Angucyclines: Total syntheses, new structures, and biosynthetic studies of an emerging new class of antibiotics

Total Synthesis of the Phenylnaphthacenoid Type II Polyketide Antibiotic Formicamycin H via Regioselective Ruthenium-Catalyzed Hydrogen Auto-Transfer [4 + 2] Cycloaddition

The first total synthesis of the pentacyclic phenylnaphthacenoid type II polyketide antibiotic formicamycin H is described. A key feature of the synthesis involves the convergent, regioselective assembly of the tetracyclic core via ruthenium-catalyzed α-ketol-benzocyclobutenone [4 + 2] cycloaddition. Double dehydration of the diol-containing cycloadduct provides an achiral enone, which upon asymmetric nucleophilic epoxidation and further manipulations delivers the penultimate tetracyclic trichloride in enantiomerically enriched form. Subsequent chemo- and atroposelective Suzuki cross-coupling of the tetracyclic trichloride introduces the E-ring to complete the total synthesis. Single-crystal X-ray diffraction analyses of two model compounds suggest that the initially assigned stereochemistry of the axially chiral C6-C7 linkage may require revision.

Enantioselective Transfer Hydrogenative Cycloaddition Unlocks the Total Synthesis of SF2446 B3: An Aglycone of Arenimycin and SF2446 Type II Polyketide Antibiotics

The first total synthesis and structure validation of an arenimycin/SF2446 type II polyketide is described, as represented by de novo construction of SF2446 B3, the aglycone shared by this family of type II polyketides. Ruthenium-catalyzed α-ketol-benzocyclobutenone [4 + 2] cycloaddition, which occurs via successive stereoablation-stereoregeneration, affects a double dynamic kinetic asymmetric transformation wherein two racemic starting materials combine to form the congested angucycline bay region with control of regio-, diastereo-, and enantioselectivity. This work represents the first application of transfer hydrogenative cycloaddition and enantioselective intermolecular metal-catalyzed C-C bond activation in target-oriented synthesis.

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.

Himalaquinones A-G, Angucyclinone-Derived Metabolites Produced by the Himalayan Isolate Streptomyces sp. PU-MM59

Himalaquinones A-G, seven new anthraquinone-derived metabolites, were obtained from the Himalayan-based Streptomyces sp. PU-MM59. The chemical structures of the new compounds were identified based on cumulative analyses of HRESIMS and NMR spectra. Himalaquinones A-F were determined to be unique anthraquinones that contained unusual C-4a 3-methylbut-3-enoic acid aromatic substitutions, while himalaquinone G was identified as a new 5,6-dihydrodiol-bearing angucyclinone. Comparative bioactivity assessment (antimicrobial, cancer cell line cytotoxicity, impact on 4E-BP1 phosphorylation, and effect on axolotl embryo tail regeneration) revealed cytotoxic landomycin and saquayamycin analogues to inhibit 4E-BP1p and inhibit regeneration. In contrast, himalaquinone G, while also cytotoxic and a regeneration inhibitor, did not affect 4E-BP1p status at the doses tested. As such, this work implicates a unique mechanism for himalaquinone G and possibly other 5,6-dihydrodiol-bearing angucyclinones.

Investigation of angucycline compounds as potential drug candidates against SARS Cov-2 main protease using docking and molecular dynamic approaches

Abstract

The emerged Coronavirus disease (COVID-19) causes severe or even fatal respiratory tract infection, and to date there is no FDA-approved therapeutics or effective treatment available to effectively combat this viral infection. This urgent situation is an attractive research area in the field of drug design and development. One of the most important targets of SARS-coronavirus-2 (SARS Cov-2) is the main protease (3CLpro). Actinomycetes are important resources for drug discovery. The angucylines that are mainly produced by Streptomyces genus of actinomycetes exhibit a broad range of biological activities such as anticancer, antibacterial and antiviral. This study aims to investigate the binding affinity and molecular interactions of 157 available angucycline compounds with 3CLpro using docking and molecular dynamics simulations. MM-PBSA calculations showed that moromycin A has a better binding energy (− 30.42 kcal mol⁻¹) compared with other ligands (in a range of − 18.66 to − 22.89 kcal mol⁻¹) including saquayamycin K4 (− 21.27 kcal mol⁻¹) except the co-crystallized ligand N3. However, in vitro and in vivo studies are essential to assess the effectiveness of angucycline compounds against coronavirus.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s11030-021-10219-1.

