Functional and Structural Insights into a Novel Promiscuous Ketoreductase of the Lugdunomycin Biosynthetic Pathway

Total Synthesis of Lugdunomycin via Sequential Photoinduced Spiroketalization and Isobenzofuran Diels-Alder Reactions

The presence of sterically rigid contiguous quaternary stereocenters in natural products imposes conformational constraints with significant effects on their biological activities. However, achieving the direct synthesis of multiple contiguous quaternary stereocenters in a single step remains a formidable challenge. Here, we present the total synthesis of the antibacterial metabolite lugdunomycin (1) in thirteen steps via a sequence of photochemical transformations. A photoenolization, keto-enol tautomerization, and spiroketalization sequence was developed to generate the spiroketal 4 from actinaphthoran B (3). Subsequently, a photoinduced isobenzofuran Diels-Alder reaction between elmonin (4) and iso-maleimycin (5) was developed to construct the polycyclic benzaza[4,3,3]propellane framework bearing three contiguous quaternary stereocenters in the compact C-ring along with a distal hydroxyl group at C19. The mechanism of these photochemical reactions was investigated using synthetic and computational approaches.

Biomimetic Total Synthesis and Paired Omics Identify an Intermolecular Diels-Alder Reaction as the Key Step in Lugdunomycin Biosynthesis

Microbial natural products are the basis of the majority of clinical drugs, where the discovery of truly novel structural scaffolds to fill the discovery pipelines is a prerequisite. Lugdunomycin is a highly rearranged angucycline polyketide produced by Streptomyces sp. QL37, with an enigmatic biosynthetic pathway. Here we show that lugdunomycin is formed by a rare intermolecular Diels-Alder reaction, with elmonin as a masked diene and iso-maleimycin as a dienophile. Genomics, mutational analysis, and heterologous expression revealed that the biosynthesis of the substrates is encoded by distinct biosynthetic gene clusters (BGCs), whereby elmonin is specified by an angucycline BGC, while the biosynthesis of iso-maleimycin is encoded by a BGC for a β-lactone-like compound. Biomimetic total synthesis of lugdunomycin showed that the Diels-Alder reaction leads to the production of a diastereomer of lugdunomycin as the main product in vitro. The diastereomeric ratio of the in vitro Diels-Alder reaction shifted toward lugdunomycin in the presence of proteinaceous material, suggesting that the in vivo Diels-Alder reaction is templated. Alphafold modeling and experimental data suggest that GarL could potentially function as a Diels-Alder template in lugdunomycin biosynthesis. The requirement of distinct biosynthetic pathways and complex chemical reactions indicates the challenges we face in discovering new chemical space.

Antibacterial and cytotoxic angucyclines discovered by heterologous expression of a type II polyketide gene cluster

Three new aromatic polyketides, spirocyclione C (1) and angumycinones E and F (2 and3), were isolated from the heterologous expression of a type II gene cluster in the strain of Streptomyces coelicolor A3(2) assisted by the one strain many compounds (OSMAC) strategy. The structures and absolute configurations of these compounds were elucidated by extensive NMR, MS, theoretical NMR calculations, DP4+ probability analysis, and ECD analyses. Notably, compound 1 represents the first example of an angucycline structure with an unusual oxaspiro[5.4]undecane architecture. Directed by molecular docking and dynamics simulations, the bioactivities of compounds 1-3 were evaluated. Compounds 1 and 2 exhibited promising cytotoxic activity against a panel of human cancer cell lines, and compound 1 showed moderate antibacterial activity against clinical pathogenic strains of B. subtilis, P. vulgaris, B. cereus, M. phlei and MRSA.

(±)-Feionemycin A and Chromonemycins A-D, Rearranged Aromatic Polyketides Uncovered by Type II Polyketide Gene Cluster Expression

Two novel spiro aromatic polyketides, (+)- and (-)-feionemycin A (1), along with four atypical angucyclinones named as chromonemycins A-D (2-5), were discovered through heterologous expression of a type II polyketide gene cluster, within which one previously characterized flavoprotein monooxygenase was deactivated. Among those structures, compound 1 features an unprecedented oxaspiro[5.4]undecane architecture, and compounds 2-5 represent novel atypical angucyclinone variants derived from unusual cyclization of the polyketide chains. The structures and absolute configurations were elucidated by NMR, MS, single-crystal X-ray diffraction, theoretical NMR calculations, DP4+ probability analysis, and ECD analyses. (+)-1 showed cytotoxic activity against NCI-H446, with an IC50 value of 2.26 μM.

