Unlocking the potential of marine biodiscovery

Efficient synthesis, stability-guided optimization and anticancer evaluation of bee venom peptide Melittin

Natural cytotoxic peptides (NCPs) are emerging sources of novel anticancer chemotherapeutics. Especially, Melittin, which is the major component of bee venom and the first-in-class NCP, has been considered as a promising anticancer scaffold. Nevertheless, as a classical linear, cationic, amphipathic, and membrane-lytic peptide, Melittin may be easily degraded by proteases, suffering from poor stability, moderate anticancer durability, and severe hemolysis. In this study, applying the terminal modification and hybridization strategies, ten Melittin-based derivatives were designed, synthesized, and investigated for their anticancer potential. The robust and economic synthetic method, in vitro anticancer efficiency, time-kill kinetics, serum stability, anti-migration activity, hemolysis effects, and anticancer mechanism were explored. As expected, the Melittin-based derivatives exhibited highly potent cytotoxicity against all six tested cancer cell lines. In particular, compared with natural Melittin, the derived peptides LJ-5 containing both N-terminal acetylation and C-terminal hydrazidation, and LJ-6, the methotrexate MTX-GFLG-Melittin conjugate exhibited significantly improved proteolytic stability, more durable anticancer efficiency, higher anti-migration activity, as well as reduced hemolysis effects. Besides, it was further verified that LJ-5 and LJ-6 could efficiently disrupt the integrity of cancer cell membrane, localize to the mitochondria and rapidly reduce the mitochondrial membrane potential of cancer cells. Collectively, the economic synthetic method and stability-guided optimization were conducted on Melittin, affording hydrolysis-resistant LJ-5 and LJ-6 that may serve as anticancer candidates and useful references for further optimizations of cytotoxic peptides.

Pan-cancer analysis of CDC7 in human tumors: Integrative multi-omics insights and discovery of novel marine-based inhibitors through machine learning and computational approaches

Cancer remains a significant global health challenge, with the Cell Division Cycle 7 (CDC7) protein emerging as a potential therapeutic target due to its critical role in tumor proliferation, survival, and resistance. However, a comprehensive analysis of CDC7 across multiple cancers is lacking, and existing therapeutic options have come with limited clinical success. The aim of this is to integrate a comprehensive pan-cancer analysis of CDC7 with the identification of novel marine-derived inhibitors, bridging the understanding of CDC7's role as a prognostic biomarker and therapeutic target across diverse cancer types. In this study, we conducted a pan-cancer analysis of CDC7 across 33 tumor types using publicly available datasets to evaluate its expression, genetic alterations, immune interactions, survival, and prognostic significance. Additionally, a marine-derived compound library of 31,492 molecules was screened to identify potential CDC7 inhibitors using chemoinformatics and machine learning. The top candidates underwent rigorous evaluations, including molecular docking, pharmacokinetics, toxicity, Density Functional Theory (DFT) calculations, and Molecular Dynamics (MD) simulations. The findings revealed that CDC7 is overexpressed in several cancers and is associated with poor survival outcomes and unfavorable prognosis. Enrichment analysis linked CDC7 to critical DNA replication pathways, while its role in modulating tumor-immune interactions highlighted its potential as a target for immunotherapy. Among all tested compounds, Tetrahydroaltersolanol D (CMNPD21999) exhibited the strongest binding affinity and stability, along with better drug-likeness and zero toxicity. These attributes highlight its potential as a promising drug candidate for CDC7 inhibition and future cancer treatment development. Furthermore, additional in vitro and in vivo studies are required to confirm the effectiveness of this drug candidate against the CDC7 protein.

Pyrrolidine Alkaloids and Polyketide Derivatives from the Marine-Derived Fungus Trichoderma harzianum ZN-4

Two unusual alkaloids with furanopyrrolidine skeleton, harzianopyrrolidones A-B (1-2), four new compounds, harzianopyridone B (3), harzianopyrone (4), (R)-1-(3,5-dihydroxy-4-methylphenyl)-1-hydroxyhept-5E-en-2-one (5), and harzianopyrrolidone C (6), together with two known compounds (7-8) were isolated from a marine-derived fungus Trichoderma harzianum ZN-4. Structures of the isolated compounds were elucidated based on their HRESIMS data, extensive NMR spectroscopic analyses, NMR calculation in combination with DP4+, ECD calculations, and a single-crystal X-ray diffraction experiment. New compounds 1, 4, and 5 exhibited potential cardiomyocyte protective activity at concentrations ranging from 5 to 20 μM. In addition, 7 showed moderate inhibitory activity against Pestalotiopsis theae with an MIC value of 25 μg/mL.

