Structure and biosynthesis of the ribosomal lipopeptide antibiotic albopeptins.

Albopeptins produced by Streptomyces albofaciens JC-82-120 were isolated as effective antibiotics for plant pathogenetic disease in 1986. However, their unusual physicochemical properties hampered the determination of their chemical structures. In this report, we describe our efforts to elucidate their structures. Initially, the structure of an unusual C13-fatty acid with an N-hydroxyguanidyl group was determined using degradation and chemical synthesis. After the linear portion of the octapeptide core was constructed based on the 2D-NMR data, the final assembly of the unusual structure, including the sulfoxide bridge, was achieved through the analysis of detailed NMR data. The proposed structure of albopeptin B was supported by MS/MS data, which also enabled us to determine the structure of 5 albopeptin family members. Bioinformatics analysis of the genomic data of the producer strain further led us to propose that their biosynthetic pathway is similar to the ribosomally derived lanthipeptides possessing a long-chain fatty acid.

Structure and Stereochemistry of Amphidinolide N Congeners from Marine Dinoflagellate Amphidinium Species.

Two highly potent cytotoxic 26-membered macrolides, isocaribenolide-I (1) and a chlorohydrin 2, together with known amphidinolide N (3), have been isolated from a free-swimming dinoflagellate Amphidinium species (KCA09053 and KCA09056 strains) collected off Iriomote Island, Japan. The structures of 1 and 2 were determined to be a congener of 3 with an isobutyl terminus and the chlorohydrin form of 3, respectively, by detailed analyses of spectroscopic data. The relative stereochemistries of 1 and 2 were elucidated by the conformational analyses based on NMR data.

Efficient Protocol for Accurately Calculating 13C Chemical Shifts of Conformationally Flexible Natural Products: Scope, Assessment, and Limitations.

An efficient protocol for calculating 13C NMR chemical shifts for natural products with multiple degrees of conformational freedom is described. This involves a multistep procedure starting from molecular mechanics and ending with a large basis set density functional model to obtain accurate Boltzmann conformer weights, followed by empirically corrected density functional NMR calculations for the individual conformers. The accuracy of the protocol (average rms <4 ppm) was determined by application to ∼925 diverse natural products, the structures of which have been confirmed either by X-ray crystallography or independent synthesis. The protocol was then applied to ∼ 2275 natural products, the structures of which were elucidated mainly by NMR and MS data. Five to ten percent of the latter compounds exhibited rms errors significantly in excess of 4 ppm, suggesting possible structural or signal assignment errors. Both data sets are available from an online browser ( NMR.wavefun.com ). The procedure can be and has been fully automated and is practical using present-generation personal computers, requiring a few hours or days depending on the size of the molecule and number of accessible conformers.

Cyclohelminthol X, a Hexa-Substituted Spirocyclopropane from Helminthosporium velutinum yone96: Structural Elucidation, Electronic Circular Dichroism Analysis, and Biological Properties.

Helminthosporium velutinum yone96 produces cyclohelminthol X (1), a unique hexa-substituted spirocyclopropane. Although its molecular formula and NMR spectral data resemble those of AD0157, being isolated from marine fungus Paraconiothyrium sp. HL-78-gCHSP3-B005, our detailed analyses disclosed a totally different structure. Chemical shift calculations and electronic circular dichroism spectral calculations were quite helpful to establish the structure, when those were performed based on density functional theory. The carbon framework of cyclohelminthols I-IV is found at the C1-C8 propenylcyclopentene substructure of 1. Thus, 1 is assumed to be biosynthesized by cyclopropanation between an oxidized form of cyclohelminthol IV and a succinic anhydride derivative 4. Cytotoxicity for two cancer cell lines and proteasome inhibition efficiency are measured.

Iriomoteolides-9a and 11a: two new odd-numbered macrolides from the marine dinoflagellate Amphidinium species.

