Low-cost, pseudo-Halbach dipole magnets for NMR

We present designs for compact, inexpensive and strong dipole permanent magnets aimed primarily at magnetic resonance applications where prepolarization and detection occur at different locations. Low-homogeneity magnets with a 7.5mm bore size and field up to nearly 2T are constructed using low-cost starting materials, standard workshop tools and only few hours of labor - an achievable project for a student or postdoc with spare time. As an application example we show how our magnet was used to polarize the nuclear spins in approximately 1mL of pure [¹³C]-methanol prior to detection of its high-resolution NMR spectrum at zero field (measurement field below 10^-10T), where signals appear at multiples of the carbon-hydrogen spin-spin coupling frequency ¹J_CH=140.7(1)Hz.

Fragment-based methods for the discovery of inhibitors modulating lysyl-tRNA synthetase and laminin receptor interaction

Lysyl-tRNA synthetase (KRS) is an enzyme that conjugates lysine to its cognate tRNAs in the process of protein synthesis. In addition to its catalytic function, KRS binds to the 67-kDa laminin receptor (LR) on the cell membrane and facilitates cell migration and metastasis. Modulation of this interaction by small-molecule inhibitors can be exploited to suppress cancer metastasis. In this study, we present fragment-based methods for the identification of inhibitors and monitoring protein-protein interactions between KRS and LR. First, we identified the amino acid residues, located on the KRS anticodon-binding domain, which interact with the C-terminal extension of the LR. One-dimensional (1D) relaxation-edited nuclear magnetic resonance spectroscopy (NMR) and competition experiments were designed and optimized to screen the fragment library. For screening using two-dimensional (2D) NMR, we identified the indicative signals in the KRS anticodon-binding domain and selected inhibitors that bind to KRS and compete with LR at the KRS-LR binding interface. These methods may offer an efficient approach for the discovery of anti-metastatic drugs.

NMR Chemical Shift Mapping of SH2 Peptide Interactions

Heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) experiments offer a rapid and high resolution approach to gaining binding and conformational insights into a protein-peptide interaction. By tracking ¹H and ¹⁵N chemical shift changes over the course of a peptide titration into isotopically labeled protein, amide NH pairs of amino acids whose chemical environment changes upon peptide binding can be identified. When mapped onto a structure of the protein, this approach can identify the peptide-binding interface or regions undergoing conformation changes within a protein upon ligand binding. Monitoring NMR chemical shift changes can also serve as a screening technique to identify novel interaction partners for a protein or to determine the binding affinity of a weak protein-peptide interaction. Here, we describe the application of NMR chemical shift mapping to the study of peptide binding to the C-terminal SH2 domain of PLCγ1.

Blood species discrimination using proton nuclear magnetic resonance spectroscopy

Blood species identification is an important challenge in forensic science. Conventional methods used for blood species analysis are destructive and associated with time-consuming sample preparation steps. Nuclear magnetic resonance (NMR) spectroscopy is known for its nondestructive properties and fast results. This research study presents a proton (¹H) NMR method to discriminate blood species including human, cat, dog, elephant, and bison. Characteristic signals acting as markers are observed for each species. Moreover, the data are evaluated by principle component analysis (PCA) and support vector machines (SVM). A 100% correct species recognition between human and nonhuman species is achieved using radial basis kernel function (RBF) and standardized data. The research study shows that ¹H NMR spectroscopy is a powerful tool for differentiating human and nonhuman blood showing a great significance to forensic science.

A Penicillium chrysogenum-based expression system for the production of small, cysteine-rich antifungal proteins for structural and functional analyses

Background

Small, cysteine-rich and cationic antifungal proteins (APs) from filamentous ascomycetes, such as NFAP from Neosartorya fischeri and PAF from Penicillium chrysogenum, are promising candidates for novel drug development. A prerequisite for their application is a detailed knowledge about their structure–function relation and mode of action, which would allow protein modelling to enhance their toxicity and specificity. Technologies for structure analyses, such as electronic circular dichroism (ECD) or NMR spectroscopy, require highly purified samples and in case of NMR milligrams of uniformly ¹⁵N-/¹³C-isotope labelled protein. To meet these requirements, we developed a P. chrysogenum-based expression system that ensures sufficient amount and optimal purity of APs for structural and functional analyses.

