Recent advances in deep-sea natural products

Xeniaphyllane and Xeniolide Diterpenes from the Deep-Sea Soft Coral Paragorgia arborea

As exploration of ocean depths >1000 m is only possible by expensive remotely operated underwater vehicles, deep-sea invertebrates represent a largely untapped source of marine metabolites for potential applications in medicine. Our current study aims to investigate these deep-sea invertebrates in Ireland to discover new biological and chemical diversity. Here, we investigate the bubble gum coral, Paragorgia arborea, collected at 1500 m depth from Whittard canyon in the Northeastern Atlantic. This species was selected following chemical profiling and biological screening. The isolation and structure elucidation of the main metabolites yielded three new diterpenes, namely, miolenol (1) and epoxymiolenol (2) characterized by the rare bicyclo[7.2.0]undec-4-ene skeleton, and the xeniolide epoxycoraxeniolide A (3), together with five known diterpenes. The structures of the new compounds were identified through extensive NMR analysis with their absolute configurations assigned by comparison between experimental and TDDFT-calculated ECD. The eight compounds were screened for cytotoxicity and antimalarial activity, and none displayed noteworthy bioactivity.

Anthoteibinenes A-E from the Irish Deep-Sea Coral Anthothela grandiflora: An Amination Puzzle

Chemical investigation of extracts from the Irish deep-sea soft coral Anthothela grandiflora revealed cadinene-like sesquiterpenes, anthoteibinenes A-E, bearing unusual dimethylamine substitution. Structure elucidation was accomplished using 1D/2D NMR spectroscopy and high-resolution mass spectrometry, while NOESY NMR experiments, gauge invariant atomic orbital (GIAO) NMR calculations coupled with DP4+ probabilities measures, and ECD comparisons were incorporated to propose their relative and absolute configurations. Anthoteibinene B (2) exhibited 49% inhibition of respiratory syncytial virus (RSV) at 3.1 μM with no cytotoxicity.

Characterization and Biosynthetic Regulation of Isoflavone Genistein in Deep-Sea Actinomycetes Microbacterium sp. B1075

Deep-sea environments, as relatively unexplored extremes within the Earth's biosphere, exhibit notable distinctions from terrestrial habitats. To thrive in these extreme conditions, deep-sea actinomycetes have evolved unique biochemical metabolisms and physiological capabilities to ensure their survival in this niche. In this study, five actinomycetes strains were isolated and identified from the Mariana Trench via the culture-dependent method and 16S rRNA sequencing approach. The antimicrobial activity of Microbacterium sp. B1075 was found to be the most potent, and therefore, it was selected as the target strain. Molecular networking analysis via the Global Natural Products Social Molecular Networking (GNPS) platform identified 25 flavonoid compounds as flavonoid secondary metabolites. Among these, genistein was purified and identified as a bioactive compound with significant antibacterial activity. The complete synthesis pathway for genistein was proposed within strain B1075 based on whole-genome sequencing data, with the key gene being CHS (encoding chalcone synthase). The expression of the gene CHS was significantly regulated by high hydrostatic pressure, with a consequent impact on the production of flavonoid compounds in strain B1075, revealing the relationship between actinomycetes' synthesis of flavonoid-like secondary metabolites and their adaptation to high-pressure environments at the molecular level. These results not only expand our understanding of deep-sea microorganisms but also hold promise for providing valuable insights into the development of novel pharmaceuticals in the field of biopharmaceuticals.

Antitumor aspochalasin and antiviral benzofuran derivatives from a marine-derived fungus Aspergillus sp. SCSIO41032

Chemical investigation of the EtOAc extract of a deep-sea derived fungus Aspergillus sp. SCSIO41032 resulted in the isolation of ten known compounds, including eight aspochalasins. Their structures were elucidated by using extensive NMR spectroscopic, mass spectrometric and single crystal X-ray diffraction analysis. The detailed crystallographic data for structures 1, 2, and 4, along with the relative configurations of aspochalasin E (3) determined by its acetonide derivative were reported for the first time. The results of antitumor and antiviral activities showed that 3 displayed moderate antitumor activities against 22Rv1, PC-3, A549, and HCT-15 cell lines with IC50 values ranged from 5.9 ± 0.8 to 19.0 ± 7.7 μM, and 9 exhibited moderate antiviral activities against HSV-1/2 with EC50 values of 9.5 ± 0.5 and 5.4 ± 0.6 μM, respectively. Plate clone formation assays results indicated that 3 inhibited the 22Rv1, PC-3 cells growth in a dose-dependent manner.

New Hydroxyphenylacetic Acids and α-Pyrone Derivative from the Deep-Sea Cold Seep Sediment-Derived Fungus Penicillium corylophilum CS-682

Two pairs of new enantiomeric hydroxyphenylacetic acid derivatives, (±)-corylophenols A and B ((±)-1 and (±)-2), a new α-pyrone analogue, corylopyrone A (3), and six andrastin-type meroterpenoids (4-9) were isolated and identified from the deep-sea cold-seep sediment-derived fungus Penicillium corylophilum CS-682. Their structures and stereo configurations were determined by detailed spectroscopic analysis of NMR and MS data, chiral HPLC analysis, J-based configuration analysis, and quantum chemical calculations of ECD, specific rotation, and NMR (with DP4+ probability analysis). Compound 3 showed inhibitory activity against some strains of pathogenic bacteria.

Anti-inflammatory monomeric sorbicillinoids from the marine-fish-derived fungus Trichoderma sp. G13

Four new monomeric sorbicillinoids, trichillinoids A - D (1-4), along with two known dimeric sorbicillinoids (5 and 6), and five known monomeric sorbicillinoids (7-11), were obtained from the marine-fish-derived fungus Trichoderma sp. G13. They were structurally characterized on the basis of comprehensive spectroscopic investigations (NMR, HRESIMS, and ECD). Compounds 1-4 displayed moderate anti-inflammatory activities, according to inhibiting the production of NO in RAW264.7 cells activated with IC50 values ranging from 14 to 20 μM.

