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Grundmann CO, Guzman J, Vilcinskas A, Pupo MT. The insect microbiome is a vast source of bioactive small molecules. Nat Prod Rep 2024; 41:935-967. [PMID: 38411238 DOI: 10.1039/d3np00054k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering: September 1964 to June 2023Bacteria and fungi living in symbiosis with insects have been studied over the last sixty years and found to be important sources of bioactive natural products. Not only classic producers of secondary metabolites such as Streptomyces and other members of the phylum Actinobacteria but also numerous bacteria from the phyla Proteobacteria and Firmicutes and an impressive array of fungi (usually pathogenic) serve as the source of a structurally diverse number of small molecules with important biological activities including antimicrobial, cytotoxic, antiparasitic and specific enzyme inhibitors. The insect niche is often the exclusive provider of microbes producing unique types of biologically active compounds such as gerumycins, pederin, dinactin, and formicamycins. However, numerous insects still have not been described taxonomically, and in most cases, the study of their microbiota is completely unexplored. In this review, we present a comprehensive survey of 553 natural products produced by microorganisms isolated from insects by collating and classifying all the data according to the type of compound (rather than the insect or microbial source). The analysis of the correlations among the metadata related to insects, microbial partners, and their produced compounds provides valuable insights into the intricate dynamics between insects and their symbionts as well as the impact of their metabolites on these relationships. Herein, we focus on the chemical structure, biosynthesis, and biological activities of the most relevant compounds.
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Affiliation(s)
| | - Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University, Giessen, Germany
| | - Mônica Tallarico Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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Tunvongvinis T, Jaitrong W, Samung Y, Tanasupawat S, Phongsopitanun W. Diversity and antimicrobial activity of the tropical ant-derived actinomycetes isolated from Thailand. AIMS Microbiol 2024; 10:68-82. [PMID: 38525037 PMCID: PMC10955170 DOI: 10.3934/microbiol.2024005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/30/2023] [Accepted: 01/15/2024] [Indexed: 03/26/2024] Open
Abstract
Antibiotic resistance is one of the most important global healthcare challenges and is responsible for the mortality of millions of people worldwide every year. It is a crisis attributed to misuse of antibiotics and a lack of new drug development. Actinomycetes constitute a group of Gram-positive bacteria known for their distinctive high guanine-cytosine (G+C) content in their genomic DNA. These microorganisms are widely recognized for their capability to generate a wide range of secondary metabolites with diverse biological activities. These versatile microorganisms are ubiquitous in diverse ecosystems, including soil, freshwater, marine sediments, and within the bodies of insects. A recent study has demonstrated that social insects, such as ants, host a diverse array of these bacteria. In this study, we involved the isolation and characterization of a total of 72 actinomycete strains obtained from 18 distinct ant species collected from various regions across Thailand. Utilizing 16S rRNA gene analysis, these isolated actinomycetes were classified into four distinct genera: Amycolatopsis (2 isolates), Micromonospora (1 isolate), Nocardia (8 isolates), and Streptomyces (61 isolates). Among the Streptomyces strains, 23 isolates exhibited antimicrobial activity against a panel of Gram-positive bacteria, including Bacillus subtilis ATCC 6633, Staphylococcus epidermidis ATCC 12228, Staphylococcus aureus ATCC 25923, Kocuria rhizophila ATCC 9341, and Methicillin-resistant Staphylococcus aureus (MRSA) DMST 20646. Additionally, two isolates displayed antifungal activity against Candida albicans TISTR 5554. Based on 16S rRNA gene sequence similarity studies, these two isolates, ODS25 and ODS28, were demonstrated to be closely related to Streptomyces lusitanus NBRC 13464T (98.07%) and Streptomyces haliclonae DSM 41970T (97.28%), respectively. The level of 16S rRNA gene sequence similarity below 98.65% cutoff indicates its potential as a novel actinomycete species. These findings underscore the potential of actinomycetes sourced from ants as a valuable reservoir of novel antimicrobials.
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Affiliation(s)
- Tuangrat Tunvongvinis
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences. Chulalongkorn University, Bangkok 10330, Thailand
| | - Weeyawat Jaitrong
- Office of Natural Science Research, National Science Museum, 39, Moo 3, Khlong 5, Khlong Luang, Pathum Thani 12120, Thailand
| | - Yudthana Samung
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences. Chulalongkorn University, Bangkok 10330, Thailand
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences. Chulalongkorn University, Bangkok 10330, Thailand
- Natural Products and Nanoparticles Research Units (NP2), Chulalongkorn University, Bangkok 10330, Thailand
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Stegmüller J, Rodríguez Estévez M, Shu W, Gläser L, Myronovskyi M, Rückert-Reed C, Kalinowski J, Luzhetskyy A, Wittmann C. Systems metabolic engineering of the primary and secondary metabolism of Streptomyces albidoflavus enhances production of the reverse antibiotic nybomycin against multi-resistant Staphylococcus aureus. Metab Eng 2024; 81:123-143. [PMID: 38072358 DOI: 10.1016/j.ymben.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/17/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Nybomycin is an antibiotic compound with proven activity against multi-resistant Staphylococcus aureus, making it an interesting candidate for combating these globally threatening pathogens. For exploring its potential, sufficient amounts of nybomycin and its derivatives must be synthetized to fully study its effectiveness, safety profile, and clinical applications. As native isolates only accumulate low amounts of the compound, superior producers are needed. The heterologous cell factory S. albidoflavus 4N24, previously derived from the cluster-free chassis S. albidoflavus Del14, produced 860 μg L-1 of nybomycin, mainly in the stationary phase. A first round of strain development modulated expression of genes involved in supply of nybomycin precursors under control of the common Perm* promoter in 4N24, but without any effect. Subsequent studies with mCherry reporter strains revealed that Perm* failed to drive expression during the product synthesis phase but that use of two synthetic promoters (PkasOP* and P41) enabled strong constitutive expression during the entire process. Using PkasOP*, several rounds of metabolic engineering successively streamlined expression of genes involved in the pentose phosphate pathway, the shikimic acid pathway, supply of CoA esters, and nybomycin biosynthesis and export, which more than doubled the nybomycin titer to 1.7 mg L-1 in the sixth-generation strain NYB-6B. In addition, we identified the minimal set of nyb genes needed to synthetize the molecule using single-gene-deletion strains. Subsequently, deletion of the regulator nybW enabled nybomycin production to begin during the growth phase, further boosting the titer and productivity. Based on RNA sequencing along the created strain genealogy, we discovered that the nyb gene cluster was unfavorably downregulated in all advanced producers. This inspired removal of a part and the entire set of the four regulatory genes at the 3'-end nyb of the cluster. The corresponding mutants NYB-8 and NYB-9 exhibited marked further improvement in production, and the deregulated cluster was combined with all beneficial targets from primary metabolism. The best strain, S. albidoflavus NYB-11, accumulated up to 12 mg L-1 nybomycin, fifteenfold more than the basic strain. The absence of native gene clusters in the host and use of a lean minimal medium contributed to a selective production process, providing an important next step toward further development of nybomycin.
