Journal of Natural Products

Boavistamide A (1), a new alkyne-containing cyclic depsipeptide featuring the rare 3-amino-2-methyl-7-octynoic acid (AMOYA) moiety, was discovered along with two structurally related analogs, boavistamides B and C (2 and 3), from a filamentous marine cyanobacterium collected on Boa Vista Island, Cabo Verde. Their isolation was guided by antiplasmodial activity, GNPS MS/MS molecular networking, LC-MS profiling, and dereplication using the MarinLit database. The planar structures of boavistamides A-C (1-3) were elucidated through comprehensive HRMS and 1D/2D NMR analyses, with annotation support from AI-based tools SMART-NMR 2.1 and DeepSAT. The absolute configurations were established using Marfeys analysis and L-Phe-OMe coupling, complemented by NMR-based conformational studies. Boavistamides A and B exhibited moderate antiplasmodial activity with no mammalian cell cytotoxicity. Microscopic observations and metagenomic binning identified the producer strain as belonging to the genus Okeania (Microcoleaceae). These results expand the chemical diversity of AMOYA-containing cyanobacterial metabolites and highlight the utility of integrated metabolomics and AI-assisted workflows for natural product discovery from environmental samples. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/732064v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@24ce2borg.highwire.dtl.DTLVardef@5ba292org.highwire.dtl.DTLVardef@e1f6dorg.highwire.dtl.DTLVardef@1312d22_HPS_FORMAT_FIGEXP M_FIG C_FIG

Microbial libraries remain an important resource for natural product discovery; however, constructing taxonomically and chemically diverse collections remains a challenge. Advances in dereplication strategies, including molecular networking, have reduced the rediscovery of known bioactive molecules and facilitated the identification of novel chemical scaffolds, but these approaches are typically applied after library construction or to existing repositories. Furthermore, many dereplication workflows require scaled fermentation and extraction, increasing the time needed to assess a microbes metabolite profile. Here, we integrate matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS/MS) into the bioinformatics platform IDBac, enabling streamlined characterization of microbial taxonomic identity, metabolite production potential, and preliminary metabolite annotation through GNPS2 molecular networking. This miniaturized high-content workflow facilitates strain prioritization by providing metabolite annotations directly from single microbial colonies prior to scale-up and extraction. Application of this approach to marine actinomycetes enabled the annotation of lavanducyanin and multiple napyradiomycin analogs. Subsequent investigation led to the discovery of napyradiomycin B8 from marine Streptomyces sp. CNZ-289, which was confirmed by 1D and 2D NMR spectroscopy and MALDI-MS/MS. Expanding this workflow to an untargeted analysis of 25 commensal marine vertebrate-derived bacterial isolates resulted in the annotation of several known bioactive natural products, including surugamides, antimycins, desferrioxamine siderophores, and the isolation and elucidation of harmane derivatives using NMR. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/733640v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@c92cfforg.highwire.dtl.DTLVardef@1a9522borg.highwire.dtl.DTLVardef@151b309org.highwire.dtl.DTLVardef@c1531f_HPS_FORMAT_FIGEXP M_FIG C_FIG

Lysolipin I (1) is a highly bioactive xanthone with strong antibacterial and cytotoxic properties. Given the limited number of lysolipin analogues, discovery of new natural lysolipin derivatives is important for understanding their structure-activity relationships. A soil-derived Streptomyces sp. P8-2B18 harbors a putative lysolipin biosynthetic gene cluster and LC-MS based metabolomic analysis revealed the production of lysolipin I along with unreported analogues. Large-scale fermentation followed by isolation led to the discovery of four new analogues, lysolipins J-M (2- 5), the structures of which were elucidated by mass spectrometric and NMR spectroscopic data analyses. Lysolipin L features a five-membered lactam F ring, which was unprecedented in reported lysolipins. Lysolipin M has a novel skeleton, with an extra methyl (Me-36) and a glycosyl group replacing a 1,3-oxane ring in lysolipin I. While lysolipins I, J and K displayed strong activity against Staphylococcus aureus and Aspergillus flavus with MIC values ranging from 0.25 to 4 g/mL and lysolipin L showed only moderate activities, lysolipin M was inactive (>50 g/mL). Lysolipins I-K showed potent cytotoxic activity against prostate cancer cell lines LNCaP and C4-2B, with IC50 values in the submicromolar range. In contrast, lysolipin L exhibited no cytotoxicity and lysolipin M exhibited substantially reduced potency. Their broad, non-selective bioactivities restricted their applicability as therapeutic agents.

