Misc

A new derivative of cannabigerolic acid, designated as iso-cannabigerolic acid (iso-CBGA), a member of the cannabinoid family, and its precursor iso-olivetolic acid (iso-OA) were discovered from the culture of the engineered Streptomyces avermitilis heterologously expressing the genes responsible for cannabigerolic acid biosynthesis. Structural determination revealed an iso-pentyl moiety, which may arise from the biosynthetic precursor pool present in S. avermitilis. We describe herein the culture, isolation, structure determination and antibacterial activities of iso-CBGA and iso-OA.

Using genome mining approach, we identified a novel biosynthetic gene cluster containing trans-AT type PKS genes from Streptomyces versipellis 4083-SVS6. A bacterial artificial chromosome (BAC) clone, pKU503JL68_PN1_P10-C12, accommodating the entire biosynthetic gene cluster was obtained from a BAC library. Heterologous expression of the biosynthetic gene cluster in Streptomyces lividans TK23 led to the production of a novel polyene compound, JBIR-159. We report herein the biosynthetic gene cluster for JBIR-159, and the heterologous expression, isolation, structure determination and a brief biological activity.

A search for anti-trypanosomal natural compounds from plants collected in El Salvador, a country particularly endemic for Chagas disease, resulted in the isolation of five lignan-type compounds (1-5) from Peperomia pseudopereskiifolia. The lignan derivatives 1, 2, and 4 are new. Their absolute configuration was determined by chemical derivatization. Compounds 1, 5, 6, and 8 exhibited anti-trypanosomal activity against the amastigote form of T. cruzi comparable to that of the existing drug benznidazole.

The biosynthetic gene clusters (BGCs) for the macrocyclic lactone-based polyketide compounds are extremely large-sized because the polyketide synthases that generate the polyketide chains of the basic backbone are of very high molecular weight. In developing a heterologous expression system for the large BGCs amenable to the production of such natural products, we selected concanamycin as an appropriate target. We obtained a bacterial artificial chromosome (BAC) clone with a 211-kb insert harboring the entire BGC responsible for the biosynthesis of concanamycin. Heterologous expression of this clone in a host strain, Streptomyces avermitilis SUKA32, permitted the production of concanamycin, as well as that of two additional aromatic polyketides. Structural elucidation identified these additional products as ent-gephyromycin and a novel compound that was designated JBIR-157. We describe herein sequencing and expression studies performed on these BGCs, demonstrating the utility of large BAC clones for the heterologous expression of cryptic or near-silent loci.

Chemical investigation of the methanolic extract of Guarea glabra Vahl (Meliaceae) led to the isolation of a new amide alkaloid containing a pyrrolidine moiety (1) and a dihydro-α-pyrone derivative (2), together with two known pimarane-type diterpenes (3, 4). The structures of the new compounds were elucidated using comprehensive spectroscopic analyses, including 1D and 2D NMR experiments. The absolute configuration of 2 was determined by comparing experimental and calculated electronic circular dichroism spectra. Compounds 1–4 demonstrated antitrypanosomal activity against the epimastigote form of Trypanosoma cruzi, with IC50 values ranging from 0.66 to 2.3 µM; compound 4 exhibited submicromolar activity. In the intracellular assay, compound 3 reduced the number of intracellular amastigotes at 10 µM. None of the isolated compounds showed significant antimalarial activity under the tested conditions. Compounds 1–4 exhibited favorable selectivity for T. cruzi over mammalian HT1080 cells. These findings highlight pimarane-type diterpenes as structurally distinct, sp3-rich scaffolds with favorable selectivity profiles and potential as leads for the development of new antitrypanosomal agents.

Baicalin and berberine are biologically active constituents of the crude drugs Scutellaria root and Coptis rhizome/Phellodendron bark, respectively. Baicalin and berberine are reported to combine together as a 1:1 complex that forms yellow precipitates by electrostatic interaction in decoctions of Kampo formulae containing these crude drugs. However, the structural basis and mechanism for the precipitate formation of this compound–compound interaction in aqueous solution remains unclarified. Herein, we searched for berberine derivatives in the Coptis rhizome that interact with baicalin and identified the chemical structures involved in the precipitation formation. Precipitation assays showed that baicalin formed precipitates with berberine and coptisine but not with palmatine and epiberberine. Thus, the 2,3-methylenedioxy structure may be crucial to the formation of the precipitates, and electrostatic interaction is necessary but is not sufficient. In this multicomponent system experiment, palmatine formed a dissociable complex with baicalin and may competitively inhibit the formation of berberine and coptisine precipitation with baicalin. Therefore, the precipitation formed by berberine and baicalin was considered to be caused by the aggregation of the berberine–baicalin complex, and the 2,3-methylenedioxy structure is likely crucial to the aggregation of the complex. Graphic abstract: (Figure presented.)

