Emestrin A, an epipolythiodioxopiperazine with a rare 15-membered ether-lactone macrocycle, exhibits significant antitumor activity. However, the late-stage enzymatic steps that establish and modify this scaffold and how these modifications influence bioactivity remain unclear. Here, targeted gene deletions in Aspergillus nidulans A6 revealed three P450 monooxygenases involved in oxidative tailoring. Among them, EmeQ was identified as a bifunctional P450 that catalyzes aromatic hydroxylation and phenol coupling, the latter of which drives the macrocyclization of the ether-lactone ring. Computational analysis delineated the coupling mechanism, and structure-guided mutagenesis successfully disentangled the dual reactivity, shedding light on how EmeQ coordinates the two sequential steps. In parallel, cytotoxicity assays demonstrated that hydroxyl groups introduced by late-stage tailoring are important for activity. This work provides a mechanistic elucidation of emestrin late-stage biosynthesis and establishes EmeQ as both a hydroxylase and a macrocyclase central to scaffold construction. The natural and engineered mutant enzymes characterized here expand the toolbox for the chemoenzymatic synthesis and synthetic biology of emestrins.

BACKGROUND:Oxysterol-binding proteins (OSBPs) serve as critical regulators throughout the oomycete life cycle. Oxathiapiprolin (OXA), a potent OSBP-targeting fungicide, represents the first commercially developed piperidine-thiazole-isooxazoline (PTI) product. Despite extensive structural modification focused on OXA, very few analogs with improved fungicidal activity have been identified to date. RESULTS:In this study, a series of OXA derivatives were designed and synthesized by introducing a flexible acetal fragment into OXA. The compounds B3 and B5 respectively exhibited excellent 77.78% and 94.44% control efficiency against cucumber downy mildew (CDM) at 0.02 mg/L concentration. The field trials showed that compounds B3 and B5 took on higher control efficiency than OXA at the same concentration. The result of environmental toxicological risk assessment indicated that compounds B3 and B5 have lower toxicity to aquatic lives than OXA. Computational chemistry indicated that the binding mode of compound B3 with Phytophthora capsici OSBP (PcOSBP) is similar to that of OXA, and kept the main binding interaction with OSBPs. CONCLUSION:Our findings suggested that a strategy focused on increasing molecular flexibility could be advantageous for optimizing OSBP inhibitors. The chemical structure of compound B3 may serve as a promising new starting point for the development of further OSBP inhibitors. © 2026 Society of Chemical Industry.

Through genome mining, we discovered a 5/8/5 fusicoccane-type diterpenoid gene cluster (named Thm) from the biocontrol fungus Trichoderma harzianum, representing the first report of such a cluster in the genus Trichoderma. Heterologous expression of Thm in Aspergillus oryzae NSAR1 led to the isolation of 33 fusicoccane-type diterpenoids (including 30 new compounds 1-30). Structurally, compounds 1-14 were tetracyclic diterpenoids, with 1 and 2 being a class of rare fusicoccane-alkaloid hybrids. Mechanistic profiling revealed that compound 6 acts as a selective GPVI pathway antagonist, potently inhibiting Syk and PLCγ2 phosphorylation and subsequent platelet activation. In contrast, compound 31 exerts its antiplatelet effect via a distinct ROCK1-dependent pathway, suppressing cytoskeletal reorganization by reducing myosin light chain (MLC) phosphorylation and key regulator expression. Critically, both compounds demonstrate a groundbreaking therapeutic dissociation, providing robust protection against arterial and venous thrombosis without impairing normal hemostasis, thereby presenting a promising strategy for safe antithrombotic therapy.

A series of 2-acyloxybenzamides were synthesized. The structures of the synthesized compounds were characterized by IR, 1H NMR, 13C NMR, and HRMS. Their antifungal activity against plant pathogenic fungi was evaluated. Compound 3i exhibited a 100.0% inhibition rate against M. oryzae, while compound 3b showed 90.0% inhibition against P. capsici. The corresponding EC50 values of compounds 3b (against P. capsici) and 3i (against M. oryzae) were determined to be 3.90 and 8.21 μg/mL, respectively. Molecular docking and MD simulations studies suggested that SCD enzyme may serve as a potential target for compound 3i and its related analogues.

Succinate dehydrogenase inhibitors (SDHIs) have emerged as one of the fastest-growing fungicides, yet their structural conservation and overuse have triggered widespread fungal resistance. Herein, we designed and synthesized a series of novel diphenyl-oxime-ether pyrazole-carboxamide derivatives by employing the fragment combination strategy. Among them, compound 8r exhibited potent SDH inhibition with an IC50 of 0.056 μM, which was approximately a 24-fold improvement over penthiopyrad (IC50 = 1.320 μM). In greenhouse trials, compounds 8t and 8z showed 50% and 40% disease control efficacy against rice sheath blight at 0.78 mg/L, comparable to Thifluzamide (50% control efficacy at 0.78 mg/L). Molecular modeling revealed that halogen substitution enhances intramolecular halogen bonding, stabilizing the cation-π interaction with the C_R46 residue. This work presents a promising scaffold for novel SDHI development.