The incorporation of non-canonical amino acids (ncAAs) into proteins, developed in the past 20 years, has opened new avenues with respect to protein structure, protein modification, protein-protein interaction or enzyme catalysis beyond what is possible with the 20 proteinogenic AAs. Although >300 unusual building blocks including several ncAAs have been described in nonribosomal peptides (NRPs) naturally, we aimed to further expand the scope of the underlying nonribosomal peptide synthetases (NRPS) to incorporate ncAAs beyond the naturally available ones. We have therefore systematically screened for ncAA accepting NRPS systems, applied NRPS engineering to transfer the respective ncAA-accepting parts into other NRPSs and thereby created novel peptides that were further derivatized in post-enzymatic chemical synthesis reactions directly in bacterial culture extracts. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/738027v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@90552forg.highwire.dtl.DTLVardef@1c8a5e0org.highwire.dtl.DTLVardef@2549dorg.highwire.dtl.DTLVardef@1012911_HPS_FORMAT_FIGEXP M_FIG C_FIG

Natural product synthesis by non-ribosomal peptide synthetases (NRPS) is greatly defined by the substrate selectivity of the adenylation (A) domains. Previous assays for specificity determination were mainly performed in vitro and were requiring protein purification. In this work, we developed - based on NRPS engineering - a novel in vivo assay suitable for high-throughput application named ASCR (A domain screening). Using the recently described XUT fusion sites, A domains and their upstream condensation domains were assembled as di-domains to characterized NRPS model system, which allowed detection of defined tripeptide products via mass spectrometry directly after cell culture extraction. We evaluated the assay by screening in total 54 A domains from five known and seven uncharacterized NRPS, covering a broad range organism taxonomy and GC content of the investigated NRPS-encoding genes. Additionally, we applied the assay to elucidate and confirm the structures of novel cyclic pentapeptides derived from three novel NRPS from Photorhabdus temperata K122.

Thiopeptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) that form complex bioactive scaffolds through extensive enzymatic tailoring. The polyglycosylated thiopeptides persiathiacins, exhibit potent activity against multidrug-resistant Mycobacterium tuberculosis (Mtb) and methicillin-resistant Staphylococcus aureus (MRSA). The persiathiacin biosynthetic gene cluster encodes six cytochrome P450 (CYP) enzymes, but the logic of their oxidative modifications was unknown. Here, we establish a protoplast-based genetic system for Actinokineospora and systematically assign functions to all P450s. We demonstrate that PerX hydroxylates the central thiazole, PerV installs the third indole-core crosslink required for macrocyclization, and PerT, not PerU, catalyses indole N-hydroxylation. Combined gene inactivation and metabolite profiling reveal a hierarchical enzymatic sequence leading to the mature scaffold prior to sugar installation. Notably, the intermediate accumulating in the {Omega}perX mutant exhibits enhanced anti-M. tuberculosis potency compared to persiathiacin A (IC50 = 0.07 vs 1.5 g mL1). These results define the enzymatic logic and temporal organization of persiathiacin biosynthesis, providing a conceptual framework for rational diversification of complex thiopeptide natural products.

