Genome Mining and Metabolomics Unveil Pseudonochelin: A Siderophore Containing 5-Aminosalicylate from a Marine-Derived Pseudonocardia sp. Bacterium

Unlocking marine treasures: isolation and mining strategies of natural products from sponge-associated bacteria

Covering: 2019 to early 2025Marine sponges form unique ecosystems through symbiosis with diverse microbial communities, producing natural products including bioactive compounds. This review comprehensively addresses the key steps in the discovery of natural products from sponge-associated microorganisms, encompassing microbial isolation and cultivation, compound identification, and characterisation. Various cultivation methods, such as floating filter cultivation, microcapsule-based cultivation, and in situ systems, are examined to highlight their applications and strategies for overcoming limitations of conventional approaches. Additionally, the integration of genome-based methodologies and compound screening is explored to enhance the discovery of novel bioactive substances and establish a sustainable platform for natural product research. This review provides insights into the latest trends in sponge-associated microbial research and offers practical perspectives for expanding the utilization of marine biological resources.

Ion Mobility-Coupled Mass Spectrometry for Metallophore Detection

Metal chelating small molecules (metallophores) play significant roles in microbial interactions and bacterial survival; however, current methods to identify metallophores are limited by low sensitivity, a lack of metal selectivity, and/or complicated data analysis. To overcome these limitations, we developed a novel approach for detecting metallophores in natural product extracts using ion mobility-coupled mass spectrometry (IM-MS). As a proof of concept, marine bacterial extracts containing known metallophores were analyzed by IM-MS with and without added metals, and the data were compared between conditions to identify metal-binding metabolites. Ions with changes in both mass and mobility were specific to metallophores, enabling their identification within these complex extracts. Additionally, we compared the use of direct infusion (DI) and liquid chromatography (LC) separation with IM-MS. For most samples, DI outperformed LC by minimizing the time required for data collection and simplifying analysis. However, for some samples, LC improved the detection of metallophores likely by reducing ion suppression. IM-MS was then used to identify 10 metallophores in an extract from a marine Micromonospora sp. Overall, incorporating IM-MS facilitated the rapid detection of metal-binding natural products in complex bacterial extracts through the comparison of mass and mobility data in the presence and absence of metals.

Cyclopeptide Avellanins D-O with Antimalarial Activity from the Mariana Trench Anemone-Derived Hamigera ingelheimensis MSC5

Marine microorganisms are a treasure trove of natural products, especially those in extreme marine environments, which may produce novel natural products. Herein, biosynthetic gene cluster analysis combined with an integrated metabolomic strategy incorporating matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), nuclear magnetic resonance (NMR), and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) based Global Natural Products Social Molecular Networking (GNPS) was used to discover new compounds from the Mariana trench anemone-derived fungus Hamigera ingelheimensis MSC5. As a result, 12 new cyclic pentapeptides, avellanins D-O (1-12), were isolated, together with a known cyclic pentapeptide avellanin C (13). All the structures and absolute configurations were elucidated using NMR, mass spectrometry, X-ray diffraction analysis, and Marfey's method. A plausible biosynthetic pathway for the avellanins was proposed based on the gene cluster analysis of H. ingelheimensis MSC5. Bioassay revealed that compound 6 exhibited potent antimalarial activity with an IC50 value of 0.19 ± 0.09 μM.

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.

1H NMR-guided isolation of hasubanan alkaloids from the alkaloidal extract of Stephania longa

1H NMR-guided fractionation led to the isolation of 16 alkaloids from the alkaloidal extract of Stephania longa, including 11 new hasubanan alkaloids (1-11) and five known alkaloids (12-16). Interestingly, compounds 2 and 11 are typically considered protonated tertiary amine compounds, whereas compounds 1 and 10 are regarded as oxidized versions of the corresponding compounds. Their gross structures were determined through an extensive analysis of spectroscopic data (NMR (nuclear magnetic resonance) and HRESIMS (high resolution electrospray ionization mass spectroscopy)), and their absolute configurations were established by comparing their experimental and calculated electronic circular dichroism (ECD) spectra. The new (3) and a known (12) compounds in all isolates displayed stronger antineuroinflammatory effects (IC50 values of 1.8 and 11.1 μM, respectively) than minocycline (IC50 value of 15.5 μM) against NO production on LPS-activated BV2 cells.

Advances in Natural Products from the Marine-Sponge-Associated Microorganisms with Antimicrobial Activity in the Last Decade

Microorganisms are the dominating source of food and nutrition for sponges and play an important role in sponge structure, chemical defense, excretion and evolution. In recent years, plentiful secondary metabolites with novel structures and specific activities have been identified from sponge-associated microorganisms. Additionally, as the phenomenon of the drug resistance of pathogenic bacteria is becoming more and more common, it is urgent to discover new antimicrobial agents. In this paper, we reviewed 270 secondary metabolites with potential antimicrobial activity against a variety of pathogenic strains reported in the literature from 2012 to 2022. Among them, 68.5% were derived from fungi, 23.3% originated from actinomycetes, 3.7% were obtained from other bacteria and 4.4% were discovered using the co-culture method. The structures of these compounds include terpenoids (13%), polyketides (51.9%), alkaloids (17.4%), peptides (11.5%), glucosides (3.3%), etc. Significantly, there are 124 new compounds and 146 known compounds, 55 of which have antifungal activity in addition to antipathogenic bacteria. This review will provide a theoretical basis for the further development of antimicrobial drugs.

1H-NMR-guided isolation of enantiomeric coumarin-monoterpenes with anti-inflammatory activity from Gerbera piloselloides

¹H-NMR guided fractionation led to the isolation of twenty-two coumarin monoterpenes from the whole plant of Gerbera piloselloides, among which fourteen were undescribed. All coumarin monoterpenes were initially found to be racemates without optical activity. Subsequently, eleven pairs of optically pure enantiomers were successfully separated by chiral phase HPLC. Their structures and absolute configurations were unambiguously determined based on their spectroscopic data, calculated/experimental electronic circular dichroism (ECD) data, and X-ray diffraction analysis. Bioassays in LPS-treated RAW 264.7 cells revealed that the four compounds possessed moderate anti-inflammatory activity. In addition, the correlations between the cotton effect (CE) from δ-lactone at approximately 210-220 nm in CD spectra and γ-C or the ring fused at γ-C of the skeleton were reported for the first time.

Hot off the Press

A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as hyperispirone A from Hypericum beanii.