Natural products as probes of cell biology: 20 years of didemnin research

Exploring the Biosynthetic Potential of Tistrella Species for Producing Didemnin Antitumor Agents

Didemnins are a class of cyclic depsipeptides derived from sea tunicates that exhibit potent anticancer, antiviral, and immunosuppressive properties. Although certain Tistrella species can produce didemnins, their complete biosynthetic potential remains largely unexplored. In this study, we utilize feature-based molecular networking to analyze the metabolomics of Tistrella mobilis and Tistrella bauzanensis, focusing on the production of didemnin natural products. In addition to didemnin B, we identify nordidemnin B and [hysp2]didemnin B, as well as several minor didemnin analogs. Heterologous expression of the didemnin biosynthetic gene cluster in a Streptomyces host results in the production of only didemnin B and nordidemnin B in limited quantities. Isotope-labeling studies reveal that the substrate promiscuity of the adenylation domains during biosynthesis leads to the accumulation of nordidemnin B and [hysp2]didemnin B. Additionally, precursor-directed biosynthesis is applied to generate eight novel didemnin derivatives by supplementing the culture with structurally related amino acids. Furthermore, we increased the titers of nordidemnin B and [hysp2]didemnin B by supplementing the fermentation medium with l-valine and l-isoleucine, respectively. Finally, both compounds undergo side-chain oxidation to enhance their biological activity, with their anticancer properties found to be as potent as plitidepsin.

A global microbiome analysis reveals the ecological feature of Tistrella and its production of the bioactive didemnins in the marine ecosystem

Marine microorganisms like Tistrella are essential for producing bioactive compounds, including didemnins with antitumor and antiviral properties. However, our understanding of Tistrella's ecological features and didemnin production in natural environments is limited. In this study, we used genomics and metagenomics to show that Tistrella is widely distributed across natural habitats, especially in marine environments from the surface to 5000 m deep, with distinct non-random distribution patterns revealed by co-occurrence analysis. Importantly, transcriptional profiling of didemnin biosynthetic gene clusters indicates active in situ production of this compound within marine ecosystems. These findings enhance our understanding of Tistrella's ecology and secondary metabolite production in natural environments. Further research is needed to explore the ecological dynamics and functional impacts of Tistrella in these ecosystems.

A Semisynthesis Platform for the Efficient Production and Exploration of Didemnin-Based Drugs

Plitidepsin (or dehydrodidemnin B), an approved anticancer drug, belongs to the didemnin family of cyclic depsipeptides, which are found in limited quantities in marine tunicate extracts. Herein, we introduce a new approach that integrates microbial and chemical synthesis to generate plitidepsin and its analogues. We screened a Tistrella strain library to identify a potent didemnin B producer, and then introduced a second copy of the didemnin biosynthetic gene cluster into its genome, resulting in a didemnin B titer of approximately 75 mg/L. Next, we developed two straightforward chemical strategies to convert didemnin B into plitidepsin, one of which involved a one-step synthetic route giving over 90 % overall yield. Furthermore, we synthesized 13 new didemnin derivatives and three didemnin probes, enabling research into structure-activity relationships and interactions between didemnin and proteins. Our study highlights the synergistic potential of biosynthesis and chemical synthesis in overcoming the challenge of producing complex natural products sustainably and at scale.

The Antioxidant Mechanism of Peptides Extracted from Tuna Protein Revealed Using a Molecular Docking Simulation

Tuna protein serves as a significant source of bioactive peptides, and its functional properties can be elucidated through predictive modeling, followed by experimental validation. In this study, the active polypeptides were obtained from tuna protein via enzymatic hydrolysis (TPP), and their peptide sequences were determined. Furthermore, the potential activity of these peptides was predicted, focusing on antioxidant peptides, and compared to the sequence library of known antioxidant peptides to identify common structural motifs. The accuracy of the prediction results was confirmed through in vitro antioxidant assays and molecular docking studies. We identified seven specific peptide segments derived from tuna protein that exhibit antioxidant potential, accounting for approximately 15% of all active peptides. Molecular docking and cell experiments were employed to provide compelling evidence for the presence of antioxidant peptides within tuna protein. This study not only lays a solid foundation for studying the structure of active peptides but also opens up a novel avenue for an expedited assessment of their properties.

Emerging pharmaceutical therapies of Ascidian-derived natural products and derivatives

In a growing multidrug-resistant environment, the identification of potential new drug candidates with an acceptable safety profile is a substantial crux in pharmaceutical discovery. This review discusses several aspects and properties of approved marine natural products derived from ascidian sources (phylum Chordata, subphylum Tunicata) and/or their deduced analogues including their biosynthetic origin, (bio)chemical preclinical assessments and known efficacy-safety profiles, clinical status in trials, but also translational developments, opportunities and final conclusions. The review also describes the preclinical assessments of a large number of other ascidian compounds that have not been involved in clinical trials yet. Finally, the emerging research on the connectivity of the ascidian hosts and their independent or obligate symbiotic guests is discussed. The review covers the latest information on the topic of ascidian-derived marine natural products over the last two decades including 2022, with the majority of publications published in the last decade.

