Three novel meroterpenoids with unique benzo-fused 10-membered carbocycle skeletons from the fungus Tricholoma sp. HD0815-7.

We expanded our previous mapping of the peptide condensation reaction mechanism from the linear dipeptide formation to the cyclization reaction that results in diketopiperazines. The overarching theme of our computational investigations is a reaction network that connects all intermediates via proton-transfer pathways. We conducted the simulations designed to be predictive in a range of environments, such as the gas phase, hydrothermal aqueous conditions, deliquescent salts, and bulk water. While the free-energy profiles are similar to the linear peptide, the presence of the cis amide bond leading to a pre-arranged vicinity of the two reacting groups and the role of explicit solvent molecules revealed new mechanistic insights that differentiate the linear versus cyclic peptide formation/hydrolysis reactions. The rate-determining step corresponds to the final water-elimination reaction using the most realistic computational models with both implicit and explicit water solvation models at neutral pH. At high pH, the highest barrier corresponds to the C-N bond formation at a significantly lower free energy, while at low pH, the water elimination step's barrier increases by close to 30%; thus, effectively shutting down the reaction in agreement with experiments. Due to the central role of proton transfer, we studied the impact of nuclear wave functions on all active H-centers. By utilizing two quantum protons, we document up to 0.1 Å impact on H positions, ca. 20 kJ mol-1 tunneling effects, and a significant change in the shape of the potential energy surface in comparison with the classical DFT calculations. The calculated reaction rates well reproduce the experimentally determined values under hydrothermal conditions.

Peptide-based approaches to quorum-sensing disruption: emerging trends and applications in antimicrobial therapy.

Design, synthesis, and biological evaluation of novel PROTACs based on unnatural dipeptide CRBN ligands.

This study is carried out to examine the in vitro probiotic properties of Bacillus subtilis B13 (= VTCC 910231), isolated from brackish water in the Cau Hai lagoon, Vietnam. The strain was confirmed to be safe, showing no hemolytic activity and exhibiting strong biofilm formation. It demonstrated notable environmental adaptability, growing across a wide pH range (5-9), showing moderate tolerance at 7% NaCl. B13 produced multiple extracellular enzymes, with the highest activities observed for lipase, protease, and cellulase, and additionally metabolized 25 of the 49 carbohydrates tested (51.0%). Antibiotic susceptibility profiling revealed broad sensitivity, with resistance detected to only 4 of 15 antibiotics, and it was highly sensitive to fluoroquinolones and phenicols. The ethyl acetate extract of its cell-free culture supernatant displayed noticeable inhibitory activity against five Vibrio species, which exhibited inhibition diameters varying from 13.3 ± 0.6 to 21.7 ± 0.6mm. Moreover, the extract exhibited significant anti-inflammatory effects, achieving concentration-dependent nitric oxide inhibition (IC50 = 28.6µg/mL) while maintaining high macrophage viability (94.9-97.1%). Chemical analysis by GC-MS and LC-ESI-QTOF/MS identified 34 metabolites, of which 26 were tentatively characterized, including organic acids, fatty acid derivatives, volatile hydrocarbons, and a diverse range of cyclic dipeptides, many of which have previously been reported with antimicrobial and anti-inflammatory activities. Notably, the detection of pre-aurantiamine and leupyrrin A1, together with the broad diversity of cyclic dipeptides, represents a rare feature among B. subtilis strains. These findings emphasise the potential of B13 as a probiotic in aquaculture practices.