Genome Mining of a Deep-Sea-Derived Penicillium allii-sativi Revealed Polyketide-Terpenoid Hybrids with Antiosteoporosis Activity

Two novel meroterpenoids, alliisativins A and B (1, 2) were discovered through a genome-based exploration of the biosynthetic gene clusters of the deep-sea-derived fungus Penicillium allii-sativi MCCC entry 3A00580. Extensive spectroscopic analysis, quantum calculations, chemical derivatization, and biogenetic considerations were utilized to establish their structures. Alliisativins A and B (1, 2) possess a unique carbon skeleton featuring a drimane sesquiterpene with a highly oxidized polyketide. Noteworthily, alliisativin A (1) showed dual activity in promoting osteogenesis and inhibiting osteoclast, indicating an antiosteoporosis potential.

Diverse indole-diterpenoids with protein tyrosine phosphatase 1B inhibitory activities from the marine coral-derived fungus Aspergillus sp. ZF-104

Eight previously undescribed indole-diterpenoids named penerpenes O-V (1-8), together with seven known analogues (9-14), were isolated from the marine soft coral-derived fungus Aspergillus sp. ZF-104. Their structures including the absolute configurations of these compounds were assigned on the basis of spectroscopic data and ECD analysis along with quantum ECD and NMR calculations. Compounds 4 and 5 bear rare indolin-2-one units in their structures and 6 bears a reconstructed novel skeleton in which the indole ring and the terpenoid substructure are cleaved before they are reconnected through the nitrogen atom. Compounds 1, 2, 7, and 10 showed protein tyrosine phosphatase 1B (PTP1B) inhibitory activities comparable to that of the positive control NaVO3.

Integration of Untargeted Metabolomics and Microbial Community Analyses to Characterize Distinct Deep-Sea Methane Seeps

Deep-sea methane seeps host highly diverse microbial communities whose biological diversity is distinct from other marine habitats. Coupled with microbial community analysis, untargeted metabolomics of environmental samples using high resolution tandem mass spectrometry provides unprecedented access to the unique specialized metabolisms of these chemosynthetic microorganisms. In addition, the diverse microbial natural products are of broad interest due to their potential applications for human and environmental health and well-being. In this exploratory study, sediment cores were collected from two methane seeps (-1000 m water depth) with very different gross geomorphologies, as well as a non-seep control site. Cores were subjected to parallel metabolomic and microbial community analyses to assess the feasibility of representative metabolite detection and identify congruent patterns between metabolites and microbes. Metabolomes generated using high resolution liquid chromatography tandem mass spectrometry were annotated with predicted structure classifications of the majority of mass features using SIRIUS and CANOPUS. The microbiome was characterized by analysis of 16S rRNA genes and analyzed both at the whole community level, as well as the small subgroup of Actinobacteria, which are known to produce societally useful compounds. Overall, the younger Dagorlad seep possessed a greater abundance of metabolites while there was more variation in abundance, number, and distribution of metabolites between samples at the older Emyn Muil seep. Lipid and lipid-like molecules displayed the greatest variation between sites and accounted for a larger proportion of metabolites found at the older seep. Overall, significant differences in composition of the microbial community mirrored the patterns of metabolite diversity within the samples; both varied greatly as a function of distance from methane seep, indicating a deterministic role of seepage. Interdisciplinary research to understand microbial and metabolic diversity is essential for understanding the processes and role of ubiquitous methane seeps in global systems and here we increase understanding of these systems by visualizing some of the chemical diversity that seeps add to marine systems.

Indonesian marine and its medicinal contribution

The archipelagic country of Indonesia is populated by the densest marine biodiversity in the world which has created strong global interest and is valued by both Indigenous and European settlements for different purposes. Nearly 1000 chemicals have been extracted and identified. In this review, a systematic data curation was employed to collate bioprospecting related manuscripts providing a comprehensive directory based on publications from 1988 to 2022. Findings with significant pharmacological activities are further discussed through a scoping data collection. This review discusses macroorganisms (Sponges, Ascidian, Gorgonians, Algae, Mangrove) and microorganism (Bacteria and Fungi) and highlights significant discoveries, including a potent microtubule stabilizer laulimalide from Hyattella sp., a prospective doxorubicin complement papuamine alkaloid from Neopetrosia cf exigua, potent antiplasmodial manzamine A from Acanthostrongylophora ingens, the highly potent anti trypanosomal manadoperoxide B from Plakortis cfr. Simplex, mRNA translation disrupter hippuristanol from Briareum sp, and the anti-HIV-1 (+)-8-hydroxymanzamine A isolated from Acanthostrongylophora sp. Further, some potent antibacterial extracts were also found from a limited biomass of bacteria cultures. Although there are currently no examples of commercial drugs from the Indonesian marine environment, this review shows the molecular diversity present and with the known understudied biodiversity, reveals great promise for future studies and outcomes.

Penidihydrocitrinins A-C: New Polyketides from the Deep-Sea-Derived Penicillium citrinum W17 and Their Anti-Inflammatory and Anti-Osteoporotic Bioactivities

Three new polyketides (penidihydrocitrinins A-C, 1-3) and fourteen known compounds (4-17) were isolated from the deep-sea-derived Penicillium citrinum W17. Their structures were elucidated by comprehensive analyses of 1D and 2D NMR, HRESIMS, and ECD calculations. Compounds 1-17 were evaluated for their anti-inflammatory and anti-osteoporotic bioactivities. All isolates exhibited significant inhibitory effects on LPS-stimulated nitric oxide production in murine brain microglial BV-2 cells in a dose-response manner. Notably, compound 14 displayed the strongest effect with the IC50 value of 4.7 µM. Additionally, compounds 6, 7, and 8 significantly enhanced osteoblast mineralization, which was comparable to that of the positive control, purmorphamine. Furthermore, these three compounds also suppressed osteoclastogenesis in a dose-dependent manner under the concentrations of 2.5 μM, 5.0 μM, and 10 μM.

