Chronic hard-to-heal skin wounds in diabetes mellitus pose a significant clinical challenge, underscoring the urgent need for additional therapeutics. Herein, we report the identification of a polyether biosynthetic gene cluster (pdm BGC) from the marine-derived Streptomyces marincola SCSIO 03032 through genome mining. By overexpressing the positive regulator gene pdmRI, we increase the product of the pdm BGC 48-fold to enable the isolation, structural determination, and biosynthesis investigation of an octalin-containing polyether ionophore polydecalinmycin (PDM). Functionally, PDM demonstrates remarkable efficacy in promoting acute skin wound healing in BALB/c mice and significantly accelerating chronic wound closure in a diabetic mouse (db/db, male) model. Mechanistically, PDM induces an elevation of mitochondrial Na+ levels to trigger a transient burst of reactive oxygen species, a critical signal for initiating acute wound closure. Upon prolonged exposure, PDM activates a robust Nrf2-mediated antioxidant response, restoring mitochondrial homeostasis and conferring cytoprotection against high-glucose-induced oxidative stress. These insights highlight the therapeutic potential of PDM as a natural polyether candidate for developing ionophore-based strategies for diabetic wound healing. Chronic skin wounds in diabetes mellitus pose a clinical challenge that requires additional therapeutics. Here the authors report a polyether biosynthetic gene cluster, engineer a bioproduction platform for the ionophore polydecalinmycin, and demonstrate its wound healing abilities.

ABSTRACT Cyanogramide ( 1 ) is a unique spirooxindole alkaloid derived from a marine actinomycete and is characterized by its distinct spirocyclic pyrrolo[1,2‐c]imidazolidin‐4‐one scaffold. Although we have successfully elucidated the biosynthetic pathway of 1 , the mechanism underlying the formation of the characteristic imidazolidin‐4‐one remains unclear. In this study, we demonstrate that the cytochrome P450 monooxygenase CyaI catalyzes an oxidation reaction through a zwitterionic intermediate and facilitates a subsequent unusual C→N acetyl migration, which triggers a spontaneous intramolecular cyclization to forge the imidazolidin‐4‐one ring during 1 biosynthesis. In addition, CyaI is identified as a bifunctional enzyme that also catalyzes N ‐demethylation. High‐resolution crystallography and mutagenesis studies determine Thr245 as a crucial catalytic residue that modulates the balance between imidazolidine‐4‐one synthesis and demethylation. This work not only expands the catalytic repertoire of P450 enzymes but also opens the way for the development of multifunctional biocatalysts in the synthesis of complex natural products.

Natural products (NPs), as a vital source of pharmaceutical agents, have contributed to the development of 60% of marketed small-molecule drugs. However, NP-based drug discovery faces a major challenge due to the combinatorial expansion of NPs' configurational space and their complex 3D-structures, which arise from atomic chirality dictated by stereospecific biosynthetic enzymes. To date, over 20% of known NPs lack complete chiral configuration annotations, and only 1–2% have fully resolved crystal structures. To address this bottleneck, we present NatGen, an innovative deep learning framework for predicting the chiral configurations and 3D conformations of natural products. NatGen leverages advanced structure augmentation and generative modeling techniques and achieves near-perfect accuracy in chiral configuration prediction: 96.87% on benchmark NP structural dataset and 100% in a prospective study involving 17 recently resolved plant-derived natural products. The average root-mean-square deviation (RMSD) of the predicted 3D structures is below 1 Å—smaller than the radius of a single atom. Using NatGen, we successfully predicted the 3D structures of 684,619 NPs from COCONUT - the largest open NP repository to date - and made the full dataset publicly available at https://www.lilab-ecust.cn/natgen/. We believe this resource significantly expands the structural landscape of natural products and will empower researchers to cross-validate findings and accelerate progress in diverse fields including natural product chemistry, enzymatic biosynthesis, physical, organic and analytical chemistry, phytochemistry, NP and NP-derived drug discovery.

Covering: up to the end of August, 2025Spirooxindole-containing natural products are widely distributed in actinomycetes, cyanobacteria, fungi, plants, and invertebrates and have attracted significant attention due to their intricate chemical skeletons and diverse biological activities. Some of these compounds have made substantial contributions to the human health, particularly in the treatment of the central nervous system disorders and cardiovascular conditions as well as in agricultural applications. Accordingly, their biosynthetic pathways have been extensively investigated. Current studies reveal that cytochrome P450 enzymes and flavin-dependent monooxygenases (FMOs) are the primary enzymes involved in triggering carbocation, radical or epoxidation reactions following semipinacol rearrangement during the formation of spirooxindole. In some cases, spontaneous intramolecular Diels-Alder cycloaddition also yields spirooxindole skeletons. This review presents a comprehensive overview of the discovery and structure of spirooxindole alkaloids (SOAs), together with their bioactivities and distinctive biosynthetic pathways.

