Structure Elucidation of Secondary Metabolites: Current Frontiers and Lingering Pitfalls

Untargeted metabolic analysis using LC-Q-TOF-MS and toxicity assessment of Eryngium foetidum in zebrafish embryos

Toxicological studies of edible plant species are important to determine the safety of their consumption. Eryngium foetidum is an edible plant used in some countries for seasoning food and as a natural remedy in folk medicine. Despite this species' gastronomic and medicinal properties, the chemical composition and toxicity have been unclear. The objective of our investigation was to determine the toxic potential of E. foetidum in the zebrafish embryo model and identify the potential compounds involved in its toxicity by electrospray ionization liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry. Acute exposure of zebrafish embryos to n-hexane extract produced higher toxicity than the other extracts in a time- and concentration-dependent fashion (coagulated embryo). A 96-h median lethal concentration (LC 50) of 2.63 µg mL-1 (CI 95 % 0.58-28.5) was calculated by probit analysis. Caudal fin hypertrophy, head, yolk sac edema, caudal region, or somite malformations were observed. Secondary metabolites such as terpenes, polyphenols, and fatty acids were identified in the n-hexane extract. Also, pollutants such as diglycidyl resorcinol ether, diisopropyl adipate, and lauryl sulfate were found in the n-hexane extract. Our study revealed that chemical pollutants could be associated with the embryonic toxicity of the n-hexane extract of E. foetidum.

A Stereoselective Oxidative Dimerization En Route to (-)-Lomaiviticin A

We describe a stereoselective synthesis of the dimeric diazofluorene 15, a potential precursor to the cytotoxic C2-symmetric bacterial metabolite (-)-lomaiviticin A (1). An efficient route was developed to convert the tetracyclic diol 5 to the diketone 4 (five steps, 30% overall). Oxidative dimerization of the enoxysilane 14 provided the C2-symmetric dimeric diazofluorene 15 in 56% yield and with 15:1:0 diastereoselectivity. Deprotection and 2D NMR analysis indicated that the major diastereomer possessed the (2S,2'S) configuration found in 1. This approach may ultimately be useful in the synthesis of 1 itself.

Unraveling the specialized metabolic pathways in medicinal plant genomes: a review

Medicinal plants are important sources of bioactive specialized metabolites with significant therapeutic potential. Advances in multi-omics have accelerated the understanding of specialized metabolite biosynthesis and regulation. Genomics, transcriptomics, proteomics, and metabolomics have each contributed new insights into biosynthetic gene clusters (BGCs), metabolic pathways, and stress responses. However, single-omics approaches often fail to fully address these complex processes. Integrated multi-omics provides a holistic perspective on key regulatory networks. High-throughput sequencing and emerging technologies like single-cell and spatial omics have deepened our understanding of cell-specific and spatially resolved biosynthetic dynamics. Despite these advancements, challenges remain in managing large datasets, standardizing protocols, accounting for the dynamic nature of specialized metabolism, and effectively applying synthetic biology for sustainable specialized metabolite production. This review highlights recent progress in omics-based research on medicinal plants, discusses available bioinformatics tools, and explores future research trends aimed at leveraging integrated multi-omics to improve the medicinal quality and sustainable utilization of plant resources.

A FRET-based multifunctional fluorescence probe for the simultaneous detection of sulfite and viscosity in living cells

Viscosity and sulfur dioxide derivatives were significant indicators for the assessment of health threat and even cancers, therefore, on-site and real time detection of viscosity and sulfur dioxide derivatives has obtained considerable attentions. An FRET-based fluorescence probe JZX was designed and synthesized based on a novel energy donor of N,N-diethyl-4-(1H-phenanthro[9,10-d]imidazol-2-yl)benzamide fluorophore. JZX exhibited a large Stokes shift (230 nm), high energy transfer efficiency, wide emission channel gap (135 nm) and excellent stability and biocompatibility. JZX detected sulfur dioxide with low detection limit (55 nM), fast responding (16 min), high selectivity and sensitivity. Additionally, JZX tend to target endoplasmic reticulum of which normal metabolism will be disturbed by the abnormal levels of viscosity and sulfur dioxide derivatives. Prominently, JZX could concurrently detect viscosity and sulfur dioxide derivatives depending on different fluorescence signals in living cells for the screening of cancer cells. Hence, probe JZX will be a promising candidate for the detection of viscosity and sulfur dioxide derivatives, and even for the diagnosis of liver cancers.