Objective: Dictyostelium differentiation-inducing factors 1 and 3 [DIF-1 (1) and DIF-3 (2), respectively], along with their derivatives, such as Ph-DIF-1 (3) and Bu-DIF-3 (4), demonstrate antibacterial activity in vitro against Gram-positive bacteria, including methicillin-sensitive Staphylococcus aureus (MSSA), methicillin-resistant S. aureus (MRSA), vancomycin-sensitive Enterococcus faecalis (VSE), and vancomycin-resistant Enterococcus faecium [VRE (VanA)]. This study investigates the therapeutic potential of DIF compounds against these Gram-positive bacteria. Results: In vitro tests revealed that the antibacterial activity of 3 and 4 was lost in the presence of human serum albumin (HSA), suggesting that HSA might inhibit their effectiveness. Further evaluation of less hydrophobic derivatives, DIF-1-NH2 (5) and NH2-Bu-DIF-3 (6), showed no antibacterial activity, even in the absence of HSA. However, ester derivatives Ph-DIF-1(AHA) (7) and Bu-DIF-3(2Ac) (8) exhibited antibacterial activity against the target bacteria in vitro, although this activity was also lost in the presence of HSA. We hypothesize that these ester derivatives may function as prodrugs, with their antibacterial activity possibly restored by hydrolysis through bacterial esterases. The results suggest that suitable ester modifications could enhance the in vivo antibacterial potential of DIF compounds, particularly if they can bypass HSA binding and be activated by bacterial enzymes.

AbstractEngineering polyketide synthases is one of the most promising ways of producing a variety of polyketide derivatives. Exploring the undiscovered chemical space of this medicinally important class of middle molecular weight natural products will aid in the development of improved drugs in the future. In previous work, we established methodology designated ‘module editing’ to precisely manipulate polyketide synthase genes cloned in a bacterial artificial chromosome. Here, in the course of investigating the engineering capacity of the rapamycin PKS, novel rapamycin derivatives 1–4, which lack the hemiacetal moiety, were produced through the heterologous expression of engineered variants of the rapamycin PKS. Three kinds of module deletions in the polyketide synthase RapC were designed, and the genetically engineered vectors were prepared by the in vitro module editing technique. Streptomyces avermitilis SUKA34 transformed with these edited PKSs produced new rapamycin derivatives. The planar structures of 1–4 established based on 1D and 2D NMR, ESI–TOF–MS and UV spectra revealed that 2 and 3 had skeletons well-matched to the designs, but 1 and 4 did not. The observations provide important insights into the mechanisms of the later steps of rapamycin skeletal formation as well as the ketone-forming oxygenase RapJ.

Cellular slime molds are excellent model organisms in the field of cell and developmental biology because of their simple developmental patterns. During our studies on the identification of bioactive molecules from secondary metabolites of cellular slime molds toward the development of novel pharmaceuticals, we revealed the structural diversity of secondary metabolites. Cellular slime molds grow by feeding on bacteria, such as Klebsiella aerogenes and Escherichia coli, without using medium components. Although changing the feeding bacteria is expected to affect dramatically the secondary metabolite production, the effect of the feeding bacteria on the production of secondary metabolites is not known. Herein, we report the isolation and structure elucidation of clavapyrone (1) from Dictyostelium clavatum, intermedipyrone (2) from D. magnum, and magnumiol (3) from D. intermedium. These compounds are not obtained from usual cultural conditions with Klebsiella aerogenes but obtained from coincubated conditions with Pseudomonas spp. The results demonstrate the diversity of the secondary metabolites of cellular slime molds and suggest that widening the range of feeding bacteria for cellular slime molds would increase their application potential in drug discovery.

Heterologous expression of natural compound biosynthetic gene clusters (BGCs) is a robust approach for not only revealing the biosynthetic mechanisms leading to the compounds, but also for discovering new products from uncharacterized BGCs. We established a heterologous expression technique applicable to huge biosynthetic gene clusters for generating large molecular secondary metabolites such as type-I polyketides. As an example, we targeted concanamycin BGC from Streptomyces neyagawaensis IFO13477 (the cluster size of 99kbp), and obtained a bacterial artificial chromosome (BAC) clone with an insert size of 211kbp that contains the entire concanamycin BGC. Interestingly, heterologous expression for this BAC clone resulted in two additional aromatic polyketides, ent-gephyromycin, and a new compound designated as JBIR-157, together with the expected concanamycin. Bioinformatic and biochemical analyses revealed that a cryptic biosynthetic gene cluster in this BAC clone was responsible for the production of these type-II polyketide synthases (PKS) compounds. Here, we describe the production, isolation, and structure elucidation of JBIR-157, determined primarily by a series of NMR spectral analyses.

