A nuclear magnetic resonance study of axial ligation for the reduced states of chloroperoxidase,cytochrome P-450cam,and porphinatoiron(II) thiolate complexes

The reduced forms of cytochrome P-450_cam and chloroperoxidase were examined by proton NMR spectroscopy. The pH and temperature dependences of the proton NMR spectra of both ferrous enzymes are reported. A series of alkyl mercaptide complexes of both synthetic and natural-derivative iron(II) porphyrins was also examined. The proton NMR spectra of these complexes facilitated the assignment of resonances due to the axial ligand in the model compounds on the basis of their isotropic shifts and multiplicities. Comparison of model compound data with that for the reduced enzymes supports assignment of the methylene protons for the axial cysteinate of ferrous cytochrome P-450_cam and ferrous chloroperoxidase to proton NMR resonances at 279 and 200 ppm (pH 7.0, 298K), respectively. Differences in the active site structure of the two enzymes are further demonstrated by ¹⁵N-NMR spectroscopy of the cyanide complexes of the ferric forms.     

Recent developments in the rapid analysis of plants and tracking their bioactive constituents

Natural products chemistry has witnessed many new developments in the last 5 years like extractions with subcritical water and ionic liquids, LC/HRMS and LC/SPE/cryo-NMR, UHPLC, TLC/MS, MS-based preparative HPLC, comprehensive chromatography (GC × GC, LC × LC), high-throughput screening, introduction of monolithic columns, miniaturisation, and automated structure identification. Nevertheless identifying bioactive constituents in complex plant extracts remains a tedious process. The classical approach of bioassay guided fractionation is time-consuming while off-line screening of extracts does not provide information on individual compounds and sometimes suffers from false positives or negatives. One way out of this is by coupling chromatography with chemical or biochemical assays, so called high resolution screening. An example is the development of HPLC on-line assays for antioxidants. By the post-column addition of a relatively stable coloured radical like DPPH^• or ABTS^•+, radical scavengers are detected as negative peaks because in a reaction coil they reduce the model radical to its reduced, non-coloured form. When combined with LC/DAD/MS and LC/SPE/NMR, reliable identification of active constituents becomes possible without the necessity of ever isolating them in a classical sense. Also for finding leads for new drugs, combining HPLC with biochemical assays is interesting but technically more difficult. Most enzymes do not work at the organic modifier concentrations commonly encountered in RP-HPLC and the reaction time is often longer requiring dilution and lengthy coils respectively. Therefore, new techniques have to be implemented to gain the required sensitivity for on-line enzyme assays. For stable analytes, high temperature LC offers a solution to the organic modifier problem. When enzymes are highly expensive, like those used in the screening for Cytochrome P450 inhibitors, miniaturisation to chip format may offer a way out. Microreactors (chips) are not only useful for miniaturising larger assays but also offer completely new prospects in phytochemical analysis. One such application is in the sample clean-up of acids and bases like alkaloids. In a lay-out of three parallel channels of 100 μm width with the middle one containing organic phase and the two outer ones water of high pH (feed phase) and low pH (trapping phase) such a chip replaces two classical LLE steps but is much faster and requires less solvents and less manpower input.     

Strategies for dereplication of natural compounds using high-resolution tandem mass spectrometry

Complete structural elucidation of natural products is commonly performed by nuclear magnetic resonance spectroscopy (NMR), but annotating compounds to most likely structures using high-resolution tandem mass spectrometry is a faster and feasible first step. The CASMI contest 2016 (Critical Assessment of Small Molecule Identification) provided spectra of eighteen compounds for the best manual structure identification in the natural products category. High resolution precursor and tandem mass spectra (MS/MS) were available to characterize the compounds. We used the Seven Golden Rules, Sirius2 and MS-FINDER software for determination of molecular formulas, and then we queried the formulas in different natural product databases including DNP, UNPD, ChemSpider and REAXYS to obtain molecular structures. We used different in-silico fragmentation tools including CFM-ID, CSI:FingerID and MS-FINDER to rank these compounds. Additional neutral losses and product ion peaks were manually investigated. This manual and time consuming approach allowed for the correct dereplication of thirteen of the eighteen natural products.     