Harnessing actinobacteria potential for cancer prevention and treatment

Actinobacteria are gram-positive bacteria with high G:C ratio in their genetic makeup. They have been noted and studied for their capacity to produce bioactive substances with a range of uses in human health, and they also exhibit a unique property of adapting to extreme environments quite well. Actinobacteria may play an essential role in cancer prevention and treatment due to their synthesis of anticancer compounds, as indicated by recent studies. The aim of this review is to give a summary of what is currently known about the connection between actinobacteria and different types of cancer. This paper delineates the diverse array of actinobacterial bioactive compounds possessing anticancer properties, elucidates their mechanisms of action and explores potential applications in cancer treatment. Furthermore, this review highlights how the microbiome influences the onset and progression of cancer, as well as the discussing the potential benefits that actinobacteria may bring in terms of controlling the microbiome and contributing to the regulation of the tumour microenvironment to cure or prevent cancer.

Rubensteroid A, a new steroid with antibacterial activity from Penicillium rubens AS-130

A new steroid with strong antibacterial activity, rubensteroid A (1), along with its decarboxylic analogue, solitumergosterol A (2), were isolated and identified from the Magellan Seamount-derived fungus Penicillium rubens AS-130. The structure and absolute configuration of compound 1 were established by detailed interpretation of NMR spectroscopic analysis, mass spectrometry data, and TDDFT-ECD calculations. Compound 1 had a rare 6/6/6/6/5 pentacyclic system, which might be the [4 + 2] Diels-Alder adduct of 14,15-didehydroergosterol (14-DHE) cycloaddition with maleic acid or maleimide, followed by decarboxylation. Rubensteroid A (1) exhibited potent antibacterial activity against Escherichia coli and Vibrio parahaemolyticus, both with MIC value of 0.5 μg/mL.

SAIF plays anti-angiogenesis via blocking VEGF-VEGFR2-ERK signal in tumor treatment

Shark cartilage was created as a cancer-fighting diet because it was believed to have an element that may suppress tumor growth. Due to overfishing, sharks have become endangered recently, making it impossible to harvest natural components from shark cartilage for therapeutic development research. Previously, we identified a peptide SAIF from shark cartilage with an-tiangiogenic and anti-tumor effects, successfully expressed it in Escherichia coli by using genetic engineering techniques. However, we did not elucidate the specific target of SAIF and its antiangiogenic molecular mechanism, which hindered its further drug development. Therefore, in this work, the exact mechanism of action was studied using various techniques, including cellular and in vivo animal models, computer-aided simulation, molecular target capture, and transcriptome sequencing analysis. With VEGF-VEGFR2 interaction and preventing the activation of VEGFR2/ERK signaling pathways, SAIF was discovered to decrease angiogenesis and hence significantly limit tumor development. The findings further demonstrated SAIF's strong safety and pharmaceutically potential. The evidence showed that SAIF, which is expressed by, is a potent and safe angiogenesis inhibitor and might be developed as a candidate peptide drug for the treatment of solid tumors such as hepatocellular carcinoma and other conditions linked with angiogenic overgrowth.

Ferroptosis Inhibitory Compounds from the Deep-Sea-Derived Fungus Penicillium sp. MCCC 3A00126

Two new xanthones (1 and 2) were isolated from the deep-sea-derived fungus Penicillium sp. MCCC 3A00126 along with 34 known compounds (3-36). The structures of the new compounds were established by spectroscopic data. The absolute configuration of 1 was validated by comparison of experimental and calculated ECD spectra. All isolated compounds were evaluated for cytotoxicity and ferroptosis inhibitory activities. Compounds 14 and 15 exerted potent cytotoxicity against CCRF-CEM cells, with IC₅₀ values of 5.5 and 3.5 μM, respectively, whereas 26, 28, 33, and 34 significantly inhibited RSL3-induced ferroptosis, with EC₅₀ values of 11.6, 7.2, 11.8, and 2.2 μM, respectively.

Current development of β-carboline derived potential antimalarial scaffolds

β-Carboline alkaloids are an eminent class of nitrogen-based natural alkaloids and therapeutic molecules which exert various pharmacological activities through diverse mechanisms. A lot of attention has recently been directed towards this moiety in order to develop effective antimalarial drugs. "Malaria", an acute febrile illness caused by diverse Plasmodium parasites, is a continuing and escalating problem that devastates economically less developed countries by significantly increased morbidity and mortality rates. The mounting parasite resistance towards the antimalarial drugs and augmenting the 'habitat of the insect vector' are creating a catastrophe, indicating an urgent need for new efficacious therapeutics to combat this tropical disease. This article comprehensively encapsulates the clinical and preclinical antimalarial scaffolds comprising β-carboline moiety in their structure. Herein, various classes of natural and semi-synthetic analogues of β-carbolines reported in the last decade (2011-2021) have been extensively studied and illustrated. This review will help the readers to develop an insight into the β-carboline based antimalarials and molecular mechanisms lying behind their mode of action, which is anticipated to be beneficial for the future development of new β-carboline based therapeutics.

Bioactivity and Metabolome Mining of Deep-Sea Sediment-Derived Microorganisms Reveal New Hybrid PKS-NRPS Macrolactone from Aspergillus versicolor PS108-62

Despite low temperatures, poor nutrient levels and high pressure, microorganisms thrive in deep-sea environments of polar regions. The adaptability to such extreme environments renders deep-sea microorganisms an encouraging source of novel, bioactive secondary metabolites. In this study, we isolated 77 microorganisms collected by a remotely operated vehicle from the seafloor in the Fram Strait, Arctic Ocean (depth of 2454 m). Thirty-two bacteria and six fungal strains that represented the phylogenetic diversity of the isolates were cultured using an One-Strain-Many-Compounds (OSMAC) approach. The crude EtOAc extracts were tested for antimicrobial and anticancer activities. While antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium was common for many isolates, only two bacteria displayed anticancer activity, and two fungi inhibited the pathogenic yeast Candida albicans. Due to bioactivity against C. albicans and rich chemical diversity based on molecular network-based untargeted metabolomics, Aspergillus versicolor PS108-62 was selected for an in-depth chemical investigation. A chemical work-up of the SPE-fractions of its dichloromethane subextract led to the isolation of a new PKS-NRPS hybrid macrolactone, versicolide A (1), a new quinazoline (-)-isoversicomide A (3), as well as three known compounds, burnettramic acid A (2), cyclopenol (4) and cyclopenin (5). Their structures were elucidated by a combination of HRMS, NMR, [α]_D, FT-IR spectroscopy and computational approaches. Due to the low amounts obtained, only compounds 2 and 4 could be tested for bioactivity, with 2 inhibiting the growth of C. albicans (IC₅₀ 7.2 µg/mL). These findings highlight, on the one hand, the vast potential of the genus Aspergillus to produce novel chemistry, particularly from underexplored ecological niches such as the Arctic deep sea, and on the other, the importance of untargeted metabolomics for selection of marine extracts for downstream chemical investigations.

