the solvent system to 100 °C for 5 h. To compare the structures of untreated cellulose and regenerated cellulose, Fourier transform infrared (FT-IR) spectroscopy was employed. Furthermore, we determined the molar mass of both untreated cellulose and regenerated cellulose, as well as CPs synthesized at higher reaction temperatures and longer durations, using intrinsic viscosity measurements. Lastly, we examined the solubility properties of CPs.

Complex I, V, and MDH2 deficient human skin fibroblasts reveal distinct metabolic signatures by 1 H HR-MAS NMR

In this study, we investigated the metabolic signatures of different mitochondrial defects (two different complex I and complex V, and the one MDH2 defect) in human skin fibroblasts (HSF). We hypothesized that using a selective culture medium would cause defect specific adaptation of the metabolome and further our understanding of the biochemical implications for the studied defects. All cells were cultivated under galactose stress condition and compared to glucose-based cell culture condition. We investigated the bioenergetic profile using Seahorse XFe96 cell analyzer and assessed the extracellular metabolic footprints and the intracellular metabolic fingerprints using NMR. The galactose-based culture condition forced a bioenergetic switch from a glycolytic to an oxidative state in all cell lines which improved overall separation of controls from the different defect groups. The extracellular metabolome was discriminative for separating controls from defects but not the specific defects, whereas the intracellular metabolome suggests CI and CV changes and revealed clear MDH2 defect-specific changes in metabolites associated with the TCA cycle, malate aspartate shuttle, and the choline metabolism, which are pronounced under galactose condition.

Three-dimensional solution structure, dynamics and binding of thioredoxin m from Pisum sativum

Thioredoxins (TRXs) are ubiquitous small, globular proteins involved in cell redox processes. In this work, we report the solution structure of TRX m from Pisum sativum (pea), which has been determined on the basis of 1444 nuclear Overhauser effect- (NOE-) derived distance constraints. The average pairwise root-mean-square deviation (RMSD) for the 20 best structures for the backbone residues (Val7-Glu102) was 1.42 ± 0.15 Å, and 1.97 ± 0.15 Å when all heavy atoms were considered. The structure corresponds to the typical fold of TRXs, with a central five-stranded β-sheet flanked by four α-helices. Some residues had an important exchange dynamic contribution: those around the active site; at the C terminus of β-strand 3; and in the loop preceding α-helix 4. Smaller NOE values were observed at the N and C-terminal residues forming the elements of the secondary structure or, alternatively, in the residues belonging to the loops between those elements. A peptide derived from pea fructose-1,6-biphosphatase (FBPase), comprising the preceding region to the regulatory sequence of FBPase (residues Glu152 to Gln179), was bound to TRX m with an affinity in the low micromolar range, as measured by fluorescence and NMR titration experiments. Upon peptide addition, the intensities of the cross-peaks of all the residues of TRX m were affected, as shown by NMR. The value of the dissociation constant of the peptide from TRX m was larger than that of the intact FBPase, indicating that there are additional factors in other regions of the polypeptide chain of the latter protein affecting the binding to thioredoxin.

Scanning mutagenesis identifies residues that improve the long-term stability and insecticidal activity of cyclotide kalata B1

Cyclotides are plant-derived disulfide-rich cyclic peptides that have a natural function in plant defense and potential for use as agricultural pesticides. Because of their highly constrained topology, they are highly resistant to thermal, chemical, or enzymatic degradation. However, the stability of cyclotides at alkaline pH for incubation times of longer than a few days is poorly studied but important since these conditions could be encountered in the environment, during storage or field application as insecticides. In this study, kalata B1 (kB1), the prototypical cyclotide, was engineered to improve its long-term stability and retain its insecticidal activity via point mutations. We found that substituting either Asn29 or Gly1 to lysine or leucine increased the stability of kB1 by twofold when incubated in an alkaline buffer (pH = 9.0) for 7 days, while retaining its insecticidal activity. In addition, when Gly1 was replaced with lysine or leucine, the mutants could be cyclized using an asparaginyl endopeptidase, in vitro with a yield of ∼90% within 5 min. These results demonstrate the potential to manufacture kB1 mutants with increased stability and insecticidal activity recombinantly or in planta. Overall, the discovery of mutants of kB1 that have enhanced stability could be useful in leading to longer term activity in the field as bioinsecticides.

