Structure—Activity Relationships in the Actinomycins

Natural Products from Actinomycetes Associated with Marine Organisms

The actinomycetes have proven to be a rich source of bioactive secondary metabolites and play a critical role in the development of pharmaceutical researches. With interactions of host organisms and having special ecological status, the actinomycetes associated with marine animals, marine plants, macroalgae, cyanobacteria, and lichens have more potential to produce active metabolites acting as chemical defenses to protect the host from predators as well as microbial infection. This review focuses on 536 secondary metabolites (SMs) from actinomycetes associated with these marine organisms covering the literature to mid-2021, which will highlight the taxonomic diversity of actinomycetes and the structural classes, biological activities of SMs. Among all the actinomycetes listed, members of Streptomyces (68%), Micromonospora (6%), and Nocardiopsis (3%) are dominant producers of secondary metabolites. Additionally, alkaloids (37%), polyketides (33%), and peptides (15%) comprise the largest proportion of natural products with mostly antimicrobial activity and cytotoxicity. Furthermore, the data analysis and clinical information of SMs have been summarized in this article, suggesting that some of these actinomycetes with multiple host organisms deserve more attention to their special ecological status and genetic factors.

Actinomycin-Producing Endophytic Streptomyces parvulus Associated with Root of Aloe vera and Optimization of Conditions for Antibiotic Production

Endophytic actinomycetes are a rich source of novel antimicrobial compounds. The aim of this study was to evaluate the production of antimicrobial compound by endophytic Streptomyces sp. Av-R5 associated with root of Aloe vera against multidrug-resistant human pathogens. The 16S rRNA sequence of the isolate Av-R5 has been identified as Streptomyces parvulus NBRC 13193^T (AB184326) and the sequence was submitted to the National Center for Biotechnology Information (NCBI) GenBank database (accession number KY771080). Streptomyces parvulus Av-R5 grown under submerged fermentation condition optimized by central composite design (glucose 11.16 g/L, soybean meal 10.25 g/L, sodium chloride 11.18 g/L, calcium carbonate 1.32 g/L at pH 7.19 at 31.42 °C with 6.04% seed inoculum for 10 days of incubation) exhibited the highest activity against multidrug-resistant Staphylococcus aureus JNMC-3, Staphylococcus epidermidis JNMC-4, Klebsiella pneumoniae MTCC-3384, Klebsiella pneumoniae JNMC-6, Pseudomonas aeruginosa MTCC-741, Proteus vulgaris JNMC-7, Candida albicans MTCC-183, and Aspergillus niger MTCC-872. The structures of the active compounds were elucidated by UV-Vis spectroscopy, ¹H and ¹³C NMR, FT-IR, and ESIMS. Actinomycin D and actinomycin X_0β were detected in crude extracts and major components were eluted by HPLC at 10.96 and 6.81 min, respectively. In this case, a high yield of actinomycin D and actinomycin X_0β (400 mg/L) was achieved with Streptomyces parvulus Av-R5, fermented in glucose soybean meal broth media, which can be used in industrial fermentation process to obtain high yields.

Comparison of actinomycin peptide synthetase formation in Streptomyces chrysomallus and Streptomyces antibioticus

Actinomycin peptide synthetase genes constitute two oppositely oriented transcriptional units, acmADR, and acmBC, separated by a non-coding intergenic region. Gene constructs of the intergenic region together with its adjoining gene acmA or acmB from the actinomycin biosynthetic gene cluster of Streptomyces chrysomallus were transferred into Streptomyces lividans TK64. Each construct expressed the respective synthetase indicating divergent promoters. Primer extension revealed for both directions -10 and -35 boxes similar to σ⁷⁰ -dependent promoters from Streptomyces and E. coli. No conspicuous regulatory sequences were detected. Accordingly, S. chrysomallus-grown in glucose-containing medium-produced the peptide synthetases AcmA and AcmB/C as well as actinomycin during logarithmic growth phase. Alignments with the corresponding intergenic region of the actinomycin biosynthetic gene cluster in Streptomyces antibioticus identified analogous -10 and -35 boxes of σ⁷⁰ consensus sequence. However, in S. antibioticus-cultivated in the same conditions-AcmA and AcmB/C were at maximum activity in late log phase and actinomycin formation peaked in stationary phase. The different patterns of formation of actinomycin and its peptide synthetases encoded by the highly homologous actinomycin biosynthetic gene clusters in S. chrysomallus and S. antibioticus suggest strain-specific control of biosynthesis in agreement with absence of pathway-specific regulatory genes.

