Class Of Natural Products Research Articles

Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters.

The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We amalgamated a pipeline of tools to predict BGCs based on shared promoter motifs and located 3800 ICS BGCs in 3300 genomes, making ICS BGCs the fifth largest class of specialized metabolites compared to canonical classes found by antiSMASH. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1/2 gene cluster family (GCF), which was prior only studied in yeast, is present in ∼30% of all Ascomycetes. The dit variety ICS exhibits greater similarity to bacterial ICS than other fungal ICS, suggesting a potential convergence of the ICS backbone domain. The evolutionary origins of the dit GCF in Ascomycota are ancient and these genes are diversifying in some lineages. Our results create a roadmap for future research into ICS BGCs. We developed a website (https://isocyanides.fungi.wisc.edu/) that facilitates the exploration and downloading of all identified fungal ICS BGCs and GCFs.

Bifurcate evolution of quinone synthetases in basidiomycetes

BackgroundThe terphenylquinones represent an ecologically remarkable class of basidiomycete natural products as they serve as central precursors of pigments and compounds that impact on microbial consortia by modulating bacterial biofilms and motility. This study addressed the phylogenetic origin of the quinone synthetases that assemble the key terphenylquinones polyporic acid and atromentin.ResultsThe activity of the Hapalopilus rutilans synthetases HapA1, HapA2 and of Psilocybe cubensis PpaA1 were reconstituted in Aspergilli. Liquid chromatography and mass spectrometry of the culture extracts identified all three enzymes as polyporic acid synthetases. PpaA1 is unique in that it features a C-terminal, yet catalytically inactive dioxygenase domain. Combined with bioinformatics to reconstruct the phylogeny, our results demonstrate that basidiomycete polyporic acid and atromentin synthetases evolved independently, although they share an identical catalytic mechanism and release structurally very closely related products. A targeted amino acid replacement in the substrate binding pocket of the adenylation domains resulted in bifunctional synthetases producing both polyporic acid and atromentin.ConclusionsOur results imply that quinone synthetases evolved twice independently in basidiomycetes, depending on the aromatic α-keto acid substrate. Furthermore, key amino acid residues for substrate specificity were identified and changed which led to a relaxed substrate profile. Therefore, our work lays the foundation for future targeted enzyme engineering.

Asymmetric Total Syntheses of Macroline-Type Alkaloids Alstomicine and Alstofolinine A

AbstractMacroline-type monoterpenoid indole alkaloids represent a fascinating class of natural products with polycyclic structures, diverse biological and pharmacological activities. Herein the asymmetric total syntheses of two of this type alkaloids, (–)-Alstomicine and (–)-Alstofolinine A are reported. Notably, these two alkaloids are divergently synthesized from a common indole-fused azabicyclo[3.3.1]nonane intermediate, which was easily obtained via a Mannich-type cyclization. An SmI2-mediated Reformatsky reaction and a Pd-catalyzed carbonylative lactonization are employed to construct the lactone moieties presented in Alstomicine and Alstofolinine A, respectively.

Steroid‐Hymecromone Conjugates with Improved Antiproliferative and Antimicrobial Potential: Synthesis, Biological Evaluation, and in silico ADME Prediction

AbstractIn this study, hymecromone with known therapeutic aspects was conjugated with steroids a class of natural products that widely exhibited broad biological functions. Cholic acid, diosgenin, cholesterol, DHEA, and testosterone were selected as steroid moiety, each of which has a different biological mechanism of action. This study focused on developing novel conjugates that can be used as multi‐targeted drugs for treating various diseases. All conjugates were evaluated in vitro for their antiproliferative and antimicrobial activities and discussed for the structure‐activity relationship. The conjugates 5 and 6 exhibited comparable cytotoxic effects to reference drugs against cancer cell lines (K562, MCF‐7, and HeLa) while showing no toxicity against healthy cells (L929). Conjugates 7 and 5 demonstrated antibacterial activity against Gram‐positive and Gram‐negative bacteria, with lower minimum inhibitory concentration (MIC) values than the standard ciprofloxacin drug. Conjugate 6, On the other hand, had the lowest MIC value against the fungus, comparable to that of the standard drug ketoconazole. The physicochemical and pharmacokinetic properties of conjugates were in silico computed and evaluated. Overall, the outputs of this study suggest that these conjugates have promising potential as therapeutic agents, offering a multi‐targeted approach for the treatment of various diseases.