Target-specific NMR detection of protein–ligand interactions with antibody-relayed <Superscript>15</Superscript>N-group selective STD

Fragment-based drug design has been successfully applied to challenging targets where the detection of the weak protein–ligand interactions is a key element. ¹H saturation transfer difference (STD) NMR spectroscopy is a powerful technique for this work but it requires pure homogeneous proteins as targets. Monoclonal antibody (mAb)-relayed ¹⁵N-GS STD spectroscopy has been developed to resolve the problem of protein mixtures and impure proteins. A ¹⁵N-labelled target-specific mAb is selectively irradiated and the saturation is relayed through the target to the ligand. Tests on the anti-Gal-1 mAb/Gal-1/lactose system showed that the approach is experimentally feasible in a reasonable time frame. This method allows detection and identification of binding molecules directly from a protein mixture in a multicomponent system.     

Identification of metabolites from liquid chromatography–coulometric array detection profiling: Gas chromatography–mass spectrometry and refractionation provide essential information orthogonal to LC–MS/microNMR

Liquid chromatography–coulometric array detection (LC–EC) is a sensitive, quantitative, and robust metabolomics profiling tool that complements the commonly used mass spectrometry (MS) and nuclear magnetic resonance (NMR)-based approaches. However, LC–EC provides little structural information. We recently demonstrated a workflow for the structural characterization of metabolites detected by LC–EC profiling combined with LC–electrospray ionization (ESI)–MS and microNMR. This methodology is now extended to include (i) gas chromatography (GC)–electron ionization (EI)–MS analysis to fill structural gaps left by LC–ESI–MS and NMR and (ii) secondary fractionation of LC-collected fractions containing multiple coeluting analytes. GC–EI–MS spectra have more informative fragment ions that are reproducible for database searches. Secondary fractionation provides enhanced metabolite characterization by reducing spectral overlap in NMR and ion suppression in LC–ESI–MS. The need for these additional methods in the analysis of the broad chemical classes and concentration ranges found in plasma is illustrated with discussion of four specific examples: (i) characterization of compounds for which one or more of the detectors is insensitive (e.g., positional isomers in LC–MS, the direct detection of carboxylic groups and sulfonic groups in ¹H NMR, or nonvolatile species in GC–MS), (ii) detection of labile compounds, (iii) resolution of closely eluting and/or coeluting compounds, and (iv) the capability to harness structural similarities common in many biologically related, LC–EC-detectable compounds.     

Towards miniaturization of a structural genomics pipeline using micro-expression and microcoil NMR

In structural genomics centers, nuclear magnetic resonance (NMR) screening is in increasing use as a tool to identify folded proteins that are promising targets for three-dimensional structure determination by X-ray crystallography or NMR spectroscopy. The use of 1D ¹H NMR spectra or 2D [¹H,¹⁵N]-correlation spectroscopy (COSY) typically requires milligram quantities of unlabeled or isotope-labeled protein, respectively. Here, we outline ways towards miniaturization of a structural genomics pipeline with NMR screening for folded globular proteins, using a high-density micro-fermentation device and a microcoil NMR probe. The proteins are micro-expressed in unlabeled or isotope-labeled media, purified, and then subjected to 1D ¹H NMR and/or 2D [¹H,¹⁵N]-COSY screening. To demonstrate that the miniaturization is functioning effectively, we processed nine mouse homologue protein targets and compared the results with those from the “macro-scale” Joint Center of Structural Genomics (JCSG) high-throughput pipeline. The results from the two pipelines were comparable, illustrating that the data were not compromised in the miniaturized approach.     