Divergence of Classical and C-Ring-Cleaved Angucyclines: Elucidation of Early Tailoring Steps in Lugdunomycin and Thioangucycline Biosynthesis

Angucyclines are an important group of microbial natural products that display tremendous chemical diversity. Classical angucyclines are composed of a tetracyclic benz[a]anthracene scaffold with one ring attached at an angular orientation. However, in atypical angucyclines, the polyaromatic aglycone is cleaved at A-, B-, or C-rings, leading to structural rearrangements and enabling further chemical variety. Here, we have elucidated the branching points in angucycline biosynthesis leading toward cleavage of the C-ring in lugdunomycin and thioangucycline biosynthesis. We showed that 12-hydroxylation and 6-ketoreduction of UWM6 are shared steps in classical and C-ring-cleaved angucycline pathways, although the bifunctional 6-ketoreductase LugOIIred harbors additional unique 1-ketoreductase activity. We identified formation of the key intermediate 8-O-methyltetrangomycin by the LugN methyltransferase as the branching point toward C-ring-cleaved angucyclines. The final common step in lugdunomycin and thioangucycline biosynthesis is quinone reduction, catalyzed by the 7-ketoreductases LugG and TacO, respectively. In turn, the committing step toward thioangucyclines is 12-ketoreduction catalyzed by TacA, for which no orthologous protein exists on the lugdunomycin pathway. Our results confirm that quinone reductions are early tailoring steps and, therefore, may be mechanistically important for subsequent C-ring cleavage. Finally, many of the tailoring enzymes harbored broad substrate promiscuity, which we utilized in combinatorial enzymatic syntheses to generate the angucyclines SM 196 A and hydranthomycin. We propose that enzyme promiscuity and the competition of many of the enzymes for the same substrates lead to a branching biosynthetic network and formation of numerous shunt products typical for angucyclines rather than a canonical linear metabolic pathway.

Unravelling key enzymatic steps in C-ring cleavage during angucycline biosynthesis

Angucyclines are type II polyketide natural products, often characterized by unusual structural rearrangements through B- or C-ring cleavage of their tetracyclic backbone. While the enzymes involved in B-ring cleavage have been extensively studied, little is known of the enzymes leading to C-ring cleavage. Here, we unravel the function of the oxygenases involved in the biosynthesis of lugdunomycin, a highly rearranged C-ring cleaved angucycline derivative. Targeted deletion of the oxygenase genes, in combination with molecular networking and structural elucidation, showed that LugOI is essential for C12 oxidation and maintaining a keto group at C6 that is reduced by LugOII, resulting in a key intermediate towards C-ring cleavage. An epoxide group is then inserted by LugOIII, and stabilized by the novel enzyme LugOV for the subsequent cleavage. Thus, for the first time we describe the oxidative enzymatic steps that form the basis for a wide range of rearranged angucycline natural products.

Total Synthesis and Structure Assignment of the Relacidine Lipopeptide Antibiotics and Preparation of Analogues with Enhanced Stability

The unabated rise of antibiotic resistance has raised the specter of a post-antibiotic era and underscored the importance of developing new classes of antibiotics. The relacidines are a recently discovered group of nonribosomal lipopeptide antibiotics that show promising activity against Gram-negative pathogens and share structural similarities with brevicidine and laterocidine. While the first reports of the relacidines indicated that they possess a C-terminal five-amino acid macrolactone, an N-terminal lipid tail, and an overall positive charge, no stereochemical configuration was assigned, thereby precluding a full structure determination. To address this issue, we here report a bioinformatics guided total synthesis of relacidine A and B and show that the authentic natural products match our predicted and synthesized structures. Following on this, we also synthesized an analogue of relacidine A wherein the ester linkage of the macrolactone was replaced by the corresponding amide. This analogue was found to possess enhanced hydrolytic stability while maintaining the antibacterial activity of the natural product in both in vitro and in vivo efficacy studies.

Characterization of the Biosynthetic Gene Cluster and Shunt Products Yields Insights into the Biosynthesis of Balmoralmycin