Unpacking policy developments in marine natural product research: a scientist's guide to DSI and BBNJ

Covering: 2014 up to February 2025Since the Nagoya Protocol came into force in 2014, scientists working with genetic resources have integrated compliance with Access and Benefit-Sharing (ABS) legislation at international and national levels into their research practices. However, two key gaps left by the Nagoya Protocol are being addressed, introducing new obligations for marine natural product scientists: under the auspices of the Convention on Biological Diversity (CBD), a compromise agreement was reached in November 2024 that regulates the use of Digital Sequence Information (DSI) on Genetic Resources. Within the next few years, the 2023 Biodiversity Beyond National Jurisdiction (BBNJ) Agreement is expected to take effect. This treaty covers the access to and use of marine biodiversity of areas beyond national jurisdiction for research and development. In a time when genetic research and marine biodiversity are key to scientific advancement, these evolving policies affect how genetic information is stored, shared, and used, raising emerging questions for the scientific community about their direct impact and the complexities of compliance. Despite continuous developments and scientific community involvement, there remains a notable gap in communication between policy changes and their accessible dissemination to researchers. Addressing this gap is crucial for the continuation of research and the effective use of relevant resources. The main goal of this viewpoint article is to provide a concise guide to recent policy developments relevant to natural product researchers that should be incorporated and harmonized into ongoing scientific activities.

Transcriptomics-driven exploration of genetic variation and peptide discovery in the sea anemones Anthopleura midori and Actinia equina

Exploring sea anemone polypeptides enables us to understand the evolutionary history and ecological adaptation strategies of species at the microscopic level. More importantly, it aims to provide a solid theoretical foundation for drug development and biodiversity conservation research. Through systematic research, we discovered a total of 51 toxin sequences in species Anthopleura midori and Acyinia equina. The toxin sequences between the two species exhibited significant differences, with notable diversity observed among individuals. In terms of genetic diversity, species Anthopleura midori primarily exhibits variations due to single nucleotide polymorphisms (SNPs), whereas species Actinia equina shows frequent insertion and deletion events. In transcription factor analysis, both species Anthopleura midori and Actinia equina share common transcription factors TEA (TEA Domain Transcription Factor), SPL(Squamosa Promoter Binding Protein-like), and bHLH (Basic Helix-Loop-Helix). Notably. Notably, bHLH is highly expressed in Actinia equina, which may give it advantages in muscle and nervous system development. On the other hand, Anthopleura midori may rely on other transcription factors. Furthermore, by employing transcriptomics and mass spectrometry techniques, two new gene families were successfully identified, and five structurally novel cyclic peptides were predicted. Kinetic simulations further confirmed that the peptide segment B3a-c29555_c4_g4 binds primarily through hydrogen bonds and hydrophobic interactions with the Cav3.1 (PDB ID:6 KZO) protein, and this peptide has the potential to act as a channel modulator for Cav3.1. Overall, this research not only deepens our understanding of the genetic basis of toxin diversity but also highlights the great potential of these toxins in the development of novel drugs.

The Benthic Dinoflagellate Coolia malayensis (Dinophyceae) Produces an Array of Compounds with Antineoplastic Activity in Cells of Tumor Origin

Among aquatic organisms, marine dinoflagellates are essential sources of bioactive metabolites. The benthic dinoflagellate Coolia malayensis produces metabolites that have exhibited substantial and specific cytotoxicity on cancer cells; however, isolation and identification of the purified compounds remain a challenge. This study reports C. malayensis biomass multi-step extraction plus chemical analyses for identifying compounds with antineoplastic activity. Through bio-directed fractionation, the cytotoxicity of extracts and fractions was tested on H1299 (lung), PC-3 (prostate), HeLa (cervical), and MCF-7 (breast) cancer cell lines. Dichloromethane (DCM) phase, hydroalcoholic (HYD) secondary extract, and methanolic (MET) extract showed cytotoxic effects on all cell lines. Active extracts and fractions were analyzed by HPLC-QTOF-MS, 1H, and 13C NMR. Cell lines H1299 and PC-3 treated with fractions F4, F7, and DCM2-AQ-Ch sub-extract showed morphological changes resembling those observed in the apoptosis control, and no signs of necrosis were observed. The selectivity of fraction F7 was above 100 μg mL-1 for healthy cells, while cytotoxic activity was observed in cancer cells. This fraction was identified as mostly fatty acids (FA) by NMR. Seventeen compounds with reported biological activities, such as antioxidant, analgesic, antiviral, and anticancer, were identified from C. malayensis extracts and fractions. Among them, the phycotoxins gambieric acid A and B, okadaic acid, and dinophysistoxin-1 were detected. Further studies are needed to reveal more significant anti-cancer potential from C. malayensis.

