Symbiodinolide, a novel polyol macrolide that activates N-type Ca2+ channel, from the symbiotic marine dinoflagellate Symbiodinium sp

The potential of marine natural products and their synthetic derivatives as drugs targeting ion channels

Ion channels are a type of protein channel that play a vital role in numerous physiological functions by facilitating the passage of ions through cell membranes, thereby enabling ion and electrical signal transmission. As a crucial target for drug action, ion channels have been implicated in various diseases. Many natural products from marine organisms, such as fungi, algae, sponges, and sea cucumber, etc. have been found to have activities related to ion channels for decades. These interesting natural product molecules undoubtedly bring good news for the treatment of neurological and cardiovascular diseases. In this review, 92 marine natural products and their synthetic derivatives with ion channel-related activities that were identified during the period 2000-2024 were systematically reviewed. The synthesis and mechanisms of action of selected compounds were also discussed, aiming to offer insights for the development of drugs targeting ion channels.

Relative stereochemical determination of the C61-C83 fragment of symbiodinolide using a stereodivergent synthetic approach

Structural determination is required in the use of marine natural products to create novel drugs and drug leads in medicinal chemistry. Symbiodinolide, which is a polyol marine natural product with a molecular weight of 2860, increases the intracellular Ca2+ concentration and exhibits inhibitory activity against cyclooxygenase-1. Seventy percent of the structure of symbiodinolide has been stereochemically clarified. Herein, we report the elucidation of the relative configuration of the C61-C83 fragment, which is among the remaining thirty percent, using a stereodivergent synthetic strategy. We first assigned the relative configuration of the C61-C74 fragment. Two candidate diastereomers of the C61-C74 fragment were synthesized, and their NMR data were compared with those of the natural product, revealing the relative stereochemistry of this component. We then narrowed down the candidate compounds for the C69-C83 fragment from 16 possible diastereomers by analyzing the NMR data of the natural product, and we thus selected eight candidate diastereomers. Stereodivergent synthesis of the candidates for this fragment and comparison of the NMR data of the natural product and the eight synthetic products resulted in the relative stereostructural clarification of the C69-C83 fragment. These individually determined relative stereochemistries of the C61-C74 and C69-C83 fragments were connected via the common C69-C73 tetrahydropyran moiety of the fragments. Finally, the relative configuration of the C61-C83 fragment of symbiodinolide was determined. The stereodivergent synthetic approach used in this study can be extended to the stereochemical determination of other fragments of symbiodinolide.

Glacier-Fed Stream Biofilms Harbor Diverse Resistomes and Biosynthetic Gene Clusters

Antimicrobial resistance (AMR) is a universal phenomenon the origins of which lay in natural ecological interactions such as competition within niches, within and between micro- to higher-order organisms. To study these phenomena, it is crucial to examine the origins of AMR in pristine environments, i.e., limited anthropogenic influences. In this context, epilithic biofilms residing in glacier-fed streams (GFSs) are an excellent model system to study diverse, intra- and inter-domain, ecological crosstalk. We assessed the resistomes of epilithic biofilms from GFSs across the Southern Alps (New Zealand) and the Caucasus (Russia) and observed that both bacteria and eukaryotes encoded twenty-nine distinct AMR categories. Of these, beta-lactam, aminoglycoside, and multidrug resistance were both abundant and taxonomically distributed in most of the bacterial and eukaryotic phyla. AMR-encoding phyla included Bacteroidota and Proteobacteria among the bacteria, alongside Ochrophyta (algae) among the eukaryotes. Additionally, biosynthetic gene clusters (BGCs) involved in the production of antibacterial compounds were identified across all phyla in the epilithic biofilms. Furthermore, we found that several bacterial genera (Flavobacterium, Polaromonas, Superphylum Patescibacteria) encode both atimicrobial resistance genes (ARGs) and BGCs within close proximity of each other, demonstrating their capacity to simultaneously influence and compete within the microbial community. Our findings help unravel how naturally occurring BGCs and AMR contribute to the epilithic biofilms mode of life in GFSs. Additionally, we report that eukaryotes may serve as AMR reservoirs owing to their potential for encoding ARGs. Importantly, these observations may be generalizable and potentially extended to other environments that may be more or less impacted by human activity. IMPORTANCE Antimicrobial resistance is an omnipresent phenomenon in the anthropogenically influenced ecosystems. However, its role in shaping microbial community dynamics in pristine environments is relatively unknown. Using metagenomics, we report the presence of antimicrobial resistance genes and their associated pathways in epilithic biofilms within glacier-fed streams. Importantly, we observe biosynthetic gene clusters associated with antimicrobial resistance in both pro- and eukaryotes in these biofilms. Understanding the role of resistance in the context of this pristine environment and complex biodiversity may shed light on previously uncharacterized mechanisms of cross-domain interactions.

