Feature-Based Molecular Networking Discovery of Bromopyrrole Alkaloids from the Marine Sponge Agelas dispar

A novel strategy for the multi-components division and discovering pharmacodynamic material basis of Chinese herbal compounds: A case study of Xian-Ling-Gu-Bao capsule

The therapeutic effects of Chinese herbal compounds are often achieved through the synergistic interactions of multiple ingredients. However, current research predominantly focuses on individual ingredients, neglecting the holistic nature of Chinese herbal compounds. This study proposes a novel strategy to elucidate the pharmacodynamic material basis of Chinese herbal compounds based on their multi-components (components named 'ZuFen' in China, it refers to multiple ingredients with similar chemical structures) composition, using the Xian-Ling-Gu-Bao (XLGB) capsule as a case study. Cheminformatics-based components partitioning was conducted after sourcing ingredients from various databases, resulting in a total of 856 ingredients which were categorized into nine major components. Furthermore, the pharmacodynamic ingredients of XLGB capsule were determined by analyzing the ingredients that were absorbed into the bloodstream. Through a combination of these ingredients and screening for absorption, the Dipsacus asper saponin components, Psoralea corylifolia coumarin components, and Epimedium flavonoid polyglycosides components were isolated. The anti-osteoporosis efficacy of these components were evaluated in zebrafish, demonstrating their capability to reverse mineralization reduction caused by prednisolone. These findings further support the idea that these components serve as the material basis for the pharmacological efficacy of XLGB capsule. This study provides a novel systematic strategy for discovering the pharmacodynamic material basis of the efficacy of Chinese herbal compounds based on a 'multi-components' perspective.

Antimicrobial metabolites produced by endophytic fungi associated with the leaves of Vochysia divergens

Investigation of the endophytic fungi Nigrospora sphaerica, Nigrospora oryzae, and Pseudofusicoccum stromaticum MeOH fractions isolated from the leaves of Vochysia divergens, a medicinal species from the Brazilian Pantanal, led to the identification of five compounds, namely a new compound (1E,8Z)-10,11-dihydroxy-5,5,8-trimethyl-4-oxocycloundeca-1,8-diene-1-carbaldehyde (1) and four known compounds: 5-methylmellein (2), sclerone (3), daldinone A (4), and lasiodiplodin (5). All compounds were identified using spectroscopic methods, and 1 was corroborated with mass spectrometry, while the known compounds were compared with data in the literature. The relative configuration of compound 1 was determined based on theoretical conformational studies as well as the J experimental values between the hydroxymethyne hydrogens. The antimicrobial activity of the compounds was evaluated. Promising results were obtained for compounds 2, 4, and 5 since they inhibited the bacterium Pseudomonas aeruginosa, an opportunistic pathogen, suggesting the potential of these microorganisms as a source of new antibacterial agents.

Marine natural products

Covering: January to the end of December 2022This review covers the literature published in 2022 for marine natural products (MNPs), with 645 citations (633 for the period January to December 2022) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, the submerged parts of mangroves and other intertidal plants. The emphasis is on new compounds (1417 in 384 papers for 2022), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. An analysis of NP structure class diversity in relation to biota source and biome is discussed.

A Survey of Recently Discovered Naturally Occurring Organohalogen Compounds

The discovery of naturally occurring organohalogen compounds has increased astronomically in the 55 years since they were first discovered─from fewer than 50 in 1968 to a combined 7,958 described examples in three comprehensive reviews. The present survey, which covers the period 2021-2023, brings the number of known natural organohalogens to approximately 8,400. The organization is according to species origin, and coverage includes marine and terrestrial plants, fungi, bacteria, marine sponges, corals, cyanobacteria, tunicates, and other marine organisms.