In silico identification of a phosphate marine steroid from Indonesian marine compounds as a potential inhibitor of phosphatidylinositol mannosyltransferase (PimA) in Mycobacterium tuberculosis

A higher death rate is associated with multiple factors, including medication resistance and co-infection with the human immunodeficiency virus (HIV). This shows the need to obtain new and effective drug candidates in improving tuberculosis (TB) treatment. In addition, the phosphatidylinositol mannosyltransferase (PimA) enzyme starts the production of phosphatidyl-myo-inositol. PimA has been identified as a key enzyme and an important area for further research in the development of anti-TB drugs. Previous research investigated various applications including marine resources driven by a deeper understanding of the distinctive features of the ecosystem and the diverse array of organisms. Therefore, this research aims to investigate the potential of Indonesian marine compounds as inhibitors of PimA, with a focus on binding energy, interaction modes, and stability using docking and molecular dynamics (MD) investigation methodologies. The results show that a total of 84 Indonesian marine compounds are effectively docked to the PimA to obtain compounds 21, 27, and 33 for further investigation. Based on the MD analysis, compound 27 (desulfohaplosamate) is the most promising candidate among the new MTB-PimA inhibitors. Compounds bind to PimA, as shown by a strong affinity of -30.09 kJ/mol, and form hydrogen bonds with the key amino acid residue Gly16. Furthermore, a stable complex is formed to easily analyze the antibacterial agents targeting MTB in the future.

Mechanisms of Action of Sea Cucumber Triterpene Glycosides Cucumarioside A0-1 and Djakonovioside A Against Human Triple-Negative Breast Cancer

Breast cancer is the most prevalent form of cancer in women worldwide. Triple-negative breast cancer is the most unfavorable for patients, but it is also the most sensitive to chemotherapy. Triterpene glycosides from sea cucumbers possess a high therapeutic potential as anticancer agents. This study aimed to identify the pathways triggered and regulated in MDA-MB-231 cells (triple-negative breast cancer cell line) by the glycosides cucumarioside A0-1 (Cuc A0-1) and djakonovioside A (Dj A), isolated from the sea cucumber Cucumaria djakonovi. Using flow cytometry, fluorescence microscopy, immunoblotting, and ELISA, the effects of micromolar concentrations of the compounds on cell cycle arrest, induction of apoptosis, the level of reactive oxygen species (ROS), mitochondrial membrane potential (Δψm), and expression of anti- and pro-apoptotic proteins were investigated. The glycosides caused cell cycle arrest, stimulated an increase in ROS production, and decreased Δψm in MDA-MB-231 cells. The depolarization of the mitochondrial membrane caused by cucumarioside A0-1 and djakonovioside A led to an increase in the levels of APAF-1 and cytochrome C. This, in turn, resulted in the activation of caspase-9 and caspase-3 and an increase in the level of their cleaved forms. Glycosides also affected the expression of Bax and Bcl-2 proteins, which are associated with mitochondria-mediated apoptosis in MDA-MB-231 cells. These results indicate that cucumarioside A0-1 and djakonovioside A activate the intrinsic apoptotic pathway in triple-negative breast cancer cells. Additionally, it was found that treatment with Cuc A0-1 resulted in in vivo inhibition of tumor growth and metastasis of murine solid Ehrlich adenocarcinoma.

Distribution and Level of Bioactive Monoacylglycerols in 12 Marine Microalgal Species

Microalgae are currently considered an attractive source of highly valuable metabolites potentially exploitable as anticancer agents, nutraceuticals and cosmeceuticals and for bioenergy purposes. Their ease of culturing and their high growth rates further promote their use as raw material for the production of specialty products. In the present paper, we focused our attention on specific glycerol-based lipid compounds, monoacylglycerols (MAGs), which displayed in our previous studies a selective cytotoxic activity against the haematological U-937 and the colon HCT-116 cancer cell lines. Here, we performed a quali/quantitative analysis of MAGs and total fatty acids (FAs) along with a profiling of the main lipid classes in a panel of 12 microalgal species, including diatoms and dinoflagellates. Our results highlight an inter- and intraspecific variability of MAG profile in the selected strains. Among them, Skeletonema marinoi (strain FE7) has emerged as the most promising source for possible biotechnological production of MAGs.

Development and Validation of a Liquid Chromatography-Tandem Mass Spectrometry Method for Screening Potential Citrate Lyase Inhibitors from a Library of Marine Compounds

Tuberculosis, a persistent illness caused by Mycobacterium tuberculosis, remains a significant global public health challenge. The widespread use of anti-tuberculosis drugs has resulted in the emergence of drug-resistant strains, which complicates treatment efforts. Addressing this issue is crucial and hinges on the development of new drugs that can effectively target the disease. This involves identifying novel therapeutic targets that can disrupt the bacterium's survival mechanisms in various environments such as granulomas and lesions. Citrate lyase, essential for the survival of Mycobacterium species at lesion sites and in granulomatous conditions, is a potential target for the treatment of tuberculosis. This manuscript aimed to construct an efficient enzyme inhibitor screening platform using ultra-high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UHPLC-QTOF MS). This system can accurately identify compounds with enzyme inhibitory activity from a library of marine terpenoids and phenolic compounds. Utilizing the screened herbal enzyme inhibitors as a starting point, we analyzed their chemical structures and skillfully built a library of marine compounds based on these structures. The results showed that all of the tested compounds from the phenolics library inhibited citrate lyase by more than 50%, and a significant portion of terpenoids also demonstrated inhibition, with these active terpenoids comprising over half of the terpenoids tested. The study underscores the potential of marine-derived phenolic and terpenoid compounds as potent inhibitors of citrate lyase, indicating a promising direction for future investigations in treating tuberculosis and associated disorders.