Antimicrobial activity of spiculisporic acid isolated from endophytic fungus Aspergillus cejpii of Hedera helix against MRSA

The surge in multidrug-resistant pathogens worldwide has jeopardized the clinical efficiency of many current antibiotics. This problem steered many researchers in their quest to discover new effective antimicrobial agents from natural origins including plants or their residing endophytes. In this work, we aimed to identify the endophytic fungi derived from Hedera helix L. and investigate their potential antimicrobial activity. Bioguided fractionation approach was conducted to isolate the pure compounds from the most active fungal fraction. Out of a total of six different isolated endophytic fungal strains, only Aspergillus cejpii showed the highest activity against all tested microbial strains. The most active fraction was the dichloromethane/methanol fraction (DCM:MeOH), where it showed significant activity against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Serratia marcescens, Acinetobacter baumannii, Salmonella typhi, and three drug-resistant clinical isolate strains including Methicillin-resistant Staphylococcus aureus (MRSA, H1), Pseudomonas aeruginosa (PS 16), and Acinetobacter baumannii (ACT 322) using tetracyline and kanamycin as the control antibiotics. Bioguided fractionation of the active fraction led to the isolation of the γ-butenolide, spiculisporic acid. Structure elucidation was carried out using 1H and 13C-NMR spectroscopic analysis. The compound showed good antimicrobial activities with minimum inhibitory concentration (MIC) values ranging from 3.9 to 31.25 μg/mL against all tested strains. Gas chromatography coupled to mass spectrometry (GC-MS) profiling was also carried out to identify the metabolites in the microbial crude extract. In conclusion, endophytic fungi, Aspergillus cejpii, isolated from Hedera helix L. roots showed promising antimicrobial activity which merits further in-depth investigations for potential utilization as a source of new antibiotics in the future. It can also be considered as a novel source for spiculisporic acid.

[4-(2-Aminoethyl)morpholine-κ2N,N']di-bromidocadmium(II): synthesis, crystal structure and Hirshfeld surface analysis

The title compound, [CdBr2(C6H14N2O)], was synthesized upon complexation of 4-(2-aminoethyl)morpholine and cadmium(II) bromide tetra-hydrate at 303 K. It crystallizes as a centrosymmetric dimer, with one cadmium atom, two bromine atoms and one N,N'-bidentate 4-(2-aminoethyl)morpholine ligand in the asymmetric unit. The metal atom is six-coordinated and has a distorted octa-hedral geometry. In the crystal, O⋯Cd inter-actions link the dimers into a polymeric double chain and inter-molecular C-H⋯O hydrogen bonds form R 2 2(6) ring motifs. Further C-H⋯Br and N-H⋯Br hydrogen bonds link the components into a three-dimensional network. As the N-H⋯Br hydrogen bonds are shorter than the C-H⋯Br inter-actions, they have a larger effect on the packing. A Hirshfeld surface analysis reveals that the largest contributions to the packing are from H⋯H (46.1%) and Br⋯H/H⋯Br (38.9%) inter-actions with smaller contributions from the O⋯H/H⋯O (4.7%), Br⋯Cd/Cd⋯Br (4.4%), O⋯Cd/Cd⋯O (3.5%), Br⋯Br (1.1%), Cd⋯H/H⋯Cd (0.9%), Br⋯O/O⋯Br (0.3%) and O⋯N/N⋯O (0.1%) contacts.

Applications of biaryl cyclization in the synthesis of cyclic enkephalin analogs with a highly restricted flexibility

A series of 10 cyclic, biaryl analogs of enkephalin, with Tyr or Phe residues at positions 1 and 4, were synthesized according to the Miyaura borylation and Suzuki coupling methodology. Biaryl bridges formed by side chains of the two aromatic amino acid residues are of the meta-meta, meta-para, para-meta, and para-para configuration. Conformational properties of the peptides were studied by CD and NMR. CD studies allowed only to compare conformations of individual peptides while NMR investigations followed by XPLOR calculations provided detailed information on their conformation. Reliability of the XPLOR calculations was confirmed by quantum chemical ones performed for one of the analogs. No intramolecular hydrogen bonds were found in all the peptides. They are folded and adopt the type IV β-turn conformation. Due to a large steric strain, the aromatic carbon atoms forming the biaryl bond are distinctly pyramidalized. Seven of the peptides were tested in vitro for their affinity for the µ-opioid receptor.

