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Kries H, Trottmann F, Hertweck C. Novel Biocatalysts from Specialized Metabolism. Angew Chem Int Ed Engl 2024; 63:e202309284. [PMID: 37737720 DOI: 10.1002/anie.202309284] [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: 06/30/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/23/2023]
Abstract
Enzymes are increasingly recognized as valuable (bio)catalysts that complement existing synthetic methods. However, the range of biotransformations used in the laboratory is limited. Here we give an overview on the biosynthesis-inspired discovery of novel biocatalysts that address various synthetic challenges. Prominent examples from this dynamic field highlight remarkable enzymes for protecting-group-free amide formation and modification, control of pericyclic reactions, stereoselective hetero- and polycyclizations, atroposelective aryl couplings, site-selective C-H activations, introduction of ring strain, and N-N bond formation. We also explore unusual functions of cytochrome P450 monooxygenases, radical SAM-dependent enzymes, flavoproteins, and enzymes recruited from primary metabolism, which offer opportunities for synthetic biology, enzyme engineering, directed evolution, and catalyst design.
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Affiliation(s)
- Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Department of Chemistry, University of Bayreuth, Universitätsstr. 30, 95440, Bayreuth, Germany
| | - Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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2
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Ho YTC, Schittenhelm RB, Iftime D, Stegmann E, Tailhades J, Cryle MJ. Exploring the Flexibility of the Glycopeptide Antibiotic Crosslinking Cascade for Extended Peptide Backbones. Chembiochem 2023; 24:e202200686. [PMID: 36534957 DOI: 10.1002/cbic.202200686] [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: 11/21/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/23/2022]
Abstract
The glycopeptide antibiotics (GPAs) are a clinically approved class of antimicrobial agents that classically function through the inhibition of bacterial cell-wall biosynthesis by sequestration of the precursor lipid II. The oxidative crosslinking of the core peptide by cytochrome P450 (Oxy) enzymes during GPA biosynthesis is both essential to their function and the source of their synthetic challenge. Thus, understanding the activity and selectivity of these Oxy enzymes is of key importance for the future engineering of this important compound class. Recent reports of GPAs that display an alternative mode of action and a wider range of core peptide structures compared to classic lipid II-binding GPAs raises the question of the tolerance of Oxy enzymes for larger changes in their peptide substrates. In this work, we explore the ability of Oxy enzymes from the biosynthesis pathways of lipid II-binding GPAs to accept altered peptide substrates based on a vancomycin template. Our results show that Oxy enzymes are more tolerant of changes at the N terminus of their substrates, whilst C-terminal extension of the peptide substrates is deleterious to the activity of all Oxy enzymes. Thus, future studies should prioritise the study of Oxy enzymes from atypical GPA biosynthesis pathways bearing C-terminal peptide extension to increase the substrate scope of these important cyclisation enzymes.
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Affiliation(s)
- Y T Candace Ho
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,EMBL Australia, Monash University, Clayton, VIC 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,Monash Proteomics and Metabolomics Facility, Monash University, Clayton, VIC 3800, Australia
| | - Dumitrita Iftime
- Interfaculty Institute of Microbiology and Infection Medicine, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, 72076, Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, 72076, Tübingen, Germany
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,EMBL Australia, Monash University, Clayton, VIC 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,EMBL Australia, Monash University, Clayton, VIC 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
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3
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Zhao Y, Ho YTC, Tailhades J, Cryle M. Understanding the Glycopeptide Antibiotic Crosslinking Cascade: In Vitro Approaches Reveal the Details of a Complex Biosynthesis Pathway. Chembiochem 2020; 22:43-51. [PMID: 32696500 DOI: 10.1002/cbic.202000309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/21/2020] [Indexed: 11/06/2022]
Abstract
The glycopeptide antibiotics (GPAs) are a fascinating example of complex natural product biosynthesis, with the nonribosomal synthesis of the peptide core coupled to a cytochrome P450-mediated cyclisation cascade that crosslinks aromatic side chains within this peptide. Given that the challenges associated with the synthesis of GPAs stems from their highly crosslinked structure, there is great interest in understanding how biosynthesis accomplishes this challenging set of transformations. In this regard, the use of in vitro experiments has delivered important insights into this process, including the identification of the unique role of the X-domain as a platform for P450 recruitment. In this minireview, we present an analysis of the results of in vitro studies into the GPA cyclisation cascade that have demonstrated both the tolerances and limitations of this process for modified substrates, and in turn developed rules for the future reengineering of this important antibiotic class.