Update on Autophagy Inhibitors in Cancer: Opening up to a Therapeutic Combination with Immune Checkpoint Inhibitors

Autophagy is a highly conserved and natural degradation process that helps maintain cell homeostasis through the elimination of old, worn, and defective cellular components, ensuring proper cell energy intake. The degradative pathway constitutes a protective barrier against diverse human diseases including cancer. Autophagy basal level has been reported to be completely dysregulated during the entire oncogenic process. Autophagy influences not only cancer initiation, development, and maintenance but also regulates cancer response to therapy. Currently, autophagy inhibitor candidates mainly target the early autophagy process without any successful preclinical/clinical development. Lessons learned from autophagy pharmaceutical manipulation as a curative option progressively help to improve drug design and to encounter new targets of interest. Combinatorial strategies with autophagy modulators are supported by abundant evidence, especially dealing with immune checkpoint inhibitors, for which encouraging preclinical results have been recently published. GNS561, a PPT1 inhibitor, is a promising autophagy modulator as it has started a phase 2 clinical trial in liver cancer indication, combined with atezolizumab and bevacizumab, an assessment without precedent in the field. This approach paves a new road, leading to the resurgence of anticancer autophagy inhibitors as an attractive therapeutic target in cancer.

Molecular structures, chemical descriptors, and pancreatic lipase (1LPB) inhibition by natural products: a DFT investigation and molecular docking prediction

Density functional theory (DFT) calculations and molecular docking have been carried out on natural products containing eugenol, gingerol, ascorbic acid, oleurpoein, piperine, hesperidin, quercetin, Luteolin, and curcumin in order to predict their biological activities and to analyze their pancreatic lipase inhibition. The biological activity predictions are based on the global and local chemical descriptors, namely, HOMO-LUMO gaps, chemical hardness, chemical potential, electrophilicity, dipole moment, and Fukui functions. Our findings show that the studied compounds can be divided into two groups based on the chemical descriptors; the first group is composed of eugenol, gingerol, ascorbic acid, and oleuropein and the second one is composed of piperine, hesperidin, quercetin, Luteolin, and curcumin depending on the HOMO-LUMO gaps and electrophilicity values predicting best reactivity for the second group than the first one. The frontier orbitals offer a deeper insight concerning the electron donor and electron acceptor capabilities, whereas the local descriptors resulting from Fukui functions put emphasis on the active sites of different candidate ligands. The molecular docking was performed in order to compare and identify the inhibition activity of the natural candidate ligands against pancreatic lipase which were compared to that of synthesized ones. The molecular docking results revealed that the Luteolin compound has the best binding affinity of -8.56 kcal/mol due to their unique molecular structure and the position of -OH aromatic substituents.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11224-023-02176-2.

Anticancer Small-Molecule Agents Targeting Eukaryotic Elongation Factor 1A: State of the Art

Eukaryotic elongation factor 1A (eEF1A) canonically delivers amino acyl tRNA to the ribosomal A site during the elongation stage of protein biosynthesis. Yet paradoxically, the oncogenic nature of this instrumental protein has long been recognized. Consistently, eEF1A has proven to be targeted by a wide assortment of small molecules with excellent anticancer activity, among which plitidepsin has been granted approval for the treatment of multiple myeloma. Meanwhile, metarrestin is currently under clinical development for metastatic cancers. Bearing these exciting advances in mind, it would be desirable to present a systematic up-to-date account of the title topic, which, to the best of our knowledge, has thus far been unavailable in the literature. The present review summarizes recent advances in eEF1A-targeting anticancer agents, both naturally occurring and synthetically crafted, with regard to their discovery or design, target identification, structure–activity relationship, and mode of action. Their structural diversity and differential eEF1A-targeting mechanisms warrant continuing research in pursuit of curing eEF1A-driven malignancy.

A Survey of Didemnin Depsipeptide Production in Tistrella

As one of the first families of marine natural products to undergo clinical trials, the didemnin depsipeptides have played a significant role in inspiring the discovery of marine drugs. Originally developed as anticancer therapeutics, the recent re-evaluation of these compounds including synthetically derived dehydrodidemnin B or Aplidine, has led to their advancement towards antiviral applications. While conventionally associated with production in colonial tunicates of the family Didemnidae, recent studies have identified their biosynthetic gene clusters from the marine-derived bacteria Tistrella mobilis. While these studies confirm the production of didemnin X/Y, the low titer and general lack of understanding of their biosynthesis in Tistrella currently prevents the development of effective microbial or synthetic biological approaches for their production. To this end, we conducted a survey of known species of Tistrella and report on their ability to produce the didemnin depsipeptides. These data were used to develop conditions to produce didemnin B at titers over 15 mg/L.

Can be marine bioactive peptides (MBAs) lead the future of foodomics for human health?