Results

The APs PAF, PAF mutants and NFAP were expressed in a P. chrysogenum ∆paf mutant strain that served as perfect microbial expression factory. This strain lacks the paf-gene coding for the endogenous antifungal PAF and is resistant towards several APs from other ascomycetes. The expression of the recombinant proteins was under the regulation of the strong paf promoter, and the presence of a paf-specific pre-pro sequence warranted the secretion of processed proteins into the supernatant. The use of defined minimal medium allowed a single-step purification of the recombinant proteins. The expression system could be extended to express PAF in the related fungus Penicillium digitatum, which does not produce detectable amounts of APs, demonstrating the versatility of the approach. The molecular masses, folded structures and antifungal activity of the recombinant proteins were analysed by ESI–MS, ECD and NMR spectroscopy and growth inhibition assays.

Conclusion

This study demonstrates the implementation of a paf promoter driven expression cassettes for the production of cysteine-rich, cationic, APs in different Penicillium species. The system is a perfect tool for the generation of correctly folded proteins with high quality for structure–function analyses.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0586-4) contains supplementary material, which is available to authorized users.

Cooperativity between verapamil and ATP bound to the efflux transporter P-glycoprotein

The P-glycoprotein (Pgp) transporter plays a central role in drug disposition by effluxing a chemically diverse range of drugs from cells through conformational changes and ATP hydrolysis. A number of drugs are known to activate ATP hydrolysis of Pgp, but coupling between ATP and drug binding is not well understood. The cardiovascular drug verapamil is one of the most widely studied Pgp substrates and therefore, represents an ideal drug to investigate the drug-induced ATPase activation of Pgp. As previously noted, verapamil-induced Pgp-mediated ATP hydrolysis kinetics was biphasic at saturating ATP concentrations. However, at subsaturating ATP concentrations, verapamil-induced ATPase activation kinetics became monophasic. To further understand this switch in kinetic behavior, the Pgp-coupled ATPase activity kinetics was checked with a panel of verapamil and ATP concentrations and fit with the substrate inhibition equation and the kinetic fitting software COPASI. The fits suggested that cooperativity between ATP and verapamil switched between low and high verapamil concentration. Fluorescence spectroscopy of Pgp revealed that cooperativity between verapamil and a non-hydrolyzable ATP analog leads to distinct global conformational changes of Pgp. NMR of Pgp reconstituted in liposomes showed that cooperativity between verapamil and the non-hydrolyzable ATP analog modulate each other's interactions. This information was used to produce a conformationally-gated model of drug-induced activation of Pgp-mediated ATP hydrolysis.

Identifying metabolite markers for preterm birth in cervicovaginal fluid by magnetic resonance spectroscopy

INTRODUCTION

Preterm birth (PTB) may be preceded by changes in the vaginal microflora and metabolite profiles.

OBJECTIVES

We sought to characterise the metabolite profile of cervicovaginal fluid (CVF) of pregnant women by 1H NMR spectroscopy, and assess their predictive value for PTB.

METHODS

A pair of high-vaginal swabs was obtained from pregnant women with no evidence of clinical infection and grouped as follows: asymptomatic low risk (ALR) women with no previous history of PTB, assessed at 20-22 gestational weeks, g.w., n = 83; asymptomatic high risk (AHR) women with a previous history of PTB, assessed at both 20-22 g.w., n = 71, and 26-28 g.w., n = 58; and women presenting with symptoms of preterm labor (PTL) (SYM), assessed at 24-36 g.w., n = 65. Vaginal secretions were dissolved in phosphate buffered saline and scanned with a 9.4 T NMR spectrometer.

