Structures Of Natural Products Research Articles

Skeletal Isomerization of Ergosterol-5,8-peroxide Leading to the Discovery of Unprecedented Ergostanes and Collective Syntheses of 5,6-Epoxysterols and (+)-Sarocladione.

Skeletal isomerization of ergosterol peroxide, a primary oxidation product of ergosterol, was investigated under thermal and iron(II)-mediated conditions. Thermal isomerization resulted in not only the isolation of the predicted 7-hydroxy-5,6-epoxides but also the discovery of the unprecedented 7/9/5-ring-fused ergostane for the first time. The iron(II)-mediated isomerization proceeded at ambient temperature, resulting in the formation of the expected 5,6-epoxysterols and a ring-opened bicyclic diketone. The diketone was further converted into novel ergostane under thermal conditions and into (+)-sarocladione under acidic conditions. All transformations from ergosterol to sarocladione, including the isolation of the unstable diketone intermediate, were achieved at ambient temperature, confirming the biosynthetic pathway of sarocladione. Several mushroom ingredients with a 5,6-epoxy group were synthesized stereoselectively from the isomerization products, leading to the confirmation or revision of the structures of natural products. The β-amyloid aggregation inhibitory activity of synthetic sterols was evaluated for the first time to gain insights into the potential for dementia prevention. This study is valuable both for supplying rare sterols found in mushrooms for biological studies and for shedding light on the oxidative metabolic pathways of ergosterol.

Hydroxylamines: From Synthetic Intermediates to Synthetic Targets.

ConspectusSynergy between the teaching and research activities of a University should be a source of new ideas, each informing the other. A classroom discussion gave rise to our concept of using hydroxylamines as a form of "tethered nitrogen" for alkaloid synthesis. The "tether" temporarily connects a nucleophilic nitrogen atom to the substrate, rendering an intermolecular reaction intramolecular, thus providing stereo- and regiochemical control for C-N bond formation. In the context of the synthesis of 1,3-amino alcohols, this necessitated the synthesis of isoxazolidines. This concept led to the exploration of methods for the synthesis of these heterocycles beyond the well-established 1,3-dipolar cycloadditions. The first two methods developed based upon this concept were palladium catalyzed cyclocarbonylation and silver catalyzed allene cyclization. These new methods were applied to two syntheses of sedamine and the synthesis of three Nuphar alkaloids. Intramolecular aza-Michael addition, combined with the use of cross-metathesis to generate the substrates, gave access to both isoxazolidines and tetrahydro-1,2-oxazines. This new method made possible a synthesis of monomorine with high stereochemical control. The extension to more complex alkaloids required the incorporation of additional chemistry. Combining allene cyclization with iminium ion chemistry allowed the extension to the more complex piperidine alkaloids porantheridine and sedinine. In these cases, successful stereocontrol relied on the ability to predict the conformation of the intermediates and the trajectory of the nucleophilic attack, which may be sterically or stereoelectronically controlled. Inspection of our collection of methods revealed that we had good methods for cis-3,5-disubstituted isoxazolidines and trans-3,6-disubstituted tetrahydro-1,2-oxazines. Inspired by earlier work involving iminium ions, methods were developed to provide the complementary trans-isoxazolidines and cis-oxazines, using an allylation reaction. This, combined with our interest in applications of hydroformylation, led to the synthesis of 5-hydroxysedamine. Venturing away from piperidines, this method was successfully applied to the synthesis of the β-amino acid antibiotic negamycin. Use of N,O-heterocycles as intermediates naturally sparked an interest in N,O-heterocycles as synthetic targets, as there are many natural products that contain the hydroxylamine moiety, often incorporated into an isoxazolidine or 1,2-oxazine ring. As the presence of the hydroxylamine moiety cannot be fully demonstrated using the usual spectroscopic methods, total synthesis can be employed to bridge this logical gap. A synthesis of raistrickindole A, utilizing an intramolecular Mitsunobu reaction of a hydroxamic acid to form a 1,2-oxazine, confirmed the structure of this diketopiperazine natural product. A synthesis of preisomide, using an aza-Michael addition to form the required 1,2-oxazine, also confirmed the structure of this natural product.

