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Structure elucidation and absolute configuration of metabolites from the soil-derived fungus Dictyosporium digitatum using spectroscopic and computational methods.

ABSTRACT: Following the discovery of a new class of compounds that inhibit the mucosa-associated lymphoid tissue lymphoma translocation 1 (MALT1) protease in a prior study, further chemical investigation of the Dictyosporium digitatum fungus resulted in the identification of 16 additional metabolites, including 12 undescribed compounds (1-12). The constitution and relative configuration of these new molecules were established by comprehensive NMR and HRMS analyses. Their absolute configurations were determined by employing Mosher's ester analysis and TDDFT ECD calculations. Two sesquiterpenes, dictyosporins A (1) and B (2), possess an undescribed eudesmen-type of structural scaffold. The ability of the isolated compounds to inhibit MALT1 proteolytic activity was evaluated, but none of them exhibited significant inhibition.

SUBMITTER: Tran TD

PROVIDER: S-EPMC7124996 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Reconciliation of chemical, enzymatic, spectroscopic and computational data to assign the absolute configuration of the DNA base lesion spiroiminodihydantoin.

Project description:The diastereomeric spiroiminodihydantoin-2'-deoxyribonucleoside (dSp) lesions resulting from 2'-deoxyguanosine (dG) or 8-oxo-7,8-dihydro-2'-deoxyguanosine (dOG) oxidation have generated much attention due to their highly mutagenic nature. Their propeller-like shape leads these molecules to display mutational profiles in vivo that are stereochemically dependent. However, there exist conflicting absolute configuration assignments arising from electronic circular dichroism (ECD) and NOESY-NMR experiments; thus, providing definitive assignments of the 3D structure of these molecules is of great interest. In the present body of work, we present data inconsistent with the reported ECD assignments for the dSp diastereomers in the nucleoside context, in which the first eluting isomer from a Hypercarb HPLC column was assigned to be the S configuration, and the second was assigned the R configuration. The following experiments were conducted: (1) determination of the diastereomer ratio of dSp products upon one-electron oxidation of dG in chiral hybrid or propeller G-quadruplexes that expose the re or si face to solvent, respectively; (2) absolute configuration analysis using vibrational circular dichroism (VCD) spectroscopy; (3) reinterpretation of the ECD experimental spectra using time-dependent density functional theory (TDDFT) with the inclusion of 12 explicit H-bonding waters around the Sp free bases; and (4) reevaluation of calculated specific rotations for the Sp enantiomers using the hydration model in the TDDFT calculations. These new insights provide a fresh look at the absolute configuration assignments of the dSp diastereomers in which the first eluting from a Hypercarb-HPLC column is (-)-(R)-dSp and the second is (+)-(S)-dSp. These assignments now provide the basis for understanding the biological significance of the stereochemical dependence of enzymes that process this form of DNA damage.

| S-EPMC3886818 | biostudies-literature

Isolation, Structure Elucidation, and Absolute Configuration of Germacrane Isomers from Carpesium divaricatum.

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Progressive-convergent elucidation of stereochemistry in complex polyols. The absolute configuration of (-)-sagittamide A.

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| S-EPMC3340292 | biostudies-literature

Meroterpenoids from the Fungus Ganoderma sinensis and First Absolute Configuration Clarification of Zizhine H.

Project description:Five new meroterpenoids, zizhines P-S and U (1-4,7), together with two known meroterpenoids (5 and 6) were isolated from Ganoderma sinensis. Their structures including absolute configurations were assigned by using spectroscopic, computational, and chemical methods. Racemics zizhines P and Q were purified by HPLC on chiral phase. Biological evaluation found that 4, 5 and 6 are cytotoxic toward human cancer cells (A549, BGC-823, Kyse30) with IC50 values in the range of 63.43-80.83 ?M towards A549, 59.2 ± 2.73 ?M and 64.25 ± 0.37 ?M towards BGC-823, 76.28 ± 1.93 ?M and 85.42 ± 2.82 ?M towards Kyse30.

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Absolute configuration of odorine.