RESULTS

Six metabolites (lactate, alanine, acetate, glutamine/glutamate, succinate and glucose) were analysed. In all study cohorts vaginal pH correlated with lactate integral (r = -0.62, p < 0.0001). Lactate integrals were higher in the term ALR compared to the AHR (20-22 g.w.) women (p = 0.003). Acetate integrals were higher in the preterm versus term women for the AHR (20-22 g.w.) (p = 0.048) and SYM (p = 0.003) groups; and was predictive of PTB < 37 g.w. (AUC 0.78; 95 % CI 0.61-0.95), and delivery within 2 weeks of the index assessment (AUC 0.84; 95 % CI 0.64-1) in the SYM women, whilst other metabolites were not.

CONCLUSION

High CVF acetate integral of women with symptoms of PTL appears predictive of preterm delivery, as well as delivery within 2 weeks of presentation.

Role of the Na(+)-translocating NADH:quinone oxidoreductase in voltage generation and Na(+) extrusion in Vibrio cholerae

For Vibrio cholerae, the coordinated import and export of Na(+) is crucial for adaptation to habitats with different osmolarities. We investigated the Na(+)-extruding branch of the sodium cycle in this human pathogen by in vivo (23)Na-NMR spectroscopy. The Na(+) extrusion activity of cells was monitored after adding glucose which stimulated respiration via the Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR). In a V. cholerae deletion mutant devoid of the Na(+)-NQR encoding genes (nqrA-F), rates of respiratory Na(+) extrusion were decreased by a factor of four, but the cytoplasmic Na(+) concentration was essentially unchanged. Furthermore, the mutant was impaired in formation of transmembrane voltage (ΔΨ, inside negative) and did not grow under hypoosmotic conditions at pH8.2 or above. This growth defect could be complemented by transformation with the plasmid encoded nqr operon. In an alkaline environment, Na(+)/H(+) antiporters acidify the cytoplasm at the expense of the transmembrane voltage. It is proposed that, at alkaline pH and limiting Na(+) concentrations, the Na(+)-NQR is crucial for generation of a transmembrane voltage to drive the import of H(+) by electrogenic Na(+)/H(+) antiporters. Our study provides the basis to understand the role of the Na(+)-NQR in pathogenicity of V. cholerae and other pathogens relying on this primary Na(+) pump for respiration.

A hemocyanin-derived antimicrobial peptide from the penaeid shrimp adopts an alpha-helical structure that specifically permeabilizes fungal membranes

BACKGROUND

Hemocyanins are respiratory proteins with multiple functions. In diverse crustaceans hemocyanins can release histidine-rich antimicrobial peptides in response to microbial challenge. In penaeid shrimp, strictly antifungal peptides are released from the C-terminus of hemocyanins.

METHODS

The three-dimensional structure of the antifungal peptide PvHCt from Litopenaeus vannamei was determined by NMR. Its mechanism of action against the shrimp pathogen Fusarium oxysporum was investigated using immunochemistry, fluorescence and transmission electron microscopy.

RESULTS

PvHCt folded into an amphipathic α-helix in membrane-mimicking media and displayed a random conformation in aqueous environment. In contact with F. oxysporum, PvHCt bound massively to the surface of fungal hyphae without being imported into the cytoplasm. At minimal inhibitory concentrations, PvHCt made the fungal membrane permeable to SYTOX-green and fluorescent dextran beads of 4 kDa. Higher size beads could not enter the cytoplasm. Therefore, PvHCt likely creates local damages to the fungal membrane. While the fungal cell wall appeared preserved, gradual degeneration of the cytoplasm most often resulting in cell lysis was observed in fungal spores and hyphae. In the remaining fungal cells, PvHCt induced a protective response by the formation of daughter hyphae.

CONCLUSION

The massive accumulation of PvHCt at the surface of fungal hyphae and subsequent insertion into the plasma membrane disrupt its integrity as a permeability barrier, leading to disruption of internal homeostasis and fungal death.

GENERAL SIGNIFICANCE

The histidine-rich antimicrobial peptide PvHCt derived from shrimp hemocyanin is a strictly antifungal peptide, which adopts an amphipathic α-helical structure, and selectively binds to and permeabilizes fungal cells.

