Botryorhodines K and L, two new cytotoxic depsidones from a fungus of the genus Arcopilus.

Botryorhodines K (1) and L (2), two new depsidone derivatives, along with one known metabolite, 4-O-demethylbarbatic acid (3), were isolated from the culture extract of a fungus of the genus Arcopilus. The structures of 1‒3 were determined by the analysis of NMR and MS spectral data and the absolute configuration of 1 was established by single-crystal X-ray diffraction analysis. Compounds 1 and 2 showed antimicrobial activity against Gram-positive bacteria and cytotoxicity against murine leukemia P388 cells.

Marinoquinolones and Marinobactoic Acid: Antimicrobial and Cytotoxic ortho-Dialkylbenzene-Class Metabolites Produced by a Marine Obligate Gammaproteobacterium of the Genus Marinobacterium.

Chemical investigation of the culture extract of a marine obligate proteobacterium, Marinobacterium sp. C17-8, isolated from scleractinian coral Euphyllia sp., led to the discovery of three new o-dialkylbenzene-class metabolites, designated marinoquinolones A (1) and B (2) and marinobactoic acid (3). Spectroscopic analysis using MS and NMR revealed the structures of 1 and 2 to be 4-quinolones with an o-dialkylbenzene-containing side chain at C3 and 3 to be a fatty acid bearing an o-dialkylbenzene substructure. The 4-quinolone form of 1 and 2 was unequivocally determined by comparison of the 1H, 13C, and 15N chemical shifts of 1 with those predicted for 2-methyl-4-quinolone A and its tautomer 2-methyl-4-quinolinol B by quantum chemical calculation. Compound 1 was proven to be racemic by X-ray crystallographic analysis and chiral-phase HPLC analysis of its chemical degradation product. Compounds 1-3 exhibited antimicrobial activity against bacteria and filamentous fungi at MIC of 6.3-50 µg/mL. In addition, all compounds showed cytotoxicity against P388 murine leukemia cells at micromolar ranges.

Kumemicinones A-G, Cytotoxic Angucyclinones from a Deep Sea-Derived Actinomycete of the Genus Actinomadura.

Chemical investigation of the fermentation products of a deep sea water-derived actinomycete, Actinomadura sp. KD439, identified seven new angucyclinones, designated as kumemicinones A-G (1-7), together with the known SF2315B and miaosporone E. NMR and MS spectroscopic analyses, combined with X-ray crystallography and quantum chemical calculations of NMR chemical shifts and electronic circular dichroism (ECD) spectra, uncovered the structures of new angucyclinones as regioisomers of SF2315B at the allyl alcohol unit (1 and 2), an epoxy ring-opened γ-hydroxy enone isomer (3), a B/C-ring-rearranged product (4), or dimers with a new mode of bridging (5-7), adding new structural variation to this antibiotic group. The absolute configuration of SF2315B was also determined by comparison of ECD spectra with those of 1 and 2. All the angucyclinones exhibited cytotoxicity against P388 murine leukemia cells, with IC50 values ranging from 1.8 to 53 µM.

Nyuzenamides A and B: Bicyclic Peptides with Antifungal and Cytotoxic Activity from a Marine-Derived Streptomyces sp.

Two bicyclic peptides, nyuzenamides A (1) and B (2), were discovered from Streptomyces isolated from suspended matter in deep sea water collected in the Sea of Japan. Their structures were determined through nuclear magnetic resonance and mass spectrometry analyses in combination with X-ray crystallography and the chiral-phase gas chromatography-mass spectrometry method to comprise ten amino acid residues containing four unusual amino acids along with aromatic acyl units. Both compounds displayed antifungal activity against pathogenic fungi and cytotoxicity against P388 murine leukemia cells.

Carapanins A-C: new limonoids from andiroba (Carapa guianensis) fruit oil.

Carapanins A-C (1-3) were isolated from the fruit oil of Carapa guianensis. Compounds 1 and 2 are limonoids with unique structures. Namely, compound 1 is an andirobin-type limonoid with a C-15/C-30 γ-lactone instead of the δ-lactone of the D-ring, and compound 2 is a mexicanolide-type limonoid with a C-16/C-30 δ-lactone ring. The absolute structures of 1 and 2 were determined using X-ray crystallography, whereas the structure of 3 was established mainly via NMR and mass spectroscopy. The inhibitory effects of 1-3 on nitric oxide production were evaluated, and it was revealed that 2 and 3 were potent nitric oxide inhibitors.

