Universal NMR Database Research Articles

Antifeedant, Antifungal Cryptic Polyketides with Six Structural Frameworks from Tea Endophyte Daldinia eschscholtzii Propelled by the Antagonistic Coculture with Phytopathogen Colletotrichum pseudomajus and Different Culture Methods.

The antagonistic coculture with tea phytopathogen Colletotrichum pseudomajus induces antifungal cryptic metabolites from isogenesis endophyte Daldinia eschscholtzii against tea phytopathogens. Sixteen new polyketides with six structural frameworks including ten cryptic ones, named coldaldols A-C (1-3), collediol (5), and daldinrins A-L (10-20 and 23), were found from the coculture of C. pseudomajus and D. eschscholtzii by different culture methods. The unique framework of compounds 11 and 12 featured a benzopyran-C7 polyketone hybrid, and compounds 13-16 were characterized by the novel benzopyran dimer. The structures were determined mainly by spectroscopic methods, including extensive one-dimensional (1D), two-dimensional (2D) NMR, high resolution electrospray ionisation mass spectroscopy (HRESIMS), ECD calculation, and single-crystal X-ray diffraction. The configuration of acyclic compounds 5 and 18 were determined by application of the universal NMR database. Most compounds showed significant antifungal activities against the tea pathogens C. pseudomajus and Alternaria sp. with MICs of 1-8 μg/mL. Compound 12 had stronger antifungal activity than that of positive drug nystatin. The ether bond at C-4 of the benzopyran derivative increased the antifungal activity. Compounds 4-9 and 11-23 showed antifeedant activities against silkworms with feeding deterrence indices of 15-100% at the concentration of 50 μg/cm2.

Dactylides A-C, three new bioactive 22-membered macrolides produced by Dactylosporangium aurantiacum.

Three new 22-membered polyol macrolides, dactylides A-C (1-3), were isolated from Dactylosporangium aurantiacum ATCC 23491 employing repeated chromatographic separations, and their structures were established based on detailed analysis of NMR and MS data. The relative configurations at the stereocenters were established via vicinal 1H-1H coupling constants, NOE correlations, and by application of Kishi's universal NMR database. In order to get insights into the biosynthetic pathway of 1-3, the genome sequence of the producer strain D. aurantiacum was obtained and the putative biosynthetic gene cluster encoding their biosynthesis was identified through bioinformatic analysis using antiSMASH. Compounds 1-3 showed significant in-vitro antimycobacterial and cytotoxic activity.

Antileishmanial macrolides from ant-associated Streptomyces sp. ISID311

Three antifungal macrolides cyphomycin (1), caniferolide C (2) and GT-35 (3) were isolated from Streptomyces sp. ISID311, a bacterial symbiont associated with Cyphomyrmex fungus-growing ants. The planar structures of these compounds were established by 1 and 2D NMR data and MS analysis. The relative configurations of 1–3 were established using Kishi's universal NMR database method, NOE/ROE analysis and coupling constants analysis assisted by comparisons with NMR data of related compounds. Detailed bioinformatic analysis of cyphomycin biosynthetic gene cluster confirmed the stereochemical assignments. Compounds 1–3 displayed high antagonism against different strains of Escovopsis sp., pathogen fungi specialized to the fungus-growing ant system. Compounds 1–3 also exhibited potent antiprotozoal activity against intracellular amastigotes of the human parasite Leishmania donovani with IC50 values of 2.32, 0.091 and 0.073 µM, respectively, with high selectivity indexes.

A Polyol-Polyol Super-Carbon-Chain Compound Containing Thirty-Six Carbon Stereocenters from the Dinoflagellate Amphidinium gibbosum: Absolute Configuration and Multi-Segment Modification

A super-carbon-chain compound, named gibbosol C, featuring a polyoxygenated C70-linear-carbon-chain backbone encompassing two acyclic polyol chains, was obtained from the South China Sea dinoflagellate Amphidinium gibbosum. Its planar structure was elucidated by extensive NMR investigations, whereas its absolute configurations, featuring the presence of 36 carbon stereocenters and 30 hydroxy groups, were successfully established by comparison of NMR data of the ozonolyzed products with those of gibbosol A, combined with J-based configuration analysis, Kishi’s universal NMR database, and the modified Mosher’s MTPA ester method. Multi-segment modification was revealed as the smart biosynthetic strategy for the dinoflagellate to create remarkable super-carbon-chain compounds with structural diversity.

