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Wang CY, Hu JQ, Wang DG, Li YZ, Wu C. Recent advances in discovery and biosynthesis of natural products from myxobacteria: an overview from 2017 to 2023. Nat Prod Rep 2024; 41:905-934. [PMID: 38390645 DOI: 10.1039/d3np00062a] [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: 02/24/2024]
Abstract
Covering: 2017.01 to 2023.11Natural products biosynthesized by myxobacteria are appealing due to their sophisticated chemical skeletons, remarkable biological activities, and intriguing biosynthetic enzymology. This review aims to systematically summarize the advances in the discovery methods, new structures, and bioactivities of myxobacterial NPs reported in the period of 2017-2023. In addition, the peculiar biosynthetic pathways of several structural families are also highlighted.
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Affiliation(s)
- Chao-Yi Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Jia-Qi Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - De-Gao Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
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2
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Sommer-Kamann C, Breiltgens J, Zou Z, Gerhardt S, Saleem-Batcha R, Kemper F, Einsle O, Andexer JN, Müller M. Structures and Protein Engineering of the α-Keto Acid C-Methyltransferases SgvM and MrsA for Rational Substrate Transfer. Chembiochem 2024:e202400258. [PMID: 38887142 DOI: 10.1002/cbic.202400258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024]
Abstract
S-adenosyl-l-methionine-dependent methyltransferases (MTs) are involved in the C-methylation of a variety of natural products. The MTs SgvM from Streptomyces griseoviridis and MrsA from Pseudomonas syringae pv. syringae catalyze the methylation of the β-carbon atom of α-keto acids in the biosynthesis of the antibiotic natural products viridogrisein and 3-methylarginine, respectively. MrsA shows high substrate selectivity for 5-guanidino-2-oxovalerate, while other α-keto acids, such as the SgvM substrates 4-methyl-2-oxovalerate, 2-oxovalerate, and phenylpyruvate, are not accepted. Here we report the crystal structures of SgvM and MrsA in the apo form and bound with substrate or S-adenosyl-l-methionine. By investigating key residues for substrate recognition in the active sites of both enzymes and engineering MrsA by site-directed mutagenesis, the substrate range of MrsA was extended to accept α-keto acid substrates of SgvM with uncharged and lipophilic β-residues. Our results showcase the transfer of the substrate scope of α-keto acid MTs from different biosynthetic pathways by rational design.
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Affiliation(s)
- Christina Sommer-Kamann
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Juliane Breiltgens
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Ziruo Zou
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Stefan Gerhardt
- Institute of Biochemistry, University of Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Raspudin Saleem-Batcha
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Florian Kemper
- Institute of Biochemistry, University of Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Oliver Einsle
- Institute of Biochemistry, University of Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Jennifer N Andexer
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
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3
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Ju S, Kuzelka KP, Guo R, Krohn-Hansen B, Wu J, Nair SK, Yang Y. A biocatalytic platform for asymmetric alkylation of α-keto acids by mining and engineering of methyltransferases. Nat Commun 2023; 14:5704. [PMID: 37709735 PMCID: PMC10502145 DOI: 10.1038/s41467-023-40980-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023] Open
Abstract
Catalytic asymmetric α-alkylation of carbonyl compounds represents a long-standing challenge in synthetic organic chemistry. Herein, we advance a dual biocatalytic platform for the efficient asymmetric alkylation of α-keto acids. First, guided by our recently obtained crystal structures, we develop SgvMVAV as a general biocatalyst for the enantioselective methylation, ethylation, allylation and propargylation of a range of α-keto acids with total turnover numbers (TTNs) up to 4,600. Second, we mine a family of bacterial HMTs from Pseudomonas species sharing less than 50% sequence identities with known HMTs and evaluated their activities in SAM regeneration. Our best performing HMT from P. aeruginosa, PaHMT, displays the highest SAM regeneration efficiencies (TTN up to 7,700) among HMTs characterized to date. Together, the synergistic use of SgvMVAV and PaHMT affords a fully biocatalytic protocol for asymmetric methylation featuring a record turnover efficiency, providing a solution to the notorious problem of asymmetric alkylation.