Marine organisms are considered a cache of biologically active metabolites with pharmaceutical, functional, and nutraceutical properties. Among these, marine bioactive peptides (MBAs) present in diverse marine species (fish, sponges, cyanobacteria, fungi, ascidians, seaweeds, & mollusks) have acquired attention owing to their broad-spectrum health-promoting benefits. Nowadays, scientists are keener exploring marine bioactive peptides precisely due to their unique structural and biological properties. These MBAs have reported ameliorating potential against different diseases like hypertension, diabetes, obesity, HIV, cancer, oxidation, and inflammation. Furthermore, MBAs isolated from various marine organisms may also have a beneficial role in the cosmetic, nutraceutical, and food industries. Few marine peptides and their derivative are approved for commercial use, while many MBAs are in various pre-clinical and clinical trials. This review mainly focuses on the diversity of marine bioactive peptides in marine organisms and their production procedures, such as chemical and enzymatic hydrolysis. Moreover, MBAs' therapeutic and biological potential has also been critically discussed herein, along with their status in drug discovery, pre-clinical and clinical trials.

The marine compound and elongation factor 1A1 inhibitor, didemnin B, provides benefit in western diet-induced non-alcoholic fatty liver disease

Inhibition of eukaryotic elongation factor 1A1 (EEF1A1) with the marine compound didemnin B decreases lipotoxic HepG2 cell death in vitro and improves early stage non-alcoholic fatty liver disease (NAFLD) in young genetically obese mice. However, the effects of didemnin B on NAFLD in a model of long-term diet-induced obesity are not known. We investigated the effects of didemnin B on NAFLD severity and metabolic parameters in western diet-induced obese mice, and on the cell types that contribute to liver inflammation and fibrosis in vitro. Male 129S6 mice were fed either standard chow or western diet for 26 weeks, followed by intervention with didemnin B (50 μg/kg) or vehicle by intraperitoneal (i.p.) injection once every 3 days for 14 days. Didemnin B decreased liver and plasma triglycerides, improved oral glucose tolerance, and decreased NAFLD severity. Moreover, didemnin B moderately increased hepatic expression of genes involved in ER stress response (Perk, Chop), and fatty acid oxidation (Fgf21, Cpt1a). In vitro, didemnin B decreased THP-1 monocyte proliferation, disrupted THP-1 monocyte-macrophage differentiation, decreased THP-1 macrophage IL-1β secretion, and decreased hepatic stellate cell (HSteC) proliferation and collagen secretion under both basal and lipotoxic (high fatty acid) conditions. Thus, didemnin B improves hepatic steatosis, glucose tolerance, and blood lipids in obesity, in association with moderate, possibly hormetic, upregulation of pathways involved in cell stress response and energy balance in the liver. Furthermore, it decreases the activity of the cell types implicated in liver inflammation and fibrosis in vitro. These findings highlight the therapeutic potential of partial protein synthesis inhibition in the treatment of NAFLD.

Phylogenetic analysis and screening of antimicrobial and cytotoxic activities of culturable bacteria associated with the ascidian Botryllus schlosseri

AIMS

Isolating culturable bacteria associated with ascidian (Botryllus schlosseri) and investigating their bioactivities to discover new marine microbial resources with potential to produce novel bioactive natural products.

METHODS AND RESULTS

A total of 357 bacteria were isolated from the ascidian B. schlosseri from the coast of Weihai in the north Yellow Sea, China. Of these, 203 isolates were identified by 16S rRNA gene sequencing and they belonged to 52 genera from 30 families in five phyla. The antimicrobial activities and cytotoxic activities of all isolates were determined. Of the 357 isolates, 135 isolates demonstrated antimicrobial activities, and the crude extracts of five isolates showed strong cytotoxicity against human hepatocellular carcinoma Bel 7402 or human cervical carcinoma HeLa cells.

CONCLUSIONS

Our study revealed the diversity of bacteria associated with the ascidian B. schlosseri and reported a broad spectrum of antimicrobial and cytotoxic activities displayed by these isolates.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results suggest that the culturable bacteria associated with the ascidian B. schlosseri may be a potential source for novel bioactive compounds.

Purification, characterization and anti-tumor activities of polysaccharides from Ecklonia kurome obtained by three different extraction methods

To investigate and compare the effects of different extraction methods on the structure and anti-tumor activity of Ecklonia kurome polysaccharides (EP), three techniques, namely hot water extraction (HW), ultrasonic-assisted extraction (UA) and enzyme-assisted extraction (EA), were used to extract EP, and three crude EPs were purified by DEAE-cellulose and gel filtration chromatography. The significant antitumor active components in each method were screened by MTT assay and named as HW-EP5, UA-EP4 and EA-EP3, respectively. The molecular weight, FT-IR assay and NMR showed that HW-EP5, UA-EP4 and EA-EP3 were pyran polysaccharides with a molecular weight of 14,466, 15,922 and 16,947 Da, respectively. HW-EP5 contained the most monosaccharides and the highest content of sulfate and uronic acid. HW-EP5 had an even and smooth sheet-like appearance, while UA-EP4 and EA-EP3 exhibited irregular and rough fragments. All three polysaccharides can inhibit the migration of human breast cancer cells (MCF-7) and promote its apoptosis. All three polysaccharides promoted caspase activity during apoptosis. HW-EP5 and UA-EP4 up-regulated the expression of proapoptotic proteins Bax and p53, while EA-EP3 only up-regulated the expression of p53. These experimental results indicate that Ecklonia kurome polysaccharides, especially HW-EP5, have great potential as a natural medicine for the treatment of breast cancer.

