LC-HRMS and NMR studies for the characterization of degradation impurities of ubrogepant along with the in silico approaches for the prediction of degradation and toxicity

Ubrogepant is the first oral calcitonin gene-related peptide (CGRP) receptor antagonist which is used for the acute treatment of migraine in adults. The present study employs liquid chromatography-high resolution mass spectrometry (LC-HRMS) and nuclear magnetic resonance spectroscopy (NMR) techniques for the identification and characterization of degradation impurities of ubrogepant. The forced degradation study of ubrogepant was performed as per the International Council for Harmonisation (ICH) Q1A and Q1B guidelines. The in silico degradation profile of ubrogepant was predicted by Zeneth. It was observed that ubrogepant was labile to acidic hydrolysis, basic hydrolysis, and oxidative degradation conditions (H2O2), although it was stable in neutral hydrolysis and photolytic (UV light and visible light) conditions. Eight degradation impurities were formed, which were separated on reversed-phase HPLC with a gradient program on an InertSustain C8 column (4.6 × 250 mm, 5 µm) using 10 mM ammonium formate (pH unadjusted) and acetonitrile as the mobile phase. The structures of all the degradation impurities were characterized using the exact masses obtained from the HRMS/MS. Further, NMR studies were conducted on two major degradation impurities (UB-4 and UB-7). A plausible mechanism was proposed to support the structures of all the degradation impurities of UBR. In silico toxicity and mutagenicity assessment were done by DEREK Nexus, SARAH Nexus, and ProTox-II.

Metabolomics-based analysis of the diatom Cheatoceros tenuissimus combining NMR and GC-MS techniques

Metabolomics, a recent addition to omics sciences, studies small molecules across plants, animals, humans, and marine organisms. Nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC-MS) are widely used in those studies, including microalgae metabolomics. NMR is non-destructive and highly reproducible but has limited sensitivity, which could be supplemented by joining GC-MS analysis. Extracting metabolites from macromolecules requires optimization for trustworthy results. Different extraction methods yield distinct profiles, emphasizing the need for optimization. The results indicated that the optimized extraction procedure successfully identified NMR and GC-MS-based metabolites in MeOH, CHCl3, and H2O extraction solvents. The findings represented the spectral information related to carbohydrates, organic molecules, and amino acids from the water-soluble metabolites fraction and a series of fatty acid chains, lipids, and sterols from the lipid fraction. Our study underscores the benefit of combining NMR and GC-MS techniques to comprehensively understand microalgae metabolomes, including high and low metabolite concentrations and abundances.•In this study, we focused on optimizing the extraction procedure and combining NMR and GC-MS techniques to overcome the low NMR sensitivity and the different detected range limits of NMR and GC-MS.•We explored metabolome diversity in a tropical strain of the small cells' diatom Cheatoceros tenuissimus.

Identification and structural characterization of a novel (+)-catechin-caffeic acid adduct present in wines

A new compound with a molecular ion mass of m/z 467 in the negative ion mode was found to occur in a white wine aged 30 months in bottle. In this latter, fragment ions compatible with the loss of a carboxylic acid (-44 a.m.u.), a caffeic acid unit (-178 a.m.u.), and a Retro-Diels Alder (-152 a.m.u.) were observed. The present work reports the synthesis of a (+)-catechin-caffeic acid adduct resulting from the condensation reaction between caffeic acid and (+)-catechin. The structural characterization by NMR showed that this adduct is formed by the linkage between carbon 8 at ring A from (+)-catechin and carbon 9 from caffeic acid. In addition, the similarity in the HPLC retention time and UV-Visible spectra of the synthesized compound with the one detected in white wine and the bottling experiments, confirms the presence of this novel (+)-catechin-derived compound in those matrices.

NMR characterization of uniformly 13C- and/or 15N-labeled, unsulfated chondroitins with high molecular weights

Solution nuclear magnetic resonance (NMR) analysis of polysaccharides can provide valuable information not only on their primary structures but also on their conformation, dynamics, and interactions under physiological conditions. One of the main problems is that non-anomeric 1H signals typically overlap, and this often hinders detailed NMR analysis. Isotope enrichment, such as with 13C and 15N, will add a new dimension to the NMR spectra of polysaccharides, and spectral analysis can be performed with enhanced sensitivity using isolated peaks. For this purpose, here we have prepared uniformly 13C- and/or 15N-labeled chondroitin polysaccharides -4)-β-D-glucuronopyranosyl-(1-3)-2-acetamido-2-deoxy-β-D-galactopyranosyl-(1- with molecular weights in the range from 310 to 460 k by bacterial fermentation. The enrichment ratios for 13C and 15N were 98.9 and 99.8%, respectively, based on the mass spectrometric analysis of the constituent chondroitin disaccharides. 1H and 13C NMR signals were assigned mainly based on HSQC and 13C-detection experiments including INADEQUATE, HETCOR, and HETCOR-TOCSY. The carbonyl carbon signal of the N-acetyl-β-D-galactosamine residue was unambiguously distinguished from the C6 carbon of the β-D-glucuronic acid residue by the observation of 13C peak splitting due to 1JCN coupling in 13C- and 15N-labeled chondroitin. The T2* and T1 were measured and indicate that both rigid and mobile sites are present in the long sequence of chondroitin. The conformation, dynamics, and interactions of chondroitin and its derivatives will be further analyzed based on the results obtained in this study.

DNA binding reveals hidden interdomain allostery of a MazE antitoxin from Mycobacterium tuberculosis

Type II toxin-antitoxin (TA) systems are ubiquitously distributed genetic elements in prokaryotes and are crucial for cell maintenance and survival under environmental stresses. The antitoxin is a modular protein consisting of the disordered C-terminal region that physically contacts and neutralizes the cognate toxin and the well-folded N-terminal DNA binding domain responsible for autorepression of TA transcription. However, how the two functional domains communicate is largely unknown. Herein, we determined the crystal structure of the N-terminal domain of the type II antitoxin MazE-mt10 from Mycobacterium tuberculosis, revealing a homodimer of the ribbon-helix-helix (RHH) fold with distinct DNA binding specificity. NMR studies demonstrated that full-length MazE-mt10 forms the helical and coiled states in equilibrium within the C-terminal region, and that helical propensity is allosterically enhanced by the N-terminal binding to the cognate operator DNA. This coil-to-helix transition may promote toxin binding/neutralization of MazE-mt10 and further stabilize the TA-DNA transcription repressor. This is supported by many crystal structures of type II TA complexes in which antitoxins form an α-helical structure at the TA interface. The hidden helical state of free MazE-mt10 in solution, favored by DNA binding, adds a new dimension to the regulatory mechanism of type II TA systems. Furthermore, complementary approaches using X-ray crystallography and NMR allow us to study the allosteric interdomain interplay of many other full-length antitoxins of type II TA systems.

Determination of fatty acid uptake and desaturase activity in mammalian cells by NMR-based stable isotope tracing

BACKGROUND

Mammalian cells both import exogenous fatty acids and synthesize them de novo. Palmitate, the end product of fatty acid synthase (FASN) is a substrate for stearoyl-CoA desaturases (Δ-9 desaturases) that introduce a single double bond into fatty acyl-CoA substrates such as palmitoyl-CoA and stearoyl-CoA. This process is particularly upregulated in lipogenic tissues and cancer cells. Tracer methodology is needed to determine uptake versus de novo synthesis of lipids and subsequent chain elongation and desaturation. Here we describe an NMR method to determine the uptake of 13C-palmitate from the medium into HCT116 human colorectal cancer cells, and the subsequent desaturation and incorporation into complex lipids.

RESULTS

Exogenous 13C16-palmitate was absorbed from the medium by HCT116 cells and incorporated primarily into complex glycerol lipids. Desaturase activity was determined from the quantification of double bonds in acyl chains, which was greatly reduced by ablation of the major desaturase SCD1.

SIGNIFICANCE

The NMR approach requires minimal sample preparation, is non-destructive, and provides direct information about the level of saturation and incorporation of fatty acids into complex lipids.