ATP Depletion Assay Led to the Isolation of New 36-Membered Polyol Macrolides Deplelides A and B from Streptomyces sp. MM581-NF15.

New 36-membered polyol macrolides deplelides A and B were isolated from the culture of Streptomyces MM581-NF15 by bioassay-guided fractionation using an ATP depletion assay. The planar structures of these novel compounds were identified by interpretation of the spectroscopic data (1D/2D NMR, MS, and IR). The relative stereochemistry was partially established using the universal NMR database method and J-based configuration analysis using 1H-1H and long-range 1H-13C coupling constants determined by 1H NMR or E.COSY and J-resolved HMBC analysis or another HMBC-based technique, respectively. The absolute stereochemistry was partially determined by a modified Mosher's method. These new compounds displayed highly potent ATP depletion activities (IC50 33 nM) and antiproliferative activities against several tumor cell lines, such as HGC-27 (IC50 47 nM).

Assignment of the Absolute Configuration of Phosphoeleganin via Synthesis of Model Compounds.

The full absolute configuration assignment of phosphoeleganin (1), a recently discovered marine-derived phosphorylated polyketide with protein tyrosine phosphatase 1B inhibitory activity, was achieved. It was based on the synthesis of model diasteroisomeric compounds of the C-8-C-12 segment portion of phosphoeleganin, chiral derivatization methods, and application of the universal NMR database concept.

Rare Polyene-polyol Macrolides from Mangrove-derived Streptomyces sp. ZQ4BG

Bioactive natural products from mangrove-derived actinomycetes are important sources for discovery of drug lead compounds. In this study, an extract prepared from culture of an actinomycete Streptomyces sp. ZQ4BG isolated from mangrove soils was found to have activity in inhibiting proliferation of glioma cells. Large culture of this mangrove actinomycete in Gause’s liquid medium resulted in isolation of seven novel polyene-polyol macrolides, named as flavofungins III–IX (3–9), together with known flavofungins I (1) and II (2) and spectinabilin (10). Structures of these isolated compounds were elucidated by extensive NMR analyses and HRESIMS data. The stereochemical assignments were achieved by a combination of NOE information, universal NMR database, and chemical reactions including preparation of acetonide derivatives and Mosher esters. Flavofungins IV–VIII (4–8) are rare 32-membered polyene-polyol macrolides with a tetrahydrofuran ring, while flavofungin IX (9) represents the first example of this type of macrolide with a unique oxepane ring. Flavofungins I (1) and II (2) and spectinabilin (10) showed anti-glioma and antifungal activities.

Yakushinamides, Polyoxygenated Fatty Acid Amides That Inhibit HDACs and SIRTs, from the Marine Sponge Theonella swinhoei.

Yakushinamides A (1) and B (2), prolyl amides of polyoxygenated fatty acids, have been isolated from the marine sponge Theonella swinhoei as inhibitors of HDACs and SIRTs. Their planar structures were determined by interpretation of the NMR data of the intact molecules and tandem FABMS data of the methanolysis products. For the assignment of the relative configurations of the three contiguous oxymethine carbons in 1 and 2, Kishi's universal NMR database was applied to the methanolysis products. During the assignments of relative configurations of the isolated 1-hydroxy-3-methyl moiety in 1 and the isolated 1-hydroxy-2-methyl moiety in 2, we found diagnostic NMR features to distinguish each pair of diastereomers. The absolute configurations of 1 and 2 were determined by a combination of the modified Mosher's method and Marfey's method. Although the modified Mosher's method was successfully applied to the methanolysis product of 1, this method gave an ambiguous result at C-20 when applied to the methanolysis product of 2, even after oxidative cleavage of the C-14 and C-15 bond.

Gargantulide A, a complex 52-membered macrolactone showing antibacterial activity from Streptomyces sp.