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Affiliation(s)
- Yongwei Zhao
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Y T Candace Ho
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Max Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
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Tailhades J, Zhao Y, Ho YTC, Greule A, Ahmed I, Schoppet M, Kulkarni K, Goode RJA, Schittenhelm RB, De Voss JJ, Cryle MJ. A Chemoenzymatic Approach to the Synthesis of Glycopeptide Antibiotic Analogues. Angew Chem Int Ed Engl 2020; 59:10899-10903. [DOI: 10.1002/anie.202003726] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/14/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Julien Tailhades
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Yongwei Zhao
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Y. T. Candace Ho
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Anja Greule
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Iftekhar Ahmed
- School of Chemistry and Molecular Biosciences The University of Queensland St Lucia Queensland 4072 Australia
| | - Melanie Schoppet
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - Rob J. A. Goode
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- Monash Proteomics & Metabolomics Facility Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- Monash Proteomics & Metabolomics Facility Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences The University of Queensland St Lucia Queensland 4072 Australia
| | - Max J. Cryle
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
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5
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Tailhades J, Zhao Y, Ho YTC, Greule A, Ahmed I, Schoppet M, Kulkarni K, Goode RJA, Schittenhelm RB, De Voss JJ, Cryle MJ. A Chemoenzymatic Approach to the Synthesis of Glycopeptide Antibiotic Analogues. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Julien Tailhades
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Yongwei Zhao
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Y. T. Candace Ho
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Anja Greule
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Iftekhar Ahmed
- School of Chemistry and Molecular Biosciences The University of Queensland St Lucia Queensland 4072 Australia
| | - Melanie Schoppet
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - Rob J. A. Goode
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- Monash Proteomics & Metabolomics Facility Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- Monash Proteomics & Metabolomics Facility Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences The University of Queensland St Lucia Queensland 4072 Australia
| | - Max J. Cryle
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
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6
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Meng S, Tang GL, Pan HX. Enzymatic Formation of Oxygen-Containing Heterocycles in Natural Product Biosynthesis. Chembiochem 2018; 19:2002-2022. [PMID: 30039582 DOI: 10.1002/cbic.201800225] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Indexed: 01/12/2023]
Abstract
Oxygen-containing heterocycles are widely encountered in natural products that display diverse pharmacological properties and have potential benefits to human health. The formation of O-heterocycles catalyzed by different types of enzymes in the biosynthesis of natural products not only contributes to the structural diversity of these compounds, but also enriches our understanding of nature's ability to construct complex molecules. This minireview focuses on the various modes of enzymatic O-heterocyclization identified in natural product biosynthesis and summarizes the possible mechanisms involved in ring closure.
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Affiliation(s)
- Song Meng
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Hai-Xue Pan
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
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Forneris CC, Ozturk S, Gibson MI, Sorensen EJ, Seyedsayamdost MR. In Vitro Reconstitution of OxyA Enzymatic Activity Clarifies Late Steps in Vancomycin Biosynthesis. ACS Chem Biol 2017; 12:2248-2253. [PMID: 28696669 DOI: 10.1021/acschembio.7b00456] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies on the biosynthesis of glycopeptide antibiotics have provided many insights into the strategies that Nature employs to build architecturally strained molecules. A key structural feature of vancomycin, the founding member of this class, is a set of three aromatic cross-links that are introduced via yet unknown mechanisms. Previous reports have identified three cytochrome P450 enzymes involved in this process and demonstrated enzymatic activity for OxyB, which installs the first aromatic cross-link. However, the activities of the remaining two P450 enzymes have not been recapitulated. Herein, we show that OxyA generates the second bis-aryl ether bond in vancomycin and that it exhibits strict substrate specificity toward the chlorinated, OxyB-cross-linked product. No OxyA product is detected with the unchlorinated substrate. Together with previous results, these data suggest that chlorination occurs after OxyB- but before OxyA-catalyzed cross-link formation. Our results have important implications for the chemo-enzymatic synthesis of vancomycin and its analogs.
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Affiliation(s)
- Clarissa C. Forneris
- Departments
of Chemistry and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Seyma Ozturk
- Departments
of Chemistry and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Marcus I. Gibson
- Departments
of Chemistry and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Erik J. Sorensen
- Departments
of Chemistry and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R. Seyedsayamdost
- Departments
of Chemistry and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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Sundaram S, Hertweck C. On-line enzymatic tailoring of polyketides and peptides in thiotemplate systems. Curr Opin Chem Biol 2016; 31:82-94. [DOI: 10.1016/j.cbpa.2016.01.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/21/2015] [Accepted: 01/15/2016] [Indexed: 11/26/2022]
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