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Saito S, Atsumi K, Zhou T, Fukaya K, Urabe D, Oku N, Karim MRU, Komaki H, Igarashi Y. A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium. Beilstein J Org Chem 2020; 16:1100-1110. [PMID: 32550925 PMCID: PMC7277628 DOI: 10.3762/bjoc.16.97] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Aside from the well-studied conventional actinomycetes such as Streptomyces, the less investigated genera of actinomycetes also represent a promising source of natural products. Genome mining indicated that members of the underexplored genus Pseudosporangium, from which no secondary metabolites have been reported to date, may harbor the biosynthetic machinery for the formation of novel natural products. The strain RD062863, that is available at a public culture collection, was obtained and subjected to metabolite analysis, which resulted in the discovery of a novel cyclopeptide, pseudosporamide (1), along with three new oligomycin-class polyketides, pseudosporamicins A–C (2–4). The unusual structure of compound 1, featured by a biaryl-bond bridging across a tripeptide scaffold, N-acetyl-ʟ-Tyr-ʟ-Pro-ʟ-Trp, was determined by a combination of spectroscopic analyses, chemical derivatization, ECD calculation, and DFT-based theoretical chemical shift calculation, revealing the presence of an (Sa)-axial chirality around the biaryl bond. Compounds 2–4 lacked hydroxylation on the side chain of the spiroacetal rings, which showed clear contrast to other oligomycin congeners and related polyketides with ring-truncation or expansion. The new macrolides 2–4 displayed potent antimicrobial activity against the Gram-positive bacterium Kocuria rhizohpila and the plant pathogenic fungus Glomerella cingulata. All compounds showed moderate cytotoxicity against P388 murine leukemia cells with IC50 values in the micromolar to submicromolar ranges. These results exemplified the validity of phylogeny-focused strain selection combined with biosynthetic gene-directed genome mining for the efficient discovery of new natural products.
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Affiliation(s)
- Shun Saito
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Kota Atsumi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Tao Zhou
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Keisuke Fukaya
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Daisuke Urabe
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Md Rokon Ul Karim
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Kisarazu, Chiba 292-0818, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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Mazur M, Włoch A, Bahri F, Pruchnik H, Pawlak A, Obmińska-Mrukowicz B, Maciejewska G, Gładkowski W. Chemoenzymatic Synthesis of Enantiomeric, Bicyclic δ-Halo-γ-lactones with a Cyclohexane Ring, Their Biological Activity and Interaction with Biological Membranes. Biomolecules 2020; 10:biom10010095. [PMID: 31935977 PMCID: PMC7022392 DOI: 10.3390/biom10010095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/24/2019] [Accepted: 12/28/2019] [Indexed: 02/07/2023] Open
Abstract
Starting from 1-acetyl-1-cyclohexene, three enantiomeric pairs (ee ≥99%) of bicyclic δ-halo-γ-lactones with cyclohexane ring were obtained in five-step synthesis. The key stereochemical steps were lipase-catalyzed kinetic resolution of racemic 1-(cyclohex-1-en-1-yl) ethanol followed by transfer of chirality to ethyl 2-(2-ethylidenecyclohexyl) acetate in the Johnson-Claisen rearrangement. Synthesized halolactones exhibited antiproliferative activity towards canine B-cell leukemia cells (GL-1) and canine B-cell chronic leukemia cells (CLB70) and the most potent (IC50 18.43 ± 1.46 μg/mL against GL-1, IC50 11.40 ± 0.40 μg/mL against CLB70) comparable with the control etoposide, was (1R,6R,1'S)-1-(1'-chloroethyl)-9- oxabicyclo[4.3.0]nonan-8-one (8b). All halolactones did not have a toxic effect on erythrocytes and did not change the fluidity of membranes in the hydrophobic region of the lipid bilayer. Only weak changes in the hydrophilic area were observed, like the degree of lipid packing and associated hydration. The racemic halolactones were also tested for their antimicrobial properties and found to exhibit selectivity towards bacteria, in particular, towards Proteus mirabilis ATCC 35659.
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Affiliation(s)
- Marcelina Mazur
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland;
- Correspondence: ; Tel.: +48-713205197
| | - Aleksandra Włoch
- Department of Physics and Biophysics, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland; (A.W.); (H.P.)
| | - Fouad Bahri
- Laboratory of Microbiology and Plant Biology, Faculty of Natural and Life Sciences, University of Abd El Hamid Ibn Badiss of Mostaganem, Mostaganem 27000, Algeria;
| | - Hanna Pruchnik
- Department of Physics and Biophysics, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland; (A.W.); (H.P.)
| | - Aleksandra Pawlak
- Department of Pharmacology and Toxicology, Wrocław University of Environmental and Life Sciences, Norwida 31, 50-375 Wrocław, Poland; (A.P.); (B.O.-M.)
| | - Bożena Obmińska-Mrukowicz
- Department of Pharmacology and Toxicology, Wrocław University of Environmental and Life Sciences, Norwida 31, 50-375 Wrocław, Poland; (A.P.); (B.O.-M.)
| | - Gabriela Maciejewska
- Central Laboratory of the Instrumental Analysis, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland;
| | - Witold Gładkowski
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland;
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Yamamoto K, Futamura Y, Uson-Lopez RA, Aono H, Shimizu T, Osada H. YO-001A, a new antifungal agent produced by Streptomyces sp. YO15-A001. J Antibiot (Tokyo) 2019; 72:986-990. [PMID: 31601980 DOI: 10.1038/s41429-019-0239-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 01/08/2023]
Abstract
A new antifungal compound YO-001A was found from the culture broth of Streptomyces sp. YO15-A001, which was isolated from a soil sample collected in Toyama Prefecture. YO-001A was identified through morphological changes-based screening of the rice blast fungus, Pyricularia oryzae (P. oryzae). YO-001A is a new 26-membered macrolide of the oligomycin family, which exhibits potent antifungal activity against P. oryzae with an IC50 of 0.012 µM by disrupting mitochondrial respiration via inhibition of the FOF1-ATPase activity.