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.

Asymmetric Total Synthesis of PD-116740

A new approach was developed to achieve the asymmetric total synthesis of (+)-PD-116740, an angucyclinone from the actinomycete isolate (WP 4669). A sequence of asymmetric dihydroxylation followed by oxidative cyclization was applied to stereoselectively construct the core trans-9,10-dihydrophenanthrene-9,10-diol B-C-D ring. A new Cu salt Cu(OH)OTf·NMI₂ was found to be the best oxidant to induce the oxidative coupling and phenol oxidation.

Unusual bridged angucyclinones and potent anticancer compounds from Streptomyces bulli GJA1

Two new unique angucyclinones (1 and 2) with unprecedented ether bridges connecting carbons 5 and 7 were isolated from the cultures of Streptomyces bulli GJA1, an endophyte of Gardenia jasminoides, together with two known ones (3 and 4). The MS2-based molecular networking system facilitated the isolation of compounds with target functionalities. The stereochemistry of 1 was completely established by ROESY and ECD experiments. Compound 3 showed antivirulence activities by inhibiting the peptide toxin (PSMs) production and the biofilm formation of MRSA. Compounds 3 and 4 showed very potent anti-proliferative effects against OV1 and ES2 ovarian cancer cells.

Monacycliones G-K and ent-Gephyromycin A, Angucycline Derivatives from the Marine-Derived Streptomyces sp. HDN15129

Six new angucycline derivatives, named monacycliones G-K (1-5) and ent-gephyromycin A (6), as well as three known ones (7-9) were discovered from the marine sediment-derived actinomycete Streptomyces sp. HDN15129 guided by Global Natural Products Social (GNPS) molecular networking. Structures including absolute configurations were elucidated by extensive NMR, MS, and ECD analyses. Among them, monacyclione G (1) possesses a unique scaffold featuring a xanthone core linked to the aminodeoxysugar ossamine, and monacycliones H-J (2-4) are rare examples of natural angucyclines with an S-methyl group. Monacycliones I and J (3 and 4) showed cytotoxic activity against multiple human cancer cell lines, with IC₅₀ values ranging from 3.5 to 10 μM.

Antibacterial and Cytotoxic Bridged and Ring Cleavage Angucyclinones From a Marine Streptomyces sp

Chemical investigation of a marine-derived Streptomyces sp. KCB-132, cultivated in liquid ISP2 medium, had led to the discovery of three C-ring cleavage angucyclinone N-heterocycles, pratensilins A–C, with a novel spiro indolinone-naphthofuran skeleton. Addition of 50 μM LaCl₃ to the same medium and subsequent chemical analysis of this strain returned a new member of this rare class, pratensilin D (1), along with two new angucyclinone derivatives, featuring ether-bridged (2) and A-ring cleavage (3) structural properties. Their structures and absolute configurations were assigned by spectroscopic analysis, single-crystal X-ray diffractions, and equivalent circulating density (ECD) calculations. (+)- and (–)-1, a pair of enantiomeric nitrogen-containing angucyclinones, exhibited different strengths of antibacterial and cytotoxic activities.

Catalytic C-C Cleavage/Alkyne-Carbonyl Metathesis Sequence of Cyclobutanones

A ring-opening/alkyne-carbonyl metathesis sequence of alkyne-tethered cyclobutanones catalyzed by AgSbF₆ is realized for the first time to furnish multisubstituted naphthyl ketones under mild conditions. A range of substrates decorated with various substituents at different positions were all well accommodated. Preliminary mechanistic studies show that silver salt acted as a Lewis acid to facilitate both C-C cleavage of the cyclobutanone moiety and the subsequent metathesis between C═O and C≡C bonds.

