Pneumonia-induced sepsis is a major cause of acute kidney injury (AKI), which can lead to high morbidity and mortality. Ceragenins, such as CSA-13, are synthetic mimics of antimicrobial peptides with known antimicrobial and immunomodulatory properties. This study aimed to evaluate the hypothesis that CSA-13, administered intraperitoneally following pneumonia-induced sepsis, was able to induce renal protection in mice. C57/BL6 female mice were randomly categorized into four groups (n = 6/group): (1) healthy control; (2) pneumonia control; (3) pneumonia followed by a low dose of CSA-13; and (4) pneumonia followed by a high dose of CSA-13. We tested CSA-13 for its effects on renal tissue IL-6 (inflammation marker) and plasma levels of cystatin C (renal injury marker). Plasma levels of hyaluronan were measured to evaluate glycocalyx degradation. Cellular integrity was assessed by histological evaluation. We found that (1) both CSA-13 doses successfully restored cystatin C; (2) high and low doses of CSA-13 decreased IL-6 levels to normal levels; (3) plasma hyaluronan remained elevated in treated and untreated mice; and (4) cellular integrity was largely maintained by the administration of either high or low doses of CSA-13. Intraperitoneal administration of CSA-13 decreases IL-6 levels in the kidneys and protects kidney function and cellular integrity in a model of pneumonia-induced sepsis. Plasma hyaluronan levels of infected mice were not substantially altered by the administration of ceragenin. CSA-13 may be helpful as a treatment protocol for pneumonia that inhibits acute kidney injury.
A novel rare actinomycete strain, WER1T, was isolated from rhizosphere soil of Broussonetia papyrifera collected from Xiangtan City, Hunan province, China. Strain WER1T contained LL-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan. The major fatty acids (>5%) were anteiso-C15:0, iso-C16:0, anteiso-C17:0 and summed feature 9 (iso-C17:1 ω9c and/or 10-methyl C16:0). The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, and phosphatidylinositol. Sequence analysis of 16S rRNA gene indicated that the strain belonged to the genus Kribbella and shared highest similarities to Kribbella karoonensis Q41T (99.57%), Kribbella speibonae YM55T (99.35%), Kribbella soli FMN22T (99.28%), Kribbella podocarpi YPL1T (99.14%), and Kribbella swartbergensis HMC25T (99.13%). Phylogenetic analysis based on 16S rRNA gene, five house-keeping genes (gyrB, rpoB, relA, recA, and atpD) and whole genome sequences showed that strain WER1T is closely related to K. karoonensis JCM 14304 T. But the average nucleotide identity and digital DNA-DNA hybridization values between strain WER1T and K. karoonensis JCM 14304 T were much less than the 95-96% and 70% cut-off points recommended for delineating species. In addition, phenotypic and chemotaxonomic characteristics further confirmed that strain WER1T represents a new Kribbella species, for which the name Kribbella broussonetiae sp. nov. ( = MCCC 1K10349T = KCTC 59685 T), is proposed.
Two new sterigmatocystin derivatives, named hyposterigmatocystin A and B (1 and 2), and three known compounds, 3a,12c-dihydro-8,12c-dihydroxy-6-methoxy-7H-furo[3',2':4,5]furo[2,3-c]xanthen-7-one (3), sterigmatocystin (4), and secosterigmatocystin (5) were isolated from the culture broth of Hypomyces sp. using various column chromatography techniques. The chemical structures of the isolated compounds were elucidated using spectroscopic methods and comparison with reported data. The isolated compounds were evaluated for their antibacterial activities against four Gram-positive bacteria, exhibiting MIC values ranging from 12.5 to exceeding 200 μg mL-1, with sterigmatocystin (4) being the most potent.