Morphology and thermal transitions of self-assembled NIPAM-DMA copolymers in aqueous media depend on copolymer composition profile

HYPOTHESIS

There is a lack of understanding of the interplay between the copolymer composition profile and thermal transition observed in aqueous solutions of N-isopropyl acrylamide (NIPAM) copolymers, as well as the correlation between this transition and the formation and structure of copolymer self-assemblies.

EXPERIMENTS

For this purpose, we investigated the response of five copolymers with the same molar mass and chemical composition, but with different composition profile in aqueous solution against temperature. Using complementary analytical techniques, we probed structural properties at different length scales, from the molecular scale with Nuclear Magnetic Resonance (NMR) to the colloidal scale with Dynamic Light Scattering (DLS) and Small Angle Neutron Scattering (SANS).

FINDINGS

NMR and SANS investigations strengthen each other and allow a clear picture of the change of copolymer solubility and related copolymer self-assembly as a function of temperature. At the molecular scale, dehydrating NIPAM units drag N,N-dimethyl acrylamide (DMA) moieties with them in a gradual collapse of the copolymer chain; this induces a morphological transition of the self-assemblies from star-like nanostructures to crew-cut micelles. Interestingly, the transition spans a temperature range which depends on the monomer distribution profile in the copolymer chain, with the asymmetric triblock copolymer specimen revealing the broadest one. We show that the broad morphological transitions associated with gradient copolymers can be mimicked and even surpassed by the use of stepwise gradient (asymmetric) copolymers, which can be more easily and reproducibly synthesized than linear gradient copolymers.

Permethylation as a strategy for high-molecular-weight polysaccharide structure analysis by nuclear magnetic resonance-Case study of Xylella fastidiosa extracellular polysaccharide

Current practices for structural analysis of extremely large-molecular-weight polysaccharides via solution-state nuclear magnetic resonance (NMR) spectroscopy incorporate partial depolymerization protocols that enable polysaccharide solubilization in suitable solvents. Non-specific depolymerization techniques utilized for glycosidic bond cleavage, such as chemical degradation or ultrasonication, potentially generate structural fragments that can complicate complete and accurate characterization of polysaccharide structures. Utilization of appropriate enzymes for polysaccharide degradation, on the other hand, requires prior structural knowledge and optimal enzyme activity conditions that are not available to an analyst working with novel or unknown compounds. Herein, we describe an application of a permethylation strategy that allows the complete dissolution of intact polysaccharides for NMR structural characterization. This approach is utilized for NMR analysis of Xylella fastidiosa extracellular polysaccharide (EPS), which is essential for the virulence of the plant pathogen that affects multiple commercial crops and is responsible for multibillion dollar losses each year.

Characterization of fatty acid forms using benchtop NMR in omega-3 oil supplements

Omega-3 fatty acid supplements, such as fish oil and plant-based oils, have gained popularity because of their potential health benefits. However, the quality and composition of these supplements can vary widely, particularly in terms of the two main forms of omega-3 fatty acids: triacylglycerols (TAGs) and ethyl esters (EEs). TAGs are the natural form found in fish oil but are prone to oxidation, whereas EEs are more stable but less well absorbed by the body. Differentiating between these forms is crucial for assessing the efficacy and tolerance of omega-3 supplements. This article describes a novel approach to differentiate between TAG and EE forms of omega-3 fatty acids in dietary supplements, utilizing a 60-MHz benchtop nuclear magnetic resonance (NMR) spectrometer. The proposed method using 1H and 1H-1H COSY NMR provides a quick and accurate approach to screen the forms of omega-3 fatty acids and evaluate their ratios. The presence of diacylglycerol (DAGs) in some supplements was also highlighted by this method and adds some information about the process used (i.e., esterification/enrichment). The affordability and user-friendliness of benchtop NMR equipment make this method feasible for food processing companies or quality control laboratories. In this study, 24 oil supplements were analyzed using NMR analysis in order to demonstrate the potential of this method for the differentiation of TAG and EE forms in omega-3 supplements.

Transient interdomain interactions in free USP14 shape its conformational ensemble

The deubiquitinase (DUB) ubiquitin-specific protease 14 (USP14) is a dual domain protein that plays a regulatory role in proteasomal degradation and has been identified as a promising therapeutic target. USP14 comprises a conserved USP domain and a ubiquitin-like (Ubl) domain separated by a 25-residue linker. The enzyme activity of USP14 is autoinhibited in solution, but is enhanced when bound to the proteasome, where the Ubl and USP domains of USP14 bind to the Rpn1 and Rpt1/Rpt2 units, respectively. No structure of full-length USP14 in the absence of proteasome has yet been presented, however, earlier work has described how transient interactions between Ubl and USP domains in USP4 and USP7 regulate DUB activity. To better understand the roles of the Ubl and USP domains in USP14, we studied the Ubl domain alone and in full-length USP14 by nuclear magnetic resonance spectroscopy and used small angle x-ray scattering and molecular modeling to visualize the entire USP14 protein ensemble. Jointly, our results show how transient interdomain interactions between the Ubl and USP domains of USP14 predispose its conformational ensemble for proteasome binding, which may have functional implications for proteasome regulation and may be exploited in the design of future USP14 inhibitors.

Challenges and opportunities in elucidating the structures of biofilm exopolysaccharides: A case study of the Pseudomonas aeruginosa exopolysaccharide called Pel

Biofilm formation protects bacteria from antibiotic treatment and host immune responses, making biofilm infections difficult to treat. Within biofilms, bacterial cells are entangled in a self-produced extracellular matrix that typically includes exopolysaccharides. Molecular-level descriptions of biofilm matrix components, especially exopolysaccharides, have been challenging to attain due to their complex nature and lack of solubility and crystallinity. Solid-state nuclear magnetic resonance (NMR) has emerged as a key tool to determine the structure of biofilm matrix exopolysaccharides without degradative sample preparation. In this review, we discuss challenges of studying biofilm matrix exopolysaccharides and opportunities to develop solid-state NMR approaches to study these generally intractable materials. We specifically highlight investigations of the exopolysaccharide called Pel made by the opportunistic pathogen, Pseudomonas aeruginosa. We provide a roadmap for determining exopolysaccharide structure and discuss future opportunities to study such systems using solid-state NMR. The strategies discussed for elucidating biofilm exopolysaccharide structure should be broadly applicable to studying the structures of other glycans.

Associations of birth weight, plasma metabolome in adulthood and risk of type 2 diabetes

AIMS

We aimed to examine the longitudinal associations of birth weight with plasma metabolites in adulthood, and further quantify the proportions of the links between birth weight and incident adult type 2 diabetes (T2D) that were mediated by plasma metabolites.

MATERIALS AND METHODS

A total of 62,033 participants with complete nuclear magnetic resonance metabolomics and birth weight data from the UK Biobank were included in this study. Linear regression was used to assess the associations between birth weight and metabolites. Cox regression was used to estimate hazard ratios for T2D associated with metabolites. We further performed mediation analyses to estimate the extent to which metabolites might mediate the association between birth weight and T2D risk.

RESULTS

Low birth weight was associated with the adverse metabolic responses across multiple metabolic pathways, including lipoprotein subclasses, amino acids, fatty acids (FA), and inflammation. Metabolites associated with higher birth weight tended to be associated with a lower risk of T2D (Pearson correlation coefficient: -0.85). A total of 62 metabolites showed statistically significant mediation effects in the protective association of higher birth weight and T2D risk, including large-sized very low-density lipoprotein particles and triglyceride concentrations as well as saturated, and monounsaturated FA and glycoprotein acetyls.

CONCLUSIONS

We identified a range of metabolites that reflect the adult metabolic response to birth weight, some of which might lie on the pathway between birth weight and adult T2D risk.