Conversion of cysteine residues to 5-thiooxazole moieties by multinuclear nonheme iron-dependent oxidative enzymes (MNIOs) is a prevalent modification in ribosomally synthesized, post-translationally modified peptide (RiPP) natural products. However, this post-translational modification (PTM) is difficult to distinguish from MNIO-produced oxazolone-coupled thioamides, such as those present in the RiPP methanobactin. The RiPP virulence factor oxazolin contains six copper-binding heterocycles installed by an MNIO. Here, we reassign these PTMs, originally described as oxazolones/thioamides, as 5-thiooxazoles on the basis of detailed comparative chemical and structural characterization of oxazolin and methanobactin. These data establish a benchmark for differentiating these two PTMs in newly discovered RiPPs. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/730506v1_ufig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@d30435org.highwire.dtl.DTLVardef@1b933fforg.highwire.dtl.DTLVardef@4b997org.highwire.dtl.DTLVardef@349ee1_HPS_FORMAT_FIGEXP M_FIG C_FIG

Pyrrolizidine alkaloids (PA) are well-known and widespread natural products from plants, which have also been identified in several different bacteria. In the latter case, the core structure is constructed by a non-ribosomal peptide synthetase (NRPS), which then undergoes oxidative ring contraction catalyzed by a Baeyer-Villiger monooxygenase. By deploying various NRPS engineering strategies, we have successfully generated five novel peptides carrying the unusual PA moiety at their C-terminus. Nonetheless, efforts to obtain a larger library of PAs were unsuccessful. Combined computational modelling and docking experiments suggest that this failure stems from the strict specificity of the thioesterase (TE) domain at the end of the NRPS, which discriminates against peptides carrying more than two amino acids. Our work thus suggests protein design strategies by which this intrinsic limitation to NRPS engineering may be overcome in future.

Endophytic fungi associated with the Himalayan yew (Taxus wallichiana) represent an underexplored source of bioactive secondary metabolites. This study investigated the extracellular metabolites of Annulohypoxylon purpureonitens isolated from Nepalese T. wallichiana using bioactivity screening combined with LCMS/MS-based metabolomics. The fungal extract exhibited broad-spectrum antibacterial activity, showing the strongest inhibition against Staphylococcus aureusand Enterococcus faecalis (MIC = 500 ug/mL). It also displayed notable antioxidant capacity(DPPH, ABTS, TPC &TFC) and cytotoxicity against HeLa and MCF-7 cancer cell lines. Metabolite profiling via GNPS molecular networking, manual MS/MS validation, and MASST reverse metabolomics putatively identified diverse compounds, including hydroquinidine, chlorogenic acid, muramic acid, and cordycepin conjugates widely distributed across public microbial datasets. Overall, A. purpureonitens is a promising source of multifunctional metabolites, laying a foundation for future compound isolation and functional characterization.

Natural product (NPs) and their derivatives are a major source of small-molecule drugs, and the building blocks of these NPs are often amino acids. These include both proteinogenic and nonproteinogenic amino acids (NPAAs), the latter of which expand the structural diversity of NPs. Homologation, or the addition of a methylene group to the amino acid side chain, is one modification that generates NPAAs. If the natural homologation pathway can be characterized and engineered, it could be used to diversify NPs. In this study, we investigated the terminal enzyme of this pathway, HphB, to determine its substrate scope. HphB was tested with various substrates that differed in backbone and/or side chain structures relative to its natural substrate. The results showed that HphB exhibits high promiscuity toward substrates with different side chains while maintaining strict specificity for the substrate backbone. Comparative analysis with two homologous enzymes from primary metabolic pathways revealed that HphB displays markedly higher substrate promiscuity. Bioinformatics analysis and structural modeling suggest that this promiscuity arises from the absence of a "lid" over the active site, resulting in increased solvent exposure of the substrate side chain. This study highlights the unique substrate flexibility of HphB and is a step toward engineering the homologation pathway to generate amino acid derivatives.