Chemoproteomic Profiling Reveals that Anticancer Natural Product Dankastatin B Covalently Targets Mitochondrial VDAC3.

Chlorinated gymnastatin and dankastatin alkaloids derived from the fungal strain Gymnascella dankaliensis have been reported to possess significant anticancer activity but their mode of action is unknown. These members possess electrophilic functional groups that can might undergo covalent bond formation with specific proteins to exert their biological activity. To better understand the mechanism of action of this class of natural products, we mapped the proteome-wide cysteine reactivity of the most potent of these alkaloids, dankastatin B, by using activity-based protein profiling chemoproteomic approaches. We identified a primary target of dankastatin B in breast cancer cells as cysteine C65 of the voltage-dependent anion-selective channel on the outer mitochondrial membrane VDAC3. We demonstrated direct and covalent interaction of dankastatin B with VDAC3. VDAC3 knockdown conferred hypersensitivity to dankastatin B-mediated antiproliferative effects in breast cancer cells, thus indicating that VDAC3 was at least partially involved in the anticancer effects of this natural product. Our study reveals a potential mode of action of dankastatin B through covalent targeting of VDAC3 and highlights the utility of chemoproteomic approaches in gaining mechanistic understanding of electrophilic natural products.

Extraction, Isolation, Characterization, and Bioactivity of Polypropionates and Related Polyketide Metabolites from the Caribbean Region.

The Caribbean region is a hotspot of biodiversity (i.e., algae, sponges, corals, mollusks, microorganisms, cyanobacteria, and dinoflagellates) that produces secondary metabolites such as polyketides and polypropionates. Polyketides are a diverse class of natural products synthesized by organisms through a biosynthetic pathway catalyzed by polyketide synthase (PKS). This group of compounds is subdivided into fatty acids, aromatics, and polypropionates such as macrolides, and linear and cyclic polyethers. Researchers have studied the Caribbean region to find natural products and focused on isolation, purification, structural characterization, synthesis, and conducting biological assays against parasites, cancer, fungi, and bacteria. These studies have been summarized in this review, including research from 1981 to 2020. This review includes about 90 compounds isolated in the Caribbean that meet the structural properties of polyketides. Out of 90 compounds presented, 73 have the absolute stereochemical configuration, and 82 have shown biological activity. We expect to motivate the researchers to continue exploring the Caribbean region's marine environments to discover and investigate new polyketide and polypropionate natural products.

Sesquiterpenoids from Meliaceae Family and Their Biological Activities.

Sesquiterpenoids, an important class of natural products possessing three isoprene-derived units, are widely distributed across plants and have a variety of biological activities. All sesquiterpenoids are derived from farnesyl pyrophosphate (FPP), a biosynthesis precursor that can form various carbon skeletons. In order to provide a reference for further research and development of these compounds, this review focused on the increasing number of isolated and volatile sesquiterpenoids found to be produced by plants of the Meliaceae family between 1968 and 2023. The related articles were collected from SciFinder, Google Scholar, and PubMed. According to a literature review, several studies were started for more than 55 years on the plant's stem barks, twigs, leaves, flowers, seeds, and pericarps, where approximately 413 sesquiterpenoid compounds from several groups such as eudesmane, aromadendrane, cadinane, guaiane, bisabolane, furanoeremophilane, humulene, germacrane, and oppositane-type were isolated and identified with some minor products. Additionally, the hypothetical route of sesquiterpenoids biosynthesis from this family was identified, and eudesmane-type was reported to be 27% of the total compounds. The antimicrobial, antidiabetic, antioxidant, antiplasmodial, antiviral, and cytotoxic activities of the isolated compounds and major volatile sesquiterpenoids constituent on essential oil were also evaluated. The result showed the fundamental of using the sesquiterpenoid compounds from the Meliaceae family in traditional medicine and the discovery of new drugs.

