Two novel types of dimeric alkaloids were isolated from the marine sediment-derived mutant strain Saccharopolyspora erythraea SCSIO 07745/Δspo11. Among them, sacchaindol A (1) represents a previously unreported class of dimeric aminoquinolinone alkaloids, whereas sacchaindols B (2) and C [(±)-3] comprise a rare fused 6/6/5/5 tetracyclic indole alkaloid framework. Their structures were elucidated using a combination of spectroscopic analyses, single-crystal X-ray diffraction, and computational methods. Hypothetical biosynthetic pathways for 1-3 were proposed. Notably, sacchaindols C [(±)-3] exhibited anti-inflammatory activity.

Two novel types of dimeric alkaloids were isolated from the marine sediment-derived mutant strain Saccharopolyspora erythraea SCSIO 07745/Delta spo11. Among them, sacchaindol A (1) represents a previously unreported class of dimeric aminoquinolinone alkaloids, whereas sacchaindols B (2) and C [(+/-)-3] comprise a rare fused 6/6/5/5 tetracyclic indole alkaloid framework. Their structures were elucidated using a combination of spectroscopic analyses, single-crystal X-ray diffraction, and computational methods. Hypothetical biosynthetic pathways for 1-3 were proposed. Notably, sacchaindols C [(+/-)-3] exhibited anti-inflammatory activity.

Mesobuthus martensii, the source species of the traditional Chinese medicine “Quanxie”, has long been utilized for its therapeutic properties. Venom peptides are recognized as the major active molecular basis of these pharmacological activities. Despite this, their development as therapeutic agents remains poorly explored. In this study, we performed an integrated multi-omics investigation to systematically explore the venom peptides of Mesobuthus martensii. We generated a chromosome-level genome assembly of Mesobuthus martensii using third-generation sequencing technologies, yielding a genome size of 1.08 Gb with a contig N50 of 46.46 Mb. Integrated genomic and transcriptomic analyses led to the identification of 51 putative novel venom peptide candidates. From the broader venom peptide set, five lysine- and arginine-rich candidates were selected for recombinant expression and functional characterization. Functional evaluation revealed that MmTX67, MmTX106 and MmTX126 modulated coagulation-related parameters in vitro, with MmTX106 further demonstrating the most pronounced antithrombotic effect in vivo. Collectively, these findings provide novel insights into the genetic basis of bioactive substances in “Quanxie” and highlight MmTX106 as the most promising antithrombotic candidate, while providing a molecular foundation for further evaluation of other scorpion venom-derived peptide candidates.

A novel andrastin-type meroterpenoid, dfpenicimeroterpenoid A (1), featuring an unprecedented fused 6/6/6/4/5 pentacyclic skeleton is described, along with four new analogues from marine-derived fungus Penicillium sp. DF71. The structures were established by analysis of their spectroscopic data, single-crystal X-ray diffraction, and quantum chemical calculations of electronic circular dichroism spectra. Compound 2 showed significant pro-angiogenic activity at a concentration of 20 μM, based on a zebrafish model. Furthermore, a plausible biosynthetic pathway for 1 is proposed.

Eight new anthraquinone analogues, namely rishirilide E (1), galvaquinones D-F (2-4), and two pairs of enantiomers, galvaquinones G (5a/5b) and H (6a/6b), together with four known compounds, rishirilide B (7), galvaquinone A (8), lupinacidin A (9), and lupinacidin B (10), were obtained from marine-derived Micromonospora sp. SCSIO 07396 by overexpressing the phosphopantetheinyl transferase (PPTase). Based on comprehensive HRESIMS data, NMR spectroscopic analyses, X-ray diffraction, and ECD calculations, their structures and absolute configurations were unambiguously elucidated. Assays for pro-angiogenic and anti-inflammatory effects in zebrafish models combined with cytotoxicity screening against six human cancer cell lines (PANC-1, TE-1, HL60, A549, MDA-MB-231, and GSC0722), showed that 1 and 5b promoted angiogenesis at 20 μM, 4 had moderate anti-inflammatory activity at 20 μM, and 8 exhibited cytotoxic activity against GSC0722 cells, with an IC50 value of 26.4 μM.