Lipophosphonoxins represent a promising class of membrane-active antimicrobial agents with potential relevance for skin-targeted antimicrobial applications. Antibacterial activity of a panel of LEGO-lipophosphonoxin (LEGO-LPPO) compounds was evaluated by minimum inhibitory concentration (MIC) profiling against selected Gram-positive and Gram-negative bacterial strains. Cellular responses were subsequently assessed in human keratinocytes (HaCaT) and primary human dermal fibroblasts using MTS-based viability assays after 3 and 7 days of exposure across a broad concentration range. The tested LEGO-LPPOs exhibited pronounced variability in antibacterial activity and cytotoxicity profiles. Cell-based screening revealed marked heterogeneity in cellular responses, with fibroblasts consistently showing higher sensitivity than keratinocytes, particularly under prolonged exposure. Based on integrated MIC and IC₅₀ profiles, four representative compounds (DR_527P1, DR_556P1, DR_34P1, and DR_33P1) were selected for further functional characterization using keratinocyte migration assays, cytoskeletal organization analysis, and protein expression profiling. These compounds exerted distinct effects on cell migration, cytoskeletal organization and protein expression. In addition, in vivo tolerability was evaluated by maximal tolerated dose assessment in mice to provide a translational perspective on compound safety. Collectively, these findings show that selected structurally diverse LEGO-LPPO derivatives display divergent biological profiles that are not predicted by antibacterial potency alone. Rather than establishing a comprehensive structure-activity relationship (SAR), this study provides integrated biological profiling of representative LEGO-LPPO compounds and identifies structural diversity points and biological liabilities that should be considered during further optimization for local anti-infective applications.
Antimicrobial Resistance (AMR) has evolved from a clinically observed phenomenon into a complex, dynamic, and partially predictable evolutionary process. Traditional approaches centered on phenotypic detection and retrospective surveillance are increasingly inadequate to address the accelerating pace of resistance emergence. This review presents a paradigm shift toward predictive antimicrobial science, driven by the convergence of Evolutionary Intelligence (EI), Artificial Intelligence (AI), genomic surveillance, molecular simulation, and digital twin technologies. Leveraging whole-genome sequencing (WGS) and resistome analytics, AI models can identify latent resistance determinants and forecast evolutionary trajectories before clinical manifestation, enabling a transition from reactive to anticipatory intervention strategies. Central to this transformation is the concept of the Computational Antimicrobial Resistance Ecosystem (C-AMRE), an integrated, multi-layered framework that unifies data acquisition, predictive modeling, mechanistic simulation, and clinical feedback into a continuous learning system. Within this ecosystem, molecular simulations provide mechanistic insights into resistance at atomic and systems levels, while AI-driven pharmacology enables the design of novel antibiotics, antimicrobial peptides, and Nano-Adjuvants through generative and optimization-based approaches. The incorporation of digital twins further advances precision medicine by simulating patient-specific infection dynamics, pharmacokinetics/pharmacodynamics (PK-PD), and resistance evolution in real time, thereby enabling adaptive and personalized therapeutic strategies. Across micro-, meso-, and macro-scales, these technologies collectively redefine AMR as a systems-level phenomenon that can be modeled, predicted, and strategically managed. However, challenges related to data integration, model interpretability, validation, ethical governance, and global accessibility remain critical barriers to implementation. Despite these limitations, the integration of AI and computational frameworks positions antimicrobial research at the forefront of a new era, where antibiotics are no longer static interventions but adaptive components of intelligent, continuously evolving systems. This review highlights the transition from detection to prediction and ultimately to adaptive intervention, emphasizing the role of computational ecosystems in shaping the future of sustainable antimicrobial therapy.