Tuaimenals B-H, Merosesquiterpenes from the Irish Deep-Sea Soft Coral Duva florida with Bioactivity against Cervical Cancer Cell Lines

Previous chemical investigation of the Irish deep-sea soft coral Duva florida led to the identification of tuaimenal A (10), a new merosesquiterpene containing a highly substituted chromene core and modest cytotoxicity against cervical cancer. Further MS/MS and NMR-guided investigation of this octocoral has resulted in the isolation and characterization of seven additional tuaimenal analogs, B-H (1-7), as well as two known A-ring aromatized steroids (8, 9), and additional tuaimenal A (10). Tuaimenals B, F, and G (1, 5, 6), bearing an oxygen at the C5 position, as well as monocyclic tuaimenal H (7), show increased cervical cancer inhibition profiles in comparison to that of 10. Tuaimenal G further displayed potent, selective cytotoxicity with an EC50 value of 0.04 μM against the C33A cell line compared to the CaSki cell line (EC50 20 μM). These data reveal the anticancer properties of tuaimenal analogs and suggest unique antiproliferation mechanisms across these secondary metabolites.

Naturally Occurring Organohalogen Compounds-A Comprehensive Review

The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.

The Diversity of Deep-Sea Actinobacteria and Their Natural Products: An Epitome of Curiosity and Drug Discovery

Bioprospecting of novel antibiotics has been the conventional norm of research fostered by researchers worldwide to combat drug resistance. With the exhaustion of incessant leads, the search for new chemical entities moves into uncharted territories such as the deep sea. The deep sea is a furthermost ecosystem with much untapped biodiversity thriving under extreme conditions. Accordingly, it also encompasses a vast pool of ancient natural products. Actinobacteria are frequently regarded as the bacteria of research interest due to their inherent antibiotic-producing capabilities. These interesting groups of bacteria occupy diverse ecological habitats including a multitude of different deep-sea habitats. In this review, we provide a recent update on the novel species and compounds of actinomycetes from the deep-sea environments within a period of 2016–2022. Within this period, a total of 24 new species of actinomycetes were discovered and characterized as well as 101 new compounds of various biological activities. The microbial communities of various deep-sea ecosystems are the emerging frontiers of bioprospecting.

Deep-sea sediment metagenome from Bay of Bengal reveals distinct microbial diversity and functional significance

Bay of Bengal (BoB) has immense significance with respect to ecological diversity and natural resources. Studies on microbial profiling and their functional significance at sediment level of BoB remain poorly represented. Herein, we describe the microbial diversity and metabolic potentials of BOB deep-sea sediment samples by subjecting the metagenomes to Nanopore sequencing. Taxonomic diversity ascertained at various levels revealed that bacteria belonging to phylum Proteobacteria predominantly represented in sediment samples NIOT_S7 and NIOT_S9. A comparative study with 16S datasets from similar ecological sites revealed depth as a crucial factor in determining taxonomic diversity. KEGG annotation indicated that bacterial communities possess sequence reads corresponding to carbon dioxide fixation, sulfur, nitrogen metabolism, but at varying levels. Additionally, gene sequences related to bioremediation of dyes, plastics, hydrocarbon, antibiotic resistance, secondary metabolite synthesis and metal resistance from both the samples as studied indicate BoB to represent a highly diverse environmental niche for further exploration.

Bacterial colonisation of plastic in the Rockall Trough, North-East Atlantic: An improved understanding of the deep-sea plastisphere

Plastic pollution has now been found within multiple ecosystems across the globe. Characterisation of microbial assemblages associated with marine plastic, or the so-called 'plastisphere', has focused predominantly on plastic in the epipelagic zone. Whether this community includes taxa that are consistently enriched on plastic compared to surrounding non plastic surfaces is unresolved, as are the ecological implications. The deep sea is likely a final sink for most of the plastic entering the ocean, yet there is limited information on microbial colonisation of plastic at depth. The aim of this study was to investigate deep-sea microbial communities associated with polystyrene (PS) and polyurethane (PU) with Bath stone used as a control. The substrates (n = 15) were deployed in the Rockall Trough (Atlantic), and recovered 420 days later from a depth of 1796 m. To characterise the bacterial communities, 16S rRNA genes were sequenced using the Illumina MiSeq platform. A dominant core microbiome (taxa shared across all substrates) comprised 8% of total ASVs (amplicon sequence variant) and accounted for 92% of the total community reads. This suggests that many commonly reported members of the plastisphere are simply opportunistic which freely colonise any hard surface. Transiently associated species consisted of approximately 7% of the total community. Thirty genera were enriched on plastic (P < 0.05), representing 1% of the total community. The discovery of novel deep-sea enriched taxa included Aurantivirga, Algivirga, IheB3-7, Spirosoma, HTCC5015, Ekhidna and Calorithrix on PS and Candidatus Obscuribacter, Haloferula, Marine Methylotrophic Group 3, Aliivibrio, Tibeticola and Dethiosulfatarculus on PU. This small fraction of the microbiome include taxa with unique metabolic abilities and show how bacterial communities can be shaped by plastic pollution at depth. This study outlines a novel approach in categorising the plastisphere to elucidate the ecological implications of enriched taxa that show an affinity for colonising plastic.

Cladosporioles A and B, Two New Indole Derivatives from the Deep-Sea-Derived Fungus Cladosporium cladosporioides 170056

Two new (cladosporioles A and B, 1 and 2) and fourteen known (3-16) compounds were isolated from the deep-sea-derived fungus Cladosporium cladosporioides 170056. The relative structures of the new compounds were elucidated mainly by detailed analysis of their NMR and HR-ESI-MS spectroscopic data. Their absolute configurations were determined by comparison of the experimental and calculated electronic circular dichroism (ECD) spectra. All isolates were tested for antimicrobial activity against Vibrio parahaemolyticus. Compound 15 exhibited weak effect with the MIC value of 156.25 μg/mL.