CYP109E1 is a novel versatile statin and terpene oxidase from Bacillus megaterium

CYP109E1 is a cytochrome P450 monooxygenase from Bacillus megaterium with a hydroxylation activity for testosterone and vitamin D3. This study reports the screening of a focused library of statins, terpene-derived and steroidal compounds to explore the substrate spectrum of this enzyme. Catalytic activity of CYP109E1 towards the statin drug-precursor compactin and the prodrugs lovastatin and simvastatin as well as biotechnologically relevant terpene compounds including ionones, nootkatone, isolongifolen-9-one, damascones, and β-damascenone was found in vitro. The novel substrates induced a type I spin-shift upon binding to P450 and thus permitted to determine dissociation constants. For the identification of conversion products by NMR spectroscopy, a B. megaterium whole-cell system was applied. NMR analysis revealed for the first time the ability of CYP109E1 to catalyze an industrially highly important reaction, the production of pravastatin from compactin, as well as regioselective oxidations generating drug metabolites (6′β-hydroxy-lovastatin, 3′α-hydroxy-simvastatin, and 4″-hydroxy-simvastatin) and valuable terpene derivatives (3-hydroxy-α-ionone, 4-hydroxy-β-ionone, 11,12-epoxy-nootkatone, 4(R)-hydroxy-isolongifolen-9-one, 3-hydroxy-α-damascone, 4-hydroxy-β-damascone, and 3,4-epoxy-β-damascone). Besides that, a novel compound, 2-hydroxy-β-damascenone, produced by CYP109E1 was identified. Docking calculations using the crystal structure of CYP109E1 rationalized the experimentally observed regioselective hydroxylation and identified important amino acid residues for statin and terpene binding.

     

The 5-hydrazino-3-methylisothiazole-4-carboxylic acid,its new 5-substituted derivatives and their antiproliferative activity

Currently, the basic method of treatment of colon cancer is surgery. The range of anticancer drugs used in the treatment of colorectal cancer is small and is based mainly on systemic combination chemotherapy. As a result of the designed syntheses, we received new isothiazole derivatives with anticancer activity. The synthesized 5-hydrazino-3-methylisothiazole-4-carboxylic acid has never been obtained before. It is also a substrate for the synthesis of its innovative derivatives, i.e. compounds that are Schiff bases. The identification of the structure of new compounds was carried out using mass spectrometry (MS), proton nuclear magnetic resonance spectroscopy (¹H NMR), carbon nuclear magnetic resonance spectroscopy (¹³C NMR) and infrared spectroscopy (IR). Potential antitumor activity was confirmed in antiproliferative MTT and SRB tests. The selected, most biologically active substances were characterized by high selectivity towards leukemia and colon cancer cell lines. They caused high inhibition of proliferation of human biphenotypic B cell myelomonocytic leukemia MV4-11 (13 compounds), human colon adenocarcinoma cell lines sensitive LoVo (8 compounds) and resistant to doxorubicin LoVo/DX (12 compounds). However, in the conducted studies, their activity against breast adenocarcinoma MCF-7 and normal non-tumorigenic epithelial cell line derived from mammary gland MCF-10A was substantially lower. The result of this work is claimed Polish patent application.     

Analytical methods to determine phytoestrogenic compounds

The analytical methods for the determination of phytoestrogenic compounds in edible plants, plant products and biological matrices are reviewed. The detection, qualitative and quantitative methods based on different chromatographic separations of gas chromatography (GC), high-performance liquid chromatography (HPLC) and capillary electrophoresis (CE) coupled with various detections by ultraviolet absorption (UV), electrochemical detection (ED), fluorescence detection, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR), as well as non-chromatographic immunoassay are each extensively examined and compared. An overview on phytoestrogen chemistry, bioactivities and health effects, plant precursors, metabolism and sample preparation is also presented.     