Ketonization of Proline Residues in the Peptide Chains of Actinomycins by a 4-Oxoproline Synthase

X-type actinomycins (Acms) contain 4-hydroxyproline (Acm X₀ ) or 4-oxoproline (Acm X₂ ) in their β-pentapeptide lactone rings, whereas their α ring contains proline. We demonstrate that these Acms are formed through asymmetric condensation of Acm half molecules (Acm halves) containing proline with 4-hydroxyproline- or 4-oxoproline-containing Acm halves. In turn, we show-using an artificial Acm half analogue (PPL 1) with proline in its peptide chain-their conversion into the 4-hydroxyproline- and 4-oxoproline-containing Acm halves, PPL 0 and PPL 2, in mycelial suspensions of Streptomyces antibioticus. Two responsible genes of the Acm X biosynthetic gene cluster of S. antibioticus, saacmM and saacmN, encoding a cytochrome P450 monooxygenase (Cyp) and a ferredoxin were identified. After coexpression in Escherichia coli, their gene products converted PPL 1 into PPL 0 and PPL 2 in vivo as well as in situ in permeabilized cell of the transformed E. coli strain in conjunction with the host-encoded ferredoxin reductase in a NADH (NADPH)-dependent manner. saAcmM has high sequence similarity to the Cyp107Z (Ema) family of Cyps, which can convert avermectin B1 into its keto derivative, 4''-oxoavermectin B1. Determination of the structure of saAcmM reveals high similarity to the Ema structure but with significant differences in residues decorating their active sites, which defines saAcmM and its orthologues as a distinct new family of peptidylprolineketonizing Cyp.

Biological and Chemical Diversity of Bacteria Associated with a Marine Flatworm

The aim of this research is to explore the biological and chemical diversity of bacteria associated with a marine flatworm Paraplanocera sp., and to discover the bioactive metabolites from culturable strains. A total of 141 strains of bacteria including 45 strains of actinomycetes and 96 strains of other bacteria were isolated, identified and fermented on a small scale. Bioactive screening (antibacterial and cytotoxic activities) and chemical screening (ultra-performance liquid chromatography–mass spectrometry (UPLC-MS)) yielded several target bacterial strains. Among these strains, the ethyl acetate (EA) crude extract of Streptomyces sp. XY-FW47 fermentation broth showed strong antibacterial activity against methicillin-resistant Staphylococcus aureus ATCC43300 (MRSA ATCC43300) and potent cytotoxic effects on HeLa cells. The UPLC-MS spectral analysis of the crude extract indicated that the strain XY-FW47 could produce a series of geldanamycins (GMs). One new geldanamycin (GM) analog, 4,5-dihydro-17-O-demethylgeldanamycin (1), and three known GMs (2–4) were obtained. All of these compounds were tested for antibacterial, cytotoxic, and antifungal activities, yet only GM (3) showed potent cytotoxic (HeLa cells, EC₅₀ = 1.12 μg/mL) and antifungal (Setosphaeria turcica MIC = 2.40 μg/mL) activities. Their structure–activity relationship (SAR) was also preliminarily discussed in this study.

The actinomycin biosynthetic gene cluster of Streptomyces chrysomallus: a genetic hall of mirrors for synthesis of a molecule with mirror symmetry

A gene cluster was identified which contains genes involved in the biosynthesis of actinomycin encompassing 50 kb of contiguous DNA on the chromosome of Streptomyces chrysomallus. It contains 28 genes with biosynthetic functions and is bordered on both sides by IS elements. Unprecedentedly, the cluster consists of two large inverted repeats of 11 and 13 genes, respectively, with four nonribosomal peptide synthetase genes in the middle. Nine genes in each repeat have counterparts in the other, in the same arrangement but in the opposite orientation, suggesting an inverse duplication of one of the arms during the evolution of the gene cluster. All of the genes appear to be organized into operons, each corresponding to a functional section of actinomycin biosynthesis, such as peptide assembly, regulation, resistance, and biosynthesis of the precursor of the actinomycin chromophore 4-methyl-3-hydroxyanthranilic acid (4-MHA). For 4-MHA synthesis, functional analysis revealed genes that encode pathway-specific isoforms of tryptophan dioxygenase, kynurenine formamidase, and hydroxykynureninase, which are distinct from the corresponding enzyme activities of cellular tryptophan catabolism in their regulation and in part in their substrate specificity. Phylogenetic analysis indicates that the pathway-specific tryptophan metabolism in Streptomyces most probably evolved divergently from the normal pathway of tryptophan catabolism to provide an extra or independent supply of building blocks for the synthesis of tryptophan-derived secondary metabolites.

