Oxygenated polyketides from Plakinastrella mamillaris as a new chemotype of PXR agonists

Chemoproteomics Reveals USP5 (Ubiquitin Carboxyl-Terminal Hydrolase 5) as Promising Target of the Marine Polyketide Gracilioether A

Mass spectrometry-based chemical proteomic approaches using limited proteolysis have become a powerful tool for the identification and analysis of the interactions between a small molecule (SM) and its protein target(s). Gracilioether A (GeA) is a polyketide isolated from a marine sponge, for which we aimed to trace the interactome using this strategy. DARTS (Drug Affinity Responsive Target Stability) and t-LiP-MS (targeted-Limited Proteolysis-Mass Spectrometry) represented the main techniques used in this study. DARTS was applied on HeLa cell lysate for the identification of the GeA target proteins, and t-LiP-MS was employed to investigate the protein's regions involved in the binding with GeA. The results were complemented through the use of binding studies using Surface Plasmon Resonance (SPR) and in silico molecular docking experiments. Ubiquitin carboxyl-terminal hydrolase 5 (USP5) was identified as a promising target of GeA, and the interaction profile of the USP5-GeA complex was explained. USP5 is an enzyme involved in the pathway of protein metabolism through the disassembly of the polyubiquitin chains on degraded proteins into ubiquitin monomers. This activity is connected to different cellular functions concerning the maintenance of chromatin structure and receptors and the degradation of abnormal proteins and cancerogenic progression. On this basis, this structural information opens the way to following studies focused on the definition of the biological potential of Gracilioether A and the rational development of novel USP5 inhibitors based on a new structural skeleton.

Natural compounds targeting nuclear receptors for effective cancer therapy

Human nuclear receptors (NRs) are a family of forty-eight transcription factors that modulate gene expression both spatially and temporally. Numerous biochemical, physiological, and pathological processes including cell survival, proliferation, differentiation, metabolism, immune modulation, development, reproduction, and aging are extensively orchestrated by different NRs. The involvement of dysregulated NRs and NR-mediated signaling pathways in driving cancer cell hallmarks has been thoroughly investigated. Targeting NRs has been one of the major focuses of drug development strategies for cancer interventions. Interestingly, rapid progress in molecular biology and drug screening reveals that the naturally occurring compounds are promising modern oncology drugs which are free of potentially inevitable repercussions that are associated with synthetic compounds. Therefore, the purpose of this review is to draw our attention to the potential therapeutic effects of various classes of natural compounds that target NRs such as phytochemicals, dietary components, venom constituents, royal jelly-derived compounds, and microbial derivatives in the establishment of novel and safe medications for cancer treatment. This review also emphasizes molecular mechanisms and signaling pathways that are leveraged to promote the anti-cancer effects of these natural compounds. We have also critically reviewed and assessed the advantages and limitations of current preclinical and clinical studies on this subject for cancer prophylaxis. This might subsequently pave the way for new paradigms in the discovery of drugs that target specific cancer types.

Chemical and biological diversity of new natural products from marine sponges: a review (2009-2018)

Marine sponges are productive sources of bioactive secondary metabolites with over 200 new compounds isolated each year, contributing 23% of approved marine drugs so far. This review describes statistical research, structural diversity, and pharmacological activity of sponge derived new natural products from 2009 to 2018. Approximately 2762 new metabolites have been reported from 180 genera of sponges this decade, of which the main structural types are alkaloids and terpenoids, accounting for 50% of the total. More than half of new molecules showed biological activities including cytotoxic, antibacterial, antifungal, antiviral, anti-inflammatory, antioxidant, enzyme inhibition, and antimalarial activities. As summarized in this review, macrolides and peptides had higher proportions of new bioactive compounds in new compounds than other chemical classes. Every chemical class displayed cytotoxicity as the dominant activity. Alkaloids were the major contributors to antibacterial, antifungal, and antioxidant activities while steroids were primarily responsible for pest resistance activity. Alkaloids, terpenoids, and steroids displayed the most diverse biological activities. The statistic research of new compounds by published year, chemical class, sponge taxonomy, and biological activity are presented. Structural novelty and significant bioactivities of some representative compounds are highlighted. Marine sponges are rich sources of novel bioactive compounds and serve as animal hosts for microorganisms, highlighting the undisputed potential of sponges in the marine drugs research and development.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00132-3.