Assessment of thimerosal effects in sublethal concentrations on zebrafish (Danio rerio) embryos exploring NMR-based metabolomics profile

Thimerosal, a preservative commonly used in the pharmaceutical and cosmetic industry, has raised concerns regarding its potentially toxic effects as an organic mercury compound. Within this context, using an NMR-based metabolomics profile and chemometric analysis, zebrafish embryos were used as an in vivo model to study the effects of thimerosal in metabolic profiles after exposure to sublethal concentrations of the mercury compound. The thimerosal concentrations of 40 and 80 nM were employed, corresponding to 40% and 80% of the LC50, respectively, for zebrafish embryos. The most significant alterations in the metabolic profile included changes in carbohydrates, amino acids, nucleotides, trimethylamine-N-oxide, ethanolamine, betaine, and ethanol. Furthermore, thimerosal exposure affects various metabolic pathways, impairing the nervous system, disrupting protein metabolism, and potentially causing oxidative damage. Therefore, adopting a metabolomics approach in this investigation provided insights into the potentially implicated metabolic pathways contributing to the deleterious effects of thimerosal in biological systems.

Through-space scalar spin-spin coupling: from rigid intramolecular cases to short-lived van der Waals complexes

We will discuss, with the help of few selected examples, how the concept of through-space scalar spin-spin coupling between non covalently bonded nuclei has evolved in recent years. We will first present systems where 'no covalent bond' actually means that the two atoms are separated by a large number of bonds; then we will see cases where it is referred to true van der Waals dimers, but with the two atoms somehow constrained in their positions; we will finish with the most recent examples of liquids and even gaseous mixtures with full translational degrees of freedom in a regime of intermolecular/interatomic fast exchange.

Degree of methyl esterification: A key factor for the encapsulation of icaritin with pectin

Pectin is a promising nano-carrier. The degree of methyl esterification (DM) influences the physiochemical properties of pectin. However, the effect of DM on the encapsulation capacity of pectin remains unclear. In this work, low methyl-esterified pectin (LMP) and high methyl-esterified pectin (HMP) were prepared. The molecular weight, rheological properties of these pectins with various DM levels were determined. Then icaritin/pectin micelles (IPMs) were prepared using HMP and LMP. Notably, higher loading capacities (18.75-20.12 %) were observed in HMP-IPMs compared to LMP-IPMs (15.72-16.64 %). Furthermore, LMP-IPMs demonstrated a DM-dependent reduction in particle sizes, ranging from 449 to 527 nm. In contrast, the particle sizes of HMP-IPMs varied between 342 and 566 nm, with smaller particle sizes observed in HMP-IPMs at higher DM levels. A significant positive correlation was found between DM and the formation of IPMs, including encapsulation efficiency, loading capacity, Zeta potential, and polydispersity index. Alkali de-esterification showed a weak impact on the pectin structure. Hydroxyl groups like 7-OH and 5-OH of icaritin might be involved in the formation of IPMs. The hydrogen-bond interactions between pectin and icaritin could be enhanced as DM increased.

Magnetic field dependence of the para-ortho conversion rate of molecular hydrogen in SABRE experiments

The use of parahydrogen - the isomer of molecular hydrogen with zero nuclear spin - is important for promising and actively developing methods for spin hyperpolarization of nuclei called parahydrogen induced polarization (PHIP). However, the dissolved parahydrogen in PHIP experiments quickly loses its spin order, resulting in the formation of orthohydrogen and reduction of the overall nuclear polarization of the substrate. This process is due to the difference of chemical shifts of hydride protons, as well as spin-spin couplings between nuclei, in the intermediate catalytic complexes, and it has not been rigorously explained so far. We proposed a new experimental technique based on magnetic field cycling for measuring the rate of molecular hydrogen para-ortho conversion in solution and applied it for non-hydrogenative PHIP Signal Amplification By Reversible Exchange (SABRE) experiments. The para-ortho conversion rate was measured over a wide range of magnetic field from 0.5 mT to 9.4 T. It was found that the conversion rate strongly depends on the magnetic field in which the reaction occurs, as well as on the concentrations of reactants. The rate decreases with increasing the concentration of pyridine ligand and increases with increasing the concentration of iridium catalyst. The model, which takes into account the reversible exchange of molecular hydrogen with the catalyst, nuclear spin-spin interaction of hydride protons with nuclei of ligands within catalytic complex and nuclear Zeeman interactions, qualitatively describes the experimental data. Two types of complexes with different spin system symmetry contribute to the molecular hydrogen conversion. In asymmetric complexes possessing hydride protons with different chemical shifts due to the presence of chlorine anion ligand the para-ortho conversion rate increases with magnetic field, while for symmetric complexes this mechanism is not operable. In the magnetic field where level anti-crossing occurs the resonant feature for the rate of para-ortho conversion is found. The results of this work can be utilized for finding the optimal conditions for obtaining the maximum hyperpolarization in the experiments employing parahydrogen.

