Metabolome Analysis of Oryza sativa (Rice) Using Liquid Chromatography-Mass Spectrometry for Characterizing Organ Specificity of Flavonoids with Anti-inflammatory and Anti-oxidant Activity.

Oryza sativa L. (rice) is an important staple crop across the world. In the previous study, we identified 36 specialized (secondary) metabolites including 28 flavonoids. In the present study, a metabolome analysis using liquid chromatography-mass spectrometry was conducted on the leaf, bran, and brown and polished rice grains to better understand the distribution of these metabolites. Principal component analysis using the metabolome data clearly characterized the accumulation patterns of the metabolites. Flavonoids, e.g., tricin, tricin 7-O-rutinoside, and tricin 7-O-ß-D-glucopyranoside, were mainly present in the leaf and bran but not in the polished grain. In addition, anti-inflammatory and anti-oxidant activity of the metabolites were assayed in vitro. Tricin 4'-O-(erythro-ß-guaiacylglyceryl)ether and isoscoparin 2″-O-(6‴-(E)-feruloyl)-glucopyranoside showed the strongest activity for inhibiting nitric oxide (NO) production and 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging, respectively.

Avenolide, a Streptomyces hormone controlling antibiotic production in Streptomyces avermitilis.

Gram-positive bacteria of the genus Streptomyces are industrially important microorganisms, producing >70% of commercially important antibiotics. The production of these compounds is often regulated by low-molecular-weight bacterial hormones called autoregulators. Although 60% of Streptomyces strains may use γ-butyrolactone-type molecules as autoregulators and some use furan-type molecules, little is known about the signaling molecules used to regulate antibiotic production in many other members of this genus. Here, we purified a signaling molecule (avenolide) from Streptomyces avermitilis--the producer of the important anthelmintic agent avermectin with annual world sales of $850 million--and determined its structure, including stereochemistry, by spectroscopic analysis and chemical synthesis as (4S,10R)-10-hydroxy-10-methyl-9-oxo-dodec-2-en-1,4-olide, a class of Streptomyces autoregulator. Avenolide is essential for eliciting avermectin production and is effective at nanomolar concentrations with a minimum effective concentration of 4 nM. The aco gene of S. avermitilis, which encodes an acyl-CoA oxidase, is required for avenolide biosynthesis, and homologs are also present in Streptomyces fradiae, Streptomyces ghanaensis, and Streptomyces griseoauranticus, suggesting that butenolide-type autoregulators may represent a widespread and another class of Streptomyces autoregulator involved in regulating antibiotic production.

Regio- and stereospecificity of filipin hydroxylation sites revealed by crystal structures of cytochrome P450 105P1 and 105D6 from Streptomyces avermitilis.

The polyene macrolide antibiotic filipin is widely used as a probe for cholesterol and a diagnostic tool for type C Niemann-Pick disease. Two position-specific P450 enzymes are involved in the post-polyketide modification of filipin during its biosynthesis, thereby providing molecular diversity to the "filipin complex." CYP105P1 and CYP105D6 from Streptomyces avermitilis, despite their high sequence similarities, catalyze filipin hydroxylation at different positions, C26 and C1', respectively. Here, we determined the crystal structure of the CYP105P1-filipin I complex. The distal pocket of CYP105P1 has the second largest size among P450 hydroxylases that act on macrolide substrates. Compared with previously determined substrate-free structures, the FG helices showed significant closing motion on substrate binding. The long BC loop region adopts a unique extended conformation without a B' helix. The binding site is essentially hydrophobic, but numerous water molecules are involved in recognizing the polyol side of the substrate. Therefore, the distal pocket of CYP105P1 provides a specific environment for the large filipin substrate to bind with its pro-S side of position C26 directed toward the heme iron. The ligand-free CYP105D6 structure was also determined. A small sub-pocket accommodating the long alkyl side chain of filipin I was observed in the CYP105P1 structure but was absent in the CYP105D6 structure, indicating that filipin cannot bind to CYP105D6 with a similar orientation due to steric hindrance. This observation can explain the strict regiospecificity of these enzymes.

Inhibitory effects of constituents from Morus alba var. multicaulis on differentiation of 3T3-L1 cells and nitric oxide production in RAW264.7 cells.