Structure‐Agnostic Bioactivity‐Driven Combinatorial Biosynthesis Reveals New Antidiabetic and Anticancer Triterpenoids

Although combinatorial biosynthesis can dramatically expand the chemical structures of bioactive natural products to identify molecules with improved characteristics, progress in this direction has been hampered by the difficulty in isolating and characterizing the numerous produced compounds. This challenge could be overcome with improved designs that enable the analysis of the bioactivity of the produced metabolites ahead of the time‐consuming isolation procedures. Herein, we showcase a structure‐agnostic bioactivity‐driven combinatorial biosynthesis workflow that introduces bioactivity assessment as a selection‐driving force to guide iterative combinatorial biosynthesis rounds towards enzyme combinations with increasing bioactivity. We apply this approach to produce triterpenoids with potent bioactivity against PTP1B, a promising molecular target for diabetes and cancer treatment. We demonstrate that the bioactivity‐guided workflow can expedite the combinatorial process by enabling the narrowing down of more than 1000 possible combinations to only five highly potent candidates. By focusing the isolation and structural elucidation effort on only these five strains, we reveal 20 structurally diverse triterpenoids, including four new compounds and a novel triterpenoid‐anthranilic acid hybrid, as potent PTP1B inhibitors. This workflow expedites hit identification by combinatorial biosynthesis and is applicable to many other types of bioactive natural products, therefore providing a strategy for accelerated drug discovery.

Structure‐Agnostic Bioactivity‐Driven Combinatorial Biosynthesis Reveals New Antidiabetic and Anticancer Triterpenoids

Although combinatorial biosynthesis can dramatically expand the chemical structures of bioactive natural products to identify molecules with improved characteristics, progress in this direction has been hampered by the difficulty in isolating and characterizing the numerous produced compounds. This challenge could be overcome with improved designs that enable the analysis of the bioactivity of the produced metabolites ahead of the time‐consuming isolation procedures. Herein, we showcase a structure‐agnostic bioactivity‐driven combinatorial biosynthesis workflow that introduces bioactivity assessment as a selection‐driving force to guide iterative combinatorial biosynthesis rounds towards enzyme combinations with increasing bioactivity. We apply this approach to produce triterpenoids with potent bioactivity against PTP1B, a promising molecular target for diabetes and cancer treatment. We demonstrate that the bioactivity‐guided workflow can expedite the combinatorial process by enabling the narrowing down of more than 1000 possible combinations to only five highly potent candidates. By focusing the isolation and structural elucidation effort on only these five strains, we reveal 20 structurally diverse triterpenoids, including four new compounds and a novel triterpenoid‐anthranilic acid hybrid, as potent PTP1B inhibitors. This workflow expedites hit identification by combinatorial biosynthesis and is applicable to many other types of bioactive natural products, therefore providing a strategy for accelerated drug discovery.

Synthesis and Structure Revision of Securingine E.

Chemical synthesis plays a crucial role in confirming and revising the structures of natural products. Through meticulous synthetic efforts, NMR spectroscopic and single-crystal X-ray diffraction analyses, DFT calculations, and mass spectrometric investigations, we revised the structure of securingine E. The revised structure of securingine E was unambiguously confirmed by its chemical synthesis.

Discovery and Folding Dynamics of a Fused Bicyclic Cysteine Knot Undecapeptide from the Marine Sponge Halichondria bowerbanki.

We describe the discovery and structure of an undecapeptide natural product from a marine sponge, termed halichondamide A, that is morphed into a fused bicyclic ring topology via two disulfide bonds. Molecular dynamics simulations allow us to posit that the installation of one disulfide bond biases the intermediate peptide conformation and predisposes the formation of the second disulfide bond. The natural product was found to be mildly cytotoxic against liver and breast cancer cell lines.