Recent bioanalytical methods for the isolation of bioactive natural products from genus Codonopsis.

Chromatography and spectroscopy are nowadays well-validated techniques allowing to isolate and purify different class of natural products from the genus Codonopsis. Several categories of phytochemicals with drug like properties have been selectively extracted, isolated, characterised by this methodology. The present review aims to provide up-to-date and comprehensive information on the chromatography, phytochemistry and pharmacology of natural products of Codonopsis with an emphasis on the search for natural products having various biological activities and the semi-synthetic derivatives of bioactive ones and to highlight current gaps in knowledge. A literature search was performed in the SciFinder Scholar, PubMed, Medline, and Scopus databases. During the period covered in this review, several classes of compounds have been reported from genus Codonopsis. Codonopsis pilosula and Codonopsis lanceolata are the most popular in the genus especially as per phytochemical and bioactive studies. Phytochemical investigation demonstrates that Codonopsis species contain mainly xanthones, flavonoids, alkaloids, polyacetylenes, phenylpropanoids, triterpenoids and polysaccharides, which contribute to numerous bioactivities. The major bioactive compounds isolated were used for semi-synthetic modification to increase the chance to discover lead compound. It can be concluded that genus Codonopsis has been used as traditional medicines and food materials around the world over years due to chemical constituents with diverse structural types, exhibiting extensive pharmacological activities in immune system, blood system, cardiovascular system, central nervous system, digestive system, and so forth, with almost no obvious toxicity and side effect. Therefore, Codonopsis can be used as a promising ethnopharmacological plant source.

Discovery of Class I Diterpene Cyclases Producing a Tetracyclic Cephalotene Skeleton in Plum Yews

The cephalotane diterpenoids (e.g., harringtonolide, cephanolides) from plum yews (Cephalotaxus) represent a rare class of tetracyclic C20 and C19 natural products with intriguing bioactivities. Here, we report the discovery and functional characterization of multiple diterpene synthases (diTPSs) from Cephalotaxus harringtonia and Cephalotaxus hainanensis. In addition to diTPSs responsible for ent-kaurene and biformene biosynthesis, two class I cephalotene synthases (CSs) were found to directly cyclize geranylgeranyl diphosphate (GGPP) into a unique cephalot-12-ene skeleton, which is a crucial step in the biogenesis of cephalotane diterpenoids. A plausible biosynthetic mechanism en route to tetracyclic ring formation was proposed based on an isotope labeling experiment combined with quantum chemical calculations. Site-directed mutagenesis indicated that residue F625 in CS is a key switch of diversifying the hydrocarbon backbone to bicyclic verticillene and tricyclic taxadiene. Altogether this report provides insight into the carbocation cascade reaction driven by active sites in class I diTPSs, promotes our understanding of how chemical diversity originates and evolves in gymnosperms, and lays a solid foundation for future investigation of Cephalotaxus diterpene metabolites.

Metabolic Engineering of Candida glycerinogenes for Sustainable Production of Geraniol.

