Krasilnikolides A and B and Detalosylkrasilnikolide A, Cytotoxic 20-Membered Macrolides from the Genus Krasilnikovia: Assignment of Anomeric Configuration by J-Based Configuration Analysis

Actinomycetes: Treasure trove for discovering novel antibiotic candidates

Actinomycetes are an important source of secondary metabolites such as antibiotics and other active natural products. Many well-known antibiotics, such as streptomycin, oxytetracycline, and tetracycline, are produced by actinomycetes. Different types of antibiotics have distinct mechanisms of action against microorganisms: inhibit protein synthesis, inhibit nucleic acid synthesis, or inhibit cell wall synthesis. For decades, actinomycetes have played a crucial role in clinical treatment for major diseases such as pathogenic bacterial infections, serving as one of the most significant sources of new discoveries. However, due to extensive use of antibiotics, the types and numbers of drug-resistant bacteria, represented by multidrug resistant (MDR) and extensively drug resistant (XDR) bacteria, have increased dramatically in clinical settings, posing a significant threat to human survival. Therefore, there is an urgent need to search for structurally novel antibacterial natural products and develop new antibiotics. In this review, a total of 170 antibacterial secondary metabolites from actinomycetes, published in the 54 literatures (2020 to September 2024) and some synthetic analogs, are discussed with emphasis on their structures and biological activities.

Cryptoic acids A and B, benzene-containing polyketides, and cyclocryptamide, a modified diketopiperazine, from an actinomycete of the genus Cryptosporangium

Two new benzene-containing polyketides, cryptoic acids A (1) and B (2), along with a new acylated diketopiperazine designated cyclocryptamide (3), were isolated from the culture extract of Cryptosporangium sp. YDKA-T02. The absolute configuration of amino acid components in 3 was determined by Marfey's method. While 3 was not cytotoxic and inactive against microbial test strains, 1 and 2 showed PPARγ agonistic activity in a reporter gene assay and cytotoxicity against P388 murine leukemia cells.

Molecular Decoration and Unconventional Double Bond Migration in Irumamycin Biosynthesis

Irumamycin (Iru) is a complex polyketide with pronounced antifungal activity produced by a type I polyketide (PKS) synthase. Iru features a unique hemiketal ring and an epoxide group, making its biosynthesis and the structural diversity of related compounds particularly intriguing. In this study, we performed a detailed analysis of the iru biosynthetic gene cluster (BGC) to uncover the mechanisms underlying Iru formation. We examined the iru PKS, including the domain architecture of individual modules and the overall spatial structure of the PKS, and uncovered discrepancies in substrate specificity and iterative chain elongation. Two potential pathways for the formation of the hemiketal ring, involving either an olefin shift or electrocyclization, were proposed and assessed using 18O-labeling experiments and reaction activation energy calculations. Based on our findings, the hemiketal ring is likely formed by PKS-assisted double bond migration and TE domain-mediated cyclization. Furthermore, putative tailoring enzymes mediating epoxide formation specific to Iru were identified. The revealed Iru biosynthetic machinery provides insight into the complex enzymatic processes involved in Iru production, including macrocycle sculpting and decoration. These mechanistic details open new avenues for a targeted architecture of novel macrolide analogs through synthetic biology and biosynthetic engineering.

Wychimicins E and F from a rare actinomycete of the genus Cryptosporangium

Two new spirotetronate class compounds designated wychimicins E (1) and F (2) were isolated from the culture extract of an actinomycete Cryptosporangium sp. RD061707. Their structures were determined through extensive NMR analysis in comparison with wychimicin C. Both compounds lack one hydroxy group in the decalin moiety, and the relative configuration of the remaining hydroxy group was assigned by NMR analysis of triacetylwychimicin E (3). Compounds 1 and 2 showed potent antimicrobial activity against Kocuria rhizophila and Staphylococcus aureus. These compounds were also modestly cytotoxic against P388 murine leukemia cells.

Herbidomicins, two pairs of polyketide tautomers produced by an actinomycete of the genus Herbidospora

Herbidospora is one of the underexplored actinomycete genera from which only a limited number of secondary metabolites are reported. In our continuing investigation on less explored actinomycetes, a liquid culture of Herbidospora sp. RD 11066 was found to contain unknown metabolites that had no match in our in-house UV database. Chromatographic separation and following structural analysis using NMR and MS identified these metabolites to be chromanone and chromene derivatives, which were respectively composed of an inseparable mixture of two isomeric forms. The former polyketides, designated to be herbidomicins A1 (1) and A2 (2), are positional isomers in terms of a methyl substituent on an aromatic ring that mutually interconvert by acetal exchange by two phenolic hydroxy groups. The latter pair, herbidomicins B1 (3) and B2 (4), is Z/E-isomers regarding an enol ether double bond. Herbidomicins 1-4 were weakly antifungal against a dermatophytic fungus Trichophyton rubrum and were moderately cytotoxic against murine leukemia P388 cells.

Survey of natural products reported by Asian research groups in 2022

The new natural products reported in 2022 in peer-reviewed articles in journals with good reputations were reviewed and analyzed. The advances made by Asian research groups in the field of natural products chemistry in 2022 were summarized. Compounds with unique structural features and/or promising bioactivities originating from Asian natural sources were discussed based on their structural classification.

Development of a drug discovery approach from microbes with a special focus on isolation sources and taxonomy

After the successful discoveries of numerous antibiotics from microorganisms, frequent reisolation of known compounds becomes an obstacle in further development of new drugs from natural products. Exploration of biological sources that can provide novel scaffolds is thus an urgent matter in drug lead screening. As an alternative source to the conventionally used soil microorganisms, we selected endophytic actinomycetes, marine actinomycetes, and actinomycetes in tropical areas for investigation and found an array of new bioactive compounds. Furthermore, based on the analysis of the distribution pattern of biosynthetic gene clusters in bacteria together with available genomic data, we speculated that biosynthetic gene clusters for secondary metabolites are specific to each genus. Based on this assumption, we investigated actinomycetal and marine bacterial genera from which no compounds have been reported, which led to the discovery of a variety of skeletally novel bioactive compounds. These findings suggest that consideration of environmental factor and taxonomic position is critically effective in the selection of potential strains producing structurally unique compounds.