Natural products from the human microbiome: an emergent frontier in organic synthesis and drug discovery

Often referred to as the "second genome", the human microbiome is at the epicenter of complex inter-habitat biochemical networks like the "gut-brain axis", which has emerged as a significant determinant of cognition, overall health and well-being, as well as resistance to antibiotics and susceptibility to diseases. As part of a broader understanding of the nexus between the human microbiome, diseases and microbial interactions, whether encoded secondary metabolites (natural products) play crucial signalling roles has been the subject of intense scrutiny in the recent past. A major focus of these activities involves harvesting the genomic potential of the human microbiome via bioinformatics guided genome mining and culturomics. Through these efforts, an impressive number of structurally intriguing antibiotics, with enhanced chemical diversity vis-à-vis conventional antibiotics have been isolated from human commensal bacteria, thereby generating considerable interest in their total synthesis and expanding their therapeutic space for drug discovery. These developments augur well for the discovery of new drugs and antibiotics, particularly in the context of challenges posed by mycobacterial resistance and emerging new diseases. The current landscape of various synthetic campaigns and drug discovery initiatives on antibacterial natural products from the human microbiome is captured in this review with an intent to stimulate further activities in this interdisciplinary arena among the new generation.

Structural Revision of Tinotufolins from Tinospora crispa Leaves Guided by Empirical Rules and DFT Calculations

Clerodane diterpenes are a class of secondary metabolites that can be classified into four types according to the configuration of the H3-19/H-10-H3-17/H3-20 fragment, i.e., trans-cis (TC), trans-trans (TT), cis-cis (CC), and cis-trans (CT). Tinotufolins A-C and E (1a-3a and 5a), isolated from the leaves of Tinospora crispa, were previously elucidated as CT-type clerodanes; however, our established 13C NMR-based empirical rules and density functional theory calculations suggested that these clerodanes belong to the CC type. Therefore, tinotufolins A-F (1-6) were reisolated from the leaves of T. crispa, along with an undescribed compound 7 and known compounds 8-11, and their structures were established by extensive spectroscopic analyses. The structures of tinotufolins A-C and E were revised to CC-type 1-3 and 5, and undescribed compound 7 was established as a CC-type clerodane. The present study demonstrates that empirical rules and calculations can efficiently identify and revise erroneous structures in clerodane diterpenes.

Anti-Xanthine Oxidase 5'-Hydroxyhericenes A-D from the Edible Mushroom Hericium erinaceus and Structure Revision of 3-[2,3-Dihydroxy-4-(hydroxymethyl)tetrahydrofuran-1-yl]-pyridine-4,5-diol

Hericium erinaceus is an edible mushroom with diverse pharmaceutical applications. Although this mushroom is an attractive source of natural products for cancer treatment, little is known about the bioactive compounds from this mushroom, which may possess antibreast cancer activity. Here, we report the isolation and structure elucidation of new compounds, 5'-hydroxyhericenes A-D (1-4) as an inseparable mixture, together with known compounds (5-16) from the fruiting body of H. erinaceus. Based on NMR spectroscopic data and MS fragmentation analysis, the structure of a previously reported natural product, 3-[2,3-dihydroxy-4-(hydroxymethyl)tetrahydrofuran-1-yl]-pyridine-4,5-diol (5), should be revised to adenosine (6). Compounds 1-4 inhibit xanthine oxidase activity, while compounds 6, 9, and 10 scavenge reactive oxygen species generated by xanthine oxidase. Moreover, hericerin (13) exhibits strong growth inhibitory activity against T47D breast cancer cells and, to a lesser extent, against MDA-MB-231 breast cancer and MRC-5 normal embryonic cells. Exposure of T47D and MDA-MB-231 cells slightly increased PARP cleavage, suggesting that the growth inhibitory effect of hericerin may be mediated through nonapoptotic pathways. Our results suggest that the bioactive compounds of mushroom H. erinaceus hold promise as antibreast cancer agents.

Penicitone: Structural Reassignment of a Proposed Natural Product Acid Chloride

The proposed structure for the natural product penicitone, which contained a chemically improbable acid chloride functional group, was reassigned to a more probable structure using a combination of chemical knowledge, computer-assisted structure elucidation, and DFT methods.

Use of carbon-13 NMR to identify known natural products by querying a nuclear magnetic resonance database-An assessment

The quick identification of known organic low molecular weight compounds, also known as structural dereplication, is a highly important task in the chemical profiling of natural resource extracts. To that end, a method that relies on carbon-13 nuclear magnetic resonance (NMR) spectroscopy, elaborated in earlier works of the author's research group, requires the availability of a dedicated database that establishes relationships between chemical structures, biological and chemical taxonomy, and spectroscopy. The construction of such a database, called acd_lotus, was reported earlier, and its usefulness was illustrated by only three examples. This article presents the results of structure searches carried out starting from 58 carbon-13 NMR data sets recorded on compounds selected in the metabolomics section of the biological magnetic resonance bank (BMRB). Two compound retrieval methods were employed. The first one involves searching in the acd_lotus database using commercial software. The second one operates through the freely accessible web interface of the nmrshiftdb2 database, which includes the compounds present in acd_lotus and many others. The two structural dereplication methods have proved to be efficient and can be used together in a complementary way.