Investigation on Metabolites in Structural Diversity from The Deep-Sea Sediment-Derived Bacterium Agrococcus sp. SCSIO 52902 and Their Biosynthesis

Deep-sea sediment-derived bacterium may make full use of self-genes to produce more bioactive metabolites to adapt to extreme environment, resulting in the discovery of novel metabolites with unique structures and metabolic mechanisms. In the paper, we systematically investigated the metabolites in structurally diversity and their biosynthesis from the deep-sea sediment-derived bacterium Agrococcus sp. SCSIO 52902 based on OSMAC strategy, Molecular Networking tool, in combination with bioinformatic analysis. As a result, three new compounds and one new natural product, including 3R-OH-1,6-diene-cyclohexylacetic acid (1), linear tetradepsipeptide (2), N¹,N⁵-di-p-(EE)-coumaroyl-N¹⁰-acetylspermidine (3) and furan fatty acid (4), together with nineteen known compounds (5–23) were isolated from the ethyl acetate extract of SCSIO 52902. Their structures were elucidated by comprehensive spectroscopic analysis, single-crystal X-ray diffraction, Marfey’s method and chiral-phase HPLC analysis. Bioinformatic analysis revealed that compounds 1, 3, 9 and 13–22 were closely related to the shikimate pathway, and compound 5 was putatively produced by the OSB pathway instead of the PKS pathway. In addition, the result of cytotoxicity assay showed that compound 5 exhibited weak cytotoxic activity against the HL-60 cell line.

New Cytochalasin Derivatives from Deep-Sea Cold Seep-Derived Endozoic Fungus Curvularia verruculosa CS-129

Two new antimicrobial cytochalasin derivatives, 6 β , 7 β -epoxydeoxaphomin C ( 1 ) and 12-hydroxydeoxaphomin C ( 2 ), a new natural occurring product 24-nor-cytochalasin B ( 3 ), together with two related known analogues ( 4 - 5 ) were isolated and identified from an endozoic fungus Curvularia verruculosa CS-129, isolated from the deep-sea squat lobster Shinkaia crosnieri which was collected in cold seep region of south China sea. The structures of new compounds were elucidated on the basis of detailed spectroscopic analysis and ECD calculation. The spectroscopic data of 24-nor-cytochalasin B ( 3 ) were reported for the first time. All compounds were tested for their antibacterial activities against human and aquatic pathogenic bacteria.

Uncommon Polyketides from Penicillium steckii AS-324, a Marine Endozoic Fungus Isolated from Deep-Sea Coral in the Magellan Seamount

Four unusual steckwaic acids E–H (1–4), possessing a rarely described acrylic acid unit at C-4 (1–3) or a double bond between C-12 and C-13 (4) are reported for the first time, along with four new analogues (5–8) and two known congeners (9 and 10). They were purified from the organic extract of Penicillium steckii AS-324, an endozoic fungus obtained from a deep-sea coral Acanthogorgiidae sp., which was collected from the Magellan Seamount at a depth of 1458 m. Their structures were determined by the interpretation of NMR and mass spectroscopic data. The relative and absolute configurations were determined by NOESY correlations, X-ray crystallographic analysis, and ECD calculations. All compounds were tested for their antimicrobial activities against human- and aquatic-pathogenic bacteria and plant-related pathogenic fungi.

Tuaimenal A, a Meroterpene from the Irish Deep-Sea Soft Coral Duva florida, Displays Inhibition of the SARS-CoV-2 3CLpro Enzyme

Cold water benthic environments are a prolific source of structurally diverse molecules with a range of bioactivities against human disease. Specimens of a previously chemically unexplored soft coral, Duva florida, were collected during a deep-sea cruise that sampled marine invertebrates along the Irish continental margin in 2018. Tuaimenal A (1), a cyclized merosesquiterpenoid representing a new carbon scaffold with a highly substituted chromene core, was discovered through exploration of the soft coral secondary metabolome via NMR-guided fractionation. The absolute configuration was determined through vibrational circular dichroism. Functional biochemical assays and in silico docking experiments found tuaimenal A selectively inhibits the viral main protease (3CLpro) of SARS-CoV-2.

Marine Microbial-Derived Resource Exploration: Uncovering the Hidden Potential of Marine Carotenoids

Microbes in marine ecosystems are known to produce secondary metabolites. One of which are carotenoids, which have numerous industrial applications, hence their demand will continue to grow. This review highlights the recent research on natural carotenoids produced by marine microorganisms. We discuss the most recent screening approaches for discovering carotenoids, using in vitro methods such as culture-dependent and culture-independent screening, as well as in silico methods, using secondary metabolite Biosynthetic Gene Clusters (smBGCs), which involves the use of various rule-based and machine-learning-based bioinformatics tools. Following that, various carotenoids are addressed, along with their biological activities and metabolic processes involved in carotenoids biosynthesis. Finally, we cover the application of carotenoids in health and pharmaceutical industries, current carotenoids production system, and potential use of synthetic biology in carotenoids production.

Cytotoxic Nitrobenzoyl Sesquiterpenoids from an Antarctica Sponge-Derived Aspergillus insulicola

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive neoplastic diseases of the pancreas with fatal proliferation and metastasis and no medicine available for treatment. From an Antarctica sponge-derived fungus, Aspergillus insulicola HDN151418, four new nitrobenzoyl sesquiterpenoids, namely, insulicolides D-G (1-4), were isolated. Compounds 3 and 4 exhibited selective inhibition against human PDAC cell lines. Further studies indicated that compound 4 could significantly suppress cell proliferation to induce apoptosis and blocked migration and invasion of PDAC cells. Compound 4 could also avoid resistance and improved the therapeutic effect of the chemotherapy drug gemcitabine. A preliminary mechanism study showed that compound 4 can significantly inhibit the expression of EGFR and XIAP in PDAC cells. Altogether, 4 is a potential lead compound for anti-PDAC drug research.