Unified Biomimetic Approach to (+)-Hippolachnin A: In-Depth Insights into Its Biosynthetic Origin

A formal biomimetic synthesis of (+)-hippolachnin A has been achieved under the guidance of its plausible biosynthetic pathway. Pivotal transformations include an intriguing 1O2-mediated [4 + 2] cycloaddition and a tandem Kornblum-DeLaMare rearrangement/hemiketalization/dehydration reaction. The current work not only offers a unified approach to access skeletally diverse plakortin-type polyketides but also provides convincing evidence to elucidate their underlying biosynthetic network.

Applications of ultrasound in total synthesis of bioactive natural products: A promising green tool

Total synthesisis frequently compared to climbing as it provides a suitable route to reach a high point from the floor, the complex natural product from simple and commercially available materials. The total synthesis has a privileged position of trust in confirming the hypothetical complex structures of natural products despite sophisticated analytical and spectroscopic instrumentation and techniques that are available presently. Moreover, total synthesis is also useful to prepare rare bioactive natural products in the laboratory as several bioactive secondary metabolites are obtained in small quantities from natural sources. The artistic aspect of the total synthesis of bioactive natural products continues to be praised today as it may provide environmental protection through the concept of green or clean chemistry. The use of ultrasound waves as a non-polluting source of energy is of great interest in the field of sustainable and pharmaceutical chemistry as it differs from conventional energy sources in terms of reaction rates, yields, selectivities, and purity of the products. The present review highlights the application of ultrasound as a green tool in the total synthesis of bioactive natural products as well as this article is also aimed to offer an overview of natural sources, structures, and biological activities of the promising natural products for the first time from 2005 to 2020 elegantly.

Searching for Small Molecules with an Atomic Sort

The discovery of biologically active small molecules requires sifting through large amounts of data to identify unique or unusual arrangements of atoms. Here, we develop, test and evaluate an atom-based sort to identify novel features of secondary metabolites and demonstrate its use to evaluate novelty in marine microbial and sponge extracts. This study outlines an important ongoing advance towards the translation of autonomous systems to identify, and ultimately elucidate, atomic novelty within a complex mixture of small molecules.

Recent advances in the synthesis of plakortin-type polyketides

Plakortin-type polyketides represent a growing family of sponge-derived marine natural products that display notable structural and biological diversity. In particular, a series of polycyclic plakortin polyketides, namely hippolachnin A and gracilioethers, have been identified in recent years, which attract immense interest from the synthetic community owing to their unique molecular architectures and promising biomedical potential. A number of elegant total syntheses of these targets and some synthetic studies have been performed through either bio-inspired or rationally designed strategies. This focused review aims to provide an up-to-date summary of the progress in the chemical synthesis of plakortin polyketides, with an emphasis on the key synthetic elements enabling the rapid assembly of their core skeletons.

Development of a novel and rapid phenotype-based screening method to assess rice seedling growth

BACKGROUND

Rice (Oryza sativa) is one of the most important model crops in plant research. Despite its considerable advantages, (phenotypic) bioassays for rice are not as well developed as for Arabidopsis thaliana. Here, we present a phenotype-based screening method to study shoot-related parameters of rice seedlings via an automated computer analysis.

RESULTS

The phenotype-based screening method was validated by testing several compounds in pharmacological experiments that interfered with hormone homeostasis, confirming that the assay was consistent with regard to the anticipated plant growth regulation and revealing the robustness of the set-up in terms of reproducibility. Moreover, abiotic stress tests using NaCl and DCMU, an electron transport blocker during the light dependent reactions of photosynthesis, confirmed the validity of the new method for a wide range of applications. Next, this method was used to screen the impact of semi-purified fractions of marine invertebrates on the initial stages of rice seedling growth. Certain fractions clearly stimulated growth, whereas others inhibited it, especially in the root, illustrating the possible applications of this novel, robust, and fast phenotype-based screening method for rice.

CONCLUSIONS

The validated phenotype-based and cost-efficient screening method allows a quick and proper analysis of shoot growth and requires only small volumes of compounds and media. As a result, this method could potentially be used for a whole range of applications, ranging from discovery of novel biostimulants, plant growth regulators, and plant growth-promoting bacteria to analysis of CRISPR knockouts, molecular plant breeding, genome-wide association, and phytotoxicity studies. The assay system described here can contribute to a better understanding of plant development in general.