Biosynthetic gene clusters (BGCs), key in synthesizing microbial secondary metabolites, are mostly hidden in microbial genomes and metagenomes. To unearth this vast potential, we present BGC-Prophet, a transformer-based language model for BGC prediction and classification. Leveraging the transformer encoder, BGC-Prophet captures location-dependent relationships between genes. As one of the pioneering ultrahigh-throughput tools, BGC-Prophet significantly surpasses existing methods in efficiency and fidelity, enabling comprehensive pan-phylogenetic and whole-metagenome BGC screening. Through the analysis of 85 203 genomes and 9428 metagenomes, BGC-Prophet has profiled an extensive array of sub-million BGCs. It highlights notable enrichment in phyla like Actinomycetota and the widespread distribution of polyketide, NRP, and RiPP BGCs across diverse lineages. It reveals enrichment patterns of BGCs following important geological events, suggesting environmental influences on BGC evolution. BGC-Prophet’s capabilities in detection of BGCs and evolutionary patterns offer contributions to deeper understanding of microbial secondary metabolites and application in synthetic biology.

To explore the chemical and biological diversities of diterpenoids from the fungus Talaromyces adpressus, a previously unknown biosynthetic gene cluster (BGC, tdn) for sordarin (a well-known fungal antibiotics) was discovered by leveraging the genome mining method. Heterologous expressions of key genes of tdn in Aspergillus oryzae, led to the determination of one new diterpenoid, cycloaraneosene-9-ol-8-one (4), and three known diterpenoids, cycloaraneosene (1), cycloaraneosene-9-ol (2), cycloaraneosene-8,9-diol (3). The structures of 1–4 was elucidated well via detailed analysis of 1D and 2D NMR, GCMS, HRESIMS, IR data, and comparison with reported data. Structurally, compounds 1–4 were belonging to fusicoccane diterpenoids with a classical tricyclic 5/8/5 ring system, which are participated in the biosynthesis of sordarin. Compound 4 maybe a key precursor for a Baeyer–Villiger like reaction with C8–C9 bond cleavage in the biosynthetic pathway of sordarin. Moreover, all isolates were evaluated for their bioactivities, compounds 3, and 4 exhibited inhibitory activities against the human cancer cell lines with IC50 values ranging from 7.8 to 32.4 µM. 3 and 4 promote cell apoptosis of HCT-116 and HepG2 cells, and suppress cell migration of HepG2 cells. As well, 3 and 4 also decrease gene expression of cell proliferation related molecules BCL-2 and cyclin D1, while increase expression of cell apoptosis related gene BAX. Targets predication and molecular docking indicate that compound 4 exhibits stronger affinity for DBL, suggesting its excellent binding potential. This finding will be enriched the structures and bioactivities of diterpenoids with a tricyclic 5/8/5 ring system, most importantly, will provide new strategies for the synthetic biological research of sordarins.

Succinate dehydrogenase (SDH) is a key fungicidal target, but rational inhibitors design has been impeded by the lack of fungal SDH structure. Here, we show the cryo-EM structure of SDH from Saccharomyces cerevisiae (ScSDH) in apo (3.36 Å) and ubiquinone-1-bound (3.25 Å) states, revealing subunits architecture and quinone-binding sites (Qp). ScSDH is classified as a heme-deficient type-D SDH, utilizing conserved redox centers (FAD, [2Fe-2S], [4Fe-4S] and [3Fe-4S] clusters) for electron transfer. A 3.23 Å structure with pydiflumetofen (PYD) identified critical interactions, including hydrogen bonds with Trp_SDHB194 and Tyr_SDHD120, and a cation-π interaction with Arg_SDHC97. Leveraging this, we designed a SDH inhibitor E8 (enprocymid), exhibiting significant fungicidal activity (Ki = 0.019 μM) and reduced zebrafish toxicity (LC50 (96 h) = 1.01 mg a.i./L). This study elucidates the structure of fungal SDH and demonstrates the potential of ScSDH for rational design of next-generation fungicides, addressing fungal resistance and environmental toxicity in agriculture.