Synthesis and antitumor activity of new flavonoid hybrid peptidomimetics

To discover new antitumor drugs based on the structure of natural products, two series of d-2-Phenylglycine/D-Leucine hybridized isoflavone derivatives were synthesized, and their anti-proliferation activities against human cancer cells were evaluated in vitro. Most target compounds exhibit potent anti-proliferative activity against HeLa cells, among which the inhibitory ability of compound 8 s is close to the positive control. Compound 8 s showed significant broad-spectrum inhibitory activity against cancer cells (HeLa, MCF-7, MDA-MB231, and H460 cells) with IC50 values of 1.94±0.26 µM, 4.75±0.38 µM, 8.56±0.19 µM, and 4.36±0.11 µM, respectively. Furthermore, compound 8 s was discovered to have certain inhibitory effects on HeLa cell proliferation, apoptosis, invasion, and migration. Molecular docking experiments and in vitro enzyme inhibition assays revealed that 8 s binds to APN and inhibits its enzyme activity, which is likely a key factor contributing to its antitumor effects. Altogether, this study proposes compound 8 s as a new lead with great promise for further antitumor research.

QNMR in natural products: practical approaches. What nobody tells you before starting your qNMR study!

NMR (Nuclear Magnetic Resonance) spectroscopy is a well-established technique for elucidating the structure and composition of Natural Products (NP). However, while NMR spectra offer qualitative insights, there is often a growing demand within the NP research community for quantitative analysis using NMR techniques. Unfortunately, this demand is sometimes met with misconceptions and lacks the methodological rigor typically associated with analytical procedures, particularly concerning validation and mandatory adjustments of quantitative NMR (qNMR) parameters. Therefore, this minireview highlights the practical approaches concerning preparation and validation for qNMR analyses of plant extracts. Specifically, we provide a concise protocol detailing experimental settings crucial for ensuring the accuracy and reliability of quantitative measurements. It is noteworthy that such guidance is often absent in existing literature, and our minireview wants to bridge this gap by offering clear methodological recommendations.

Characterization of HphA: The First Enzyme in the Homologation Pathway of l-Phenylalanine and l-Tyrosine.

Homologation of amino acids is the insertion or deletion of a methylene group to their side chain, which is a relatively uncommon chemical transformation observed in peptide natural product (NP) structure. Homologated amino acids can potentially make the NP more stable in a biological system, but its biosynthesis is yet to be understood. This study biochemically characterized the first of three unexplored enzymes in the homologation pathway of l-phenylalanine and l-tyrosine. Previously proposed reactions catalyzed by HphA were confirmed by reversed-phase high-performance liquid chromatography and tandem mass spectrometry analysis. The substrate profile and kinetic parameters showed high selectivity for the natural substrates and their close analogs. The comparability of HphA to homologous enzymes in primary metabolic pathways, 2-isopropylmate synthase and homocitrate synthase which are involved in l-leucine and l-lysine biosynthesis, respectively, was validated by bioinformatical and site-directed mutagenesis studies. The knowledge obtained from this study has deepened the understanding of the homologation of amino acids, which can lead to future combinatorial biosynthesis and metabolic engineering studies.

Gut microbiome-derived hydrolases-an underrated target of natural product metabolism.

In recent years, there has been increasing interest in studying gut microbiome-derived hydrolases in relation to oral drug metabolism, particularly focusing on natural product drugs. Despite the significance of natural product drugs in the field of oral medications, there is a lack of research on the regulatory interplay between gut microbiome-derived hydrolases and these drugs. This review delves into the interaction between intestinal microbiome-derived hydrolases and natural product drugs metabolism from three key perspectives. Firstly, it examines the impact of glycoside hydrolases, amide hydrolases, carboxylesterase, bile salt hydrolases, and epoxide hydrolase on the structure of natural products. Secondly, it explores how natural product drugs influence microbiome-derived hydrolases. Lastly, it analyzes the impact of interactions between hydrolases and natural products on disease development and the challenges in developing microbial-derived enzymes. The overarching goal of this review is to lay a solid theoretical foundation for the advancement of research and development in new natural product drugs and personalized treatment.