Marine Invertebrate Extracts Induce Colon Cancer Cell Death via ROS-Mediated DNA Oxidative Damage and Mitochondrial Impairment

Marine compounds are a potential source of new anticancer drugs. In this study, the antiproliferative effects of 20 invertebrate marine extracts on three colon cancer cell models (HGUE-C-1, HT-29, and SW-480) were evaluated. Extracts from two nudibranchs (Phyllidia varicosa, NA and Dolabella auricularia, NB), a holothurian (Pseudocol ochirus violaceus, PS), and a soft coral (Carotalcyon sp., CR) were selected due to their potent cytotoxic capacities. The four marine extracts exhibited strong antiproliferative effects and induced cell cycle arrest at the G2/M transition, which evolved into early apoptosis in the case of the CR, NA, and NB extracts and necrotic cell death in the case of the PS extract. All the extracts induced, to some extent, intracellular ROS accumulation, mitochondrial depolarization, caspase activation, and DNA damage. The compositions of the four extracts were fully characterized via HPLC-ESI-TOF-MS analysis, which identified up to 98 compounds. We propose that, among the most abundant compounds identified in each extract, diterpenes, steroids, and sesqui- and seterterpenes (CR); cembranolides (PS); diterpenes, polyketides, and indole terpenes (NA); and porphyrin, drimenyl cyclohexanone, and polar steroids (NB) might be candidates for the observed activity. We postulate that reactive oxygen species (ROS) accumulation is responsible for the subsequent DNA damage, mitochondrial depolarization, and cell cycle arrest, ultimately inducing cell death by either apoptosis or necrosis.

Marine Ligands of the Pregnane X Receptor (PXR): An Overview

Pregnane X Receptor (PXR) is a ligand-activated transcription factor which binds many structurally different molecules. The receptor is able to regulate the expression of a wide array of genes and is involved in cancer and different key physiological processes such as the metabolism of drugs/xenobiotics and endogenous compounds including lipids and carbohydrates, and inflammation. Algae, sponges, sea squirts, and other marine organisms are some of the species from which structurally new molecules have been isolated that have been subsequently identified in recent decades as ligands for PXR. The therapeutic potential of these natural compounds is promising in different areas and has recently resulted in the registration of trabectedin by the FDA as a novel antineoplastic drug. Apart from being potentially novel drugs, these compounds can also serve as models for the development of new molecules with improved activity. The aim of this review is to succinctly summarize the currently known natural molecules isolated from marine organisms with a proven ability to interact with PXR.

Advances in the Asymmetric Total Synthesis of Natural Products Using Chiral Secondary Amine Catalyzed Reactions of α,β-Unsaturated Aldehydes

Chirality is one of the most important attributes for its presence in a vast majority of bioactive natural products and pharmaceuticals. Asymmetric organocatalysis methods have emerged as a powerful methodology for the construction of highly enantioenriched structural skeletons of the target molecules. Due to their extensive application of organocatalysis in the total synthesis of bioactive molecules and some of them have been used in the industrial synthesis of drugs have attracted increasing interests from chemists. Among the chiral organocatalysts, chiral secondary amines (MacMillan's catalyst and Jorgensen's catalyst) have been especially considered attractive strategies because of their impressive efficiency. Herein, we outline advances in the asymmetric total synthesis of natural products and relevant drugs by using the strategy of chiral secondary amine catalyzed reactions of α,β-unsaturated aldehydes in the last eighteen years.

Natural Products from Sponges

The sponge is one of the oldest multicellular invertebrates in the world. Marine sponges represent one of the extant metazoans of 700–800 million years. They are classified in four major classes: Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha. Among them, three genera, namely, Haliclona, Petrosia, and Discodemia have been identified to be the richest source of biologically active compounds. So far, 15,000 species have been described, and among them, more than 6000 species are found in marine and freshwater systems throughout tropical, temperate, and polar regions. More than 5000 different compounds have been isolated and structurally characterized to date, contributing to about 30% of all marine natural products. The chemical diversity of sponge products is high with compounds classified as alkaloids, terpenoids, peptides, polyketides, steroids, and macrolides, which integrate a wide range of biological activities, including antibacterial, anticancer, antifungal, anti-HIV, anti-inflammatory, and antimalarial. There is an open debate whether all natural products isolated from sponges are produced by sponges or are in fact derived from microorganisms that are inhaled though filter-feeding or that live within the sponges. Apart from their origin and chemoecological functions, sponge-derived metabolites are also of considerable interest in drug development. Therefore, development of recombinant microorganisms engineered for efficient production of sponge-derived products is a promising strategy that deserves further attention in future investigations in order to address the limitations regarding sustainable supply of marine drugs.

