Genome Mining of α-Pyrone Natural Products from Ascidian-Derived Fungus Amphichordafelina SYSU-MS7908

Genome mining of nonenzymatic ortho-quinone methide-based pseudonatural products from ascidian-derived fungus Diaporthe sp.SYSU-MS4722

Ortho-quinone methides (o-QMs), generated by oxidative dehydration of clavatol, are highly reactive intermediates in biosynthesis that give rise to a variety of clavatol-containing pseudonatural products (PNPs) in fungi through intra- and intermolecular nonenzymatic cyclization/addition reaction, and some compounds have significant biological activities. Here we report our genome mining efforts on a cryptic clavatol biosynthetic gene cluster (BGC) from an ascidian-derived fungus Diaporthe sp. SYSU-MS4722. The core genes NR-PKS (DiaG), Esterase (DiaF) derived from the fungus Diaporthe sp. SYSU-MS4722 clavatol BGC and the known α-ketoglutarate-dependent nonheme iron enzymes (ClaD) were heterologously expressed in the Aspergillus oryzae NSAR1 (A. oryzae NSAR1). Thirteen new monomeric, dimeric, and trimeric clavatol-based PNPs (7-19), together with three known compounds (20-22) were isolated from the above transformant. Their structures including absolute configurations were elucidated by spectroscopic analysis (UV, IR, HR-ESI-MS, 1D and 2D NMR data), complemented with the X-ray crystallography, the comparison of the experimental and calculated ECD spectra, and gauge-independent atomic orbital (GIAO) NMR calculations. Based on the structural characteristics, their plausible biosynthetic pathways were proposed. Notably, Compounds 8, 9, 14 and 16 exhibited potent anti-fibrotic activity with EC50 values of 28.9, 10.0, 3.5 and 30.1 μM, respectively.

Genome mining and biosynthetic pathways of marine-derived fungal bioactive natural products

Marine fungal natural products (MFNPs) are a vital source of pharmaceuticals, primarily synthesized by relevant biosynthetic gene clusters (BGCs). However, many of these BGCs remain silent under standard laboratory culture conditions, delaying the development of novel drugs from MFNPs to some extent. This review highlights recent efforts in genome mining and biosynthetic pathways of bioactive natural products from marine fungi, focusing on methods such as bioinformatics analysis, gene knockout, and heterologous expression to identify relevant BGCs and elucidate the biosynthetic pathways and enzyme functions of MFNPs. The research efforts presented in this review provide essential insights for future gene-guided mining and biosynthetic pathway analysis in MFNPs.

Natural Products from Marine-Derived Fungi with Anti-Inflammatory Activity

Inflammation is considered as one of the most primary protective innate immunity responses, closely related to the body's defense mechanism for responding to chemical, biological infections, or physical injuries. Furthermore, prolonged inflammation is undesirable, playing an important role in the development of various diseases, such as heart disease, diabetes, Alzheimer's disease, atherosclerosis, rheumatoid arthritis, and even certain cancers. Marine-derived fungi represent promising sources of structurally novel bioactive natural products, and have been a focus of research for the development of anti-inflammatory drugs. This review covers secondary metabolites with anti-inflammatory activities from marine-derived fungi, over the period spanning August 2018 to July 2024. A total of 285 anti-inflammatory metabolites, including 156 novel compounds and 11 with novel skeleton structures, are described. Their structures are categorized into five categories: terpenoids, polyketides, nitrogen-containing compounds, steroids, and other classes. The biological targets, as well as the in vitro and in vivo screening models, were surveyed and statistically summarized. This paper aims to offer valuable insights to researchers in the exploration of natural products and the discovery of anti-inflammatory drugs.

Recent Advances in Anti-Inflammatory Compounds from Marine Microorganisms

Marine microbial secondary metabolites with diversified structures have been found as promising sources of anti-inflammatory lead compounds. This review summarizes the sources, chemical structures, and pharmacological properties of anti-inflammatory natural products reported from marine microorganisms in the past three years (2021-2023). Approximately 252 anti-inflammatory compounds, including 129 new ones, were predominantly obtained from marine fungi and they are structurally divided into polyketides (51.2%), terpenoids (21.0%), alkaloids (18.7%), amides or peptides (4.8%), and steroids (4.3%). This review will shed light on the development of marine microbial secondary metabolites as potential anti-inflammatory lead compounds with promising clinical applications in human health.