Two new picolinic acid derivatives, ethylfusaric acid A (1) and ethylfusaric acid B (2), along with two known picolinic acid derivatives (3-4), were isolated from the culture of Rehmannia glutinosa endophytic fungus Epicoccum sorghinum SDU-F549. The chemical structures of the compounds were elucidated by the combination of 1D and 2D nuclear magnetic resonance spectroscopy and electronic circular dichroism calculations. Compounds 1-4 exhibited antibacterial activity against a panel of Staphylococcus aureus strains, with MIC values ranging from 16 to 32 μg/mL. In contrast, they showed no significant cytotoxic activity against a range of human tumor cell lines at 10 μM. Furthermore, bioinformatic analysis revealed that the bty biosynthetic gene cluster in E. sorghinum SDU-F549 is responsible for assembling the picolinic acid derivatives, enabling us to propose the biosynthetic pathways of compounds 1-4.

Seven pairs of new enantiomers, Paecilomyces A-G (1-7), were isolated from the deep-sea-derived fungus Paecilomyces sp. YD-8. Their unprecedented structures, featuring symmetric or single C8-aliphatic chain substitutions on the 1,4-epoxynaphthalene-2,3-dicarboxylic acid core, were elucidated via spectroscopic analysis, X-ray diffraction, and ECD calculations. Several enantiomers (1b, 3a, 4a/4b, and 5b) showed better antithrombotic activity at 6.25 μM than aspirin at 124.9 μM in a zebrafish model, highlighting their therapeutic potential. Moreover, plausible biosynthetic pathways of 1-7 were proposed.

Covering: up to Oct, 2025Cinnamoyl-containing non-ribosomal peptides (CCNPs) are characterized by a cinnamoyl group, which is substituted at the ortho position with an alkyl side chain and linked to a peptide scaffold, representing a structurally unique and pharmacologically promising family of microbial natural products. Here, the current knowledge of their chemical diversity, biological activities, and intricate biosynthetic mechanisms is systematically summarized. Their characteristic biosynthetic logic centers on the conserved coupling of a highly reducing type II polyketide synthase (hrPKS II) with a non-ribosomal peptide synthetase (NRPS). Particular emphasis is placed on two fundamental principles: first, the conserved pathway for cinnamoyl benzene ring formation, initiated by an isomerase and proceeding via 6π-electrocyclization catalyzed by three distinct enzymes classes, namely, YsfF (4-hydroxybenzoyl-CoA thioesterase (4-HBT)-like enzymes), Kcn17-19 (DsrE family enzyme components) and YssX/YsfX, thereby providing a reliable signature for genome mining. Second, the remarkable diversity of cinnamoyl tailoring, peptide modification, and NRPS assembly collectively offers substantial opportunities for structural diversification through combinatorial biosynthesis strategies. Elucidating these biosynthetic features has shifted the research paradigm from discovery to rational engineering. However, this shift has not yet translated into comprehensive pharmacological evaluation, as most reported activities have been only briefly assessed, and extensive studies are still needed to fully realize their therapeutic potential. This review not only consolidates recent advances but also provides a strategic framework for future research aimed at unlocking the full potential of these fascinating natural products.

Three new pyrrole alkaloids, streptopyrroles D–F (1–3), along with four known analogs (4–7) were isolated from Sea Anemone-Associated Streptomyces sp. S1502 via an OSMAC (One Strain Many Compounds)-based strategy. Their structures were elucidated through comprehensive spectroscopic analyses, including HRESIMS and 1D/2D NMR experiments (COSY, HSQC, and HMBC), and further confirmed by X-ray crystallography. Biological evaluation identified streptopyrrole (4) as an anti-MRSA (methicillin-resistant Staphylococcus aureus) agent, while 4 and 6 displayed broad-spectrum cytotoxicity and good selectivity against a panel of human cancer cell lines. Notably, 4 and 6 showed particularly potent activity against the lung cancer cell lines H1299, SW1573, and A549, with IC50 values ranging from 5.43 to 16.24 μM. Further mechanistic investigation revealed that both compounds suppress the proliferation of lung cancer cells by inducing cell cycle arrest at the G0/G1 phase and impair metastatic potential by inhibiting migration and invasion. These findings not only expand the structural diversity of marine-derived pyrrole alkaloids but also reveal the anticancer mechanisms of 4 and 6, highlighting their promise as active candidates for further antitumor drug development, particularly in lung cancer.