Genome mining has become a powerful method for linking biosynthetic gene clusters to chemical structures of their encoded natural products, driven by advances in genomic sequencing and the accumulated knowledge of natural product biosynthesis. Guided by this strategy, Actinoalloteichus hymeniacidonis DSM 45092 was identified as a potential producer of pentangular polyketides. Subsequently, five pentangular polyphenols were isolated from this strain, including two new compounds 19-hydroxy-KS-619-1 (1) and 19,20-dehydro-KS-619-1 (2), and three known analogues 3-5. Their structures were elucidated through comprehensive spectroscopic analysis and electronic circular dichroism calculations, and all compounds were evaluated for antibacterial and cytotoxic activities.

Nenestatins (NENs) belong to benzo[b]fluorene-containing atypical angucyclines, a structurally diverse class of microbial natural products. Bioinformatic analysis of the NEN biosynthetic gene cluster (nes BGC) from the deep-sea sediment-derived Micromonospora echinospora SCSIO 04089 implicated Nes5 as an α/β hydrolase. The targeted inactivation of the nes5 gene led to the accumulation of five new analogs, NENs E-I (1-5), together with the known monomer homo-dehydrorabelomycin E (6). Their structures were elucidated by comprehensive spectroscopic analysis and electronic circular dichroism calculations. Notably, both NEN A and NEN B were absent in the Δnes5 mutant, indicating that Nes5 is essential for their biosynthesis; however, the exact function of Nes5 requires further exploration.

We decipher functions of three monooxygenases (PasO1, PasO3, and PasO4) in early biosynthetic steps in spirotetronate PA-46101 and demonstrate a PasO4/PasO3 cascade for forging the signature macrocyclic lactone. The P450 PasO4 oxidizes a methyl group to a carboxylate, enabling a regiospecific Baeyer-Villiger oxidation by PasO3. Structural analysis of a PasO3 homologue identifies a carboxylate-binding pocket essential for this strict substrate specificity. This two-enzyme cascade can serve as a portable biocatalytic tool for diversifying spirotetronates.

Fusarium wilt of banana (FWB), caused by Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 (TR4), poses a severe threat to the global banana industry. The screening of endophytic fungi from the mangrove plant led to the identification of Medicopsis sp. SCSIO 40440, which exhibited potent antifungal activity against Fusarium. The further fraction of the extract yielded ten compounds, including MK8383 (1) and nine new analogues, MK8383s B-J (2-10). The structures of 1-10 were elucidated using extensive spectroscopic data and single-crystal X-ray diffraction analysis. In vitro antifungal assays revealed that 1 showed strongly antifungal activities against Foc TR4, with an EC50 of 0.28 μg/mL, surpassing nystatin and hygromycin B (32 and 16 μg/mL, respectively). Pot experiments showed that 1 or spores of SCSIO 40440 could significantly reduce the virulence of Foc TR4 on Cavendish banana.

N-Methyltransferases involved in indole methylation have seldom been discovered in natural product biosynthesis. This study focuses on the enzyme CyaF, which catalyzes a critical N-methylation step of indole in the β-carboline skeleton during cyanogramide biosynthesis. Seven β-carboline analogues (3-9) were isolated from the recombinant strain Streptomyces coelicolor YF11/cyaABC, including three new compounds (5-7). In vitro assays revealed CyaF's substrate flexibility. The crystal structure of the CyaF/S-adenosyl-L-homocysteine (SAH) complex, combined with the AlphaFold-predicted model and site-directed mutagenesis, elucidated the catalytic mechanism and structural features that enable CyaF to accommodate diverse substrates, highlighting its potential for biocatalytic applications.