Antimicrobial peptides (AMPs) represent promising alternatives to conventional antibiotics, but their therapeutic application is often hindered by suboptimal stability and poorly defined mechanisms of action. To overcome these limitations, we engineered a peptide named CAMP502NC3 through chemical modification of its parent peptide, CAMP502, which originates from marine biofilm microorganisms. The design included N-terminal acetylation, C-terminal amidation, and N-methylation of the lysine at position 3 to improve stability. CAMP502NC3 demonstrated potent activity against Staphylococcus aureus and remained stable under diverse conditions, including varying pH, high salinity, and protease exposure. Mechanistically, CAMP502NC3 leads to bacterial membrane depolarization. Transcriptomic and biochemical analyses further revealed that it interferes with key metabolic pathways, notably the fructose-specific phosphotransferase system. Molecular docking indicated direct binding of CAMP502NC3 to the fructose transporter FruA. This study illustrates how rational peptide engineering can generate stable and potent AMPs with precise membrane-associated targets, as exemplified by CAMP502NC3.
Two new agmatine derivatives, luteoagmacins A (1) and B (2), were isolated from the culture extract of the hot spring water-associated actinomycete Luteococcus sp. RD000023. The chemical structures of 1 and 2 were elucidated by spectroscopic analyses, including 1D and 2D NMR spectroscopy, and the structure of 2 was further confirmed by chemical synthesis. Based on disk diffusion and broth microdilution assays using the synthetic material, 2 exhibited broad-spectrum antimicrobial activity against Gram-positive and Gram-negative bacteria, as well as yeast.
One new α-pyrone derivative, acremopyrone A (1) was isolated from the soil-derived fungus Acremonium persicinum 3.2858. The structure of 1 was elucidated by comprehensive spectroscopic analysis including nuclear magnetic resonance (NMR) and high-resolution electrospray ionization mass spectrometry (HRESIMS). Compound 1 showed significant inhibitory activity against α-glucosidase. Enzyme kinetic analysis revealed a mixed-type mode of inhibition, which was further supported by molecular docking studies.
A Gram-positive actinomycete, designated strain C-140ᵀ, was isolated from the crustose lichen Arthonia leioplacella collected in Thailand. A polyphasic taxonomic study demonstrated that the strain represents a member of the genus Actinomycetospora. The 16S rRNA gene sequence analysis showed that strain C-140ᵀ exhibited the highest sequence similarity to Actinomycetospora lutea TT00-04ᵀ (98.62%), followed by Actinomycetospora lemnae DW7H6ᵀ (98.55%). Phylogenomic analysis indicated that Actinomycetospora chlora JCM 17979ᵀ is the closest phylogenetic relative of strain C-140ᵀ. Morphologically, the strain formed extensively branched substrate mycelium that fragmented into cylindrical spores, with swollen spores observed at the tips of the mycelia. The whole-cell hydrolysate contained ribose, arabinose, glucose, and galactose, and the peptidoglycan contained meso-diaminopimelic acid. The predominant menaquinone was MK-8(H₄). The major cellular fatty acid (>10%) was iso-C16:0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, four unidentified phospholipids, two unidentified glycolipids, and five unidentified lipids. Genome-based comparisons revealed that digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain C-140ᵀ and A. chlora JCM 17979ᵀ were below the accepted thresholds for species delineation, supporting the conclusion that strain C-140ᵀ represents a novel species of the genus Actinomycetospora, for which the name Actinomycetospora lichenicola sp. nov. is proposed (=TBRC 20748T = NBRC 117442T). Genome analysis identified several biosynthetic gene clusters, including NRPS, siderophore, and terpene clusters. The strain exhibited weak antimicrobial activity against Kocuria rhizophila.