Iriomoteolides-9a (1) and 11a (2), new 15- and 19-membered macrolides, respectively, have been isolated from the marine dinoflagellate Amphidinium species (strain KCA09052). Compounds 1 and 2 were obtained from the extracts of the algal cells inoculated in the PES and TKF seawater medium, respectively. The structures of 1 and 2 were assigned on the basis of detailed NMR analyses. Compounds 1 and 2 exhibited cytotoxic activity against human cervix adenocarcinoma HeLa cells.

Structural Analysis of Novel Low-Digestible Sucrose Isomers Synthesized from D-Glucose and D-Fructose by Thermal Treatment.

The synthesis of the saccharide ß-D-fructopyranosyl-(2→6)-D-glucopyranose, which was isolated from Super Ohtaka®, has recently been reported. During the synthesis of this saccharide, the formation of two novel saccharides from D-glucose and D-fructose was observed. The present study aimed to confirm the structures of the two disaccharides synthesized from D-glucose and D-fructose by thermal treatment. Furthermore, various properties of the saccharides were investigated. Both saccharides were isolated from the reaction mixture by carbon-Celite column chromatography and an HPLC system and were determined to be novel sucrose-isomers, ß-D-fructopyranosyl-(2↔1)-ß-D-glucopyranoside (1) and ß-D-fructofuranosyl-(2↔1)-ß-D-glucopyranoside (2), by MALDI-TOF MS and NMR analyses. Both saccharides showed low digestibility in vitro, and the sweetness of saccharide 2 was 0.45 times that of sucrose.

Structural Analysis of a Novel Oligosaccharide Isolated from Fermented Beverage of Plant Extracts.

A fermented beverage of plant extracts (Super Ohtaka®) was prepared from about 50 kinds of fruits and vegetables. This natural fermentation was performed by yeast (Zygosaccharomyces spp. and Pichia spp.) and lactic acid bacteria (Leuconostoc spp.) and resulted in the production of a novel fructopyranose-containing saccharide, which was subsequently isolated using carbon-Celite column chromatography and preparative-HPLC. The structure of the saccharide was determined using MALDI-TOF MS and NMR, and the saccharide was identified as ß-D-fructopyranosyl-(2→6)-ß-D-fructofuranosyl-(2↔1)-α-D-glucopyranoside. This is the first description of this novel saccharide and its isolation from a natural source.

Iriomoteolides-10a and 12a, Cytotoxic Macrolides from Marine Dinoflagellate Amphidinium Species.

Two new macrolides, iriomoteolides-10a (1) and -12a (2), have been isolated from a marine dinoflagellate Amphidinium sp. (KCA09053 strain), and their structures were elucidated on the basis of a detailed two dimensional (2D)-NMR analysis. Compound 1 is a novel 21-membered Amphidinium macrolide, which contains one tetrahydrofuran ring, two ketone carbonyls, two hydroxyl groups, and six one-carbon branches. Compound 2 is a new 12-membered macrolide related to amphidinolide Q. Compound 1 exhibited cytotoxic activity against human cervix adenocarcinoma HeLa and murine hepatocellular carcinoma MH134 cells.

Structural confirmation of novel oligosaccharides isolated from sugar beet molasses.

Eleven oligosaccharides were isolated from sugar beet molasses using carbon-Celite column chromatography and HPLC. The constituent sugars and linkage positions were determined using methylation analysis, MALDI-TOF-MS, and NMR measurements. The configurations of isolated oligosaccharides were confirmed based on detailed NMR analysis. Based on our results, three of the 11 oligosaccharides were novel.

Structural analysis of novel kestose isomers isolated from sugar beet molasses.