Structural determination of virus protein U from HIV-1 by NMR in membrane environments

Virus protein U (Vpu) from HIV-1, a small membrane protein composed of a transmembrane helical domain and two α-helices in an amphipathic cytoplasmic domain, down modulates several cellular proteins, including CD4, BST-2/CD317/tetherin, NTB-A, and CCR7. The interactions of Vpu with these proteins interfere with the immune system and enhance the release of newly synthesized virus particles. It is essential to characterize the structure and dynamics of Vpu in order to understand the mechanisms of the protein-protein interactions, and potentially to discover antiviral drugs. In this article, we describe investigations of the cytoplasmic domain of Vpu as well as full-length Vpu by NMR spectroscopy. These studies are complementary to earlier analysis of the transmembrane domain of Vpu. The results suggest that the two helices in the cytoplasmic domain form a U-shape. The length of the inter-helical loop in the cytoplasmic domain and the orientation of the third helix vary with the lipid composition, which demonstrate that the C-terminal helix is relatively flexible, providing accessibility for interaction partners.

Rapid-melt Dynamic Nuclear Polarization

In recent years, Dynamic Nuclear Polarization (DNP) has re-emerged as a means to ameliorate the inherent problem of low sensitivity in nuclear magnetic resonance (NMR). Here, we present a novel approach to DNP enhanced liquid-state NMR based on rapid melting of a solid hyperpolarized sample followed by 'in situ' NMR detection. This method is applicable to small (10nl to 1μl) sized samples in a microfluidic setup. The method combines generic DNP enhancement in the solid state with the high sensitivity of stripline (1)H NMR detection in the liquid state. Fast cycling facilitates options for signal averaging or 2D structural analysis. Preliminary tests show solid-state (1)H enhancement factors of up to 500 for H2O/D2O/d6-glycerol samples doped with TEMPOL radicals. Fast paramagnetic relaxation with nitroxide radicals, In nonpolar solvents such as toluene, we find proton enhancement factors up to 400 with negligible relaxation losses in the liquid state, using commercially available BDPA radicals. A total recycling delay (including sample freezing, DNP polarization and melting) of about 5s can be used. The present setup allows for a fast determination of the hyper-polarization as function of the microwave frequency and power. Even at the relatively low field of 3.4T, the method of rapid melting DNP can facilitate the detection of small quantities of molecules in the picomole regime.

Properties of phosphorylated thymidylate synthase

Thymidylate synthase (TS) may undergo phosphorylation endogenously in mammalian cells, and as a recombinant protein expressed in bacterial cells, as indicated by the reaction of purified enzyme protein with Pro-Q® Diamond Phosphoprotein Gel Stain (PGS). With recombinant human, mouse, rat, Trichinella spiralis and Caenorhabditis elegans TSs, expressed in Escherichia coli, the phosphorylated, compared to non-phosphorylated recombinant enzyme forms, showed a decrease in Vmax(app), bound their cognate mRNA (only rat enzyme studied), and repressed translation of their own and several heterologous mRNAs (human, rat and mouse enzymes studied). However, attempts to determine the modification site(s), whether endogenously expressed in mammalian cells, or recombinant proteins, did not lead to unequivocal results. Comparative ESI-MS/analysis of IEF fractions of TS preparations from parental and FdUrd-resistant mouse leukemia L1210 cells, differing in sensitivity to inactivation by FdUMP, demonstrated phosphorylation of Ser(10) and Ser(16) in the resistant enzyme only, although PGS staining pointed to the modification of both L1210 TS proteins. The TS proteins phosphorylated in bacterial cells were shown by (31)P NMR to be modified only on histidine residues, like potassium phosphoramidate (KPA)-phosphorylated TS proteins. NanoLC-MS/MS, enabling the use of CID and ETD peptide fragmentation methods, identified several phosphohistidine residues, but certain phosphoserine and phosphothreonine residues were also implicated. Molecular dynamics studies, based on the mouse TS crystal structure, allowed one to assess potential of several phosphorylated histidine residues to affect catalytic activity, the effect being phosphorylation site dependent.