Nitrogen-Containing Secondary Metabolites from a Deep-Sea Fungus Aspergillus unguis and Their Anti-Inflammatory Activity

Aspergillus is well-known as the second-largest contributor of fungal natural products. Based on NMR guided isolation, three nitrogen-containing secondary metabolites, including two new compounds, variotin B (1) and coniosulfide E (2), together with a known compound, unguisin A (3), were isolated from the ethyl acetate (EtOAc) extract of the deep-sea fungus Aspergillus unguis IV17-109. The planar structures of 1 and 2 were elucidated by an extensive analysis of their spectroscopic data (HRESIMS, 1D and 2D NMR). The absolute configuration of 2 was determined by comparison of its optical rotation value with those of the synthesized analogs. Compound 2 is a rare, naturally occurring substance with an unusual cysteinol moiety. Furthermore, 1 showed moderate anti-inflammatory activity with an IC₅₀ value of 20.0 µM. These results revealed that Aspergillus unguis could produce structurally diverse nitrogenous secondary metabolites, which can be used for further studies to find anti-inflammatory leads.

Australindolones, New Aminopyrimidine Substituted Indolone Alkaloids from an Antarctic Tunicate Synoicum sp

Five new alkaloids have been isolated from the lipophilic extract of the Antarctic tunicate Synoicum sp. Deep-sea specimens of Synoicum sp. were collected during a 2011 cruise of the R/V Nathanial B. Palmer to the southern Scotia Arc, Antarctica. Crude extracts from the invertebrates obtained during the cruise were screened in a zebrafish-based phenotypic assay. The Synoicum sp. extract induced embryonic dysmorphology characterized by axis truncation, leading to the isolation of aminopyrimidine substituted indolone (1–4) and indole (5–12) alkaloids. While the primary bioactivity tracked with previously reported meridianins A–G (5–11), further investigation resulted in the isolation and characterization of australindolones A–D (1–4) and the previously unreported meridianin H (12).

Streptoglycerides E-H, Unsaturated Polyketides from the Marine-Derived Bacterium Streptomyces&nbsp;specialis and Their Anti-Inflammatory Activity

Four new streptoglycerides E-H (1-4), with a rare 6/5/5/-membered ring system, were isolated from a marine-derived actinomycete Streptomyces specialis. The structures of 1-4 were elucidated by detailed analysis of HRESIMS, 1D and 2D NMR data and ECD spectra as well as comparison of their spectroscopic data with those reported in literature. Compounds 1-4 showed significant anti-inflammatory activity by inhibiting lipopolysaccharide (LPS)-induced nitric oxide (NO) production in Raw 264.7 cells with IC₅₀ values ranging from 3.5 to 10.9 µM. Especially, 2 suppressed mRNA expression levels of iNOS and IL-6 without cytotoxicity.

Cytochalasin Derivatives from the Endozoic Curvularia verruculosa CS-129, a Fungus Isolated from the Deep-Sea Squat Lobster Shinkaia crosnieri Living in the Cold Seep Environment

A new cytochalasin dimer, verruculoid A (1), three new cytochalasin derivatives, including 12-nor-cytochalasin F (2), 22-methoxycytochalasin B₆ (3), and 19-hydroxycytochalasin B (4), and 20-deoxycytochalasin B (5), a synthetic product obtained as a natural product for the first time, together with four known analogues (6-9), were isolated and identified from the culture extract of Curvularia verruculosa CS-129, an endozoic fungus obtained from the inner fresh tissue of the deep-sea squat lobster Shinkaia crosnieri, which was collected from the cold seep area of the South China Sea. Structurally, verruculoid A (1) represents the first cytochalasin homodimer containing a thioether bridge, while 12-nor-cytochalasin F (2) is the first 12-nor-cytochalasin derivative. Their structures were elucidated by detailed interpretation of the NMR spectroscopic and mass spectrometric data. X-ray crystallographic analysis and ECD calculations confirmed their structures and absolute configurations. Compound 1 displayed activity against the human pathogenic bacterium Escherichia coli (MIC = 2 μg/mL), while compounds 4, 8, and 9 showed cytotoxicity against three tumor cell lines (HCT-116, HepG-2, and MCF-7) with IC₅₀ values from 5.2 to 12 μM. The structure-activity relationship was briefly discussed.

A Treasure of Bioactive Compounds from the Deep Sea

The deep-sea environment is a unique, challenging extreme habitat where species have had to adapt to the absence of light, low levels of oxygen, high pressure and little food. In order to survive such harsh conditions, these organisms have evolved different biochemical and physiological features that often have no other equivalent in terrestrial habitats. Recent analyses have highlighted how the deep sea is one of the most diverse and species-rich habitats on the planet but less explored compared to more accessible sites. Because of their adaptation to this extreme environment, deep-sea species have the potential to produce novel secondary metabolites with potent biological activities. Recent advances in sampling and novel techniques in microorganism culturing and chemical isolation have promoted the discovery of bioactive agents from deep-sea organisms. However, reports of natural products derived from deep-sea species are still scarce, probably because of the difficulty in accessing deep-sea samples, sampling costs and the difficulty in culturing deep-sea organisms. In this review, we give an overview of the potential treasure represented by metabolites produced by deep marine species and their bioactivities for the treatment and prevention of various human pathologies.

Ultrastructural changes in methicillin-resistant Staphylococcus aureus (MRSA) induced by metabolites of thermophilous fungi Acrophialophora levis

Staphylococcus aureus and Methicillin-resistant S. aureus (MRSA) remains one of the major concerns of healthcare associated and community-onset infections worldwide. The number of cases of treatment failure for infections associated with resistant bacteria is on the rise, due to the decreasing efficacy of current antibiotics. Notably, Acrophialophora levis, a thermophilous fungus species, showed antibacterial activity, namely against S. aureus and clinical MRSA strains. The ethyl acetate extract of culture filtrate was found to display significant activity against S. aureus and MRSA with a minimum inhibitory concentration (MIC) of 1 μg/mL and 4 μg/mL, respectively. Scanning electron micrographs demonstrated drastic changes in the cellular architecture of metabolite treated cells of S. aureus and an MRSA clinical isolate. Cell wall disruption, membrane lysis and probable leakage of cytoplasmic are hallmarks of the antibacterial effect of fungal metabolites against MRSA. The ethyl acetate extract also showed strong antioxidant activity using two different complementary free radicals scavenging methods, DPPH and ABTS with efficiency of 55% and 47% at 1 mg/mL, respectively. The total phenolic and flavonoid content was found to be 50 mg/GAE and 20 mg/CAE, respectively. More than ten metabolites from different classes were identified: phenolic acids, phenylpropanoids, sesquiterpenes, tannins, lignans and flavonoids. In conclusion, the significant antibacterial activity renders this fungal strain as a bioresource for natural compounds an interesting alternative against resistant bacteria.