Enriching cancer pharmacology with drugs of marine origin

Marine natural products have proven, over the last half-century, to be effective biological modulators. These molecules have revealed new targets for cancer therapy as well as dissimilar modes of action within typical classes of drugs. In this scenario, innovation from marine-based pharmaceuticals has helped advance cancer chemotherapy in many aspects, as most of these are designated as first-in-class drugs. Here, by examining the path from discovery to development of clinically approved drugs of marine origin for cancer treatment-cytarabine (Cytosar-U®), trabectedin (Yondelis®), eribulin (Halaven®), brentuximab vedotin (Adcetris®), and plitidepsin (Aplidin®)- together with those in late clinical trial phases-lurbinectedin, plinabulin, marizomib, and plocabulin-the present review offers a critical analysis of the contributions given by these new compounds to cancer pharmacotherapy.

Oceans as a Source of Immunotherapy

Marine flora is taxonomically diverse, biologically active, and chemically unique. It is an excellent resource, which offers great opportunities for the discovery of new biopharmaceuticals such as immunomodulators and drugs targeting cancerous, inflammatory, microbial, and fungal diseases. The ability of some marine molecules to mediate specific inhibitory activities has been demonstrated in a range of cellular processes, including apoptosis, angiogenesis, and cell migration and adhesion. Immunomodulators have been shown to have significant therapeutic effects on immune-mediated diseases, but the search for safe and effective immunotherapies for other diseases such as sinusitis, atopic dermatitis, rheumatoid arthritis, asthma and allergies is ongoing. This review focuses on the marine-originated bioactive molecules with immunomodulatory potential, with a particular focus on the molecular mechanisms of specific agents with respect to their targets. It also addresses the commercial utilization of these compounds for possible drug improvement using metabolic engineering and genomics.

Anticancer Activity of Natural Compounds from Plant and Marine Environment

This paper describes the substances of plant and marine origin that have anticancer properties. The chemical structure of the molecules of these substances, their properties, mechanisms of action, their structure⁻activity relationships, along with their anticancer properties and their potential as chemotherapeutic drugs are discussed in this paper. This paper presents natural substances from plants, animals, and their aquatic environments. These substances include the vinca alkaloids, mistletoe plant extracts, podophyllotoxin derivatives, taxanes, camptothecin, combretastatin, and others including geniposide, colchicine, artesunate, homoharringtonine, salvicine, ellipticine, roscovitine, maytanasin, tapsigargin, and bruceantin. Compounds (psammaplin, didemnin, dolastin, ecteinascidin, and halichondrin) isolated from the marine plants and animals such as microalgae, cyanobacteria, heterotrophic bacteria, invertebrates (e.g., sponges, tunicates, and soft corals) as well as certain other substances that have been tested on cells and experimental animals and used in human chemotherapy.

Therapeutic Properties and Biological Benefits of Marine-Derived Anticancer Peptides

Various organisms exist in the oceanic environment. These marine organisms provide an abundant source of potential medicines. Many marine peptides possess anticancer properties, some of which have been evaluated for treatment of human cancer in clinical trials. Marine anticancer peptides kill cancer cells through different mechanisms, such as apoptosis, disruption of the tubulin-microtubule balance, and inhibition of angiogenesis. Traditional chemotherapeutic agents have side effects and depress immune responses. Thus, the research and development of novel anticancer peptides with low toxicity to normal human cells and mechanisms of action capable of avoiding multi-drug resistance may provide a new method for anticancer treatment. This review provides useful information on the potential of marine anticancer peptides for human therapy.

Antiviral potential of medicinal plants against HIV, HSV, influenza, hepatitis, and coxsackievirus: A systematic review

Viral infections are being managed therapeutically through available antiviral regimens with unsatisfactory clinical outcomes. The refractory viral infections resistant to available antiviral drugs are alarming threats and a serious health concern. For viral hepatitis, the interferon and vaccine therapies solely are not ultimate solutions due to recurrence of hepatitis C virus. Owing to the growing incidences of viral infections and especially of resistant viral strains, the available therapeutic modalities need to be improved, complemented with the discovery of novel antiviral agents to combat refractory viral infections. It is widely accepted that medicinal plant heritage is nature gifted, precious, and fueled with the valuable resources for treatment of metabolic and infectious disorders. The aims of this review are to assemble the facts and to conclude the therapeutic potential of medicinal plants in the eradication and management of various viral diseases such as influenza, human immunodeficiency virus (HIV), herpes simplex virus (HSV), hepatitis, and coxsackievirus infections, which have been proven in diverse clinical studies. The articles, published in the English language since 1982 to 2017, were included from Web of Science, Cochrane Library, AMED, CISCOM, EMBASE, MEDLINE, Scopus, and PubMed by using relevant keywords including plants possessing antiviral activity, the antiviral effects of plants, and plants used in viral disorders. The scientific literature mainly focusing on plant extracts and herbal products with therapeutic efficacies against experimental models of influenza, HIV, HSV, hepatitis, and coxsackievirus were included in the study. Pure compounds possessing antiviral activity were excluded, and plants possessing activity against viruses other than viruses in inclusion criteria were excluded. Hundreds of plant extracts with antiviral effect were recognized. However, the data from only 36 families investigated through in vitro and in vivo studies met the inclusion criteria of this review. The inferences from scientific literature review, focusing on potential therapeutic consequences of medicinal plants on experimental models of HIV, HSV, influenza, hepatitis, and coxsackievirus have ascertained the curative antiviral potential of plants. Fifty-four medicinal plants belonging to 36 different families having antiviral potential were documented. Out of 54 plants, 27 individually belong to particular plant families. On the basis of the work of several independent research groups, the therapeutic potential of medicinal plants against listed common viral diseases in the region has been proclaimed. In this context, the herbal formulations as alternative medicine may contribute to the eradication of complicated viral infection significantly. The current review consolidates the data of the various medicinal plants, those are Sambucus nigra, Caesalpinia pulcherrima, and Hypericum connatum, holding promising specific antiviral activities scientifically proven through studies on experimental animal models. Consequently, the original research addressing the development of novel nutraceuticals based on listed medicinal plants is highly recommended for the management of viral disorders.