Integrative Genomics and Bioactivity-Guided Isolation of Novel Antimicrobial Compounds from Streptomyces sp. KN37 in Agricultural Applications

Actinomycetes have long been recognized as an important source of antibacterial natural products. In recent years, actinomycetes in extreme environments have become one of the main research directions. Streptomyces sp. KN37 was isolated from the cold region of Kanas in Xinjiang. It demonstrated potent antimicrobial activity, but the primary active compounds remained unclear. Therefore, we aimed to combine genomics with traditional isolation methods to obtain bioactive compounds from the strain KN37. Whole-genome sequencing and KEGG enrichment analysis indicated that KN37 possesses the potential for synthesizing secondary metabolites, and 41 biosynthetic gene clusters were predicted, some of which showed high similarity to known gene clusters responsible for the biosynthesis of antimicrobial antibiotics. The traditional isolation methods and activity-guided fractionation were employed to isolate and purify seven compounds with strong bioactivity from the fermentation broth of the strain KN37. These compounds were identified as 4-(Diethylamino)salicylaldehyde (1), 4-Nitrosodiphenylamine (2), N-(2,4-Dimethylphenyl)formamide (3), 4-Nitrocatechol (4), Methylsuccinic acid (5), Phenyllactic acid (6) and 5,6-Dimethylbenzimidazole (7). Moreover, 4-(Diethylamino)salicylaldehyde exhibited the most potent inhibitory effect against Rhizoctonia solani, with an EC50 value of 14.487 mg/L, while 4-Nitrosodiphenylamine showed great antibacterial activity against Erwinia amylovora, with an EC50 value of 5.715 mg/L. This study successfully isolated several highly active antimicrobial compounds from the metabolites of the strain KN37, which could contribute as scaffolds for subsequent chemical synthesis. On the other hand, the newly predicted antibiotic-like substances have not yet been isolated, but they still hold significant research value. They are instructive in the study of active natural product biosynthetic pathways, activation of silent gene clusters, and engineering bacteria construction.

Marine natural products

Covering: January to the end of December 2022This review covers the literature published in 2022 for marine natural products (MNPs), with 645 citations (633 for the period January to December 2022) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, the submerged parts of mangroves and other intertidal plants. The emphasis is on new compounds (1417 in 384 papers for 2022), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. An analysis of NP structure class diversity in relation to biota source and biome is discussed.

Total biosynthesis of fungal tetraketide pyrones

Fungal tetraketide pyrones possess important and potent bioactivities, but their detailed biosynthetic pathways are unknown and synthetic routes to their production are lengthy. Here we investigated the fungal pathways to the multiforisins and compounds related to islandic acid. Heterologous expression experiments yield high titres of these compounds and pathway intermediates. The results both elucidate the pathway and offer a platform for the total biosynthesis of this class of metabolites.

Highlights of bioinformatic tools and methods for validating bioinformatics derived hypotheses for microbial natural products research

Historically, bacterial natural products have served as an excellent source of drug leads, however, in recent decades the rate of discovery has slowed due to multiple challenges. Rapid advances in genome sequencing science in recent years have revealed the vast untapped encoded potential of bacteria to make natural products. To access these molecules, researchers can employ the ever-growing array of bioinformatic tools at their disposal and leverage newly developed experimental approaches to validate these bioinformatic-driven hypotheses. When used together effectively, bioinformatic and experimental tools enable researchers to deeply examine the full diversity of bacterial natural products. This review briefly outlines recent bioinformatic tools that can facilitate natural product research in bacteria including the use of CRISPR, co-occurrence network analysis, and combinatorial generation of microbial natural products to test bioinformatic hypotheses in the lab.

Emerging pharmaceutical therapies of Ascidian-derived natural products and derivatives

In a growing multidrug-resistant environment, the identification of potential new drug candidates with an acceptable safety profile is a substantial crux in pharmaceutical discovery. This review discusses several aspects and properties of approved marine natural products derived from ascidian sources (phylum Chordata, subphylum Tunicata) and/or their deduced analogues including their biosynthetic origin, (bio)chemical preclinical assessments and known efficacy-safety profiles, clinical status in trials, but also translational developments, opportunities and final conclusions. The review also describes the preclinical assessments of a large number of other ascidian compounds that have not been involved in clinical trials yet. Finally, the emerging research on the connectivity of the ascidian hosts and their independent or obligate symbiotic guests is discussed. The review covers the latest information on the topic of ascidian-derived marine natural products over the last two decades including 2022, with the majority of publications published in the last decade.

Two New Picoline-Derived Meroterpenoids with Anti-Acetylcholinesterase Activity from Ascidian-Derived Fungus Amphichorda felina

Amphichoterpenoids D (1) and E (2), two new picoline-derived meroterpenoids with a rare 6/6/6 tricyclic pyrano[3,2-c]pyridinyl-γ-pyranone scaffold, were isolated from the ascidian-derived fungus Amphichorda felina SYSU-MS7908. Their structures, including the absolute configurations, were established by extensive spectroscopic methods (1D and 2D NMR and high-resolution mass spectrometry) and ECD calculations. Compounds 1 and 2 showed anti-acetylcholinesterase (anti-AChE) activities with IC50 values of 12.5 μM and 11.6 μM, respectively. The binding interactions between 1, 2, and AChE were investigated using molecular docking analyses.