Voratins A-C: Pyridinium Alkaloids from the Marine Dinoflagellate Effrenium voratum with Inhibitory Effects on Biomarkers for Benign Prostatic Hyperplasia

Three voratin compounds (1-3) were isolated from the symbiotic marine dinoflagellate Effrenium voratum. The planar structures of 1-3 were determined by 1D and 2D NMR spectroscopy and HRESIMS, and the relative and absolute configurations were established using ROESY correlations, Mosher's method, and quantum calculations. All of the compounds are zwitterionic and contain a dihydroindolizinium ring and a spiroketal moiety. Compounds 1-3 were found to exhibit therapeutic effects against benign prostatic hyperplasia (BPH), as evaluated using testosterone propionate-treated LNCap and RWPE-1 human prostate cells. This excellent activity suggests that 1-3 are promising for the development of BPH treatments.

Bioactivity and Biotechnological Overview of Naturally Occurring Compounds from the Dinoflagellate Family Symbiodiniaceae: A Systematic Review

Marine invertebrates are a significant source of biologically active compounds. Recent studies have highlighted the role of microbiota associated with marine invertebrates in the production of bioactive compounds. Corals and sponges are the main marine invertebrates producing bioactive substances, and Symbiodiniaceae dinoflagellates are well-recognized endosymbionts with corals and sponges playing vital functions. The biological properties of Symbiodiniaceae-derived compounds have garnered attention in the past decades owing to their ecological implications and potentiality for bioprospecting initiatives. This study aims to systematically review studies on bioactivities and potential biotechnological applications of Symbiodiniaceae-derived compounds. The PRISMA guidelines were followed. Our study showed that anti-inflammatory and vasoconstrictive activities of Symbiodiniaceae-derived compounds have been the most investigated. However, very few studies have been published, with in vitro culturing of Symbiodiniaceae being the most significant challenge. Therefore, we surveyed for the metabolites reported so far, analyzed their chemodiversity, and discussed approaches to overcome culturing-related limitations.

Discovery of benthol A and its challenging stereochemical assignment: opening up a new window for skeletal diversity of super-carbon-chain compounds

Super-carbon-chain compounds (SCCCs) are marine organic molecules featuring long polyol carbon chains with numerous stereocenters. Polyol-polyene compounds (PPCs) and ladder-frame polyethers (LFPs) are two major families. It is highly challenging to establish the absolute configurations of SCCCs. In this century, few new SCCC families have been reported. Benthol A, an aberrant SCCC, was obtained from a South China Sea benthic dinoflagellate that should belong to a new taxon. Its planar structure and absolute configuration, containing thirty-five carbon stereocenters, were unambiguously established by a combination of extensive NMR spectroscopic investigations, periodate degradation of the 1,2-diol groups, ozonolysis of the carbon-carbon double bonds, J-based configurational analysis, NOE interactions, modified Mosher's MTPA ester method, and DFT-NMR ¹³C chemical-shift calculations aided by DP4+ statistical analysis. Benthol A displayed potent antimalarial activity against Plasmodium falciparum 3D7 parasites. This new molecule combines extraordinary structural features, particularly eight scattered ether rings on a C₇₂ backbone chain, which places it within a new SCCC family between PPCs and LFPs, herein termed polyol-polyether compounds. This suggestion was strongly supported by principal component analysis. The discovery of benthol A does not only provide new insights into the untapped biosynthetic potential of marine dinoflagellates, but also opens up a new window for skeletal diversity of SCCCs.