Activating silent biosynthetic gene clusters (BGCs) within various microorganisms is an important approach to uncover valuable natural products. In this study, we reported the capture and activation of two large silent BGCs from a marine-derived Streptomyces sp. SCSGAA 0027 in the heterologous host Streptomyces albus J1074 by inserting a widely used constitutive promoter kasOp∗ upstream of the core biosynthetic genes, which led to the production of coprisamides (COPs) and padanamides (PADs), respectively. Interestingly, the yields of COPs and PADs were significantly enhanced when potassium or sodium salts were supplemented in the fermentation media, especially 1 % KCl. The promoting strength of kasOp∗ was found to be obviously increased upon KCl addition by using the eGFP (enhanced green fluorescent protein) as an indicator. These findings revealed for the first time that the exogenous promoter kasOp∗ performed unexpectedly as a salt-enhanced element in S. albus J1074. Consequently, a "kasOp∗-KCl" strategy was developed to achieve the highest production of COPs A/B at 97.9 mg/L in fermentation with shaking flasks, along with the coproduction of a pair of new analogues, COPs E/F at 151.8 mg/L, leading to a maximum isolation titer of COPs at 171.7 mg/L, about 170-fold improvement comparing to previous reports. Similarly, the strategy increased the titers of the antimalarial agent PAD A to 76.7 mg/L and the diisonitrile copper chelator SF2768 to 72.8 mg/L in S. albus J1074, representing the highest yields reported to date for both compounds. Moreover, a small library of kasOp∗ variants were generated and validated to also be KCl-responsive, expanding the promoter toolkits for metabolic engineering and genome mining. These findings provide new insights into the salt-enhancing property of the widely used promoter kasOp∗, and offer a simple "kasOp∗-KCl" approach to efficiently activate silent BGCs and improve the production of the encoding natural products in multiple commonly used Streptomyces hosts.

4-Hydroxy-2-pyridone alkaloids are a significant class of natural products with notable biological activities, including antitumor, antimicrobial, and anti-inflammatory properties, attracting increasing research interest in recent years. The continuous isolation of novel 4-hydroxy-2-pyridones has significantly broadened the scope of this compound class. To provide a comprehensive understanding of their current research status and potential applications in human health, this review summarizes 133 novel 4-hydroxy-2-pyridone alkaloids from fungi reported between 2010 and 2024, and explores their chemical synthesis, biosynthesis, and bioactivities. By synthesizing valuable insights and data, this article aims to support and inform ongoing research endeavors focused on 4-hydroxy-2-pyridone and its potential therapeutic applications, serving as a resource for scientists interested in drug discovery and development.

Bacterial tryptophan dimers comprise a large family of natural products with promising biological activities. Herein, we report the identification of a methyltransferase, SpmM1, which acts as a gatekeeping enzyme to govern the divergent biosynthesis of tryptophan dimers spiroindimicins (SPMs) and indimicins (IDMs) in Streptomyces marincola SCSIO 03032. Bioinformatics, genetic, and biochemical studies revealed that SpmM1-catalyzed carboxyl O-methylation enabled the common precursor of SPMs and IDMs to flux into the spiro-forming pathway to generate SPMs.

Inspired by naturally occurring bis-isochromans such as penicisteckins, we envisaged the first synthesis of biaryl-type bis-1-arylisochromans containing a stereogenic ortho-trisubstituted biaryl axis. We achieved the stereoselective synthesis of 5,5′-linked heterodimeric bis-isochromans containing both central and axial chirality elements by performing diastereoselective Suzuki–Miyaura biaryl coupling reactions on two optically active 1-arylpropan-2-ol derivatives, followed by two oxa-Pictet–Spengler cyclizations with aryl aldehydes or methoxymethyl chloride. We studied the diastereoselectivity of the cyclization step, separated the stereoisomeric products with chiral preparative HPLC and determined the absolute configuration through a combination of vibrational circular dichroism (VCD), NMR and single-crystal X-ray diffraction analysis. We demonstrated that different aryl groups could be introduced into the two isochroman subunits, since the dimethoxyaryl subunit reacted faster, enabling the two oxa-Pictet–Spengler cyclizations to be performed separately with different aryl aldehydes. We also explored the acid-catalyzed isomerization and oxidation to axially chiral ortho-quinones in order to produce stereoisomeric and oxidized analogs, respectively. We identified the antibacterial activity of our target bis-isochromans against Bacillus subtilis and Enterococcus faecalis with minimum inhibitory concentrations down to 4.0 and 0.5 μg/mL, respectively, which depend on the stereochemistry and substitution pattern of the bis-isochroman skeleton.

Lipounguisins (LPUs) A‒K (9‒19), eleven novel lipopeptides were isolated from the sponge-associated fungus Aspergillus sp. SCSIO 40435. LPUs represent a rare class of lipopeptides (LPs), featuring cyclic heptapeptides conjugated to diverse octadecadienoic acids (either trans Δ10, Δ12 or trans Δ9, Δ11) via a C‒C or C‒N bond, and showed bioactivities including anti-Gram-positive bacteria, inhibitory activity of α-glucosidase, and cytotoxicity to Huh-7 (half-maximal inhibitory concentration (IC50) = 5.42 μmol/L). A radical-mediated coupling reaction between unguisins and octadecadienoic acids was proposed to account for LPU formation.

A non-enzymatic method to synthesize C-methylated Fluostatins by using DMSO to methylate C(sp2)–H bonds under mild conditions without any catalysts is described here. A mechanism for this reaction was proposed.

