Importance of microbial natural products and the need to revitalize their discovery

Natural sideromycins and siderophore-conjugated natural products as inspiration for novel antimicrobial agents

The widespread emergence of multidrug-resistant (MDR) Gram-negative pathogens has posed a major challenge to clinical anti-infective therapy, and new effective treatments are urgently needed. A promising "Trojan horse" strategy involves conjugating antibiotics to siderophore molecules; the resulting siderophore-antibiotic conjugates (SACs) deliver antibiotics directly into cells by hijacking the sophisticated iron transport systems of Gram-negative bacteria, bypassing the outer membrane permeability barrier to enhance uptake and antibacterial efficacy. The clinical release of the first siderophore-antibiotic conjugate, cefiderocol, has aroused tremendous interest in the field among researchers and pharmaceutical companies. To date, most of the reported SACs have focused on the conjugation of siderophores to traditional antibacterial drugs. However, these antibacterial agents designed on the basis of the traditional antibiotic skeleton theoretically bear the risk of cross-resistance caused by shared molecular scaffolds. In this case, exploring novel natural product antibacterial conjugate scaffolds to circumvent the risk of early cross-resistance represents a presumably more sustainable approach for the development of SACs. In this review, we systematically summarize the research progress on siderophore-natural product conjugates as novel antimicrobial agents reported since 2010. Additionally, we propose challenges to be overcome and prospects for future development in this field.

Microbial secondary metabolites: advancements to accelerate discovery towards application

Microbial secondary metabolites not only have key roles in microbial processes and relationships but are also valued in various sectors of today's economy, especially in human health and agriculture. The advent of genome sequencing has revealed a previously untapped reservoir of biosynthetic capacity for secondary metabolites indicating that there are new biochemistries, roles and applications of these molecules to be discovered. New predictive tools for biosynthetic gene clusters (BGCs) and their associated pathways have provided insights into this new diversity. Advanced molecular and synthetic biology tools and workflows including cell-based and cell-free expression facilitate the study of previously uncharacterized BGCs, accelerating the discovery of new metabolites and broadening our understanding of biosynthetic enzymology and the regulation of BGCs. These are complemented by new developments in metabolite detection and identification technologies, all of which are important for unlocking new chemistries that are encoded by BGCs. This renaissance of secondary metabolite research and development is catalysing toolbox development to power the bioeconomy.

Assessing Normandy Soil Microbial Diversity for Antibacterial Activities Using Traditional Culture and iChip Methods

Uncultured microorganisms represent a promising and untapped source of antibacterial compounds, crucial in the fight against the significant threat of antimicrobial resistance (AMR). In this study, both traditional and isolation chip (iChip) cultivation techniques were employed to enhance the recovery of known and unknown microorganisms from soils located in Normandy, France. The isolates obtained were identified using 16S rDNA or ITS regions analysis and MALDI-TOF mass spectrometry and were screened for antibacterial activity. A total of 386 isolates, belonging to 6 microbial phyla and distributed across 65 genera, were recovered using both methods. In total, 11 isolates are potentially new bacterial species, and 34 were associated with 22 species described recently. The iChip method yielded a higher diversity of microorganisms (47 genera) than the traditional method (38 genera) and was particularly effective in enriching Actinomycetota. Antibacterial screening against target bacteria showed that 85 isolates (22%) exhibited antibacterial activity. The Streptomyces, Pseudomonas, and Bacillaceae taxa accounted for most antibacterial-producing bacteria with some presenting promising undescribed characteristics. Other active isolates were affiliated with less-known antibacterial producers such as Arthrobacter, Chryseobacterium, Delftia, Ensifer, Flavobacterium, Rahnella, and Stenotrophomonas, among others. These results highlight the potential of our microbial collection as a source of new antibacterial natural products.

Aspergillus-Penicillium co-culture: An investigation of bioagents for controlling Fusarium proliferatum-induced basal rot in onion

Fungal co-culture is a method that allows the detection of interactions between fungi, enabling the examination of bioactive novel metabolites induction that may not be produced in monocultures. Worldwide, Fusarium basal rot is a primary limitation to onion yield, being caused by different Fusarium species. Current research directions encourage biological control of plant diseases as a replacement for routine chemical treatments. The current study aimed to investigate the co-culturing technique for mining new sources of bioagents that could be used as fungicides. Aspergillus ochraceus AUMC15539 was co-cultured with Penicillium chrysogenum AUMC15504, and their ethyl acetate extract was tested in vitro and in a greenhouse against Fusarium proliferatum AUMC15541. The results showed that Aspergillus-Penicillium (AP) co-culture extract significantly inhibited the growth of F. proliferatum with an MIC value of 0.78 mg/mL and showed antioxidant efficiency with an IC50 value of 1.31 mg/mL. The brine shrimp toxicity testing showed a LC50 value of 2.77 mg/mL. In addition, the co-culture extract showed the highest phenolic content at 114.71 GAE mg/g, with a 27.82 QE mg/g flavonoid content. Profiling of AP co-culture and its monoculture extracts by HPLC revealed a change in the metabolites profile in AP co-culture. Principal component analysis verified a positive correlation between the obtained HPLC data of A. ochraceus (A), P. chrysogenum (P), and AP extracts. Greenhouse experiments demonstrated that treating infected onion plants with the AP co-culture extract significantly enhanced all growth parameters. Additionally, the co-culture extract treatment resulted in the highest levels of total pigments (3.46 mg/g), carbohydrates (52.10 mg/g dry weight), proteins (131.44 mg/g), phenolics (41.66 GAE mg/g), and flavonoids (9.43 QE mg/g) compared with other treatments. This indicates a promising potential for fungal co-cultures in discovering new bioagents with antifungal properties and growth-promoting capabilities.

Broad-spectrum antimicrobial activities of a food fermentate of Aspergillus oryzae

Amid persistent concerns over microbial foodborne illnesses and escalating antibiotic resistance, we introduce "NP," a novel and effective broad-spectrum natural antimicrobial product derived from the filtered culture broth of Aspergillus oryzae grown in a food-grade liquid medium. NP demonstrates potent bactericidal activity against a range of food-borne and ESKPAE pathogens, including Staphylococcus aureus (including eight distinct drug-resistant methicillin-resistant Staphylococcus aureus strains), Listeria monocytogenes, Salmonella typhimurium, Klebsiella pneumonia, Pseudomonas aeruginosa, and Escherichia coli (including O157:H7) with minimal inhibitory strength ranging from 25% to 100%. In addition, NP exhibits robust antifungal activity against several human pathogenic fungi including Aspergillus fumigatus, Candida albicans, and the prevalent food spoilage mold Penicillium species, arresting spore germination and vegetative cell growth. Mechanistically, NP disrupts the structural integrity of bacterial and fungal cell membranes, increasing membrane permeability and leading to cell death. Furthermore, genome-wide expression analyses of A. fumigatus vegetative cells exposed to NP reveal the downregulation of genes associated with the liveness of the fungal cells including ergosterol biosynthesis, cell wall maintenance, and development, with network analysis highlighting NP's impact on various metabolic pathways. Notably, NP is presumed safe and thermally stable, holding promise for addressing foodborne illnesses and drug-resistant infections through the development and widespread application of a new generation of antimicrobials.