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Affiliation(s)
- Julian Stegmüller
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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4
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Liu K, Zhang J, Zhang G, Zhang L, Meng Z, Ma L, Zhang W, Xiong W, Zhu Y, Wang B, Zhang C. Deciphering Deoxynybomycin Biosynthesis Reveals Fe(II)/α-Ketoglutarate-Dependent Dioxygenase-Catalyzed Oxazoline Ring Formation and Decomposition. J Am Chem Soc 2023; 145:27886-27899. [PMID: 38055632 DOI: 10.1021/jacs.3c11772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The antibacterial agents deoxynybomycin (DNM) and nybomycin (NM) have a unique tetracyclic structure featuring an angularly fused 4-oxazoline ring. Here, we report the identification of key enzymes responsible for forming the 4-oxazoline ring in Embleya hyalina NBRC 13850 by comparative bioinformatics analysis of the biosynthetic gene clusters encoding structurally similar natural products DNM, deoxynyboquinone (DNQ), and diazaquinomycins (DAQs). The N-methyltransferase DnmS plays a crucial role in catalyzing the N-dimethylation of a tricyclic precursor prenybomycin to generate NM D; subsequently, the Fe(II)/α-ketoglutarate-dependent dioxygenase (Fe/αKGD) DnmT catalyzes the formation of a 4-oxazoline ring from NM D to produce DNM; finally, a second Fe/αKGD DnmU catalyzes the C-12 hydroxylation of DNM to yield NM. Strikingly, DnmT is shown to display unexpected functions to also catalyze the decomposition of the 4-oxazoline ring and the N-demethylation, thereby converting DNM back to prenybomycin, to putatively serve as a manner to control the intracellular yield of DNM. Structure modeling, site-directed mutagenesis, and quantum mechanics calculations provide mechanistic insights into the DnmT-catalyzed reactions. This work expands our understanding of the functional diversity of Fe/αKGDs in natural product biosynthesis.
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Affiliation(s)
- Kai Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Jinyan Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Guangtao Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Meng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Liang Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Weiliang Xiong
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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5
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Paranjpe M, Marina V, Grachev A, Maviza T, Tolicheva O, Paleskava A, Osterman I, Sergiev P, Konevega A, Polikanov Y, Gagnon M. Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin. Nucleic Acids Res 2023; 51:449-462. [PMID: 36546783 PMCID: PMC9841432 DOI: 10.1093/nar/gkac1189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/11/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Thermorubin (THR) is an aromatic anthracenopyranone antibiotic active against both Gram-positive and Gram-negative bacteria. It is known to bind to the 70S ribosome at the intersubunit bridge B2a and was thought to inhibit factor-dependent initiation of translation and obstruct the accommodation of tRNAs into the A site. Here, we show that thermorubin causes ribosomes to stall in vivo and in vitro at internal and termination codons, thereby allowing the ribosome to initiate protein synthesis and translate at least a few codons before stalling. Our biochemical data show that THR affects multiple steps of translation elongation with a significant impact on the binding stability of the tRNA in the A site, explaining premature cessation of translation. Our high-resolution crystal and cryo-EM structures of the 70S-THR complex show that THR can co-exist with P- and A-site tRNAs, explaining how ribosomes can elongate in the presence of the drug. Remarkable is the ability of THR to arrest ribosomes at the stop codons. Our data suggest that by causing structural re-arrangements in the decoding center, THR interferes with the accommodation of tRNAs or release factors into the ribosomal A site.