A new arylbenzofuran, 3',5'-dihydroxy-6-methoxy-7-prenyl-2-arylbenzofuran (1), and 25 known compounds, including moracin R (2), moracin C (3), moracin O (4), moracin P (5), artoindonesianin O (6), moracin D (7), alabafuran A (8), mulberrofuran L (9), mulberrofuran Y (10), kuwanon A (11), kuwanon C (12), kuwanon T (13), morusin (14), kuwanon E (15), sanggenon F (16), betulinic acid (17), uvaol (18), ursolic acid (19), ß-sitosterol (20), oxyresveratrol 2-O-ß-D-glucopyranoside (21), mulberroside A (22), mulberroside B (23), 5,7-dihydroxycoumarin 7-O-ß-D-glucopyranoside (24), 5,7-dihydroxycoumarin 7-O-ß-D-apiofuranosyl-(1→6)-O-ß-D-glucopyranoside (25) and adenosine (26), were isolated from Morus alba var. multicaulis Perro. (Moraceae). Their structures were determined by spectroscopic methods. The prenyl-flavonoids 11-14, 16, triterpenoids 17,18 and 20 showed significant inhibitory activity towards the differentiation of 3T3-L1 adipocytes. The arylbenzofurans 1-10 and prenyl-flavonoids 11-16 also showed significant nitric oxide (NO) production inhibitory effects in RAW264.7 cells.

Genome mining in Streptomyces avermitilis: A biochemical Baeyer-Villiger reaction and discovery of a new branch of the pentalenolactone family tree.

Incubation of 1-deoxy-11-oxopentalenic acid (12) with recombinant PtlE protein from Streptomyces avermitilis in the presence of NADPH and catalytic FAD gave the Baeyer-Villiger oxidation product, the previously unknown compound neopentalenolactone D (13), representing a new branch of the pentalenolactone biosynthetic pathway. The structure and stereochemistry of the derived neopentalenolactone D methyl ester (13-Me) were fully assigned by a combination of GC-MS and NMR analysis and confirmed by X-ray crystallography. Neopentalenolactone D (13) was also isolated from engineered cultures of S. avermitilis from which the ptlD gene within the 13.4-kb (neo)-ptl biosynthetic gene cluster had been deleted. The DeltaptlEDeltaptlD double deletion mutant accumulated 12, the substrate for the ptlE gene product, while the corresponding single DeltaptlE mutant produced 12 as well as the related oxidation products 14 and 15. Engineered strains of S. avermitilis, SUKA5 and pKU462::ermRp-ptl cluster, harboring the complete (neo)ptl cluster produced the oxidized lactone 18 and the closely related seco acid hydrolysis products 16 and 17.

Effects of chemically induced contraction of a coordination polyhedron on the dynamical magnetism of bis(phthalocyaninato)disprosium, a single-4f-ionic single-molecule magnet with a Kramers ground state.

Chemically induced longitudinal contraction of the square-antiprism coordination polyhedron of a peripherically substituted bis(phthalocyaninato)dysprosiumate(III), a dysprosium-based single-4f-ionic single-molecule magnet having a J z = +/- (13)/ 2 Kramers doublet ground state, resulted in drastic changes in dynamical magnetism including a doubling of the energy barrier, a 2-order-of-magnitude decrease of the spin reversal rate, a significant rise of the blocking temperature, and the first observation of the emergence of a large remanent magnetization.

Correction to: Naturally occurring cell adhesion inhibitors.

The article Naturally occurring cell adhesion inhibitors, written by Satoshi Takamatsu, was originally published electronically on the publisher's internet portal.

Naturally occurring cell adhesion inhibitors.

This paper reviews naturally occurring cell adhesion inhibitors derived from a plant, microbial and marine origin. Plant-derived inhibitors are classified according to a type of structure. Microbially and marine-derived inhibitors were described according to age. In addition, effects of inhibitors on cell proliferation and that of standards on cell adhesion are listed as much as possible.

Corrigendum: Total synthesis and absolute configuration of avenolide, extracellular factor in Streptomyces avermitilis.

This corrects the article DOI: 10.1038/ja.2011.90.

Screening for free radical scavenging and cell aggregation inhibitory activities by secondary metabolites from Turkish Verbascum species.