Aromatic polyketides have emerged as an important source of fluorescent natural products, which hold significant value for research and diagnostic applications. In this study, we reported the discovery of three new (5, 6, and 9) and ten known (1-4, 7, 8, and 10-13) fluorescent aromatic polyketides representing seven sets of carbon skeletons. Compounds 3-13 exhibited fluorescence ranging from cyan to orange-yellow and displayed varied behaviors in terms of excitation wavelength, emission wavelength, and Stokes shift, indicating their diverse spectral characteristics and environmental responsiveness. Notably, globismycin A (5) features an unprecedented 2,3-dihydrobenzofuro[4,5,6-de]chromene scaffold. Compound 5 not only exhibited high quantum yields in both water and organic solvents, with visible green fluorescence to the naked eye, but also showed potent selective cytotoxicity against three cancer cell lines. Biosynthetic investigations through a combination of gene inactivation, heterologous expression, and 13C-labeled acetate feeding studies revealed that these fluorescent compounds, despite differing in size and shape, are all derived from a type II polyketide synthase (PKS) gene cluster sgl, and their diverse skeletons are generated through seven distinct cyclization patterns. More importantly, compound 5 uniquely involves a characteristic fungal F-mode first-ring cyclization step, although 5 has been proven to be a bacterial aromatic polyketide. These findings not only provide excellent fluorescent candidates potentially useful for various biological applications but also expand our understanding on the biosynthetic mechanisms driving the production of diverse aromatic polyketides by type II gene clusters.

Four new 2-hydroxyphenylthiazoline natural products, methyl thiazostatin A (6), methyl watasemycin B (7), pulicatin K (8), and pulicatin L (9), alongside five known analogues (1-5) were isolated from a shrimp-associated strain Streptomyces ardesiacus SCSIO XS006. The planar structures of the new compounds were determined on the basis of NMR and HRESIMS spectroscopic analysis, and their absolute configurations were assigned by ECD and X-ray single-crystal diffraction studies. The biosynthetic gene cluster (BGC) governing the biosynthesis of these 2-hydroxyphenylthiazoline compounds was identified using bioinformatic analysis of the whole genome sequence of strain XS006 coupled with the in vivo gene inactivation. Based on the bioinformatics characterization of the BGC, a plausible biosynthetic pathway for compounds 1-9 was proposed. Antimicrobial activity assays showed that compound 2 was active against a clinic strain of Candida albicans with an MIC of 64 mu g/mL, and compound 5 exhibited activities against methicillin-resistant Staphylococcus epidermidis SRH-Sep, Mycolicibacterium smegmatis mc2155 and Enterococcus faecalis ATCC 29212, with MICs of 64 mu g/mL, 128 mu g/mL and 64 mu g/mL, respectively.

The deep-sea-derived Streptomyces atratus SCSIO ZH16 is a promising host for producing nanomole-level anti-tuberculosis ilamycins. However, limited research on regulating the ilamycins biosynthetic gene cluster (BGC) has hindered industrial production. Our previous study found that nitrogen metabolism-related genes were upregulated in strains with enhanced ilamycins production. Since amino acids from nitrogen metabolism are key precursors, we aimed to optimize ilamycins production by balancing BGC expression and nitrogen metabolism. Using RNA-seq and hierarchical clustering, we identified the native promoter P20605 and its modified version P20605-400, which regulate the positive regulator IlaB in ilamycins BGC. To synchronously boost ilamycins synthesis and precursor supply, we analyzed P20605's function via bioinformatics and validated it using an indigoidine biosynthetic model. The engineered strain ΔilaR::P20605-400-ilaB::PermE*-phoP achieved over a dozen-fold increase in ilamycins yield. Fermentation was successfully scaled up in 5-L and 500-L bioreactors, reaching titers of 2,546.4 mg/L and 1,993.9 mg/L, respectively, significantly surpassing previously reported yields. This study highlights the industrial potential of ilamycins and provides insights into enhancing peptide compound production in Streptomyces.