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Affiliation(s)
- Kai Yamamoto
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama-shi, Saitama, 338-8570, Japan
| | - Yushi Futamura
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Rachael A Uson-Lopez
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Harumi Aono
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takeshi Shimizu
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama-shi, Saitama, 338-8570, Japan.
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Kim MC, Machado H, Jang KH, Trzoss L, Jensen PR, Fenical W. Integration of Genomic Data with NMR Analysis Enables Assignment of the Full Stereostructure of Neaumycin B, a Potent Inhibitor of Glioblastoma from a Marine-Derived Micromonospora. J Am Chem Soc 2018; 140:10775-10784. [PMID: 30085661 DOI: 10.1021/jacs.8b04848] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microbial metabolites known as the macrolides are some of the most successful natural products used to treat infectious and immune diseases. Describing the structures of these complex metabolites, however, is often extremely difficult due to the presence of multiple stereogenic centers inherent in this class of polyketide-derived metabolites. With the availability of genome sequence data and a better understanding of the molecular genetics of natural product biosynthesis, it is now possible to use bioinformatic approaches in tandem with spectroscopic tools to assign the full stereostructures of these complex metabolites. In our quest to discover and develop new agents for the treatment of cancer, we observed the production of a highly cytotoxic macrolide, neaumycin B, by a marine-derived actinomycete bacterium of the genus Micromonospora. Neaumycin B is a complex polycyclic macrolide possessing 19 asymmetric centers, usually requiring selective degradation, crystallization, derivatization, X-ray diffraction analysis, synthesis, or other time-consuming approaches to assign the complete stereostructure. As an alternative approach, we sequenced the genome of the producing strain and identified the neaumycin gene cluster ( neu). By integrating the known stereospecificities of biosynthetic enzymes with comprehensive NMR analysis, the full stereostructure of neaumycin B was confidently assigned. This approach exemplifies how mining gene cluster information while integrating NMR-based structure data can achieve rapid, efficient, and accurate stereostructural assignments for complex macrolides.
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Affiliation(s)
- Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Henrique Machado
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Kyoung Hwa Jang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Lynnie Trzoss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States.,Center for Microbiome Innovation , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093-0204 , United States.,Moores Comprehensive Cancer Center , University of California, San Diego , La Jolla , California 92093-0204 , United States
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5
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Zhu S, Wu Y. Synthesis and Configuration of Neomaclafungin A. Chem Asian J 2017; 12:2211-2215. [DOI: 10.1002/asia.201700950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/06/2017] [Indexed: 01/25/2023]
Affiliation(s)
- Shijun Zhu
- State Key Laboratory of Bioorganic and Natural Products Chemistry; Collaborative Innovative Center for Chemistry and Life Sciences; Shanghai Institute of Organic Chemistry and the University of Chinese Academy of Sciences; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Yikang Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry; Collaborative Innovative Center for Chemistry and Life Sciences; Shanghai Institute of Organic Chemistry and the University of Chinese Academy of Sciences; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
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Simone M, Maffioli SI, Tocchetti A, Tretter S, Cattaneo M, Biunno I, Gaspari E, Donadio S. Additional congeners of the macrolide neaumycin: structure revision and biological activity. J Antibiot (Tokyo) 2015; 68:406-8. [DOI: 10.1038/ja.2014.168] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/28/2014] [Accepted: 12/04/2014] [Indexed: 11/09/2022]
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Gładkowski W, Skrobiszewski A, Mazur M, Siepka M, Pawlak A, Obmińska-Mrukowicz B, Białońska A, Poradowski D, Drynda A, Urbaniak M. Synthesis and anticancer activity of novel halolactones with β-aryl substituents from simple aromatic aldehydes. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.09.094] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sato S, Iwata F, Yamada S, Katayama M. Neomaclafungins A-I: oligomycin-class macrolides from a marine-derived actinomycete. JOURNAL OF NATURAL PRODUCTS 2012; 75:1974-1982. [PMID: 23102410 DOI: 10.1021/np300719g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Nine new 26-membered macrolides of the oligomycin subfamily, neomaclafungins A-I, were isolated from the fermentation broth of Actinoalloteichus sp. NPS702, which was isolated from marine sediment collected from Usa Bay, Kochi Prefecture, Japan. Their structures were identified through mass spectrometry and NMR experiments. They belong to the oligomycin class and have several distinct features including the presence of alkane or alkanol branches. Neomaclafungins A-I exhibited significant antifungal activity in vitro against Trichophyton mentagrophytes (ATCC 9533), showing MIC values between 1 and 3 μg/mL.
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Affiliation(s)
- Seizo Sato
- Central Research Laboratory, Tokyo Innovation Center , Nippon Suisan Kaisha, Ltd. 32-3 Nanakuni 1 chome, Hachioji, Tokyo 192-0991, Japan
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Gładkowski W, Grabarczyk M, Konopka M, Wawrzeñczyk C. Lactones 20 : Biohydroxylation of saturated bicyclic γ-lactones with the substituted cyclohexane system. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.molcatb.2003.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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