Geraniol is a class of natural products that are widely used in the aroma industry due to their unique aroma. Here, to achieve the synthesis of geraniol and alleviate the intense competition from the yeast ergosterol pathway, a transcription factor-mediated ergosterol feedback system was developed in this study to autonomously regulate ergosterol metabolism and redirect carbon flux to geraniol synthesis. In addition, the modification of ergosterol-responsive promoters, the optimization of transcription factor expression intensity, and stepwise metabolic engineering resulted in a geraniol titer of 531.7 mg L-1. For sustainable production of geraniol, we constructed a xylose assimilation pathway in Candida glycerinogenes (C. glycerinogenes). Then, the xylose metabolic capacity was ameliorated and the growth of the engineered strain was rescued by activating the pentose phosphate (PP) pathway. Finally, we obtained 1091.6, 862.4, and 921.8 mg L-1 of geraniol in a 5 L bioreactor by using pure glucose, simulated wheat straw hydrolysates, and simulated sugarcane bagasse hydrolysates, with yields of 47.5, 57.9, and 59.1 mg g-1 DCW, respectively. Our study demonstrated that C. glycerinogenes has the potential to produce geraniol from lignocellulosic biomass, providing a powerful tool for the sustainable synthesis of other valuable monoterpenes.

The discovery of 3-fluoroalkyl indoles as potential antifungal agents to control tomato gray mold caused by Botrytis cinerea

Indole derivatives are a class of important heterocyclic natural products, which usually possess extensive bioactivities. In order to develop indole derivatives as potential fungicidal agents, a series of 3-perfluoroalkyl indole derivatives were prepared and investigated for their antifungal activities. The present data revealed that compound 3a was effective against eight test phytopathogenic fungi in vitro, and had the highest antifungal activity against B. cinerea, with an EC50 value of 0.94 µg/mL. Additionally, this indole exhibited excellent protective and curative efficacies against tomato gray mold in vivo. A possible mechanism of antifungal action for this compound was also explored. This study demonstrated that 3-perfluoroalkyl indole derivatives could potentially have utility as botanical fungicides for the management of phytopathogenic fungi.

Ni-catalyzed unnatural prenylation and cyclic monoterpenation of heteroarenes with isoprene

Terpenoids, such as hemiterpenoids and monoterpenoids, are the largest class of natural products, which widely exist in plants and marine organisms. Herein, a divergent strategy is developed for the introduction of unnatural prenyl and cyclic monoterpene skeleton through relay catalysis from basic feedstock isoprene. In the presence of catalytic amount of base, the unnatural prenylation of heteroarenes proceeds through Markovnikov addition onto isoprene with less hindered NHC (IMes) ligand under Ni catalysis. With the aid of extra base, a further in situ isomerization of Markovnikov addition products delivered unnatural hemiterpenoids with tetrasubstituted alkene motif in high selectivities. It was found that bulky NHC (IPr) ligand could further promote sequential hydroheteroarylation between isoprene dimers and heterocycles and gave monoterpenoids in one pot. This work provides a new strategy for regulating the synthesis of hemiterpenoids and monoterpenoids.

The campfire stories of Russell Marker, a pioneer of chemistry

The maverick American chemist Russell Earl Marker (1902–1995) is known for his studies on the fragmentation of organic mercury compounds, establishing the concept of the octane number, investigating the rearrangements of hydrocarbons and exploring the relationship between optical rotation and the configuration of organic compounds. His greatest achievement, however, is the elaboration of seminal isolation and synthetic methods of an important class of natural products that helped found a new industry, based on the pharmaceutical chemistry of steroids. The nomadic life of this extraordinary man demonstrates that the enormous obstacles thwarting the progress of science and technology can be surmounted by serendipity, acumen and devotion. However, his premature retirement from chemistry is a warning sign that every scientist is vulnerable and even the toughest man's perseverance can fade if the conditions worsen.

Fragmentation and [4 + 3] cycloaddition in sodorifen biosynthesis.