Free radical scavenging and cell aggregation inhibitory activities of 36 secondary metabolites isolated from the methanolic extracts of Verbascum cilicicum Boiss., V. lasianthum Boiss. ex Bentham, V pterocalycinum var. mutense Hub.-Mor., and V. salviifolium Boiss. (Scrophulariaceae) were investigated. The isolated compounds, 6-O-vaniloyl ajugol (1), ilwensisaponin A (2), ilwensisaponin C (3), verbascoside (4), beta-hydroxyacteoside (5), martynoside (6), poliumoside (7), forsythoside B (8), angoroside A (9), dehydrodiconiferyl alcohol-9-O-beta-D-glucopyranoside (10), dehydrodiconiferyl alcohol-9'-O-beta-D-glucopyranoside (11), apigenin 7-O-beta-glucopyranoside (12), luteolin 7-O-beta-glucopyranoside (13), luteolin 3'-O-beta-glucopyranoside (14) and chrysoeriol 7-O-beta-glucopyranoside (15), exhibited a dose-dependent inhibition of bioautographic and spectrophotometric DPPH activities. Verbascoside (4) was the most active (IC50 4.0 microg/ml) comparing it to vitamin C (IC50 4.4 microg/ml) to inhibit phorbol 12-myristate 13-acetate (PMA)-induced peroxide-catalyzed oxidation of 2',7'-dichlorofluorescein (DCFH) by reactive oxygen species (ROS) within human promyelocytic HL-60 cells. Ilwensisaponin A (2) (MIC 6.9 microg/ml) showed moderate in vitro activity on lymphocyte-associated antigen-1 (LFA-1)/intercellular adhesion molecule-1 (ICAM-1)-mediated aggregation using the HL-60 cell line [positive control was cytochalasin B (MIC 2.3 microg/ml)]. None of the other compounds showed free radical scavenging and cell aggregation inhibitory activities.

Antioxidant lignans from Larrea tridentata.

Three lignans, (7S,8S,7'S,8'S)-3,3',4'-trihydroxy-4-methoxy-7,7'-epoxylignan, meso-(rel 7S,8S,7'R,8'R)-3,4,3',4'-tetrahydroxy-7,7'-epoxylignan, and (E)-4,4'-dihydroxy-7,7'-dioxolign-8(8')-ene, together with 10 known compounds, were isolated from the leaves of Larrea tridentata. The structures of the new compounds were determined primarily from 1D and 2D NMR spectroscopic analysis. Their antioxidant activities against intracellular reactive oxygen species were evaluated in HL-60 cells.

Biologically active secondary metabolites from Ginkgo biloba.

Three new compounds, (7E)-2beta,3alpha-dihydroxy-megastigm-7-en-9-one (1), 3-[5,7-dihydroxy-2-(4-methoxyphenyl)-4-oxo-4H-chromen-8-yl]-4-methoxybenzoic acid (2), and 4'-O-methyl myricetin 3-O-(6-O-alpha-L-rhamnopyranosyl)-beta-D-glucopyranoside (3), were isolated from Ginkgo biloba, together with 27 known compounds. The structures of the new compounds were determined primarily from 1D- and 2D-NMR analysis. The 4-O-methylbenzoic acid structural feature at C-8 in 2 is encountered for the first time. The antioxidant activities of 29 compounds isolated from Ginkgo biloba were evaluated on intracellular reactive oxygen species in HL-60 cells. It was found that quercetin, kampferol, and tamarixetin had antioxidant activity that was approximately 3-fold greater than that of their respective glycosides and also approximately 3-fold greater than that of a standard ascorbic acid with an IC(50) at maximum effectiveness.

New cell-cell adhesion inhibitors from Streptomyces sp. UMA-044.

Three compounds, NP25301 (1), NP25302 (2) and bohemamine (3), inhibitors of cell adhesion based on LFA-1/ICAM-1, were isolated from the cultured broth of the strain Streptomyces sp. UMA-044. New compounds 1 and 2 were identified as 2-(3'-carbamoylphenoxy)acrylic acid methyl ester and deoxybohemamine, respectively, based on spectroscopic analyses. Compounds 1 approximately 3 inhibited adhesion of HL-60 cells to CHO-ICAM-1 cells at IC50 values of 29.5 microg/ml for 1, 24.3 microg/ml for 2, and 27.2 microg/ml for 3.

Characterization of Mycotypha metabolites found to be inhibitors of cell adhesion molecules.