Irpetones A and B, Anti-Osteoclastic Heptaketides from a Marine Mesophotic Zone Ircinia Sponge-Associated Fungus Irpex sp. NBUF088

Chemical investigation of Irpex sp. NBUF088, associated with an Ircinia sp. sponge located at an 84 m deep mesophotic zone, led to the discovery of two new heptaketides, named irpetones A (1) and B (2). Their structures were identified by analysis of spectroscopic data and quantum-chemical calculations. Compound 1 exhibited inhibition against the receptor activator of NF-κB ligand-induced osteoclastogenesis in bone marrow monocytes with an IC50 of 6.3 ± 0.2 μM, causing no notable cytotoxicity. It was also determined that 1 inhibited the phosphorylation of ERK1/2-JNK1/2-p38 MAPKs and the nuclear translocation of NF-κB, consequently suppressing the activation of MAPK and NF-κB signaling pathways induced by the NF-κB ligand.

Chemical Investigation of the Calcareous Marine Sponge Pericharax heteroraphis, Clathridine-A Related Derivatives Isolation, Synthesis and Osteogenic Activity

As a result of screening a panel of marine organisms to identify lead molecules for the stimulation of endochondral bone formation, the calcareous sponge Pericharax heteroraphis was identified to exhibit significant activity during endochondral differentiation. On further molecular networking analysis, dereplication and chemical fractionation yielded the known clathridine A-related metabolites 3-6 and the homodimeric complex (clathridine A)2 Zn2+ (9), together with the new unstable heterodimeric complex (clathridine A-clathridimine)Zn2+ (10). With the presence of the zinc complexes annotated through the LC-MS analysis of the crude extract changing due to the instability of some metabolites and complexes constituting the mixture, we combined the isolation of the predicted molecules with their synthesis in order to confirm their structure and to understand their reactivity. Interestingly, we also found a large quantity of the contaminant benzotriazoles BTZ (7) and its semi-dimer (BTZ)2CH2 (8), which are known to form complexes with transition metals and are used for preventing corrosion in water. All isolated 2-aminoimidazole derivatives and complexes were synthesized not only for structural confirmation and chemical understanding but to further study their bioactivity during endochondral differentiation, particularly the positively screened imidazolone derivatives. Compounds leucettamine B, clathridine A and clathridimine were found to increase type X collagen transcription and stimulate endochondral ossification in the ATDC5 micromass model.

Marine-Derived Bisindoles for Potent Selective Cancer Drug Discovery and Development

Marine-derived bisindoles exhibit structural diversity and exert anti-cancer influence through multiple mechanisms. Comprehensive research has shown that the development success rate of drugs derived from marine natural products is four times higher than that of other natural derivatives. Currently, there are 20 marine-derived drugs used in clinical practice, with 11 of them demonstrating anti-tumor effects. This article provides a thorough review of recent advancements in anti-tumor exploration involving 167 natural marine bisindole products and their derivatives. Not only has enzastaurin entered clinical practice, but there is also a successfully marketed marine-derived bisindole compound called midostaurin that is used for the treatment of acute myeloid leukemia. In summary, investigations into the biological activity and clinical progress of marine-derived bisindoles have revealed their remarkable selectivity, minimal toxicity, and efficacy against various cancer cells. Consequently, they exhibit immense potential in the field of anti-tumor drug development, especially in the field of anti-tumor drug resistance. In the future, these compounds may serve as promising leads in the discovery and development of novel cancer therapeutics.

Computational insights into potential marine natural products as selective inhibitors of Mycobacterium tuberculosis InhA: A structure-based virtual screening study