We discovered JBIR-155 as a novel specific class D β-lactamase inhibitor from Streptomyces polymachus SoB100815Hv02. JBIR-155 consists of a 6-oxabicyclo[3.2.0]heptan-7-one skeleton and a long unsaturated alkyl chain moiety of which absolute configuration was determined by spectroscopic data, modified Mosher's method, and analyses of the relative configuration of chemically modified derivative. JBIR-155 specifically exhibited inhibitory activity against the class D β-lactamase, with an IC50 value of 0.36 μM.

Oomycetes are eukaryotic microorganisms widely distributed in aquatic and terrestrial environments. Although they morphologically resemble fungi, they belong to the kingdom Stramenopila. Saprolegnia parasitica is an agriculturally and economically important oomycete and is well-known as a freshwater fish pathogen. Despite its significance, this organism has received little attention in natural product chemistry and is generally regarded as having limited secondary metabolite productivity. Nevertheless, oomycetes are known to produce small molecules that mediate interspecies and host communication and are therefore expected to generate secondary metabolites derived from components associated with the host and growth medium. Herein, we report the isolation, structural elucidation, and preliminary biological activities of parasitisterols A–C, newly identified 24,25-oxygenated cholestane-type triterpenes isolated from S. parasitica. These findings demonstrate that oomycetes represent an underexplored, yet promising, resource for natural product discovery.

Assembly line biosynthesis creates numerous structurally diverse natural products using a common modular synthetic strategy. The collinearity between the architectures of modular polyketide synthases (PKS) and the structures of their polyketide products would seem to render these biosynthetic machineries excellent platforms for designer biosynthesis, yet reliable strategies to reprogram these assembly lines without diminishing their activities have not been identified. Here, as a best practice for PKS engineering, we demonstrate the reprogramming of the mediomycin PKS without significant loss of productivity. Using in vitro CRISPR/Cas9 gene editing followed by heterologous expression, we reconstruct an inaccessible drug lead of the fibrinogen receptor, tetrafibricin, at 82 ± 3 mg/L yield, retaining 26% productivity after five-step module editing using an evolution-supported cut site, downstream of the acyltransferase domain. A macrocyclic aminopolyol is also accessed through thioesterase swapping. These results pave the way toward the rational reprogramming of PKSs to access desired complex organic molecules.

The construction of a chemical library based on natural products is a promising method for the synthesis of natural product-like compounds. In this study, we synthesized a terpenoid alkaloid-like compound library based on the humulene skeleton. Our strategy, which enables access to diverse ring systems such as 11-membered monocyclic, oxabicyclic, and medium-sized aza ring-containing scaffolds, involves the introduction of a nitrogen atom, an intermolecular C-O bond formation via Lewis acid-mediated epoxide-opening transannulation, and a ring-reconstruction strategy based on olefin metathesis. A cheminformatics analysis based on their structural and physicochemical properties revealed that the synthesized compounds have high three-dimensionality and high natural product likeness scores but with structural novelty. The usefulness of the terpenoid alkaloid-like compound library for drug discovery and the accessibility to structure-activity relationship studies were validated by performing an assay for osteoclast-specific tartrate-resistant acid phosphatase activity, resulting in the identification of a lead compound for bone-resorptive diseases such as osteoporosis.

植物から得られた生物活性分子のなかには，植物に共生する微生物が真の生産者である場合がある．このような微生物の多くは，特定の共生環境でのみ生育が可能で，一般的な実験室環境下では培養が困難であり，工業生産などへの応用が難しい．Kudoらは，in vitro Cas9反応とバクテリア人工染色体(bacterial artificial chromosome: BAC)上でのギブソンアセンブリーを応用し，相同性が高い配列が繰り返されるI型モジュール型ポリケチド合成酵素遺伝子の標的領域を制約なく編集できる革新的な技術「in vitroモジュール編集」を報告している．本技術を用いて天然物の設計図とも言える生合成遺伝子を編集し，異種発現ホストに発酵生産させることができれば，自由にデザインされた化合物の生産が可能になると期待できる．本稿では，培養困難な微生物由来化合物生産における課題の解決策の1つとして，in vitroモジュール編集を活用したFR900359の生産に関する文献を紹介する．