Marine Pharmacology in 2012-2013: Marine Compounds with Antibacterial, Antidiabetic, Antifungal, Anti-Inflammatory, Antiprotozoal, Antituberculosis, and Antiviral Activities; Affecting the Immune and Nervous Systems, and Other Miscellaneous Mechanisms of Action

The peer-reviewed marine pharmacology literature from 2012 to 2013 was systematically reviewed, consistent with the 1998–2011 reviews of this series. Marine pharmacology research from 2012 to 2013, conducted by scientists from 42 countries in addition to the United States, reported findings on the preclinical pharmacology of 257 marine compounds. The preclinical pharmacology of compounds isolated from marine organisms revealed antibacterial, antifungal, antiprotozoal, antituberculosis, antiviral and anthelmitic pharmacological activities for 113 marine natural products. In addition, 75 marine compounds were reported to have antidiabetic and anti-inflammatory activities and affect the immune and nervous system. Finally, 69 marine compounds were shown to display miscellaneous mechanisms of action which could contribute to novel pharmacological classes. Thus, in 2012–2013, the preclinical marine natural product pharmacology pipeline provided novel pharmacology and lead compounds to the clinical marine pharmaceutical pipeline, and contributed significantly to potentially novel therapeutic approaches to several global disease categories.

Gain-of-Function Alleles in Caenorhabditis elegans Nuclear Hormone Receptor nhr-49 Are Functionally Distinct

Nuclear hormone receptors (NHRs) are transcription factors that regulate numerous physiological and developmental processes and represent important drug targets. NHR-49, an ortholog of Hepatocyte Nuclear Factor 4 (HNF4), has emerged as a key regulator of lipid metabolism and life span in the nematode worm Caenorhabditis elegans. However, many aspects of NHR-49 function remain poorly understood, including whether and how it regulates individual sets of target genes and whether its activity is modulated by a ligand. A recent study identified three gain-of-function (gof) missense mutations in nhr-49 (nhr-49(et7), nhr-49(et8), and nhr-49(et13), respectively). These substitutions all affect the ligand-binding domain (LBD), which is critical for ligand binding and protein interactions. Thus, these alleles provide an opportunity to test how three specific residues contribute to NHR-49 dependent gene regulation. We used computational and molecular methods to delineate how these mutations alter NHR-49 activity. We find that despite originating from a screen favoring the activation of specific NHR-49 targets, all three gof alleles cause broad upregulation of NHR-49 regulated genes. Interestingly, nhr-49(et7) and nhr-49(et8) exclusively affect nhr-49 dependent activation, whereas the nhr-49(et13) surprisingly affects both nhr-49 mediated activation and repression, implicating the affected residue as dually important. We also observed phenotypic non-equivalence of these alleles, as they unexpectedly caused a long, short, and normal life span, respectively. Mechanistically, the gof substitutions altered neither protein interactions with the repressive partner NHR-66 and the coactivator MDT-15 nor the subcellular localization or expression of NHR-49. However, in silico structural modeling revealed that NHR-49 likely interacts with small molecule ligands and that the missense mutations might alter ligand binding, providing a possible explanation for increased NHR-49 activity. In sum, our findings indicate that the three nhr-49 gof alleles are non-equivalent, and highlight the conserved V411 residue affected by et13 as critical for gene activation and repression alike.

Collaborative Total Synthesis: Routes to (±)-Hippolachnin A Enabled by Quadricyclane Cycloaddition and Late-Stage C-H Oxidation

Described herein are synthetic efforts toward the synthesis of hippolachnin A. Two independently devised routes from the Brown and Wood groups allowed for the synthesis of hippolachnin A from the unusual starting material, quadricyclane, by harnessing the power of late-stage C-H oxidation. Collaborative union of the best features of the two routes allowed for preparation of the molecule with improved efficiency.

Structural diversity and chemical synthesis of peroxide and peroxide-derived polyketide metabolites from marine sponges

The structural elucidation, chemical synthesis and therapeutic potential of peroxide and peroxide-derived sponge metabolites, with special focus on their intriguing structural similarities and differences from a biogenetic perspective, are reviewed.

Diethylstilbestrol-scaffold-based pregnane X receptor modulators

Due to its function as a regulator of drug-metabolizing enzymes and transporters, pregnane X receptor (PXR) represents an important factor involved in drug metabolism. In this work, we describe the discovery of diethylstilbestrol-based PXR modulators, which were designed from marine sulfated steroids with PXR agonistic activity, solomonsterols A and B, and our recently reported bazedoxifene scaffold-derived PXR antagonists. The methylated diethylstilbestrol derivative 1 displayed potent PXR agonistic activity with an EC50 value of 10.5 μM, whereas compounds 3, 4 and 6 (IC50 for 6 = 27.4 μM) and diethylstilbestrol (2) itself (IC50 = 14.6 μM) exhibited PXR antagonistic effects in HepG2 cells. The PXR modulatory effects of the synthesized diethylstilbestrol derivatives were further confirmed by the induction of PXR-regulated CYP3A4 expression with compound 1, as well as by the inhibition of the rifaximin-promoted up-regulation of CYP3A4 expression with 2 and its derivative 6.