Eight kestose isomers were isolated from sugar beet molasses by carbon-Celite column chromatography and HPLC. GC-FID and GC-MS analyses of methyl derivatives, MALD-TOF-MS measurements and NMR spectra were used to confirm the structural characteristics of the isomers. The (1)H and (13)C NMR signals of each isomer saccharide were assigned using COSY, E-HSQC, HSQC-TOCSY, HMBC and H2BC techniques. These kestose isomers were identified as α-D-fructofuranosyl-(2- > 2)-α-D-glucopyranosyl-(1 < ->2)-ß-D-fructofuranoside, α-D-fructofuranosyl-(2- > 3)-ß-D-fructofuranosyl-(2 < ->1)-α-D-glucopyranoside, α-D-fructofuranosyl-(2- > 4)-ß-D-fructofuranosyl-(2 < ->1)-α-D-glucopyranoside, ß-D-fructofuranosyl-(2- > 4)-ß-D-fructofuranosyl-(2 < ->1)-α-D-glucopyranoside, ß-D-fructofuranosyl-(2- > 3)-α-D-glucopyranosyl-(1 < ->2)-ß-D-fructofuranoside, α-D-fructofuranosyl-(2- > 1)-ß-D-fructofuranosyl-(2 < ->1)-α-D-glucopyranoside, α-D-fructofuranosyl-(2- > 6)-α-D-glucopyranosyl-(1 < ->2)-ß-D-fructofuranoside, and α-D-fructofuranosyl-(2- > 6)-ß-D-fructofuranosyl-(2 < ->1)-α-D-glucopyranoside. The former five compounds are novel saccharides.

Amphirionin-2, a novel linear polyketide with potent cytotoxic activity from a marine dinoflagellate Amphidinium species.

A novel linear polyketide, amphirionin-2 (1), with two unique hexahydrofuro[3,2-b]furan moieties has been isolated from the cultivated algal cells of a benthic dinoflagellate Amphidinium sp. (strain KCA09051). The structure was elucidated on the basis of detailed analyses of 2D NMR data, and the absolute configuration of C-5 was determined by using modified Mosher's method. Amphirionin-2 (1) exhibited potent cytotoxic activity against human colon carcinoma Caco-2 cells and human lung adenocarcinoma A549 cells.

Amphirionin-4 with potent proliferation-promoting activity on bone marrow stromal cells from a marine dinoflagellate amphidinium species.

A linear polyketide, amphirionin-4 (1), has been isolated from cultivated algal cells of the marine dinoflagellate Amphidinium species. The structure was elucidated on the basis of detailed analyses of 1D and 2D NMR data, and the absolute configurations of C-4 and C-8 were determined using the modified Mosher's method. Amphirionin-4 (1) exhibited extremely potent proliferation-promoting activity on murine bone marrow stromal ST-2 cells (950% promotion) at a concentration of 0.1 ng/mL.

Observation of glycolytic metabolites in tumor cell lysate by using hyperpolarization of deuterated glucose.

Hyperpolarization of stable isotope-labeled substrates and subsequent NMR measurement of the metabolic reactions allow for direct tracking of cellular reactions in vitro and in vivo. Here, we report the hyperpolarization of (13)C6-glucose-d7 and evaluate its use as probes to observe glucose flux in cells. We measured the lifetime of the polarized signal governed by the spin-lattice relaxation time T1. (13)C6-Glucose-d7 exhibited a T1 that was over ten times as long as that of (13)C6-glucose, and metabolic NMR studies of hyperpolarized (13)C6-glucose-d7 using tumor cell lysate led to observation of the resonances due to phosphorylated fluctofuranoses generated through aerobic glycolysis.

Roussoellols A and B, tetracyclic fusicoccanes from Roussoella hysterioides.

The structures of the tetracyclic fusicoccanes roussoellols A (1) and B (2) from Roussoella hysterioides KT1651 are described. NMR spectroscopic analyses involving NOESY experiments revealed that these molecules possessed unique bent structures that were supported by chemical derivatizations as well as chemical shift comparisons with theoretical shifts based on the density functional theory (DFT) at the EDF2/6-31G* level. Absolute configurations were established by the ECD couplet of positive chirality in both 1 and 2 at vacuum UV (VUV) region, which were further confirmed by successful reproduction of VUVCD spectra using theoretical calculations.