How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins

Despite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self-avoiding random walks (SARWs) under physiological conditions. Here, we tested how temperature and ionic conditions influence the dimensions of the N-terminal domain of pertactin (PNt), an IDP with an amino acid composition typical of folded proteins. While PNt contracts somewhat with temperature, it nevertheless remains expanded over 10-58°C, with a Flory exponent, ν, >0.50. Both low and high ionic strength also produce contraction in PNt, but this contraction is mitigated by reducing charge segregation. With 46% glycine and low hydrophobicity, the reduced form of snow flea anti-freeze protein (red-sfAFP) is unaffected by temperature and ionic strength and persists as a near-SARW, ν ~ 0.54, arguing that the thermal contraction of PNt is due to stronger interactions between hydrophobic side chains. Additionally, red-sfAFP is a proxy for the polypeptide backbone, which has been thought to collapse in water. Increasing the glycine segregation in red-sfAFP had minimal effect on ν. Water remained a good solvent even with 21 consecutive glycine residues (ν > 0.5), and red-sfAFP variants lacked stable backbone hydrogen bonds according to hydrogen exchange. Similarly, changing glycine segregation has little impact on ν in other glycine-rich proteins. These findings underscore the generality that many disordered states can be expanded and unstructured, and that the hydrophobic effect alone is insufficient to drive significant chain collapse for typical protein sequences.

Uptake of vanadium and its intracellular metabolism by Coprinellus truncorum mycelial biomass

BACKGROUND

Fungi absorb and solubilize a broad spectrum of heavy metals such as vanadium (V), which makes them a main route of its entry into the biosphere. V as vanadate (V5+) is a potential medical agent due to its many metabolic actions such as interaction with phosphates in the cell, and especially its insulin-mimetic activity. Antidiabetic activity of V-enriched fungi has been studied in recent years, but the biological and chemical bases of vanadium action and status in fungi in general are poorly understood, with almost no information on edible fungi.

METHODS

This manuscript gives a deeper insight into the interaction of V5+ with Coprinellus truncorum, an edible autochthonous species widely distributed in Europe and North America. Vanadium uptake and accumulation as V5+ was studied by 51V NMR, while the reducing abilities of the mycelium were determined by EPR. 31P NMR was used to determine its effects on the metabolism of phosphate compounds, with particular focus on phosphate sugars identified using HPLC.

RESULTS

Vanadate enters the mycelium in monomeric form and shows no immediate detrimental effects on intracellular pH or polyphosphate (PPc) levels, even when applied at physiologically high concentrations (20 mM Na3VO4). Once absorbed, it is partially reduced to less toxic vanadyl (V4+) with notable unreduced portion, which leads to a large increase in phosphorylated sugar levels, especially glucose-1-phosphate (G1P) and fructose-6-phosphate (F6P).

CONCLUSIONS

Preservation of pH and especially PPc reflects maintenance of the energy status of the mycelium, i.e., its tolerance to high V5+ concentrations. Rise in G1P and F6P levels implies that the main targets of V5+ are most likely phosphoglucomutase and phosphoglucokinase(s), enzymes involved in early stages of G6P transformation in glycolysis and glycogen metabolism. This study recommends C. truncorum for further investigation as a potential antidiabetic agent.

Myotubularin-related-protein-7 inhibits mutant (G12V) K-RAS by direct interaction

Inhibition of K-RAS effectors like B-RAF or MEK1/2 is accompanied by treatment resistance in cancer patients via re-activation of PI3K and Wnt signaling. We hypothesized that myotubularin-related-protein-7 (MTMR7), which inhibits PI3K and ERK1/2 signaling downstream of RAS, directly targets RAS and thereby prevents resistance. Using cell and structural biology combined with animal studies, we show that MTMR7 binds and inhibits RAS at cellular membranes. Overexpression of MTMR7 reduced RAS GTPase activities and protein levels, ERK1/2 phosphorylation, c-FOS transcription and cancer cell proliferation in vitro. We located the RAS-inhibitory activity of MTMR7 to its charged coiled coil (CC) region and demonstrate direct interaction with the gastrointestinal cancer-relevant K-RASG12V mutant, favouring its GDP-bound state. In mouse models of gastric and intestinal cancer, a cell-permeable MTMR7-CC mimicry peptide decreased tumour growth, Ki67 proliferation index and ERK1/2 nuclear positivity. Thus, MTMR7 mimicry peptide(s) could provide a novel strategy for targeting mutant K-RAS in cancers.

The Fundamental Disorder Unit in (Si, P)-(O, N) Networks

This study presents the synthesis and characterization of oxonitridosilicate phosphates Sr3SiP3O2N7, Sr5Si2P4ON12, and Sr16Si9P9O7N33 as the first of their kind. These compounds were synthesized under high-temperature (1400 °C) and high-pressure (3 GPa) conditions. A unique structural feature is their common fundamental building unit, a vierer single chain of (Si, P)(O, N)4 tetrahedra. All tetrahedra comprise substitutional disorder which is why we refer to it as the fundamental disorder unit (FDU). We classified four different FDU motifs, revealing systematic bonding patterns. Including literature known Sr5Si2P6N16, three of the four patterns were found in the presented compounds. Common techniques like single-crystal X-ray diffraction (SCXRD), elemental analyses, and 31P nuclear magnetic resonance (NMR) spectroscopy were utilized for structural analysis. Additionally, low-cost crystallographic calculations (LCC) provided insights into the structure of Sr16Si9P9O7N33 where NMR data were unavailable due to the lack of bulk samples. The optical properties of these compounds, when doped with Eu2+, were investigated using photoluminescence excitation (PLE), photoluminescence (PL) measurements, and density functional theory (DFT) calculations. Factors influencing the emission properties, including thermal quenching mechanisms, were discussed. This research reveals the new class of oxonitridosilicate phosphates with unique systematic structural features that offer potential for theoretical studies of luminescence and band gap tuning in insulators.

Solution NMR chemical shift assignment of apo and molybdate-bound ModA at two pHs

ModA is a soluble periplasmic molybdate-binding protein found in most gram-negative bacteria. It is part of the ABC transporter complex ModABC that moves molybdenum into the cytoplasm, to be used by enzymes that carry out various redox reactions. Since there is no clear analog for ModA in humans, this protein could be a good target for antibacterial drug design. Backbone 1H, 13C and 15N chemical shifts of apo and molybdate-bound ModA from E. coli were assigned at pHs 6.0 and 4.5. In addition, side chain atoms were assigned for apo ModA at pH 6.0. When comparing apo and molybdate-bound ModA at pH 6.0, large chemical shift perturbations are observed, not only in areas near the bound metal, but also in regions that are distant from the metal-binding site. Given the significant conformational change between apo and holo ModA, we might expect the large chemical shift changes to be more widespread; however, since they are limited to specific regions, the residues with large perturbations may reveal allosteric sites that could ultimately be important for the design of antibiotics that target ModA.

NMR metabolomic modeling of age and lifespan: A multicohort analysis

Metabolomic age models have been proposed for the study of biological aging, however, they have not been widely validated. We aimed to assess the performance of newly developed and existing nuclear magnetic resonance spectroscopy (NMR) metabolomic age models for prediction of chronological age (CA), mortality, and age-related disease. Ninety-eight metabolic variables were measured in blood from nine UK and Finnish cohort studies (N ≈31,000 individuals, age range 24-86 years). We used nonlinear and penalized regression to model CA and time to all-cause mortality. We examined associations of four new and two previously published metabolomic age models, with aging risk factors and phenotypes. Within the UK Biobank (N ≈102,000), we tested prediction of CA, incident disease (cardiovascular disease (CVD), type-2 diabetes mellitus, cancer, dementia, and chronic obstructive pulmonary disease), and all-cause mortality. Seven-fold cross-validated Pearson's r between metabolomic age models and CA ranged between 0.47 and 0.65 in the training cohort set (mean absolute error: 8-9 years). Metabolomic age models, adjusted for CA, were associated with C-reactive protein, and inversely associated with glomerular filtration rate. Positively associated risk factors included obesity, diabetes, smoking, and physical inactivity. In UK Biobank, correlations of metabolomic age with CA were modest (r = 0.29-0.33), yet all metabolomic model scores predicted mortality (hazard ratios of 1.01 to 1.06/metabolomic age year) and CVD, after adjustment for CA. While metabolomic age models were only moderately associated with CA in an independent population, they provided additional prediction of morbidity and mortality over CA itself, suggesting their wider applicability.