Anticancer potential of bioactive peptides from animal sources (Review)

Cancer is the most common cause of human death worldwide. Conventional anticancer therapies, including chemotherapy and radiation, are associated with severe side effects and toxicities as well as low specificity. Peptides are rapidly being developed as potential anticancer agents that specifically target cancer cells and are less toxic to normal tissues, thus making them a better alternative for the prevention and management of cancer. Recent research has focused on anticancer peptides from natural animal sources, such as terrestrial mammals, marine animals, amphibians, and animal venoms. However, the mode of action by which bioactive peptides inhibit the proliferation of cancer cells remains unclear. In this review, we present the animal sources from which bioactive peptides with anticancer activity are derived and discuss multiple proposed mechanisms by which these peptides exert cytotoxic effects against cancer cells.

Natural Products Diversity of Marine Ascidians (Tunicates; Ascidiacea) and Successful Drugs in Clinical Development

This present study reviewed the chemical diversity of marine ascidians and their pharmacological applications, challenges and recent developments in marine drug discovery reported during 1994-2014, highlighting the structural activity of compounds produced by these specimens. Till date only 5% of living ascidian species were studied from <3000 species, this study represented from family didemnidae (32%), polyclinidae (22%), styelidae and polycitoridae (11-12%) exhibiting the highest number of promising MNPs. Close to 580 compound structures are here discussed in terms of their occurrence, structural type and reported biological activity. Anti-cancer drugs are the main area of interest in the screening of MNPs from ascidians (64%), followed by anti-malarial (6%) and remaining others. FDA approved ascidian compounds mechanism of action along with other compounds status of clinical trials (phase 1 to phase 3) are discussed here in. This review highlights recent developments in the area of natural products chemistry and biotechnological approaches are emphasized.

Preparation and Antitumor Activity of CS5931, A Novel Polypeptide from Sea Squirt Ciona Savignyi

CS5931 is a novel anticancer agent isolated from the sea squirt Ciona savignyi. However, its content in the species is very low, and developing a novel approach for production of the polypeptide is promising. In the present study, we expressed and purified the polypeptide from E. coli, and the fermentation conditions were studied using response surface methodology. The yield of CS5931 was increased from 2.0 to 7.5 mg/L. The denaturing and renaturation conditions were also studied. Using the optimized renaturation condition, the anticancer activity of refolding CS5931 was increased significantly; the value of IC₅₀ was decreased from 23.2 to 11.6 μM. In vivo study using xenograft nude mice bearing HCT116 cancer cells revealed that CS5931 was able to inhibit the growth of tumor significantly. The study provides a useful approach for obtaining enough amount of CS5931 for further study. This study is also important for developing the polypeptide as a novel anticancer agent.

Ternatin and improved synthetic variants kill cancer cells by targeting the elongation factor-1A ternary complex

Cyclic peptide natural products have evolved to exploit diverse protein targets, many of which control essential cellular processes. Inspired by a series of cyclic peptides with partially elucidated structures, we designed synthetic variants of ternatin, a cytotoxic and anti-adipogenic natural product whose molecular mode of action was unknown. The new ternatin variants are cytotoxic toward cancer cells, with up to 500-fold greater potency than ternatin itself. Using a ternatin photo-affinity probe, we identify the translation elongation factor-1A ternary complex (eEF1A·GTP·aminoacyl-tRNA) as a specific target and demonstrate competitive binding by the unrelated natural products, didemnin and cytotrienin. Mutations in domain III of eEF1A prevent ternatin binding and confer resistance to its cytotoxic effects, implicating the adjacent hydrophobic surface as a functional hot spot for eEF1A modulation. We conclude that the eukaryotic elongation factor-1A and its ternary complex with GTP and aminoacyl-tRNA are common targets for the evolution of cytotoxic natural products.

DOI:http://dx.doi.org/10.7554/eLife.10222.001

Many plants, fungi, and bacteria have evolved to produce small molecules that have powerful effects on the cells of other living organisms, and can even kill them. These naturally produced compounds are often used as starting points for developing new drugs. One such class of compounds are the cyclic peptides, which can be relatively easily produced in the laboratory and are able to penetrate cells. Some cyclic peptides have also proved to be useful for treating cancer and immune diseases, so researchers are keen to identify others that have similar effects. One promising prospect, called ternatin, is produced by several species of fungi. In high doses, ternatin can kill mammalian cells, but it was not clear how it does so.