Structural confirmation of oligosaccharides newly isolated from sugar beet molasses.

BACKGROUND: Sugar beet molasses is a viscous by-product of the processing of sugar beets into sugar. The molasses is known to contain sucrose and raffinose, a typical trisaccharide, with a well-established structure. Although sugar beet molasses contains various other oligosaccharides as well, the structures of those oligosaccharides have not been examined in detail. The purpose of this study was isolation and structural confirmation of these other oligosaccharides found in sugar beet molasses. RESULTS: Four oligosaccharides were newly isolated from sugar beet molasses using high-performance liquid chromatography (HPLC) and carbon-Celite column chromatography. Structural confirmation of the saccharides was provided by methylation analysis, matrix-assisted laser desorption/ionaization time of flight mass spectrometry (MALDI-TOF-MS), and nuclear magnetic resonance (NMR) measurements. CONCLUSION: The following oligosaccharides were identified in sugar beet molasses: ß-D-galactopyranosyl-(1- > 6)-ß-D-fructofuranosyl-(2 <-> 1)-α-D-glucopyranoside (named ß-planteose), α-D-galactopyranosyl-(1- > 1)-ß-D-fructofuranosyl-(2 <-> 1)-α-D-glucopyranoside (named1-planteose), α-D-glucopyranosyl-(1- > 6)-α-D-glucopyranosyl-(1 <-> 2)-ß-D-fructofuranoside (theanderose), and ß-D-glucopyranosyl-(1- > 3)-α-D-glucopyranosyl-(1 <-> 2)-ß-D-fructofuranoside (laminaribiofructose). 1-planteose and laminaribiofructose were isolated from natural sources for the first time.

Isolation and structural confirmation of the oligosaccharides containing α-D-fructofuranoside linkages isolated from fermented beverage of plant extracts.

Fermented beverage of plant extracts was prepared from the extracts of approximately 50 types of vegetables and fruits. Natural fermentation was carried out mainly by lactic acid bacteria (Leuconostoc spp.) and yeast (Zygosaccharomyces spp. and Pichia spp.). Two oligosaccharides containing an α-fructofuranoside linkage were detected in this beverage and isolated using carbon-Celite column chromatography and preparative HPLC. The structural confirmation of the saccharides was determined by methylation analysis, MALDI-TOF-MS, and NMR measurements. These saccharides were identified as α-D-fructofuranosyl-(2→6)-D-glucopyranose, which was isolated from a natural source for the first time, and a novel saccharide ß-D-fructopyranosyl-(2→6)-α-D-fructofuranosyl-(2↔1)-α-D-glucopyranoside.

Novel fructopyranose oligosaccharides isolated from fermented beverage of plant extract.

Four oligosaccharides containing a fructopyranosyl residue have been found from fermented beverage of plant extract and isolated from the beverage using carbon-Celite column chromatography and preparative high performance liquid chromatography. Structure confirmation of the saccharides was provided by methylation analysis, MALDI-TOF-MS and NMR measurements. These saccharides were identified as oligosaccharides of fructopyranoside series; beta-D-fructopyranosyl-(2-->6)-D-fructofuranose (1), beta-D-fructopyranosyl-(2-->1)-D-fructopyranose (2), beta-D-fructopyranosyl-(2-->1)-beta-D-fructofuranosyl-(2<-->1)-alpha-D-glucopyranoside (3), and beta-D-fructopyranosyl-(2-->6)-alpha-D-glucopyranosyl-(1<-->2)-beta-D-fructofuranoside (4). Saccharides 3 and 4 among novel saccharides 1, 3, and 4 were named 'pyrano-1-kestose (pyrano-isokestose)' and 'pyrano-neokestose', respectively.

Potato tuber cell expansion-inducing activity of stereochemically restricted JA analogs.