A unique chaperoning mechanism in class A JDPs recognizes and stabilizes mutant p53

J-domain proteins (JDPs) constitute a large family of molecular chaperones that bind a broad spectrum of substrates, targeting them to Hsp70, thus determining the specificity of and activating the entire chaperone functional cycle. The malfunction of JDPs is therefore inextricably linked to myriad human disorders. Here, we uncover a unique mechanism by which chaperones recognize misfolded clients, present in human class A JDPs. Through a newly identified β-hairpin site, these chaperones detect changes in protein dynamics at the initial stages of misfolding, prior to exposure of hydrophobic regions or large structural rearrangements. The JDPs then sequester misfolding-prone proteins into large oligomeric assemblies, protecting them from aggregation. Through this mechanism, class A JDPs bind destabilized p53 mutants, preventing clearance of these oncoproteins by Hsp70-mediated degradation, thus promoting cancer progression. Removal of the β-hairpin abrogates this protective activity while minimally affecting other chaperoning functions. This suggests the class A JDP β-hairpin as a highly specific target for cancer therapeutics.

Pectic-AGP is a major form of Arabidopsis AGPs

As a key component in cell walls of numerous organisms ranging from green algae to higher plants, AGPs play principal roles in many biological processes such as cell-cell adhesion and regulating Ca2+ signaling pathway as a Ca2+-capacitor. Consistently, AGP structures vary from species to species and from tissue to tissue. To understand the functions of AGPs, it is vital to know their structural differences relative to their location in the plant. Thus, AGPs were purified from different Arabidopsis tissues. Analyses of these AGPs demonstrated that the AGPs comprised covalently linked pectin and AGP, referred to as pectic-AGPs. Importantly, these pectic-AGPs were glycosylated with a remarkable variety of polysaccharides including homogalacturonan, rhamnogalacturonan-I, and type II arabinogalactan at different ratios and lengths. This result not only suggests that pectic-AGP is a major form of Arabidopsis AGPs, but also supports AGPs serve as crosslinkers covalently connecting pectins with structures tailored for tissue-specific functions.

Synthesis of Rupestonic Acid L-Ephedrine Derivatives with Preliminary In vitro Anti-influenza Viral Activity

BACKGROUND

Influenza virus is a kind of RNA virus. Nowadays, the high incidence of influenza and the morbidity and mortality of epidemic influenza are substantial. It has been reported that one hundred million people in the world are infected with influenza viruses, and two hundred and fifty thousand to five hundred thousand people die from the flu per year. In 2021, the number of infected persons in China was reported to be 654,700, and 0.07% of the infected persons died. The flu has caused a serious threat to human survival. Although several drugs, such as Zanamivir, Oseltamivir, Peramivir, and Laninamivir, have been used in clinics for the treatment of the influenza virus, there are some shortcomings of these drugs. The strain of influenza H5N1 (avian influenza) has been found to resist the effective drug Oseltamivir. Thus, there is an urgent demand to discover new anti-influenza virus inhibitors to overcome the emergence of influenza antigens.

AIMS

This study aimed to develop new anti-influenza virus inhibitors based on the rupestonic acid parent core.

OBJECTIVE

The rupestonic acid L-ephedrine ester (A) and rupestonic acid L-ephedrine complex (B) were synthesized in this work for the development of anti-influenza virus inhibitors.

METHODS

The target compounds were synthesized using rupestonic acid and L-ephedrine as starting materials. Their structures were characterized by 1H NMR and 13C NMR, and the purity was determined by HPLC. Then, their preliminary in vitro anti-influenza activity was evaluated using Oseltamivir as a reference drug.

RESULTS

The results showed that the synthesized rupestonic acid L-ephedrine derivatives A and B were more potent anti-influenza virus agents against the strains of A/PR/8/34 (H1N1) and A/FM/1/47 (H1N1) with the IC50 values of 51.0, 51.0 μM and 441.0, 441.0 μM, respectively, than that of rupestonic acid. By comparing the IC50 of compounds A and B, compound A can be regarded as a very promising lead compound for the development of anti-influenza inhibitors.

CONCLUSION

The rupestonic acid L-ephedrine ester (A) and rupestonic acid L-ephedrine complex (B) were synthesized and characterized using 1H NMR and 13C NMR. Moreover, their purity was determined by HPLC. Both compounds A and B exhibited more potent activities against the strains of A/PR/8/34 (H1N1) and A/FM/1/47 (H1N1) than rupestonic acid. Compound A can be regarded as a very promising lead compound for the development of anti-influenza inhibitors. Based on these results, more rupestonic acid derivatives will be designed and synthesized in the future for the development of anti-influenza inhibitors.

1H-NMR-based urine metabolomics of prostate cancer and benign prostatic hyperplasia

Background

Prostate cancer (PCa) and benign prostatic hyperplasia (BPH) are prevalent conditions affecting a significant portion of the male population, particularly with advancing age. Traditional diagnostic methods, such as digital rectal examination (DRE) and prostate-specific antigen (PSA) tests, have limitations in specificity and sensitivity, leading to potential overdiagnosis and unnecessary biopsies.

Significance

This study explores the effectiveness of 1H NMR urine metabolomics in distinguishing PCa from BPH and in differentiating various PCa grades, presenting a non-invasive diagnostic alternative with the potential to enhance early detection and patient-specific treatment strategies.

Results

The study demonstrated the capability of 1H NMR urine metabolomics in detecting distinct metabolic profiles between PCa and BPH, as well as among different Gleason grade groups. Notably, this method surpassed the PSA test in distinguishing PCa from BPH. Untargeted metabolomics analysis also revealed several metabolites with varying relative concentrations between PCa and BPH cases, suggesting potential biomarkers for these conditions.

Increasing the complexity of lipoprotein characterization for cardiovascular risk in type 2 diabetes

The burden of cardiovascular disease is particularly high among individuals with diabetes, even when LDL cholesterol is normal or within the therapeutic target. Despite this, cholesterol accumulates in their arteries, in part, due to persistent atherogenic dyslipidaemia characterized by elevated triglycerides, remnant cholesterol, smaller LDL particles and reduced HDL cholesterol. The causal link between dyslipidaemia and atherosclerosis in T2DM is complex, and our contention is that a deeper understanding of lipoprotein composition and functionality, the vehicle that delivers cholesterol to the artery, will provide insight for improving our understanding of the hidden cardiovascular risk of diabetes. This narrative review covers three levels of complexity in lipoprotein characterization: 1-the information provided by routine clinical biochemistry, 2-advanced nuclear magnetic resonance (NMR)-based lipoprotein profiling and 3-the identification of minor components or physical properties of lipoproteins that can help explain arterial accumulation in individuals with normal LDLc levels, which is typically the case in individuals with T2DM. This document highlights the importance of incorporating these three layers of lipoprotein-related information into population-based studies on ASCVD in T2DM. Such an attempt should inevitably run in parallel with biotechnological solutions that allow large-scale determination of these sets of methodologically diverse parameters.

LDHB contributes to the regulation of lactate levels and basal insulin secretion in human pancreatic β cells

Using 13C6 glucose labeling coupled to gas chromatography-mass spectrometry and 2D 1H-13C heteronuclear single quantum coherence NMR spectroscopy, we have obtained a comparative high-resolution map of glucose fate underpinning β cell function. In both mouse and human islets, the contribution of glucose to the tricarboxylic acid (TCA) cycle is similar. Pyruvate fueling of the TCA cycle is primarily mediated by the activity of pyruvate dehydrogenase, with lower flux through pyruvate carboxylase. While the conversion of pyruvate to lactate by lactate dehydrogenase (LDH) can be detected in islets of both species, lactate accumulation is 6-fold higher in human islets. Human islets express LDH, with low-moderate LDHA expression and β cell-specific LDHB expression. LDHB inhibition amplifies LDHA-dependent lactate generation in mouse and human β cells and increases basal insulin release. Lastly, cis-instrument Mendelian randomization shows that low LDHB expression levels correlate with elevated fasting insulin in humans. Thus, LDHB limits lactate generation in β cells to maintain appropriate insulin release.