Adaptive resistance to immunotherapy remains a significant challenge in cancer treatment. The reshaping of the tumor immune microenvironment in response to therapeutic pressures is a crucial factor contributing to this resistance. In this study, by comprehensive metabolic profiling of tumor tissues, we identified elevated itaconate in response to anti-PD-1 therapy as an adaptive resistance mechanism that promoted immune escape and tumor progression. CD8+ T-cell-derived IFNγ induced a significant upregulation of cis-aconitate decarboxylase 1 (ACOD1) in macrophages via the JAK-STAT1 pathway, thereby rewiring the Krebs cycle toward itaconate production. In murine models, macrophage-specific deletion of Acod1 increased the antitumor efficacy of anti-PD-1 therapy and improved survival. Additionally, itaconate and its derivative, 4-octyl itaconate, suppressed the tumor antigen presentation and cross-priming ability of dendritic cells, resulting in the impairment of antigen-specific T-cell antitumor responses. In summary, these findings identify an IFNγ-dependent immunometabolic mechanism of anti-PD-1 resistance, providing a promising strategy for combination therapy. Significance: Elevated itaconate production by macrophages induced by IFNγ is a critical negative feedback immunoregulatory metabolic response to anti-PD-1 immunotherapy that inhibits the cross-priming function of dendritic cells and confers immunotherapy resistance.

The building blocks-based molecular network (BBMN) strategy is effective for targeted natural product identification but depends on existing MS/MS data. To address this, we propose the simulated MS/MS-guided molecular network (SMMN) strategy, which combines virtual molecule design and MS/MS simulation to identify novel compounds containing target building blocks. We developed the MZmol Analyzer, a user-friendly web tool, to automate the SMMN strategy. Using this approach and the target 6-methyl-l-pipecolate (6-MeP), we identified two new indole alkaloid hybrids, crienamides A and B. In vitro immunosuppressive assays showed that both compounds inhibited ConA-induced cell proliferation, with IC50 values of 2.86 ± 1.33 μM and 0.96 ± 1.22 μM, respectively.