To learn more, Carelli et al. searched a chemical database for cyclic peptides related to ternatin and identified several similar compounds that were reported to kill cancer cells. Inspired by the structures of these cyclic peptides, Carelli et al. synthesized modified versions of ternatin. One of these was 500 times more potent than ternatin, which means a much lower dose of the compound is still able to kill cancer cells.

Further experiments showed that ternatin blocks the production of new proteins in cells. Specifically, ternatin binds to a complex that includes a protein called elongation factor-1A (eEF1A). Mutations in a particular region of eEF1A prevent ternatin from killing cells, suggesting a potential binding site for ternatin.

The next challenge is to dissect the mechanism by which compounds binding to this site on eEF1A block protein synthesis and kill cells. A related challenge is to understand why certain cancer cells are hypersensitive to ternatin and other eEF1A inhibitors, while other cancer cells are relatively resistant. These questions are relevant to the development of eEF1A inhibitors as cancer treatments.

DOI:http://dx.doi.org/10.7554/eLife.10222.002

Differential action of pateamine A on translation of genomic and subgenomic mRNAs from Sindbis virus

Pateamine A (Pat A) is a natural marine product that interacts specifically with the translation initiation factor eIF4A leading to the disruption of the eIF4F complex. In the present study, we have examined the activity of Pat A on the translation of Sindbis virus (SINV) mRNAs. Translation of genomic mRNA is strongly suppressed by Pat A, as shown by the reduction of nsP1 or nsP2 synthesis. Notably, protein synthesis directed by subgenomic mRNA is resistant to Pat A inhibition when the compound is added at late times following infection; however, subgenomic mRNA is sensitive to Pat A in transfected cells or in cell free systems, indicating that this viral mRNA exhibits a dual mechanism of translation. A detailed kinetic analysis of Pat A inhibition in SINV-infected cells demonstrates that a switch occurs approximately 4h after infection, rendering subgenomic mRNA translation more resistant to Pat A inhibition.

Mode of action and pharmacogenomic biomarkers for exceptional responders to didemnin B

Modern cancer treatment employs many effective chemotherapeutic agents originally discovered from natural sources. The cyclic depsipeptide didemnin B has demonstrated impressive anticancer activity in preclinical models. Clinical use has been approved but is limited by sparse patient responses combined with toxicity risk and an unclear mechanism of action. From a broad-scale effort to match antineoplastic natural products to their cellular activities, we found that didemnin B selectively induces rapid and wholesale apoptosis through dual inhibition of PPT1 and EEF1A1. Furthermore, empirical discovery of a small panel of exceptional responders to didemnin B allowed the generation of a regularized regression model to extract a sparse-feature genetic biomarker capable of predicting sensitivity to didemnin B. This may facilitate patient selection in a fashion that could enhance and expand the therapeutic application of didemnin B against neoplastic disease.

Identification of eusynstyelamide B as a potent cell cycle inhibitor following the generation and screening of an ascidian-derived extract library using a real time cell analyzer

Ascidians are marine invertebrates that have been a source of numerous cytotoxic compounds. Of the first six marine-derived drugs that made anticancer clinical trials, three originated from ascidian specimens. In order to identify new anti-neoplastic compounds, an ascidian extract library (143 samples) was generated and screened in MDA-MB-231 breast cancer cells using a real-time cell analyzer (RTCA). This resulted in 143 time-dependent cell response profiles (TCRP), which are read-outs of changes to the growth rate, morphology, and adhesive characteristics of the cell culture. Twenty-one extracts affected the TCRP of MDA-MB-231 cells and were further investigated regarding toxicity and specificity, as well as their effects on cell morphology and cell cycle. The results of these studies were used to prioritize extracts for bioassay-guided fractionation, which led to the isolation of the previously identified marine natural product, eusynstyelamide B (1). This bis-indole alkaloid was shown to display an IC₅₀ of 5 µM in MDA-MB-231 cells. Moreover, 1 caused a strong cell cycle arrest in G2/M and induced apoptosis after 72 h treatment, making this molecule an attractive candidate for further mechanism of action studies.

Possible involvement of eEF1A in Tomato spotted wilt virus RNA synthesis

Tomato spotted wilt virus (TSWV) is a negative-strand RNA virus in the family Bunyaviridae and propagates in both insects and plants. Although TSWV can infect a wide range of plant species, host factors involved in viral RNA synthesis of TSWV in plants have not been characterized. In this report, we demonstrate that the cell-free extract derived from one of the host plants can activate mRNA transcriptional activity of TSWV. Based on activity-guided fractionation of the cell-free extract, we identified eukaryotic elongation factor (eEF) 1A as a possible host factor facilitating TSWV transcription and replication. The RNA synthesis-supporting activity decreased in the presence of an eEF1A inhibitor, suggesting that eEF1A plays an important role in RNA synthesis of TSWV.