Screening for antibacterial and cytotoxic activities of Sri Lankan marine sponges through microfractionation: Isolation of bromopyrrole alkaloids from Stylissa massa

Sri Lanka is a biodiversity hotspot and one of the richest geographical locations of marine sponges in the Indian ocean. However, the most extensive taxonomical study on Sri Lankan sponge biodiversity dates back ~100 years and only a limited number of studies have been conducted on sponge natural products. In the current study, 35 marine sponge specimens (collected from 16 sponge habitats around Sri Lanka) were identified, microfractionated and evaluated for antibacterial and anticancer assays. In total, 30 species were characterized, of which 19 species gave extracts with antibacterial and/or cytotoxic activities. Microfractionated organic extract of Aciculites orientalis gave the most potent antibacterial activity against Staphylococcus aureus and strongest lymphoma cell toxicity was exhibited by the organic extract of Acanthella sp. Guided by the molecular ion peaks in the bioactive fractions, large-scale extraction of Stylissa massa led to the isolation of three bromopyrrole alkaloids, sceptrin, hymenin and manzacidin A/C. Of these, sceptrin exhibited broad spectrum antibacterial activity against both Escherichia coli and S. aureus (MIC of 62.5 μM against both species). Based on natural product literature, seven promising species were identified as understudied. Their further exploration may lead to the discovery of structurally novel compounds.

Targeted chemical profiling for p-HAP glycosides by using molecular networking and comparative analysis of their contents between Artemisia japonica and Artemisia capillaris

A total of 65 phenolic acid compounds were annotated or identified by UHPLC-MS/MS method, among them, 17 p-HAP (p-hydroxyacetophenone) glycosides were firstly targeted profiled based on molecular networking. Their characteristic product ions of MS/MS spectra were found and examined on the guideline of targeted isolation. As a result, a new p-HAP glycoside was thus obtained and determined as 2'-O-caffeoyl-p-HAP-4-O-β-D-glucopyranoside (33) based on 1D and 2D NMR data. Besides, multicomponents quantitative analysis indicated the distinct regional variability in chemicals distribution of A. japonica, and meanwhile, the contents of p-HAP glycosides from A. japonica were higher than those in A. capillaris as a whole, which further suggested the potential medicinal value of A. japonica.

Comparative Chemical Profiling and Antimicrobial/Anticancer Evaluation of Extracts from Farmed versus Wild Agelas oroides and Sarcotragus foetidus Sponges

Marine sponges are highly efficient in removing organic pollutants and their cultivation, adjacent to fish farms, is increasingly considered as a strategy for improving seawater quality. Moreover, these invertebrates produce a plethora of bioactive metabolites, which could translate into an extra profit for the aquaculture sector. Here, we investigated the chemical profile and bioactivity of two Mediterranean species (i.e., Agelas oroides and Sarcotragus foetidus) and we assessed whether cultivated sponges differed substantially from their wild counterparts. Metabolomic analysis of crude sponge extracts revealed species-specific chemical patterns, with A. oroides and S. foetidus dominated by alkaloids and lipids, respectively. More importantly, farmed and wild explants of each species demonstrated similar chemical fingerprints, with the majority of the metabolites showing modest differences on a sponge mass-normalized basis. Furthermore, farmed sponge extracts presented similar or slightly lower antibacterial activity against methicillin-resistant Staphylococcus aureus, compared to the extracts resulting from wild sponges. Anticancer assays against human colorectal carcinoma cells (HCT-116) revealed marginally active extracts from both wild and farmed S. foetidus populations. Our study highlights that, besides mitigating organic pollution in fish aquaculture, sponge farming can serve as a valuable resource of biomolecules, with promising potential in pharmaceutical and biomedical applications.

In Situ Capture and Real-Time Enrichment of Marine Chemical Diversity

Analyzing the chemical composition of seawater to understand its influence on ecosystem functions is a long-lasting challenge due to the inherent complexity and dynamic nature of marine environments. Describing the intricate chemistry of seawater requires optimal in situ sampling. Here is presented a novel underwater hand-held solid-phase extraction device, I-SMEL (In Situ Marine moleculELogger), which aims to concentrate diluted molecules from large volumes of seawater in a delimited zone targeting keystone benthic species. Marine benthic holobionts, such as sponges, can impact the chemical composition of their surroundings possibly through the production and release of their specialized metabolites, hence termed exometabolites (EMs). I-SMEL was deployed in a sponge-dominated Mediterranean ecosystem at a 15 m depth. Untargeted MS-based metabolomics was performed on enriched EM extracts and showed (1) the chemical diversity of enriched seawater metabolites and (2) reproducible recovery and enrichment of specialized sponge EMs such as aerothionin, demethylfurospongin-4, and longamide B methyl ester. These EMs constitute the chemical identity of each targeted species: Aplysina cavernicola, Spongia officinalis, and Agelas oroides, respectively. I-SMEL concentrated sponge EMs from 10 L of water in a 10 min sampling time. The present proof of concept with I-SMEL opens new research perspectives in marine chemical ecology and sets the stage for further sustainable efforts in natural product chemistry.