InfoMetricsFiguresRef.SI Journal of Agricultural and Food ChemistryASAPArticle This publication is free to access through this site. Learn More CiteCitationCitation and abstractCitation and referencesMore citation options ShareShare onFacebookX (Twitter)WeChatLinkedInRedditEmailJump toExpandCollapse ViewpointFebruary 18, 2025l-Histidinol Dehydrogenase (HDH) Represents a Potential Molecular Target of Herbicides, Bactericides, and FungicidesClick to copy article linkArticle link copied!Xing-Xing Shi*Xing-Xing ShiState Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. China*[email protected]More by Xing-Xing ShiHui-Min ChenHui-Min ChenState Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. ChinaMore by Hui-Min ChenWu-Yingzheng GuoWu-Yingzheng GuoState Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. ChinaMore by Wu-Yingzheng GuoZhi-Zheng WangZhi-Zheng WangState Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan 430061, P. R. ChinaMore by Zhi-Zheng Wanghttps://orcid.org/0009-0009-4847-5797Ying YeYing YeState Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. ChinaMore by Ying YeGuang-Fu Yang*Guang-Fu YangState Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. China*[email protected]More by Guang-Fu Yanghttps://orcid.org/0000-0003-4384-2593Open PDFJournal of Agricultural and Food ChemistryCite this: J. Agric. Food Chem. 2025, XXXX, XXX, XXX-XXXClick to copy citationCitation copied!https://pubs.acs.org/doi/10.1021/acs.jafc.5c01206https://doi.org/10.1021/acs.jafc.5c01206Published February 18, 2025 Publication History Received 25 January 2025Published online 18 February 2025article-commentary© 2025 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissionsThis publication is licensed for personal use by The American Chemical Society. ACS Publications© 2025 American Chemical SocietySubjectswhat are subjectsArticle subjects are automatically applied from the ACS Subject Taxonomy and describe the scientific concepts and themes of the article.BacteriaInhibitorsMonomersPeptides and proteinsPest controlThe global population is projected to reach nearly 10 billion by 2050, posing enormous challenges for worldwide agricultural production. The use of pesticides is one of the most cost-effective means to increase food productivity by protecting crops from weeds, diseases, and insect infestation. Twenty to forty percent of the world's total crop yield loss could be saved by pesticides each year.Nevertheless, with the overuse of traditional pesticides, many agricultural pests have developed resistance to them. Since the late 19th century, the number of cases of resistance to herbicides, fungicides, and insecticides has increased dramatically. Pesticide resistance can easily cause the failure of pesticides or other compounds with the same mode of action, costing agriculture billions of dollars each year. The problem of pesticide resistance poses a serious threat to sustainable food production. In this context, the development of pesticides based on novel targets has become one of the most effective strategies to address resistance and ensure food security.Function and Structure of HDHClick to copy section linkSection link copied!l-Histidinol dehydrogenase (HDH) is essential for primary metabolism in bacteria, fungi, lower eukaryotes, and plants by participating in histidine biosynthesis (Figure 1A). Among the 20 natural amino acid, histidine is the most versatile in protein structures or biological functions. For example, histidine is often the key residue in enzyme catalytic sites. HDH catalyzes the final two steps in the histidine biosynthesis pathway, oxidizing l-histidinol via l-histidinal into l-histidine. A loss of HDH function impairs histidine biosynthesis and often results in abnormal phenotypes. The knockout of hisn8, the HDH gene in Arabidopsis, showed ovule abortion phenotypes. (1) BsHDH has been identified as an essential factor for its intracellular replication in macrophages. (2) Inhibition of HDH activity can reduce the in vitro growth and intramacrophagic multiplication of Brucella suis. (3) Similarly, histidine auxotroph mutants of Mycobacterium tuberculosis, Salmonella typhimurium, or Burkholderia pseudomallei showed reduced virulence. (4) In addition to bacteria, deletion of the essential gene in the histidine biosynthesis pathway in the fungus Aspergillus fumigatus leads to attenuated pathogenicity and decreased resistance to starvation. (5) Notably, HDH is absent in humans and other mammals. Therefore, targeting HDH to block the histidine biosynthesis pathway provides a promising path for the development of novel herbicides, bactericides, and fungicides.Figure 1Figure 1. (A) HDH-catalyzed oxidation reaction and HDH-related biological functions. (B) Homodimeric structure of MtHDH. (C) Structure of MtHDH in a complex with histidine and NAD+ (Protein Data Bank entry 5VLD). (D) Evolutionary conservation of HDH. (E) Reported HDH inhibitors.High Resolution ImageDownload MS PowerPoint SlideHDH is a Zn2+- and NAD+-dependent enzyme with a dimeric nature (Figure 1B). Some HDH crystal structures have been reported, covering Escherichia coli, Elizabethkingia anopheles, B. suis, and Medicago truncatula. The overall architecture of these HDH structures is similar. Among plant species, only MtHDH has been structurally characterized and is described here as an example (Figure 1C). The MtHDH monomer consists of four domains (I–IV). Domains I and II adopt a Rossmann fold in their core and together constitute a globular architecture with a cleft at their interface. Domain III is almost perpendicular to domain IV, and they together form an L-shaped tail occupying the cleft between domains I and II in the other monomer. Surrounded by domains I, II, and IV, the active site is located at the dimer interface, containing a substrate-binding subpocket and a cofactor NAD+-binding groove. In the substrate-binding pocket, Zn2+ is octahedrally coordinated to residues Gln299, Asp401, His460*, and His302 and the two nitrogen atoms of l-histidinol. NAD+ binds to only one monomer primarily through polar interactions. In the catalytic mechanism of MtHDH, Zn2+ is critical for the proper positioning of the substrate and other reaction intermediates, while NAD+ binding allows for hydride transfer and requires specific loop rearrangement induced by substrate binding. (6) Although the degree of sequence similarity of HDH among different species is relatively low, the active site is highly conserved (Figure 1D). These structural and mechanistic studies of HDH provide a basis for designing novel inhibitors as pesticide leads.Progress in HDH Inhibitor DiscoveryClick to copy section linkSection link copied!In recent decades, a number of plant or bacterial HDH inhibitors have been reported (Figure 1E). (7,8) Most of the existing HDH inhibitors contain a (R)-(α)-methylhistamine fragment, which is also the party of the substrate histidinol that coordinates with Zn2+. In 1989, histidinol analogue compound 1 (Ki = 35 μM) was found to exhibit micromolar inhibitory activity against StHDH. In 1996, a series derivative of compound 1 was reported to exhibit an inhibitory effect on BoHDH, among which compounds 2a and 2b showed better bioactivities (IC50 = 40 nM). In 2007, histidine-derived substituted benzylic ketones were synthesized as BsHDH inhibitors. Compound 3 was the most effective (IC50 = 3 nM) and exhibited good in vitro anti-B. suis activity. The crystal structure of BsHDH in a complex with compound 3 was later determined. (9) Two nitrogen atoms in the imidazole moiety and -NH2 group form two coordinate bonds with Zn2+, while the aromatic side chain forms a hydrophobic interaction with the surrounding residues and is directed toward the groove responsible for NAD+ recognition. In 2008, a series of BsHDH inhibitors containing sulfonyl hydrazide were reported, represented by compound 4 (IC50 = 25 μM). In 2012, via extension of the aromatic tail, compound 5 was obtained as a novel BsHDH inhibitor (IC50 = 3 nM), which had a certain inhibitory effect on B. suis growth and replication. In 2014, oxo- and thioxo-imidazo[1,5-c]pyrimidines was designed by replacing the aminomethyl imidazole moiety, but these compounds failed to improve the inhibitory effect on BsHDH. Compounds 6a (IC50 = 18 μM) and 6b (IC50 = 5 μM) showed relatively high bioactivities. In 2016, l-histidine-derived hydrazones were synthesized as the first low-micromolar M. tuberculosis (Mtb) HDH inhibitors. They showed moderate in vitro anti-Mtb activity, represented by compound 7 (IC50 = 1.1 nM). These inhibitors demonstrate the great potential of HDH as a novel molecular target for controlling plant growth or plant diseases.Future ProspectsClick to copy section linkSection link copied!This study highlights the potential of metalloenzyme HDH as a biochemical target for the development of herbicides, bactericides, and fungicides. Our retrospective investigation of HDH biological functions, structures, and inhibitors supports the good prospects for HDH-inhibiting pesticides, which present a novel mode of action to overcome resistance. In the future, the design of HDH inhibitors is a prospective direction for pesticide discovery.Author InformationClick to copy section linkSection link copied!Corresponding AuthorsXing-Xing Shi - State Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. China; Email: [email protected]Guang-Fu Yang - State Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. China; https://orcid.org/0000-0003-4384-2593; Email: [email protected]AuthorsHui-Min Chen - State Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. ChinaWu-Yingzheng Guo - State Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. ChinaZhi-Zheng Wang - State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan 430061, P. R. China; https://orcid.org/0009-0009-4847-5797Ying Ye - State Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. ChinaAuthor ContributionsX.