IMPORTANCE

The development of NP, a potent broad-spectrum antimicrobial, is a significant breakthrough in the ongoing challenge against microbial foodborne illnesses and the growing threat of antibiotic resistance. This food-grade culture broth of Aspergillus oryzae demonstrates exceptional broad-spectrum efficacy against a variety of harmful bacteria and fungi, including drug-resistant strains such as methicillin-resistant Staphylococcus aureus and prevalent food spoilage molds. NP exhibits strong bactericidal activity against various foodborne and ESKAPE pathogens, and strong antifungal activity against Penicillium species, Aspergillus fumigatus, and Candida albicans. The potent bactericidal and antifungal properties of NP are a result of its ability to disrupt microbial cell membranes leading to increased permeability. Furthermore, the genome-wide impact of NP on fungal gene expression and metabolic pathways underscores its comprehensive antimicrobial action, leading to transcriptomic and metabolic changes associated with cell death in A. fumigatus.

Biotechnological and pharmaceutical potential of twenty-eight novel type strains of Actinomycetes from different environments worldwide

Actinomycetes are a prolific source of bioactive natural compounds many of which are used as antibiotics or other drugs. In this study we investigated the genomic and biochemical diversity of 32 actinobacterial strains that had been deposited at the DSMZ-German Collection of Microorganisms and Cell Cultures decades ago. Genome-based phylogeny and in silico DNA-DNA hybridization supported the assignment of these strains to 26 novel species and two novel subspecies and a reclassification of a Streptomyces species. These results were consistent with the biochemical, enzymatic, and chemotaxonomic features of the strains. Most of the strains showed antimicrobial activities against a range of Gram-positive and Gram-negative bacteria, and against yeast. Genomic analysis revealed the presence of numerous unique biosynthetic gene clusters (BGCs) encoding for potential novel antibiotic and anti-cancer compounds. Strains DSM 41636T and DSM 61640T produced the antibiotic compounds A33853 and SF2768, respectively. Overall, this reflects the significant pharmaceutical and biotechnological potential of the proposed novel type strains and underlines the role of prokaryotic systematics for drug discovery. In order to compensate for the gender gap in naming prokaryotic species, we propose the eponyms for all newly described species to honour female scientists.

Anti-cancer activity of secreted aspartyl proteinase protein from Candida tropicalis on human cervical cancer HeLa cells

Cervical cancer is the fourth leading cause of cancer-related death in women worldwide. Microbial products are valuable sources of anti-cancer drugs. The aim of this study was to isolate secreted aspartyl proteinase protein from Candida tropicalis, investigate its inhibitory effect on human cervical cancer HeLa cells, and analyze the expression profiling of selected nuclear stem cell-associated transcription factors. The presence of secreted aspartyl proteinase protein was confirmed by the expression of SAP2 and SAP4 genes in C. tropicalis during the yeast-hyphae transition phase. The enzyme was purified and characterized using the aqueous two-phase system purification method, as well as proteolytic activity and the Bradford and micro-Kjeldahl methods, respectively. The in vitro anti-cancer properties of secreted aspartyl proteinase protein were evaluated by MTT assay, microscopic image analysis, nitric oxide (NO) scavenging activity assay, intracellular reactive oxygen species (ROS) production assay, and RT-qPCR. The isolated C. tropicalis secreted aspartyl proteinase protein exhibited proteinase activity with values ranging from 93.72 to 130.70 μg/mL and 89.88-127.72 μg/mL according to the Bradford and micro-Kjeldahl methods, respectively. Secreted aspartyl proteinase showed effective cytotoxicity in HeLa cell line leading to significant morphological changes. Additionally, it exhibited increased free radical scavenging activity compared to the untreated control group, as evidenced by nitrite inhibition. ROS production increased in HeLa cells exposed to secreted aspartyl proteinase. The expression levels of the nuclear stem cell-associated transcription factors octamer-binding transcription factor 4 (OCT4), sex determining region Y-box 2 (SOX2), and Nanog homeobox (NANOG) were significantly downregulated in the HeLa cells treated with secreted aspartyl proteinase. Secreted aspartyl proteinase protein may be a promising anti-cancer agent, as it effectively affects gene expression and may ultimately reduce the development and progression of cervical cancer. Targeting the genes related to nuclear stem cell-associated transcription factors may provide a novel amenable to cancer treatment.

New cyclic dipeptide discovered from deep-sea derived Aspergillus sp. HDN20-1401

A new alkaloid named aspergilalkaloid A (1) with pyridoindole hydroxymethyl piperazine dione structure along with six known compounds 2-7 were isolated from deep-sea derived fungus Aspergillus sp. HDN20-1401. The structure including absolute configuration was elucidated by extensive NMR analyses, HRESIMS, ECD calculation, and theoretical NMR calculation with DP4+ analysis. All isolated compounds were tested for antimicrobial and anticancer activity. Aspergilalkaloid A (1) showed inhibitive activity against Bacillus cereus with MIC value of 12.5 μM and weak activity against MRCNS.

High-Throughput Mining of Novel Compounds from Known Microbes: A Boost to Natural Product Screening

Advanced techniques can accelerate the pace of natural product discovery from microbes, which has been lagging behind the drug discovery era. Therefore, the present review article discusses the various interdisciplinary and cutting-edge techniques to present a concrete strategy that enables the high-throughput screening of novel natural compounds (NCs) from known microbes. Recent bioinformatics methods revealed that the microbial genome contains a huge untapped reservoir of silent biosynthetic gene clusters (BGC). This article describes several methods to identify the microbial strains with hidden mines of silent BGCs. Moreover, antiSMASH 5.0 is a free, accurate, and highly reliable bioinformatics tool discussed in detail to identify silent BGCs in the microbial genome. Further, the latest microbial culture technique, HiTES (high-throughput elicitor screening), has been detailed for the expression of silent BGCs using 500-1000 different growth conditions at a time. Following the expression of silent BGCs, the latest mass spectrometry methods are highlighted to identify the NCs. The recently emerged LAESI-IMS (laser ablation electrospray ionization-imaging mass spectrometry) technique, which enables the rapid identification of novel NCs directly from microtiter plates, is presented in detail. Finally, various trending 'dereplication' strategies are emphasized to increase the effectiveness of NC screening.

Insights into docking in megasynthases from the investigation of the toblerol trans-AT polyketide synthase: many α-helical means to an end

The fidelity of biosynthesis by modular polyketide synthases (PKSs) depends on specific moderate affinity interactions between successive polypeptide subunits mediated by docking domains (DDs). These sequence elements are notably portable, allowing their transplantation into alternative biosynthetic and metabolic contexts. Herein, we use integrative structural biology to characterize a pair of DDs from the toblerol trans-AT PKS. Both are intrinsically disordered regions (IDRs) that fold into a 3 α-helix docking complex of unprecedented topology. The C-terminal docking domain (CDD) resembles the 4 α-helix type (4HB) CDDs, which shows that the same type of DD can be redeployed to form complexes of distinct geometry. By carefully re-examining known DD structures, we further extend this observation to type 2 docking domains, establishing previously unsuspected structural relations between DD types. Taken together, these data illustrate the plasticity of α-helical DDs, which allow the formation of a diverse topological spectrum of docked complexes. The newly identified DDs should also find utility in modular PKS genetic engineering.