The effects of biological crowders on fibrillization, structure, diffusion, and conformational dynamics of α-synuclein

α-synuclein is an intrinsically disordered protein (IDP) whose aggregation in presynaptic neuronal cells is a pathological hallmark of Lewy body formation and Parkinson's disease. This aggregation process is likely affected by the crowded macromolecular cellular environment. In this study, α-synuclein was studied in the presence of both a synthetic crowder, Ficoll70, and a biological crowder composed of lysed cells that better mimics the biocomplexity of the cellular environment. 15 N-1 H HSQC NMR results show similar α-synuclein chemical shifts in non-crowded and all crowded conditions implying that it remains similarly unstructured in all conditions. Nevertheless, both HSQC NMR and fluorescence measurements indicate that, only in the cell lysate, α-synuclein forms aggregates over a timescale of 48 h. 15 N-edited diffusion measurements indicate that all crowders slow down the α-synuclein's diffusivity. Interestingly, at high concentrations, α-synuclein diffuses faster in cell lysate than in Ficoll70, possibly due to additional soft (e.g., electrostatic or hydrophobic) interactions. 15 N-edited relaxation measurements show that some residues are more mobile in cell lysate than in Ficoll70; the rates that are most different are predominantly in hydrophobic residues. We thus examined cell lysates with reduced hydrophobicity and found slower dynamics (higher relaxation rates) in several α-synuclein residues. Taken together, these experiments suggest that while cell lysate does not substantially affect α-synuclein structure (HSQC spectra), it does affect chain dynamics and translational diffusion, and strongly affects aggregation over a timescale of days, in a manner that is different from either no crowder or an artificial crowder: soft hydrophobic interactions are implicated.

Structural characterization of the antimicrobial peptides myxinidin and WMR in bacterial membrane mimetic micelles and bicelles

Antimicrobial peptides are a promising class of potential antibiotics that interact selectively with negatively charged lipid bilayers. This paper presents the structural characterization of the antimicrobial peptides myxinidin and WMR associated with bacterial membrane mimetic micelles and bicelles by NMR, CD spectroscopy, and molecular dynamics simulations. Both peptides adopt a different conformation in the lipidic environment than in aqueous solution. The location of the peptides in micelles and bicelles has been studied by paramagnetic relaxation enhancement experiments with paramagnetic tagged 5- and 16-doxyl stearic acid (5-/16-SASL). Molecular dynamics simulations of multiple copies of the peptides were used to obtain an atomic level of detail on membrane-peptide and peptide-peptide interactions. Our results highlight an essential role of the negatively charged membrane mimetic in the structural stability of both myxinidin and WMR. The peptides localize predominantly in the membrane's headgroup region and have a noticeable membrane thinning effect on the overall bilayer structure. Myxinidin and WMR show a different tendency to self-aggregate, which is also influenced by the membrane composition (DOPE/DOPG versus DOPE/DOPG/CL) and can be related to the previously observed difference in the ability of the peptides to disrupt different types of model membranes.

Comparative Conformational Analysis of Acyclic Sugar Alcohols Ribitol, Xylitol and d-Arabitol by Solution NMR and Molecular Dynamics Simulations

Ribitol (C5H12O5) is an acyclic sugar alcohol that was recently identified in O-mannose glycan on mammalian α-dystroglycan. The conformation and dynamics of acyclic sugar alcohols such as ribitol are dependent on the stereochemistry of the hydroxyl groups; however, the dynamics are not fully understood. To gain insights into the conformation and dynamics of sugar alcohols, we carried out comparative analyses of ribitol, d-arabitol and xylitol by a crystal structure database search, solution NMR analysis and molecular dynamics (MD) simulations. The crystal structures of the sugar alcohols showed a limited number of conformations, suggesting that only certain stable conformations are prevalent among all possible conformations. The three-bond scholar coupling constants and exchange rates of hydroxyl protons were measured to obtain information on the backbone torsion angle and possible hydrogen bonding of each hydroxyl group. The 100 ns MD simulations indicate that the ribitol backbone has frequent conformational transitions with torsion angles between 180∘ and ±60∘, while d-arabitol and xylitol showed fewer conformational transitions. Taking our experimental and computational data together, it can be concluded that ribitol is more flexible than d-arabitol or xylitol, and the flexibility is at least in part defined by the configuration of the OH groups, which may form intramolecular hydrogen bonds.

