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Dubovik V, Dalinova A, Berestetskiy A. Natural ten-membered lactones: sources, structural diversity, biological activity, and intriguing future. Nat Prod Rep 2024; 41:85-112. [PMID: 37885339 DOI: 10.1039/d3np00013c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Covering: 2012 to 2022Ten-membered lactones (TMLs) are an interesting and diverse group of natural polyketides that are abundant in fungi and, to a lesser extent, in bacteria, marine organisms, and insects. TMLs are known for their ability to exhibit a wide spectrum of biological activity, including phytotoxic, cytotoxic, antifungal, antibacterial, and others. However, the random discovery of these compounds by scientific groups with various interests worldwide has resulted in patchy information about their distribution among different organisms and their biological activity. Therefore, despite more than 60 years of research history, there is still no common understanding of the natural sources of TMLs, their structural type classification, and most characteristic biological activities. The controversial nomenclature, incorrect or erroneous structure elucidation, poor identification of producing organisms, and scattered information on the biological activity of compounds - all these factors have led to the problems with dereplication and the directed search for TMLs. This review consists of two parts: the first part (Section 2) covers 104 natural TMLs, published between 2012 and 2022 (after the publishing of the previous review), and the second part (Section 3) summarizes information about 214 TMLs described during 1964-2022 and as a result highlights the main problems and trends in the study of these intriguing natural products.
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Affiliation(s)
- Vsevolod Dubovik
- Laboratory of Phytotoxicology and Biotechnology, All-Russian Institute of Plant Protection, Pushkin, 196608 Saint-Petersburg, Russia.
| | - Anna Dalinova
- Laboratory of Phytotoxicology and Biotechnology, All-Russian Institute of Plant Protection, Pushkin, 196608 Saint-Petersburg, Russia.
| | - Alexander Berestetskiy
- Laboratory of Phytotoxicology and Biotechnology, All-Russian Institute of Plant Protection, Pushkin, 196608 Saint-Petersburg, Russia.
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2
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Ushimaru R, Abe I. Unusual Dioxygen-Dependent Reactions Catalyzed by Nonheme Iron Enzymes in Natural Product Biosynthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c05247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- ACT-X, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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3
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Panth N, Wenger ES, Krebs C, Bollinger JM, Grossman RB. Synthesis of 6,6- and 7,7-difluoro-1-acetamidopyrrolizidines and their oxidation catalyzed by the nonheme Fe oxygenase LolO. Chembiochem 2022; 23:e202200081. [PMID: 35482316 DOI: 10.1002/cbic.202200081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/26/2022] [Indexed: 11/11/2022]
Abstract
LolO, a 2-oxoglutarate-dependent nonheme Fe oxygenase, catalyzes both the hydroxylation and cycloetherification of 1- exo -acetamidopyrrolizidine (AcAP), a pathway intermediate in the biosynthesis of the loline alkaloids. We have prepared fluorinated AcAP analogs to aid in continued mechanistic investigation of the unusual LolO-catalyzed cycloetherification step. LolO was able to first hydroxylate and then cycloetherify 6,6-difluoro-AcAP (prepared from N , O -protected 4-oxoproline), forming a difluorinated analog of N -acetylnorloline (NANL) and providing evidence for a cycloetherification mechanism involving a C(7) radical as opposed to a C(7) carbocation. By contrast, LolO was able to hydroxylate 7,7-difluoro-AcAP (prepared from 3-oxoproline) but failed to cycloetherify it, forming (1 R , 2 R , 8 S )-7,7-difluoro-2-hydroxy-AcAP as the sole product. Because it completely blocks the cycloetherification step, 7,7-difluoro-AcAP has the potential to become an important tool for accumulating and characterizing the LolO intermediate responsible for catalyzing cycloetherification of 2-hydroxy-AcAP.
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Affiliation(s)
- Nabin Panth
- University of Kentucky, Chemistry, UNITED STATES
| | | | - Carsten Krebs
- The Pennsylvania State University, Chemistry; Biochemistry and Molecular Biology, UNITED STATES
| | - J Martin Bollinger
- The Pennsylvania State University, Chemistry; Biochemistry and Molecular Biology, UNITED STATES
| | - Robert B Grossman
- University of Kentucky, Chemistry, Chemistry-Physics Building, 40506-0055, Lexington, UNITED STATES
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Engelbrecht A, Saad H, Gross H, Kaysser L. Natural Products from Nocardia and Their Role in Pathogenicity. Microb Physiol 2021; 31:217-232. [PMID: 34139700 DOI: 10.1159/000516864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/26/2021] [Indexed: 11/19/2022]
Abstract
Nocardia spp. are filamentous Actinobacteria of the order Corynebacteriales and mostly known for their ability to cause localized and systemic infections in humans. However, the onset and progression of nocardiosis is only poorly understood, in particular the mechanisms of strain-specific presentations. Recent genome sequencing has revealed an extraordinary capacity for the production of specialized small molecules. Such secondary metabolites are often crucial for the producing microbe to survive the challenges of different environmental conditions. An interesting question thus concerns the role of these natural products in Nocardia-associated pathogenicity and immune evasion in a human host. In this review, a summary and discussion of Nocardia metabolites is presented, which may play a part in nocardiosis because of their cytotoxic, immunosuppressive and metal-chelating properties or otherwise vitally important functions. This review also contains so far unpublished data concerning the biosynthesis of these molecules that were obtained by detailed bioinformatic analyses.