Actinomycetota bioprospecting from ore-forming environments

Natural products from Actinomycetota have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.

Exploring halophilic environments as a source of new antibiotics

Microbial natural products from microbes in extreme environments, including haloarchaea, and halophilic bacteria, possess a huge capacity to produce novel antibiotics. Additionally, enhanced isolation techniques and improved tools for genomic mining have expanded the efficiencies in the antibiotic discovery process. This review article provides a detailed overview of known antimicrobial compounds produced by halophiles from all three domains of life. We summarize that while halophilic bacteria, in particular actinomycetes, contribute the vast majority of these compounds the importance of understudied halophiles from other domains of life requires additional consideration. Finally, we conclude by discussing upcoming technologies- enhanced isolation and metagenomic screening, as tools that will be required to overcome the barriers to antimicrobial drug discovery. This review highlights the potential of these microbes from extreme environments, and their importance to the wider scientific community, with the hope of provoking discussion and collaborations within halophile biodiscovery. Importantly, we emphasize the importance of bioprospecting from communities of lesser-studied halophilic and halotolerant microorganisms as sources of novel therapeutically relevant chemical diversity to combat the high rediscovery rates. The complexity of halophiles will necessitate a multitude of scientific disciplines to unravel their potential and therefore this review reflects these research communities.

A flexible, modular and versatile functional part assembly toolkit for gene cluster engineering in Streptomyces

Streptomyces has enormous potential to produce novel natural products (NPs) as it harbors a huge reservoir of uncharacterized and silent natural product biosynthetic gene clusters (BGCs). However, the lack of efficient gene cluster engineering strategies has hampered the pace of new drug discovery. Here, we developed an easy-to-use, highly flexible DNA assembly toolkit for gene cluster engineering. The DNA assembly toolkit is compatible with various DNA assembling approaches including Biobrick, Golden Gate, CATCH, yeast homologous recombination-based DNA assembly and homing endonuclease-mediated assembly. This compatibility offers great flexibility in handling multiple genetic parts or refactoring large gene clusters. To demonstrate the utility of this toolkit, we quantified a library of modular regulatory parts, and engineered a gene cluster (act) using characterized promoters that led to increased production. Overall, this work provides a powerful part assembly toolkit that can be used for natural product discovery and optimization in Streptomyces.

Proposing of fungal endophyte secondary metabolites as a potential inhibitors of 2019-novel coronavirus main protease using docking and molecular dynamics

In this study, the inhibitory potential of 99 fungal derived secondary metabolites was predicted against SARS-CoV-2 main protease by using of computational approaches. This protein plays an important role in replication and is one of the important targets to inhibit viral reproduction. Among the 99 reported compounds, the 9 of them with the highest binding energy to Mpro obtained from the molecular docking method were selected for the molecular dynamic simulations. The compounds were then investigated by using the SwissADME serve to evaluate the compounds in terms of pharmacokinetic and druglikness properties. The overall results of different analysis show that the compound RKS-1778 is potentially more effective than others and form strong complexes with viral protease. It also had better pharmacokinetic properties than other metabolites, so predicted to be a suitable candidate as anti SARS-CoV-2 bioactive.Communicated by Ramaswamy H. Sarma.

A proteomic landscape of pharmacologic perturbations for functional relevance

Pharmacological perturbation studies based on protein-level signatures are fundamental for drug discovery. In the present study, we used a mass spectrometry (MS)-based proteomic platform to profile the whole proteome of the breast cancer MCF7 cell line under stress induced by 78 bioactive compounds. The integrated analysis of perturbed signal abundance revealed the connectivity between phenotypic behaviors and molecular features in cancer cells. Our data showed functional relevance in exploring the novel pharmacological activity of phenolic xanthohumol, as well as the noncanonical targets of clinically approved tamoxifen, lovastatin, and their derivatives. Furthermore, the rational design of synergistic inhibition using a combination of histone methyltransferase and topoisomerase was identified based on their complementary drug fingerprints. This study provides rich resources for the proteomic landscape of drug responses for precision therapeutic medicine.

Rapid Discovery of Substances with Anticancer Potential from Marine Fungi Based on a One Strain-Many Compounds Strategy and UPLC-QTOF-MS

The secondary metabolites of marine fungi with rich chemical diversity and biological activity are an important and exciting target for natural product research. This study aimed to investigate the fungal community in Quanzhou Bay, Fujian, and identified 28 strains of marine fungi. A total of 28 strains of marine fungi were screened for small-scale fermentation by the OSMAC (One Strain-Many Compounds) strategy, and 77 EtOAc crude extracts were obtained and assayed for cancer cell inhibition rate. A total of six strains of marine fungi (P-WZ-2, P-WZ-3-2, P-WZ-4, P-WZ-5, P56, and P341) with significant changes in cancer cell inhibition induced by the OSMAC strategy were analysed by UPLC-QTOF-MS. The ACD/MS Structure ID Suite software was used to predict the possible structures with inhibitory effects on cancer cells. A total of 23 compounds were identified, of which 10 compounds have been reported to have potential anticancer activity or cytotoxicity. In this study, the OSMAC strategy was combined with an untargeted metabolomics approach based on UPLC-QTOF-MS to efficiently analyse the effect of changes in culture conditions on anticancer potentials and to rapidly find active substances that inhibit cancer cell growth.

Optimization of multi-enzyme cascade process for the biosynthesis of benzylamine

Benzylamine is a valuable intermediate in the synthesis of organic compounds such as curing agents and antifungal drugs. To improve the efficiency of benzylamine biosynthesis, we identified the enzymes involved in the multi-enzyme cascade, regulated the expression strength by using RBS engineering in Escherichia coli, and established a regeneration-recycling system for alanine. This is a cosubstrate, coupled to cascade reactions, which resulted in E. coli RARE-TP and can synthesize benzylamine using phenylalanine as a precursor. By optimizing the supply of cosubstrates alanine and ammonia, the yield of benzylamine produced by whole-cell catalysis was increased by 1.5-fold and 2.7-fold, respectively, and the final concentration reached 6.21 mM. In conclusion, we achieved conversion from l-phenylalanine to benzylamine and increased the yield through enzyme screening, expression regulation, and whole-cell catalytic system optimization. This demonstrated a green and sustainable benzylamine synthesis method, which provides a reference and additional information for benzylamine biosynthesis research.