Marine-Derived Macrolides 1990-2020: An Overview of Chemical and Biological Diversity

Macrolides are a significant family of natural products with diverse structures and bioactivities. Considerable effort has been made in recent decades to isolate additional macrolides and characterize their chemical and bioactive properties. The majority of macrolides are obtained from marine organisms, including sponges, marine microorganisms and zooplankton, cnidarians, mollusks, red algae, bryozoans, and tunicates. Sponges, fungi and dinoflagellates are the main producers of macrolides. Marine macrolides possess a wide range of bioactive properties including cytotoxic, antibacterial, antifungal, antimitotic, antiviral, and other activities. Cytotoxicity is their most significant property, highlighting that marine macrolides still encompass many potential antitumor drug leads. This extensive review details the chemical and biological diversity of 505 macrolides derived from marine organisms which have been reported from 1990 to 2020.

N,N-Dimethylaminopyrene as a fluorescent affinity mass tag for ligand-binding mode analysis

Elucidation of the binding mode of protein–ligand interactions provides insights for the design of new pharmacological tools and drug leads. Specific labeling of target proteins with chemical probes, in which the ligands are conjugated with reacting and detecting groups, can establish the binding positions of ligands. Label-assisted laser desorption/ionization mass spectrometry (LA-LDI MS) is a promising detection method to selectively detect labeled molecules. However, previous LDI MS tags, such as nitrogen-substituted pyrenes, had problems with low sensitivity and stability. Here we show 6-N,N-dimethylaminopyrene (dmpy) as a versatile mass tag, which was detected at an amount of 0.1 fmol by LA-LDI MS and applicable for MS/MS analysis. By using ligand-dissociation-type dmpy probes and affinity purification with a polystyrene gel, we demonstrated that dmpy-labeled peptides were predominantly detected by MALDI MS. Our dmpy-probe-labeling method might be highly useful for determining the target biomacromolecules of various ligands and their binding sites.

Determination of the Absolute Configuration of Polyhydroxy Compound Ostreol B Isolated from the Dinoflagellate Ostreopsis cf. ovata

Following isolation of the polyhydroxy compound, ostreol B, from cultivated cells of the toxic dinoflagellate Ostreopsis cf. ovata collected in South Korea, 1D and 2D NMR spectroscopy were employed to determine the planar chemical structure of this compound, which contained a tetrahydropyran ring, two terminal double bonds, and 21 hydroxyl groups. The absolute configurations of all stereogenic carbon centers in ostreol B were then determined through a combination of the J-based configuration analysis, rotating frame Overhauser effect correlations, and the modified Mosher method following cleavage of the 1,2-diol bonds. Ostreol B was also found to exhibit moderate cytotoxicity in HepG2, Neuro-2a and HCT-116 cells.

Achmatowicz Reaction and its Application in the Syntheses of Bioactive Molecules

Substituted pyranones and tetrahydropyrans are structural subunits of many bioactive natural products. Considerable efforts are devoted toward the chemical synthesis of these natural products due to their therapeutic potential as well as low natural abundance. These embedded pyranones and tetrahydropyran structural motifs have been the subject of synthetic interest over the years. While there are methods available for the syntheses of these subunits, there are issues related to regio and stereochemical outcomes, as well as versatility and compatibility of reaction conditions and functional group tolerance. The Achmatowicz reaction, an oxidative ring enlargement of furyl alcohol, was developed in the 1970s. The reaction provides a unique entry to a variety of pyranone derivatives from functionalized furanyl alcohols. These pyranones provide convenient access to substituted tetrahydropyran derivatives. This review outlines general approaches to the synthesis of tetrahydropyrans, covering general mechanistic aspects of the Achmatowicz reaction or rearrangement with an overview of the reagents utilized for the Achmatowicz reaction. The review then focuses on the synthesis of functionalized tetrahydropyrans and pyranones and their applications in the synthesis of natural products and medicinal agents.