The human RNA polymerase II interacts with the terminal stem-loop regions of the hepatitis delta virus RNA genome

The hepatitis delta virus (HDV) is an RNA virus that depends on DNA-dependent RNA polymerase (RNAP) for its transcription and replication. While it is generally accepted that RNAP II is involved in HDV replication, its interaction with HDV RNA requires confirmation. A monoclonal antibody specific to the carboxy terminal domain of the largest subunit of RNAP II was used to establish the association of RNAP II with both polarities of HDV RNA in HeLa cells. Co-immunoprecipitations using HeLa nuclear extract revealed that RNAP II interacts with HDV-derived RNAs at sites located within the terminal stem-loop domains of both polarities of HDV RNA. Analysis of these regions revealed a strong selection to maintain a rod-like conformation and demonstrated several conserved features. These results provide the first direct evidence of an association between human RNAP II and HDV RNA and suggest two transcription start sites on both polarities of HDV RNA.

Nonribosomal biosynthesis of microbial chromopeptides

Nonribosomal chromopeptides and mixed chromopeptide-polyketides contain aromatic or heteroaromatic side groups which are important recognition elements for interaction with cellular targets such as DNA and proteins, resulting in the biological activities of these natural products. In the chromopeptide lactones and arylpeptide-siderophores from bacteria, the chromophore moiety--an aryl carboxylate amidated to the peptide chain--constitutes the formal amino terminus and is the starter residue of peptide assembly. Common to many arylpeptide systems is the activation by stand-alone adenylation domains and loading of the starter to discrete aryl carrier proteins (ArCPs) or ArCP domains which interact with the modules of the respective nonribosomal peptide synthetase (NRPS), assembling the next residues of the chain. Chain modification is another mechanism of nonribosomal chromopeptide synthesis where heteroaromatic rings such as thiazoles and oxazoles in peptides and polyketides are generated by heterocylizations of acyl- or peptidyl-cysteinyl or -serinyl/threonyl intermediates in each elongation step. In this review the basic mechanisms of chromophore acquisition in nonribosomal chromopeptide synthesis and mixed peptide/polyketide synthesis are illustrated by comparing the biosynthesis systems of various chromopeptides and chromopeptidic polyketide compounds.

Molecular characterization of the genes of actinomycin synthetase I and of a 4-methyl-3-hydroxyanthranilic acid carrier protein involved in the assembly of the acylpeptide chain of actinomycin in Streptomyces

Actinomycin synthetase I (ACMS I) activates 4-methyl-3-hydroxyanthranilic acid, the precursor of the chromophoric moiety of the actinomycin, as adenylate. The gene acmA of ACMS I was identified upstream of the genes acmB and acmC encoding the two peptide synthetases ACMS II and ACMS III, respectively, which assemble the pentapeptide lactone rings of the antibiotic. Sequence analysis and expression of acmA in Streptomyces lividans as enzymatically active hexa-His-fusion confirmed the acmA gene product to be ACMS I. An open reading frame of 234 base pairs (acmD), which encodes a 78-amino acid protein with similarity to various acyl carrier proteins, is located downstream of acmA. The acmD gene was expressed in Escherichia coli as hexa-His-fusion protein (Acm acyl carrier protein (AcmACP)). ACMS I in the presence of ATP acylated the purified AcmACP with radioactive p-toluic acid, used as substrate in place of 4-MHA. Only 10% of the AcmACP from E. coli was acylated, suggesting insufficient modification with 4'-phosphopantetheine cofactor. Incubation of this AcmACP with a holo-ACP synthase and coenzyme A quantitatively established the holo-form of AcmACP. Enzyme assays in the presence of ACMS II showed that toluyl-AcmACP directly acylated the thioester-bound threonine on ACMS II. Thus, AcmACP is a 4-MHA carrier protein in the peptide chain initiation of actinomycin synthesis.

Effect of actinomycin D and cycloheximide on human sperm function

The effects of actinomycin D and cycloheximide on human spermatozoal function were examined to investigate the potential transcriptional and translational activities of human sperm cell during capacitation/acrosome reaction. Treatment with actinomycin D significantly increased and treatment with cycloheximide decreased the acrosome reaction, and the penetration rates in the human sperm penetration of zona-free hamster oocytes assay (SPA). [35(S)]Methionine got incorporated into 3-9 de novo synthesized proteins present in the head and midpiece regions of the swim-up population of human sperm. Treatment with actinomycin D completely blocked and treatment with cycloheximide slightly reduced the synthesis of proteins. There seem to be some transcriptional and translational activities in the head and midpiece regions of human sperm during capacitation/acrosome reaction.