Gargantulide A (1), an extremely complex 52-membered macrolactone, was isolated from Streptomyces sp. A42983 and displayed moderate activity against MRSA. The planar structure of 1 was determined using 2D NMR, and its stereochemistry was partially established on the basis of NOESY correlations, J-based configuration analysis, and Kishi's universal NMR database.

Stereochemistry of theonezolides A–C

Theonezolides A–C (1–3) are cytotoxic 37-membered macrolides with a long side chain isolated from an Okinawan marine sponge Theonella sp. The relative stereochemistry of 1–3 was investigated by combination of NMR analysis including application of a JBCA method, a Universal NMR database, and a 13C-acetonide method. Furthermore, the absolute configurations at 14 chiral centers in 1–3 were found to be 19S, 22R, 24S, 28S, 44S, 45S, 47R, 49S, 53R, 55S, 57S, 59S, 60S, and 63S by application of a modified Mosher’s method.

The relative configurations of azalomycins F5a, F4a and F3a

Azalomycins F5a (1), F4a (2) and F3a (3) are three 36-membered polyhydroxyl macrolides with remarkable antifungal activity. By comparing the NMR spectral data of 1 and its degradation products with those of several universal NMR databases and identical fragments of known compounds, the relative configuration of 1 was assigned for the first time except that the stereochemistry of stereoclusters C6–C11 to C14–C36 was undefined. Moreover, the relative configurations of 2 and 3 were respectively established by comparing their NMR spectral data with those of 1.

Caylobolide B, a Macrolactone from Symplostatin 1-Producing Marine Cyanobacteria Phormidium spp. from Florida

A Phormidium spp. collection from Key West, Florida, afforded caylobolide B (1), an analogue of the known macrolactone caylobolide A, previously isolated from a Lyngbya majuscula collection from the Bahamas. The planar structure of 1 was determined using NMR and MS experiments. The relative configuration for subunits C7-C9 and C25-C29 was assigned using Kishi's Universal NMR Database. Caylobolide B (1) displayed cytotoxic activity against HT29 colorectal adenocarcinoma and HeLa cervical carcinoma cells with IC(50) values of 4.5 and 12.2 μM, respectively.

Advances in the Universal NMR Database: Toward the Determination of the Relative Configurations of Large Polypropionates

AbstractThe relative stereochemical determination of naturally occurring large polyketides has proved to be critical, especially when the polyketides are available only in small quantities. Difficulties are often circumvented by the tedious synthesis either of adapted compound libraries (databases) or of all the presumed structures, because both methods allow efficient NMR comparison. To predict the stereochemistries of these frameworks, we have developed a straightforward method requiring neither the derivatisation of the natural product nor the synthesis of a new database of model stereoisomers. With the aid of 13C NMR spectroscopy, the relative configurations of the considered polypropionate segments are determined through a statistical UDB analysis of each included tetrad subunit followed by superposition of all predicted relative configurations of these tetrads. Examination of the different tetrads by statistical analysis consists of alternatively ruling out the Δδ values at positions where γ and δ effects could interfere. In most cases this statistical 13C NMR UDB approach leads to the stereochemical assignment of large polypropionate structures in a reliable way. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

Marinisporolides, Polyene-Polyol Macrolides from a Marine Actinomycete of the New Genus Marinispora

Two new polyene macrolides, marinisporolides A and B (1, 2), were isolated from the saline culture of the marine actinomycete, strain CNQ-140, identified as a member of the new marine genus Marinispora. The marinisporolides are 34-membered macrolides composed of a conjugated pentaene and several pairs of 1,3-dihydroxyl functionalities. Marinisporolide A (1) contains a bicyclic spiro-bis-tetrahydropyran ketal functionality, while marinisporolide B (2) is the corresponding hemiketal. The structures of these new compounds were assigned by combined spectral and chemical methods including extensive 2D NMR experiments and correlations of (13)C NMR data with Kishi's Universal NMR Database. Chemical modifications, including methanolysis, acetonide formation, and application of the modified Mosher method, provided the full stereostructures of these molecules. Three additional macrolides, marinisporolides C-E (3-5), which are olefin geometric isomers of marinisporolide A (1), were also isolated and their structures defined. Under room light, marinisporolides A and B readily photoisomerize to C-E indicating that they are most likely produced by photochemical conversion during the cultivation or isolation procedures. Although polyenes, marinisporolides A (1) and B (2) showed weak to no antifungal activity against Candida albicans.