Nonthmicin, a Polyether Polyketide Bearing a Halogen-Modified Tetronate with Neuroprotective and Antiinvasive Activity from Actinomadura sp.

Nonthmicin (1), a new polyether polyketide bearing a chlorinated tetronic acid, was isolated from the culture extract of a soil-derived Actinomadura strain. The structure of 1 was elucidated by interpretation of NMR and MS spectroscopic data, and the absolute configuration of 1 was proposed on the basis of the crystal structure of its dechloro congener ecteinamycin (2) also isolated from the same strain. Tetronic acids modified by halogenation have never been reported from natural products. Compounds 1 and 2 were found to have neuroprotective activity and antimetastatic properties at submicromolar concentrations in addition to antibacterial activity.

Six new ergostane-type steroids from king trumpet mushroom (Pleurotus eryngii) and their inhibitory effects on nitric oxide production.

Six new ergostane-type steroids; (22E)-3ß,5α,6α,11-tetrahydroxy-9(11)-seco-ergosta-7,22-dien-9-one (1), (22E)-8,14-epoxyergosta-6,22-diene-3ß,5α,9α-triol (2), (22E)-4α,5α-epoxyergosta-7,22-diene-3ß,6ß-diol (3), (22E)-3ß,4ß,5α-trihydroxyergosta-7,22-dien-6-one (4), (22E)-ergosta-7,22-diene-3ß,5ß,6α-triol (5), and (22E)-6ß-methoxyergosta-7,22-diene-3ß,5α-diol 3-O-ß-d-glucopyranoside (6) were isolated from the fruiting bodies of king trumpet mushroom (Pleurotus eryngii), along with fourteen known compounds (7-20). All isolated compounds were evaluated for their inhibitory effects on macrophage activation using a nitric oxide production inhibition assay.

Ulbactins F and G, Polycyclic Thiazoline Derivatives with Tumor Cell Migration Inhibitory Activity from Brevibacillus sp.

Two new structurally unique compounds bearing a nitrogen- and sulfur-containing tricyclic ring system, ulbactin F (1) and its diastereomeric isomer ulbactin G (2), were isolated from the culture extract of a sponge-derived Brevibacillus sp. The structures and absolute configurations of 1 and 2 were determined by NMR analysis and X-ray crystallographic analysis. These compounds inhibit the migration of tumor cells in the submicromolar to micromolar range.

Carapanolides C-I from the seeds of andiroba (Carapa guianensis, Meliaceae).

Five new mexicanolide-type limonoids, carapanolides C-G (1-5), together with two new phragmalin-type limonoids, carapanolides H-I (6, 7), were isolated from the oil of Carapa guianasis AUBLET (Meliaceae) seeds. Their structures were elucidated on the basis of spectroscopic analyses using 1D and 2D NMR spectra and FABMS. Carapanolides C (1), E (3), and I (7) exhibited moderate activity in the P388 (IC50 17.9 µM in 1, 15.8 µM in 3) and L1210 cell lines (IC50 13.3 µM in 1, 18.1 µM in 3, 16.9 µM in 7). On the other hand, Carapanolide D (2) exhibited a strong inhibitory effect in the HL-60 cell line (IC50 11.0 µM), Carapanolides F (4) showed inhibitory activity in the L1210 cell line (IC50 15.9 µM), and the cytotoxic activity of Carapanolides I (7) was moderate in all cell lines.

CH-π interaction in VQIVYK sequence elucidated by NMR spectroscopy is essential for PHF formation of tau.

One of the histopathological features of Alzheimer's disease (AD) is higher order neurofibrillary tangles formed by abnormally aggregated tau protein. Investigation of the mechanism of tau aggregation is important for the clarifying the cause of AD and the development of therapeutic drugs. The microtubule-binding domain, which consists of repeats of similar amino acids (R1-R4) is thought to form the core component of paired helical filament (PHF). The hexapeptide(306) VQIVYK(311) of R3 has been shown to take a key role of promoting tau aggregation and assumed that its CH-π interaction between the side chains of Ile308 and Tyr310 would contribute in stabilizing the filament. In this work, we investigated a short isoform of tau (4RTau), R3, VQIVYK peptide and their mutants by thioflavin S (ThS) fluorescence, and NMR measurements, and proved for the first time that this CH-π interaction stabilizes the filament at the atomic level. In addition, by molecular modeling, we revealed that this interaction further supports an extended amphipathic structure for molecular self-association during the process of PHF formation of tau protein. The present work indicates new approach that inhibits the CH-π interaction for developing a therapeutic agent for AD.