Could multivariate statistics exploit HPTLC and NMR data to reveal bioactive compounds? The case of Paeonia mascula

Bioassay screening or pharmacological evaluation is a common approach to guide the isolation process towards the pure bioactive component. Nevertheless, plenteous time is wasted on isolation, purification and structural elucidation of already known compounds. The tendency over the last years for implementation of high-throughput screening (HTS) technologies leads to the prior identification of the compounds that contribute to the demonstrated activity, avoiding the constant re-isolation of known compounds, reducing workload and cost. The extract of Paeonia mascula ssp. hellenica, which was discriminated for its tyrosinase inhibition among other extracts from Greek flora, was fractionated by FCPC and the resulted fractions were assayed for tyrosinase inhibition potential and further analyzed by HPTLC and NMR. An integrated HPTLC-based procedure for the tracing of compounds that contributed to tyrosinase inhibitory effect in active fractions was established with the use of multivariate data analysis. Additionally, NMR spectral data were correlated with the activity towards tyrosinase resulting in the identification of bioactive compounds through the combination of the Heterocovariance approach (HetCA) and the statistical total correlation spectroscopy (STOCSY). The combined data deriving from NMR and HPTLC correlated to the results of the biological activity by the statistically driven approach, revealed potent whitening agents, providing a major reduction in workload by direct use of routine information.     

Degradation of Morpholine by an Environmental Mycobacterium Strain Involves a Cytochrome P-450

A Mycobacterium strain (RP1) was isolated from a contaminated activated sludge collected in a wastewater treatment unit of a chemical plant. It was capable of utilizing morpholine and other heterocyclic compounds, such as pyrrolidine and piperidine, as the sole source of carbon, nitrogen, and energy. The use of in situ ¹H nuclear magnetic resonance (¹H NMR) spectroscopy allowed the determination of two intermediates in the biodegradative pathway, 2-(2-aminoethoxy)acetate and glycolate. The inhibitory effects of metyrapone on the degradative abilities of strain RP1 indicated the involvement of a cytochrome P-450 in the biodegradation of morpholine. This observation was confirmed by spectrophotometric analysis and ¹H NMR. Reduced cell extracts from morpholine-grown cultures, but not succinate-grown cultures, gave rise to a carbon monoxide difference spectrum with a peak near 450 nm, which indicated the presence of a soluble cytochrome P-450. ¹H NMR allowed the direct analysis of the incubation medium containing metyrapone, a specific inhibitor of cytochrome P-450. The inhibition of morpholine degradation was dependent on the morpholine/metyrapone ratio. The heme-containing monooxygenase was also detected in pyrrolidine- and piperidine-grown cultures. The abilities of different compounds to support strain growth or the induction of a soluble cytochrome P-450 were assayed. The results suggest that this enzyme catalyzes the cleavage of the C—N bond of the morpholine ring.     

4D Non-uniformly sampled C,C-NOESY experiment for sequential assignment of 13C,15N-labeled RNAs

¹³C spin diluted protein samples can be produced using [1-¹³C] and [2-¹³C]-glucose (Glc) carbon sources in the bacterial growth medium. The ¹³C spin dilution results in favorable ¹³C spectral resolution and polarization transfer behavior. We recently reported the combined use of [1-¹³C]- and [2-¹³C]-Glc labeling to facilitate the structural analysis of insoluble and non-crystalline biological systems by solid-state NMR (ssNMR), including sequential assignment, detection of long-range contacts and structure determination of macromolecular assemblies. In solution NMR the beneficial properties of sparsely labeled samples using [2-¹³C]-glycerol (¹³C labeled Cα sites on a ¹²C diluted background) have recently been exploited to provide a bi-directional assignment method (Takeuchi et al. in J Biomol NMR 49(1):17–26, 2011 ). Inspired by this approach and our own recent results using [2-¹³C]-Glc as carbon sources for the simplification of ssNMR spectra, we present a strategy for a bi-directional sequential assignment of solid-state NMR resonances and additionally the detection of long-range contacts using the combination of ¹³C spin dilution and 3D NMR spectroscopy. We illustrate our results with the sequential assignment and the collection of distance restraints on an insoluble and non-crystalline supramolecular assembly, the Salmonella typhimurium type III secretion system needle.     