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Affiliation(s)
- Shuyun Ju
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Kaylee P Kuzelka
- Department of Biochemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rui Guo
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Benjamin Krohn-Hansen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Jianping Wu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Satish K Nair
- Department of Biochemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA.
- Biomolecular Science and Engineering (BMSE) Program, University of California, Santa Barbara, CA, USA.
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Atanasov AG, Zotchev SB, Dirsch VM, Supuran CT. Natural products in drug discovery: advances and opportunities. Nat Rev Drug Discov 2021; 20:200-216. [PMID: 33510482 PMCID: PMC7841765 DOI: 10.1038/s41573-020-00114-z] [Citation(s) in RCA: 1770] [Impact Index Per Article: 590.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2020] [Indexed: 02/07/2023]
Abstract
Natural products and their structural analogues have historically made a major contribution to pharmacotherapy, especially for cancer and infectious diseases. Nevertheless, natural products also present challenges for drug discovery, such as technical barriers to screening, isolation, characterization and optimization, which contributed to a decline in their pursuit by the pharmaceutical industry from the 1990s onwards. In recent years, several technological and scientific developments - including improved analytical tools, genome mining and engineering strategies, and microbial culturing advances - are addressing such challenges and opening up new opportunities. Consequently, interest in natural products as drug leads is being revitalized, particularly for tackling antimicrobial resistance. Here, we summarize recent technological developments that are enabling natural product-based drug discovery, highlight selected applications and discuss key opportunities.
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Affiliation(s)
- Atanas G Atanasov
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Jastrzebiec, Poland.
- Department of Pharmacognosy, University of Vienna, Vienna, Austria.
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria.
| | - Sergey B Zotchev
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Verena M Dirsch
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Claudiu T Supuran
- Università degli Studi di Firenze, NEUROFARBA Dept, Sezione di Scienze Farmaceutiche, Florence, Italy.
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Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
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Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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Bader CD, Panter F, Müller R. In depth natural product discovery - Myxobacterial strains that provided multiple secondary metabolites. Biotechnol Adv 2019; 39:107480. [PMID: 31707075 DOI: 10.1016/j.biotechadv.2019.107480] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/28/2022]
Abstract
In recognition of many microorganisms ability to produce a variety of secondary metabolites in parallel, Zeeck and coworkers introduced the term "OSMAC" (one strain many compounds) around the turn of the century. Since then, additional efforts focused on the systematic characterization of a single bacterial species ability to form multiple secondary metabolite scaffolds. With the beginning of the genomic era mainly initiated by a dramatic reduction of sequencing costs, investigations of the genome encoded biosynthetic potential and especially the exploitation of biosynthetic gene clusters of undefined function gained attention. This was seen as a novel means to extend range and diversity of bacterial secondary metabolites. Genome analyses showed that even for well-studied bacterial strains, like the myxobacterium Myxococcus xanthus DK1622, many biosynthetic gene clusters are not yet assigned to their corresponding hypothetical secondary metabolites. In contrast to the results from emerging genome and metabolome mining techniques that show the large untapped biosynthetic potential per strain, many newly isolated bacterial species are still used for the isolation of only one target compound class and successively abandoned in the sense that no follow up studies are published from the same species. This work provides an overview about myxobacterial bacterial strains, from which not just one but multiple different secondary metabolite classes were successfully isolated. The underlying methods used for strain prioritization and natural product discovery such as biological characterization of crude extracts against a panel of pathogens, in-silico prediction of secondary metabolite abundance from genome data and state of the art instrumental analytics required for new natural product scaffold discovery in comparative settings are summarized and classified according to their output. Furthermore, for each approach selected studies performed with actinobacteria are shown to underline especially innovative methods used for natural product discovery.
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Affiliation(s)
- Chantal D Bader
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Fabian Panter
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany.