Health-Promoting Effects of Bioactive Compounds from Plant Endophytic Fungi

The study examines the intricate relationship between plants and the endophytic fungi inhabiting their tissues. These fungi harmoniously coexist with plants, forming a distinct symbiotic connection that has caught scientific attention due to its potential implications for plant health and growth. The diverse range of bioactive compounds produced by these fungi holds significant promise for human health. The review covers various aspects of this topic, starting by introducing endophytic microorganisms, explaining their colonization of different plant parts, and illuminating their potential roles in enhancing plant defense against diseases and promoting growth. The review emphasizes the widespread occurrence and diversity of these microorganisms among plant species while highlighting the complexities and significance of isolating and extracting bioactive compounds from them. It focuses on the health benefits of these bioactive compounds, including their capacity to exhibit antioxidant, anti-inflammatory, antimicrobial, and anticancer effects. The review delves into the mechanisms behind these health-promoting effects, spotlighting how the compounds interact with cellular receptors, signaling pathways, and gene expression. In conclusion, the review provides a comprehensive overview of health-promoting bioactive compounds from plant endophytic fungi. It outlines their multifaceted impact, potential applications, and future research avenues in health and medicine.

Complete Genome Sequence of Streptomyces sp. HP-A2021, a Promising Bacterium for Natural Product Discovery

Streptomyces are one of the most prolific sources of bioactive and structurally diverse secondary metabolites for natural product drug discovery. Genome sequencing and bioinformatics analysis revealed that the genomes of Streptomyces harbor a wealth of cryptic secondary metabolite biosynthetic gene clusters that could encode novel compounds. In this work, a genome mining approach was employed to investigate the biosynthetic potential of Streptomyces sp. HP-A2021, isolated from rhizosphere soil of Ginkgo biloba L. The complete genome of HP-A2021 was sequenced and contained the 9,607,552 base pair linear chromosome with a GC content of 71.07%. The annotation results revealed the presence of 8534 CDSs, 76 tRNA genes, and 18 rRNA genes in HP-A2021. The highest dDDH and ANI values based on genome sequences between HP-A2021 and the most closely related type strain, Streptomyces coeruleorubidus JCM 4359, were 64.2% and 92.41%, respectively. In total, 33 secondary metabolite biosynthetic gene clusters with an average length of 105,594 bp were identified, including the putative thiotetroamide, alkylresorcinol, coelichelin, and geosmin. The antibacterial activity assay confirmed that the crude extracts of HP-A2021 showed potent antimicrobial activity against human pathogenic bacteria. Our study demonstrated that Streptomyces sp. HP-A2021 will propose a potential use in biotechnological and novel bioactive secondary metabolite biosynthetic applications.

Iseoic acids and bisiseoate: three new naphthohydroquinone/naphthoquinone-class metabolites from a coral-derived Streptomyces

Two new naphthohydroquinone derivatives designated iseoic acids A (1) and B (2) and a new symmetrical glycerol bisester of naphthoquinonepropanoic acid designated bisiseoate (3) were isolated from the culture extract of a marine-derived actinomycete Streptomyces sp. DC4-5. The structures of 1-3 were determined by analyzing one- and two-dimensional NMR data and MS analytical data. The absolute configurations were determined by NOESY analysis and the phenylglycine methyl ester (PGME) method for 1 and by considering the structural similarity and biosynthesis for 2 and 3. Compound 3 exhibited modest cytotoxicity against P388 murine leukemia cells with an IC50 value of 19 μM.

Protocatechuic acid inhibits LPS-induced mastitis in mice through activating the pregnane X receptor

Mastitis refers to the inflammation in the mammary gland caused by various reasons. Protocatechuic acid (PCA) exerts anti-inflammatory effect. However, no studies have shown the protective role of PCA on mastitis. We investigated the protective effect of PCA on LPS-induced mastitis in mice and elucidated its possible mechanism. LPS-induced mastitis model was established by injection of LPS into the mammary gland. The pathology of mammary gland, MPO activity and inflammatory cytokine production were detected to evaluate the effects of PCA on mastitis. In vivo, PCA significantly attenuated LPS-induced mammary pathological changes, MPO activity, TNF-α and IL-1β production. In vitro, the production of inflammatory cytokines TNF-α and IL-1β was significantly reduced by PCA. Furthermore, LPS-induced NF-κB activation was also inhibited by PCA. In addition, PCA was found to activate pregnane X receptor (PXR) transactivation and PCA dose-dependently increased the expression of PXR downstream molecule CYP3A4. In addition, the inhibitory effect of PCA on inflammatory cytokine production was also reversed when PXR was knocked down. In conclusion, the protective effects of PCA on LPS-induced mastitis in mice through regulating PXR.

Chemical constituents of Aspergillus udagawae isolated from the soil of the Xingren coal areas and their antibacterial activities

A new helvolic acid derivative (1), together with nine known compounds (2-10) were isolated from the metabolites of Aspergillus udagawae MST1-10 with the bioassay-guided fractionation method. Their structures were identified on the basis of spectroscopic analysis. The absolute configuration of compound 1 was elucidated through NOESY and ECD spectra. Compound 2 displayed significant antibacterial activities against Stenotrophomonas maltophilia with MIC value of 2 μg/mL (Trimethoprim, MIC = 64 μg/mL), and with biofilm inhibition rates of 96.41%, 87.77%, and 41.70% at 4MIC, 2MIC, and MIC, respectively.

Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic

Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. Here, we investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans spanning 100 kya to the present and reconstructed 459 bacterial metagenome-assembled genomes (MAGs). We identified a biosynthetic gene cluster (BGC) shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites we name paleofurans. This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.

Secondary Metabolic Potential of Kutzneria

Kutzneria is a rare genus of Actinobacteria that harbors a variety of secondary metabolite gene clusters and produces several interesting types of bioactive secondary metabolites. Recent efforts have partially elucidated the biosynthetic pathways of some of these bioactive natural products, suggesting the diversity and specificity of secondary metabolism within this genus. Here, we summarized the chemical structures, biosynthetic pathways, and key metabolic enzymes of the secondary metabolites isolated from Kutzneria strains. In-depth comparative genomic analysis of all six available high-quality Kutzneria genomes revealed that the majority (77%) of the biosynthetic gene cluster families of Kutzneria were untapped and identified homologues of key metabolic enzymes in the putative gene clusters, including cytochrome P450s, halogenases, and flavin-dependent N-hydroxylases. The present study suggests that Kutzneria exhibits great potential to synthesize novel secondary metabolites, encodes a variety of valuable metabolic enzymes, and also provides valuable information for the targeted discovery and biosynthesis of novel natural products from Kutzneria.

Discovery and excavation of lichen bioactive natural products

Lichen natural products are a tremendous source of new bioactive chemical entities for drug discovery. The ability to survive in harsh conditions can be directly correlated with the production of some unique lichen metabolites. Despite the potential applications, these unique metabolites have been underutilized by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability, and technical challenges involved in their artificial cultivation. At the same time, DNA sequence data have revealed that the number of encoded biosynthetic gene clusters in a lichen is much higher than in natural products, and the majority of them are silent or poorly expressed. To meet these challenges, the one strain many compounds (OSMAC) strategy, as a comprehensive and powerful tool, has been developed to stimulate the activation of silent or cryptic biosynthetic gene clusters and exploit interesting lichen compounds for industrial applications. Furthermore, the development of molecular network techniques, modern bioinformatics, and genetic tools is opening up a new opportunity for the mining, modification, and production of lichen metabolites, rather than merely using traditional separation and purification techniques to obtain small amounts of chemical compounds. Heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offer a promising means for a sustainable supply of specialized metabolites. In this review, we summarized the known lichen bioactive metabolites and highlighted the application of OSMAC, molecular network, and genome mining-based strategies in lichen-forming fungi for the discovery of new cryptic lichen compounds.