Structures and Dynamics of Complex Guest Molecules in Confinement, Revealed by Solid-State NMR, Molecular Dynamics, and Calorimetry

This review gives an overview of current trends in the investigation of confined molecules such as water, small and higher alcohols, carbonic acids, ethylene glycol, and non-ionic surfactants, such as polyethylene glycol or Triton-X, as guest molecules in neat and functionalized mesoporous silica materials employing solid-state NMR spectroscopy, supported by calorimetry and molecular dynamics simulations. The combination of steric interactions, hydrogen bonds, and hydrophobic and hydrophilic interactions results in a fascinating phase behavior in the confinement. Combining solid-state NMR and relaxometry, DNP hyperpolarization, molecular dynamics simulations, and general physicochemical techniques, it is possible to monitor these confined molecules and gain deep insights into this phase behavior and the underlying molecular arrangements. In many cases, the competition between hydrogen bonding and electrostatic interactions between polar and non-polar moieties of the guests and the host leads to the formation of ordered structures, despite the cramped surroundings inside the pores.

The molecular basis of Abelson kinase regulation by its αI-helix

Abelson tyrosine kinase (Abl) is regulated by the arrangement of its regulatory core, consisting sequentially of the SH3, SH2, and kinase (KD) domains, where an assembled or disassembled core corresponds to low or high kinase activity, respectively. It was recently established that binding of type II ATP site inhibitors, such as imatinib, generates a force from the KD N-lobe onto the SH3 domain and in consequence disassembles the core. Here, we demonstrate that the C-terminal αI-helix exerts an additional force toward the SH2 domain, which correlates both with kinase activity and type II inhibitor-induced disassembly. The αI-helix mutation E528K, which is responsible for the ABL1 malformation syndrome, strongly activates Abl by breaking a salt bridge with the KD C-lobe and thereby increasing the force onto the SH2 domain. In contrast, the allosteric inhibitor asciminib strongly reduces Abl's activity by fixating the αI-helix and reducing the force onto the SH2 domain. These observations are explained by a simple mechanical model of Abl activation involving forces from the KD N-lobe and the αI-helix onto the KD/SH2SH3 interface.

Structural determinants for membrane binding of the EGFR juxtamembrane domain

Overactivation of the epidermal growth factor receptor (EGFR) is critical for the development of multiple cancers. Previous studies have shown that the cell membrane is a key regulator of EGFR kinase activity through its interaction with the EGFR juxtamembrane domain (JM). However, the lipid recognition specificity of EGFR-JM and its interaction details remain unclear. Using lipid strip and liposome pulldown assays, we showed that EGFR-JM could specifically interact with PI(4,5)P2-or phosphatidylserine-containing membranes. We further characterized the JM-membrane interaction using NMR-titration-based chemical shift perturbation and paramagnetic relaxation enhancement analyses, and found that residues I649 - L659 comprised the membrane-binding site. Furthermore, the membrane-binding region contains the predicted dimerization motif of JM, 655LRRLL659, suggesting that membrane binding may affect JM dimerization and, therefore, regulate kinase activation.

Direct Observation of Polaritonic Chemistry by Nuclear Magnetic Resonance Spectroscopy

Polaritonic chemistry is emerging as a powerful approach to modifying the properties and reactivity of molecules and materials. However, probing how the electronics and dynamics of molecular systems change under strong coupling has been challenging due to the narrow range of spectroscopic techniques that can be applied in situ. Here we develop microfluidic optical cavities for vibrational strong coupling (VSC) that are compatible with nuclear magnetic resonance (NMR) spectroscopy using standard liquid NMR tubes. VSC is shown to influence the equilibrium between two conformations of a molecular balance sensitive to London dispersion forces, revealing an apparent change in the equilibrium constant under VSC. In all compounds studied, VSC does not induce detectable changes in chemical shifts, J-couplings, or spin-lattice relaxation times. This unexpected finding indicates that VSC does not substantially affect molecular electron density distributions, and in turn has profound implications for the possible mechanisms at play in polaritonic chemistry under VSC and suggests that the emergence of collective behavior is critical.

Application of an NMR/crystallography fragment screening platform for the assessment and rapid discovery of new HIV-CA binding fragments

Identification and assessment of novel targets is essential to combat drug resistance in the treatment of HIV/AIDS. HIV Capsid (HIV-CA), the protein playing a major role in both the early and late stages of the viral life cycle, has emerged as an important target. We have applied an NMR fragment screening platform and identified molecules that bind to the N-terminal domain (NTD) of HIV-CA at a site close to the interface with the C-terminal domain (CTD). Using X-ray crystallography, we have been able to obtain crystal structures to identify the binding mode of these compounds. This allowed for rapid progression of the initial, weak binding, fragment starting points to compounds 37 and 38, which have 19F-pKi values of 5.3 and 5.4 respectively.

C19-diterpene alkaloids from delphinium turkmenum lipsky

The genus Delphinium is a rich source of diterpene alkaloids. Chemical investigation on an alkaloid rich extract of the whole parts of Delphinium turkmenum resulted in the isolation of three C19-diterpene alkaloids (1-3) and a palmitic acid derivative (4). The chemical structures were elucidated by analysis of 1D and 2D-NMR and comparison the data with those reported in the literature. Notably, all isolated compounds were reported for the first time from D. turkmenum.

Antimicrobial macrozones interact with biological macromolecules via two-site binding mode of action: Fluorimetric, NMR and docking studies

Macrozones are novel conjugates of azithromycin and thiosemicarbazones, which exhibit very good in vitro antibacterial activities against susceptible and some resistant bacterial strains thus showing a potential for further development. A combination of spectrometric (fluorimetry, STD and WaterLOGSY NMR) and molecular docking studies provided insights into atomic details of interactions between selected macrozones and biological receptors such as E. coli ribosome and bovine serum albumin. Fluorimetric measurements revealed binding constants in the micro-molar range while NMR experiments provided data on binding epitopes. It has been demonstrated that both STD and WaterLOGSY gave comparable and consistent results unveiling atoms in intimate contacts with biological receptors. Docking studies pointed towards main interactions between macrozones and E. coli ribosome which included specific π - π stacking and hydrogen bonding interactions with thiosemicarbazone part extending down the ribosome exit tunnel. The results of the docking experiments were in fine correlation with those obtained by NMR and fluorimetry. Our investigation pointed towards a two-site binding mechanism of interactions between macrozones and E. coli ribosome which is the most probable reason for their activity against azithromycin-resistant strains. Much better activity of macrozone-nickel coordinated compound against E. coli ribosome compared to other macrozones has been attributed to the higher polarity which enabled better bacterial membrane penetration and binding of the two thiosemicarbazone units thus additionally contributing to the overall binding energy. The knowledge gained in this study should play an important role in anti-infective macrolide design in the future.

Purification of andibenin and a chromanone analogue from rhizospheric Aspergillus flavus and soil-borne Penicillium notatum exhibiting cytotoxic and antibacterial properties

The discovery of bioactive compounds from fungal natural sources holds immense potential for the development of novel therapeutics. The present study investigates the extracts of soil-borne Penicillium notatum and rhizosphere-inhabiting Aspergillus flavus for their antibacterial, antifungal, and cytotoxic potential. Additionally, two compounds were purified using chromatographic and spectroscopic techniques. The results demonstrated that the ethyl acetate fraction of A. flavus exhibited prominent cytotoxic activity against Artemia salina, whereas the ethyl acetate fraction of P. notatum displayed promising antibacterial potential. At dose concentrations of 10, 100, and 1000 µg mL-1, the ethyl acetate fraction of A. flavus showed mortality percentages of 7.6%, 66.4%, and 90%, respectively. The ethyl acetate fraction of P. notatum extract exhibited significant antibacterial activity, forming inhibition zones measuring 41, 38, 34, 34, and 30 mm against B. subtilis, S. flexneri, E. coli, K. pneumoniae, and S. aureus, respectively, at 1000 µg mL-1. At this concentration, inhibition zones of 28, 27, and 15 mm were recorded for P. vulgaris, S. typhi, and X. oryzae. Using bioassay-guided approach, one compound each was purified from the fungal extracts. The initial purification involved mass spectroscopic analysis, followed by structural elucidation using 500 MHz nuclear magnetic resonance (NMR) spectroscopy. Compound 1, derived from A. flavus, was identified as ethyl 2-hydroxy-5,6-dimethyl-4-oxocyclohex-2-ene-1-carboxylate, with a mass of 212, whereas compound 2, isolated from P. notatum, was identified as 3-amino-2-(cyclopenta-2,4-dien-1-ylamino)-8-methoxy-4H-chromen-4-one, with an exact mass of 270. Based on bioassay results, compound 1 was subjected to brine shrimp lethality assay and compound 2 was tested for its antibacterial potential. Compound 1 exhibited 30% lethality against brine shrimp larvae at a concentration of 100 µg mL-1, whereas at 1000 µg mL-1 the mortality increased to 70%. Compound 2 displayed notable antibacterial potential, forming inhibition zones of 30, 24, 19, and 12 mm against S. aureus, E. coli, B. subtilis, and S. flexneri, respectively. In comparison, the standard antibiotic tetracycline produced inhibition zones of 18, 18, 15, and 10 mm against the respective bacterial strains at the same concentration.