Changes in urinary metabolic profiles of colorectal cancer patients enrolled in a prospective cohort study (ColoCare)

INTRODUCTION

Metabolomics is a valuable tool for biomarker screening of colorectal cancer (CRC). In this study, we profiled the urinary metabolomes of patients enrolled in a prospective patient cohort (ColoCare). We aimed to describe changes in the metabolome in the longer clinical follow-up and describe initial predictors as candidate markers with possibly prognostic significance.

METHODS

In total, 199 urine samples from CRC patients pre-surgery (n=97), 1-8 days post-surgery (n=12) and then after 6 and 12 months (n=52 and 38, respectively) were analyzed using both GC-MS and ¹H-NMR. Both datasets were analyzed separately with built in uni- and multivariate analyses of Metaboanalyst 2.0. Furthermore, adjusted linear mixed effects regression models were constructed.

RESULTS

Many concentrations of the metabolites derived from the gut microbiome were affected by CRC surgery, presumably indicating a tumor-induced shift in bacterial species. Associations of the microbial metabolites with disease stage indicate an important role of the gut microbiome in CRC.We were able to differentiate the metabolite profiles of CRC patients prior to surgery from those at any post-surgery timepoint using a multivariate model containing 20 marker metabolites (AUCROC=0.89; 95% CI:0.84-0.95).

CONCLUSION

To the best of our knowledge, this is one of the first metabolomic studies to follow CRC patients in a prospective setting with repeated urine sampling over time. We were able to confirm markers initially identified in case-control studies and pin point metabolites which may serve as candidates for prognostic biomarkers of CRC.

Analytical solution of cross polarization dynamics

The first analytical solution under Hartman-Hahn match (ω1I=ω1S) for a stationary sample was derived by Müller et al. After the introduction of magic angle spinning (MAS), the dynamics becomes much more complicated. By transferring the Hamiltonian into a rotating frame, Stejskal et al. derived the effective Hamiltonian and the new condition of Hartman-Hahn match (ω1I-ω1S=nωr,n=±1,±2), which leads to an analytical solution of CP dynamics under very fast MAS. For both stationary and fast MAS results, the effective Hamiltonians are time-independent in the rotating frame. Under Hartman-Hahn match (ω1I=ω1S) and arbitrary MAS speed condition, the Hamiltonian is no longer time-independent, making the CP dynamics very intriguing. In this work, the solution is derived analytically in the zero- and double-quantum spaces. The initial polarization in the double-quantum space is a constant of motion under strong pulse condition (|ω1I+ω1S|≫|d(t)|), while the Hamiltonian in the zero-quantum space reduces to d(t)σz(Δ), which is time dependent but self commuting all the time. This Hamilontian acts on the initial density matrix successively, leading to an analytical solution of CP dynamics. Based on the result, a phenomenological solution is derived. When the MAS speed ωr→0 , this solution reduces to Müller's formula except a spin-lattice relaxation time in the rotating frame (T1ρ). Computer simulations and experimental results agree well with the solutions.

Structural insights into endoplasmic reticulum stored calcium regulation by inositol 1,4,5-trisphosphate and ryanodine receptors

The two major calcium (Ca²⁺) release channels on the sarco/endoplasmic reticulum (SR/ER) are inositol 1,4,5-trisphosphate and ryanodine receptors (IP3Rs and RyRs). They play versatile roles in essential cell signaling processes, and abnormalities of these channels are associated with a variety of diseases. Structural information on IP3Rs and RyRs determined using multiple techniques including X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (EM), has significantly advanced our understanding of the mechanisms by which these Ca²⁺ release channels function under normal and pathophysiological circumstances. In this review, structural advances on the understanding of the mechanisms of IP3R and RyR function and dysfunction are summarized. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.