Ethenolysis: A Green Catalytic Tool to Cleave Carbon-Carbon Double Bonds

Remarkable innovations have been made in the field of olefin metathesis due to the design and preparation of new catalysts. Ethenolysis, which is cross-metathesis with ethylene, represents one catalytic transformation that has been used with the purpose of cleaving internal carbon-carbon double bonds. The objectives were either the ring opening of cyclic olefins to produce dienes or the shortening of unsaturated hydrocarbon chains to degrade polymers or generate valuable shorter terminal olefins in a controlled manner. This Review summarizes several aspects of this reaction: the catalysts, their degradation in the presence of ethylene, some parameters driving their productivity, the side reactions, and the applications of ethenolysis in organic synthesis and in potential industrial applications.

Multifunctional polyketide synthase genes identified by genomic survey of the symbiotic dinoflagellate, Symbiodinium minutum

Background

Dinoflagellates are unicellular marine and freshwater eukaryotes. They possess large nuclear genomes (1.5–245 gigabases) and produce structurally unique and biologically active polyketide secondary metabolites. Although polyketide biosynthesis is well studied in terrestrial and freshwater organisms, only recently have dinoflagellate polyketides been investigated. Transcriptomic analyses have characterized dinoflagellate polyketide synthase genes having single domains. The Genus Symbiodinium, with a comparatively small genome, is a group of major coral symbionts, and the S. minutum nuclear genome has been decoded.

Results

The present survey investigated the assembled S. minutum genome and identified 25 candidate polyketide synthase (PKS) genes that encode proteins with mono- and multifunctional domains. Predicted proteins retain functionally important amino acids in the catalytic ketosynthase (KS) domain. Molecular phylogenetic analyses of KS domains form a clade in which S. minutum domains cluster within the protist Type I PKS clade with those of other dinoflagellates and other eukaryotes. Single-domain PKS genes are likely expanded in dinoflagellate lineage. Two PKS genes of bacterial origin are found in the S. minutum genome. Interestingly, the largest enzyme is likely expressed as a hybrid non-ribosomal peptide synthetase-polyketide synthase (NRPS-PKS) assembly of 10,601 amino acids, containing NRPS and PKS modules and a thioesterase (TE) domain. We also found intron-rich genes with the minimal set of catalytic domains needed to produce polyketides. Ketosynthase (KS), acyltransferase (AT), and acyl carrier protein (ACP) along with other optional domains are present. Mapping of transcripts to the genome with the dinoflagellate-specific spliced leader sequence, supports expression of multifunctional PKS genes. Metabolite profiling of cultured S. minutum confirmed production of zooxanthellamide D, a polyhydroxy amide polyketide and other unknown polyketide secondary metabolites.

Conclusion

This genomic survey demonstrates that S. minutum contains genes with the minimal set of catalytic domains needed to produce polyketides and provides evidence of the modular nature of Type I PKS, unlike monofunctional Type I PKS from other dinoflagellates. In addition, our study suggests that diversification of dinoflagellate PKS genes comprises dinoflagellate-specific PKS genes with single domains, multifunctional PKS genes with KS domains orthologous to those of other protists, and PKS genes of bacterial origin.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2195-8) contains supplementary material, which is available to authorized users.

Stereoselective synthesis of the C79-C97 fragment of symbiodinolide

Symbiodinolide is a polyol marine natural product with a molecular weight of 2860. Herein, a streamlined synthesis of the C79–C97 fragment of symbiodinolide is described. In the synthetic route, a spiroacetalization, a Julia–Kocienski olefination, and a Sharpless asymmetric dihydroxylation were utilized as the key transformations.