Marine natural products

This review covers the literature published in 2013 for marine natural products (MNPs), with 982 citations (644 for the period January to December 2013) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1163 for 2013), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.

Total synthesis of gracilioether F: development and application of lewis Acid promoted ketene-alkene [2+2] cycloadditions and late-stage C-H oxidation

The first synthesis of gracilioether F, a polyketide natural product with an unusual tricyclic core and five contiguous stereocenters, is described. Key steps of the synthesis include a Lewis acid promoted ketene-alkene [2+2] cycloaddition and a late-stage carboxylic acid directed C(sp(3) )H oxidation. The synthesis requires only eight steps from norbornadiene.

Marine and semi-synthetic hydroxysteroids as new scaffolds for pregnane X receptor modulation

In recent years many sterols with unusual structures and promising biological profiles have been identified from marine sources. Here we report the isolation of a series of 24-alkylated-hydroxysteroids from the soft coral Sinularia kavarattiensis, acting as pregnane X receptor (PXR) modulators. Starting from this scaffold a number of derivatives were prepared and evaluated for their ability to activate the PXR by assessing transactivation and quantifying gene expression. Our study reveals that ergost-5-en-3β-ol (4) induces PXR transactivation in HepG2 cells and stimulates the expression of the PXR target gene CYP3A4. To shed light on the molecular basis of the interaction between these ligands and PXR, we investigated, through docking simulations, the binding mechanism of the most potent compound of the series, 4, to the PXR. Our findings provide useful functional and structural information to guide further investigations and drug design.

Plakilactones G and H from a marine sponge. Stereochemical determination of highly flexible systems by quantitative NMR-derived interproton distances combined with quantum mechanical calculations of (13)C chemical shifts

In this paper the stereostructural investigation of two new oxygenated polyketides, plakilactones G and H, isolated from the marine sponge Plakinastrella mamillaris collected at Fiji Islands, is reported. The stereostructural studies began on plakilactone H by applying an integrated approach of the NOE-based protocol and quantum mechanical calculations of (13)C chemical shifts. In particular, plakilactone H was used as a template to extend the application of NMR-derived interproton distances to a highly flexible molecular system with simultaneous assignment of four non-contiguous stereocenters. Chemical derivatization and quantum mechanical calculations of (13)C on plakilactone G along with a plausible biogenetic interconversion between plakilactone G and plakilactone H allowed us to determine the absolute configuration in this two new oxygenated polyketides.

Solomonsterol A, a marine pregnane-X-receptor agonist, attenuates inflammation and immune dysfunction in a mouse model of arthritis

In the present study we provide evidence that solomonsterol A, a selective pregnane X receptor (PXR) agonist isolated from the marine sponge Theonella swinhoei, exerts anti-inflammatory activity and attenuates systemic inflammation and immune dysfunction in a mouse model of rheumatoid arthritis. Solomonsterol A was effective in protecting against the development of arthritis induced by injecting transgenic mice harboring a humanized PXR, with anti-collagen antibodies (CAIA) with beneficial effects on joint histopathology and local inflammatory response reducing the expression of inflammatory markers (TNFα, IFNγ and IL-17 and chemokines MIP1α and RANTES) in draining lymph nodes. Solomonsterol A rescued mice from systemic inflammation were assessed by measuring arthritis score, CRP and cytokines in the blood. In summary, the present study provides a molecular basis for the regulation of systemic local and systemic immunity by PXR agonists.

Insights on pregnane-X-receptor modulation. Natural and semisynthetic steroids from Theonella marine sponges

Pregnane-X-receptor (PXR) is a member of nuclear receptors superfamily that activates gene transcription by binding to responsive elements in the promoter of target genes. PXR is a master gene orchestrating the expression/activity of genes involved in the metabolism of endobiotics including bilirubin, bile acids, glucose and lipid. In addition PXR oversights the metabolism of the large majority of xenobiotics including a large amount of prescribing drugs. Thus, developing PXR ligands represents a great opportunity for a therapeutic intervention on human diseases including diabetes, obesity, dyslipidemias and liver disorders. To this end, natural compounds represent an arsenal of new chemical scaffolds useful for the identification of novel PXR ligands. Here, we report a series of 4-methylenesteroid derivatives isolated from Theonella marine sponges as novel PXR modulators. In addition, combining medicinal chemistry, pharmacological experiments and computational studies, we have investigated the effects of different modifications on ring A and on the side chain of 4-methylenesteroid derivatives toward PXR modulation. This study provides the molecular bases of ligand/PXR interaction useful for designing novel PXR modulators.