Several factors are associated with the emergence of drug resistance mechanisms, such as impermeable cell walls, gene mutations, and drug efflux systems. Consequently, bacteria acquire resistance, leading to a decrease in drug efficacy. A new and innovative strategy is required to combat drug resistance in tuberculosis (TB) effectively. Therefore, targeting the mycolic acid biosynthesis pathway, which is involved in synthesising mycolic acids (MAs), essential structural components responsible for mycobacterial pathogenicity, has garnered interest in TB research and the concept of drug resistance. In this context, InhA, which plays a crucial role in the fatty acid synthase-II (FAS-II) system of the MA biosynthetic pathway, was selected as a druggable target for screening investigation. To identify potential lead molecules against InhA, diverse marine natural products (MNPs) were collected from the comprehensive marine natural products database (CMNPD). Virtual screening studies aided in selecting potential lead molecules that best fit within the substrate-binding pocket (SBP) of InhA, forming crucial hydrogen bond interaction with the catalytic residue Tyr158. Three MNPs, CMNPD30814, CMNPD1702, and CMNPD27355, were chosen as prospective alternative molecules due to their favorable pharmacokinetic properties and lack of toxicity according to ProTox-II predictions. Additionally, improved reactivity of the MNPs was observed in the results of density functional theory (DFT) studies. Furthermore, comparative molecular dynamics simulation (MDS), principal component (PC)-based free energy landscape (FEL) analysis, and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) were employed to show enhanced structural stability, increased H-bond potential, and high binding affinity toward the target InhA. Moreover, the hot spot residues that contributed to the high binding energy profile and anchored the stability of the complexes were revealed with their individual interaction energy. The computational insights from this study provide potential avenues to combat TB through the multifaceted mode of action of these marine lead molecules, which can be further explored in future experimental investigations.

Profiling Prokaryotic Communities and Aaptamines of Sponge Aaptos suberitoides from Tulamben, Bali

Sponges (Porifera) harbor a diversity of microorganisms that contribute largely to the production a vast array of bioactive compounds. The microorganisms associated with sponge have an important impact on the chemical diversity of the natural products. Herein, our study focuses on an Aaptos suberitoides commonly found in Indonesia. The objective of this study was to investigate the profile of prokaryotic community and the presence of aaptamine metabolites in sponge Aaptos suberitoides. Sponges were collected from two site locations (Liberty Wreck and Drop Off) in Tulamben, Bali. The sponges were identified by barcoding DNA cytochrome oxidase subunit I (COI) gene. The profile of prokaryotic composition was investigated by amplifying the 16S rRNA gene using primers 515f and 806r to target the V4 region. The metabolites were analyzed using LC-MS, and dereplication was done to identify the aaptamines and its derivates. The barcoding DNA of the sponges confirmed the identity of samples as Aaptos suberitoides. The prokaryotic communities of samples A. suberitoides were enriched and dominated by taxa Proteobacteria, Chloroflexi, Actinobacteria, and Acidobacteria. The chemical analysis showed that all sponges produce aaptamine and isoaaptamine except A. suberitoides S2421 produce analog of aaptamines. This is the first report on the profile of prokaryotic community and the aaptamine of tropical marine sponges, A. suberitoides, from Tulamben, Bali.

Red Fluorescent Protein Variant with a Dual-Peak Emission of Fluorescence

The marine environment is a rich reservoir of diverse biological entities, many of which possess unique properties that are of immense value to biotechnological applications. One such example is the red fluorescent protein derived from the coral Discosoma sp. This protein, encoded by the DsRed gene, has been the subject of extensive research due to its potential applications in various fields. In the study, a variant of the red fluorescent protein was generated through random mutagenesis using the DsRed2 gene as a template. The process employed error-prone PCR (epPCR) to introduce random mutations, leading to the isolation of twelve gene variants. Among these, one variant stood out due to its unique spectral properties, exhibiting dual fluorescence emission at both 480 nm (green) and 550 nm (red). This novel variant was expressed in both Escherichia coli and zebrafish (Danio rerio) muscle, confirming the dual fluorescence emission in both model systems. One of the immediate applications of this novel protein variant is in ornamental aquaculture. The dual fluorescence can serve as a unique marker or trait, enhancing the aesthetic appeal of aquatic species in ornamental settings.

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.

A critical review of machine-learning for "multi-omics" marine metabolite datasets

During the last decade, genomic, transcriptomic, proteomic, metabolomic, and other omics datasets have been generated for a wide range of marine organisms, and even more are still on the way. Marine organisms possess unique and diverse biosynthetic pathways contributing to the synthesis of novel secondary metabolites with significant bioactivities. As marine organisms have a greater tendency to adapt to stressed environmental conditions, the chance to identify novel bioactive metabolites with potential biotechnological application is very high. This review presents a comprehensive overview of the available "-omics" and "multi-omics" approaches employed for characterizing marine metabolites along with novel data integration tools. The need for the development of machine-learning algorithms for "multi-omics" approaches is briefly discussed. In addition, the challenges involved in the analysis of "multi-omics" data and recommendations for conducting "multi-omics" study were discussed.

MariClus: Your One-Stop Platform for Information on Marine Natural Products, Their Gene Clusters and Producing Organisms

BACKGROUND

The marine environment hosts the vast majority of living species and marine microbes that produce natural products with great potential in providing lead compounds for drug development. With over 70% of Earth's surface covered in water and the high interaction rate associated with liquid environments, this has resulted in many marine natural product discoveries. Our improved understanding of the biosynthesis of these molecules, encoded by gene clusters, along with increased genomic information will aid us in uncovering even more novel compounds.