Fusarium species are major fungal pathogens causing root rot in Lonicera macranthoides and other agriculturally and medicinally important plants. They exhibit a broad host range and high pathogenicity, leading to yield losses, reduced quality, and plant mortality. Current control measures rely primarily on chemical pesticides, with few sustainable biological options available. This study compared rhizosphere microbial diversity between healthy and diseased Lonicera macranthoides, revealing increased pathogenic fungi abundance (Fusarium, Plectosphaerella, p < 0.01) and reduced beneficial fungi abundance (Trichoderma) along with significantly lower Chao1 and Shannon diversity indices (p < 0.05). An endophytic Bacillus velezensis strain, NS13, was isolated from healthy roots. Plate confrontation assays showed strong inhibition of Fusarium oxysporum from L. macranthoides and other Fusarium species (Fusarium solani, Fusarium graminearum, Fusarium fujikuroi). The 3.95 Mb genome encoded 4,060 proteins, including 96 biocontrol-related genes. AntiSMASH identified 15 biosynthetic gene clusters, including antifungal (fengycin, surfactin), antibacterial (bacillaene, difficidin), and other bioactive metabolites (bacilysin, bacillibactin), alongside seven potentially novel clusters. The presence of these BGCs was further corroborated by LC-MS/MS metabolomic profiling, which detected multiple corresponding antifungal metabolites, including cyclic dipeptides, fatty acid amides (e.g., erucamide), and oleanolic acid. These results demonstrate soil microbial dysbiosis in L. macranthoides affected by root rot and confirm the broad-spectrum anti-Fusarium potential of NS13, highlighting its promise as a biocontrol resource against Fusarium pathogens in medicinal plants. The findings provide both theoretical insights and practical guidance for developing sustainable biocontrol strategies against Fusarium and other soil-borne pathogens, benefiting both the scientific community and agricultural practitioners.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12866-025-04551-x.

Metabolomic profiling of antifungal Lactiplantibacillus plantarum strains and their inhibition of Aspergillus niger and Penicillium chrysogenum in a cheese matrix.

Molecular networking guided discovery of non-limonoids type ingredients from Citrus medica var. Sarcodactylis fruits.

LC-HRMS-based identification and quantification of novel 2,5-diketopiperazines in roasted coffee.

Genistein and daidzein are isoflavonoid phytoalexins that increase rapidly during bean hypersensitive immunity to Pseudomonas savastanoi pv. phaseolicola. To understand how genistein and daidzein affect P. savastanoi pv. phaseolicola, non-targeted metabolomic mass spectrometry was performed on the bacterium treated in vitro. The bacterium catabolized genistein and daidzein and responded by producing several different classes of compounds including auxin-like indoles and cyclic dipeptides. Non-targeted metabolomic investigation of bean leaves infiltrated with the cyclic dipeptides revealed no similarities to auxin-induced metabolic changes, but one cyclic dipeptide, cyclo-Trp-Pro (cWP), induced the accumulation of phytoalexins. This implied that cWP application might make beans more resistant to pathogens. Challenge with Uromyces appendiculatus, a rust fungal pathogen, revealed that beans pretreated with cWP had 90% reductions in disease. Arabidopsis thaliana sprayed with cWP had activated salicylic acid-mediated immune responses. Overall, these results reveal that P. savastanoi pv. phaseolicola is adapted to tolerate bean genistein and daidzein, likely sensing the compounds as host signals and producing cyclic dipeptides in response. In turn, beans respond to at least one cyclic dipeptide, cWP, by producing phytoalexins to increase resistance. cWP may be useful for protecting beans and other plants from microbial disease.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-33515-4.

A new cyclic dipeptide, cyclo(phenylalanine-proline) (cFP), was isolated from the marine bacterium Exiguobacterium profundum SW22 and characterized by NMR and high-resolution mass spectrometry. In silico profiling predicted favorable pharmacokinetic and drug-like properties for cFP. The compound demonstrated dose-dependent cytotoxicity against human breast (MDA MB-231), pancreatic (PAN C1), and prostate (PC 3) cancer cell lines with IC₅₀ values of 47.24 ± 0.42, 40.96 ± 0.68, and 110 ± 1.48 µM, respectively, accompanied by apoptosis-associated morphological changes. Biophysical studies demonstrated strong binding affinity between cFP and human serum albumin (HSA), confirmed through UV-visible absorption spectroscopy, fluorescence quenching, and circular dichroism analyses, with validation using well-characterized reference ligand warfarin as control. Results suggest static quenching via ground-state complex formation with negligible lifetime changes, consistent with control molecule (warfarin) binding via hydrogen bonding and van der Waals interactions, accompanied by ligand-induced decreases in HSA α-helical content. Molecular docking studies of HSA with cFP and warfarin revealed strong binding affinities for both compounds. Further, the molecular dynamics simulations over a 50 ns timeframe confirmed the enhanced stability and persistent interaction of the cFP-HSA complex. Results highlight the cFP as a promising bioactive peptide with potential anticancer, pharmacokinetic and serum binding efficacies advocating further preclinical development for anticancer therapy.