Allantopyrone A is an α-pyrone metabolite produced by the plant endophytic fungus Allantophomopsis lycopodina KS-97. We previously demonstrated that allantopyrone A decreased the abundance of many components of 26S proteasome fractions while inducing the appearance of an additional protein with a higher apparent molecular mass than known proteasome components. In the present study, we identified this protein as ubiquitin-specific protease 5 (USP5) using mass spectrometry. In cell-based assays, allantopyrone A promoted the cross-linked form of USP5, which was shown by immunoprecipitation to represent a USP5 dimer. The cross-linked form of USP5 was markedly reduced when the C-terminal zinc finger ubiquitin-binding domain (cUBP; residues 175-283) was deleted or when Cys195 was substituted with alanine. Allantopyrone A was also found to reduce the activity of multiple deubiquitinases. USP5 labeling by ubiquitin-vinyl methyl ester was markedly reduced by allantopyrone A or by a Cys335 substitution. Consistent with these biological effects of allantopyrone A on USP5, in silico docking studies suggested that allantopyrone A interacts with Cys195 on the surface of the cUBP domain and is positioned near Cys335 within the catalytic center of the USP domain. These results demonstrate that allantopyrone A promotes USP5 cross-linking and inhibits its deubiquitinase activity through interactions with distinct domains.
Streptomyces species are prolific producers of structurally diverse secondary metabolites with a broad spectrum of biological activities. In this study, we isolated a novel angucyclinone compound, tsukubacyclinone (1), from the culture broth of Streptomyces sp. K21-0141. Tsukubacyclinone (1) exhibited potent anti-inflammatory effects in vitro. RNA sequencing of TNF-α-stimulated synovial cell line, SW982 revealed that tsukubacyclinone (1) downregulated pro-inflammatory genes, including IL1B and IL6, which was further validated by qPCR, without increasing LDH activity. KEGG pathway analysis indicated modulation of TNF, NF-κB, cytokine-cytokine receptor interaction, and JAK-STAT signaling. ELISA further confirmed a dose-dependent suppression of IL-1β and IL-6 protein. These findings suggest that tsukubacyclinone (1), as a novel angucyclinone-type compound, may target upstream cytokine signaling pathways to attenuate synovial inflammation, highlighting its potential as a disease-modifying agent for osteoarthritis and other chronic joint diseases. Future studies are warranted to investigate its in vivo pharmacological effects and molecular targets.
Macrolide antibiotics inhibit bacterial translation and are characterized by the presence of a macrocyclic lactone ring. First discovered as natural products of Streptomyces species, the potency of macrolide antibiotics against a diverse swath of bacterial pathogens has inspired continued efforts to develop semisynthetic derivatives with enhanced efficacy. Often used to treat community-acquired pneumonia, sexually-transmitted diseases, and gut infections, macrolides constitute one of the most commonly prescribed out-patient antibiotic classes in the world. However, those clinical successes have been tempered by the prevalence of macrolide resistance, observations of tolerance, and limited activity against many Gram-negative bacteria. Here, we review the macrolide antibiotic class by summarizing their discovery, biosynthesis, mechanism of action, and causes of failure, which include resistance and tolerance. We then discuss recent work that seeks to identify adjuvant compounds that could be delivered with macrolides to extend their spectrum of activity to more Gram-negative species, including those with multidrug-resistant strains.
Understanding the mechanisms by which silent biosynthetic genes of secondary metabolites in microorganisms are activated is critical to developing ways to enhance natural product production. Our laboratory previously showed that co-culturing fungi with animal immune cells induces the production of secondary metabolites. In this study, we cultured cells at 37 °C (the optimal temperature for human cells) with thermotolerant fungi that can grow at this temperature. This optimized condition was expected to enhance production of otherwise silent metabolite genes. Eight thermotolerant fungi were co-cultured with J774.1 mouse macrophage-like cells at 28 or 37 °C. By comparing extracts, we identified metabolites specifically induced-or markedly enhanced-by co-culture at each temperature. Co-culture of Hamigera avellanea IFM 52957 with J774.1 cells at 37 °C enhanced the expression of two compounds, 1 and 2. Structural analyses identified 1 as 4-hydroxybenzaldehyde and 2 as (Z,Z)-N,N'-[1-[(4-hydroxyphenyl)methylene]-2-[(4-methoxyphenyl)methylene]-1,2-ethanediyl]bis-formamide, designated hamiformamide. Compound 2 inhibited nitric oxide production (IC50 = 49.1 µM), indicating its potential for modulating host immune signaling. In addition, the production of 2 increased under iron-depleted conditions, suggesting it is induced by iron competition with host immune cells.