Isotopic labeling of mammalian G protein-coupled receptors heterologously expressed in Caenorhabditis elegans

High-resolution structural determination and dynamic characterization of membrane proteins by nuclear magnetic resonance (NMR) require their isotopic labeling. Although a number of labeled eukaryotic membrane proteins have been successfully expressed in bacteria, they lack post-translational modifications and usually need to be refolded from inclusion bodies. This shortcoming of bacterial expression systems is particularly detrimental for the functional expression of G protein-coupled receptors (GPCRs), the largest family of drug targets, due to their inherent instability. In this work, we show that proteins expressed by a eukaryotic organism can be isotopically labeled and produced with a quality and quantity suitable for NMR characterization. Using our previously described expression system in Caenorhabditis elegans, we showed the feasibility of labeling proteins produced by these worms with (15)N,(13)C by providing them with isotopically labeled bacteria. (2)H labeling also was achieved by growing C. elegans in the presence of 70% heavy water. Bovine rhodopsin, simultaneously expressed in muscular and neuronal worm tissues, was employed as the "test" GPCR to demonstrate the viability of this approach. Although the worms' cell cycle was slightly affected by the presence of heavy isotopes, the final protein yield and quality was appropriate for NMR structural characterization.

Evaluation of saffron (Crocus sativus L.) adulteration with plant adulterants by (1)H NMR metabolite fingerprinting

In the present work, a preliminary study for the detection of adulterated saffron and the identification of the adulterant used by means of (1)H NMR and chemometrics is reported. Authentic Greek saffron and four typical plant-derived materials utilised as bulking agents in saffron, i.e., Crocus sativus stamens, safflower, turmeric, and gardenia were investigated. A two-step approach, relied on the application of both OPLS-DA and O2PLS-DA models to the (1)H NMR data, was adopted to perform authentication and prediction of authentic and adulterated saffron. Taking into account the deficiency of established methodologies to detect saffron adulteration with plant adulterants, the method developed resulted reliable in assessing the type of adulteration and could be viable for dealing with extensive saffron frauds at a minimum level of 20% (w/w).

Two dimensional NMR spectroscopic approaches for exploring plant metabolome: A review

Today, most investigations of the plant metabolome tend to be based on either nuclear magnetic resonance (NMR) spectroscopy or mass spectrometry (MS), with or without hyphenation with chromatography. Although less sensitive than MS, NMR provides a powerful complementary technique for the identification and quantification of metabolites in plant extracts. NMR spectroscopy, well appreciated by phytochemists as a particularly information-rich method, showed recent paradigm shift for the improving of metabolome(s) structural and functional characterization and for advancing the understanding of many biological processes. Furthermore, two dimensional NMR (2D NMR) experiments and the use of chemometric data analysis of NMR spectra have proven highly effective at identifying novel and known metabolites that correlate with changes in genotype or phenotype. In this review, we provide an overview of the development of NMR in the field of metabolomics with special focus on 2D NMR spectroscopic techniques and their applications in phytomedicines quality control analysis and drug discovery from natural sources, raising more attention at its potential to reduce the gap between the pace of natural products research and modern drug discovery demand.

Changes in the metabolome of lettuce leaves due to exposure to mancozeb pesticide

This paper describes a proton high resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) metabolomic study of lettuce (Lactuca sativa L.) leaves to characterise metabolic adaptations during leaf growth and exposure to mancozeb. Metabolite variations were identified through multivariate analysis and checked through spectral integration. Lettuce growth was accompanied by activation of energetic metabolism, preferential glucose use and changes in amino acids, phospholipids, ascorbate, nucleotides and nicotinate/nicotinamide. Phenylalanine and polyphenolic variations suggested higher oxidative stress at later growth stages. Exposure to mancozeb induced changes in amino acids, fumarate and malate, suggesting Krebs cycle up-regulation. In tandem disturbances in sugar, phospholipid, nucleotide and nicotinate/nicotinamide metabolism were noted. Additional changes in phenylalanine, dehydroascorbate, tartrate and formate were consistent with a higher demand for anti-oxidant defence mechanisms. Overall, lettuce exposure to mancozeb was shown to have a significant impact on plant metabolism, with mature leaves tending to be more extensively affected than younger leaves.