Enantioselective Synthesis of Oasomycin A, Part I: Synthesis of the C1–C12 and C13–C28 Subunits

Oasomycin A (I) is a member of the desertomycin family of macrolide natural products and was isolated in 1993 by Thiericke and co-workers during the screening of secondary metabolites of Streptoverticillium baldacii. The overall structure of oasomycin A was established through extensive NMR spectroscopic studies and by direct comparison to other members of the desertomycin family. In 2001, Kishi and coworkers issued a proposal for the relative and absolute stereochemistry of oasomycin A through the use of their “universal NMR database” (Scheme 1). To validate the structural assignment of oasomycin A, we decided to pursue the synthesis of the reported structure, I. Herein, and in the following Communications, we describe our efforts which culminated in the synthesis of oasomycin A (I) and confirm the stereochemical assignment by Kishi and co-workers. First, we describe the synthesis of the C1–C12 and C13–C28 subunits II and III, respectively, which will be united by using the Julia coupling reaction (Scheme 1). Our plan for the synthesis of the C13–C28 fragment III is outlined in Scheme 2. Aldehyde III could be derived from a chelate-controlled reduction of the a,b-unsaturated ketone IV, which in turn can be disconnected at the C21 C22 bond to afford fragments V and VI. We predict successful union of these two fragments because of the greater reactivity of the Weinreb amide VI, which is required to avoid self-condensation of V (M=Li, MgX). This prediction is based on the supposition that the inductive effect of the a-alkoxy substituent should elevate the amide reactivity of VI above that of its reaction partner V. Synthesis of subunit II commenced with the aldol addition of known b-ketoimide 1 to aldehyde 2, which afforded the desired anti,anti aldol adduct as an 84:16 mixture of Scheme 1. Retrosynthetic analysis of oasomycin A (I).

Attempts to Assemble a Universal NMR Database without Synthesis of NMR Database Compounds

[structure: see text] The feasibility of assembling 3JH,H profiles from NMR data collected on relevant, but not necessarily specific, NMR database compounds representing a given stereocluster was demonstrated. By this approach, the 3JH,H profile was created for the contiguous tetraol peracetate stereocluster. The reliability and applicability of the database thus assembled were demonstrated for known peracetates derived from two heptoses.

Mycapolyols A−F, New Cytotoxic Metabolites of Mixed Biogenesis from the Marine Sponge Mycale izuensis1

[structure: see text]. Mycapolyols A-F (1-6), six new unusual PKS/NRPS metabolites, were isolated from the marine sponge Mycale izuensis. The gross structures were elucidated by analysis of spectroscopic data, while the stereochemistry was established using chemical method and the universal NMR database.

2′-Methyl taxanes: synthesis and NMR configurational assignment

Capitalizing on an oxidation–alkylation approach, a non-diastereoselective entry into 2′-methyl taxanes was developed. The issue of configurational assignment at the newly formed side-chain quaternary stereocenter was solved and put into a more general context by integrating information from an alternative diastereoselective synthesis of model compounds and from spectroscopic measurements, critically comparing the J-Based and the Universal NMR Database approaches.

Advances in the Universal NMR Database Approach. 2‘-Substituted Taxanes as Probes for an Improved Protocol of Diastereomeric Differentiation

[structure: see text] The configuration of the alpha-substituted alpha-hydroxy-beta-aminoester moiety in a series of 2'-substituted taxanes was analyzed according to the recently proposed Universal NMR Database (UDB) approach. A critical analysis of the results showed that modifications regarding chemical shift adjustment (so as to render the shifts virtually connectivity independent) were necessary to get consistent stereoassignments in this set of compounds. On this basis, a modified UDB-based strategy, especially tailored to the configurational assignment of densely substituted diastereomeric fragments, is proposed.

Palytoxin: An Inexhaustible Source of Inspiration — Personal Perspective

AbstractFor Abstract see ChemInform Abstract in Full Text.