Abstract Background Cordyceps militaris (Cordycipitaceae) is a parasitic fungus that infects insects or larvae hosts and has been widely used to boost energy and enhance the immune system. A well-known nucleoside from C. militaris , cordycepin (3′-deoxyadenosine), has been reported to exhibit anti-inflammatory, anti-microbial, and anti-oxidant activities. Methods In this study, nine compounds were isolated from C. militaris using chromatographic purification techniques, and their structures were elucidated using spectroscopic analyses, including UV and NMR. Results Four tryptophan-containing cyclic dipeptides ( 1 – 4 ) were isolated from this species for the first time along with five known compounds, and the separation techniques for diketopiperazines were explained. The skeleton of the compounds 1 – 4 is reported for the first time from this species. Conclusion By expanding the chemical profile of C. militaris , our results may open new avenues for investigating its various biological potentials. Graphical abstract

A mild and highly diastereoselective strategy for the direct C3-quaternary carbonation of cyclic dipeptides (CDPs) has been explored using DBU as a base. This approach enabled the efficient functionalization of the C3 position in CDPs that contain a C6 chiral center, affording diverse CDPs with fully substituted carbon stereocenters without protecting amide N-H bonds. Through downstream derivatization, novel quaternary serine analogues have been successfully synthesized.

Cyclic peptides are peptidic macrocycles with ring-constrained backbones that have distinct physicochemical and biological properties, with the simplest being cyclic dipeptides. Four cyclic dipeptides, cyclo(Pro-Pro), cyclo(Pip-Pip), cyclo(PrS-PrS), and the unique sulfur-rich cyclo(PipS-PipS), were synthesized from unprotected amino acids by using a one-pot thionyl chloride-mediated cyclization process, producing 19%-40% without the use of protective-group strategies. FTIR, NMR, and high-resolution mass spectrometry (HRMS) were used to confirm the structures. The 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay was used to assess antioxidant activity, and it was discovered that sulfur incorporation and six-membered ring size significantly increase radical quenching. A cloud-based platform was used to predict electronic properties, such as HOMO-LUMO gaps, dipole moments, and oxidation potential. Compounds with smaller HOMO-LUMO gaps and lower oxidation potentials had higher DPPH scavenging efficiencies, establishing a clear structure-property-activity relationship. This study identifies promising sulfur-containing cyclic dipeptides for future development as antioxidant therapeutics and presents a scalable pathway to diverse cyclic dipeptides.

Cyclic dipeptides, derivatives of 2,5-diketopiperazines, possessing a wide spectrum of biological activity and the ability to self-assemble are of interest for medicine and various technologies. Therefore, the development of methods for their preparation is a topical issue. Synthesis of cyclic dipeptides from their linear analogs in the solid state upon heating is a simple, effective, and atom-economical method. However, for widespread use of this method, the problems associated with a decrease in the yield of a product due to its thermal destruction, epimerization, and sublimation should be solved. One of the ways to increase the yield of the reaction product may be the development of methods for reducing the reaction temperature. In this work, the possibility of obtaining cyclic dipeptide cyclo(GlyGly) from linear GlyGly in the solid state using its amorphous phase instead of the crystalline phase was studied. A method for obtaining the amorphous phase of GlyGly was developed; its thermal properties were studied, and a kinetic analysis of the cyclization reaction was carried out. The effect of the initial dipeptide phase on the yield of the cyclic products was estimated.

CDIS V1.0: A program for non-targeted rapid identification of cyclic dipeptides.