Purification and Characterization of Bioactive Compounds fromStyela clava

The immunomodulatory activity of extract fromStyela clavawas studied systematically based on activity trackingin vitroin order to find out novel-structured secondary metabolite. The proliferation rates of mouse splenic lymphocytes and peritoneal macrophages were used as screening index, as well as NO release promoting activities. The crude extract (CE) and its different polar fractions fromS. clavaall exhibited proliferative activity of splenolymphocytes and mouse macrophages, as well as NO release promoting activities, among which petroleum ether fraction (PE) showed the strongest effect. The antioxidant experimentin vitroshowed that CE demonstrated antioxidant ability in 1,1-diphenyl-2-picrylhydrazyl (DPPH) system and the beta carotene-linoleic acid system; the activity of ethyl acetate fraction (ET) was much stronger than that of the others. Further isolated by silica gel column chromatography, ET was classified into seven sub-components (E1~E7) listed in the order of activity asE5>E6>E4>E3>E7>E2>E1. Five compounds were separated as (1) cholesteric-7-en-3β-ol, (2) cholesteric-4-en-3β,6β-diol, (3) cholesterol, (4) batilol, and (5) ceramide, among which (1), (2), and (4) were isolated for the first time fromS. clava.

Immunosuppressive peptides and their therapeutic applications

•

T cell signaling has a pivotal role in autoimmunity and immunosuppression.

•

Immunosuppressive pharmaceuticals often exhibit severe side-effects in patients.

•

Gene-encoded peptides have potential as immunosuppressive drug candidates.

•

Cyclotides are stable peptides that offer enhanced oral administration properties.

The immune system is vital for detecting and evading endogenous and exogenous threats to the body. Failure to regulate this homeostasis leads to autoimmunity, which is often associated with malfunctioning T cell signaling. Several medications are available to suppress over-reactive T lymphocytes, but many of the currently marketed drugs produce severe and life-threatening side-effects. Ribosomally synthesized peptides are gaining recognition from the pharmaceutical industry for their enhanced selectivity and decreased toxicity compared with small molecules; in particular, circular peptides exhibit remarkable stability and increased oral administration properties. For example, plant cyclotides effectively inhibit T lymphocyte proliferation. They are composed of a head-to-tail cyclized backbone and a cystine-knot motif, which confers them with remarkable stability, thus making them attractive pharmaceutical tools.

"Head-to-side-chain" cyclodepsipeptides of marine origin

Since the late 1980s, a large number of depsipeptides that contain a new topography, referred to as "head-to-side-chain" cyclodepsipeptides, have been isolated and characterized. These peptides present a unique structural arrangement that comprises a macrocyclic region closed through an ester bond between the C-terminus and a β-hydroxyl group, and terminated with a polyketide moiety or a more simple branched aliphatic acid. This structural pattern, the presence of unique and complex residues, and relevant bioactivity are the main features shared by all the members of this new class of depsipeptides, which are reviewed herein.

Case studies of the synthesis of bioactive cyclodepsipeptide natural products

Cyclodepsipeptide natural products often display intriguing biological activities that along with their complex molecular scaffolds, makes them interesting targets for chemical synthesis. Although cyclodepsipeptides feature highly diverse chemical structures, their synthesis is often associated with similar synthetic challenges such as the establishment of a suitable macrocyclization methodology. This review therefore compiles case studies of synthetic approaches to different bioactive cyclodepsipeptide natural products, thereby illustrating obstacles of cyclodepsipeptide synthesis as well as their overcomings.

Bioactive peptides and depsipeptides with anticancer potential: sources from marine animals

Biologically active compounds with different modes of action, such as, antiproliferative, antioxidant, antimicrotubule, have been isolated from marine sources, specifically algae and cyanobacteria. Recently research has been focused on peptides from marine animal sources, since they have been found as secondary metabolites from sponges, ascidians, tunicates, and mollusks. The structural characteristics of these peptides include various unusual amino acid residues which may be responsible for their bioactivity. Moreover, protein hydrolysates formed by the enzymatic digestion of aquatic and marine by-products are an important source of bioactive peptides. Purified peptides from these sources have been shown to have antioxidant activity and cytotoxic effect on several human cancer cell lines such as HeLa, AGS, and DLD-1. These characteristics imply that the use of peptides from marine sources has potential for the prevention and treatment of cancer, and that they might also be useful as molecular models in anticancer drug research. This review focuses on the latest studies and critical research in this field, and evidences the immense potential of marine animals as bioactive peptide sources.

Recent insights into natural venoms

Toxic substances that occur in nature have various structures and functions. In fact, the very novelty of their structures and functions sometimes extends far beyond the realm of human imagination, and the capabilities of these compounds are still largely untapped despite the major advances of modern science. In this report we focus on the most recent developments in this field, with a particular emphasis on natural venoms, marine sunscreen, and marine huge molecules.

Didemnins, tamandarins and related natural products

Since the discovery and isolation of the didemnin family of marine depsipeptides in 1981, the synthesis and biological activity of its congeners have been of great interest to the scientific community. The didemnins have demonstrated antitumor, antiviral, and immunosuppressive activity at low nano- and femtomolar levels. Of the congeners, didemnin B was the first marine natural product to reach phase II clinical trials in the United States, stimulating many analogue syntheses to date. About two decades later, tamandarins A and B were isolated, and were found to possess very similar structure and biological activity to that of the didemnin B. These compounds have shown impressive biological activity and some progress has been made in establishing structure-activity relationships. However, their molecular mechanism of action still remains unclear. This review highlights the long-standing study of didemnins and its critical application towards the understanding of the molecular mechanism of action of tamandarins and their potential use as therapeutic agents.