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Affiliation(s)
- Alicia Engelbrecht
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany
| | - Hamada Saad
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany.,Department of Phytochemistry and Plant Systematics, Division of Pharmaceutical Industries, National Research Centre, Cairo, Egypt
| | - Harald Gross
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany
| | - Leonard Kaysser
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany.,Institute for Drug Discovery, University of Leipzig, Leipzig, Germany
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Zhang X, Chen S, Zhang L, Zhang Q, Zhang W, Chen Y, Zhang W, Zhang H, Zhang C. Dassonmycins A and B, Polycyclic Thioalkaloids from a Marine Sponge-Derived Nocardiopsis dassonvillei SCSIO 40065. Org Lett 2021; 23:2858-2862. [PMID: 33703905 DOI: 10.1021/acs.orglett.1c00328] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Two polycyclic thioalkaloides dassonmycins A (1) and B (2) were isolated from Nocardiopsis dassonvillei SCSIO 40065 associated with marine sponge Petrosia sp. Structures of 1 and 2 were elucidated by comprehensive spectroscopic analysis and confirmed by single-crystal X-ray diffraction experiments, to have a 6/6/6/6-fused tetracyclic ring featuring a naphthoquinone[2,3-e]piperazine[1,2-c]thiomorpholine scaffold. Compound 2 formed a caged core through an additional ether bridge. Both compounds exhibited moderate antibacterial and cytotoxic activities.
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Affiliation(s)
- Xinya Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Siqiang Chen
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
| | - Yuchan Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou 510070, China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou 510070, China
| | - Haibo Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China.,Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya 572000, China
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A [6+4]-cycloaddition adduct is the biosynthetic intermediate in streptoseomycin biosynthesis. Nat Commun 2021; 12:2092. [PMID: 33828077 PMCID: PMC8027225 DOI: 10.1038/s41467-021-22395-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/10/2021] [Indexed: 12/14/2022] Open
Abstract
Streptoseomycin (STM, 1) is a bacterial macrolactone that has a unique 5/14/10/6/6-pentacyclic ring with an ether bridge. We have previously identified the biosynthetic gene cluster for 1 and characterized StmD as [6 + 4]- and [4 + 2]-bispericyclase that catalyze a reaction leading to both 6/10/6- and 10/6/6-tricyclic adducts (6 and 7). The remaining steps, especially how to install and stabilize the required 10/6/6-tricyclic core for downstream modifications, remain unknown. In this work, we have identified three oxidoreductases that fix the required 10/6/6-tryciclic core. A pair of flavin-dependent oxidoreductases, StmO1 and StmO2, catalyze the direct hydroxylation at [6 + 4]-adduct (6). Subsequently, a spontaneous [3,3]-Cope rearrangement and an enol-ketone tautomerization result in the formation of 10/6/6-tricyclic intermediate 12b, which can be further converted to a stable 10/6/6-tricyclic alcohol 11 through a ketoreduction by StmK. Crystal structure of the heterodimeric complex NtfO1-NtfO2, homologues of StmO1-StmO2 with equivalent function, reveals protein-protein interactions. Our results demonstrate that the [6 + 4]-adduct instead of [4 + 2]-adduct is the bona fide biosynthetic intermediate.
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Kenshole E, Herisse M, Michael M, Pidot SJ. Natural product discovery through microbial genome mining. Curr Opin Chem Biol 2020; 60:47-54. [PMID: 32853968 DOI: 10.1016/j.cbpa.2020.07.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/17/2020] [Accepted: 07/24/2020] [Indexed: 02/06/2023]
Abstract
The advent of the genomic era has opened up enormous possibilities for the discovery of new natural products. Also known as specialized metabolites, these compounds produced by bacteria, fungi, and plants have long been sought for their bioactive properties. Innovations in both DNA sequencing technologies and bioinformatics now allow the wealth of sequence data to be mined at both the genome and metagenome levels for new specialized metabolites. However, a key problem that remains is rapidly and efficiently linking these identified genes to their corresponding compounds. Within this review, we provide specific examples of studies that have used the power of genomic or metagenomic data to overcome these problems and identify new small molecules and their biosynthetic pathways.
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Affiliation(s)
- Emma Kenshole
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia, 3000
| | - Marion Herisse
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia, 3000
| | - Michael Michael
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia, 3000
| | - Sacha J Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia, 3000.