Extracts of marine algae show inhibitory activity against osteoclast differentiation

Osteoclasts are multinucleated cells that play a crucial role in bone resorption. The imbalance between bone resorption and bone formation results in osteoporosis. Therefore, substances that can suppress osteoclast formation are potential candidate materials for drug development or functional foods. There have been reports that extracts or purified compounds from marine micro- and macroalgae can suppress osteoclast differentiation. Symbioimine, isolated from the cultured dinoflagellate Symbiodinium sp., had suppressive effects against osteoclast differentiation in osteoclast-like cells. Norzoanthamine, isolated from the colonial zoanthid Zoanthas sp., has been shown to have antiosteoporosis activity in ovariectomized mice. With regard to marine extracts, the fucoxanthin-rich component from brown algae has been shown to have suppressive effects against osteoclast differentiation. An extract of Sargassum fusiforme has recently been shown to have antiosteoporosis activity. This extract suppressed both osteoclast differentiation and accelerated osteoblast formation in separate in vitro experiments. It also showed antiosteoporosis activity in ovariectomized mice by regulating the balance between bone resorption and bone formation. These marine algae and their extracts may be sources of marine medicinal foods for the prevention of osteoporosis.

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.

Survey of marine natural product structure revisions: a synergy of spectroscopy and chemical synthesis

The structural assignment of new natural product molecules supports research in a multitude of disciplines that may lead to new therapeutic agents and or new understanding of disease biology. However, reports of numerous structural revisions, even of recently elucidated natural products, inspired the present survey of techniques used in structural misassignments and subsequent revisions in the context of constitutional or configurational errors. Given the comparatively recent development of marine natural products chemistry, coincident with modern spectroscopy, it is of interest to consider the relative roles of spectroscopy and chemical synthesis in the structure elucidation and revision of those marine natural products that were initially misassigned. Thus, a tabulated review of all marine natural product structural revisions from 2005 to 2010 is organized according to structural motif revised. Misassignments of constitution are more frequent than perhaps anticipated by reliance on HMBC and other advanced NMR experiments, especially when considering the full complement of all natural products. However, these techniques also feature prominently in structural revisions, specifically of marine natural products. Nevertheless, as is the case for revision of relative and absolute configuration, total synthesis is a proven partner for marine, as well as terrestrial, natural products structure elucidation. It also becomes apparent that considerable 'detective work' remains in structure elucidation, in spite of the spectacular advances in spectroscopic techniques.

Marine pharmacology in 2007-8: Marine compounds with antibacterial, anticoagulant, antifungal, anti-inflammatory, antimalarial, antiprotozoal, antituberculosis, and antiviral activities; affecting the immune and nervous system, and other miscellaneous mechanisms of action

The peer-reviewed marine pharmacology literature in 2007-8 is covered in this review, which follows a similar format to the previous 1998-2006 reviews of this series. The preclinical pharmacology of structurally characterized marine compounds isolated from marine animals, algae, fungi and bacteria is discussed in a comprehensive manner. Antibacterial, anticoagulant, antifungal, antimalarial, antiprotozoal, antituberculosis and antiviral activities were reported for 74 marine natural products. Additionally, 59 marine compounds were reported to affect the cardiovascular, immune and nervous systems as well as to possess anti-inflammatory effects. Finally, 65 marine metabolites were shown to bind to a variety of receptors and miscellaneous molecular targets, and thus upon further completion of mechanism of action studies, will contribute to several pharmacological classes. Marine pharmacology research during 2007-8 remained a global enterprise, with researchers from 26 countries, and the United States, contributing to the preclinical pharmacology of 197 marine compounds which are part of the preclinical marine pharmaceuticals pipeline. Sustained preclinical research with marine natural products demonstrating novel pharmacological activities, will probably result in the expansion of the current marine pharmaceutical clinical pipeline, which currently consists of 13 marine natural products, analogs or derivatives targeting a limited number of disease categories.

Symbiopolyol, a VCAM-1 inhibitor from a symbiotic dinoflagellate of the jellyfish Mastigias papua

A super-carbon-chain compound, symbiopolyol (1a), was isolated from a symbiotic dinoflagellate of the jellyfish Mastigias papua. Although a direct comparison between symbiopolyol (1a) and lingshuiol B has not been completed, symbiopolyol (1a) is suggested to be the enantiomer of lingshuiol B. The structure of 1a, including its partial relative configuration, was elucidated on the basis of interpretation of spectroscopic data and chemical transformations. This compound exhibited significant inhibitory activity against the expression of VCAM-1 in human umbilical vein endothelial cells (HUVEC).