Plant-Derived Caffeic Acid and Its Derivatives: An Overview of Their NMR Data and Biosynthetic Pathways

In recent years, caffeic acid and its derivatives have received increasing attention due to their obvious physiological activities and wide distribution in nature. In this paper, to clarify the status of research on plant-derived caffeic acid and its derivatives, nuclear magnetic resonance spectroscopy data and possible biosynthetic pathways of these compounds were collected from scientific databases (SciFinder, PubMed and China Knowledge). According to different types of substituents, 17 caffeic acid and its derivatives can be divided into the following classes: caffeoyl ester derivatives, caffeyltartaric acid, caffeic acid amide derivatives, caffeoyl shikimic acid, caffeoyl quinic acid, caffeoyl danshens and caffeoyl glycoside. Generalization of their 13C-NMR and 1H-NMR data revealed that acylation with caffeic acid to form esters involves acylation shifts, which increase the chemical shift values of the corresponding carbons and decrease the chemical shift values of the corresponding carbons of caffeoyl. Once the hydroxyl group is ester, the hydrogen signal connected to the same carbon shifts to the low field (1.1~1.6). The biosynthetic pathways were summarized, and it was found that caffeic acid and its derivatives are first synthesized in plants through the shikimic acid pathway, in which phenylalanine is deaminated to cinnamic acid and then transformed into caffeic acid and its derivatives. The purpose of this review is to provide a reference for further research on the rapid structural identification and biofabrication of caffeic acid and its derivatives.

Protocol to identify the ligand binding site of Mincle using NMR spectroscopy

Mincle (macrophage-inducible C-type lectin, CLEC4E) is a C-type lectin immune-stimulatory receptor that can be targeted for inducing potent adjuvant effects. Mincle can recognize trehalose dimycolate and related glycolipids. Here, we present a protocol to identify the ligand binding mode of Mincle. We describe steps for preparing labeled Mincle ectodomain, data acquisition, and analysis of nuclear magnetic resonance experiments using non-detergent sulfobetaine-195. This protocol can be applied to other protein-ligand interactions that have aggregation problems for complex formation. For complete details on the use and execution of this protocol, please refer to Furukawa et al.1.

Proanthocyanidins and Phenolic Compounds from the Twigs of Salix chaenomeloides and Their Anti-Lipogenic Effects on 3T3-L1 Preadipocytes

The present study investigated potential bioactive natural products from the EtOH extract of Salix chaenomeloides twigs using column chromatography, leading to the isolation of six compounds (1-6), which were characterized as two proanthocyanidins, procyanidin B2 (1) and procyanidin B1 (2), and four phenolic compounds, 4-hydroxybenzoic acid β-D-glucosyl ester (3), di-O-methylcrenatin (4), p-coumaric acid glucoside (5), and syringin (6) by the comparison of their NMR spectra with the reported data and high-resolution (HR)-electrospray ionization mass spectroscopy (ESI-MS) analysis. We investigated the potential of six compounds (1-6) to inhibit adipogenesis in 3T3-L1 preadipocytes, which showed that the compounds (1-6) significantly reduced lipid accumulation in 3T3-L1 adipocytes without affecting cell proliferation. Notably, compound 1 demonstrated a remarkable 60% and 90% reduction in lipid levels with 50 and 100 µM treatments, respectively. Oil Red O staining results indicated that compound 1 significantly inhibits the formation of lipid droplets, comparable to the effect of T863, an inhibitor of triglyceride used as a positive control, in adipocytes. Compound 1 had no effect on the regulators PPARγ, C/EBPα, and SREBF1 of adipocyte differentiation in 3T3-L1 preadipocytes, but compound 1 activated the fatty acid oxidation regulator, PPARα, compared to the lipogenic-induced control. It also suppressed fatty acid synthesis by downregulating the expression of fatty acid synthase (FAS). Finally, compound 1 induced the mRNA and protein levels of CPT1A, an initial marker of mitochondrial fatty acid oxidation in 3T3-L1. This finding substantiates the anti-lipogenic and lipolytic effects of procyanidin B2 (1) in 3T3-L1 preadipocytes, emphasizing its pivotal role in modulating obesity-related markers.

Essentials in the acquisition, interpretation, and reporting of plant metabolite profiles

Plant metabolite profiling reveals the diversity of secondary or specialized metabolites in the plant kingdom with its hundreds of thousands of species. Specialized plant metabolites constitute a vast class of chemicals posing significant challenges in analytical chemistry. In order to be of maximum scientific relevance, reports dealing with these compounds and their source species must be transparent, make use of standards and reference materials, and be based on correctly and traceably identified plant material. Essential aspects in qualitative plant metabolite profiling include: (i) critical review of previous literature and a reasoned sampling strategy; (ii) transparent plant sampling with wild material documented by vouchers in public herbaria and, optimally, seed banks; (iii) if possible, inclusion of generally available reference plant material; (iv) transparent, documented state-of-the art chemical analysis, ideally including chemical reference standards; (v) testing for artefacts during preparative extraction and isolation, using gentle analytical methods; (vi) careful chemical data interpretation, avoiding over- and misinterpretation and taking into account phytochemical complexity when assigning identification confidence levels, and (vii) taking all previous scientific knowledge into account in reporting the scientific data. From the current stage of the phytochemical literature, selected comments and suggestions are given. In the past, proposed revisions of botanical taxonomy were sometimes based on metabolite profiles, but this approach ("chemosystematics" or "chemotaxonomy") is outdated due to the advent of DNA sequence-based phylogenies. In contrast, systematic comparisons of plant metabolite profiles in a known phylogenetic framework remain relevant. This approach, known as chemophenetics, allows characterizing species and clades based on their array of specialized metabolites, aids in deducing the evolution of biosynthetic pathways and coevolution, and can serve in identifying new sources of rare and economically interesting natural products.

The impact of glycosylation on the structure, function, and interactions of CD14

CD14 is an innate immune receptor that senses pathogen-associated molecular patterns, such as lipopolysaccharide, to activate the innate immune response. Although CD14 is known to be glycosylated, detailed understanding about the structural and functional significance of this modification is still missing. Herein, an NMR and MS-based study, assisted by MD simulations, has provided a 3D-structural model of glycosylated CD14. Our results reveal the existence of a key N-glycosylation site at Asn282 that exclusively contains unprocessed oligomannnose N-glycans that perfectly fit the concave cavity of the bent-solenoid shaped protein. This site is not accessible to glycosidases and is fundamental for protein folding and secretion. A second N-site at Asn151 displays mostly complex N-glycans, with the typical terminal epitopes of the host cell-line expression system (i.e. βGal, α2,3 and α2,6 sialylated βGal, here), but also particularities, such as the lack of core fucosylation. The glycan at this site points outside the protein surface, resulting in N-glycoforms fully exposed and available for interactions with lectins. In fact, NMR experiments show that galectin-4, proposed as a binder of CD14 on monocytes to induce their differentiation into macrophages-like cells, interacts in vitro with CD14 through the recognition of the terminal glycoepitopes on Asn151. This work provides key information about CD14 glycosylation, which helps to better understand its functional roles and significance. Although protein glycosylation is known to be dynamic and influenced by many factors, some of the features found herein (presence of unprocessed N-glycans and lack of core Fuc) are likely to be protein specific.