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Affiliation(s)
- Madhura N Paranjpe
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Valeria I Marina
- Department of Chemistry and Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Aleksandr A Grachev
- Peter the Great St.Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Tinashe P Maviza
- Department of Chemistry and Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Olga A Tolicheva
- Peter the Great St.Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Alena Paleskava
- Peter the Great St.Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Ilya A Osterman
- Department of Chemistry and Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Petr V Sergiev
- Department of Chemistry and Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Andrey L Konevega
- Peter the Great St.Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Matthieu G Gagnon
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX77555, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
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6
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Conjugates of Chloramphenicol Amine and Berberine as Antimicrobial Agents. Antibiotics (Basel) 2022; 12:antibiotics12010015. [PMID: 36671216 PMCID: PMC9854996 DOI: 10.3390/antibiotics12010015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022] Open
Abstract
In order to obtain antimicrobial compounds with improved properties, new conjugates comprising two different biologically active agents within a single chimeric molecule based on chloramphenicol (CHL) and a hydrophobic cation were synthesized and studied. Chloramphenicol amine (CAM), derived from the ribosome-targeting antibiotic CHL, and the plant isoquinoline alkaloid berberine (BER) are connected by alkyl linkers of different lengths in structures of these conjugates. Using competition binding, double reporter system, and toeprinting assays, we showed that synthesized CAM-Cn-BER compounds bound to the bacterial ribosome and inhibited protein synthesis like the parent CHL. The mechanism of action of CAM-C5-BER and CAM-C8-BER on the process of bacterial translations was similar to CHL. Experiments with bacteria demonstrated that CAM-Cn-BERs suppressed the growth of laboratory strains of CHL and macrolides-resistant bacteria. CAM-C8-BER acted against mycobacteria and more selectively inhibited the growth of Gram-positive bacteria than the parent CHL and the berberine derivative lacking the CAM moiety (CH3-C8-BER). Using a potential-sensitive fluorescent probe, we found that CAM-C8-BER significantly reduced the membrane potential in B. subtilis cells. Crystal violet assays were used to demonstrate the absence of induction of biofilm formation under the action of CAM-C8-BER on E. coli bacteria. Thus, we showed that CAM-C8-BER could act both on the ribosome and on the cell membrane of bacteria, with the alkylated berberine fragment of the compound making a significant contribution to the inhibitory effect on bacterial growth. Moreover, we showed that CAM-Cn-BERs did not inhibit eukaryotic translation in vitro and were non-toxic for eukaryotic cells.
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Baranova AA, Zakalyukina YV, Ovcharenko AA, Korshun VA, Tyurin AP. Antibiotics from Insect-Associated Actinobacteria. BIOLOGY 2022; 11:1676. [PMID: 36421390 PMCID: PMC9687666 DOI: 10.3390/biology11111676] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 11/10/2023]
Abstract
Actinobacteria are involved into multilateral relationships between insects, their food sources, infectious agents, etc. Antibiotics and related natural products play an essential role in such systems. The literature from the January 2016-August 2022 period devoted to insect-associated actinomycetes with antagonistic and/or enzyme-inhibiting activity was selected. Recent progress in multidisciplinary studies of insect-actinobacterial interactions mediated by antibiotics is summarized and discussed.
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Affiliation(s)
- Anna A. Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, Bol’shaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Yuliya V. Zakalyukina
- Department of Soil Science, Lomonosov Moscow State University, Leninskie Gory 1-12, 119991 Moscow, Russia
| | - Anna A. Ovcharenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Higher Chemical College RAS, Mendeleev University of Chemical Technology of Russia, Miusskaya sq. 9, 125047 Moscow, Russia
| | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anton P. Tyurin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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Zakalyukina YV, Pavlov NA, Lukianov DA, Marina VI, Belozerova OA, Tashlitsky VN, Guglya EB, Osterman IA, Biryukov MV. A New Albomycin-Producing Strain of Streptomyces globisporus subsp. globisporus May Provide Protection for Ants Messor structor. INSECTS 2022; 13:1042. [PMID: 36421945 PMCID: PMC9693239 DOI: 10.3390/insects13111042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
There are several well-studied examples of protective symbiosis between insect host and symbiotic actinobacteria, producing antimicrobial metabolites to inhibit host pathogens. These mutualistic relationships are best described for some wasps and leaf-cutting ants, while a huge variety of insect species still remain poorly explored. For the first time, we isolated actinobacteria from the harvester ant Messor structor and evaluated the isolates' potential as antimicrobial producers. All isolates could be divided into two morphotypes of single and mycelial cells. We found that the most common mycelial morphotype was observed among soldiers and least common among larvae in the studied laboratory colony. The representative of this morphotype was identified as Streptomyces globisporus subsp. globisporus 4-3 by a polyphasic approach. It was established using a E. coli JW5503 pDualRep2 system that crude broths of mycelial isolates inhibited protein synthesis in reporter strains, but it did not disrupt the in vitro synthesis of proteins in cell-free extracts. An active compound was extracted, purified and identified as albomycin δ2. The pronounced ability of albomycin to inhibit the growth of entomopathogens suggests that Streptomyces globisporus subsp. globisporus may be involved in defensive symbiosis with the Messor structor ant against infections.
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Affiliation(s)
- Yuliya V. Zakalyukina
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Department of Soil Science, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Nikolay A. Pavlov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Valeria I. Marina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Olga A. Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, 117997 Moscow, Russia
| | - Vadim N. Tashlitsky
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Elena B. Guglya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova st. 1, 117997 Moscow, Russia
| | - Ilya A. Osterman
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Mikhail V. Biryukov
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
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9
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Sarmiento-Vizcaíno A, Martín J, Ortiz-López FJ, Reyes F, García LA, Blanco G. Natural products, including a new caboxamycin, from Streptomyces and other Actinobacteria isolated in Spain from storm clouds transported by Northern winds of Arctic origin. Front Chem 2022; 10:948795. [DOI: 10.3389/fchem.2022.948795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Actinobacteria, mostly Streptomyces species, are the main source of natural products essential in medicine. While the majority of producer microorganisms of secondary metabolite are reported from terrestrial or marine environments, there are limited reports of their isolation from atmospheric precipitations. Clouds are considered as atmospheric oases for microorganisms and there is a recent paradigm shift whereby atmospheric-derived Actinobacteria emerge as an alternative source for drug discovery. In this context, we studied a total of 18 bioactive Actinobacteria strains, isolated by sampling nine precipitation events with prevailing Northern winds in the Cantabrian Sea coast, Northern Spain. Backward trajectories meteorological analyses indicate that air masses were originated mostly in the Arctic Ocean, and their trajectory to downwind areas involved the Atlantic Ocean and also terrestrial sources from continental Europe, and in some events from Canada, Greenland, Mauritania and Canary Islands. Taxonomic identification of the isolates, by 16S rRNA gene sequencing and phylogenetic analyses, revealed that they are members of three Actinobacteria genera. Fifteen of the isolates are Streptomyces species, thus increasing the number of bioactive species of this genus in the atmosphere to a 6.8% of the total currently validated species. In addition, two of the strains belong to the genus Micromonospora and one to genus Nocardiopsis. These findings reinforce a previous atmospheric dispersal model, extended herein to the genus Micromonospora. Production of bioactive secondary metabolites was screened in ethyl acetate extracts of the strains by LC-UV-MS and a total of 94 secondary metabolites were detected after LC/MS dereplication. Comparative analyses with natural products databases allowed the identification of 69 structurally diverse natural products with contrasted biological activities, mostly as antibiotics and antitumor agents, but also anti-inflammatory, antiviral, antiparasitic, immunosuppressant and neuroprotective among others. The molecular formulae of the 25 remaining compounds were determined by HRMS. None of these molecules had been previously reported in natural product databases indicating potentially novel metabolites. As a proof of concept, a new metabolite caboxamycin B (1) was isolated from the culture broth of Streptomyces sp. A-177 and its structure was determined by various spectrometric methods. To the best of our knowledge, this is the first novel natural product obtained from an atmospheric Streptomyces, thus pointing out precipitations as an innovative source for discovering new pharmaceutical natural products.