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Sekurova ON, Schneider O, Zotchev SB. Novel bioactive natural products from bacteria via bioprospecting, genome mining and metabolic engineering. Microb Biotechnol 2019; 12:828-844. [PMID: 30834674 PMCID: PMC6680616 DOI: 10.1111/1751-7915.13398] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/15/2019] [Accepted: 02/21/2019] [Indexed: 12/21/2022] Open
Abstract
For over seven decades, bacteria served as a valuable source of bioactive natural products some of which were eventually developed into drugs to treat infections, cancer and immune system-related diseases. Traditionally, novel compounds produced by bacteria were discovered via conventional bioprospecting based on isolation of potential producers and screening their extracts in a variety of bioassays. Over time, most of the natural products identifiable by this approach were discovered, and the pipeline for new drugs based on bacterially produced metabolites started to run dry. This mini-review highlights recent developments in bacterial bioprospecting for novel compounds that are based on several out-of-the-box approaches, including the following: (i) targeting bacterial species previously unknown to produce any bioactive natural products, (ii) exploring non-traditional environmental niches and methods for isolation of bacteria and (iii) various types of 'genome mining' aimed at unravelling genetic potential of bacteria to produce secondary metabolites. All these approaches have already yielded a number of novel bioactive compounds and, if used wisely, will soon revitalize drug discovery pipeline based on bacterial natural products.
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Affiliation(s)
- Olga N. Sekurova
- Department of PharmacognosyUniversity of ViennaAlthanstraße 141090ViennaAustria
| | - Olha Schneider
- Department of PharmacognosyUniversity of ViennaAlthanstraße 141090ViennaAustria
| | - Sergey B. Zotchev
- Department of PharmacognosyUniversity of ViennaAlthanstraße 141090ViennaAustria
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8
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Li Z, Zhu D, Shen Y. Discovery of novel bioactive natural products driven by genome mining. Drug Discov Ther 2018; 12:318-328. [DOI: 10.5582/ddt.2018.01066] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zhongyue Li
- Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences, Shandong University
| | - Deyu Zhu
- School of Basic Medical Sciences, Shandong University
| | - Yuemao Shen
- Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences, Shandong University
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Ueoka R, Bhushan A, Probst SI, Bray WM, Lokey RS, Linington RG, Piel J. Genome-Based Identification of a Plant-Associated Marine Bacterium as a Rich Natural Product Source. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Agneya Bhushan
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Silke I. Probst
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Walter M. Bray
- Chemistry & Biochemistry Department; University of California Santa Cruz; 1156 High Street 95064 Santa Cruz California USA
| | - R. Scott Lokey
- Chemistry & Biochemistry Department; University of California Santa Cruz; 1156 High Street 95064 Santa Cruz California USA
| | - Roger G. Linington
- Department of Chemistry; Simon Fraser University; 8888 University Drive Bumaby BC V5A 1S6 Canada
| | - Jörn Piel
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
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Ueoka R, Bhushan A, Probst SI, Bray WM, Lokey RS, Linington RG, Piel J. Genome-Based Identification of a Plant-Associated Marine Bacterium as a Rich Natural Product Source. Angew Chem Int Ed Engl 2018; 57:14519-14523. [PMID: 30025185 DOI: 10.1002/anie.201805673] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/12/2018] [Indexed: 01/14/2023]
Abstract
The large number of sequenced bacterial genomes provides the opportunity to bioinformatically identify rich natural product sources among previously neglected microbial groups. Testing this discovery strategy, unusually high biosynthetic potential was suggested for the Oceanospirillales member Gynuella sunshinyii, a Gram-negative marine bacterium from the rhizosphere of the halophilic plant Carex scabrifolia. Its genome contains numerous unusual biosynthetic gene clusters for diverse types of metabolites. Genome-guided isolation yielded representatives of four different natural product classes, of which only alteramide A was known. Cytotoxic lacunalides were identified as products of a giant trans-acyltransferase polyketide synthase gene cluster, one of six present in this strain. Cytological profiling against HeLa cells suggested that lacunalide A disrupts CDK signaling in the cell cycle. In addition, chemical studies on model compounds were conducted, suggesting the structurally unusual ergoynes as products of a conjugated diyne-thiourea cyclization reaction.
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Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Agneya Bhushan
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Silke I Probst
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Walter M Bray
- Chemistry & Biochemistry Department, University of California Santa Cruz, 1156 High Street, 95064, Santa Cruz, California, USA
| | - R Scott Lokey
- Chemistry & Biochemistry Department, University of California Santa Cruz, 1156 High Street, 95064, Santa Cruz, California, USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Bumaby, BC, V5A 1S6, Canada
| | - Jörn Piel
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
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