Project description:The title compound, known as odorine or roxburghiline {systematic name: (S)-N-[(R)-1-cinnamoylpyrrolidin-2-yl]-2-methyl-butanamide}, C(18)H(24)N(2)O(2), is a nitro-genous compound isolated from the leaves of Aglaia odorata. The absolute configuration was determined by refinement of the Flack parameter with data collected using Cu Kα radiation showing positions 2 and 2' to be S and R, respectively. The pyrrolidine ring adopts an envelope conformation. In the crystal, mol-ecules are linked into chains along [010] by inter-molecular N-H⋯O hydrogen bonds.

| S-EPMC3007931 | biostudies-literature

Cytotoxic metabolites from the soil-derived fungus Exophiala pisciphila.

Project description:A new polyketide compound 1 and a new naturally occurring chromone derivative 2, along with two known indole alkaloids 3-4 were characterized from the ethyl acetate extract of a soil-derived fungal strain, Exophiala pisciphila PHF-9. The structures of compounds 1-4 were established by detailed spectroscopic analysis and comparison with literature data. The absolute configuration of 1 was determined by a modified Mosher's method. Compound 1 exhibited moderate cytotoxicity against A-549, Hela, PANC-28 and BEL-7402 cell lines.

| S-EPMC6260601 | biostudies-literature

Elucidation of the Relationship between CD Cotton Effects and the Absolute Configuration of Sixteen Stereoisomers of Spiroheterocyclic-Lactams.

Project description:As part of research to search for antitumor agents in fungi originating from marine organisms, cephalimysins E?L were isolated from a culture broth of Aspergillus fumigatus that was separated from the marine fish Mugil cephalus. One- and two-dimensional nuclear magnetic resonance spectra revealed their planar structures, which are diastereomers of each other. Their absolute stereostructures were established by epimerization at C-8 with acidic methanol, nuclear Overhauser effect spectroscopy (NOESY), and circular dichroism (CD) spectroscopy. These demonstrated the detailed relationships between absolute configuration and CD Cotton effects. Additionally, in the growth inhibition assay against P388, HL-60, L1210, and KB cell lines, some of the fungal metabolites or reaction products exhibited moderate activities.

| S-EPMC6071047 | biostudies-literature

Absolute configuration of isoeichlerialactone.

Project description:The title seco-dammarane triterpenoid, C(27)H(42)O(4) (systematic name: 3-{(3S,3aR,5aR,6S,7S,9aR,9bR)-6,9a,9b-trimethyl-3-[(R)-2-methyl-5-oxotetra-hydro-furan-2-yl]-7-(prop-1-en-2-yl)dodeca-hydro-1H-cyclo-penta-[a]naphthalen-6-yl}propanoic acid), has been isolated for the first time from the seeds of Aglaia forbesii. The mol-ecule has three fused rings and all rings are in trans-fused. The two cyclo-hexane rings are in standard chair conformations and the cyclo-pentane ring adopts an envelope conformation. Its absolute configuration was determined by the refinement of the Flack parameter to 0.26?(17). In the crystal, mol-ecules are linked into chains along [010] by O-H?O hydrogen bonds.

| S-EPMC2984085 | biostudies-other

Absolute configuration of micromelin.

Project description:The title compound {systematic name: 7-meth-oxy-6-[(1R,2R,5R)-5-methyl-4-oxo-3,6-dioxabicyclo-[3.1.0]hexan-2-yl]-2H-chromen-2-one}, C(15)H(12)O(6), is a coumarin, which was isolated from the roots of Micromelum glanduliferum. There are two mol-ecules in the asymmetric unit with slight differences in bond angles. In both mol-ecules, the furan ring adopts a flattened envelope conformation. In the crystal, mol-ecules are linked by weak C-H?O inter-actions into chains along the a axis. Aromatic ?-? stacking inter-actions with centroid-centroid distances in the range 3.6995?(11)-3.8069?(11)?Å and C?O short contacts [3.030?(2)-3.171?(3)?Å] also occur.

| S-EPMC3151812 | biostudies-other

Absolute configuration of dolichol.

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