The construction and editing of heterocycles are fascinating and challenging in both biosynthesis and chemical synthesis. The furan ring, as a fundamental structural unit, plays a significant scaffolding role in many bioactive natural products. In this study, we report a furan assembly strategy in linfuranone A (1) and its associated natural products, characterized by the presence of a furanone at the terminus of their linear polyketide chains. An FAD-dependent monooxygenase, LfnO1, performs the skeletal editing of alpha-pyrones to the corresponding furanones. We show through combinatorial expression, in vitro biochemical assays, isotope labeling experiments, and comprehensive structural prediction analysis that the multifunctional LfnO1 converts alpha-pyrone substrates to furanone products displaying two distinct levels of oxidation via ring contraction. Additionally, we demonstrate that LfnO1 possesses broad substrate compatibility, enabling it to recognize and transform a variety of alpha-pyrone natural products commonly found in nature. Our findings shed light on an unconventional approach to furanone formation in natural products and show the great potential of LfnO1 as a skeletal editing tool in biocatalysis.

Chlocarbazomycins are bioactive carbazoles with therapeutic potential. Here, we report a conserved gene cluster (ccz) that directs its biosynthesis via a novel pathway. This cluster encodes a versatile tailoring system, including a regioselective halogenase (CczH), dedicated hydroxylases (CczA/J/D), and a bifunctional methyltransferase (CczI) that iteratively methylates and accelerates N-OH dehydroxylation. Our findings provide new enzymes for carbazole pathway engineering and structural diversification.

Depsidones are structurally diverse polyketides with significant pharmacological potential. Their structural variability in the marine-derived fungus Aspergillus sp. SCSIO SX7S7 stems from the substrate promiscuity of key enzymes, particularly the starter-unit acyltransferase (SAT) domain of non-reducing polyketide synthase (NR-PKS). In this study, we combined a metabolic blockade with the inherent biosynthetic flexibility to access rare depsidone derivatives. Inactivation of the highly reducing polyketide synthase (HR-PKS) gene depD redirected metabolic flux to potential branching pathways, leading to the isolation of (i) aspergillol A (1), an unprecedented depsidone featuring a unique benzene substitution, (ii) four new orsellinic acid homodimer-derived depsidones aspergillol B-E (2-5), (iii) a new diphenyl ether derivative aspergillol F (6), and (iv) two known compounds (7 and 8) but lacking complete NMR data from a previous publication. Further structure-activity relationship analyses revealed that the ester linkage in compounds 1-5 is essential for antimicrobial activities, while the distinctive benzene extension in compound 1 is responsible for its significantly enhanced activity. These findings not only expand the known structural diversity of fungal depsidones but also reveal the complex metabolic network underlying their biosynthesis while establishing an effective approach for discovering bioactive natural product scaffolds through rational pathway manipulation.

The mycobacterial caseinolytic protease (Clp) system has been recognized as a promising therapeutic target. In this study, we identify two novel ilamycin analogs, ilamycin E (ILE) and ilamycin F (ILF), both targeting the ClpC1 component of the ClpC1P1P2 proteasome. ILE potently disrupts ClpC1P1P2-mediated proteolysis, leading to delayed bactericidal activity, while ILF also binds ClpC1, albeit with lower affinity. Notably, we discover and validate a unique mutation in clpX and a novel insertion in clpC1 both conferring resistance to ILE and ILF in mycobacterium by gene editing. Furthermore, ILE can also inhibit the proteolytic activity of ClpXP1P2 in a manner dependent on the substrate's tag sequence and adaptor. This first demonstration of clpX- and clpC1-mediated ilamycins resistance underscores the potential of ilamycins to target multiple components of the Clp protease system, offering a novel dual-target strategy for combating mycobacterial infections.

Covering: up to 2025Invertebrates, as the majority of macroscopic species on the Earth, are important resources for natural products. Chemical investigations of animals can date back to the early 20th century and have led to the discovery of thousands of compounds with diverse biological functions. These natural products can be structurally classified as terpenoids, polyketides, and alkaloids. Additionally, many compounds have been isolated from symbionts, leading to the widespread belief that animals lack the capability for secondary metabolism. Recent biochemical studies challenge this notion, revealing great potential for animal biosynthesis research. Animals possess larger genomes and more complex metabolic pathways, suggesting untapped biosynthetic potential. In contrast to microorganisms, studies on the biosynthesis of natural products in animals remain limited. Characterized genes represent only a small fraction of their vast genomes. The discovery of biosynthetic gene clusters suggests that the methods used to mine the biosynthetic genes of microorganisms may also be applicable to animals. The characterization of 4-vinylanisole in locusts demonstrates that the pathways lacking clear core biosynthesis enzymes still require multidisciplinary experimental approaches. In summary, further biosynthesis studies will expand methodological approaches and accelerate the characterization of remaining natural product pathways.

