Structure Elucidation Of Secondary Metabolites Research Articles

Chemical Constituents Isolated from the Lichen Biome of Selected Species Native to North America.

A lichen is a symbiotic association composed of a primary mycobionts and one or more photobionts living mutualistically together, forming a distinct morphological entity beneficial to their partnership and to other associated fungi, photobionts, and bacteria that collectively make up the lichen biome. The taxonomic identification of a lichen species often requires determination of the primary mycobiont's secondary metabolites, the key morphological characteristics of the thallus, and how it relates to other lichen species as seen in DNA phylogeny. This chapter covers lichens and their bionts, taxonomic identification, and their chemical constituents as exemplified by what is found in lichen biomes, especially those endemic to North America. Extraction and isolation, as well as updates on dereplication methods using mass spectrometric GNPS and NMR spectroscopic spin network fingerprint procedures, and marker-based techniques to identify lichens are discussed. The isolation and structure elucidation of secondary metabolites of an endolichenic Penicillium species that produces bioactive compounds will be described in detail.

Structure Elucidation of Secondary Metabolites: Current Frontiers and Lingering Pitfalls.

Analytical methods allow for the structure determination of submilligram quantities of complex secondary metabolites. This has been driven in large part by advances in NMR spectroscopic capabilities, including access to high-field magnets equipped with cryogenic probes. Experimental NMR spectroscopy may now be complemented by remarkably accurate carbon-13 NMR calculations using state-of-the-art DFT software packages. Additionally, microED analysis stands to have a profound effect on structure elucidation by providing X-ray-like images of microcrystalline samples of analytes. Nonetheless, lingering pitfalls in structure elucidation remain, particularly for isolates that are unstable or highly oxidized. In this Account, we discuss three projects from our laboratory that highlight nonoverlapping challenges to the field, with implications for chemical, synthetic, and mechanism of action studies. We first discuss the lomaiviticins, complex unsaturated polyketide natural products disclosed in 2001. The original structures were derived from NMR, HRMS, UV-vis, and IR analysis. Owing to the synthetic challenges presented by their structures and the absence of X-ray crystallographic data, the structure assignments remained untested for nearly two decades. In 2021, the Nelson group at Caltech carried out microED analysis of (-)-lomaiviticin C, leading to the startling discovery that the original structure assignment of the lomaiviticins was incorrect. Acquisition of higher-field (800 MHz 1H, cold probe) NMR data as well as DFT calculations provided insights into the basis for the original misassignment and lent further support to the new structure identified by microED. Reanalysis of the 2001 data set reveals that the two structure assignments are nearly indistinguishable, underscoring the limitations of NMR-based characterization. We then discuss the structure elucidation of colibactin, a complex, nonisolable microbiome metabolite implicated in colorectal cancer. The colibactin biosynthetic gene cluster was detected in 2006, but owing to colibactin's instability and low levels of production, it could not be isolated or characterized. We used a combination of chemical synthesis, mechanism of action studies, and biosynthetic analysis to identify the substructures in colibactin. These studies, coupled with isotope labeling and tandem MS analysis of colibactin-derived DNA interstrand cross-links, ultimately led to a structure assignment for the metabolite. We then discuss the ocimicides, plant secondary metabolites that were studied as agents against drug-resistant P. falciparum. We synthesized the core structure of the ocimicides and found significant discrepancies between our experimental NMR spectroscopic data and that reported for the natural products. We determined the theoretical carbon-13 NMR shifts for 32 diastereomers of the ocimicides. These studies indicated that a revision of the connectivity of the metabolites is likely needed. We end with some thoughts on the frontiers of secondary metabolite structure determination. As modern NMR computational methods are straightforward to execute, we advocate for their systematic use in validating the assignments of novel secondary metabolites.

Isolation and Structure Elucidation of Secondary Metabolites From an Endophytic Fungus Annulohypoxylon ilanense

Fractionation of the EtOAc-soluble fraction of the liquid fermentation of an endophytic fungus Annulohypoxylon ilanense associated with the wood of medicinal plant Cinnamomum species resulted in th...