Angucyclines are a family of structurally diverse, aromatic polyketides with some members that exhibit potent bioactivity. Angucyclines have also attracted considerable attention due to the intriguing biosynthetic origins that underlie their structural complexity and diversity. Balmoralmycin (compound 1) represents a unique group of angucyclines that contain an angular benz[α]anthracene tetracyclic system, a characteristic C-glycosidic bond-linked deoxy-sugar (d-olivose), and an unsaturated fatty acid chain. In this study, we identified a Streptomyces strain that produces balmoralmycin and seven biosynthetically related coproducts (compounds 2-8). Four of the coproducts (compounds 5-8) are novel compounds that feature a highly oxygenated or fragmented lactone ring, and three of them (compounds 3-5) exhibited cytotoxicity against the human pancreatic cancer cell line MIA PaCa-2 with IC₅₀ values ranging from 0.9 to 1.2 μg/mL. Genome sequencing and CRISPR/dCas9-assisted gene knockdown led to the identification of the ~43 kb balmoralmycin biosynthetic gene cluster (bal BGC). The bal BGC encodes a type II polyketide synthase (PKS) system for assembling the angucycline aglycone, six enzymes for generating the deoxysugar d-olivose, and a hybrid type II/III PKS system for synthesizing the 2,4-decadienoic acid chain. Based on the genetic and chemical information, we propose a mechanism for the biosynthesis of balmoralmycin and the shunt products. The chemical and genetic studies yielded insights into the biosynthetic origin of the structural diversity of angucyclines. IMPORTANCE Angucyclines are structurally diverse aromatic polyketides that have attracted considerable attention due to their potent bioactivity and intriguing biosynthetic origin. Balmoralmycin is a representative of a small family of angucyclines with unique structural features and an unknown biosynthetic origin. We report a newly isolated Streptomyces strain that produces balmoralmycin in a high fermentation titer as well as several structurally related shunt products. Based on the chemical and genetic information, a biosynthetic pathway that involves a type II polyketide synthase (PKS) system, cyclases/aromatases, oxidoreductases, and other ancillary enzymes was established. The elucidation of the balmoralmycin pathway enriches our understanding of how structural diversity is generated in angucyclines and opens the door for the production of balmoralmycin derivatives via pathway engineering.

Discovery of actinomycin L, a new member of the actinomycin family of antibiotics

Streptomycetes are major producers of bioactive natural products, including the majority of the naturally produced antibiotics. While much of the low-hanging fruit has been discovered, it is predicted that less than 5% of the chemical space of natural products has been mined. Here, we describe the discovery of the novel actinomycins L₁ and L₂ produced by Streptomyces sp. MBT27, via application of metabolic analysis and molecular networking. Actinomycins L₁ and L₂ are diastereomers, and the structure of actinomycin L₂ was resolved using NMR and single crystal X-ray crystallography. Actinomycin L is formed via spirolinkage of anthranilamide to the 4-oxoproline moiety of actinomycin X_2, prior to the condensation of the actinomycin halves. Such a structural feature has not previously been identified in naturally occurring actinomycins. Adding anthranilamide to cultures of the actinomycin X₂ producer Streptomyces antibioticus, which has the same biosynthetic gene cluster as Streptomyces sp. MBT27, resulted in the production of actinomycin L. This supports a biosynthetic pathway whereby actinomycin L is produced from two distinct metabolic routes, namely those for actinomycin X₂ and for anthranilamide. Actinomycins L₁ and L₂ showed significant antimicrobial activity against Gram-positive bacteria. Our work shows how new molecules can still be identified even in the oldest of natural product families.

A Standalone β-Ketoreductase Acts Concomitantly with Biosynthesis of the Antimycin Scaffold

Antimycins are anticancer compounds produced by a hybrid nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) pathway. The biosynthesis of these compounds is well characterized, with the exception of the standalone β-ketoreductase enzyme AntM that is proposed to catalyze the reduction of the C8 carbonyl of the antimycin scaffold. Inactivation of antM and structural characterization suggested that rather than functioning as a post-PKS tailoring enzyme, AntM acts upon the terminal biosynthetic intermediate while it is tethered to the PKS acyl carrier protein. Mutational analysis identified two amino acid residues (Tyr185 and Phe223) that are proposed to serve as checkpoints controlling substrate access to the AntM active site. Aromatic checkpoint residues are conserved in uncharacterized standalone β-ketoreductases, indicating that they may also act concomitantly with synthesis of the scaffold. These data provide novel mechanistic insights into the functionality of standalone β-ketoreductases and will enable their reprogramming for combinatorial biosynthesis.

Disclosing biosynthetic connections and functions of atypical angucyclinones with a fragmented C-ring

This review on atypical angucyclinones possessing an aromatic cleavage of the C-ring covers literature between 1995 and early 2020.The unusual framework of the middle C-ring, "broken" as a result of biotransformations and oxidations in vivo and bearing an sp³-C connection, is of interest for biosynthetic investigations. The reported 39 natural compounds (55 including stereoisomers) have been analyzed and arranged into three structural groups. The biosynthetic origin of all these compounds has been thoroughly reviewed and revised, based on the found connections with oxidized angucyclinone structures. The data on biological activities has been summarized. Careful consideration of the origin of the structure allowed us to outline a hypothesis on the biological function as well as prospective applications of such atypical angucyclinones.