As a representative example of biosynthetic genome mining aimed at identifying biosynthetic gene clusters whose target is unknown core enzymes for known natural products, we review the biosynthesis of altemicidin (1), SB-203207 (2), and SB-203208 (3). Self-resistance gene-guided genome mining led to the identification of the responsible biosynthetic gene cluster, and heterologous expression of the cluster successfully confirmed the production of compounds 1-3. Biochemical analyses and single-gene expression studies demonstrated that the PLP-dependent enzyme SbzP is a core enzyme of this gene cluster. SbzP accepts β-NAD and SAM as substrates to generate the azaindane scaffold common to compounds 1-3. Subsequent in vitro assays revealed the downstream tailoring reactions, involving the α-ketoglutarate-dependent dioxygenase SbzQ, GNAT-type acyltransferase SbzI, ADP-ribose transferases SbzNHO, F420-dependent reductase SbzF, SAM-dependent methyltransferase SbzE, acyl-tRNA-dependent transferase SbzA, and GNAT-type acyltransferase SbzC, which collectively modify the SbzP product to yield the final structure of compound 3. Structural studies of SbzP and SbzI elucidated the molecular basis for substrate recognition and protein-protein interactions. This review highlights the novelty and utility of investigating biosynthetic gene clusters categorized as Group III and provides new insights into the biosynthesis of β-NAD-derived natural products.
The increased incidence of multi-drug resistant (MDR) Proteus mirabilis highlights the need for novel antibiotics targeting P. mirabilis. In this study, we examined the potential antibacterial effects of gallium-based antimicrobials on P. mirabilis. We performed in vitro susceptibility testing of gallium compounds against P. mirabilis UTI isolates. Ga(NO3)3 and gallium protoporphyrin IX (GaPP) effectively inhibited P. mirabilis growth, with minimum inhibitory concentrations (MIC) of 64 μg/ml and 2.5 μg/ml, respectively. To further assess the effects of gallium compounds on P. mirabilis growth we performed time-kill assays. Ga(NO3)3 was bacteriostatic and prevented P. mirabilis growth over time, while GaPP was bactericidal, effectively killing P. mirablis over time. Free iron in the form of ferric ammonium citrate (FAC) reversed the inhibitory effects of Ga(NO3)3, while the addition of hemin reversed the effects of GaPP on P. mirabilis growth. In vivo, GaPP administered intravesically to the bladder reduced bacterial burden in an animal model of P. mirabilis urinary tract infection. Our results demonstrate that Ga(NO3)3 and GaPP disrupt free iron/heme and siderophore-based iron acquisition in P. mirabilis to inhibit growth. Further work is needed to better determine the effectiveness of gallium in vivo and the potential utility of gallium in treating P. mirabilis infections.
When treated with various compounds, fungi exhibit characteristic morphological changes depending on their mode of action. Previously, we constructed morphology-based databases of the rice blast fungus Pyricularia oryzae and human pathogenic fungus Candida albicans and used them for antifungal screening. As these databases are manually created by human experts, objectivity and throughput may be a concern. To overcome these limitations, we developed a new artificial intelligence (AI)-based automated classification system for morphological changes in the filamentous fungus Aspergillus oryzae. Using this system, we screened a library of 7602 microbial broths and found that the culture broth of Streptomyces sp. RK21-A1205 exhibited potent antifungal activity and induced unique morphological changes distinct from those induced by conventional antifungal agents. Antifungal-activity-guided purification yielded the active metabolite RK-1205-I (1), whose chemical structure was identified as a new fostriecin derivative. 1 showed strong growth inhibitory activity against A. oryzae and other fungi, including A. fumigatus and C. auris, with IC50 value of 0.020 and 0.21 µM, respectively. Furthermore, 1 inhibited protein phosphatase 2A (PP2A) activity in the fungal cells. This study demonstrates that our newly developed AI-based phenotypic screening system can effectively distinguish morphological changes induced by microbial broths and facilitates the identification of novel antifungal compounds.