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10
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Volynkina IA, Zakalyukina YV, Alferova VA, Belik AR, Yagoda DK, Nikandrova AA, Buyuklyan YA, Udalov AV, Golovin EV, Kryakvin MA, Lukianov DA, Biryukov MV, Sergiev PV, Dontsova OA, Osterman IA. Mechanism-Based Approach to New Antibiotic Producers Screening among Actinomycetes in the Course of the Citizen Science Project. Antibiotics (Basel) 2022; 11:antibiotics11091198. [PMID: 36139977 PMCID: PMC9495171 DOI: 10.3390/antibiotics11091198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/22/2022] Open
Abstract
Since the discovery of streptomycin, actinomycetes have been a useful source for new antibiotics, but there have been diminishing rates of new finds since the 1960s. The decreasing probability of identifying new active agents led to reduced interest in soil bacteria as a source for new antibiotics. At the same time, actinomycetes remain a promising reservoir for new active molecules. In this work, we present several reporter plasmids encoding visible fluorescent protein genes. These plasmids provide primary information about the action mechanism of antimicrobial agents at an early stage of screening. The reporters and the pipeline described have been optimized and designed to employ citizen scientists without specialized skills or equipment with the aim of essentially crowdsourcing the search for new antibiotic producers in the vast natural reservoir of soil bacteria. The combination of mechanism-based approaches and citizen science has proved its effectiveness in practice, revealing a significant increase in the screening rate. As a proof of concept, two new strains, Streptomyces sp. KB-1 and BV113, were found to produce the antibiotics pikromycin and chartreusin, respectively, demonstrating the efficiency of the pipeline.
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Affiliation(s)
- Inna A. Volynkina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
- Correspondence: (I.A.V.); (I.A.O.)
| | - Yuliya V. Zakalyukina
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Department of Soil Science, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia
| | - Albina R. Belik
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
| | - Daria K. Yagoda
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Arina A. Nikandrova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia
| | - Yuliya A. Buyuklyan
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
| | - Andrei V. Udalov
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
| | - Evgenii V. Golovin
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
| | - Maxim A. Kryakvin
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Mikhail V. Biryukov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Olga A. Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Correspondence: (I.A.V.); (I.A.O.)
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11
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Khairullina ZZ, Makarov GI, Tereshchenkov AG, Buev VS, Lukianov DA, Polshakov VI, Tashlitsky VN, Osterman IA, Sumbatyan NV. Conjugates of Desmycosin with Fragments of Antimicrobial Peptide Oncocin: Synthesis, Antibacterial Activity, Interaction with Ribosome. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:871-889. [PMID: 36180983 DOI: 10.1134/s0006297922090024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 06/16/2023]
Abstract
Design and synthesis of conjugates consisting of the macrolide antibiotic desmycosin and fragments of the antibacterial peptide oncocin were performed in attempt to develop new antimicrobial compounds. New compounds were shown to bind to the E. coli 70S ribosomes, to inhibit bacterial protein synthesis in vitro, as well as to suppress bacterial growth. The conjugates of N-terminal hexa- and tripeptide fragments of oncocin and 3,2',4''-triacetyldesmycosin were found to be active against some strains of macrolide-resistant bacteria. By simulating molecular dynamics of the complexes of these compounds with the wild-type bacterial ribosomes and with ribosomes, containing A2059G 23S RNA mutation, the specific structural features of their interactions were revealed.