Isolation and structure elucidation of secondary metabolites of two Greek endemic Inula species. Biological activities

In the framework of phytochemical studies on Greek endemic Inula species, Inula candida subsp. candida and Inula candida subsp. decalvans have been analyzed. The aerial parts were extracted with increasing polarity solvents and sixteen secondary metabolites from I. candida subsp. candida and eight from I. candida subsp. decalvans were isolated. From I. candida subsp. decalvans a sesquiterpene lactone (3aS,8aR)-6-methyl-3-methylidene-7-(3-oxobutyl)-3a,4,5,8a-tetrahydro-2H-cyclohepta[b]furan-2,8(3H)dione (1), was determined as a new natural product, additionally to five known triterpenes: β-amyrin (2), dammaradienol (3), dammaradienyl acetate (4), epifriedelanol (5), stigmasterol (6) and two known lactones: inusoniolide (7) and tomentosine (8). The chemical investigation of I. candida subsp. candida resulted in the isolation of ten known triterpenes: β-amyrin (2), stigmasterol (6), β-sitosterol (9), α-amyrone (10), α-amyrin (11), friedelin (12), lupenone (13), 3β-acetoxy-24-hydroxydammara-20,25-diene (14), 3β-acetoxy-25-hydroxydammara-20,23-diene (15), 3β-acetoxy-24-oxo-dammara-20,25-diene (16), as well as five lactones: inusoniolide (7), 4-O-dihydroinusoniolide (17), 9β-(3-hydroxyisovaleryloxy) parthenolide (18), 9β-hydroxyparthenolide (19), 9β-(3-hydroxy-2-methylbutyryloxy) parthenolide (20), together with the phenolic aldehyde: vanillin (21). The crude extracts and the isolated compounds were also evaluated for their antimicrobial activity against a panel of selected human pathogenic bacteria and fungi showing that the new lactone (1) and 9β-hydroxyparthenolide (19) showed the strongest activity against the tested bacteria (MIC 3•10−2–5•10−1 μg/ml), while (1) and tomentosin (8) appeared as the most active against the assayed fungi (MIC 2,5•10−2–12•10−2 μg/ml). The antiproliferative effect for the new lactone was also evaluated in vitro against the human non-small-cell bronchopulmonary carcinoma cell line NSCLC-N6 and the epidermoid lung cancer cell line A549.

Isolation and Structure Elucidation of Secondary Metabolites from a Microcystis sp. Bloom Material Collected in Southern Israel

The hydrophilic extract of Microcystis sp. bloom material collected from Bror Hayil Reservoir in southern Israel afforded four new metabolites, (2 S,3 S)-3-hydeoxy-1,4-diphenylbutan-2-yl-acetate, aeruginosins BH604, BH462A and BH462B, and two known metabolites cyanopeptolins S and SS. The planar structure of 1–4 was established by analyses of their 1D and 2D NMR data and mass spectrometric data. The absolute configurations of the chiral centers of 1 were established by Mosher method and analysis of the coupling constants between H-2 and H-3, and those of 2–4 by Merfay's method and advanced Merfay's method and chiral HPLC. The compounds do not inhibit the serine proteases trypsin and thrombin.

Isolation and Structure Elucidation of Secondary Metabolites from the Roots of the Tunisian Convolvulus dorycnium

A phytochemical investigation of the roots of Convolvulus dorycnium led to the isolation of a new phenolic metabolite methyl 3-(3-caffeoyl-1,2-dihydroxycyclobutyl)-3-hydroxypropanoate (1) named convoldorine and the previously known dorycnic acid (2), chlorogenic acid (3), scopolin (4) and scopolitin (5). Their structures were elucidated on the basis of spectroscopic evidence, including 1D and 2D NMR experiments and by comparison with authentic samples.

Characterization of Secondary Metabolites from Various Solvent Extracts of Saffron Floral Waste

Isolation of secondary metabolites from saffron flower waste (stamens), and their identification using chromatographic techniques was carried out. Extraction was carried out with solvents (methanol, ethanol, ethyl acetate, diethylether and hexane) with different polarity. Gas chromatography–mass spectroscopy (GC–MS) technique was used for identification and structure elucidation of secondary metabolites obtained from saffron flower stamens. Chromatogram of ethanol showed higher peak area as compared to other solvents. Ethanol extract showed maximum number of peaks while chromatogram of hexane extract showed minimum number of peaks indicating that polarity of the solvent plays an important role in the extraction process. GC–MS analysis confirmed presence of many important compounds in saffron stamens such as α-tocopherol or vitamin E, dibutyl para-cresol, hydroquinone, and certain esters.

Structure elucidation of secondary metabolites isolated from the leaves of Ixora undulate and their inhibitory activity toward advanced glycation end-products formation

Three aromatic glycosides (1–3), two sulfur and nitrogen-containing compound glucosides (4, 5), and one flavonoid glycoside (6) were isolated from the leaves of Ixora undulata. Their structures were established by extensive 1D, 2D NMR, and HRESIMS experiments, and structure 4 was further confirmed by single crystal X-ray diffraction analysis. Of the assayed compounds, 7, 11 and 12 showed strong inhibitory activity toward advanced glycation end-products formation with IC50 values of 86.0μM, 76.6μM and 98.6μM, respectively.

Bioassay directed structure elucidation of secondary metabolites in Tanacetum abratonifolium (Compositae)

Bioassay directed structure elucidation of secondary metabolites in Tanacetum abratonifolium (Compositae)