Monitoring the metabolite content of seasoned zucchinis during storage by NMR-based metabolomics

This study applied 1H NMR metabolomics to monitor the metabolite content of baked and seasoned zucchinis packaged in both compostable and plastic trays. Polar extracts of samples stored at 4 °C up to 35 days were investigated to check for metabolite changes upon shelf life. The evolution of the integral values of only the main metabolites responsible for sample differentiation (lactate, acetate, malate, α and β glucose and sucrose) were further analysed and compared. In particular, the evaluation of lactate and acetate amount, considered markers of fermentation progress, showed a comparable performance for the two types of packaging in preserving the freshness of seasoned zucchinis, confirming the maintenance of food product composition within the declared shelf life period in the recommended storage conditions. Albeit preliminary, the results support the NMR metabolomics as a tool for identifying candidate metabolites to monitor the shelf life of foods, thereby improving the understanding of molecular changes during storage.

Molecular structure, vibrational spectral, electron density analysis on linaloe oil and molecular docking efficacy against the therapeutic target on human immunodeficiency virus-1 organism (VIRAL protein)

Natural traditional medicine extensively uses certain terpenes and gives plants their flavor, aroma, and color. Treatments for bacterial infections, malaria, and cardiovascular disorders, anti-inflammatory, promote circulation, and heal wounds. 3,7-Dimethyl-1,6-octadien-3-ol (Linalool) is a naturally occurring monoterpene alcohol with no cycle and is a colorless liquid. Spectral analysis such as UV absorption spectra, NMR for structure determination, and IR and Raman for vibrational analysis. The Quantum mechanical approach uses DFT, ELF, and LOL-promolecular electron density, non-relaxed, and atomic density analysis. The biomolecular studies such as molecular dynamics using protein-ligand complex with HIV-1 organism (energy minimization). ADMET for the usage of linalool in different metabolism studies and Molecular docking for binding affinity, its reactive site estimation, and macromolecules that come into contact with protein receptors and conclude ligand binding affinity with protein.

Tiegun maturity by NMR-based metabolomics and LC-MS/MS analysis

BACKGROUND

Dioscorea opposita Thunb. cv. Tiegun maturity (DM) is an important factor influencing its quality. However, there are few studies on the impact of harvest time on its maturation. In the present study, a NMR-based metabolomics approach was applied to investigate the dynamic metabolic changes of D. opposita Thunb. cv. Tiegun at six different harvest stages: stage 1 (S1), stage 2 (S2), Stage 3 (S3), stage 4 (S4), stage 5 (S5) and stage 6 (S6).

RESULTS

Principal component analysis showed distinct segregation of samples obtained from S1, S2 and S3 compared to those derived from S4, S5 and S6. Interestingly, these samples from the two periods were obtained before and after frost, indicating that frost descent might be important for DM. Eight differential metabolites responsible for good separation of different groups were identified by the principal component analysis loading plot and partial least squares-discriminant analysis. In addition, quantitative analysis of these metabolites using liquid chromatography-tandem mass spectrometry determined the effects of harvest time on these metabolite contents, two of which, sucrose and allantoin, were considered as potential biomarkers to determine DM.

CONCLUSION

The present study demonstrated that NMR-based metabolomics approach could serve as a powerful tool to identify differential metabolites during harvesting processes, also offering a fresh insight into understanding the DM and the potential mechanism of quality formation. © 2024 Society of Chemical Industry.

Formation of Furan from Linoleic Acid Thermal Oxidation: (E,E)-2,4-Decadienal as a Critical Intermediate Product

The linoleic acid reaction models were set at 150 °C for 120 min, and its oxidation process was monitored by nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC-MS). Results showed that no furan was formed from linoleic acid without heating, while furan accumulated throughout the heating process. Linoleic acid ran out within 30 min, which indicated that furan was formed mainly from the intermediate oxidation products of linoleic acid after 30 min. It should be noticed that the content of (E,E)-2,4-decadienal reached maximum once the linoleic acid ran out and then decreased with the formation of furan. Multivariate statistical analysis suggested that (E,E)-2,4-decadienal was the most important aldehyde related to furan formation during linoleic acid oxidation. To prove this assumption, the variation of furan from (E,E)-2,4-decadienal reaction models heating at 150 °C for 60 min was also studied. Results showed that the content of furan increased with the oxidation of (E,E)-2,4-decadienal. Furthermore, NMR and GC-MS data proved that (E,E)-2,4-decadienal could be oxidized to 4,5-epoxy-(E)-2-decenal. In conclusion, our results supported (E,E)-2,4-decadienal and trans-4,5-epoxy-(E)-2-decenal as critical intermediate products of furan formation from linoleic acid oxidation.