Electrochemical and electron spin resonance studies of actinomycin D and other phenoxazones

Electrochemical studies on actinomycin D (1) and two analogs, 2-amino-3-phenoxazone (2) and 1,2,4-trichloro-7-nitrophenoxazone (3) were analyzed by polarography and ESR spectroscopy. The polarograms of the three compounds in acetonitrile all show two reduction waves. ESR experiments confirm that the first reduction wave corresponds to a one-electron transfer process which produces a phenoxazone free radical anion and the second wave corresponds to a subsequent one-electron transfer producing a diamagnetic dianion. Substitution with electron-withdrawing groups such as NO2 (at C-7) and chloro (at C-1, C-2 and C-4)3 facilitated the reduction of the phenoxazone ring system to a free radical (i.e., half-wave potentials; 1, -0.815 V; 2, -0.920 V; 3, -0.135 V). It was found, by computer simulation of the ESR spectra, that the spin density in the electrochemically generated free radicals from 1, 2 and 3 was preferentially located in the benzenoid ring and at the N-10 nitrogen. For radicals obtained from 1 and 2, only a small residual spin density could be detected in the quinoid ring. Since 1 can be metabolized to a free radical in cells, these free radical forms of 1 and its analogs may represent reactive forms of the phenoxazone nucleus.

Control of actinomycin D biosynthesis in Streptomyces parvullus: regulation of tryptophan oxygenase activity

Tryptophan oxygenase (tryptophan 2,3-dioxygenase) activity increases immediately before the initiation of actinomycin D production by Streptomyces parvullus. We have attempted to discern whether this increase is due to a release from catabolite repression or to the synthesis of an inducer substance. The standard culture medium (glutamic acid-histidine-fructose medium) used in antibiotic production studies with S. parvullus contains l-glutamate as a major constituent. l-Glutamate is almost totally consumed before the onset of actinomycin D synthesis. The addition of 10 mM l-glutamate at this stage completely abolished actinomycin D production as well as tryptophan oxygenase synthesis. Fourteen amino acids were tested for a similar effect. Of these, l-glutamate and l-aspartate had the most dramatic effect on tryptophan oxygenase and beta-galactosidase (beta-d-galactosidase), another inducible enzyme. Standard glutamic acid-histidine-fructose medium, preincubated for 23 h to remove l-glutamate, allowed the synthesis of actinomycin D and tryptophan oxygenase by cells at a stage of growth normally considered too early for antibiotic production. A chemically defined medium lacking l-glutamate and adjusted to pH 8.0 was designed to simulate the preincubation medium. The transfer of cells to this artificial preincubation medium resulted in the appearance of tryptophan oxygenase as early as 19 h before normal synthesis occurred, eliminating the possibility that an inducer molecule is synthesized and excreted during the preincubation period. The results of these studies suggest that the increase in tryptophan oxygenase activity before the onset of actinomycin D synthesis, as well as the synthesis of actinomycin D itself, is due to a release from l-glutamate catabolite repression.

Natural products from microorganisms

Microorganisms are capable of producing natural products with widely divergent chemical structures. Greatest attention in the past has been paid to natural products that have antibiotic properties. Natural products accumulate in fermentation broths during secondary metabolism, a characteristic of the incomplete metabolic control operative in growth-inhibited microorganisms. With this general mechanism of biosynthesis, the natural products synthesized by microorganisms would be expected to have a broad range of pharmacological activities. The directed screening for non-antibiotic natural products has been of limited scope. The expectation that new compounds of interest would be found has been validated. The pharmacologically active natural products provide previously unrecognized structures as tools for fundamental research programs, as well as offering the possibility of direct use in medicine or in industrial processes.

NMR studies of the structure and stability of the 1 : 2 actinomycin D-d-pG-C complex in aqueous solution

We describe NMR studies at superconducting fields which characterize aspects of the structure and stability of the 1 : 2 actinomycin-d-pG-C complex in solution as monitored at the Watson-Crick base pairs and backbone phosphate groups. Two guanine N1H resonances (12.17 and 11.66 ppm) are observed in the 360 MHz proton NMR spectra of the complex in water at -4 degrees C. These slowly exchangeable resonances, which demonstrate the presence of two Watson-Crick G + C base pairs in the complex, broaden in a sequential manner with increasing temperature. The terminal and internucleotide phosphates of both d-pG-C molecules are observable in the 145.7 MHz 31P spectra of the 1 : 2 actinomycin-d-pG-C complex at 0 degrees C. The internucleotide phosphate resonance at 1.905 ppm broadens prior to that at 2.385 ppm with increasing temperature, consistent with a sequential breakage of the G + C base pairs in the complex. The lifetime of the complex (4.5 +/- 0.5 X 10(-4) s, 33 degrees C) was deduced from the variation of the d-pG-D internucleotide 31P resonance line width on gradual addition of the antibiotic in solution.