On Finding Natural Antibiotics based on TCM Formulae

CONTEXT

Novel kinds of antibiotics are needed to combat the emergence of antibacterial resistance. Natural products (NPs) have shown potential as antibiotic candidates. Current experimental methods are not yet capable of exploring the massive, redundant, and noise-involved chemical space of NPs. In silico approaches are needed to select NPs as antibiotic candidates.

OBJECTIVE

This study screens out NPs with antibacterial efficacy guided by both TCM and modern medicine and constructed a dataset aiming to serve the new antibiotic design.

METHOD

A knowledge-based network is proposed in this study involving NPs, herbs, the concepts of TCM, and the treatment protocols (or etiologies) of infectious in modern medicine. Using this network, the NPs candidates are screened out and compose the dataset. Feature selection of machine learning approaches is conducted to evaluate the constructed dataset and statistically validate the im- portance of all NPs candidates for different antibiotics by a classification task.

RESULTS

The extensive experiments prove the constructed dataset reaches a convincing classification performance with a 0.9421 weighted accuracy, 0.9324 recall, and 0.9409 precision. The further visu- alizations of sample importance prove the comprehensive evaluation for model interpretation based on medical value considerations.

Polyene Carboxylic Acids from a Streptomyces sp. Isolated from Tibet Soil

Six new polyene carboxylic acids named serpentemycins E–J (1–6), together with three known analogs (7–9), were isolated from the fermentation medium of Streptomyces sp. TB060207, which was isolated from arid soil collected from Tibet, China. The structures of the new compounds were elucidated mainly on the basis of HR-ESI-MS and NMR spectroscopic analyses. The inhibitory activities of compounds 1–9 against NO production in LPS-activated RAW264.7 cells were evaluated. Compound 9 has an inhibition rate of 87.09% to 60.53% at concentrations ranging from 5.0 to 40.0 µM.

Decrypting the programming of β-methylation in virginiamycin M biosynthesis

During biosynthesis by multi-modular trans-AT polyketide synthases, polyketide structural space can be expanded by conversion of initially-formed electrophilic β-ketones into β-alkyl groups. These multi-step transformations are catalysed by 3-hydroxy-3-methylgluratryl synthase cassettes of enzymes. While mechanistic aspects of these reactions have been delineated, little information is available concerning how the cassettes select the specific polyketide intermediate(s) to target. Here we use integrative structural biology to identify the basis for substrate choice in module 5 of the virginiamycin M trans-AT polyketide synthase. Additionally, we show in vitro that module 7, at minimum, is a potential additional site for β-methylation. Indeed, analysis by HPLC-MS coupled with isotopic labelling and pathway inactivation identifies a metabolite bearing a second β-methyl at the expected position. Collectively, our results demonstrate that several control mechanisms acting in concert underpin β-branching programming. Furthermore, variations in this control - whether natural or by design - open up avenues for diversifying polyketide structures towards high-value derivatives.

Species-specific secondary metabolism by actinomycetes of the genus Phytohabitans and discovery of new pyranonaphthoquinones and isatin derivatives

To further exploit secondary metabolic potential of a minor actinomycete genus Phytohabitans within the family Micromonosporaceae, metabolite profiling by HPLC-UV analysis, combined with 16S rDNA sequence-based phylotyping were attempted on seven Phytohabitans strains available at the public culture collection. The strains were grouped into three clades and each exhibited unique and distinct metabolite profiles, which were highly conserved among strains within the same clade. These results were consistent with previous observations on two other actinomycetes genera, reconfirming species-specificity of secondary metabolite production, which were conventionally thought to be strain-specific. A strain RD003215, belonging to the P. suffuscus clade, produced multiple metabolites, some of which were presumed to be naphthoquinones. Liquid fermentation followed by chromatographic separation of the broth extract led to the discovery of three new pyranonaphthoquinones, designated habipyranoquinones A-C (1-3), and one new isatin derivative, (R)-N-methyl-3-hydroxy-5,6-dimethoxyoxindole (4), along with three known synthetic compounds, 6,8-dihydroxydehydro-α-lapachone (5), N-methyl-5,6-dimethoxyisatin (6), and 5,6-dimethoxyisatin (7). Structures of 1-4 were unequivocally elucidated by NMR, MS, and CD spectral analysis, with assistance of density functional theory-based NMR chemical shift prediction and ECD spectral calculation. Compound 2 displayed antibacterial activity against Kocuria rhizophila and Staphylococcus aureus with MIC 50 µg/mL and cytotoxicity against P388 murine leukemia cells with an IC₅₀ value of 34 µM. Compounds 1 and 4 also showed cytotoxicity against P388 cells with IC₅₀ values of 29 and 14 µM, respectively.

Mass Spectrometry-Based High-Throughput Quantification of Bioproducts in Liquid Culture

To meet the ever-increasing need for high-throughput screening in metabolic engineering, information-rich, fast screening methods are needed. Mass spectrometry (MS) provides an efficient and general approach for metabolite screening and offers the capability of characterizing a broad range of analytes in a label-free manner, but often requires a range of sample clean-up and extraction steps. Liquid extraction surface analysis (LESA) coupled MS is an image-guided MS surface analysis approach that directly samples and introduces metabolites from a surface to MS. Here, we combined the advantages of LESA-MS and an acoustic liquid handler with stable isotope-labeled internal standards. This approach provides absolute quantitation of target chemicals from liquid culture-dried droplets and enables high-throughput quantitative screening for microbial metabolites. In this study, LESA-MS was successfully applied to quantify several different metabolites (itaconic acid, triacetic acid lactone, and palmitic acid) from different yeast strains in different mediums, demonstrating its versatility, accuracy, and efficiency across a range of microbial engineering applications.

Computer-aided, resistance gene-guided genome mining for proteasome and HMG-CoA reductase inhibitors

Secondary metabolites (SMs) are biologically active small molecules, many of which are medically valuable. Fungal genomes contain vast numbers of SM biosynthetic gene clusters (BGCs) with unknown products, suggesting that huge numbers of valuable SMs remain to be discovered. It is challenging, however, to identify SM BGCs, among the millions present in fungi, that produce useful compounds. One solution is resistance gene-guided genome mining, which takes advantage of the fact that some BGCs contain a gene encoding a resistant version of the protein targeted by the compound produced by the BGC. The bioinformatic signature of such BGCs is that they contain an allele of an essential gene with no SM biosynthetic function, and there is a second allele elsewhere in the genome. We have developed a computer-assisted approach to resistance gene-guided genome mining that allows users to query large databases for BGCs that putatively make compounds that have targets of therapeutic interest. Working with the MycoCosm genome database, we have applied this approach to look for SM BGCs that target the proteasome β6 subunit, the target of the proteasome inhibitor fellutamide B, or HMG-CoA reductase, the target of cholesterol reducing therapeutics such as lovastatin. Our approach proved effective, finding known fellutamide and lovastatin BGCs as well as fellutamide- and lovastatin-related BGCs with variations in the SM genes that suggest they may produce structural variants of fellutamides and lovastatin. Gratifyingly, we also found BGCs that are not closely related to lovastatin BGCs but putatively produce novel HMG-CoA reductase inhibitors.