RESULTS

We introduce MariClus (https://www.mariclus.com), an online user-friendly platform for mining and visualizing marine gene clusters. The first version contains information on clusters and the predicted molecules for over 500 marine-related prokaryotes. The user-friendly interface allows scientists to easily search by species, cluster type or molecule and visualize the information in table format or graphical representation.

CONCLUSIONS

This new online portal simplifies the exploration and comparison of gene clusters in marine species for scientists and assists in characterizing the bioactive molecules they produce. MariClus integrates data from public sources, like GenBank, MIBiG and PubChem, with genome mining results from antiSMASH. This allows users to access and analyze various aspects of marine natural product biosynthesis and diversity.

Convergent evolution for antibiotic biosynthesis in bacteria and animals

Convergent evolution has been described for several metabolic pathways across the kingdoms of life. However, there is hitherto no evidence for such an interkingdom process for antimicrobials. A new report suggests that marine animals have evolved the ability to biosynthesize antimicrobial polyketides, in parallel with bacteria.

Recent Advancement in Anticancer Compounds from Marine Organisms: Approval, Use and Bioinformatic Approaches to Predict New Targets

In recent years, the study of anticancer bioactive compounds from marine sources has received wide interest. Contextually, world regulatory authorities have approved several marine molecules, and new synthetic derivatives have also been synthesized and structurally improved for the treatment of numerous forms of cancer. However, the administration of drugs in cancer patients requires careful evaluation since their interaction with individual biological macromolecules, such as proteins or nucleic acids, determines variable downstream effects. This is reflected in a constant search for personalized therapies that lay the foundations of modern medicine. The new knowledge acquired on cancer mechanisms has certainly allowed advancements in tumor prevention, but unfortunately, due to the huge complexity and heterogeneity of cancer, we are still looking for a definitive therapy and clinical approaches. In this review, we discuss the significance of recently approved molecules originating from the marine environment, starting from their organism of origin to their structure and mechanism of action. Subsequently, these bio-compounds are used as models to illustrate possible bioinformatics approaches for the search of new targets that are useful for improving the knowledge on anticancer therapies.

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.

Molecular Diversity and Biochemical Content in Two Invasive Alien Species: Looking for Chemical Similarities and Bioactivities

The biochemical composition, molecular diversity, and two different bioactivities of Asparagopsis armata and Rugulopteryx okamurae (two alien species with different invasive patterns in the southern Iberian Peninsula) were analyzed through spectrophotometric methods and Fourier transform ion cyclotron mass spectroscopy (FT-ICR-MS). A total of 3042 molecular formulas were identified from the different extracts. The dH2O extracts were the most molecularly different. A. armata presented the highest content of nitrogenous compounds (proteins, CHON) and sulphur content, whereas R. okamurae was rich in carbonated compounds (total carbon, lipids, CHO, and CHOP). Antioxidant capacity and phenolic content were higher in R. okamurae than in A. armata. Antimicrobial activity was detected from both species. A. armata showed capacity to inhibit human and fish pathogens (e.g., Staphylococcus aureus or Vibrio anguillarum), whereas R. okamurae only showed inhibition against human bacteria (Staphylococcus aureus and Cutibacterium acnes). In R. okamurae, molecules with a great number of pharmaceutical activities (e.g., anti-inflammatory or antitumoral), antibacterial, biomaterial, and other utilities were found. The main molecules of A. armata had also pharmaceutical applications (e.g., antimalarian, antithrombotic, anti-inflammatory, or antiarthritis). The valorization of these species can help to counteract the environmental effects of the bioinvasions.

Secondary Metabolites from Coral-Associated Fungi: Source, Chemistry and Bioactivities

Our study of the secondary metabolites of coral-associated fungi produced a valuable and extra-large chemical database. Many of them exhibit strong biological activity and can be used for promising drug lead compounds. Serving as an epitome of the most promising compounds, which take the ultra-new skeletons and/or remarkable bioactivities, this review presents an overview of new compounds and bioactive compounds isolated from coral-associated fungi, covering the literature from 2010 to 2021. Its scope included 423 metabolites, focusing on the bioactivity and structure diversity of these compounds. According to structure, these compounds can be roughly classified as terpenes, alkaloids, peptides, aromatics, lactones, steroids, and other compounds. Some of them described in this review possess a wide range of bioactivities, such as anticancer, antimicrobial, antifouling, and other activities. This review aims to provide some significant chemical and/or biological enlightenment for the study of marine natural products and marine drug development in the future.