Research Progress in Anti-Inflammatory Bioactive Substances Derived from Marine Microorganisms, Sponges, Algae, and Corals

Inflammation is the body's defense reaction in response to stimulations and is the basis of various physiological and pathological processes. However, chronic inflammation is undesirable and closely related to the occurrence and development of diseases. The ocean gives birth to unique and diverse bioactive substances, which have gained special attention and been a focus for anti-inflammatory drug development. So far, numerous promising bioactive substances have been obtained from various marine organisms such as marine bacteria and fungi, sponges, algae, and coral. This review covers 71 bioactive substances described during 2015-2020, including the structures (65 of which), species sources, evaluation models and anti-inflammatory activities of these substances. This review aims to provide some reference for the research progress of marine-organism-derived anti-inflammatory metabolites and give more research impetus for their conversion to novel anti-inflammatory drugs.

Genome-Directed Discovery of Tetrahydroisoquinolines from Deep-Sea Derived Streptomyces niveus SCSIO 3406

A genome-directed discovery strategy to identify new tetrahydroisoquinolines (THIQs) was applied to deep-sea derived Streptomyces niveus SCSIO 3406; 11 THIQs were found representing three THIQ classes. Known aclidinomycins A (1) and B (2) were isolated along with nine new compounds, aclidinomycins C-K (3-11). The structures were elucidated using extensive spectroscopic analyses and single-crystal X-ray diffraction methods. The core skeleton of compounds 6-9 contains a fused tetrahydropyran (THP) as an integral part of a distinct type of 6/6/6/6/5/5 polycyclic motif. This is the first report of such a system. Beyond their discovery, we also report here a proposed biosynthetic route to these interesting natural products as well as a preliminary survey of their antimicrobial activities.

A New Fusicoccane-Type Norditerpene and a New Indone from the Marine-Derived Fungus Aspergillus aculeatinus WHUF0198

A new norditerpene named aculeaterpene A (1) and a new indone named aculeaindone A (2), along with eight known compounds 3-10 were isolated from the culture extract of Aspergillus aculeatinus WHUF0198. The structural characterization of compounds 1 and 2 were performed by spectroscopic analysis, including 1D and 2D NMR and HR-ESI-MS experiments, whereas the absolute configurations were determined by comparing their experimental or calculated ECD spectra. Compound 1 was the first report of fusicoccane-based norditerpene, in which the C-20 was degraded and tured into a hydroxy group.

Penicacids E-G, three new mycophenolic acid derivatives from the marine-derived fungus Penicillium parvum HDN17-478

Three new mycophenolic acid derivatives, penicacids E-G (1-3), together with three known analogues, mycophenolic acid (4), 4'-hydroxy-mycophenolic acid (5) and mycophenolic methyl ester (6), were isolated from a marine-derived fungus Penicillium parvum HDN17-478 from a South China Sea marine sediment sample. The structures of compounds 1-3 were elucidated by HRMS, NMR, and Mosher's method. Among them, compounds 1 and 2 were the first examples of mycophenolic acid analogs with a double bond at C-3'/C-4' position. The cytotoxicity of 1-6 was evaluated against the HCT-116, BEL-7402, MGC-803, SH-SY5Y, HO-8910 and HL-60 cell lines, and compounds 4 and 6 showed potent cytotoxicity with IC₅₀ values ranging from 1.69 to 12.98 μmol·L^-1.

Deep-sea hydrothermal vent sediments reveal diverse fungi with antibacterial activities

Relatively little is known about the diversity of fungi in deep-sea, hydrothermal sediments. Less thoroughly explored environments are likely untapped reservoirs of unique biodiversity with the potential to augment our current arsenal of microbial compounds with biomedical and/or industrial applications. In this study, we applied traditional culture-based methods to examine a subset of the morphological and phylogenetic diversity of filamentous fungi and yeasts present in 11 hydrothermally influenced sediment samples collected from eight sites on the seafloor of Guaymas Basin, Mexico. A total of 12 unique isolates affiliating with Ascomycota and Basidiomycota were obtained and taxonomically identified on the basis of morphological features and analyses of marker genes including actin, β-tubulin, small subunit ribosomal DNA (18S rRNA), internal transcribed spacer (ITS) and large subunit ribosomal DNA (26S rRNA) D1/D2 domain sequences (depending on taxon). A total of 11 isolates possess congeners previously detected in, or recovered from, deep-sea environments. A total of seven isolates exhibited antibacterial activity against human bacterial pathogens Staphylococcus aureus ATCC-35556 and/or Escherichia coli ATCC-25922. This first investigation suggests that hydrothermal environments may serve as promising reservoirs of much greater fungal diversity, some of which may produce biomedically useful metabolites.

Design and synthesis of β-carboline derivatives with nitrogen mustard moieties against breast cancer

To discover the promising antitumor agents, a series of β-carboline derivatives with nitrogen mustard moieties were designed and synthesized. Most target derivatives showed antiproliferative activity against MCF-7 and MDA-MB-231 cells. Among them, (1-methyl-9H-pyrido[3,4-b]indol-3-yl)methyl (S)-3-(4-(bis(2-chloroethyl)amino)phenyl)-2-formamidopropanoate possessed the most potent antiproliferative activity with IC₅₀ values of 1.79 μM and 4.96 μM, respectively, which were significantly higher than that of the parent compounds, and the efficacy was comparable to that of the positive control doxorubicin. More importantly, it showed weak cytotoxicity against human normal breast cell line MCF-10A (IC₅₀ > 20 μM), exhibiting certain selectivity. Subsequently, further mechanism exploration indicated that it induced G2/M phase cell cycle arrest and apoptosis in MDA-MB-231 cells. The DCFH-DA fluorescent probe assay and comet assay showed that this compound could cause intracellular ROS accumulation and DNA damage. In addition, it exerted potent inhibitory effect on the migration, invasion and adhesion of MDA-MB-231 cells in vitro. In short, (1-methyl-9H-pyrido[3,4-b]indol-3-yl)methyl (S)-3-(4-(bis(2-chloroethyl)amino)phenyl)-2-formamidopropanoate was considered as a promising compound for anti-breast cancer.