ONE-SENTENCE SUMMARY

A new computer-assisted approach to resistance gene-directed genome mining is reported along with its use to identify fungal biosynthetic gene clusters that putatively produce proteasome and HMG-CoA reductase inhibitors.

Antibacterial natural products from microbial and fungal sources: a decade of advances

Throughout the ages the world has witnessed the outbreak of many infectious diseases. Emerging microbial diseases pose a serious threat to public health. Increasing resistance of microorganisms towards the existing drugs makes them ineffective. In fact, anti-microbial resistance is declared as one of the top public health threats by WHO. Hence, there is an urge for the discovery of novel antimicrobial drugs to combat with this challenge. Structural diversity and unique pharmacological effects make natural products a prime source of novel drugs. Staggeringly, in spite of its extensive biodiversity, a prominent portion of microorganism species remains unexplored for the identification of bioactives. Microorganisms are a predominant source of new chemical entities and there are remarkable number of antimicrobial drugs developed from it. In this review, we discuss the contributions of microorganism based natural products as effective antibacterial agents, studied during the period of 2010-2020. The review encompasses over 140 structures which are either natural products or semi-synthetic derivatives of microbial natural products. 65 of them are identified as newly discovered natural products. All the compounds discussed herein, have exhibited promising efficacy against various bacterial strains.

Advances in Mass Spectrometry-Metabolomics Based Approaches

Highly selective and sensitive analytical techniques are necessary for microbial metabolomics due to the complexity of the microbial sample matrix. Hence, mass spectrometry (MS) has been successfully applied in microbial metabolomics due to its high precision, versatility, sensitivity, and wide dynamic range. The different analytical tools using MS have been employed in microbial metabolomics investigations and can contribute to the discovery or accelerate the search for bioactive substances. The coupling with chromatographic and electrophoretic separation techniques has resulted in more efficient technologies for the analysis of microbial compounds occurring in trace levels. This book chapter describes the current advances in the application of mass spectrometry-based metabolomics in the search for new biologically active agents from microbial sources; the development of new approaches for in silico annotation of natural products; the different technologies employing mass spectrometry imaging to deliver more comprehensive analysis and elucidate the metabolome involved in ecological interactions as they enable visualization of the spatial dispersion of small molecules. We also describe other ambient ionization techniques applied to the fingerprint of microbial natural products and modern techniques such as ion mobility mass spectrometry used to microbial metabolomic analyses and the dereplication of natural microbial products through MS.

Artificial intelligence in microbial natural product drug discovery: current and emerging role

Covering: up to the end of 2022Microorganisms are exceptional sources of a wide array of unique natural products and play a significant role in drug discovery. During the golden era, several life-saving antibiotics and anticancer agents were isolated from microbes; moreover, they are still widely used. However, difficulties in the isolation methods and repeated discoveries of the same molecules have caused a setback in the past. Artificial intelligence (AI) has had a profound impact on various research fields, and its application allows the effective performance of data analyses and predictions. With the advances in omics, it is possible to obtain a wealth of information for the identification, isolation, and target prediction of secondary metabolites. In this review, we discuss drug discovery based on natural products from microorganisms with the help of AI and machine learning.

Genomic Investigation of Desert Streptomyces huasconensis D23 Reveals Its Environmental Adaptability and Antimicrobial Activity

The harsh climatic conditions of deserts may lead to unique adaptations of microbes, which could serve as potential sources of new metabolites to cope with environmental stresses. However, the mechanisms governing the environmental adaptability and antimicrobial activity of desert Streptomyces remain inadequate, especially in extreme temperature differences, drought conditions, and strong radiation. Here, we isolated a Streptomyces strain from rocks in the Kumtagh Desert in Northwest China and tested its antibacterial activity, resistance to UV-C irradiation, and tolerance to hydrogen peroxide (H2O2). The whole-genome sequencing was carried out to study the mechanisms underlying physiological characteristics and ecological adaptation from a genomic perspective. This strain has a growth inhibitory effect against a variety of indicator bacteria, and the highest antibacterial activity recorded was against Bacillus cereus. Moreover, strain D23 can withstand UV-C irradiation up to 100 J/m2 (D10 = 80 J/m2) and tolerate stress up to 70 mM H2O2. The genome prediction of strain D23 revealed the mechanisms associated with its adaptation to extreme environmental and stressful conditions. In total, 33 biosynthetic gene clusters (BGCs) were predicted based on anti-SMASH. Gene annotation found that S. huasconensis D23 contains several genes and proteins associated with the biosynthesis of factors required to cope with environmental stress of temperature, UV radiation, and osmotic pressure. The results of this study provide information about the genome and BGCs of the strain S. huasconensis D23. The experimental results combined with the genome sequencing data show that antimicrobial activity and stress resistance of S. huasconensis D23 was due to the rich and diverse secondary metabolite production capacity and the induction of stress-responsive genes. The environmental adaptability and antimicrobial activity information presented here will be valuable for subsequent work regarding the isolation of bioactive compounds and provide insight into the ecological adaptation mechanism of microbes to extreme desert environments.

Evolution and regulation of microbial secondary metabolism

Microbes have disproportionate impacts on the macroscopic world. This is in part due to their ability to grow to large populations that collectively secrete massive amounts of secondary metabolites and alter their environment. Yet, the conditions favoring secondary metabolism despite the potential costs for primary metabolism remain unclear. Here we investigated the biosurfactants that the bacterium Pseudomonas aeruginosa makes and secretes to decrease the surface tension of surrounding liquid. Using a combination of genomics, metabolomics, transcriptomics, and mathematical modeling we show that the ability to make surfactants from glycerol varies inconsistently across the phylogenetic tree; instead, lineages that lost this ability are also worse at reducing the oxidative stress of primary metabolism on glycerol. Experiments with different carbon sources support a link with oxidative stress that explains the inconsistent distribution across the P. aeruginosa phylogeny and suggests a general principle: P. aeruginosa lineages produce surfactants if they can reduce the oxidative stress produced by primary metabolism and have excess resources, beyond their primary needs, to afford secondary metabolism. These results add a new layer to the regulation of a secondary metabolite unessential for primary metabolism but important to change physical properties of the environments surrounding bacterial populations.

Identification of Anticryptococcal Bornyl Compounds from Verbesina turbacensis and Their Structure-Activity Relationships

Cryptococcus neoformans is an opportunistic fungal pathogen that has limited treatment options. Natural product plant extracts offer a cost-effective option for the discovery of new anticryptococcal lead compounds. The acetone bark extract of Verbesina turbacensis was found to potently inhibit C. neoformans and was subjected to bioautography. Two compounds that inhibited the growth of C. neoformans were isolated and displayed minimum inhibitory concentration values of 10 and 310 µg/mL. The compounds were identified as the bornyl hydroxycinnamic esters bornyl caffeate and bornyl ferulate, respectively. To better understand initial structure-activity relationships, anticryptococcal activity was characterized for similar compounds. All compounds were further evaluated for mammalian cell toxicity using the MTT assay with MCF-7 and HEK-293 cell lines. Overall, bornyl caffeate demonstrated promising anticryptococcal potential given its potent inhibition of C. neoformans and low mammalian cell toxicity.