Marine huge molecules: the longest carbon chains in natural products

Marine huge polyol and polyether compounds are remarkable molecules owing to their extraordinary structures and significant biological activities. Currently, palytoxin and maitotoxin are believed to have the longest carbon chains in nature (more than 100 A in length), except for biopolymers. The structural properties of such marine huge molecules are highlighted, especially with regard to the length and shape of their carbon chains.

Exploratory research on bioactive natural products with a focus on biological phenomena

The discovery of new basic compounds holds the key for advancing material sciences. We have focused on the identification and characterization of natural key compounds that control biologically and physiologically intriguing phenomena. The discovery of new bioactive molecules, facilitated by a deeper understanding of nature, should advance our knowledge of biological processes and lead to new strategies to treat disease. The structure and function of natural compounds are sometimes unexpectedly original. Based on our past experience and results, we have carried out research to find new directions for compound exploration by directly learning from dynamic biological phenomena in the field, and have succeeded in creating a new research field in biological molecular sciences.

Stereoselective synthesis and absolute configuration of the C1'-C25' fragment of symbiodinolide

Stereoselective synthesis of the C1'-C25' fragment of symbiodinolide, which was obtained as a degraded product from symbiodinolide by alkaline hydrolysis, has been accomplished. The synthetic route features Kotsuki coupling and Julia-Kocienski olefination in the introduction of the side chains. This enantio- and stereoselective synthesis has established the absolute configuration of the C1'-C25' fragment.

Recent aspects of chemical ecology: Natural toxins, coral communities, and symbiotic relationships

The discovery of new ecologically active compounds often triggers the development of basic scientific concepts in the field of biological sciences, since such compounds have direct physiological and behavioral effects on other living organisms. We have focused on the identification of natural key compounds that control biologically and physiologically intriguing phenomena. We describe three recent aspects of chemical ecology that we have investigated: natural toxins, coral communities, and symbiotic relationships. Blarina toxin (BLTX) is a lethal mammalian venom that was isolated from the short-tailed shrew. Duck-billed platypus venom shows potent Ca2+ influx in neuroblastoma cells. The venom of the solitary wasp contains arginine kinase-like protein and is used to paralyze its prey to feed its larva. The ecological behaviors of corals are controlled by combinations of small molecules. The polyol compound symbiodinolide may serve as a defense substance for symbiotic dinoflagellates to prevent digestion of their host animals. These compounds reveal the wonder of nature, in both terrestrial and marine ecological systems.

Marine toxins: an overview

Oceans provide enormous and diverse space for marine life. Invertebrates are conspicuous inhabitants in certain zones such as the intertidal; many are soft-bodied, relatively immobile and lack obvious physical defenses. These animals frequently have evolved chemical defenses against predators and overgrowth by fouling organisms. Marine animals may accumulate and use a variety of toxins from prey organisms and from symbiotic microorganisms for their own purposes. Thus, toxic animals are particularly abundant in the oceans. The toxins vary from small molecules to high molecular weight proteins and display unique chemical and biological features of scientific interest. Many of these substances can serve as useful research tools or molecular models for the design of new drugs and pesticides. This chapter provides an initial survey of these toxins and their salient properties.

Marine natural products

This review covers the literature published in 2007 for marine natural products, with 948 citations(627 for the period January to December 2007) referring to compounds isolated from marine microorganisms and phytoplankton, green algae, brown algae, red algae, sponges, cnidarians,bryozoans, molluscs, tunicates, echinoderms and true mangrove plants. The emphasis is on new compounds (961 for 2007), together with the relevant biological activities, source organisms and country of origin. Biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.1 Introduction, 2 Reviews, 3 Marine microorganisms and phytoplankton, 4 Green algae, 5 Brown algae, 6 Red algae, 7 Sponges, 8 Cnidarians, 9 Bryozoans, 10 Molluscs, 11 Tunicates (ascidians),12 Echinoderms, 13 Miscellaneous, 14 Conclusion, 15 References.