Terpenes constitute the largest class of natural products. Their skeletons are formed by terpene cyclases (TCs) from acyclic oligoprenyl diphosphates through sophisticated enzymatic conversions. These enzyme reactions start with substrate ionization through diphosphate abstraction, followed by a cascade reaction via cationic intermediates. Based on isotopic-labelling experiments in combination with a computational study, the cyclization mechanism for sodorifen, a highly methylated sesquiterpene from the soil bacterium Serratia plymuthica, was resolved. A peculiar problem in its biosynthesis lies in the formation of several methyl groups from chain methylene carbons. The underlying mechanism involves a methyltransferase-mediated cyclization and unprecedented ring contraction with carbon extrusion from the chain to form a methyl group. A terpene cyclase subsequently catalyses a fragmentation into two reactive intermediates, followed by hydrogen transfers between them and recombination of the fragments by [4 + 3] cycloaddition. This study solves the intricate mechanistic problem of extra methyl group formation in sodorifen biosynthesis.

Enantioselective Intramolecular Decarboxylative C-H Bond Func-tionalization of Quinazolinones with Amino Acids by Visible Light Photoredox Catalysis.

The direct visible light-mediated intramolecular decarboxylative C-H functionalization of Csp2 -H bond adjacent to the nitrogen of a heteroarene has been achieved by iridium-catalyzed photodecarboxylative radical cyclization. This method offers rapid entry to the synthesis of quinazolinone scaffolds from easily accessible starting materials. The newly developed protocol is mild, operationally simple, oxidant free and general. The utility of this unique Csp3 -Csp2 bond forming reaction has been demonstrated in the syntheses of Circumdatin, Sclerotigenine and Benzomalvin A class of quinazolinone natural products and their congeners. The present work represents an interesting example of use of memory of chirality in decarboxylative C-C bond forming enantioselective photoredox reaction.

Natural Products and Derivatives as Potential Zika virus Inhibitors: A Comprehensive Review.

Zika virus (ZIKV) is an arbovirus whose infection in humans can lead to severe outcomes. This article reviews studies reporting the anti-ZIKV activity of natural products (NPs) and derivatives published from 1997 to 2022, which were carried out with NPs obtained from plants (82.4%) or semisynthetic/synthetic derivatives, fungi (3.1%), bacteria (7.6%), animals (1.2%) and marine organisms (1.9%) along with miscellaneous compounds (3.8%). Classes of NPs reported to present anti-ZIKV activity include polyphenols, triterpenes, alkaloids, and steroids, among others. The highest values of the selectivity index, the ratio between cytotoxicity and antiviral activity (SI = CC50/EC50), were reported for epigallocatechin gallate (SI ≥ 25,000) and anisomycin (SI ≥ 11,900) obtained from Streptomyces bacteria, dolastane (SI = 1246) isolated from the marine seaweed Canistrocarpus cervicorni, and the flavonol myricetin (SI ≥ 862). NPs mostly act at the stages of viral adsorption and internalization in addition to presenting virucidal effect. The data demonstrate the potential of NPs for developing new anti-ZIKV agents and highlight the lack of studies addressing their molecular mechanisms of action and pre-clinical studies of efficacy and safety in animal models. To the best of our knowledge, none of the active compounds has been submitted to clinical studies.

Developing TeroENZ and TeroMAP modules for the terpenome research platform TeroKit.

Terpenoids and their derivatives are collectively known as the terpenome and are the largest class of natural products, whose biosynthesis refers to various kinds of enzymes. To date, there is no terpenome-related enzyme database, which is a desire for enzyme mining, metabolic engineering and discovery of new natural products related to terpenoids. In this work, we have constructed a comprehensive database called TeroENZ (http://terokit.qmclab.com/browse_enz.html) containing 13 462 enzymes involved in the terpenoid biosynthetic pathway, covering 2541 species and 4293 reactions reported in the literature and public databases. At the same time, we classify enzymes according to their catalytic reactions into cyclase, oxidoreductase, transferase, and so on, and also make a classification according to species. This meticulous classification is beneficial for users as it can be retrieved and downloaded conveniently. We also provide a computational module for isozyme prediction. Moreover, a module named TeroMAP (http://terokit.qmclab.com/browse_rxn.html) is also constructed to organize all available terpenoid enzymatic reactions into an interactive network by interfacing with the previously established database of terpenoid compounds, TeroMOL. Finally, all these databases and modules are integrated into the web server TeroKit (http://terokit.qmclab.com/) to shed light on the field of terpenoid research. Database URL http://terokit.qmclab.com/.