Psammaplin A analogues with modified disulfide bond targeting histone deacetylases: Synthesis and biological evaluation

Psammaplin A (PsA), a symmetrical bromotyrosine-derived disulfide marine metabolite, has been reported could inhibit HDAC1/2/3 through its thiol monomer. Inspired by the disuflide bond structure of this marine natural product, we designed and synthesized a series of PsA analogues, in which the disulfide bond of PsA was replaced with diselenide bond or cyclic disulfide/diselenide/selenenylsulfide motifs. We also studied the HDAC inhibition, cell growth inhibition, and apoptosis induction of these PsA analogues. The results showed that, all the synthetic diselenide analogues and cyclic selenenyl sulfide compounds exhibited better antiproferative activity than their counterpart of disulfide analogues. Among the prepared analogues, diselenide analogue P-503 and P-116 significantly increased the ability of inhibiting HDAC6 and induced apoptosis and G2/M cell cycle arrest. However, cyclic selenenylsulfides analogues P-111 lost its HDAC inhibitory ability and exhibited no effect on cell cycle and apoptosis, indicating that the anti-proliferative mechanism of cyclic selenenylsulfides analogues has changed.

A natural diphenolic glucoside, sonnerphenolic C: Chemical synthesis, structural revision, redox transformation, and identification as an antioxidant

To investigate the redox o-hydroxylation of epirhododendrin (1) with tyrosinase and vitamin C, the possible product, sonnerphenolic C (2), and its epimer, tripodantoside (3), were synthesized for the first time via key steps including glycosylation and epimeric separation. The NMR data of synthetic compounds 2 and 3 were completely consistent with those of natural products 2 and 3, respectively. However, the specific rotation value of synthesized 2 (−15.5, c 1.8 in MeOH) was different from that of the previously reported data (+33.4, c 1.8 in MeOH) of natural product 2. L-Glucoside 5, the enantiomer of 2, was successively prepared through a similar synthetic route using l-glucose as the sugar material. The specific rotation value of 5 was recorded as +18.5 (c 1.8 in MeOH), indicating that the structure of natural product 2 should be revised to that of 5. Additionally, 1 and its epimer rhododendrin (4), were concisely synthesized using the same steps for 2 and 3. The initially proposed redox transformation of 1 to 2 was confirmed by the analysis of the reaction mixture with 1, tyrosinase, and vitamin C. Furthermore, 2 was newly identified in Acer nikoense extract as a natural antioxidant by HPLC and 2,2-diphenyl-1-picrylhydrazyl radical scavenging experiments.

Calcium complexes with sulfonic acid-containing flavonoids from the fruits of Phyllanthus acidus

Two rare flavonoid-sulfonic acids complexed with calcium ions, Ca (II)-6‑methoxy-8- sulfonic acid-naringenin complexes and Ca (II)-8-sulfonic acid-isoprunetin complexes, were isolated from the fruits of Phyllanthus acidus (L.) Skeels (Phyllanthaceae). Their planar structures were unambiguously established by extensive interpretation of the HRESIMS, 1D and 2D NMR data, and comparison to the literature data. The single crystal X-ray diffraction analysis revealed the location of sulfonic acid group on flavonoid C-8 position and the existence of metal atom in molecules, which was confirmed further to be calcium by elemental analysis. The two molecules represent the first examples of sulfonic flavonoids coordinated with calcium ions from the natural products. This example enriched the variety of natural product structures. All the isolates were evaluated for their antioxidant and anti-inflammatory activity.

One-pot synthesis of cysteine-rich peptide via ‘2,2’-dithiobispyridine’ mediated sulfur exchange reaction

The cyclization of polypeptides confers enhanced stability, specificity, binding affinity, and cell permeability, making it a common feature in the backbone structure of natural products. Disulfide bonds are widely found in active peptides and play a crucial role in maintaining their secondary structure. In this study, we present a sulfur exchange reaction-based method for constructing disulfide bonds using 2,2′-dithiobis(5-nitropyridine) as a mediator. This method exhibits excellent substrate adaptability and compatibility with conventional functional groups. It also demonstrates rapid reaction efficiency, allowing successful disulfide bond formation under various pH conditions. Moreover, the products and additives can be easily separated, showing the potential of this method for screening disulfide bond-rich peptides in future research.

Natural Products That Contain Higher Homologated Amino Acids.