Screening Peptide-Binding Partners for GenX via Phage Display

Per- and poly-fluoroalkyl substances (PFAS), such as GenX, are a class of highly stable synthetic compounds that have recently become the focus of environmental remediation endeavors due to their toxicity. While considerable strides have been made in PFAS remediation, the diversity of these compounds, and the costs associated with approaches such as ion exchange resins and advanced oxidation technologies, remain challenging for widespread application. In addition, little is known about the potential binding and impacts of GenX on human proteins. To address these issues, we applied phage display and screened short peptides that bind specifically to GenX, with the ultimate goal of identifying human proteins that bind with GenX. In this study we identified the amino acids that contribute to the binding and measured the binding affinities of the two discovered peptides with NMR. A human protein, ankyrin-repeat-domain-containing protein 36B, with matching sequences of one of the peptides, was identified, and the binding positions were predicted by docking and molecular dynamics simulation. This study created a platform to screen peptides that bind with toxic chemical compounds, which ultimately helped us identify biologically relevant molecules that could be inhibited by the GenX, and also provided information that will contribute to future bioengineered GenX-binding device design.

Cytotoxic constituents from the fruit of Solanum aculeastrum

A new triterpene, aculeastrumone A (1), a new triterpene saponin aculeastrumoside A (2), and eleven known compounds (3-13) were isolated from MeOH/Water (80/20) extract of the fruits of Solanum aculeastrum (Solanaceae). Their structures were established by detailed 1D and 2D NMR spectroscopic studies and mass spectrometry. The isolated compounds were evaluated against three human cancer cells ((MCF-7 (breast cancer), NCI-H460 (lung cancer), and Hela (cervical cancer)) and normal human fibroblast (BJ) cell lines. Among them, saponins 2-5, 7-8, and Carpesterol 10 possess significant cytotoxic activity with IC50 ≤ 10 µM against the three cancer cell lines.

NMR Analyses and Statistical Modeling of Biobased Polymer Microstructures-A Selected Review

NMR analysis combined with statistical modeling offers a useful approach to investigate the microstructures of polymers. This article provides a selective review of the developments in both the NMR analysis of biobased polymers and the statistical models that can be used to characterize these materials. The information obtained from NMR and statistical models can provide insights into the microstructure and stereochemistry of appropriate biobased polymers and establish a systematic approach to their analysis. In suitable cases, the analysis can help optimize the synthetic procedures and facilitate the development of new or modified polymeric materials for various applications. Examples are given of the studies of poly(hydroxyalkanoates), poly(lactic acid), and selected polysaccharides, e.g., alginate, pectin, and chitosan. This article may serve as both a reference and a guide for future workers interested in the NMR sequence analysis of biobased materials.

NMR-Based Analysis of Plasma Lipoprotein Subclass and Lipid Composition Demonstrate the Different Dietary Effects in ApoE-Deficient Mice

Plasma lipid levels are commonly measured using traditional methods such as triglycerides (TG), high-density lipoprotein (HDL), low-density lipoprotein (LDL), and cholesterol (CH). However, the use of newer technologies, such as nuclear magnetic resonance (NMR) with post-analysis platforms, has made it easier to assess lipoprotein profiles in research. In this study involving ApoE-deficient mice that were fed high-fat diets, significant changes were observed in TG, CH, free cholesterol (FC), and phospholipid (PL) levels within the LDL fraction. The varied proportions of TG in wild-type mice and CH, FC, and PL in ApoE-/- mice were strikingly different in very low-density lipoproteins (VLDL), LDL, intermediate-density lipoprotein (IDL), and HDL. This comprehensive analysis expands our understanding of lipoprotein subfractions and the impacts of the APOE protein and high-fat diet in mouse models. The new testing method allows for a complete assessment of plasma lipids and their correlation with genetic background and diet in mice.