-X.S. and H.-M.C. contributed equally to this work.NotesThe authors declare no competing financial interest.AcknowledgmentsClick to copy section linkSection link copied!This work was supported by the National Key Research and Development Program of China (2021YFD1700103), the fellowship from the China National Postdoctoral Program for Innovative Talent (BX20240133), the National Natural Science Foundation of China (22207037), the Postdoctoral Fellowship Program of CPSF (GZB20230198), the China Postdoctoral Science Foundation (2024M760857), and the Postdoctor Project of Hubei Province (2024HBBHCXA004).ReferencesClick to copy section linkSection link copied! This article references 9 other publications. 1Muralla, R.; Sweeney, C.; Stepansky, A.; Leustek, T.; Meinke, D. Genetic dissection of histidine biosynthesis in Arabidopsis. Plant Physiol. 2007, 144 (2), 890– 903, DOI: 10.1104/pp.107.096511 Google ScholarThere is no corresponding record for this reference.2Köhler, S.; Foulongne, V.; Ouahrani-Bettache, S.; Bourg, G.; Teyssier, J.; Ramuz, M.; Liautard, J. The analysis of the intramacrophagic virulome of Brucella suis deciphers the environment encountered by the pathogen inside the macrophage host cell. Proc. Natl. Acad. Sci. U. S. A. 2002, 99 (24), 15711– 15716, DOI: 10.1073/pnas.232454299 Google ScholarThere is no corresponding record for this reference.3Joseph, P.; Abdo, M. R.; Boigegrain, R. A.; Montero, J. L.; Winum, J. Y.; Kohler, S. Targeting of the Brucella suis virulence factor histidinol dehydrogenase by histidinol analogues results in inhibition of intramacrophagic multiplication of the pathogen. Antimicrob. Agents Chemother. 2007, 51 (10), 3752– 5, DOI: 10.1128/AAC.00572-07 Google ScholarThere is no corresponding record for this reference.4M. Monti, S.; De Simone, G.; D'Ambrosio, K. L-Histidinol Dehydrogenase as a New Target for Old Diseases. Curr. Top. Med. Chem. 2016, 16 (21), 2369– 2378, DOI: 10.2174/1568026616666160413140000 Google ScholarThere is no corresponding record for this reference.5Dietl, A. M.; Amich, J.; Leal, S.; Beckmann, N.; Binder, U.; Beilhack, A.; Pearlman, E.; Haas, H. Histidine biosynthesis plays a crucial role in metal homeostasis and virulence of Aspergillus fumigatus. Virulence 2016, 7 (4), 465– 76, DOI: 10.1080/21505594.2016.1146848 Google ScholarThere is no corresponding record for this reference.6Ruszkowski, M.; Dauter, Z. Structures of Medicago truncatula L-Histidinol Dehydrogenase Show Rearrangements Required for NAD+ Binding and the Cofactor Positioned to Accept a Hydride. Sci. Rep. 2017, 7 (1), 10476, DOI: 10.1038/s41598-017-10859-0 Google ScholarThere is no corresponding record for this reference.7Lopez, M.; Köhler, S.; Winum, J.-Y. Zinc metalloenzymes as new targets against the bacterial pathogen Brucella. J. Inorg. Biochem. 2012, 111, 138– 145, DOI: 10.1016/j.jinorgbio.2011.10.019 Google ScholarThere is no corresponding record for this reference.8Winum, J.-Y. Chapter 3.7 - Histidinol dehydrogenase. In Metalloenzymes; Supuran, C. T., Donald, W. A., Eds.; Academic Press, 2024; pp 255– 263.Google ScholarThere is no corresponding record for this reference.9D'Ambrosio, K.; Lopez, M.; Dathan, N. A.; Ouahrani-Bettache, S.; Köhler, S.; Ascione, G.; Monti, S. M.; Winum, J.-Y.; De Simone, G. Structural basis for the rational design of new anti-Brucella agents: The crystal structure of the C366S mutant of l-histidinol dehydrogenase from Brucella suis. Biochimie 2014, 97, 114– 120, DOI: 10.1016/j.biochi.2013.09.028 Google ScholarThere is no corresponding record for this reference.Cited By Click to copy section linkSection link copied!This article has not yet been cited by other publications.Download PDFFiguresReferencesSupporting Information Get e-AlertsGet e-AlertsJournal of Agricultural and Food ChemistryCite this: J. Agric. Food Chem. 2025, XXXX, XXX, XXX-XXXClick to copy citationCitation copied!https://doi.org/10.1021/acs.jafc.5c01206Published February 18, 2025 Publication History Received 25 January 2025Published online 18 February 2025© 2025 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissionsArticle Views-Altmetric-Citations-Learn about these metrics closeArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.Recommended Articles FiguresReferencesSupporting InfoAbstractHigh Resolution ImageDownload MS PowerPoint SlideFigure 1Figure 1. (A) HDH-catalyzed oxidation reaction and HDH-related biological functions. (B) Homodimeric structure of MtHDH. (C) Structure of MtHDH in a complex with histidine and NAD+ (Protein Data Bank entry 5VLD). (D) Evolutionary conservation of HDH. (E) Reported HDH inhibitors.High Resolution ImageDownload MS PowerPoint SlideReferences This article references 9 other publications. 1Muralla, R.; Sweeney, C.; Stepansky, A.; Leustek, T.; Meinke, D. Genetic dissection of histidine biosynthesis in Arabidopsis. Plant Physiol. 2007, 144 (2), 890– 903, DOI: 10.1104/pp.107.096511 There is no corresponding record for this reference.2Köhler, S.; Foulongne, V.; Ouahrani-Bettache, S.; Bourg, G.; Teyssier, J.; Ramuz, M.; Liautard, J. The analysis of the intramacrophagic virulome of Brucella suis deciphers the environment encountered by the pathogen inside the macrophage host cell. Proc. Natl. Acad. Sci. U. S. A. 2002, 99 (24), 15711– 15716, DOI: 10.1073/pnas.232454299 There is no corresponding record for this reference.3Joseph, P.; Abdo, M. R.; Boigegrain, R. A.; Montero, J. L.; Winum, J. Y.; Kohler, S. Targeting of the Brucella suis virulence factor histidinol dehydrogenase by histidinol analogues results in inhibition of intramacrophagic multiplication of the pathogen. Antimicrob. Agents Chemother. 2007, 51 (10), 3752– 5, DOI: 10.1128/AAC.00572-07 There is no corresponding record for this reference.4M. Monti, S.; De Simone, G.; D'Ambrosio, K. L-Histidinol Dehydrogenase as a New Target for Old Diseases. Curr. Top. Med. Chem. 2016, 16 (21), 2369– 2378, DOI: 10.2174/1568026616666160413140000 There is no corresponding record for this reference.5Dietl, A. M.; Amich, J.; Leal, S.; Beckmann, N.; Binder, U.; Beilhack, A.; Pearlman, E.; Haas, H. Histidine biosynthesis plays a crucial role in metal homeostasis and virulence of Aspergillus fumigatus. Virulence 2016, 7 (4), 465– 76, DOI: 10.1080/21505594.2016.1146848 There is no corresponding record for this reference.6Ruszkowski, M.; Dauter, Z. Structures of Medicago truncatula L-Histidinol Dehydrogenase Show Rearrangements Required for NAD+ Binding and the Cofactor Positioned to Accept a Hydride. Sci. Rep. 2017, 7 (1), 10476, DOI: 10.1038/s41598-017-10859-0 There is no corresponding record for this reference.7Lopez, M.; Köhler, S.; Winum, J.-Y. Zinc metalloenzymes as new targets against the bacterial pathogen Brucella. J. Inorg. Biochem. 2012, 111, 138– 145, DOI: 10.1016/j.jinorgbio.2011.10.019 There is no corresponding record for this reference.8Winum, J.-Y. Chapter 3.7 - Histidinol dehydrogenase. In Metalloenzymes; Supuran, C. T., Donald, W. A., Eds.; Academic Press, 2024; pp 255– 263.There is no corresponding record for this reference.9D'Ambrosio, K.; Lopez, M.; Dathan, N. A.; Ouahrani-Bettache, S.; Köhler, S.; Ascione, G.; Monti, S. M.; Winum, J.-Y.; De Simone, G. Structural basis for the rational design of new anti-Brucella agents: The crystal structure of the C366S mutant of l-histidinol dehydrogenase from Brucella suis. Biochimie 2014, 97, 114– 120, DOI: 10.1016/j.biochi.2013.09.028 There is no corresponding record for this reference.PDB: 5VLD