Alchivemycin A, a bioactive polycyclic polyketide with an unprecedented skeleton from Streptomyces sp.

Alchivemycin A, a novel polycyclic polyketide, was isolated from the culture extract of a plant-derived actinomycete Streptomyces sp. The structure and relative configuration were elucidated by spectroscopic analysis and X-ray crystallography, and the absolute configuration was determined by a (1)H NMR anisotropy method using MPA ester derivatization. The new compound contains an unprecedented heterocyclic ring system, 2H-tetrahydro-4,6-dioxo-1,2-oxazine. Alchivemycin A showed potent antimicrobial activity against Micrococcus luteus and inhibitory effects on tumor cell invasion.

Cancer chemopreventive activity of oleanane-type triterpenoids from the stem bark of Betula ermanii.

In search for cancer chemopreventive agents from natural sources, three oleanane- and four known lupane-type triterpenoids, and sitosterol from the stem bark of Betula ermanii were tested for their inhibitory effects on Epstein-Barr virus early antigen (EBV-EA) activation induced by 12-O-tetradecanoylphorbol-13-acetate (TPA). Among them, 3beta-acetoxy-12alpha-hydroxyoleanan-13beta,28-olide (1) and 3beta-acetoxy-11alpha,12alpha-epoxyoleanan-13beta,28-olide (2) were investigated for the inhibitory effect in a two-stage carcinogenesis test on mouse skin using 7,12-dimethylbenz[a]anthracene (DMBA) as an initiator and TPA as a promoter. 3beta-Acetoxy-11alpha,12alpha-epoxyoleanan-13beta,28-olide (2) was found to exhibit the potent antitumor promoting activity in the in vivo carcinogenesis test.

Aggregation feature of fluorine-substituted benzene rings and intermolecular C-H.F interaction: crystal structure analyses of mono- and trifluoro-L-phenylalanines.

X-Ray crystal structures of four different fluorine-substituted phenylalanines (two mono- and two tri-substitutions) were analyzed to investigate the effect of fluorine atom on the association pattern of benzene rings. Although respective structures showed similar molecular packing in such a way that the layers of hydrophobic benzene rings and hydrophilic amino/carboxyl groups were alternately running along a crystallographic axis, the association patterns of benzene rings were different depending on the substitution position and number of fluorine atoms. The general features could be that the partially displaced face-to-face interactions are increased with increase in the number of fluorine atoms, whereas the edge-to-face interactions are decreased. The C-H bond next to a fluorine-substituted carbon atom could serve as a donor of an intermolecular C-H.F hydrogen bond.

Structural basis for development of cathepsin B-specific noncovalent-type inhibitor: crystal structure of cathepsin B-E64c complex.

In order to elucidate the substrate specificity of the Sn subsites (n=1-3) of cathepsin B, its crystal structure inhibited by E64c [(+)-(2S,3S)-3-(1-[N-(3-methylbutyl)amino]-leucylcarbonyl)oxirane-2-carboxylic acid] was analyzed by the X-ray diffraction method. Iterative manual rebuilding and convenient conjugate refinement of structure decreased R- and free R-factors to 19.7% and to 23.9%, respectively, where 130 water molecules were included for the refinement using 14,759 independent reflections from 10 to 2.3 A resolution. The epoxy carbonyl carbon of E64c was covalently bonded to the Cys(29) S(gamma) atom and the remaining parts were located at Sn subsites (n=1-3). The substrate specificity of these subsites was characterized based on their interactions with the inhibitor. Base on these structural data, we developed a novel cathepsin B-specific noncovalent-type inhibitor, which may bind to S2'-S3. The molecular design of possessing structural elements of both CA074 and E64c, assisted by energy minimization and molecular dynamics (MD) simulation, may lead to a new lead noncovalent-type inhibitor.