A novel linear acylated tripeptide, catenulamide A (1), was isolated from a culture extract of Catenuloplanes sp. RD061694. Comprehensive spectroscopic analyses coupled with Marfey's analysis established that 1 comprised n-butyric acid, N-methyl-L-isoleucine, L-valine, and a lactamized new amino acid, 5-methoxy-L-kynurenine lactam. Compound 1 exhibited dual PPARα and PPARγ agonist activities in a luciferase reporter gene assay and anti-inflammatory potential by inhibiting nitric oxide production in lipopolysaccharide-stimulated murine macrophages with an IC50 value of 29 µM. Furthermore, 1 at 1 μM promoted radicle elongation of germinated lettuce seeds by 40% compared to vehicle-treated seeds.
Strain K20-0274T was isolated from a soil sample collected from a sweet potato field fertilized with compost at the Tsukuba-Plant Innovation Research Center farm in Ibaraki Prefecture, Japan. 16S rRNA gene sequence analysis indicated that the strain belonged to the genus Longispora and was most closely related to Longispora fulva DSM 45356T (98.71%) and Longispora urticae DSM 105119T (98.47%). However, both average nucleotide identity and digital DNA-DNA hybridization values between strain K20-0274T and its closely related strains were below the proposed thresholds for bacterial species delineation. Strain K20-0274T formed short sporophores arising from the substrate mycelium that bore chains of more than 20 spores. Strain K20-0274T contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were MK-10(H4) and MK-10(H6). The whole-cell hydrolysates contained galactose, xylose, and mannose. The phospholipid profile comprised phosphatidylethanolamine and phosphatidylinositol. The acyl type of the peptidoglycan was glycolyl. Strain K20-0274T produced γ-L-glutamyl-L-tryptophan, which showed antibacterial activity. Based on a polyphasic approach, strain K20-0274T represents a novel species of the genus Longispora, for which the name Longispora agrisoli sp. nov. is proposed. The type strain of the novel species is K20-0274T (=NBRC 115957T = JCM 37382T = TBRC 17379T).
Streptomyces produce various antibiotics and bioactive compounds as secondary metabolites. Although they are normally found in soil, strains of Streptomyces have also been discovered in non-soil environments, including marine habitats. These non-terrestrial strains may have specific metabolic features compared with those of soil-dwelling Streptomyces. In this study, we investigated phenotypic and taxonomic characteristics, and antibiotic production of a Streptomyces sp. strain TUA-HK1GM that we previously isolated from kusaya gravy, a fermented fish gravy high in salt content. Microbiological analysis revealed distinct properties compared to closely related species, particularly in its ability to grow at 7% NaCl. Phylogenetic analysis suggested that strain TUA-HK1GM is a novel actinomycete species. We investigated the effects of NaCl supplementation on secondary metabolite biosynthesis, with a focus on antibiotic production. This strain produced antifungal compounds in the absence of NaCl, and these compounds were identified as oligomycins A and B. On the other hand, a large amount of anti-Staphylococcus compound was produced alongside oligomycin in the presence of NaCl. This compound had m/z values of 543.2813 [M + H]⁺ and 565.2633 [M+Na]⁺, which were consistent with those of 7-deoxypactamycin. Enhancement (32-fold) of oligomycin A production was also observed in a manner dependent on the duration of NaCl exposure. Supplementation with NaCl during cultivation demonstrated that prolonged exposure to NaCl increased the antibiotic production. These results indicate that the novel strain TUA-HK1GM has a characteristic mechanism that involves secondary metabolic activation by NaCl.