(±)-Talapyrones A-F (1-6), six pairs of dimeric polyketide enantiomers featuring unusual 6/6/6 and 6/6/6/5 ring systems, were isolated from the fungus Talaromyces adpressus. Their structures were determined by spectroscopic analysis and HR-ESI-MS data, and their absolute configurations were elucidated using a modified Mosher's method and electronic circular dichroism (ECD) calculations. (±)-Talapyrones A-F (1-6) possess a 6/6/6 tricyclic skeleton, presumably formed through a Michael addition reaction between one molecule of α-pyrone derivative and one molecule of C8 poly-β-keto chain. In addition, compounds 2/3 and 4/5 are two pairs of C-18 epimers, respectively. Putative biosynthetic pathways of 1-6 were discussed.

Microbial secondary metabolites, synthesized by biosynthetic gene clusters (BGCs), offer vast potential for biotechnological applications. Among BGC profiling techniques, computational detection methods face challenges, including time-consuming alignment and reliance on predefined profiles. To address these, we present BGC-Finder, an end-to-end pipeline utilizing protein language models for BGC detection and annotation from microbial genomes and metagenomes. This approach achieves remarkable increase in profiling speed of up to 100-fold, and employs genomic context-aware modeling to facilitate interpretable genetic essentiality assessment and large-scale BGC clustering. BGC-Finder outperformed traditional methods, successfully detecting 9.49% more biosynthetic-core genes and 27.70% more cytochrome P450s in 742 experimentally-validated BGCs. Notably, it retrieved 31 remote biosynthetic homologs from 210 polar marine metagenomes and identified 4,585 BGCs with 6,388 core genes from 256 fungal genomes. These findings highlight BGC-Finder’s capability to illuminate “microbial biosynthesis dark matter” (sequence-unrelated, function-similar biosynthetic enzymes) and expedite natural product discovery. BGC-Finder is an accurate and ultrafast pipeline leveraging protein language models (pLMs) to predict and annotate biosynthetic gene clusters (BGCs) from microbial genomes and metagenomes. The genomic context-aware model enables interpretable analysis: attention-driven identification of essential biosynthetic genes and embedding-guided BGC clustering. BGC-Finder sensitively retrieves remote homologous BGCs from both bacteria and fungi genomes, uncovering hidden ‘microbial biosynthesis dark matter’. We discovered a non-ribosomal peptide synthetase (NRPS) family, which involved into function-specific BGCs in two evolutionarily distant fungi.