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Affiliation(s)
| | | | - Andrey G Tereshchenkov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Vitaly S Buev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Dmitrii A Lukianov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vadim N Tashlitsky
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ilya A Osterman
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Natalia V Sumbatyan
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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12
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Wu Y, Liu Y, Yu J, Xu Y, Chen S. Observation of the Antimicrobial Activities of Two Actinomycetes in the Harvester Ant Messor orientalis. INSECTS 2022; 13:insects13080691. [PMID: 36005316 PMCID: PMC9408877 DOI: 10.3390/insects13080691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/24/2022] [Accepted: 07/28/2022] [Indexed: 11/28/2022]
Abstract
Simple Summary Observations in the animal room have shown that the seeds stored by harvester ants, although in a damp environment, are less likely to mold. It was hypothesized that harvester ants may use actinomycetes to protect their seed stores, given that leafcutter ants use actinomycetes as producers of defensive substances. Two actinomycetes were isolated from the harvester ant Messor orientalis. The fermentation broth of the actinomycetes showed significant inhibitory effects on the three indicator fungi. Coculture experiments supported the observed inhibitory effects. The antifungal activities of actinomycetes in harvester ants were revealed. This research provides a significant theoretical reference for the abovementioned hypothesis and for the potential agricultural applications of these actinomycetes for multiple crops. Abstract Observations have shown that seeds collected by harvester ants are less likely to mold. Based on evolutionary analysis and other research, it was hypothesized that harvester ants could apply actinomycetes to protect seeds, similar to the protection of mutualistic fungi by leafcutter ants. Two actinomycetes were successfully isolated from the harvester ant Messor orientalis. The taxonomic status of the actinomycetes was determined by 16S rRNA sequence analysis and biochemical experimental observations. Their inhibitory effects on plant pathogens were measured. One of the bacteria was identified as Brachybacterium phenoliresistens and denoted as B. phenoliresistens MO. The other belonged to the genus Microbacterium. It was named Microbacterium sp. Growth rate determination and coculture experiments were performed to explore the inhibitory effect of actinomycetes on indicator plant pathogens. The inhibition rates of the actinomycetes toward Peronophythora litchii and Rhizoctonia solani were 100% in media containing 30% or more fermentation broth, and they also showed an inhibitory effect on Colletotrichum siamense. The coculture experiment supported this result by showing that the growth of P. litchii and R. solani was inhibited in the presence of actinomycetes. Therefore, the results of this study show the agricultural application potential of these bacteria and may provide a reference for research on the symbiosis of harvester ants with actinomycetes.
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Affiliation(s)
- Yiyang Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, Red Imported Fire Ant Research Center, South China Agricultural University, Guangzhou 510642, China;
- Sendelta International Academy, Shenzhen 518000, China
| | - Yaxuan Liu
- Department of Material Science and Engineering, College of Engineering, Carnegie Mellon University, Pittsburgh, PA 15213-2683, USA;
| | - Jinyong Yu
- College of Agronomy and Biotechnology, Hebei Normal University of Science & Technology, Qinhuangdao 066600, China;
| | - Yijuan Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, Red Imported Fire Ant Research Center, South China Agricultural University, Guangzhou 510642, China;
- Correspondence: (Y.X.); (S.C.)
| | - Siqi Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Red Imported Fire Ant Research Center, South China Agricultural University, Guangzhou 510642, China;
- Correspondence: (Y.X.); (S.C.)
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13
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Zakalyukina YV, Osterman IA, Wolf J, Neumann-Schaal M, Nouioui I, Biryukov MV. Amycolatopsis camponoti sp. nov., new tetracenomycin-producing actinomycete isolated from carpenter ant Camponotus vagus. Antonie Van Leeuwenhoek 2022; 115:533-544. [PMID: 35218449 PMCID: PMC8930869 DOI: 10.1007/s10482-022-01716-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/30/2022] [Indexed: 01/15/2023]
Abstract
An actinobacterial strain A23T, isolated from adult ant Camponotus vagus collected in Ryazan region (Russia) and established as tetracenomycin X producer, was subjected to a polyphasic taxonomic study. Morphological characteristics of this strain included well-branched substrate mycelium and aerial hyphae fragmented into rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain A23T was most closely related to Amycolatopsis pretoriensis DSM 44654T. Average nucleotide identity and digital DNA-DNA hybridization values between the genome sequences of isolate A23T and its closest relative, Amycolatopsis pretoriensis DSM 44654T, were 39.5% and 88.6%, which were below the 70% and 95-96% cut-off point recommended for bacterial species demarcation, respectively. The genome size of the isolate A23T was 10,560,374 bp with a DNA G + C content of 71.2%. The whole-cell hydrolysate contained meso-diaminopimelic acid and arabinose and galactose as main diagnostic sugars as well as ribose and rhamnose. It contained MK-9(H4) as the predominant menaquinone and iso-C16:0, iso-C15:0, anteiso-C17:0 and C16:0 as the major cellular fatty acids. Diphosphatidylglycerol and phosphatidylethanolamine prevailed among phospholipids. Mycolic acids were not detected. Based on the phenotypic, genomic and phylogenetic data, isolate A23T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis camponoti sp. nov. is proposed, and the type strain is A23T (= DSM 111725T = VKM 2882T).
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Affiliation(s)
- Yuliya V Zakalyukina
- Scientific Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia, 354340.
- Department of Soil Science, Lomonosov Moscow State University, Moscow, Russia, 119991.
| | - Ilya A Osterman
- Scientific Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia, 354340
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia, 143025
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Imen Nouioui
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Mikhail V Biryukov
- Scientific Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia, 354340
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
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14
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Alferova VA, Maviza TP, Biryukov MV, Zakalyukina YV, Lukianov DA, Skvortsov DA, Vasilyeva LA, Tashlitsky VN, Polshakov VI, Sergiev PV, Korshun VA, Osterman IA. Biological evaluation and spectral characterization of a novel tetracenomycin X congener. Biochimie 2021; 192:63-71. [PMID: 34592388 DOI: 10.1016/j.biochi.2021.09.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 01/15/2023]
Abstract
The aromatic polyketide tetracenomycin X (TcmX) was recently found to be a potent inhibitor of protein synthesis; its binding site is located in a unique locus within the tunnel of the large ribosomal subunit. The distinct mode of action makes this relatively narrow class of aromatic polyketides promising for drug development in the quest to prevent the spread of drug-resistant pathogens. Here we report the isolation and structure elucidation of a novel natural tetracenomycin X congener - 6-hydroxytetraceonomycin X (6-OH-TcmX). In contrast to TcmX, 6-OH-TcmX exhibited lower antimicrobial and cytotoxic activity, but comparable in vitro protein synthesis inhibition ability. A survey on spectral properties of tetracenomycins revealed profound differences in both UV-absorption and fluorescence spectra between TcmX and 6-OH-TcmX, suggesting a significant influence of 6-hydroxylation on the tetracenomycin X chromophore. Nonetheless, characteristic spectral properties of tetracenomycins make them suitable candidates for semi-synthetic drug development (e.g., for targeted delivery, chemical biology, or cell imaging).