Carbon-13 Radiofrequency Amplification by Stimulated Emission of Radiation of the Hyperpolarized Ketone and Hemiketal Forms of Allyl [1-13C]Pyruvate

13C hyperpolarized pyruvate is an emerging MRI contrast agent for sensing molecular events in cancer and other diseases with aberrant metabolic pathways. This metabolic contrast agent can be produced via several hyperpolarization techniques. Despite remarkable success in research settings, widespread clinical adoption faces substantial roadblocks because the current sensing technology utilized to sense this contrast agent requires the excitation of 13C nuclear spins that also need to be synchronized with MRI field gradient pulses. Here, we demonstrate sensing of hyperpolarized allyl [1-13C]pyruvate via the stimulated emission of radiation that mitigates the requirements currently blocking broader adoption. Specifically, 13C Radiofrequency Amplification by Stimulated Emission of Radiation (13C RASER) was obtained after pairwise addition of parahydrogen to a pyruvate precursor, detected in a commercial inductive detector with a quality factor (Q) of 32 for sample concentrations as low as 0.125 M with 13C polarization of 4%. Moreover, parahydrogen-induced polarization allowed for the preparation of a mixture of ketone and hemiketal forms of hyperpolarized allyl [1-13C]pyruvate, which are separated by 10 ppm in 13C NMR spectra. This is a good model system to study the simultaneous 13C RASER signals of multiple 13C species. This system models the metabolic production of hyperpolarized [1-13C]lactate from hyperpolarized [1-13C]pyruvate, which has a similar chemical shift difference. Our results show that 13C RASER signals can be obtained from both species simultaneously when the emission threshold is exceeded for both species. On the other hand, when the emission threshold is exceeded only for one of the hyperpolarized species, 13C stimulated emission is confined to this species only, therefore enabling the background-free detection of individual hyperpolarized 13C signals. The reported results pave the way to novel sensing approaches of 13C hyperpolarized pyruvate, potentially unlocking hyperpolarized 13C MRI on virtually any MRI system─an attractive vision for the future molecular imaging and diagnostics.

Rational Approach to Optimizing Conformation-Switching Aptamers for Biosensing Applications

The utilization of structure-switching aptamers (SSAs) has enabled the development of novel sensing platforms for the sensitive and continuous detection of molecules. De novo development of SSAs, however, is complex and laborious. Here we describe a rational approach to SSA optimization that simultaneously improves aptamer binding affinity and introduces target-dependent conformation-switching for compatibility with real-world biosensor applications. Key structural features identified from NMR and computational modeling were used to optimize conformational switching in the presence of target, while large-scale, microarray-based mutation analysis was used to map regions of the aptamer permissive to mutation and identify combinations of mutations with stronger binding affinity. Optimizations were carried out in a relevant biofluid to ensure a seamless transition of the aptamer to a biosensing platform. Initial proof-of-concept for this approach is demonstrated with a cortisol binding aptamer but can easily be translated to other relevant aptamers. Cortisol is a hormone correlated with the stress response that has been associated with various medical conditions and is present at quantifiable levels in accessible biofluids. The ability to continuously track levels of stress in real-time via cortisol monitoring, which can be enabled by the aptamers reported here, is crucial for assessing human health and performance.

Total cucurbitacins from Herpetospermum pedunculosum pericarp do better than Hu-lu-su-pian (HLSP) in its safety and hepatoprotective efficacy

The pericarp of Herpetospermum pedunculosum (HPP) has traditionally been used for treating jaundice and hepatitis. However, the specific hepatoprotective components and their safety/efficacy profiles remain unclear. This study aimed to characterize the total cucurbitacins (TCs) extracted from HPP and evaluate their hepatoprotective potential. As a reference, Hu-lu-su-pian (HLSP), a known hepatoprotective drug containing cucurbitacins, was used for comparison of chemical composition, effects, and safety. Molecular networking based on UHPLC-MS/MS identified cucurbitacin B, isocucurbitacin B, and cucurbitacin E as the major components in TCs, comprising 70.3%, 26.1%, and 3.6% as determined by RP-HPLC, respectively. TCs treatment significantly reversed CCl4-induced metabolic changes associated with liver damage in a dose-dependent manner, impacting pathways including energy metabolism, oxidative stress and phenylalanine metabolism, and showed superior efficacy to HLSP. Safety evaluation also showed that TCs were safe, with higher LD50 and no observable adverse effect level (NOAEL) values than HLSP. The median lethal dose (LD50) and NOAEL values of TCs were 36.21 and 15 mg/kg body weight (BW), respectively, while the LD50 of HLSP was 14 mg/kg BW. In summary, TCs extracted from HPP demonstrated promising potential as a natural hepatoprotective agent, warranting further investigation into synergistic effects of individual cucurbitacin components.