Automated nuclear magnetic resonance fingerprinting of mixtures

Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for qualitative and quantitative analysis. However, for complex mixtures, determining the speciation from NMR spectra can be tedious and sometimes even unfeasible. On the other hand, identifying and quantifying structural groups in a mixture from NMR spectra is much easier than doing the same for components. We call this group-based approach "NMR fingerprinting." In this work, we show that NMR fingerprinting can even be performed in an automated way, without expert knowledge, based only on standard NMR spectra, namely, 13C, 1H, and 13C DEPT NMR spectra. Our approach is based on the machine-learning method of support vector classification (SVC), which was trained here on thousands of labeled pure-component NMR spectra from open-source data banks. We demonstrate the applicability of the automated NMR fingerprinting using test mixtures, of which spectra were taken using a simple benchtop NMR spectrometer. The results from the NMR fingerprinting agree remarkably well with the ground truth, which was known from the gravimetric preparation of the samples. To facilitate the application of the method, we provide an interactive website (https://nmr-fingerprinting.de), where spectral information can be uploaded and which returns the NMR fingerprint. The NMR fingerprinting can be used in many ways, for example, for process monitoring or thermodynamic modeling using group-contribution methods-or simply as a first step in species analysis.

ASAP: An automatic sequential assignment program for congested multidimensional solid state NMR spectra

Accurate signal assignments can be challenging for congested solid-state NMR (ssNMR) spectra. We describe an automatic sequential assignment program (ASAP) to partially overcome this challenge. ASAP takes three input files: the residue type assignments (RTAs) determined from the better-resolved NCACX spectrum, the full peak list of the NCOCX spectrum, and the protein sequence. It integrates our auto-residue type assignment strategy (ARTIST) with the Monte Carlo simulated annealing (MCSA) algorithm to overcome the hurdle for accurate signal assignments caused by incomplete side-chain resonances and spectral congestion. Combined, ASAP demonstrates robust performance and accelerates signal assignments of large proteins (>200 residues) that lack crystalline order.

Changes in primary metabolite content may affect thrips feeding preference in soybean crops

Past research has characterized the induction of plant defenses in response to chewing insect damage. However, little is known about plant responses to piercing-sucking insects that feed on plant cell-contents like thrips (Caliothrips phaseoli). In this study, we used NMR spectroscopy to measure metabolite changes in response to six days of thrips damage from two field-grown soybean cultivars (cv.), known for their different susceptibility to Caliothrips phaseoli. We observed that thrips damage reduces sucrose concentration in both cultivars, while pinitol, the most abundant leaf soluble carbohydrate, is induced in cv. Charata but not in cv. Williams. Thrips did not show preference for leaves where sucrose or pinitol were externally added, at tested concentration. In addition, we also noted that cv. Charata was less naturally colonized and contained higher levels of trigonelline, tyrosine as well as several compounds that we have not yet identified. We have established that preference-feeding clues are not dependent on the plants major soluble carbohydrates but may depend on other types of compounds or leaf physical characteristics.

High-resolution liquid chromatography mass spectrometry (HR-LCMS) and 1H NMR analysis of methanol extracts from marine seaweed Gracilaria edulis

A wide variety of bioactive secondary metabolites that seaweeds are claimed to generate can be used by the pharmaceutical industry to create novel medications. The primary goal of the current study was to use the HR-LCMS and NMR approach to analyse the phytochemical content of a methanolic extract of Gracilaria edulis. The HR-LCMS and NMR analysis reveals the presence of bioactive compounds (amino acid, fatty acid, triterpenoids, carotenoid, aromatic compounds, flavonoids, secondary alcohols, diterpenes, lipid, phenolic compounds, sesquiterpenoids, quinolizidine alkaloid, and benzoquinone). The present study's findings support the existence of significant phytocompounds in G. edulis and are useful for future in-depth investigation to create medications from marine algae to treat a variety of ailments. The goal of current research is to discover all-natural treatments for a wide variety of illnesses and conditions.

Purification of SRSF1 from E. coli for Biophysical and Biochemical Assays

The Ser/Arg-rich splicing factors (SR proteins) constitute a crucial protein family in alternative splicing, comprising twelve members characterized by unique repetitive Arg-Ser dipeptide sequences (RS) and one to two RNA-recognition motifs (RRM). The RS regions of SR proteins undergo variable phosphorylation, resulting in unphosphorylated, partially phosphorylated, or hyper-phosphorylated states based on functional requirements. Despite the identification of the SR protein family over 30 years ago, the purification of native SR proteins in soluble form at large quantities has presented challenges due to their low solubility. This protocol delineates a method for acquiring soluble, full-length, unphosphorylated, hypo- and hyper-phosphorylated SRSF1, a prototypical SR family member. Notably, this protocol facilitates the purification of SRSF1 in ample quantities suitable for NMR, as well as various biophysical and biochemical studies. The methodologies and principles outlined herein are expected to extend beyond SRSF1 protein production and can be adapted for purifying other SR protein family members or SR-related proteins, such as snRNP70 and U2AF-35. Given the involvement of these proteins in numerous essential biological processes, this protocol will prove beneficial to researchers in related fields. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Purification of SRSF1 from E. coli Support Protocol: Purification of ULP1 Basic Protocol 2: Purification of hypo-phosphorylated SRSF1 from E. coli Basic Protocol 3: Purification of hyper-phosphorylated SRSF1 from E. coli.

Structure of KOH-soluble polysaccharides from сoniferous greens of Norway spruce (Picea abies): The pectin-xylan-AGPs complex. Part 1

Using 7 % KOH, the polysaccharide PAK has been isolated from the coniferous greens of Norway spruce. PAK was found to contain predominantly arabinoglucuronoxylan, xyloglucan and arabinan, but also pectic polysaccharides, glucomannan and arabinogalactan proteins (AGPs), as determined by 1D/2D NMR analysis. It was found that fractionation of PAK on DEAE-cellulose resulted in simultaneous elution of pectins, arabinoglucuronoxylans and AGPs. It was evident that the content of 4-OMe-α-D-GlcpA and xylose, 1,4-β-D-GlcpA, and T-β-D-GlcpA increased with an increase in NaCl concentration. However, 1,4-α-D-GalpA content was almost independent of NaCl concentration, indicating unchanged pectic polysaccharide concentration. Interestingly, pectins extracted with 0.1-0.3 M NaCl solutions were richer in rhamnogalacturonan-I (RG-I) than those extracted with water and 0.01 M NaCl. Conclusion: The content of RG-I, AGPs and arabinoglucuronoxylan rises with rising NaCl concentration. An intense signal indicating an intermolecular linkage between the xylan and RG-I domains, i.e. that part of the arabinoglucuronoxylan is covalently bound to RG-I, is observed in the HMBC spectra of the polysaccharides obtained. The discovery here of a new relationship between rhamnogalacturonan I and xylan contradicts the prevailing cell wall model.

Unveiling the fungal color palette: pigment analysis of Fusarium solani species complex and Curvularia verruculosa clinical isolates

Fungal species in the Nectriaceae, such as Fusarium spp. (Hypocreales: Nectriaceae), are etiologic agents of hyalohyphomycosis capable of producing violaceous or yellowish pigments under certain conditions, while Curvularia spp. (Pleosporales: Pleosporaceae) are agents of phaeohyphomycosis and typically produce melanin in their cell walls. In nectriaceous and pleosporaceous fungi, these pigments are mainly constituted by polyketides (e.g., azaphilones, naphthoquinones, and hydroxyanthraquinones). Considering the importance of pigments synthesized by these genera, this work focused on the selective extraction of pigments produced by eight Fusarium solani species complex and one Curvularia verruculosa isolate recovered from dermatomycosis specimens, their separation, purification, and posterior chemical analysis. The pigments were characterized through spectral and acid-base analysis, and their maximum production time was determined. Moreover, spectral identification of isolates was carried out to approach the taxonomic specificity of pigment production. Herein we describe the isolation and characterization of three acidic pigments, yellowish and pinkish azaphilones (i.e., coaherin A and sclerotiorin), and a purplish xanthone, reported for the first time in the Nectriaceae and Pleosporaceae, which appear to be synthesized in a species-independent manner, in the case of fusaria.