We investigated the functional plasticity of two P450 enzymes, AbnK and AbnG, in the brassicicene biosynthetic pathway. Through in vivo heterologous expression, feeding assays, and in vitro reactions, we show that these enzymes regio- and stereoselectively transform both 5-8-5 and 5-9-5 terpenoid scaffolds in different ways, supported by computational simulations. AbnK also bridges a missing step in brassicicene A biosynthesis. Our findings demonstrate how controlled promiscuity underpins structural diversity, informing strategies to expand chemoenzymatic synthesis.

Meroaspochalasins (mAPOs) are a group of intricate heteromers comprising two distinct subunits, dienophile aspochalasin, and diene isobenzofuran, of which the biosynthetic mechanism is of great interest yet unrevealed. In this study, two independent biosynthetic gene clusters (BGCs), flas and epi, being responsible for the biosynthesis of aspochalasin B (7) and pre-diene hemiacetal 21 (or 26), respectively, were identified in the filamentous fungus Aspergillus flavipes. In vivo and in vitro studies proved that a flavin adenine dinucleotide (FAD)-dependent oxidase FlasF in the flas cluster catalyzes the crucial oxidation to generate diverse aspochalasin monomers, particularly the dienophile 7. Interactive reduction catalyzed by the short-chain alcohol dehydrogenase/reductase (SDR) FlasG and endogenous NADPH further increases the complexity of this anabolic network. The cytochrome P450 enzyme EpiC and SDR enzyme EpiD in the epi cluster collaboratively catalyze the formation of pre-diene 21 (or 26), which can spontaneously dehydrate to yield a diene, leading to the nonenzymatic cascade of [4π + 2π] Diels-Alder and formal [5π + 2π] cycloaddition reaction to generate mAPO dimers and trimer progressively. Moreover, the FAD-dependent oxidase EpiG catalyzes the hydroxylation at the C3 position of the diene as a critical step in the formation of mAPO trimers.