MALDI-TOF mass spectrometry of naturally occurring mixtures of monorhamnolipids and dirhamnolipids

MALDI-TOFMS approaches have been developed for high-throughput screening of naturally occurring mixtures of rhamnolipids from Pseudomonas spp. Monorhamnolipids and dirhamnolipids are readily distinguished by characteristic molecular adduct ions, [M+Na]⁺ and [M−H+Na₂]⁺, with variously acylated rhamnolipids differing by 28 mu. Following proton-deuterium exchange, deuterated [M+Na−4¹H+4²H]⁺ and [M+Na−6¹H+6²H]⁺ ions are observed for the monorhamnolipids and dirhamnolipids, respectively, which allows rapid identification of these molecules. The described approach has been validated by compositional analysis using GC/MS, fractionation by RPHPLC, and analysis by 1D and 2D NMR spectroscopy. MALDI-TOFMS analysis allows the rapid screening of variously acylated rhamnolipids, and has potential for selective identification of new surfactants from microbial strains.     

Fast screening and structural elucidation of G-quadruplex ligands from a mixture via G-quadruplex recognition and NMR methods

Currently, there is a considerable interest in discovering G-quadruplex ligands. Plant-derived agents, because of their diversity in structure and bioactivity and low toxicity, may be a very diverse source of G-quadruplex ligands. However, up to now, the screening of G-quadruplex ligands from natural plant extract has not been reported. Herein, in order to develop a simple method for fast identifying G-quadruplex ligands from plant extract, we intended to substitute the spectral shift in the imino region (δ 10–12) in ¹H NMR spectra of G-quadruplex for in vitro bioassay to judge the existence/nonexistence of G-quadruplex ligand(s) in plant extract, and then couple G-quadruplex recognition with NMR based structure elucidation to identify the structure of the ligand(s) without the need of prior separation. In this paper, we successfully screened a G-quadruplex ligand from a simulated plant extract using this approach. This research work provides a promising tactic to find new leading compounds from nature plant extract.     

Synthesis,crystal structure,optical properties and antibacterial evaluation of novel imidazo[1, 5‐a]pyridine derivatives bearing a hydrazone moiety

A series of novel imidazo[1,5‐a]pyridine‐hydrazone derivatives were synthesized and characterized by infrared spectroscopy (IR), ¹H NMR, ¹³C NMR and high resolution mass spectrometer (HRMS). Typically, the spatial structure of compound 3j was determined using X‐ray diffraction analysis. The UV–vis absorption and fluorescence spectral characteristics of the compounds in dichloromethane and acetonitrile were investigated. Absorption peaks could be observed in the wavelength range 290–450 nm. It can also be seen that they display very similar maximum emission. The group attached to hydrazone hardly influenced the maximum emission. Furthermore, all the compounds were evaluated for antibacterial activity and were found to be more effective against Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa and Shigella compared with chloramphenicol. Copyright © 2013 John Wiley & Sons, Ltd.     

Identification and structural analysis of a glycophospholipid component from the venom of ant Paraponera clavata

The venom of South American ant Paraponera clavata and its low-molecular-mass fraction were shown to possess insectotoxic and pore-forming activities. A number of glycophospholipid components were isolated from this ant venom by means of gel filtration and reversed-phase chromatography. Some of the compounds cause conductivity fluctuations in lipid bilayer membranes within the ranges 3–25 pS and 200–400 pS at concentrations of 10^?6 to 10^?7 M. N-Acetylglucosamine, a fatty acid, and phosphoric acid residues were found in their structures. A full structure, 3-myristoyl-2-acetamido-2-deoxy-α-D-glucopyranosyl phosphate, was elucidated for one of the compounds by the use of ¹H-, ¹³C-, and ³¹P NMR spectroscopy and mass spectrometry.     