Combinatorial strategies for production improvement of anti-tuberculosis antibiotics ilamycins E1/E2 from deep sea-derived Streptomyces atratus SCSIO ZH16 ΔilaR

Ilamycins E1/E2 are novel cyclic heptapeptides from Streptomyces atratus SCSIO ZH16, which have the MIC value of 9.8 nM against Mycobacterium tuberculosis H37Rv. However, the lower fermentative titer of ilamycins E1/E2 cut off further development for novel anti-TB lead drugs. In order to break the obstacle, the combinatorial strategy of medium optimization, fermentative parameters optimization, exogenous addition of metal ions, precursors, and surfactants was developed to promoted the production of ilamycins E1/E2. Addition of 1 mM ZnCl2 at 0 h, 1 g/L tyrosine at 96 h, and 2 g/L shikimic acid at 48 h increased the production of ilamycins E1/E2 from 13.51 to 762.50 ± 23.15, 721.39 ± 19.13, and 693.83 ± 16.86 mg/L, respectively. qRT-PCR results showed that the transcription levels of key genes in Embden-Meyerhof-Parnas pathway, hexose phosphate shunt pathway, and shikimic acid pathway were upregulated. In addition, the production of ilamycins E1/E2 reached 790.34 mg/L in a 5-L bioreactor by combinatorial strategy. Combinatorial strategies were used for improving ilamycins E1/E2 production in S. atratus ΔilaR and provided a sufficient basis on further clinic development.

Metabolites of medicine food homology-derived endophytic fungi and their activities

Medicine food homology (MFH) substances not only provide essential nutrients as food but also have corresponding factors that can prevent and help treat nutritional imbalances, chronic disease, and other related issues. Endophytic fungi associated with plants have potential for use in drug discovery and food therapy. However, the endophytic fungal metabolites from MFH plants and their effects have been overlooked. Therefore, this review focuses on the various biological activities of 108 new metabolites isolated from 53 MFH-derived endophytic fungi. The paper explores the potential nutritional and medicinal value of metabolites of MFH-derived endophytic fungi for food and medical applications. This research is important for the future development of effective, safe, and nontoxic therapeutic nutraceuticals for the prevention and treatment of human diseases.

Genome mining as a biotechnological tool for the discovery of novel biosynthetic genes in lichens

Natural products (NPs) and their derivatives are a major contributor to modern medicine. Historically, microorganisms such as bacteria and fungi have been instrumental in generating drugs and lead compounds because of the ease of culturing and genetically manipulating them. However, the ever-increasing demand for novel drugs highlights the need to bioprospect previously unexplored taxa for their biosynthetic potential. Next-generation sequencing technologies have expanded the range of organisms that can be explored for their biosynthetic content, as these technologies can provide a glimpse of an organism's entire biosynthetic landscape, without the need for cultivation. The entirety of biosynthetic genes can be compared to the genes of known function to identify the gene clusters potentially coding for novel products. In this study, we mine the genomes of nine lichen-forming fungal species of the genus Umbilicaria for biosynthetic genes, and categorize the biosynthetic gene clusters (BGCs) as "associated product structurally known" or "associated product putatively novel". Although lichen-forming fungi have been suggested to be a rich source of NPs, it is not known how their biosynthetic diversity compares to that of bacteria and non-lichenized fungi. We found that 25%-30% of biosynthetic genes are divergent as compared to the global database of BGCs, which comprises 1,200,000 characterized biosynthetic genes from plants, bacteria, and fungi. Out of 217 BGCs, 43 were highly divergant suggesting that they potentially encode structurally and functionally novel NPs. Clusters encoding the putatively novel metabolic diversity comprise polyketide synthases (30), non-ribosomal peptide synthetases (12), and terpenes (1). Our study emphasizes the utility of genomic data in bioprospecting microorganisms for their biosynthetic potential and in advancing the industrial application of unexplored taxa. We highlight the untapped structural metabolic diversity encoded in the lichenized fungal genomes. To the best of our knowledge, this is the first investigation identifying genes coding for NPs with potentially novel properties in lichenized fungi.

Revealing Genome-Based Biosynthetic Potential of Streptomyces sp. BR123 Isolated from Sunflower Rhizosphere with Broad Spectrum Antimicrobial Activity

Actinomycetes, most notably the genus Streptomyces, have great importance due to their role in the discovery of new natural products, especially for finding antimicrobial secondary metabolites that are useful in the medicinal science and biotechnology industries. In the current study, a genome-based evaluation of Streptomyces sp. isolate BR123 was analyzed to determine its biosynthetic potential, based on its in vitro antimicrobial activity against a broad range of microbial pathogens, including gram-positive and gram-negative bacteria and fungi. A draft genome sequence of 8.15 Mb of Streptomyces sp. isolate BR123 was attained, containing a GC content of 72.63% and 8103 protein coding genes. Many antimicrobial, antiparasitic, and anticancerous compounds were detected by the presence of multiple biosynthetic gene clusters, which was predicted by in silico analysis. A novel metabolite with a molecular mass of 1271.7773 in positive ion mode was detected through a high-performance liquid chromatography linked with mass spectrometry (HPLC-MS) analysis. In addition, another compound, meridamycin, was also identified through a HPLC-MS analysis. The current study reveals the biosynthetic potential of Streptomyces sp. isolate BR123, with respect to the synthesis of bioactive secondary metabolites through genomic and spectrometric analysis. Moreover, the comparative genome study compared the isolate BR123 with other Streptomyces strains, which may expand the knowledge concerning the mechanism involved in novel antimicrobial metabolite synthesis.

Indispensable role of microbes in anticancer drugs and discovery trends

Recent years have seen an increased focus on the advancement of naturally derived products for the treatment of cancer. Since the beginning of recorded history, nature has provided a variety of medicinal agents, and an overwhelming number of drugs that we have today are derived from natural sources. Such natural agents are prominently used to treat several diseases such as diabetes, malaria, Alzheimer's, pulmonary disorders, etc. with cancer being the highlight of this review. Due to the rapid development of resistance to chemotherapeutic drugs, the hunt for effective novel drugs is still a paramount concern in cancer treatment. Moreover, many chemotherapy drugs typically have high toxicity and adverse side effects, which necessitates the need to develop anti-tumor drugs that can be employed to treat deadly tumors with fewer negative effects on health and better efficacy. Isolation of several chemotherapeutic drugs has been conducted from a wide range of natural sources which include plants, microbes, fungi, and marine microorganisms. Considering the trends of previous decades, microbial diversity has grown to play a significant role in the formulation of pharmaceuticals and drugs, especially antibiotics and anti-cancer medications. Microbe-derived antitumor antibiotics such as anthracycline, epothilones, bleomycin, actinomycin, and staurosporine are amongst the widely used cancer chemotherapeutic agents. This review deals majorly with microbe-derived anticancer drugs taking into account their derivatives, mechanism of action, isolation procedures, limitations, and tumors targeted by them. This article also reports the phase of clinical study these drugs are undergoing. Moreover, it intends to portray the indispensable part that these microbes have been playing since time immemorial in the odyssey of chemotherapeutic agents. KEY POINTS: • Microbial diversity contributes heavily towards the formulation of anticancer drugs. • Polypeptides, carbohydrates, and alkaloids are prevalent microbe-based drug classes. • Microbe-derived anticancer agents target various sarcomas, carcinomas, and lymphomas.