This review focuses on discussing natural products (NPs) that contain higher homologated amino acids (homoAAs) in the structure as well as the proposed and characterized biosynthesis of these non-proteinogenic amino acids. Homologation of amino acids includes the insertion of a methylene group into its side chain. It is not a very common modification found in NP biosynthesis as approximately 450 homoAA-containing NPs have been isolated from four bacterial phyla (Cyanobacteria, Actinomycetota, Myxococcota, and Pseudomonadota), two fungal phyla (Ascomycota and Basidiomycota), and one animal phylum (Porifera), except for a few examples. Amino acids that are found to be homologated and incorporated in the NP structures include the following ten amino acids: alanine, arginine, cysteine, isoleucine, glutamic acid, leucine, phenylalanine, proline, serine, and tyrosine, where isoleucine, leucine, phenylalanine, and tyrosine share the comparable enzymatic pathway. Other amino acids have their individual homologation pathway (arginine, proline, and glutamic acid for bacteria), likely utilize the primary metabolic pathway (alanine and glutamic acid for fungi), or have not been reported (cysteine and serine). Despite its possible high potential in the drug discovery field, the biosynthesis of homologated amino acids has a large room to explore for future combinatorial biosynthesis and metabolic engineering purpose.

Visible-Light-Mediated Three-Component Strategy for the Synthesis of Isoxazolines and Isoxazoles.

Isoxazolines and isoxazoles commonly serve as core structures of many therapeutic agents and natural products. However, the metal-free and catalysis-free strategy for the synthesis of these privileged motifs at room temperature remains a challenging task. Herein, we report a three-component strategy to afford diverse isoxazolines and isoxazoles via [3 + 2] cycloadditions of in situ-formed nitronates and olefins/alkynes under visible-light irradiation.

Exploring Type II Diabetes Inhibitors from Genus Daphne Plant-species: An Integrated Computational Study.

Plant species of the genus Daphne clasps a historical background with a potential source of bioactive phytochemicals such as flavonoids and daphnodorins. These compounds manifest a significant chemotaxonomic value in drug discovery. Their flair comprehensive pharmacological, phytochemical, biological, catalytic, and clinical utilities make them exclusively unique. This study was conducted to investigate the optimization and structure-based virtual screening of these peculiar analogs. The majority of the active constituents of medicines are obtained from natural products. Previously, before the invention of virtual screening methods or techniques, almost 80% of drugs were obtained from natural resources. Comparing reported data to drug discovery from 1981 to 2007 signifies that half of the FDA-approved drugs are obtained from natural resources. It has been reported that structures of natural products that have particularities of structural diversity, biochemical specification, and molecular properties make them suitable products for drug discovery. These products basically have unique chiral centers which increase their structural complexity than the synthesized drugs. This work aimed to probe the use of daphnodorins analogs for the first time as antidiabetic inhibitors based on significant features and to determine the potential of daphnodorin analogs as antidiabetic inhibitors through computational analysis and structure-based virtual screening. A dataset of 38 compounds was selected from different databases, including PubChem and ZINC, for computational analysis, and optimized compounds were docked against various co-crystallized structures of inhibitors, antagonists, and receptors which were downloaded from PDB by using AutoDock Vina (by employing Broyden-Fletcher-Goldfarb-Shanno method), Discovery studio visualizer 2020, PYMOL (Schrodinger). Docking results were further validated by Molecular dynamic simulation and MM-GBSA calculation. Quantitative structure-activity relationship (QSAR) was reported by using Gaussian 09W by intimating Density Functional Theory (DFT). Using this combination of multi-approach computational strategy, 14 compounds were selected as potential exclusive lead compounds, which were analyzed through ADMET studies to pin down their druglike properties and toxicity. At significant phases of drug design approaches regular use of molecular docking has helped to promote the separation of important representatives from 38 pharmaceutically active compounds by setting a threshold docking score of -9.0 kcal/mol which was used for their exposition. Subsequently, by employing a threshold it was recognized that 14 compounds proclaimed this threshold for antidiabetic activity. Further, molecular dynamic simulation, MM-GBSA, ADMET, and DFT results screened out daphnegiralin B4 (36) as a potential lead compound for developing antidiabetic agents. Our analysis took us to the conclusion that daphnegiralin B4 (36) among all ligands comes out to be a lead compound having drug-like properties among 38 ligands being non-carcinogenic and non-cytotoxic which would benefit the medical community by providing significant drugs against diabetes. Pragmatic laboratory investigations identified a new precursor to open new doors for new drug discovery.