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Affiliation(s)
- Vera A Alferova
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, Moscow, 119021, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Tinashe P Maviza
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia
| | - Mikhail V Biryukov
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, Moscow, 119021, Russia; Department of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia; Genetics and Life Sciences Research Center, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Yuliya V Zakalyukina
- Genetics and Life Sciences Research Center, Sirius University of Science and Technology, Sochi, 354340, Russia; Department of Soil Science, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Dmitrii A Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia
| | - Dmitry A Skvortsov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Lilia A Vasilyeva
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Vadim N Tashlitsky
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Vladimir I Polshakov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Petr V Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Vladimir A Korshun
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, Moscow, 119021, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Ilya A Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia; Genetics and Life Sciences Research Center, Sirius University of Science and Technology, Sochi, 354340, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia.
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15
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Pavlova JA, Khairullina ZZ, Tereshchenkov AG, Nazarov PA, Lukianov DA, Volynkina IA, Skvortsov DA, Makarov GI, Abad E, Murayama SY, Kajiwara S, Paleskava A, Konevega AL, Antonenko YN, Lyakhovich A, Osterman IA, Bogdanov AA, Sumbatyan NV. Triphenilphosphonium Analogs of Chloramphenicol as Dual-Acting Antimicrobial and Antiproliferating Agents. Antibiotics (Basel) 2021; 10:antibiotics10050489. [PMID: 33922611 PMCID: PMC8145938 DOI: 10.3390/antibiotics10050489] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
In the current work, in continuation of our recent research, we synthesized and studied new chimeric compounds, including the ribosome-targeting antibiotic chloramphenicol (CHL) and the membrane-penetrating cation triphenylphosphonium (TPP), which are linked by alkyl groups of different lengths. Using various biochemical assays, we showed that these CAM-Cn-TPP compounds bind to the bacterial ribosome, inhibit protein synthesis in vitro and in vivo in a way similar to that of the parent CHL, and significantly reduce membrane potential. Similar to CAM-C4-TPP, the mode of action of CAM-C10-TPP and CAM-C14-TPP in bacterial ribosomes differs from that of CHL. By simulating the dynamics of CAM-Cn-TPP complexes with bacterial ribosomes, we proposed a possible explanation for the specificity of the action of these analogs in the translation process. CAM-C10-TPP and CAM-C14-TPP more strongly inhibit the growth of the Gram-positive bacteria, as compared to CHL, and suppress some CHL-resistant bacterial strains. Thus, we have shown that TPP derivatives of CHL are dual-acting compounds targeting both the ribosomes and cellular membranes of bacteria. The TPP fragment of CAM-Cn-TPP compounds has an inhibitory effect on bacteria. Moreover, since the mitochondria of eukaryotic cells possess qualities similar to those of their prokaryotic ancestors, we demonstrate the possibility of targeting chemoresistant cancer cells with these compounds.
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Affiliation(s)
- Julia A. Pavlova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (D.A.S.); (A.A.B.)
| | - Zimfira Z. Khairullina
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (D.A.S.); (A.A.B.)
| | - Andrey G. Tereshchenkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119992 Moscow, Russia; (A.G.T.); (P.A.N.); (Y.N.A.)
| | - Pavel A. Nazarov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119992 Moscow, Russia; (A.G.T.); (P.A.N.); (Y.N.A.)
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143028 Skolkovo, Russia;
| | - Inna A. Volynkina
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - Dmitry A. Skvortsov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (D.A.S.); (A.A.B.)
| | - Gennady I. Makarov
- Laboratory of the Multiscale Modeling of Multicomponent Materials, South Ural State University, 454080 Chelyabinsk, Russia;
| | - Etna Abad
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
| | - Somay Y. Murayama
- Department of Chemotherapy and Mycoses, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8340, Japan;
| | - Susumu Kajiwara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan;
| | - Alena Paleskava
- Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
| | - Andrey L. Konevega
- Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
- NRC “Kurchatov Institute”, 123182 Moscow, Russia
| | - Yuri N. Antonenko
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119992 Moscow, Russia; (A.G.T.); (P.A.N.); (Y.N.A.)
| | - Alex Lyakhovich
- Institute of Molecular Biology and Biophysics, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia;
- Vall D’Hebron Institut de Recerca, 08035 Barcelona, Spain
| | - Ilya A. Osterman
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (D.A.S.); (A.A.B.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143028 Skolkovo, Russia;
- Genetics and Life Sciences Research Center, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
- Correspondence: (I.A.O.); (N.V.S.)
| | - Alexey A. Bogdanov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (D.A.S.); (A.A.B.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119992 Moscow, Russia; (A.G.T.); (P.A.N.); (Y.N.A.)
| | - Natalia V. Sumbatyan
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (D.A.S.); (A.A.B.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119992 Moscow, Russia; (A.G.T.); (P.A.N.); (Y.N.A.)
- Correspondence: (I.A.O.); (N.V.S.)