Identifying Candidate Flavonoids for Non-Alcoholic Fatty Liver Disease by Network-Based Strategy

Nonalcoholic fatty liver disease (NAFLD) is the most common type of chronic liver disease and lacks guaranteed pharmacological therapeutic options. In this study, we applied a network-based framework for comprehensively identifying candidate flavonoids for the prevention and/or treatment of NAFLD. Flavonoid-target interaction information was obtained from combining experimentally validated data and results obtained using a recently developed machine-learning model, AI-DTI. Flavonoids were then prioritized by calculating the network proximity between flavonoid targets and NAFLD-associated proteins. The preventive effects of the candidate flavonoids were evaluated using FFA-induced hepatic steatosis in HepG2 and AML12 cells. We reconstructed the flavonoid-target network and found that the number of re-covered compound-target interactions was significantly higher than the chance level. Proximity scores have successfully rediscovered flavonoids and their potential mechanisms that are reported to have therapeutic effects on NAFLD. Finally, we revealed that discovered candidates, particularly glycitin, significantly attenuated lipid accumulation and moderately inhibited intracellular reactive oxygen species production. We further confirmed the affinity of glycitin with the predicted target using molecular docking and found that glycitin targets are closely related to several proteins involved in lipid metabolism, inflammatory responses, and oxidative stress. The predicted network-level effects were validated at the levels of mRNA. In summary, our study offers and validates network-based methods for the identification of candidate flavonoids for NAFLD.

Metabolic Profiling and In Vitro Assessment of the Biological Activities of the Ethyl Acetate Extract of Penicillium chrysogenum “Endozoic of Cliona sp. Marine Sponge” from the Red Sea (Egypt)

Marine sponge-derived endozoic fungi have been gaining increasing importance as promising sources of numerous and unique bioactive compounds. This study investigates the phytochemical profile and biological activities of the ethyl acetate extract of Penicillium chrysogenum derived from Cliona sp. sponge. Thirty-six compounds were tentatively identified from P. chrysogenum ethyl acetate extract along with the kojic acid (KA) isolation. The UPLC-ESI-MS/MS positive ionization mode was used to analyze and identify the extract constituents while 1D and 2D NMR spectroscopy were used for kojic acid (KA) structure confirmation. The antimicrobial, antioxidant, and cytotoxic activities were assessed in vitro. Both the extract and kojic acid showed potent antibacterial activity against Staphylococcus aureus and Pseudomonas aeruginosa with MIC 250 ± 0.82 µg/mL. Interestingly, the extract showed strong antifungal activity against Candida albicans and Cryptococcus neoformans with MIC 93.75 ± 0.55 and 19.53 ± 0.48 µg/mL, respectively. Furthermore, KA showed the same potency against Fusarium oxysporum and Cryptococcus neoformans with MIC 39.06 ± 0.85 and 39.06 ± 0.98 µg/mL, respectively. Ultimately, KA showed strong antioxidant activity with IC₅₀ 33.7 ± 0.8 µg/mL. Moreover, the extract and KA showed strong cytotoxic activity against colon carcinoma (with IC₅₀ 22.6 ± 0.8 and 23.4 ± 1.4 µg/mL, respectively) and human larynx carcinoma (with equal IC₅₀ 30.8 ± 1.3 and ± 2.1 µg/mL, respectively), respectively. The current study represents the first insights into the phytochemical profile and biological properties of P. chrysoenum ethyl acetate extract, which could be a promising source of valuable secondary metabolites with potent biological potentials.

Plant-Derived Toxin Inhibitors as Potential Candidates to Complement Antivenom Treatment in Snakebite Envenomations

Snakebite envenomations (SBEs) are a neglected medical condition of global importance that mainly affect the tropical and subtropical regions. Clinical manifestations include pain, edema, hemorrhage, tissue necrosis, and neurotoxic signs, and may evolve to functional loss of the affected limb, acute renal and/or respiratory failure, and even death. The standard treatment for snake envenomations is antivenom, which is produced from the hyperimmunization of animals with snake toxins. The inhibition of the effects of SBEs using natural or synthetic compounds has been suggested as a complementary treatment particularly before admission to hospital for antivenom treatment, since these alternative molecules are also able to inhibit toxins. Biodiversity-derived molecules, namely those extracted from medicinal plants, are promising sources of toxin inhibitors that can minimize the deleterious consequences of SBEs. In this review, we systematically synthesize the literature on plant metabolites that can be used as toxin-inhibiting agents, as well as present the potential mechanisms of action of molecules derived from natural sources. These findings aim to further our understanding of the potential of natural products and provide new lead compounds as auxiliary therapies for SBEs.

Investigation of chetomin as a lead compound and its biosynthetic pathway

Chaetomium fungi produce a diversity of bioactive compounds. Chaetomium cochliodes SD-280 possesses 91 secondary metabolite gene clusters and exhibits strong antibacterial activity. One of the active compounds responsible for that activity, chetomin, has a minimum inhibitory concentration (MIC) for anti-methicillin-resistant Staphylococcus aureus (MRSA) of 0.05 μg/mL (vancomycin: 0.625 μg/mL). This study demonstrated that the addition of glutathione (GSH) can enhance chetomin yield dramatically, increasing its production 15.43-fold. Following genome sequencing, cluster prediction, and transcriptome and proteome analyses of the fungus were carried out. Furthermore, a relatively complete chetomin biosynthetic gene cluster was proposed, and the coding sequences were acquired. In the cluster of GSH-treated cells, proteome analysis revealed two up-regulated proteins that are critical enzymes for chetomin biosynthesis. One of these enzymes, a nonribosomal peptide synthetase (NRPS), was heterologously expressed in Aspergillus nidulans, and one of its metabolites was determined to be an intermediate in the chetomin biosynthetic pathway. We present here, to our knowledge, the first experimental evidence that chetomin exhibits strong bioactivity against MRSA. Our work also provides extensive insights into the biosynthetic pathway of chetomin, in particular identifying two key enzymes (glutathione S-transferase (CheG) and NRPS (CheP)) that substantially up-regulate chetomin. These mechanistic insights into chetomin biosynthesis will provide the foundation for further investigation into the anti-pathogenic properties and applications of chetomin. KEY POINTS: • Chetomin exhibits strong anti-MRSA activity with MIC of 0.05 μg/mL. • Addition of glutathione improved the yield of chetomin by 15.43-fold. • CheG and CheP involved in the chetomin biosynthesis were revealed for the first time.