Thiazole scaffold-based small molecules exhibit a range of biological activities and play important roles in drug discovery. Based on bioinformatics analysis, a putative biosynthetic gene cluster (BGC) for thiazole-containing compounds was identified from Streptomyces sp. SCSIO 40020. Heterologous expression of this BGC led to the production of eight new thiazole-containing compounds, grisechelins E, F, and I-N (1, 2, 5-10), and two quinoline derivatives, grisechelins G and H (3 and 4). The structures of 1-10, including their absolute configurations, were elucidated by HRESIMS, NMR spectroscopic data, ECD calculations, and single-crystal X-ray diffraction analysis. Grisechelin F (2) is a unique derivative, distinguished by the presence of a salicylic acid moiety. The biosynthetic pathway for 2 was proposed based on bioinformatics analysis and in vivo gene knockout experiments. Grisechelin E (1) displayed moderate antimycobacterial activity against Mycobacterium tuberculosis H37Ra (MIC of 8 mu g mL(-1)).

Naturally occurring resistances diminish the effectiveness of antibiotics, and present significant challenges to human health. Human activities are usually considered as the main drivers of the dissemination of antibiotic resistance, however, the origin of the clinical antibiotic resistance can be traced to the environmental microbes, and the clinically relevant resistance determinants have already pre-existed in nature before the antibiotics come into clinic. In this concept, we present the naturally occurring and widespread resistance determinants recently discovered during the biosynthesis study of bioactive compounds. These widely prevalent resistances in environmental microbes, including antibiotic producers and non-producers, advance the understanding of the origin of resistance, and provide prediction for the clinically relevant resistance to aid in the rational design of more effective drug analogues to combat resistance.

For advanced synthetic intermediates or natural products with multiple unactivated and energetically similar C(sp3)-H bonds, controlling regioselectivity for the C-H activation is particularly challenging. The use of cytochrome P450 enzymes (CYPs) is a promising solution to the 'regioelectivity' challenge in remote C-H activation. Notably, CYPs and organic catalysts share a fundamental principle: they strive to control the distance and geometry between the metal reaction center and the target C-H site. Most structural analyses of the regioselectivity of CYPs are limited to the active pocket, particularly when explaining why regioselectivity could be altered by enzyme engineering through mutagenesis. However, the substructures responsible for forming the active pocket in CYPs are well known to display complex dynamic changes and substrate-induced plasticity. In this context, we highlight a comparative study of the recently reported paralogous CYPs, IkaD and CftA, which achieve different regioselectivity towards the same substrate ikarugamycin by distinct substructure conformations. We propose that substructural conformation-controlled regioselectivity might also be present in CYPs of other natural product biosynthesis pathways, which should be considered when engineering CYPs for regioselective modifications.

Optically active heterodimeric 5,5′-linked bis-isochromans, containing a stereogenic ortho-trisubstituted biaryl axis and up to four chirality centers, were synthesized stereoselectively by using a Suzuki–Miyaura biaryl coupling reaction of optically active isochroman and 1-arylpropan-2-ol derivatives, providing the first access to synthetic biaryl-type isochroman dimers. Enantiomeric pairs and stereoisomers up to seven derivatives were prepared with four different substitution patterns, which enabled us to test how OR, ECD, and VCD measurements and DFT calculations can be used to determine parallel central and axial chirality elements in three isolated blocks of chirality. In contrast to natural penicisteckins A–D and related biaryls, the ECD spectra and OR data of (aS) and (aR) atropodiastereomers did not reflect the opposite axial chirality, but they were characteristic of the central chirality. The atropodiastereomers showed consistently near-mirror-image VCD curves, allowing the determination of axial chirality with the aid of DFT calculation or by comparison of characteristic VCD transitions.

Mangrove derived actinomycetes are a rich reservoir of bioactive natural products and play important roles in pharmaceutical chemistry. In a screen of actinomycetes from mangrove rhizosphere sedimental environments, the isolated strain Streptomyces sp. SCSIO 40068 displayed strong antibacterial activity. Further fractionation of the extract yielded four new compounds kebanmycins A-D (1-4) and two known analogues FD-594 (5) and the aglycon (6). The structures of 1-6 were determined based on extensive spectroscopic data and single-crystal X-ray diffraction analysis. 1-3 featured a fused pyranonaphthaxanthene as an integral part of a 6/6/6/6/6/6 polycyclic motif, and showed bioactivity against a series of Gram-positive bacteria and cytotoxicity to several human tumor cells. In addition, the kebanmycins biosynthetic gene cluster (keb) was identified in Streptomyces sp. SCSIO 40068, and KebMT2 was biochemically characterized as a tailoring sugar-O-methyltransferase, leading to a proposed biosynthetic route to 1-6. This study paves the way to further investigate 1 as a potential lead compound.