Gephyyamycin and cysrabelomycin, two new angucyclinone derivatives from the Streptomyces sp. HN-A124

Gephyyamycin (1) owned the rare 3,12a-epoxybenz[a]anthracene ring system, and cysrabelomycin (2) possessed an acetylated cysteine group, two new angucyclinone derivatives were isolated from the rice solid fermentation of the marine-derived Streptomyces sp. HN-A124, an actinobacterium isolated from the marine sediments collected from Hainan Province, China. Their structures were elucidated on the basis of MS, NMR spectroscopic, X-ray diffration data analyses and quantum chemical calculations of the electronic circular dichroism (ECD) spectra. Compound 2 appeared to show moderate cytotoxicity against human prostate cancer PC3 and human ovarian carcinoma A2780 cell lines with IC₅₀ values of 19.39 and 10.23 μM, respectively; on the other hand, compound 2 also exhibited moderate antibacterial activities against Staphylococcus aureus and Candida albicans with an MIC value of 20.0 and 20 μM, respectively.

Synthesis and antitumor activities of aquayamycin and analogues of derhodinosylurdamycin A

An analogue without the sugar moiety of natural derhodinosylurdamycin A is better.

Nocardiopsistins A-C: New angucyclines with anti-MRSA activity isolated from a marine sponge-derived Nocardiopsis sp. HB-J378

Marine natural products have become an increasingly important source of new drug leads during recent years. In an attempt to identify novel anti-microbial natural products by bioprospecting deep-sea Actinobacteria, three new angucyclines, nocardiopsistins A-C, were isolated from Nocardiopsis sp. strain HB-J378. Notably, the supplementation of the rare earth salt Lanthanum chloride (LaCl₃) during fermentation of HB-J378 significantly increased the yield of these angucyclines. The structures of nocardiopsistins A-C were identified by 1D and 2D NMR and HR-MS data. Nocardiopsistins A-C have activity against MRSA (methicillin-resistant Staphylococcus aureus) with MICs of 3.12–12.5 μg/mL; the potency of nocardiopsistin B is similar to that of the positive control, chloramphenicol. Bioinformatic analysis of the draft genome of HB-J378 identified a set of three core genes in a biosynthetic gene cluster that encode a typical aromatic or type II polyketide synthase (PKS) system, including ketoacyl:ACP synthase α-subunit (KS_α), β-subunit (KS_β) and acyl carrier protein (ACP). The production of nocardiopsistins A-C was abolished when the three genes were knocked out, indicating their indispensable role in the production of nocardiopsistins.

Antibiotic Activity of Actinobacteria from the Digestive Tract of Millipede Nedyopus dawydoffiae (Diplopoda)

Because of the spread of drug resistance, it is necessary to look for new antibiotics that are effective against pathogenic microorganisms. The purpose of this study was to analyse the species composition of actinobacteria isolated from the digestive tract of the millipedes Nedyopus dawydoffiae and to determine their antimicrobial properties. Species identification was carried out on the basis of the morphological and culture properties and the sequence of the 16S rRNA gene. Actinobacteria were grown in different liquid media. Antibiotic properties were determined against some Gram-positive and Gram-negative bacteria as well as fungi. Of the 15 isolated strains, 13 have antibiotic activity against Gram-positive bacteria (including methicillin-resistant Staphylococcus aureus—MRSA) and fungi, but there was no antibiotic activity against Gram-negative test strains Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 27853. It was established that antibiotic-producing actinobacteria belong to eight species of the genus Streptomyces. Depending on the nutrient medium, actinobacteria demonstrate different antimicrobial activities. As an example, S. hydrogenans shows that even strains selected in one population differ by the range of antimicrobial activity and the level of biosynthesis. Since the antibiotic production is considered as a feature for species competition in the microbiota community, the variability of antibiotic production among different strains of the same species is an adaptive characteristic for the competition in millipedes’ digestive tract community.

Enantioselective Ruthenium-Catalyzed Benzocyclobutenone-Ketol Cycloaddition: Merging C-C Bond Activation and Transfer Hydrogenative Coupling for Type II Polyketide Construction

The first enantioselective intermolecular metal-catalyzed cycloadditions of benzocyclobutenones via C-C bond oxidative addition are described. In the presence of a ruthenium(0) complex modified by ( R)-DM-SEGPHOS, tetralone-derived ketols and benzocyclobutenones combine to form cycloadducts with complete regio- and diastereoselectivity and high enantioselectivity. Using this method, the "bay region" substructure of the angucycline natural product arenimycin was prepared.