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16
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Nybomycin inhibits both types of E. coli DNA gyrase - fluoroquinolone-sensitive and fluoroquinolone-resistant. Antimicrob Agents Chemother 2021; 95:AAC.00777-20. [PMID: 33593838 PMCID: PMC8092900 DOI: 10.1128/aac.00777-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial type II topoisomerases, DNA gyrase and topoisomerase IV, are targets of many antibiotics including fluoroquinolones (FQs). Unfortunately, a number of bacterial species easily acquire resistance to FQs by mutations in either DNA gyrase or topoisomerase IV genes. The emergence of resistant pathogenic strains is a global problem in healthcare, therefore, identifying alternative pathways to thwart their persistence is the current frontier in drug discovery. An attractive class of compounds is nybomycins, reported to be "reverse antibiotics" that selectively inhibit growth of some Gram-positive FQ-resistant bacteria by targeting the mutant form of DNA gyrase, while being inactive against wild-type strains with FQ-sensitive gyrases. The strong "reverse" effect was demonstrated only for a few Gram-positive organisms resistant to FQs due to the S83L/I mutation in GyrA subunit of DNA gyrase. However, the activity of nybomycins has not been extensively explored among Gram-negative species. Here, we observed that in Gram-negative E. coli ΔtolC strain with enhanced permeability, wild-type gyrase and GyrA S83L mutant, resistant to fluoroquinolones, are both similarly sensitive to nybomycin.
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17
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Chen CW, Pavlova JA, Lukianov DA, Tereshchenkov AG, Makarov GI, Khairullina ZZ, Tashlitsky VN, Paleskava A, Konevega AL, Bogdanov AA, Osterman IA, Sumbatyan NV, Polikanov YS. Binding and Action of Triphenylphosphonium Analog of Chloramphenicol upon the Bacterial Ribosome. Antibiotics (Basel) 2021; 10:390. [PMID: 33916420 PMCID: PMC8066774 DOI: 10.3390/antibiotics10040390] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
Chloramphenicol (CHL) is a ribosome-targeting antibiotic that binds to the peptidyl transferase center (PTC) of the bacterial ribosome and inhibits peptide bond formation. As an approach for modifying and potentially improving the properties of this inhibitor, we explored ribosome binding and inhibitory properties of a semi-synthetic triphenylphosphonium analog of CHL-CAM-C4-TPP. Our data demonstrate that this compound exhibits a ~5-fold stronger affinity for the bacterial ribosome and higher potency as an in vitro protein synthesis inhibitor compared to CHL. The X-ray crystal structure of the Thermus thermophilus 70S ribosome in complex with CAM-C4-TPP reveals that, while its amphenicol moiety binds at the PTC in a fashion identical to CHL, the C4-TPP tail adopts an extended propeller-like conformation within the ribosome exit tunnel where it establishes multiple hydrophobic Van der Waals interactions with the rRNA. The synthesized compound represents a promising chemical scaffold for further development by medicinal chemists because it simultaneously targets the two key functional centers of the bacterial ribosome-PTC and peptide exit tunnel.
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Affiliation(s)
- Chih-Wei Chen
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA;
| | - Julia A. Pavlova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143028 Skolkovo, Russia;
| | - Andrey G. Tereshchenkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Gennady I. Makarov
- Laboratory of Multiscale Modeling of Multicomponent Materials, South Ural State University, 454080 Chelyabinsk, Russia;
| | - Zimfira Z. Khairullina
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
| | - Vadim N. Tashlitsky
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
| | - Alena Paleskava
- Petersburg Nuclear Physics Institute, National Research Center (NRC) “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Peter the Great St.Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
| | - Andrey L. Konevega
- Petersburg Nuclear Physics Institute, National Research Center (NRC) “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Peter the Great St.Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
- National Research Center (NRC) “Kurchatov Institute”, 123182 Moscow, Russia
| | - Alexey A. Bogdanov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Ilya A. Osterman
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143028 Skolkovo, Russia;
| | - Natalia V. Sumbatyan
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Yury S. Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA;
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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18
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Baranova AA, Chistov AA, Tyurin AP, Prokhorenko IA, Korshun VA, Biryukov MV, Alferova VA, Zakalyukina YV. Chemical Ecology of Streptomyces albidoflavus Strain A10 Associated with Carpenter Ant Camponotus vagus. Microorganisms 2020; 8:microorganisms8121948. [PMID: 33316994 PMCID: PMC7763447 DOI: 10.3390/microorganisms8121948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/22/2022] Open
Abstract
Antibiotics produced by symbiotic microorganisms were previously shown to be of crucial importance for ecological communities, including ants. Previous works on ant–actinobacteria symbiosis are mainly focused on farming ants, which use antifungal microbial secondary metabolites to control pathogens in their fungal gardens. In this work, we studied microorganisms associated with carpenter ant Camponotus vagus. Pronounced antifungal activity of isolated actinobacteria strain A10 was found to be facilitated by biosynthesis of the antimycin A complex, consisting of small hydrophobic depsipeptides with high antimicrobial and cytotoxic activity. The actinomycete strain A10 was identified as Streptomyces albidoflavus. We studied the antagonistic activity of strain A10 against several entomopathogenic microorganisms. The antifungal activity of this strain potentially indicates a defensive symbiosis with the host ant, producing antimycins to protect carpenter ants against infections. The nature of this ant-microbe association however remains to be established.
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Affiliation(s)
- Anna A. Baranova
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (A.A.B.); (A.P.T.); (I.A.P.); (V.A.K.); (M.V.B.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Alexey A. Chistov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
- Orekhovich Research Institute of Biomedical Chemistry, Pogodinskaya 10, 119121 Moscow, Russia
| | - Anton P. Tyurin
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (A.A.B.); (A.P.T.); (I.A.P.); (V.A.K.); (M.V.B.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Igor A. Prokhorenko
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (A.A.B.); (A.P.T.); (I.A.P.); (V.A.K.); (M.V.B.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Vladimir A. Korshun
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (A.A.B.); (A.P.T.); (I.A.P.); (V.A.K.); (M.V.B.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Mikhail V. Biryukov
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (A.A.B.); (A.P.T.); (I.A.P.); (V.A.K.); (M.V.B.)