A forgotten element of the blue economy: marine biomimetics and inspiration from the deep sea

The morphology, physiology, and behavior of marine organisms have been a valuable source of inspiration for solving conceptual and design problems. Here, we introduce this rich and rapidly expanding field of marine biomimetics, and identify it as a poorly articulated and often overlooked element of the ocean economy associated with substantial monetary benefits. We showcase innovations across seven broad categories of marine biomimetic design (adhesion, antifouling, armor, buoyancy, movement, sensory, stealth), and use this framing as context for a closer consideration of the increasingly frequent focus on deep-sea life as an inspiration for biomimetic design. We contend that marine biomimetics is not only a "forgotten" sector of the ocean economy, but has the potential to drive appreciation of nonmonetary values, conservation, and stewardship, making it well-aligned with notions of a sustainable blue economy. We note, however, that the highest ambitions for a blue economy are that it not only drives sustainability, but also greater equity and inclusivity, and conclude by articulating challenges and considerations for bringing marine biomimetics onto this trajectory.

Marine Actinomycetes Associated with Stony Corals: A Potential Hotspot for Specialized Metabolites

Microbial secondary metabolites are an important source of antibiotics currently available for combating drug-resistant pathogens. These important secondary metabolites are produced by various microorganisms, including Actinobacteria. Actinobacteria have a colossal genome with a wide array of genes that code for several bioactive metabolites and enzymes. Numerous studies have reported the isolation and screening of millions of strains of actinomycetes from various habitats for specialized metabolites worldwide. Looking at the extent of the importance of actinomycetes in various fields, corals are highlighted as a potential hotspot for untapped secondary metabolites and new bioactive metabolites. Unfortunately, knowledge about the diversity, distribution and biochemistry of marine actinomycetes compared to hard corals is limited. In this review, we aim to summarize the recent knowledge on the isolation, diversity, distribution and discovery of natural compounds from marine actinomycetes associated with hard corals. A total of 11 new species of actinomycetes, representing nine different families of actinomycetes, were recovered from hard corals during the period from 2007 to 2022. In addition, this study examined a total of 13 new compounds produced by five genera of actinomycetes reported from 2017 to 2022 with antibacterial, antifungal and cytotoxic activities. Coral-derived actinomycetes have different mechanisms of action against their competitors.

Aerophobin-1 from the Marine Sponge Aplysina aerophoba Modulates Osteogenesis in Zebrafish Larvae

Longer life expectancy has led to an increase in efforts directed to the discovery of new healing agents for disorders related to aging, such as bone diseases. Harboring an incredible variety of bioactive metabolites, marine organisms are standing out as fruitful sources also in this therapeutic field. On the other hand, the in vivo zebrafish model has proven to be an excellent low-cost screening platform for the fast identification of molecules able to regulate bone development. By using zebrafish larvae as a mineralization model, we have thus evaluated the effects of the crude acetonic extract from the marine sponge Aplysina aerophoba and its bromotyrosine components on bone development. Obtained results led to the selection of aerophobin-1 (1) as a promising candidate for applications in regenerative medicine, paving the way for the development of a novel therapeutic option in osteoporosis treatment.

Novel Alkaloids from Marine Actinobacteria: Discovery and Characterization

The marine environment is an excellent resource for natural products with therapeutic potential. Its microbial inhabitants, often associated with other marine organisms, are specialized in the synthesis of bioactive secondary metabolites. Similar to their terrestrial counterparts, marine Actinobacteria are a prevalent source of these natural products. Here, we discuss 77 newly discovered alkaloids produced by such marine Actinobacteria between 2017 and mid-2021, as well as the strategies employed in their elucidation. While 12 different classes of alkaloids were unraveled, indoles, diketopiperazines, glutarimides, indolizidines, and pyrroles were most dominant. Discoveries were mainly based on experimental approaches where microbial extracts were analyzed in relation to novel compounds. Although such experimental procedures have proven useful in the past, the methodologies need adaptations to limit the chance of compound rediscovery. On the other hand, genome mining provides a different angle for natural product discovery. While the technology is still relatively young compared to experimental screening, significant improvement has been made in recent years. Together with synthetic biology tools, both genome mining and extract screening provide excellent opportunities for continued drug discovery from marine Actinobacteria.

Acorenone C: A New Spiro-Sesquiterpene from a Mangrove-Associated Fungus, Pseudofusicoccum sp. J003

Mangrove-derived endophytes are rich in bioactive secondary metabolites with a variety of biological activities. Recently, a fungus Pseudofusicoccum sp. J003 was first isolated by our research group from mangrove species Sonneratia apetala Buch.-Ham. The subsequent chemical investigation of the methanol extract of the culture broth of this strain has led to the isolation of a new sesquiterpenoid named acorenone C (1), two alkaloids (2-3), four phenolic compounds (4-7), and four steroid derivatives (8-11). The new structure of 1 was established by extensive spectroscopic analysis, including 1D, 2D NMR spectroscopy, and HRESIMS. Its absolute configuration was elucidated by experimental ECD and ECD calculation. The in vitro AChE inhibitory, anti-inflammatory, and cytotoxic activities of the selected compounds were evaluated. The results showed that compound 1 showed mild AChE inhibitory activity, with an inhibition rate of 23.34% at the concentration of 50 μM. Compound 9 exerted a significant inhibitory effect against nitric oxide (NO) production in LPS-stimulated RAW 264.7 mouse macrophages, with an inhibition rate of 72.89% at the concentration of 25 μM, better than that of positive control L-NMMA. Compound 9 also displayed obvious inhibition effects on the growth of two human tumor cell lines, HL-60 and SW480 (inhibition rates 98.68 ± 0.97% and 60.40 ± 4.51%, respectively). The antimicrobial activities of the compounds (1-11) against Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Pseudomonas aeruginosa were also tested; however, none of them showed antimicrobial activities.