Bacterial production of the tunicate-derived antitumor cyclic depsipeptide didemnin B

Natural products obtained from marine invertebrates such as sponges and tunicates are attractive sources of drugs. However, a critical obstacle in the development of these compounds is the problem of supply. In most cases, neither chemical synthesis nor mariculture of invertebrates is economically feasible. Due to structural similarities, many marine natural products are suspected to be produced by associated microorganisms. A favorable strategy for the production of such compounds is to use culturable microorganisms. Here we report that didemnin B, a tunicate-derived depsipeptide, has been isolated from a culturable bacterium, Tistrella mobilis YIT 12409.

Bioactive substances with anti-neoplastic efficacy from marine invertebrates: Bryozoa, Mollusca, Echinodermata and Urochordata

The marine environment provides a rich source of natural products with potential therapeutic application. This has resulted in an increased rate of pharmaceutical agents being discovered in marine animals, particularly invertebrates. Our objective is to summarize the most promising compounds which have the best potential and may lead to use in clinical practice, show their biological activities and highlight the compounds currently being tested in clinical trials. In this paper, we focused on Bryozoa, Mollusca, Echinodermata and Urochordata.

Total synthesis of a depsidomycin analogue by convergent solid-phase peptide synthesis and macrolactonization strategy for antitubercular activity

Depsidomycin is a cyclic heptadepsi-peptide isolated from the cultured broth of Streptomyces lavendofoliae MI951-62F2. It exhibits significant antimicrobial and immunosuppressive activity. The total synthesis of a depsidomycin analogue in which 1,2-piperazine-3-carboxylic acid was substituted with proline is described. After several trials using different strategies, the desired depsidomycin analogue was obtained via stepwise synthesis starting by the amino acid 'head' and macrolactonization under Yamaguchi conditions. The cyclic depsipeptide was evaluated to have an minimum inhibitory concentration (MIC) of 4 µg/ml against H37RV and 16 µg/ml against MDR clinical strains of MTB (MDR-MTB), while the linear precursor 8 also had MICs of 4 and 16 µg/ml for the susceptible and resistant strains, respectively.

N,N'-methyleno-didemnin A from the ascidian Trididemnum solidum. Complete NMR assignments and confirmation of the imidazolidinone ring by strategic analysis of 1J(CH)

The complete NMR assignments of N,N'-methyleno-didemnin A from Trididemnum solidum Van Name 1902 are reported along with a strategic analysis of (1)J(CH) coupling constants that confirm the presence of the imidazolidinone ring.

Pharmacological Developments Obtained from Marine Natural Products and Current Pipeline Perspective

Marine organisms represent a new extensive source for bioactive molecules. They have the potential to provide new therapeutic alternatives to treat human diseases. In this paper, we describe and discuss a variety of isolated and semisynthetic molecules obtained from marine sources. These compounds are in phase II, phase III and at the commercialization stage of new drug development. A description of the mechanism of action, dosage used and side effects are also reported. The positive results obtained from these studies have triggered the development of new studies to evaluate the prospects for utilization of marine organisms.

Translation elongation factor 1A facilitates the assembly of the tombusvirus replicase and stimulates minus-strand synthesis

Replication of plus-strand RNA viruses depends on host factors that are recruited into viral replicase complexes. Previous studies showed that eukaryotic translation elongation factor (eEF1A) is one of the resident host proteins in the highly purified tombusvirus replicase complex. Using a random library of eEF1A mutants, we identified one mutant that decreased and three mutants that increased Tomato bushy stunt virus (TBSV) replication in a yeast model host. Additional in vitro assays with whole cell extracts prepared from yeast strains expressing the eEF1A mutants demonstrated several functions for eEF1A in TBSV replication: facilitating the recruitment of the viral RNA template into the replicase complex; the assembly of the viral replicase complex; and enhancement of the minus-strand synthesis by promoting the initiation step. These roles for eEF1A are separate from its canonical role in host and viral protein translation, emphasizing critical functions for this abundant cellular protein during TBSV replication.

Plus-stranded RNA viruses are important pathogens of plants, animals and humans. They replicate in the infected cells by assembling viral replicase complexes consisting of viral- and host-coded proteins. In this paper, we show that the eukaryotic translation elongation factor (eEF1A), which is one of the resident host proteins in the highly purified tombusvirus replicase complex, is important for Tomato bushy stunt virus (TBSV) replication in a yeast model host. Based on a random library of eEF1A mutants, we identified eEF1A mutants that either decreased or increased TBSV replication. In vitro studies revealed that eEF1A facilitated the recruitment of the viral RNA template for replication and the assembly of the viral replicase complex, as well as eEF1A enhanced viral RNA synthesis in vitro. Altogether, this study demonstrates that eEF1A has several functions during TBSV replication.

Total synthesis of Lys(3) tamandarin M: a potential affinity ligand

The synthesis of Lys(3) tamandarin M is described. This analogue can be used as a protein affinity ligand to probe the mechanism of action of this unique class of molecules.