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vera A. Alferova
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (A.A.B.); (A.P.T.); (I.A.P.); (V.A.K.); (M.V.B.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
- Correspondence: (V.A.A.); (Y.V.Z.); Tel.: +7-9266113649 (V.A.A.); +7-9175548004 (Y.V.Z.)
| | - Yuliya V. Zakalyukina
- Department of Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (V.A.A.); (Y.V.Z.); Tel.: +7-9266113649 (V.A.A.); +7-9175548004 (Y.V.Z.)
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19
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Osterman IA, Wieland M, Maviza TP, Lashkevich KA, Lukianov DA, Komarova ES, Zakalyukina YV, Buschauer R, Shiriaev DI, Leyn SA, Zlamal JE, Biryukov MV, Skvortsov DA, Tashlitsky VN, Polshakov VI, Cheng J, Polikanov YS, Bogdanov AA, Osterman AL, Dmitriev SE, Beckmann R, Dontsova OA, Wilson DN, Sergiev PV. Tetracenomycin X inhibits translation by binding within the ribosomal exit tunnel. Nat Chem Biol 2020; 16:1071-1077. [PMID: 32601485 DOI: 10.1038/s41589-020-0578-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/28/2020] [Indexed: 11/09/2022]
Abstract
The increase in multi-drug resistant pathogenic bacteria is making our current arsenal of clinically used antibiotics obsolete, highlighting the urgent need for new lead compounds with distinct target binding sites to avoid cross-resistance. Here we report that the aromatic polyketide antibiotic tetracenomycin (TcmX) is a potent inhibitor of protein synthesis, and does not induce DNA damage as previously thought. Despite the structural similarity to the well-known translation inhibitor tetracycline, we show that TcmX does not interact with the small ribosomal subunit, but rather binds to the large subunit, within the polypeptide exit tunnel. This previously unappreciated binding site is located adjacent to the macrolide-binding site, where TcmX stacks on the noncanonical basepair formed by U1782 and U2586 of the 23S ribosomal RNA. Although the binding site is distinct from the macrolide antibiotics, our results indicate that like macrolides, TcmX allows translation of short oligopeptides before further translation is blocked.
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Affiliation(s)
- Ilya A Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia. .,Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Maximiliane Wieland
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Tinashe P Maviza
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Kseniya A Lashkevich
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitrii A Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Ekaterina S Komarova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yuliya V Zakalyukina
- Department of Soil Science and Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Robert Buschauer
- Gene Center, Department of Biochemistry, University of Munich, Munich, Germany
| | - Dmitrii I Shiriaev
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Jaime E Zlamal
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Mikhail V Biryukov
- Department of Soil Science and Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A Skvortsov
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vadim N Tashlitsky
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir I Polshakov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Jingdong Cheng
- Gene Center, Department of Biochemistry, University of Munich, Munich, Germany
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Alexey A Bogdanov
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sergey E Dmitriev
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Roland Beckmann
- Gene Center, Department of Biochemistry, University of Munich, Munich, Germany
| | - Olga A Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
| | - Petr V Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia. .,Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
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20
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Wang X, Elshahawi SI, Ponomareva LV, Ye Q, Liu Y, Copley GC, Hower JC, Hatcher BE, Kharel MK, Van Lanen SG, She QB, Voss SR, Thorson JS, Shaaban KA. Structure Determination, Functional Characterization, and Biosynthetic Implications of Nybomycin Metabolites from a Mining Reclamation Site-Associated Streptomyces. JOURNAL OF NATURAL PRODUCTS 2019; 82:3469-3476. [PMID: 31833370 PMCID: PMC7084111 DOI: 10.1021/acs.jnatprod.9b01015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We report the isolation and characterization of three new nybomycins (nybomycins B-D, 1-3) and six known compounds (nybomycin, 4; deoxynyboquinone, 5; α-rubromycin, 6; β-rubromycin, 7; γ-rubromycin, 8; and [2α(1E,3E),4β]-2-(1,3-pentadienyl)-4-piperidinol, 9) from the Rock Creek (McCreary County, KY) underground coal mine acid reclamation site isolate Streptomyces sp. AD-3-6. Nybomycin D (3) and deoxynyboquinone (5) displayed moderate (3) to potent (5) cancer cell line cytotoxicity and displayed weak to moderate anti-Gram-(+) bacterial activity, whereas rubromycins 6-8 displayed little to no cancer cell line cytotoxicity but moderate to potent anti-Gram-(+) bacterial and antifungal activity. Assessment of the impact of 3 or 5 cancer cell line treatment on 4E-BP1 phosphorylation, a predictive marker of ROS-mediated control of cap-dependent translation, also revealed deoxynyboquinone (5)-mediated downstream inhibition of 4E-BP1p. Evaluation of 1-9 in a recently established axolotl embryo tail regeneration assay also highlighted the prototypical telomerase inhibitor γ-rubromycin (8) as a new inhibitor of tail regeneration. Cumulatively, this work highlights an alternative nybomycin production strain, a small set of new nybomycin metabolites, and previously unknown functions of rubromycins (antifungal activity and inhibition of tail regeneration) and also provides a basis for revision of the previously proposed nybomycin biosynthetic pathway.
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Affiliation(s)
- Xiachang Wang
- Jiangsu Key Laboratory for Functional Substances of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
- Center for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Sherif I. Elshahawi
- Center for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
| | - Larissa V. Ponomareva
- Center for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Qing Ye
- Markey Cancer Center, Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yang Liu
- Center for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Gregory C. Copley
- Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40511, United States
| | - James C. Hower
- Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40511, United States
| | - Bruce E. Hatcher
- Division of Water, Kentucky Energy and Environment Cabinet, 2642 Russellville Road, Bowling Green, Kentucky 42101, United States
| | - Madan K. Kharel
- School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Steven G. Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Qing-Bai She
- Markey Cancer Center, Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - S. Randal Voss
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky 40536, United States
- Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky 40536, United States
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Jon S. Thorson
- Center for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Khaled A. Shaaban
- Center for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
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