Ultraviolet and tandem mass spectrometry for simultaneous quantification of 21 pivotal metabolites in plasma from patients with diabetic nephropathy

A sensitive and specific method was developed for simultaneous determination of 21 compounds related to the diabetic nephropathy (DN) in a single analysis using high-performance liquid chromatography coupled to ultraviolet and tandem mass spectrometry (HPLC–UV/MS/MS) in human plasma. With retention times and MS/MS for peak identification, both UV and MS detectors were used for quantification. Calibration curves suitable for the analysis of plasma were linear (r² > 0.998) with limits of detection (LOD) from 10 to 1000 ng/mL. Intraday relative standard deviation (R.S.D.) and interday R.S.D. were both lower than 15%. With the case and control study, we found five potential biomarkers of DN, including adenosine, inosine, uric acid, xanthine and creatinine.     

The intact muscle lipid composition of bulls: an investigation by MALDI-TOF MS and 31P NMR

The analysis of beef lipids is normally based on chromatographic techniques and/or gas chromatography in combination with mass spectrometry (GC/MS). Modern techniques of soft-ionization MS were so far scarcely used to investigate the intact lipids in muscle tissues of beef. The objective of the study was to investigate whether matrix-assisted laser desorption and ionization time-of-flight (MALDI-TOF) mass spectrometry and ³¹P nuclear magnetic resonance (NMR) spectroscopy are useful tools to study the intact lipid composition of beef. For the MALDI-TOF MS and ³¹P NMR investigations muscle samples were selected from a feeding experiment with German Simmental bulls fed different diets. Beside the triacylglycerols (TAGs), phosphatidylethanolamine (PE), phosphatidylcholine (PC) and phosphatidylinositol (PI) species the MALDI-TOF mass spectra of total muscle lipids gave also intense signals of cardiolipin (CL) species.The application of different matrix compounds, 2,5-dihydroxybenzoic acid (DHB) and 9-aminoacridine (9-AA), leads to completely different mass spectra: 9-AA is particularly useful for the detection of (polar) phospholipids, whereas apolar lipids, such as cholesterol and triacylglycerols, are exclusively detected if DHB is used. Finally, the quality of the negative ion mass spectra is much higher if 9-AA is used.     

The synthesis and characterization of nucleotide complexes involving an asymmetric metal

The synthesis of cobalt and chromium complexes of H₄ATP and H₄GTP in which the metal is asymmetric are reported. These compounds were characterized by visible spectroscopy, fast atom bombardment mass spectroscopy (FAB MS), and ³¹P NMR. The mass spectral data allow identification of the complexes to be made from ions in the molecular weight region. The effect of an asymmetric metal greatly alters the appearance of the ³¹P NMR spectra in comparison to complexes which do not have this feature. Complexes of uridine diphosphoglucose, UDPG, are also reported. The effect of an asymmetric metal ion on the chromatographic and spectral properties of the complexes are discussed.     

Highly selective screening of the bioactive compounds in Huoxue capsule using immobilized β2-adrenoceptor affinity chromatography

A highly selective assay was developed for screening compounds that bind to the porcine recombinant β₂-adrenoceptor (β₂-AR) with affinity chromatography coupled to quadrupole time-of-flight mass spectrometry (Q-TOF–MS). The methodology involved selective screening with immobilized β₂-AR, a highly accurate identification via Q-TOF–MS, and a functional evaluation of the screened compounds with a sensitive myograph system. Ferulic acid, hydroxysafflor yellow A (HSYA), and naringin were confirmed to be the bioactive compounds in Huoxue capsule that specifically bound to the β₂-AR. These compounds produced a concentration-dependent relaxation of arteries that were contracted by treatment with phenylephrine, and the relaxation caused by these compounds was attenuated in the presence of ICI 118551, a type of β₂-AR antagonist. Our data indicate that the use of an immobilized receptor is potentially an alternative method for the rapid screening of bioactive compounds in a complex matrix because of its high specificity. β₂-AR affinity chromatography was valuable in focusing attention on the further investigation of ferulic acid, HSYA, and naringin as β₂-AR agonists.