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8
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Robinson SL, Terlouw BR, Smith MD, Pidot SJ, Stinear TP, Medema MH, Wackett LP. Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia. J Biol Chem 2020; 295:14826-14839. [PMID: 32826316 DOI: 10.1074/jbc.ra120.013528] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/07/2020] [Indexed: 12/31/2022] Open
Abstract
Enzymes that cleave ATP to activate carboxylic acids play essential roles in primary and secondary metabolism in all domains of life. Class I adenylate-forming enzymes share a conserved structural fold but act on a wide range of substrates to catalyze reactions involved in bioluminescence, nonribosomal peptide biosynthesis, fatty acid activation, and β-lactone formation. Despite their metabolic importance, the substrates and functions of the vast majority of adenylate-forming enzymes are unknown without tools available to accurately predict them. Given the crucial roles of adenylate-forming enzymes in biosynthesis, this also severely limits our ability to predict natural product structures from biosynthetic gene clusters. Here we used machine learning to predict adenylate-forming enzyme function and substrate specificity from protein sequences. We built a web-based predictive tool and used it to comprehensively map the biochemical diversity of adenylate-forming enzymes across >50,000 candidate biosynthetic gene clusters in bacterial, fungal, and plant genomes. Ancestral phylogenetic reconstruction and sequence similarity networking of enzymes from these clusters suggested divergent evolution of the adenylate-forming superfamily from a core enzyme scaffold most related to contemporary CoA ligases toward more specialized functions including β-lactone synthetases. Our classifier predicted β-lactone synthetases in uncharacterized biosynthetic gene clusters conserved in >90 different strains of Nocardia. To test our prediction, we purified a candidate β-lactone synthetase from Nocardia brasiliensis and reconstituted the biosynthetic pathway in vitro to link the gene cluster to the β-lactone natural product, nocardiolactone. We anticipate that our machine learning approach will aid in functional classification of enzymes and advance natural product discovery.
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Affiliation(s)
- Serina L Robinson
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA; Graduate Program in Bioinformatics and Computational Biology, University of Minnesota, Rochester, Minnesota, USA; Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, Minneapolis, Minnesota, USA.
| | - Barbara R Terlouw
- Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Megan D Smith
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA; Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sacha J Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Lawrence P Wackett
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA; Graduate Program in Bioinformatics and Computational Biology, University of Minnesota, Rochester, Minnesota, USA; Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, Minneapolis, Minnesota, USA
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9
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Herisse M, Ishida K, Porter JL, Howden B, Hertweck C, Stinear TP, Pidot SJ. Identification and Mobilization of a Cryptic Antibiotic Biosynthesis Gene Locus from a Human-Pathogenic Nocardia Isolate. ACS Chem Biol 2020; 15:1161-1168. [PMID: 31697466 DOI: 10.1021/acschembio.9b00763] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The genus Nocardia contains >50 human pathogenic species that cause a range of illnesses from skin and soft tissue infections to lung and brain infections. However, despite their membership in the most prominent family of secondary metabolite producers (the Actinomycetes), the ability of Nocardia species, especially those that cause human infections, to produce secondary metabolites has not been as well studied. Using genome mining, we have investigated cryptic secondary metabolite biosynthesis gene clusters from Nocardia species and identified a conserved locus within human pathogenic strains of Nocardia brasiliensis and Nocardia vulneris. Direct capture and heterologous expression in a Streptomyces host activated the biosynthetic locus, revealing it to be the source of the brasiliquinones, benz[a]anthraquinone antibiotics whose biosynthetic pathway has remained hidden for over two decades, until now. Our findings highlight these hitherto neglected human pathogenic Nocardia as a source of diverse and important natural products.
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Affiliation(s)
- Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Jessica L. Porter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Ben Howden
- Microbiological Diagnostic Unit, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
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Pidot SJ, Rizzacasa MA. The Nargenicin Family of Oxa-Bridged Macrolide Antibiotics. Chemistry 2020; 26:2780-2792. [PMID: 31667915 DOI: 10.1002/chem.201904053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Indexed: 11/06/2022]
Abstract
The nargenicin family of antibiotic macrolides comprise a group of bacterial natural products with a rare ether bridged cis-decalin moiety and a narrow spectrum of activity. Most family members were identified almost four decades ago and were placed on the shelf due to the numbers of broad-spectrum compounds available at the time. However, in light of rising rates of antimicrobial resistance, there has been a renewed interest in the use of narrow-spectrum antimicrobials. Here, we review the history of this family of compounds, including synthetic approaches, and highlight the recently uncovered genetic basis for nargenicin production. Given the renewed pharmaceutical interest in these compounds, we also investigate structure-activity relationships among these molecules, with a view to the future development of members of this unusual antibiotic family.
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Affiliation(s)
- Sacha J Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, 3000, Melbourne, VIC, Australia
| | - Mark A Rizzacasa
- School of Chemistry, The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 3000, Melbourne, VIC, Australia
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Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as niduterpenoid A from Aspergillus nidulans.
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