Malbranchea circinata SDU050, a fungus derived from deep-sea sediment, is a prolific producer of diverse secondary metabolites. Genome sequencing revealed the presence of at least 69 biosynthetic gene clusters (BGCs), including 30 encoding type I polyketide synthases (PKSs). This study reports the isolation and identification of four classes of secondary metabolites from wild-type M. circinata SDU050, alongside five additional metabolite classes, including three novel cytochalasins (7–9), obtained from a mutant strain through the metabolic blockade strategy. Furthermore, bioinformatic analysis of the BGC associated with the isocoumarin sclerin (1) enabled the deduction of its biosynthetic pathway based on gene function predictions. Bioactivity assays demonstrated that sclerin (1) and (−)-mycousnine (10) exhibited weak antibacterial activity against Gram-positive bacteria such as Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA), and Bacillus subtilis. These findings underscore the chemical diversity and biosynthetic potential of M. circinata SDU050 and highlight an effective strategy for exploring marine fungal metabolites.

Guided by comprehensive bioinformatic analysis and global molecular networking, four previously undescribed peptidic natural products, pepticinnamins Q-T (1-4), along with two known analogues (5, 6), were isolated from cultures of the marine-derived Streptomyces sp. SCSIO 68065. Heterologous expression of the pcn biosynthetic gene cluster in the engineered chassis strain Streptomyces atratus ZH16NSEPK enabled the production of pepticinnamin analogues and led to the targeted isolation of two undescribed biosynthetic intermediates, pepticinnamins U and V (7, 8), as well as the known compound pepticinnamin M (9). The structures of these compounds were elucidated by spectroscopic analyses (including 1D and 2D NMR), HRESIMS, time-dependent density functional theory electronic circular dichroism (TDDFT-ECD) calculations, single-crystal X-ray diffraction studies, and advanced Marfey's method. Pepticinnamins Q-S (1-3) and U (7) are characterized by an unusual epoxidized cinnamoyl moiety. Comparative genomic analysis with homologous gene clusters allowed the proposal of their plausible biosynthetic pathways. Moreover, the cytochrome P450 monooxygenase Pcn29 was experimentally confirmed to catalyze the key epoxidation of the cinnamoyl moiety through a combination of targeted gene deletion and in vitro enzymatic reconstitution studies.

Spiromarmycin-type natural products are rare fungal tricyclic aromatic polyketides with remarkable biological activities. However, the enzymatic processes for assembling the lactone and pyran ring of spiromarmycin and its analogues are unclear. Here, we identify a rare benzolactone formation process differing from typical thioesterase domain-catalyzed transesterification. In this process, a short-chain dehydrogenase/reductase (SDR-Spm14)-catalyzed reduction on the phenylacetic acid core plays a critical role in promoting the lactonization process. Then, prenyltransferase (Spm5)-catalyzed prenylation on the benzolactone intermediate, along with monooxygenase (Spm6)-mediated epoxidation, produces an epoxide intermediate. Interestingly, a C6 hydroxy preset by a hydroxylase (Spm12) plays a role instead of an epoxide hydrolase, allowing a unique spontaneous anti-Baldwin cyclization and benzopyran formation for producing a toxic final product in the extracellular space and thus avoiding self-toxicity. Furthermore, structural analysis of Spm14 proteins in apo form and in complex with NADP+ indicates dramatic conformational changes for substrate accommodation. Subsequent molecular docking and structure-based mutagenesis analyses reveal a Tyr-based catalytic mechanism and a Lys-assisted substrate binding mode for Spm14. Importantly, Spm14 shows promiscuous substrate specificity toward diverse phenyl ketones with high stereoselectivity, expanding the potential application of Spm14 in the drug precursor synthesis. This study advances the understanding of benzolactone and benzopyran biosynthesis and expands the biocatalytic toolbox for future drug discovery.