Integrated biorefinery based on hydrothermal and alkaline treatments: investigation of sorghum hemicelluloses

An integrated process based on hydrothermal pretreatment (HTP) and alkaline post-treatment was proposed to treat sweet sorghum stem. The structural features of the alkali-soluble hemicelluloses (ASHs) obtained from the un-pretreated and hydrothermally pretreated materials were comprehensively investigated by HPAEC, GPC, NMR, FT-IR, and TGA techniques. The ASH with the highest yield (60.6%) was obtained from the HTP residue performed at 130 °C for 1.0 h. All the results indicated that the ASHs had a more linear structure with increasing the pretreatment temperature (110-170 °C). The molecular weights of the ASHs were decreased with increasing the pretreatment temperature, suggesting that C-O bonds in the ASHs were gradually cleaved, especially at the higher temperatures (≥ 170 °C). Interestingly, the integrated process yielded more homogeneous ASHs than hemicelluloses obtained from the un-pretreated material. Based on the spectral analyses, the structure of the ASHs was assumed to be L-arabino-4-O-methyl-D-glucurono-D-xylan.

Analysis of the restorative effect of Bu-zhong-yi-qi-tang in the spleen-qi deficiency rat model using (1)H-NMR-based metabonomics

ETHNOPHARMACOLOGICAL RELEVANCE

Bu-zhong-yi-qi-tang (BT) is a classical formula for the treatment of spleen-qi descending, visceroptosis with hyposplenic qi, uterine prolapse, and rectal prolapse due to chronic diarrhea in traditional Chinese medicine (TCM) and has been identified as an effective drug for the treatment of TCM spleen-qi deficiency in clinical practice. The present study aimed to investigate the restorative effect and the potential mechanisms of Bu-zhong-yi-qi-tang in a rat spleen-qi deficiency model using (1)H-NMR-based metabonomics.

MATERIALS AND METHODS

The rat spleen-qi deficiency model was established as follows: oral administration of Radix Rhei extract (equivalent to 10g/kg body weight of the crude drug), loaded swimming, and starvation for 24h. Each of these treatments was administered consecutively every three days. Sixty male SD rats were randomly divided into five groups, and three of the groups received a different oral dose of the aqueous extract of Bu-zhong-yi-qi-tang during the last seven days of the three-week experimental period. The body weight and motor behavior of the rats were measured and recorded once a week. The endogenous metabolites in the plasma were analyzed using NMR in conjunction with multivariate and statistical techniques. In addition, the liver and spleen were removed and weighed.

RESULTS

All of the rats in the spleen-qi deficiency group presented pasty loose stools, inactiveness, grouping, a decrease in swimming endurance, and lackluster, loose, and disorderly behavior in addition to a significant decrease in body weight, spleen weight, and liver weight. In contrast, the abovementioned demonstrations were reversed to a certain extent in the rats treated with Bu-zhong-yi-qi-tang compared with the model group (p<0.05, p<0.01). A significant separation was determined between the control and model groups in the PCA score plot, which indicates that the spleen-qi deficiency model was successfully duplicated. The changes in the levels of endogenous metabolites in the plasma included lower levels of valine, leucine, and O-acetyl-glycoprotein and a higher concentration of lactate in the spleen-qi deficiency group compared with the control group. Treatment with Bu-zhong-yi-qi-tang at least partially returned the levels of these metabolites to the normal levels.

CONCLUSIONS

The restorative effects of Bu-zhong-yi-qi-tang in rats with spleen-qi deficiency were confirmed, and four endogenous metabolites were identified as potential biomarkers of the symptoms of spleen-qi deficiency and most likely play roles in the changes observed in certain metabolic pathways, such as the energy, protein, and glycolytic metabolisms.