Deep-Sea Coral Garden Invertebrates and Their Associated Fungi Are Genetic Resources for Chronic Disease Drug Discovery

Chronic diseases characterized by bone and cartilage loss are associated with a reduced ability of progenitor cells to regenerate new tissues in an inflammatory environment. A promising strategy to treat such diseases is based on tissue repair mediated by human mesenchymal stem cells (hMSCs), but therapeutic outcomes are hindered by the absence of small molecules to efficiently modulate cell behaviour. Here, we applied a high-throughput drug screening technology to bioprospect a large library of extracts from Irish deep-sea organisms to induce hMSC differentiation toward musculoskeletal lineages and reduce inflammation of activated macrophages. The library included extracts from deep-sea corals, sponges and filamentous fungi representing a novel source of compounds for the targeted bioactivity. A validated hit rate of 3.4% was recorded from the invertebrate library, with cold water sea pens (octocoral order Pennatulacea), such as Kophobelemnon sp. and Anthoptilum sp., showing the most promising results in influencing stem cell differentiation toward osteogenic and chondrogenic lineages. Extracts obtained from deep-sea fungi showed no effects on stem cell differentiation, but a 6.8% hit rate in reducing the inflammation of activated macrophages. Our results demonstrate the potential of deep-sea organisms to synthetize pro-differentiation and immunomodulatory compounds that may represent potential drug development candidates to treat chronic musculoskeletal diseases.

Recent highlights of biosynthetic studies on marine natural products

Marine bacteria are excellent yet often underexplored sources of structurally unique bioactive natural products. In this review we cover the diversity of marine bacterial biomolecules and highlight recent studies on structurally novel natural products. We include different compound classes and discuss the latest progress related to their biosynthetic pathway analysis and engineering: examples range from fatty acids over terpenes to PKS, NRPS and hybrid PKS-NRPS biomolecules.

Oshimalides A and B, Sesterterpenes of the Manoalide Class from a Luffariella sp. Deep-Sea Marine Sponge: Application of Asymmetric Dihydroxylation in Structure Elucidation

Oshimalides A (1) and B (2) were isolated from a Luffariella sp. marine sponge. The absolute configurations of the stereogenic centers in the cyclohexenone ring were determined by the modified Mosher's analysis of the reduction product. The absolute configuration of the stereogenic center in the dihydropyran ring was assigned by analysis of the ¹H NMR data of the vicinal diols which were prepared by AD-mix reagents stereoselectively.

Structure Elucidation of Calyxoside B, a Bipolar Sphingolipid from a Marine Sponge Cladocroce sp. through the Use of Beckmann Rearrangement

Marine sponges are an excellent source of biologically active secondary metabolites. We focus on deep-sea sponges for our discovery study. A marine sponge Cladocroce sp. exhibited cytotoxic activity in the bioactivity screening. From this sponge a previously unreported cytotoxic glycosphingolipid, calyxoside B, was isolated and the structure of this compound was elucidated by analyses of MS and NMR spectra and chemical derivatization. We converted the ketone in the middle of a long aliphatic chain into an oxime to which was applied Beckmann rearrangement to afford two positional isomers of amides. The products were subjected to acidic hydrolysis followed by LC-MS analysis, permitting us to assign unequivocally the position of the ketone. Calyxoside B shows cytotoxicity against HeLa cells with an IC50 value of 31 µM and also weakly stimulated the production of cytokines in mice.

Fungi populate deep-sea coral gardens as well as marine sediments in the Irish Atlantic Ocean

Fungi populate deep Oceans in extreme habitats characterized by high hydrostatic pressure, low temperature and absence of sunlight. Marine fungi are potential major contributors to biogeochemical events, critical for marine communities and food web equilibrium under climate change conditions and a valuable source of novel extremozymes and small molecules. Despite their ecophysiological and biotechnological relevance, fungal deep-sea biodiversity has not yet been thoroughly characterized. In this study, we describe the culturable mycobiota associated with the deepest margin of the European Western Continental Shelf: sediments sampled at the Porcupine Bank and deep-water corals and sponges sampled in the Whittard Canyon. Eighty-seven strains were isolated, belonging to 43 taxa and mainly Ascomycota. Ten species and four genera were detected for the first time in the marine environment and a possible new species of Arachnomyces was isolated from sediments. The genera Cladosporium and Penicillium were the most frequent and detected on both substrates, followed by Candida and Emericellopsis. Our results showed two different fungal communities: sediment-associated taxa which were predominantly saprotrophic and animal-associated taxa which were predominantly symbiotic. This survey supports selective fungal biodiversity in the deep North Atlantic, encouraging further mycological studies on cold water coral gardens, often overexploited marine habitats.

Cellular Signal Transductions and Their Inhibitors Derived from Deep-Sea Organisms

Not only physiological phenomena but also pathological phenomena can now be explained by the change of signal transduction in the cells of specific tissues. Commonly used cellular signal transductions are limited. They consist of the protein-tyrosine kinase dependent or independent Ras-ERK pathway, and the PI3K-Akt, JAK-STAT, SMAD, and NF-κB-activation pathways. In addition, biodegradation systems, such as the ubiquitin-proteasome pathway and autophagy, are also important for physiological and pathological conditions. If we can control signaling for each by a low-molecular-weight agent, it would be possible to treat diseases in new ways. At present, such cell signaling inhibitors are mainly looked for in plants, soil microorganisms, and the chemical library. The screening of bioactive metabolites from deep-sea organisms should be valuable because of the high incidence of finding novel compounds. Although it is still an emerging field, there are many successful examples, with new cell signaling inhibitors. In this review, we would like to explain the current view of the cell signaling systems important in diseases, and show the inhibitors found from deep-sea organisms, with their structures and biological activities. These inhibitors are possible candidates for anti-inflammatory agents, modulators of metabolic syndromes, antimicrobial agents, and anticancer agents.