Synthesis, characterization and differentiation of the structural isomers of valine and tert-leucine derived synthetic cannabinoids

The identification of the synthetic cannabinoids receptor agonists (SCRAs) has always posed a great challenge to drug testing laboratories with slight structural modifications aimed at evading drug legislation. In addition, the most prevalent synthetic cannabinoids have valine and tert-leucine amino acid moieties where re-arrangement of the carbon chains can result in structural isomers that are very similar to the parent synthetic cannabinoids. This makes their analysis and identification challenging, and the problem is compounded with the difficulty in purchasing reference standards quickly and a lack of literature for comparison. Therefore, in this investigation, four series of synthetic cannabinoids (AB-PINACA, AB-CHMINACA, MMB-FUBINACA and 5-fluoro-MDMB-PINACA) and their alkyl chain structural isomers at the amino acid moieties were synthesized and characterized using various analytical techniques-gas chromatography-mass spectrometry (GC-MS), gas chromatography-infrared detection (GC-IRD) and nuclear magnetic resonance (NMR) spectroscopy to evaluate the ability of each analytical technique to differentiate the respective isomers for their identification. A total of 12 isomers were synthesized and analysed together with the four parent synthetic cannabinoids. NMR was able to differentiate between all the compounds, whereas GC-IRD was able to discern between most of the synthetic cannabinoids and their isomers. GC-MS had the least discriminating power and was not able to differentiate some of the compounds that has very similar mass spectra. The results from this work will be useful to other drug testing laboratories that are facing the identification of related synthetic cannabinoids.

Structure and dynamics of the cyanobacterial regulator SipA

The small, 78-residue long, regulator SipA interacts with the non-bleaching sensor histidine kinase (NblS). We have solved the solution structure of SipA on the basis of 990 nuclear Overhauser effect- (NOE-) derived distance constraints. The average pairwise root-mean-square deviation (RMSD) for the twenty best structures for the backbone residues, obtained by CYANA, was 1.35 ± 0.21 Å, and 1.90 ± 0.16 Å when all heavy atoms were considered (the target function of CYANA was 0.540 ± 0.08). The structure is that of a β-II class protein, basically formed by a five-stranded β-sheet composed of antiparallel strands following the arrangement: Gly6-Leu11 (β-strand 1), which packs against Leu66-Val69 (β-strand 5) on one side, and against Gly36-Thr42 (β-strand 2) on the other side; Trp50-Phe54 (β-strand 3); and Gly57-Leu60 (β-strand 4). The protein is highly mobile, as shown by measurements of R1, R2, NOE and ηxy relaxation parameters, with an average order parameter () of 0.70; this mobility encompasses movements in different time scales. We hypothesize that this high flexibility allows the interaction with other proteins (among them NblS), and it explains the large conformational stability of SipA.

Exploring the therapeutic potential of Derris elliptica (Wall.) Benth in Streptozotocin-Induced diabetic Rats: Phytochemical characterization and antidiabetic evaluation

Derris elliptica (Wall.) Benth, a native medicinal plant, has been used to treat diabetes for centuries; however, comprehensive documentation of its bioactive constituents and therapeutic effectiveness is lacking. In this study, we investigated the phytochemical profile and antidiabetic potential of D. elliptica methanolic leaf extract (DEME) in diabetic Sprague Dawley rats induced with streptozotocin (STZ). In normal rats, acute oral toxicity evaluations were conducted, and in STZ-induced rats, antidiabetic properties were investigated. 14 days of oral administration of standard glibenclamide and the extract at 200 and 400 mg/kg body weight to diabetic rodents. Assessed parameters included blood glucose levels, alterations in body weight, biochemical markers, and histological analysis of the pancreas, liver, and kidney. Numerous phytoconstituents were uncovered through qualitative phytochemical assays, 1H NMR, and 1H-13C HSQC screening. Quercetin was identified by 1H NMR characterization, and a ceramide analogue compound was isolated and partially characterized by 1H NMR. There were no indications of toxicity or mortality. The treatment with DEME significantly (p < 0.001) decreased body weight and had a remarkable hypoglycemic effect. Both 200 mg/kg and 400 mg/kg extract concentrations decreased total cholesterol levels significantly (p < 0.01 and p < 0.05, respectively). In addition, glibenclamide and the 400 mg/kg dose of extract increased serum insulin levels substantially (p < 0.05) and decreased total bilirubin, lactic acid dehydrogenase, aspartate aminotransferase, and alanine aminotransferase levels. In addition to glibenclamide, treatment with DEME has exhibited cytoprotective effects and increased insulin secretion, thereby exerting a potent antihyperglycemic effect. These results suggest that D. elliptica may have therapeutic potential for the treatment of diabetes mellitus.

Combined nuclear magnetic resonance methods in quality control of lubricants in green energy production

NMR methods were applied for lubricant analysis. Different factors influence the real aging of lubricants on diverse length scales and are captured by NMR. Chemical conversion of additives is addressed by NMR spectroscopy. High-field NMR experiments allow the identification and quantification of chemical components and are transferred to benchtop devices. Molecular dynamics and contaminations like fuel or abrasion are addressed via NMR relaxation and diffusion. Quality parameters were extracted via suitable data analysis of NMR raw data, which allow the detection of aging and indicate changes in the oil composition. At the same time, the methodology is optimized to the conditions in quality control. The feasibility is shown the example of a series of lubricants from applications in regenerative energy production, namely, wind turbine oils and biogas motor oils.

A cellulosomal double-dockerin module from Clostridium thermocellum shows distinct structural and cohesin-binding features

Cellulosomes are intricate cellulose-degrading multi-enzymatic complexes produced by anaerobic bacteria, which are valuable for bioenergy development and biotechnology. Cellulosome assembly relies on the selective interaction between cohesin modules in structural scaffolding proteins (scaffoldins) and dockerin modules in enzymes. Although the number of tandem cohesins in the scaffoldins is believed to determine the complexity of the cellulosomes, tandem dockerins also exist, albeit very rare, in some cellulosomal components whose assembly and functional roles are currently unclear. In this study, we characterized the structure and mode of assembly of a tandem bimodular double-dockerin, which is connected to a putative S8 protease in the cellulosome-producing bacterium, Clostridium thermocellum. Crystal and NMR structures of the double-dockerin revealed two typical type I dockerin folds with significant interactions between them. Interaction analysis by isothermal titration calorimetry and NMR titration experiments revealed that the double-dockerin displays a preference for binding to the cell-wall anchoring scaffoldin ScaD through the first dockerin with a canonical dual-binding mode, while the second dockerin module was unable to bind to any of the tested cohesins. Surprisingly, the double-dockerin showed a much higher affinity to a cohesin from the CipC scaffoldin of Clostridium cellulolyticum than to the resident cohesins from C. thermocellum. These results contribute valuable insights into the structure and assembly of the double-dockerin module, and provide the basis for further functional studies on multiple-dockerin modules and cellulosomal proteases, thus highlighting the complexity and diversity of cellulosomal components.

Stability of 20 Biogenic Amino Acids in Concentrated Sulfuric Acid: Implications for the Habitability of Venus' Clouds

Scientists have long speculated about the potential habitability of Venus, not at the 700K surface, but in the cloud layers located at 48-60 km altitudes, where temperatures match those found on Earth's surface. However, the prevailing belief has been that Venus' clouds cannot support life due to the cloud chemical composition of concentrated sulfuric acid-a highly aggressive solvent. In this work, we study 20 biogenic amino acids at the range of Venus' cloud sulfuric acid concentrations (81% and 98% w/w, the rest water) and temperatures. We find 19 of the biogenic amino acids we tested are either unreactive (13 in 98% w/w and 12 in 81% w/w) or chemically modified in the side chain only, after 4 weeks. Our major finding, therefore, is that the amino acid backbone remains intact in concentrated sulfuric acid. These findings significantly broaden the range of biologically relevant molecules that could be components of a biochemistry based on a concentrated sulfuric acid solvent.