A new and informative [a,b,c,d] nomenclature for one-pot multistep transformations: a simple tool to measure synthetic efficiency

Domino, cascade and tandem reactions constitute the most efficient and creative chemical transformations with a huge domain of synthetic utility and applications. A number of reactions may be achieved in a single pot, accompanied by the formation of new rings and new bonds, leading towards higher molecular complexity. A lack of one unified, yet informative descriptor often understates the synthetic ingenuity of certain highly creative transformations. In this review, we propose a new tetra-coordinated [a,b,c,d] nomenclature which takes into account and displays the basic parameters which generally indicate the level of efficiency of a chemical transformation. An almost exhaustive set of one-pot multistep reactions may be described by this system and this review is an attempt to display the one-pot multistep transformations reported from our group and to classify them based on our proposed descriptor.

Streptomyces globosus DK15 and Streptomyces ederensis ST13 as new producers of factumycin and tetrangomycin antibiotics

Fifty seven soil-borne actinomycete strains were assessed for the antibiotic production. Two of the most active isolates, designed as Streptomyces ST-13 and DK-15 exhibited a broad range of antimicrobial activity and therefore they were selected for HPLC fractionation against the most suppressed bacteria Staphylococcus aureus (ST-13) and Chromobacterium violaceum (DK-15). LC/MS analysis of extracts showed the presence of polyketides factumycin (DK15) and tetrangomycin (ST13). The taxonomic position of the antibiotic-producing actinomycetes was determined using a polyphasic approach. Phenotypic characterization and 16S rRNA gene sequence analysis of the isolates matched those described for members of the genus Streptomyces. DK-15 strain exhibited the highest 16S rRNA gene sequence similarity to Streptomyces globosus DSM-40815 (T) and Streptomyces toxytricini DSM-40178 (T) and ST-13 strain to Streptomyces ederensis DSM-40741 (T) and Streptomyces phaeochromogenes DSM-40073 (T). For the proper identification, MALDI-TOF/MS profile of whole-cell proteins led to the identification of S. globosus DK-15 (accession number: KX527570) and S. ederensis ST13 (accession number: KX527568). To our knowledge, there is no report about the production of these antibiotics by S.globosus and S. ederensis, thus isolates DK15 and ST13 identified as S. globosus DK-15 and S.ederensis ST-13 can be considered as new sources of these unique antibacterial metabolites.

2-Deoxyglycosyl 3-benzoylpropionates as novel donors for the direct and stereoselective synthesis of 2-deoxy-glycosides

Lewis acid mediated stereoselective synthesis of 2-deoxy-O-glycosides has been demonstrated using 2-deoxyglycosyl 3-benzoylpropionates as novel glycosyl donors.

Ruthenium-Catalyzed Transfer Hydrogenation for C-C Bond Formation: Hydrohydroxyalkylation and Hydroaminoalkylation via Reactant Redox Pairs

Merging the chemistry of transfer hydrogenation and carbonyl or imine addition, a broad new family of redox-neutral or reductive hydrohydroxyalkylations and hydroaminomethylations have been developed. In these processes, hydrogen redistribution between alcohols and π-unsaturated reactants is accompanied by C-C bond formation, enabling direct conversion of lower alcohols to higher alcohols. Similarly, hydrogen redistribution between amines to π-unsaturated reactants results in direct conversion of lower amines to higher amines. Alternatively, equivalent products of hydrohydroxyalkylation and hydroaminomethylation may be generated through the reaction of carbonyl compounds or imines with π-unsaturated reactants under the conditions of 2-propanol-mediated reductive coupling. Finally, using vicinally dioxygenated reactants, that is, diol, ketols, or diones, successive transfer hydrogenative coupling occurs to generate 2 C-C bonds, resulting in products of formal [4+2] cycloaddition.

Insights into Complex Oxidation during BE-7585A Biosynthesis: Structural Determination and Analysis of the Polyketide Monooxygenase BexE

Cores of aromatic polyketides are essential for their biological activities. Most type II polyketide synthases (PKSs) biosynthesize these core structures involving the minimal PKS, a PKS-associated ketoreductase (KR) and aromatases/cyclases (ARO/CYCs). Oxygenases (OXYs) are rarely involved. BE-7585A is an anticancer polyketide with an angucyclic core. (13)C isotope labeling experiments suggest that its angucyclic core may arise from an oxidative rearrangement of a linear anthracyclinone. Here, we present the crystal structure and functional analysis of BexE, the oxygenase proposed to catalyze this key oxidative rearrangement step that generates the angucyclinone framework. Biochemical assays using various linear anthracyclinone model compounds combined with docking simulations narrowed down the substrate of BexE to be an immediate precursor of aklaviketone, possibly 12-deoxy-aklaviketone. The structural analysis, docking simulations, and biochemical assays provide insights into the role of BexE in BE-7585A biosynthesis and lay the groundwork for engineering such framework-modifying enzymes in type II PKSs.