Marine drugs: Biology, pipelines, current and future prospects for production

The marine environment is a huge reservoir of biodiversity and represents an excellent source of chemical compounds, some of which have large economical values. In the urgent quest for new pharmaceuticals, marine-based drug discovery has progressed significantly over the past several decades and we now benefit from a series of approved marine natural products (MNPs) to treat cancer and pain while an additional collection of promising leads are in clinical trials. However, the discovery and supply of MNPs has always been challenging given their low bioavailability and structural complexity. Their manufacture for pre-clinical and clinical development but also commercialization mainly relies upon marine source extraction and chemical synthesis, which are associated with high costs, unsustainability and severe environmental problems. In this review, we discuss how metabolic engineering now raises reasonable expectations for the implementation of microbial cell factories, which may provide a sustainable approach for MNP-based drug supply in the near future.

Marine Biodiscovery in a Changing World

The term "marine biodiscovery" has been recently been adopted to describe the area of marine natural products dedicated to the search of new drugs. Several maritime countries such as Australia, New Zealand, South Korea, and Japan as well as some European countries have invested significantly in this area of research over the last 50 years. In the late 2000s, research in this field has received significant interest and support in Ireland for exploring new marine bioresources from the nutrient-rich waters of the Northeastern Atlantic Ocean. Despite undeniable success exemplified by the marketing of new drugs, especially in oncology, the integration of new technical but also environmental aspects should be considered. Indeed, global change, particularly in our oceans, such as climate change, biodiversity loss, and the emergence of microbial pathogens, not only affects the environment but ultimately contributes to social inequalities. In this contribution, new avenues and best practices are proposed, such as the development of biorepositories and shared data for the future of marine biodiscovery research. The extension of this type of scientific work will allow humanity to finally make the optimum use of marine bioresources.

Application of Networking Approaches to Assess the Chemical Diversity, Biogeography, and Pharmaceutical Potential of Verongiida Natural Products

This study provides a review of all isolated natural products (NPs) reported for sponges within the order Verongiida (1960 to May 2020) and includes a comprehensive compilation of their geographic and physico-chemical parameters. Physico-chemical parameters were used in this study to infer pharmacokinetic properties as well as the potential pharmaceutical potential of NPs from this order of marine sponge. In addition, a network analysis for the NPs produced by the Verongiida sponges was applied to systematically explore the chemical space relationships between taxonomy, secondary metabolite and drug score variables, allowing for the identification of differences and correlations within a dataset. The use of scaffold networks as well as bipartite relationship networks provided a platform to explore chemical diversity as well as the use of chemical similarity networks to link pharmacokinetic properties with structural similarity. This study paves the way for future applications of network analysis procedures in the field of natural products for any order or family.

Diversity, Bioactivity Profiling and Untargeted Metabolomics of the Cultivable Gut Microbiota of Ciona intestinalis

It is widely accepted that the commensal gut microbiota contributes to the health and well-being of its host. The solitary tunicate Ciona intestinalis emerges as a model organism for studying host-microbe interactions taking place in the gut, however, the potential of its gut-associated microbiota for marine biodiscovery remains unexploited. In this study, we set out to investigate the diversity, chemical space, and pharmacological potential of the gut-associated microbiota of C. intestinalis collected from the Baltic and North Seas. In a culture-based approach, we isolated 61 bacterial and 40 fungal strains affiliated to 33 different microbial genera, indicating a rich and diverse gut microbiota dominated by Gammaproteobacteria. In vitro screening of the crude microbial extracts indicated their antibacterial (64% of extracts), anticancer (22%), and/or antifungal (11%) potential. Nine microbial crude extracts were prioritized for in-depth metabolome mining by a bioactivity- and chemical diversity-based selection procedure. UPLC-MS/MS-based metabolomics combining automated (feature-based molecular networking and in silico dereplication) and manual approaches significantly improved the annotation rates. A high chemical diversity was detected where peptides and polyketides were the predominant classes. Many compounds remained unknown, including two putatively novel lipopeptides produced by a Trichoderma sp. strain. This is the first study assessing the chemical and pharmacological profile of the cultivable gut microbiota of C. intestinalis.