Oxalyl-coenzyme A (oxalyl-CoA) is a key intermediate in oxalate metabolism in plants, fungi and oxalate-degrading bacteria, but its limited availability has restricted biochemical investigations of oxalyl-CoA-dependent enzymes. Here, we describe a practical semisynthetic procedure for the preparation of oxalyl-CoA based on rapid oxalyl transfer from S-oxalyl p-thiocresol to coenzyme A. The reaction was monitored directly by 1H NMR spectroscopy, allowing optimisation of pD and reaction conditions. Following removal of thiocresol and purification by reversed-phase HPLC, oxalyl-CoA was obtained in 39% yield as determined by quantitative 1H NMR. The product was characterised by high-resolution electrospray mass spectrometry and comprehensive 1H, 13C and 31P NMR spectroscopy, confirming its structure unequivocally. During the study, the limited stability of oxalyl-CoA in aqueous solution was documented, leading to recommendations for its purification and storage. The semisynthetic protocol provides a convenient source of analytically pure oxalyl-CoA suitable for biochemical assays and supplies reference spectroscopic data for its unambiguous identification. The biological utility of the semisynthetic oxalyl-CoA was demonstrated by its application as an acyl donor substrate in assays of PnBAHD15, enabling quantitative kinetic characterisation of the enzyme and illustrating its suitability for biochemical studies of oxalyl-CoA-dependent enzymes.

Lanthipeptides are one of the largest classes of ribosomally synthesized and post-translationally modified peptides (RiPPs). The coi biosynthetic gene cluster (BGC) from Streptomyces coelicolor A3(2) encodes a canonical class I lanthipeptide dehydratase (CoiB) and cyclase (CoiC), a bifunctional enzyme (CoiSA) with an O-methyltransferase (MT) and glutamyl lyase (GL) domain, and a protein of unknown function (CoiH). The product of the coi BGC was recently shown to impart anti-phage activity, but its structure is still unresolved. Previous work investigated the regioselectivity of the GL domains in CoiB and CoiSA and the stereochemistry of the cyclized precursor peptide, but the function of CoiH was not addressed. In this study, co-expression of the peptide CoiA1 with CoiBCSAH resulted in a +16 Da addition on the cyclized peptide compared to when CoiH was omitted. LC-MS/MS analysis indicated that this modification occurred in the first thioether ring. A combination of site-directed mutagenesis, comparison of linear and cyclized peptide substrates, hydrogen peroxide (H2O2) treatment, and collision-induced dissociation (CID) mass spectrometric analysis suggested that the sulfur atom in the first methyllanthionine was oxidized to a sulfoxide group by CoiH. This hypothesis was confirmed by NMR analysis. CoiH represents a previously uncharacterized oxygenase family catalyzing sulfoxide formation. Structure prediction tools suggest a novel enzyme fold without obvious metal or cofactor binding sites, raising the possibility that CoiH is a cofactor independent oxidation enzyme.

Tandem mass spectrometry has become central to untargeted metabolomics. The translation of unknown spectra into biological insight depends on assigning chemical identities to detected metabolites. Structural characterization typically begins with mass spectral library matching, in which experimental spectra are compared against reference libraries and candidate annotations are ranked by their spectral similarity to the query. As spectral libraries and experimental datasets grow, however, more candidates achieve comparable similarity scores for a single query, and similarity scores give no indication of how reproducible a candidate match is or how sensitive it is to the underlying fragment evidence. Existing false-discovery-rate approaches can indicate annotation error at the dataset level but do not provide a per-match estimate of reliability. Here, we introduce a SpecReBoot-inspired query-focused bootstrapping approach that resamples the fragment evidence of each query spectrum. This approach relies on recomputing query similarity to candidate library spectra across bootstrap replicates, which provides a statistical distribution of scores rather than a single value. From this distribution we define the match support, a per-match reliability estimate quantifying the reproducibility of a match under spectral perturbation, together with measures of ranking stability that describe how often a candidate remains among the top-ranked matches across replicates. Applied to a forensic drug-of-abuse case, match support distinguished previously identified annotations from high-scoring false positives: a distinction cosine similarity failed to make. Furthermore, match support values remained stable as the reference library was expanded, whereas ranking stability metrics shifted significantly. In a cross-instrument endogenous metabolite library search, match support further revealed metric-specific annotation behavior, identifying metabolites consistently supported across different similarity metrics, while flagging annotations whose reliability depended strongly on the chosen scoring metric. Benchmarking against a natural-product reference library demonstrated that ranking based on match support values promoted true matches by four ranks on average compared with cosine-based ranking, without promoting analogs. Under controlled spectral perturbation experiments, match support flagged incorrect annotations with an AUROC of 0.75, whereas the cosine similarity score alone of the same match reached only 0.56. Query-focused bootstrapping thus provides a practical, per-match measure of annotation reliability, bringing the field a step toward reliable annotations at scale. We anticipate that incorporation of our annotation reliability scoring into computational metabolomics workflows will further promote the growth of spectral libraries and enhance their applicability across scientific disciplines.