Phomactinine, the First Nitrogen-Bearing Phomactin, Produced by Biatriospora sp. CBMAI 1333

Metabolomics analyses and improvement of growth conditions were applied toward diversification of phomactin terpenoids by the fungus Biatriospora sp. CBMAI 1333. Visualization of molecular networking results on Gephi assisted the observation of phomactin diversification and guided the isolation of new phomactin variants by applying a modified version of chemometrics based on a fractional factorial design. Consequentially, the first nitrogen-bearing phomactin, phomactinine (1), with a new rearranged carbon skeleton, was isolated and identified. The strategy combining metabolomics and chemometrics can be extended to include bioassay potency, structure novelty, and metabolic diversification connected or not to genomic analyses.

Targeted Isolation of Dolabellane Diterpenoids from the Soft Coral Clavularia viridis Using Molecular Networking

LC-MS/MS-based molecular networking annotation coupled ¹H NMR detection allowed the depiction of the soft coral Clavularia viridis to produce a profile of dolabellane-type diterpenoids. Chromatographic separation of the EtOAc fraction resulted in the isolation of 12 undescribed dolabellane-type diterpenoids, namely, clavirolides J-U (1-12). Their structures were characterized by the extensive analysis of the spectroscopic data, including the calculated ECD and X-ray diffraction for the configurational assignments. Clavirolides J-K are characterized by a 1,11- and 5,9-fused tricyclic tetradecane scaffold fused with a α,β-unsaturated-δ-lactone, and clavirolide L possesses a 1,11- and 3,5-fused tricyclic tetradecane scaffold, which extend the dolabellane-type scaffolds. Clavirolides L and G showed significant inhibition against HIV-1 without RT enzyme inhibition, providing additional non-nucleosides with different mechanisms from efavirenz.

Dimeric pyrrole-imidazole alkaloids: sources, structures, bioactivities and biosynthesis

Pyrrole-imidazole alkaloids (PIAs) constitute a highly diverse and densely functionalized subclass of marine natural products. Among them, the uncommon dimeric PIAs with ornate molecular architectures, attractive biological properties and interesting biosynthetic origin have spurred a considerable interest of chemists and biologists. The present review comprehensively summarized 84 dimeric PIAs discovered during the period from 1981 to September 2022, covering their source organisms, chemical structures, biological activities as well as biosynthesis. For a better understanding, these structurally intricate PIA dimers are firstly classified and presented according to their carbon skeleton features as well as biosynthesis pathways. Furthermore, relevant summaries focusing on the source organisms and the associated bioactivities of these compounds belonging to different chemical classes are also provided, which will help elucidate the fascinating chemistry and biology of these unusual PIA dimers.

β-Lactams from the Ocean

The title of this essay is as much a question as it is a statement. The discovery of the β-lactam antibiotics-including penicillins, cephalosporins, and carbapenems-as largely (if not exclusively) secondary metabolites of terrestrial fungi and bacteria, transformed modern medicine. The antibiotic β-lactams inactivate essential enzymes of bacterial cell-wall biosynthesis. Moreover, the ability of the β-lactams to function as enzyme inhibitors is of such great medical value, that inhibitors of the enzymes which degrade hydrolytically the β-lactams, the β-lactamases, have equal value. Given this privileged status for the β-lactam ring, it is therefore a disappointment that the exemplification of this ring in marine secondary metabolites is sparse. It may be that biologically active marine β-lactams are there, and simply have yet to be encountered. In this report, we posit a second explanation: that the value of the β-lactam to secure an ecological advantage in the marine environment might be compromised by its close structural similarity to the β-lactones of quorum sensing. The steric and reactivity similarities between the β-lactams and the β-lactones represent an outside-of-the-box opportunity for correlating new structures and new enzyme targets for the discovery of compelling biological activities.