Recent advances in target-based pesticide design have identified numerous novel candidate targets, although their agrochemical potential requires rigorous validation. Fluorescent probes serve as critical tools for tracing molecular interactions and elucidating the target functionality. Herein, we developed a complementary fluorescent probe pair (HDP1 and HDP2) to systematically reveal the challenge of targeting histidinol dehydrogenase (HDH) as an agrochemical target. HDP1 exhibits an outstanding detection limit (0.17 μg/mL), while HDP2 demonstrates excellent imaging capabilities in vivo. HDP1 was used to probe the interactions between inhibitors and substrates with HDH, confirming that HOL, the natural substrate of HDH, exhibits a strong and competitive affinity for HDH similar to that of HDH inhibitors (HDHIs). HDP2 was employed to image HDH in Arabidopsis thaliana, Escherichia coli, and Saccharomyces cerevisiae during treatment with HDHIs or under other stresses to show the change of the flux through the histidine biosynthesis pathway. The results indicate that HDHIs, non-HDH-targeting pesticides, and abiotic stresses can all affect His biosynthesis in plants, bacteria, and fungi. The results also show that various stresses can influence the histidine biosynthesis pathway through the regulation of the pentose phosphate pathway and inhibition of the expression of ATP-phosphoribosyltransferase. It can be concluded that the development of competitive inhibitors for HDH that can compete with HOL and show activity in vivo is a significant challenge. The sensitivity of the His biosynthesis pathway to other stresses complicates the picture and, under different conditions, may provide a positive or negative factor for HDH inhibition by synthetic ligands.

Microbial secondary metabolites, synthesized by biosynthetic gene clusters (BGCs), play critical roles in ecological interactions and offer vast potential for biotechnological and pharmaceutical applications. Despite advances in computational BGC detection, current methods face challenges, including time-consuming sequence alignments, dependence on known homologs and manually defined rules, limiting its robustness and generalizability. To address these, we present CoreFinder, a deep learning framework that integrates protein language models (pLMs) and genomic contexts to predict product class and decipher gene functions within BGCs without alignment. CoreFinder demonstrated higher precision of 0.945 (842/891) and recall of 0.821 (842/1,025) than antiSMASH for core gene annotation in over 700 experimentally validated fungal BGCs. Built on CoreFinder, we introduced an end-to-end scalable workflow for BGC screening and deciphering, which is about 240 times faster than antiSMASH. Applied to 256 genomes spanning 197 taxa, CoreFinder identified 6,414 core genes within 4,585 BGCs. Further analysis indicates that a non-ribosomal peptide synthetase (NRPS) family likely existed prior to the divergence of Fusarium and Aspergillus and evolved into function-specific gene clusters. These findings emphasize the potential of CoreFinder as a powerful tool for accelerating natural product discovery and driving innovation in synthetic biology by unlocking novel biosynthetic pathways for biotechnological and pharmaceutical advancements. Highlights ### Competing Interest Statement The authors have declared no competing interest. National Key R&D Program of China, , 2023YFA1800900, 2021YFA0910500, 2018YFC0910502 National Natural Science Foundation of China, , 32071465, 31871334, 81827901, 22277035

By integrating heterologous expression of the entire biosynthetic gene cluster in Aspergillus nidulans and a building blocks-based molecular networking (BBMN) strategy, six novel aspertetronin dimers (diasperonins A-F, 1-6) with three unprecedented skeletons and two additional novel congeners (7-8) were characterized from the engineered strain. High monomer levels from gene cluster overexpression likely triggered nonenzymatic dimerization. Compound 7 suppressed the NF-κB pathway in LPS-induced RAW264.7 cells and mouse model, demonstrating potent anti-inflammatory activity.

A novel strategy for the synthesis of fusicoccane diterpenoids is reported. By harnessing the biosynthetic pathways of brassicicenes and fusicoccins, cotylenol was produced in an engineered Aspergillus oryzae strain. We further achieved the concise synthesis of three fusicoccane diterpenoids, including alterbrassicicene E and brassicicenes A and R in 4 or 5 chemical steps from brassicicene I. This strategy lays the foundation for the preparation of fusicoccane diterpenoids and their analogues for biological studies.

Genome sequencing on an intertidal zone-derived Aspergillus flavipes strain revealed its great potential to produce secondary metabolites. To activate the cryptic compounds of A. flavipes, the global regulator flLaeA was knocked out, leading to substantial up-regulation of the expression of two NRPS-like biosynthetic gene clusters in the Delta flLaeA mutant. With a scaled-up fermentation of the Delta flLaeA strain, five compounds, including two previously undescribed piperazine derivatives flavipamides A and B (1 and 2), along with three known compounds (3-5), were obtained by LC-MS guided isolation. The new compounds were elucidated by spectroscopic analysis and electronic circular dichroism (ECD) calculations, and the biosynthetic pathway was proposed on the bias of bioinformatic analysis and 13C isotope labeling evidence. This is the first report to access cryptic fungi secondary metabolites by inactivating global regulator LaeA and may provide a new approach to discovering new secondary metabolites by such genetic manipulation.