Resistance to {beta}-lactam antibiotics, including carbapenems, mediated by metallo-{beta}-lactamases (MBLs), including the New Delhi metallo-{beta}-lactamase (NDM) MBL subfamily, is increasing. No MBL inhibitors are currently approved for clinical use with most reported MBL inhibitors are metal ion chelators, acting either at the Zn(II) ion active site and/or in solution. The hexokinase inhibitor 3-bromopyruvate (3-BP) is reported to inhibit NDM-1. We found that 3-BP selectively restored the antimicrobial activity of meropenem against carbapenem resistant Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii strains, obtained from clinical and environmental isolates from Tanzania and Malawi, containing genes that encode NDM-1 or NDM-5, but not against strains containing genes encoding for serine {beta}-lactamases. Mass spectrometry studies with NDM-1 and NDM-5 support a mechanism involving covalent reaction of 3-BP with an active site cysteine residue. The results will promote work on the development of covalently reacting MBL inhibitors, a strategy that has been successful for inhibition of the nucleophilic serine {beta}-lactamases.

Premarineosin A undergoes rapid, chemoselective C12 halogenation under mild conditions, providing brominated, chlorinated, fluorinated, and iodinated analogs. These derivatives retained potent antiplasmodial activity against both chloroquine-sensitive and -resistant Plasmodium falciparum strains and displayed smaller reductions in potency against the resistant strain than the parent compound.

It was recently reported that Methylobacterium extorquens AM1 produces the citrate-hydroxamate siderophore N-deoxyschizokinen A, identified by LC-HRMS. Multiple properties were inconsistent with the assignment: the feature eluted far later than the other schizokinen derivatives (17 min versus 6-8 min), a reversed-phase shift larger than a single-hydroxyl difference in a molecule can explain, further its accurate mass deviated from the calculated one by 28 ppm, well outside the error on the co-analyzed standards and its diagnostic m/z 105 and 77 fragments suggest a molecule with an aromatic moiety. A replicate comparison of identical samples in plastic versus glass autosampler vials was decisive: the m/z 387 feature was reproducibly present with plastic vials and absent with glass. We therefore conclude that the reported detection of N-deoxyschizokinen A in M. extorquens AM1 is an artifact, and recommend glass-vial and solvent-blank controls, an explicit accurate-mass threshold, and narrow MS/MS isolation when assigning trace siderophore-like features from complex extracts.

We present a generative machine learning pipeline for the design of linear antimicrobial peptides (AMPs). To extend diversity beyond synthetically validated peptide datasets ([~]7,000 entries), we apply transfer learning by training a Generative Pre-trained Transformer (GPT) on the genomically derived AMPSphere dataset ([~]863,000 entries), before fine-tuning on the Database of Antimicrobial Activity and Structure of Peptides (DBAASP). We assess the filtered sequences with a committee of Minimum Inhibitory Concentration (MIC) predictive models built with a Bi-LSTM architecture, and ESM-2 and QSAR feature vectors. The fine-tuned GPT model produced a 28% reduction in test loss compared to training on DBAASP alone, and generates peptides that are simultaneously more novel and more physicochemically plausible. Our top-ranked candidates are predicted to possess antimicrobial activity comparable to polymyxin B. We anticipate this transfer-learning approach is broadly applicable for leveraging massive, unlabelled genomic datasets to enrich targeted peptide discovery. Our identified sequences have been submitted to the 2027 AMP Challenge1 (team name VINCI) for experimental validation, and the complete codebase and workflow are open source2.