Three inhibitors of cell adhesion based on LFA-1/ICAM-1 were isolated from the cultured broth of the fungal strain Mycotypha sp. UMF-006. These compounds were identified by spectroscopy to be cytochalasin E (1), 5,6-dehydro-7-hydroxy derivative of cytochalasin E (2) and delta 6,12-isomer of 2 (3). All these components inhibited adhesion of HL-60 cells to CHO-ICAM-1 cells at IC50 values of 30 micrograms/ml for 1, 75 micrograms/ml for 2, and 90 micrograms/ml for 3.

An industrial process for synthesizing Lodenosine (FddA).

Two industrial synthetic approaches to Lodenosine (1, FddA, 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl) adenine) via a purine riboside or a purine 3'-deoxyriboside are described. Several novel applications of deoxygenation and fluorination methods are compared considering reaction yields, economy, safety and environmental concerns.

A facile synthetic method for 3'-alpha-fluoro-2',3'-dideoxyadenosine.

A facile method for the synthesis of 3'-alpha-fluoro-2',3'-dideoxyadenosine (5) has been developed using a novel rearrangement of 3'-beta-bromine to the 2'-beta position during 3'-alpha fluorination.

Convenient synthesis of fluorinated nucleosides with perfluoroalkanesulfonyl fluorides.

Perfluoroalkanesulfonyl fluorides are effective dehydroxy-fluorination agents for the hydroxyl group at the sugar moiety of nucleoside derivatives and give the corresponding fluorinated nucleosides in good yield with an inversion of configuration in a single step.

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.

Effects of the herbal medicine composition "Saiko-ka-ryukotsu-borei-To" on the function of endothelial progenitor cells in hypertensive rats.

Endothelial progenitor cells (EPCs) are known to repair vascular injuries. Recent studies suggest that Saiko-ka-ryukotsu-borei-To (SKRBT), a traditional herbal medicine that has been used to treat stress-related neuropsychiatric disorders, has protective effects on cardiovascular diseases such as hypertension and arteriosclerosis. Spontaneously hypertensive rats (SHRs) were fed diets containing lyophilized SKRBT extract for 6 weeks. Peripheral blood mononuclear cells (MNCs) were isolated and cultured to assay EPC colony formation. Oxidative stress in MNCs was evaluated by thiobarbituric acid reactive substance (TBARS) assay and flowcytometric analyses. Treatment with SKRBT increased EPC colony numbers significantly (p<0.05) with decrease in oxidative stress and without affecting blood pressure in SHRs. Treatment with SKRBT did not reduce the expression of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase subunits in cardiovascular organs. Serum IL-6 level was significantly reduced. SKRBT is a feasible herbal medicine that protects against cardiovascular diseases through an increase in EPC function along with anti-oxidative effects, and may affect the link between chronic inflammation and cardiovascular disease.

Characterization of a silent sesquiterpenoid biosynthetic pathway in Streptomyces avermitilis controlling epi-isozizaene albaflavenone biosynthesis and isolation of a new oxidized epi-isozizaene metabolite.

The genome-sequenced, Gram-positive bacterium Streptomyces avermitilis harbours an orthologue (SAV_3032) of the previously identified epi-isozizaene synthase (SCO5222) in Streptomyces coelicolor A3(2). The sav3032 is translationally coupled with the downstream sav3031 gene encoding the cytochrome P450 CYP170A2 analogous to SCO5223 (CYP170A1) of S. coelicolor A3(2), which exhibits a similar translation coupling. Streptomyces avermitilis did not produce epi-isozizaene or any of its oxidized derivatives, albaflavenols and albaflavenone, under in any culture conditions examined. Nonetheless, recombinant SAV_3032 protein expressed in Escherichia coli catalysed the Mg²+-dependent cyclization of farnesyl diphosphate to epi-isozizaene. To effect the production of epi-isozizaene in S. avermitilis, the sav3032 gene was cloned and placed under control of a copy of the native S. avermitilis promoter rpsJp (sav4925). The derived expression construct was introduced by transformation into a large-deletion mutant of S. avermitilis SUKA16 and the resulting transformants accumulated epi-isozizaene. The previously characterized oxidized epi-isozizaene metabolites (4R)- and (4S)-albaflavenols and albaflavenone, as well as a previously undescribed doubly oxidized epi-isozizaene derivative were isolated from cultures of S. avermitilis SUKA16 transformants in which sav3032 was coexpressed with the P450-encoding sav3031. This new metabolite was identified as 4ß,5ß-epoxy-2-epi-zizaan-6ß-ol which is most likely formed by oxidation of (4S)-albaflavenol.