Napyradiomycin B4 Suppresses RANKL-Induced Osteoclastogenesis and Prevents Alveolar Bone Destruction in Experimental Periodontitis.

The unique structure and beneficial biological properties of marine natural products have drawn interest in drug development. Here, we examined the therapeutic potential of napyradiomycin B4 isolated from marine-derived Streptomyces species for osteoclast-related skeletal diseases. Bone marrow-derived macrophages were treated with napyradiomycin B4 in an osteoclast-inducing medium, and osteoclast formation, osteoclast-specific gene expression, and nuclear factor of activated T-cells cytoplasmic 1 (NFATc1) localization were evaluated using tartrate-resistant acid phosphatase staining, real-time PCR, and immunostaining, respectively. Phosphorylation levels of signaling proteins were assessed by immunoblot analysis to understand the molecular action of napyradiomycin B4. The in vivo efficacy of napyradiomycin B4 was examined under experimental periodontitis, and alveolar bone destruction was evaluated by microcomputed tomography (micro-CT) and histological analyses. Among the eight napyradiomycin derivatives screened, napyradiomycin B4 considerably inhibited osteoclastogenesis. Napyradiomycin B4 significantly suppressed the receptor activator of nuclear factor-κB ligand (RANKL)-induced osteoclast formation and disrupted the expression of NFATc1 and its target genes. Mitogen-activated extracellular signal-regulated kinase (MEK) and extracellular signal-regulated kinase (ERK) phosphorylation levels were reduced by napyradiomycin B4 in response to RANKL. Under in vivo experimental periodontitis, napyradiomycin B4 significantly attenuated osteoclast formation and decreased the distance between the cementoenamel junction and alveolar bone crest. Our findings demonstrate the antiosteoclastogenic activity of napyradiomycin B4 by inhibiting the RANKL-induced MEK-ERK signaling pathway and its protective effect on alveolar bone destruction.

Design, synthesis and biological evaluation of tanshinone IIA derivatives as NLRP3 inflammasome inhibitors

Natural product structures have long provided valuable pharmacophores and even candidates for drug discovery. Tanshinone scaffold showed moderately inhibitory activity in NLRP3 inflammasome/IL-1β pathway. Herein, we designed a series of derivatives on different regions of Tanshinone IIA (TNA) scaffold. The biological evaluation identified compound T10, a scaffold hybrid of TNA and salicylic acid, as a potent NLRP3 inflammasome inhibitor. Mechanistically, T10 inhibits the production of ROS and prevents NLRP3 inflammasome-dependent IL-1β production. In addition, treatment with T10 significantly attenuated inflammatory response in DSS-induced peritonitis. Our work describes a potential tanshinone-based derivative, which needs to be further structurally optimized as NLRP3 inflammasome inhibitors for treating inflammatory disorders.

Structures and Biological Activities of Secondary Metabolites from Xylaria spp.

The fungus genus Xylaria is an important source of drug discoveries in scientific fields and in the pharmaceutical industry due to its potential to produce a variety of structured novel and bioactive secondary metabolites. This review prioritizes the structures of the secondary metabolites of Xylaria spp. from 1994 to January 2024 and their relevant biological activities. A total of 445 new compounds, including terpenoids, nitrogen-containing compounds, polyketides, lactones, and other classes, are presented in this review. Remarkably, among these compounds, 177 compounds show various biological activities, including cytotoxic, antimicrobial, anti-inflammatory, antifungal, immunosuppressive, and enzyme-inhibitory activities. This paper will guide further investigations into the structures of novel and potent active natural products derived from Xylaria and their potential contributions to the future development of new natural drug products in the agricultural and medicinal fields.