This study investigates the genetic, metabolic, and probiotic characteristics of Levilactobacillus brevis DY55bre, a strain isolated from the traditional Turkish fermented beverage, shalgam. Whole-genome sequencing revealed a circular genome of 2.485Mb with a GC content of 45.72%, predicted 2791 genes, and multiple CRISPR-Cas systems. Pangenome analysis demonstrated an open structure, with 18.9% core genes and 103 strain-specific genes, highlighting its genetic diversity. The DY55bre exhibits heterofermentative carbohydrate metabolism due to the presence of the araBAD operon and the lack of 1-phosphofructokinase (pfK) and fructose-1,6-bisphosphate aldolase enzymes. Probiotic evaluation revealed firm survival under simulated gastrointestinal conditions, including resistance to acidic pH (as low as 3.0) and bile salts (up to 1%), along with significant adhesion to intestinal epithelial cell lines (HT29;59.3%, Caco-2;87%, and DLD-1;60.8%). The strain exhibited high auto-aggregation (84.55%) and cell surface hydrophobicity (56.69%), essential for gut colonization. Safety assessments confirmed its non-hemolytic nature and absence of horizontally acquired antibiotic resistance genes. Notably, GC-MS analysis identified bioactive cyclic dipeptides, Cyclo(D-Phe-L-Pro) and Cyclo(L-Leu-L-Pro), which demonstrated cytotoxic effects against colorectal cancer cell lines, with IC50 values of 7.71mg/mL for HT29 and 3.19mg/mL for DLD-1. The cell-free supernatant exhibited antimicrobial activity against pathogens, likely due to the synergistic effects of cyclic dipeptides, organic acids, and other metabolites. Antioxidant assays revealed significant ABTS+ (76.63%) and DPPH (34.25%) radical scavenging activities, while cholesterol assimilation tests showed a 27.29% reduction. These findings position the DY55bre as a promising candidate for functional foods, nutraceuticals, and therapeutic applications, warranting further in vivo validation.

A total of six secondary metabolites were isolated for the first time from the endophytic bacterium Bacillus halotolerans XJB-35, which was obtained from the stem of the medicinal plant Baccharoides anthelmintica. These metabolites include a cyclic dipeptide, cyclo(L-phenylalanine-L-proline) (1), 1-methylquinolin-4(1H)-one (2), the diketopiperazine cyclo(R-proline-R-phenylalanine) (3), the diketopiperazine cyclo(D-Pro-D-Phe) (4), the indole alkaloid 3-hydroxyacetylindole (5), and tryptophol (6). All isolated compounds were evaluated for their cytotoxic activity and their effects on melanin synthesis in murine B16 cells.

This study aimed to provide the first genomic, functional, and metabolic characterization of Bacillus siamensis B03 from Lang Co Bay, Vietnam, and to evaluate the hypothesis that it harbors unique metabolic traits and antimicrobial potential against Vibrio spp.. B03 showed no hemolytic activity, moderate biofilm formation, tolerance to 10% NaCl, and broad extracellular enzyme secretion. Ethyl acetate extracts from the cell-free supernatant exhibited in vitro antibacterial activity against five Vibrio species, with inhibition zones of 14.7-22.3mm. Metabolomic analysis tentatively identified 20 compounds, mainly cyclic dipeptides, some previously reported to possess antimicrobial properties. Draft, plasmid-free genome (3,745,205bp; 46.4% GC) encodes 3,561 proteins and 72 tRNAs, with genes mainly for amino acid and carbohydrate metabolism, and contains gene clusters for bacillaene, fengycin, difficidin, bacillibactin (100% similarity), and surfactin (78%). Pan-genome analysis of 24 B. siamensis genomes revealed 2,254 core genes, with B03 contributing 31 unique genes, including those encoding NAD-dependent malic enzyme and adenylation domain proteins. These findings suggest B. siamensis B03 as a potential control agent against Vibrio pathogens.

Synthesis and active evaluation of LecB-targeted cyclic dipeptide quorum sensing inhibitors