MS/MS-Based Molecular Networking: An Efficient Approach for Natural Products Dereplication

Natural products (NPs) have historically played a primary role in the discovery of small-molecule drugs. However, due to the advent of other methodologies and the drawbacks of NPs, the pharmaceutical industry has largely declined in interest regarding the screening of new drugs from NPs since 2000. There are many technical bottlenecks to quickly obtaining new bioactive NPs on a large scale, which has made NP-based drug discovery very time-consuming, and the first thorny problem faced by researchers is how to dereplicate NPs from crude extracts. Remarkably, with the rapid development of omics, analytical instrumentation, and artificial intelligence technology, in 2012, an efficient approach, known as tandem mass spectrometry (MS/MS)-based molecular networking (MN) analysis, was developed to avoid the rediscovery of known compounds from the complex natural mixtures. Then, in the past decade, based on the classical MN (CLMN), feature-based MN (FBMN), ion identity MN (IIMN), building blocks-based molecular network (BBMN), substructure-based MN (MS2LDA), and bioactivity-based MN (BMN) methods have been presented. In this paper, we review the basic principles, general workflow, and application examples of the methods mentioned above, to further the research and applications of these methods.

Chemodiversity and Anti-Leukemia Effect of Metabolites from Penicillium setosum CMLD 18

Penicillium setosum represents a Penicillium species recently described, with little up-to-date information about its metabolic and biological potential. Due to this scenario, we performed chemical and biological studies of P. setosum CMLD18, a strain isolated from Swinglea glutinosa (Rutaceae). HRMS-MS guided dereplication strategies and anti-leukemia assays conducted the isolation and characterization of six compounds after several chromatographic procedures: 2-chloroemodic acid (2), 2-chloro-1,3,8-trihydroxy-6- (hydroxymethyl)-anthraquinone (7), 7-chloroemodin (8), bisdethiobis(methylthio)acetylaranotine (9), fellutanine C (10), and 4-methyl-5,6-diihydro-2H-pyran-2-one (15). From the assayed metabolites, (10) induced cellular death against Kasumi-1, a human leukemia cell line, as well as good selectivity for it, displaying promising cytotoxic activity. Here, the correct NMR signal assignments for (9) are also described. Therefore, this work highlights more detailed knowledge about the P. setosum chemical profile as well as its biological potential, offering prospects for obtaining natural products with anti-leukemia capabilities.

Targeted isolation of diterpenoids and sesquiterpenoids from Daphne gemmata E. Pritz. ex Diels using molecular networking together with network annotation propagation and MS2LDA

Investigation of the whole plant of Daphne gemmata E. Pritz. ex Diels (Thymelaeaceae) using molecular networking coupled to Network Annotation Propagation (NAP) and unsupervised substructure annotation (MS2LDA) led to the discovery of five tigliane diterpenoids, 14 guaiane sesquiterpenoids, one rhamnofolane diterpenoid and three carotene sesquiterpenoids. The structures of the eight undescribed compounds, daphnorbol A and daphnegemmatoids A-G, were characterized by detailed spectroscopic analyses, NMR and ECD calculations, application of Snatzke's method and single-crystal X-ray diffraction analysis. All isolated compounds were evaluated for their cytotoxic activities against HepG2, A549, and MCF-7 cells by MTT assay. Daphnorbol A exhibited significant cytotoxic activity against HepG2 and A549 cells with IC50 values of 4.06 μM and 6.35 μM, respectively. Prostratin showed potent cytotoxic activity against HepG2 and A549 cells with IC50 values of 6.06 μM and 5.45 μM, respectively. Further Hoechst 33,258 and AO-EB staining assays indicated that daphnorbol A and prostratin could induce apoptosis in HepG2 and A549 cells.