N-acylethanolamines (NAEs), including the endocannabinoid anandamide, are bioactive fatty acid amides that are normally hydrolyzed by fatty acid amide hydrolase (FAAH) or N-acyl acid amidohydrolase (NAAA). Strikingly, when canonical NAE degradation is blocked, NAE levels do not increase indefinitely but instead reach a plateau. This apparent metabolic ceiling suggests that additional, underexplored pathways contribute to NAE homeostasis. Identifying these pathways is essential to determine whether NAEs are converted into inactive metabolites or products with distinct biological properties. Here, we identify NAE glycosylation as a metabolic pathway that links endocannabinoid-related lipid metabolism to glycosphingolipid turnover. We synthesized glycosylated NAEs and their isotope-encoded standards and developed targeted LC-MS/MS assays to monitor their enzymatic processing and quantify their abundance in mouse and human cells, tissues, and plasma. We show that non-lysosomal glucosylceramidase GBA2 transfers glucose or galactose to anandamide, N-oleoylethanolamine and N-palmitoylethanolamine, and lysosomal glucosylceramidase GCase hydrolyses {beta}-Glycosylated-NAEs ({beta}-Glyco-NAE) back to their parent NAEs. {beta}-Glyco-NAEs occur endogenously in macrophages and neuronal cells, increase when canonical NAE degradation is impaired, and accumulate in human samples with GCase deficiency, including Gaucher disease and GBA1-associated Parkinsons disease. {beta}-Glyco-NAEs do not engage the cannabinoid receptors, TRPV1, or PPAR, and potentiate inflammatory cytokine release, including IL6 and TNF, from microglia. Based on these findings, we pose that GBA2-dependent NAE glycosylation may constitute an overflow lipid-remodeling pathway that connects NAE metabolism to lysosomal dysfunction, inflammation and neurodegeneration.

Mycosporine-like amino acids (MAAs) are among nature's most effective sunscreen compounds, capable of converting harmful ultraviolet radiation into harmless heat, and are widely distributed in marine organisms such as red macroalgae. Although decades of research have led to numerous discoveries, the rate of new MAA identifications has declined. To address this, we considerably expanded our previously developed combinatorial MAA database, increasing the number of covered structures tenfold. Following a comprehensive literature search for plausible but undescribed building blocks, the database now incorporates an extensive set of proteinogenic and non-proteinogenic amino acids, as well as other marine organic osmolytes, in combination with all (currently) known MAA scaffolds. This expanded resource was integrated into our identification platform, which combines UHPLC-VWD-HRMS2 analysis, feature-based molecular networking, and bioinformatics-driven annotation. Application of this updated workflow enabled the isolation and structural elucidation of a novel MAA, mycosporine-cysteinolic acid, from the red marine macroalga Vertebrata lanosa. Altogether, this study provides a valuable extension of the bioinformatics-based MAA screening pipeline, enhancing the annotation and discovery of novel MAAs in natural matrices.

Iron is widely considered the first metallocofactor, evolving as iron-sulfur clusters in early life. While iron-chelating siderophores have been widely characterized across microbial life, the lanthanide-chelating metallophore, methylolanthanin, has only recently been described in Methylobacterium extorquens AM1. Methylolanthanin shares structural similarities to the siderophore rhodopetrobactin but contains 4-hydroxybenzoate chelating moieties in place of canonical 3,4-dihydroxybenzoates. Here we compare Methylobacterium extorquens AM1, which produces methylolanthanin, and the closely related Methylobacterium extorquens PA1, which produces rhodopetrobactin. We present a pathway for the biosynthesis of both metallophores and describe the unusual synthesis of the 4-HB moieties of methylolanthanin from tyrosine. We uncover a frameshift mutation in the predicted 3-dehydroshikimate dehydratase, mllF, that prevents production of rhodopetrobactin in AM1 through truncation of the catalytically essential N-terminus. We find that deletion of the uncharacterized gene mllG reveals a cryptic branch of the pathway, leading to production of both methylolanthanin and rhodopetrobactin. Finally, we discover that rhodopetrobactin production in this mutant is enabled through the activity of a 3-dehydroshikimate dehydratase in a separate biosynthetic gene cluster. These insights highlight an evolutionary mechanism for metallophore diversification through pseudogenization and regulation of distinct biosynthetic gene clusters with shared aromatic intermediates.