Stereochemically restricted analogues of C-7 substituted 7-epi-jasmonate, together with 12-hydroxy jasmonic acid, 12-hydroxy jasmonic acid glucoside, and jasmonic acid conjugated with L-isoleucine (JA-Ile), were synthesized and then tested for potato tuber cell expansion-inducing activity. JA-Ile showed almost the same activity as JA, while the C-7 substituted 7-epi-jasmonates exhibited weaker activity than JA and showed an antagonist effect against JA.

Structural analysis of three novel trisaccharides isolated from the fermented beverage of plant extracts.

BACKGROUND: A fermented beverage of plant extracts was prepared from about fifty kinds of vegetables and fruits. Natural fermentation was carried out mainly by lactic acid bacteria (Leuconostoc spp.) and yeast (Zygosaccharomyces spp. and Pichia spp.). We have previously examined the preparation of novel four trisaccharides from the beverage: O-beta-D-fructopyranosyl-(2->6)-O-beta-D-glucopyranosyl-(1->3)-D-glucopyranose, O-beta-D-fructopyranosyl-(2->6)-O-[beta-D-glucopyranosyl-(1->3)]-D-glucopyranose, O-beta-D-glucopyranosyl-(1->1)-O-beta-D-fructofuranosyl-(2<->1)-alpha-D-glucopyranoside and O-beta-D-galactopyranosyl-(1->1)-O-beta-D-fructofuranosyl-(2<->1)- alpha-D-glucopyranoside. RESULTS: Three further novel oligosaccharides have been found from this beverage and isolated from the beverage using carbon-Celite column chromatography and preparative high performance liquid chromatography. Structural confirmation of the saccharides was provided by methylation analysis, MALDI-TOF-MS and NMR measurements. CONCLUSION: The following novel trisaccharides were identified: O-beta-D-fructofuranosyl-(2->1)-O-[beta-D-glucopyranosyl-(1->3)]-beta-D-glucopyranoside (named "3G-beta-D-glucopyranosyl beta, beta-isosucrose"), O-beta-D-glucopyranosyl-(1->2)-O-[beta-D-glucopyranosyl-(1->4)]-D-glucopyranose (4(1)-beta-D-glucopyranosyl sophorose) and O-beta-D-fructofuranosyl-(2->6)-O-beta-D-glucopyranosyl-(1->3)-D-glucopyranose (6(2)-beta-D-fructofuranosyl laminaribiose).

Escherichia coli allows efficient modular incorporation of newly isolated quinomycin biosynthetic enzyme into echinomycin biosynthetic pathway for rational design and synthesis of potent antibiotic unnatural natural product.

Natural products display impressive activities against a wide range of targets, including viruses, microbes, and tumors. However, their clinical use is hampered frequently by their scarcity and undesirable toxicity. Not only can engineering Escherichia coli for plasmid-based pharmacophore biosynthesis offer alternative means of simple and easily scalable production of valuable yet hard-to-obtain compounds, but also carries a potential for providing a straightforward and efficient means of preparing natural product analogs. The quinomycin family of nonribosomal peptides, including echinomycin, triostin A, and SW-163s, are important secondary metabolites imparting antibiotic antitumor activity via DNA bisintercalation. Previously we have shown the production of echinomycin and triostin A in E. coli using our convenient and modular plasmid system to introduce these heterologous biosynthetic pathways into E. coli. However, we have yet to develop a novel biosynthetic pathway capable of producing bioactive unnatural natural products in E. coli. Here we report an identification of a new gene cluster responsible for the biosynthesis of SW-163s that involves previously unknown biosynthesis of (+)-(1S, 2S)-norcoronamic acid and generation of aliphatic side chains of various sizes via iterative methylation of an unactivated carbon center. Substituting an echinomycin biosynthetic gene with a gene from the newly identified SW-163 biosynthetic gene cluster, we were able to rationally re-engineer the plasmid-based echinomycin biosynthetic pathway for the production of a novel bioactive compound in E. coli.