Antibacterial metabolites from the Actinomycete Streptomyces sp. P294

The Actinomycete strain P294 was isolated from soil and identified as Streptomyces sp. based upon the results of 16S rRNA sequence analysis. Three compounds obtained from the solid fermentation products of this strain have been determined by 1D, 2D NMR and HRMS experiments. These compounds include two new compounds angumycinones C (1) and D (2), and the known compound X-14881 E (3). All compounds were assayed for antibacterial and nematicidal activity. The results showed the three compounds had different degrees of inhibitory activity against several target bacteria but no significant toxicity against the nematode Caenorhabditis elegans.

Ruthenium(0)-Catalyzed [4+2] Cycloaddition of Acetylenic Aldehydes with α-Ketols: Convergent Construction of Angucycline Ring Systems

Ruthenium(0) complexes modified by CyJohnPhos or RuPhos catalyze the successive C-C coupling of acetylenic aldehydes with α-ketols to form [4+2] cycloadducts as single diastereomers. This method enables convergent construction of type II polyketide ring systems of the angucycline class.

A comprehensive review of glycosylated bacterial natural products

A systematic analysis of all naturally-occurring glycosylated bacterial secondary metabolites reported in the scientific literature up through early 2013 is presented. This comprehensive analysis of 15 940 bacterial natural products revealed 3426 glycosides containing 344 distinct appended carbohydrates and highlights a range of unique opportunities for future biosynthetic study and glycodiversification efforts.

Synthesis of a landomycinone skeleton via Masamune–Bergmann cyclization

In this report, a synthetic study of landomycinone via Masamune–Bergmann cyclization is described.

Preparation of C-arylglycals via Suzuki-Miyaura cross-coupling of dihydropyranylphosphates

The preparation of C-arylglycals has been accomplished employing the Suzuki-Miyaura cross-coupling reaction of dihydropyranylphosphates with arylboronate esters. The reaction is tolerant of both electron-donating (EDG) and electron-withdrawing (EWG) groups on the aromatic ring and affords the corresponding C-arylglycals in good to excellent yields (68-97%). Additionally, the ketene acetal phosphate derived from 6-deoxy-3,4-di-O-benzyl-L-rhamnal also couples efficiently to yield C-arylglycals in excellent yields.

Convergent de novo synthesis of vineomycinone B2 methyl ester

An efficient de novo synthesis of vineomycinone B2 methyl ester has been achieved. The longest linear route required only 14 steps from achiral commercially available starting materials (4.0% overall yield). The key transformations included the de novo asymmetric synthesis of two key fragments, which were joined by a convergent late stage Suzuki's glycosylation for the construction of the aryl β-C-glycoside. A subsequent BBr3 one-pot debenzylation, demethylation and air oxidation provided vineomycinone B2 methyl ester.

Saccharosporones A, B and C, cytotoxic antimalarial angucyclinones from Saccharopolyspora sp. BCC 21906

Three new angucyclinones, saccharosporones A, B and C, together with (+)-ochromycinone, (+)-rubiginone B2, tetrangulol methyl ether and fujianmycin A, were obtained from fermentation of the terrestrial actinomycete of the genus Saccharopolyspora BCC 21906 isolated from a soil collected in Chanthaburi Province, Thailand. Structures of the new compounds and their relative configurations were assigned by NMR spectral data interpretation. Saccharosporones A and B exhibited antimalarial activity against Plasmodium falciparum K1 with IC50 values of 4.1 and 3.9 μM. Both metabolites also possessed cytotoxic activities against cancer cell lines (KB, MCF-7 and NCI-H187) and nonmalignant Vero cell, while saccharosporone C only showed cytotoxic activity against NCI-H187.