Highly Efficient Biosorption of Cationic Dyes via Biopolymeric Adsorbent-Material-Based Pectin Extract Polysaccharide and Carrageenan Grafted to Cellulosic Nonwoven Textile

Water scarcity and contamination have emerged as critical global challenges, requiring the development of effective and sustainable solutions for the treatment of contaminated water. Recently, functionalized polymer biomaterials have garnered significant interest because of their potential for a wide range of water treatment applications. Accordingly, this paper highlights the design of a new adsorbent material based on a cellulosic nonwoven textile grafted with two extracted biopolymers. The layer-by-layer grafting technique was used for the polyelectrolyte multi-layer (PEM) biosorbent production. Firstly, we extracted a Suaeda fruticosa polysaccharide (SFP) and confirmed its pectin-like polysaccharide structure via SEC, NMR spectroscopy, and chemical composition analyses. Afterward, the grafting was designed via an alternating multi-deposition of layers of SFP polymer and carrageenan crosslinked with 1,2,3,4-butanetetracarboxylic acid (BTCA). FT-IR and SEM were used to characterize the chemical and morphological characteristics of the designed material. Chemical grafting via polyesterification reactions of the PEM biosorbent was confirmed through FT-IR analysis. SEM revealed the total filling of material microspaces with layers of grafted biopolymers and a rougher surface morphology. The assessment of the swelling behavior revealed a significant increase in the hydrophilicity of the produced adsorbent system, a required property for efficient sorption potential. The evaluation of the adsorption capabilities using the methylene blue (MB) as cationic dye was conducted in various experimental settings, changing factors such as the pH, time, temperature, and initial concentration of dye. For the untreated and grafted materials, the greatest adsorbed amounts of MB were 130.6 mg/g and 802.6 mg/g, respectively (pH = 4, T = 22 C, duration = 120 min, and dye concentration = 600 mg/L). The high adsorption performance, compared to other reported materials, was due to the presence of a large number of hydroxyl, sulfonate, and carboxylic functional groups in the biosorbent polymeric system. The adsorption process fitted well with the pseudo-first-order kinetic model and Langmuir/Temkin adsorption isotherms. This newly developed multi-layered biosorbent shows promise as an excellent adsorption resultant and cheap-cost/easy preparation alternative for treating industrial wastewater.

Isolation and Structure Determination of Drought-Induced Multihexose Benzoxazinoids from Maize (Zea mays)

Benzoxazinoids (BXDs) are plant specialized metabolites exerting a pivotal role in plant nutrition, allelopathy, and defenses. Multihexose benzoxazinoids were previously observed in cereal-based food products such as whole-grain bread. However, their production in plants and exact structure have not been fully elucidated. In this study, we showed that drought induced the production of di-, tri-, and even tetrahexose BXDs in maize roots and leaves. We performed an extensive nuclear magnetic resonance study and elucidated the nature and linkage of the sugar units, which were identified as gentiobiose units β-linked (1″ → 6') for the dihexoses and (1″ → 6')/(1‴ → 6″) for the trihexoses. Drought induced the production of DIMBOA-2Glc, DIMBOA-3Glc, HMBOA-2Glc, HMBOA-3Glc, and HDMBOA-2Glc. The induction was common among several maize lines and the strongest in seven-day-old seedlings. This work provides ground to further characterize the BXD synthetic pathway, its relevance in maize-environment interactions, and its impact on human health.

Host-Guest Chemosensor Ensembles based on Water-Soluble Sulfonated Calix[n]arenes and a Pyranoflavylium Dye for the Optical Detection of Biogenic Amines

Biogenic amines (BAs) are biologically active nitrogen-containing compounds formed during the food spoilage process and are often related as key markers of food quality, safety, and freshness. Because their presence in foods at high levels can cause significant health problems, researchers have been focused on developing novel strategies and methods for early detection and capture of these analytes. Herein, water-soluble sulfonated calix[n]arene macrocycles (SC4, SC6, and SC8) and a pH-sensitive dye (4'-hydroxy-10-methylpyranoflavylium) were investigated as host-guest systems for BA sensing. The hosts were able to bind the flavylium cation of the dye with association constants of 103 to 104 M-1. The dye complexation also allowed tuning its pKa from 6.72 (free) toward high values: 7.68 (SC4), 7.79 (SC6), and 8.45 (SC8). These data were crucial to optimize the host-guest complexes as optical sensing systems for putrescine/tyramine (pH 7.2-7.6), yielding a colorimetric redshift from yellow to red. The BA sensing was also demonstrated by fluorescence quenching for the calix[n]arene/dye complexes and fluorescence recovery after the addition of BAs. 1H NMR spectroscopy was used to demonstrate the interaction mode, confirming an encapsulation-driven mechanism. Overall, these host-guest systems demonstrated great potential for the detection of BAs, one of the main key markers of food spoilage.