Isolation and structural characterization of sugarcane bagasse lignin after dilute phosphoric acid plus steam explosion pretreatment and its effect on cellulose hydrolysis

The structure of lignin after dilute phosphoric acid plus steam explosion pretreatment process of sugarcane bagasse in a pilot scale and the effect of the lignin extracted by ethanol on subsequent cellulose hydrolysis were investigated. The lignin structural changes caused by pretreatment were identified using advanced nondestructive techniques such as gel permeation chromatography (GPC), quantitative (13)C, and 2-D nuclear magnetic resonance (NMR). The structural analysis revealed that ethanol extractable lignin preserved basic lignin structure, but had relatively lower amount of β-O-4 linkages, syringyl/guaiacyl units ratio (S/G), p-coumarate/ferulate ratio, and other ending structures. The results also indicated that approximately 8% of mass weight was extracted by pure ethanol. The bagasse after ethanol extraction had an approximate 22% higher glucose yield after enzyme hydrolysis compared to pretreated bagasse without extraction.

Toward better annotation in plant metabolomics: isolation and structure elucidation of 36 specialized metabolites from Oryza sativa (rice) by using MS/MS and NMR analyses

Metabolomics plays an important role in phytochemical genomics and crop breeding; however, metabolite annotation is a significant bottleneck in metabolomic studies. In particular, in liquid chromatography-mass spectrometry (MS)-based metabolomics, which has become a routine technology for the profiling of plant-specialized metabolites, a substantial number of metabolites detected as MS peaks are still not assigned properly to a single metabolite. Oryza sativa (rice) is one of the most important staple crops in the world. In the present study, we isolated and elucidated the structures of specialized metabolites from rice by using MS/MS and NMR. Thirty-six compounds, including five new flavonoids and eight rare flavonolignan isomers, were isolated from the rice leaves. The MS/MS spectral data of the isolated compounds, with a detailed interpretation of MS fragmentation data, will facilitate metabolite annotation of the related phytochemicals by enriching the public mass spectral data depositories, including the plant-specific MS/MS-based database, ReSpect.

Intermolecular interaction of voriconazole analogues with model membrane by DSC and NMR, and their antifungal activity using NMR based metabolic profiling

The development of novel antifungal agents with high susceptibility and increased potency can be achieved by increasing their overall lipophilicity. To enhance the lipophilicity of voriconazole, a second generation azole antifungal agent, we have synthesized its carboxylic acid ester analogues, namely p-methoxybenzoate (Vpmb), toluate (Vtol), benzoate (Vbz) and p-nitrobenzoate (Vpnb). The intermolecular interactions of these analogues with model membrane have been investigated using nuclear magnetic resonance (NMR) and differential scanning calorimetric (DSC) techniques. The results indicate varying degree of changes in the membrane bilayer's structural architecture and physico-chemical characteristics which possibly can be correlated with the antifungal effects via fungal membrane. Rapid metabolite profiling of chemical entities using cell preparations is one of the most important steps in drug discovery. We have evaluated the effect of synthesized analogues on Candida albicans. The method involves real time (1)H NMR measurement of intact cells monitoring NMR signals from fungal metabolites which gives Metabolic End Point (MEP). This is then compared with Minimum Inhibitory Concentration (MIC) determined using conventional methods. Results indicate that one of the synthesized analogues, Vpmb shows reasonably good activity.

Inhibition of human neutrophil activity by an RNA aptamer bound to interleukin-8

Interleukin-8 (IL-8) is a proinflammatory CXC chemokine that has been associated with the promotion of neutrophil chemotaxis, degranulation, and the pathogenesis of several neutrophil-infiltrating chronic inflammatory diseases. In the current study, we generated and characterized a 2'-fluoro-pyrimidine modified RNA aptamer (8A-35) against human IL-8. The 8A-35 aptamer binds to IL-8 with high specificity and affinity, yielding an estimated K(D) of 1.72 pM. NMR data revealed that the residues of Lys8, Leu10, Val63, Val66, Lys69 and Ala74 of IL-8 interact with aptamer. Moreover, the 8A-35 aptamer has a potent IL-8-neutralizing activity that can modulate multiple biological activities of IL-8 in human neutrophils, including migration, intracellular signaling, and intracellular Ca(2+) mobilization. Our results suggest that the 8A-35 aptamer has great potential to be a lead structure in the development of effective therapeutic agents against inflammatory diseases.