Silica Gel-mediated Oxidation of Prenyl Motifs Generates Natural Product-Like Artifacts

Exploring the Nonenzymatic Origin of Duclauxin-like Natural Products

Chemical-biological efforts to increase the diversity of duclauxin (1)-like molecules for medicinal chemistry purposes unveiled the reactivity of duclauxin (1) toward amines and alcohols. To expand the compound class, a semisynthetic strategy conjugating amines to duclauxin (1) was employed. Insights gained from this approach led to the hypothesis that certain duclauxin-like "natural products" such as talaromycesone B (2), bacillisporin G (3), xenoclauxin (4), bacillisporins F (5/6), bacillisporins J (8/9), bacillisporins I (12/13), and verruculosin A (38) may be isolation artifacts rather than enzymatic products. Further experimentation, involving adsorption of 1 onto silica gel, resulted in the production of 2-6. To gain insights into the conditions that generate such molecules, one-step reactions under mild conditions were set. Outcomes from both experiments confirmed that duclauxin-like molecules are generated via nonenzymatic reactions. This article presents analytical evidence, indicating that these molecules originate from 1, with the epimeric mixture of bacillisporins J (8 and 9) acting as the primary intermediate.

Trivialities in metabolomics: Artifacts in extraction and analysis

The aim of this review is to show the risks of artifact formation in metabolomics analyses. Metabolomics has developed in a major tool in system biology approaches to unravel the metabolic networks that are the basis of life. Presently TLC, LC-MS, GC-MS, MS-MS and nuclear magnetic resonance are applied to analyze the metabolome of all kind of biomaterials. These analytical methods require robust preanalytical protocols to extract the small molecules from the biomatrix. The quality of the metabolomics analyses depends on protocols for collecting and processing of the biomaterial, including the methods for drying, grinding and extraction. Also the final preparation of the samples for instrumental analysis is crucial for highly reproducible analyses. The risks of artifact formation in these steps are reviewed from the point of view of the commonly used solvents. Examples of various artifacts formed through chemical reactions between solvents or contaminations with functional groups in the analytes are discussed. These reactions involve, for example, the formation of esters, trans-esterifications, hemiacetal and acetal formation, N-oxidations, and the formation of carbinolamines. It concerns chemical reactions with hydroxyl-, aldehyde-, keto-, carboxyl-, ester-, and amine functional groups. In the analytical steps, artifacts in LC may come from the stationary phase or reactions of the eluent with analytes. Differences between the solvent of the injected sample and the LC-mobile phase may cause distortions of the retention of analytes. In all analytical methods, poorly soluble compounds will be in all samples at saturation level, thus hiding a potential marker function. Finally a full identification of compounds remains a major hurdle in metabolomics, it requires a full set of spectral data, including methods for confirming the absolute stereochemistry. The putative identifications found in supplemental data of many studies, unfortunately, often become “truly” identified compounds in papers citing these results. Proper validation of the protocols for preanalytical and analytical procedures is essential for reproducible analyses in metabolomics.

Investigation of red clover (Trifolium pratense) isoflavonoid residual complexity by off-line CCS-qHNMR

The importance of Trifolium pratense L. as a dietary supplement and its use in traditional medicine prompted the preparation of a thorough metabolite profile. This included the identification and quantitation of principal constituents as well as low abundant metabolites that constitute the residual complexity (RC) of T. pratense bioactives. The purity and RC of isoflavonoid fractions from standardized red clover extract (RCE) was determined using an off-line combination of countercurrent separation (CCS) and two orthogonal analytical methodologies: quantitative ¹H NMR spectroscopy with external calibration (EC-qHNMR) and LC-MS. A single-step hydrostatic CCS methodology (Centrifugal Partition Chromatography [CPC]) was developed that fractionated the isoflavonoids with a hexanes-ethyl acetate-methanol-water (HEMWat) 5.5/4.5/5/5, v/v solvent system (SS) into 75 fractions containing 3 flavonolignans, 2 isoflavonoid glycosides, as well as 17 isoflavonoids and related compounds. All metabolites were identified and quantified by qHNMR spectroscopy. The data led to the creation of a complete isoflavonoid profile to complement the biological evaluation. For example, fraction 69 afforded 90.5% w/w biochanin A (17), with 0.33% w/w of prunetin (16), and 0.76% w/w of maackiain (15) as residual components. Fraction 27 with 89.4% w/w formononetin (13) as the major component had, in addition, a residual complexity consisting of 3.37%, 0.73%, 0.68% w/w of pseudobaptigenin (11), kaempferol (10) and pratensein (8), respectively. Despite the relatively high resolving power of CPC, and not unexpectedly, the chromatographic fractions retained varying degrees of the original metabolomic diversity. Collectively, the extent of metabolomic diversity should be recognized and used to guide the development of isolation strategies, especially when generating samples for bioactivity evaluation. The simultaneous structural and quantitative characterization enabled by qNMR, supported by LC-MS measurements, enables the evaluation of a relatively large number of individual fractions and, thereby, advances both the chemical and biological evaluation of active principles in complex natural products.