Direct Utilization of Peroxisomal Acetyl-CoA for the Synthesis of Polyketide Compounds in Saccharomyces cerevisiae.

Polyketides are a class of natural products with many applications but are mainly appealing as pharmaceuticals. Heterologous production of polyketides in the yeast Saccharomyces cerevisiae has been widely explored because of the many merits of this model eukaryotic microorganism. Although acetyl-CoA and malonyl-CoA, the precursors for polyketide synthesis, are distributed in several yeast subcellular organelles, only cytosolic synthesis of polyketides has been pursued in previous studies. In this study, we investigate polyketide synthesis by directly using acetyl-CoA in the peroxisomes of yeast strain CEN.PK2-1D. We first demonstrate that the polyketide flaviolin can be synthesized in this organelle upon peroxisomal colocalization of native acetyl-CoA carboxylase and 1,3,6,8-tetrahydroxynaphthalene synthase (a type III polyketide synthase). Next, using the synthesis of the polyketide triacetic acid lactone as an example, we show that (1) a new peroxisome targeting sequence, pPTS1, is more effective than the previously reported ePTS1 for peroxisomal polyketide synthesis; (2) engineering peroxisome proliferation is effective to boost polyketide production; and (3) peroxisomes provide an additional acetyl-CoA reservoir and extra space to accommodate enzymes so that utilizing the peroxisomal pathway plus the cytosolic pathway produces more polyketide than the cytosolic pathway alone. This research lays the groundwork for more efficient heterologous polyketide biosynthesis using acetyl-CoA pools in subcellular organelles.

Development of a Streptomyces-based system for facile thioholgamide library generation and analysis

Derivatizing natural products (NPs) is essential in structure-activity relationship (SAR) studies, compound optimization, and drug development. Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent one of the major classes of natural products. Thioholgamide represents thioamitide – a recently emerged family of RiPPs with unique structures and great potential in anticancer drug development. Although the method for generating the RiPP library by codon substitutions in the precursor peptide gene is straightforward, the techniques to perform RiPP derivatization in Actinobacteria remain limited and time-consuming. Here, we report a facile system for producing a library of randomized thioholgamide derivatives utilizing an optimized Streptomyces host. This technique enabled us to access all possible amino acid substitutions of the thioholgamide molecule, one position at a time. Out of 152 potential derivatives, 85 were successfully detected, revealing the impact of amino acid substitutions on thioholgamide post-translational modifications (PTMs). Moreover, new PTMs were observed among thioholgamide derivatives: thiazoline heterocycles, which have not yet been reported for thioamitides, and S-methylmethionine, which is very rare in nature. The obtained library was subsequently used for thioholgamide SAR studies and stability assays.

The natural product chlorotonil A preserves colonization resistance and prevents relapsing Clostridioides difficile infection

Clostridioides difficile infections (CDIs) remain a healthcare problem due to high rates of relapsing/recurrent CDIs (rCDIs). Breakdown of colonization resistance promoted by broad-spectrum antibiotics and the persistence of spores contribute to rCDI. Here, we demonstrate antimicrobial activity of the natural product class of chlorotonils against C.difficile. In contrast to vancomycin, chlorotonil A (ChA) efficiently inhibits disease and prevents rCDI in mice. Notably, ChA affects the murine and porcine microbiota to a lesser extent than vancomycin, largely preserving microbiota composition and minimally impacting the intestinal metabolome. Correspondingly, ChA treatment does not break colonization resistance against C.difficile and is linked to faster recovery of the microbiota after CDI. Additionally, ChA accumulates in the spore and inhibits outgrowth of C.difficile spores, thus potentially contributing to lower rates of rCDI. We conclude that chlorotonils have unique antimicrobial properties targeting critical steps in the infection cycle of C.difficile.