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  1. Article: Ribosome-independent peptide biosynthesis: the challenge of a unifying nomenclature

    Dell, Maria / Dunbar, Kyle L. / Hertweck, Christian

    Natural product reports. 2022 Mar. 23, v. 39, no. 3

    2022  

    Abstract: The first machineries for non-ribosomal peptide (NRP) biosynthesis were uncovered over 50 years ago, and the dissection of these megasynthetases set the stage for the nomenclature system that has been used ever since. Although the number of exceptions to ...

    Abstract The first machineries for non-ribosomal peptide (NRP) biosynthesis were uncovered over 50 years ago, and the dissection of these megasynthetases set the stage for the nomenclature system that has been used ever since. Although the number of exceptions to the canonical biosynthetic pathways has surged in the intervening years, the NRP synthetase (NRPS) classification system has remained relatively unchanged. This has led to the exclusion of many biosynthetic pathways whose biosynthetic machineries violate the classical rules for NRP assembly, and ultimately to a rupture in the field of NRP biosynthesis. In an attempt to unify the classification of NRP pathways and to facilitate the communication within the research field, we propose a revised framework for grouping ribosome-independent peptide biosynthetic pathways based on recognizable commonalities in their biosynthetic logic. Importantly, the framework can be further refined as needed.
    Keywords biosynthesis ; dissection ; nonribosomal peptides
    Language English
    Dates of publication 2022-0323
    Size p. 453-459.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ZDB-ID 2002546-4
    ISSN 1460-4752 ; 0265-0568
    ISSN (online) 1460-4752
    ISSN 0265-0568
    DOI 10.1039/d1np00019e
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Ribosome-independent peptide biosynthesis: the challenge of a unifying nomenclature.

    Dell, Maria / Dunbar, Kyle L / Hertweck, Christian

    Natural product reports

    2022  Volume 39, Issue 3, Page(s) 453–459

    Abstract: The first machineries for non-ribosomal peptide (NRP) biosynthesis were uncovered over 50 years ago, and the dissection of these megasynthetases set the stage for the nomenclature system that has been used ever since. Although the number of exceptions to ...

    Abstract The first machineries for non-ribosomal peptide (NRP) biosynthesis were uncovered over 50 years ago, and the dissection of these megasynthetases set the stage for the nomenclature system that has been used ever since. Although the number of exceptions to the canonical biosynthetic pathways has surged in the intervening years, the NRP synthetase (NRPS) classification system has remained relatively unchanged. This has led to the exclusion of many biosynthetic pathways whose biosynthetic machineries violate the classical rules for NRP assembly, and ultimately to a rupture in the field of NRP biosynthesis. In an attempt to unify the classification of NRP pathways and to facilitate the communication within the research field, we propose a revised framework for grouping ribosome-independent peptide biosynthetic pathways based on recognizable commonalities in their biosynthetic logic. Importantly, the framework can be further refined as needed.
    MeSH term(s) Biosynthetic Pathways ; Peptide Biosynthesis, Nucleic Acid-Independent ; Peptide Synthases/metabolism ; Peptides/metabolism ; Ribosomes/metabolism
    Chemical Substances Peptides ; Peptide Synthases (EC 6.3.2.-)
    Language English
    Publishing date 2022-03-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2002546-4
    ISSN 1460-4752 ; 0265-0568
    ISSN (online) 1460-4752
    ISSN 0265-0568
    DOI 10.1039/d1np00019e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Trapping of a Polyketide Synthase Module after C-C Bond Formation Reveals Transient Acyl Carrier Domain Interactions.

    Dell, Maria / Tran, Mai Anh / Capper, Michael J / Sundaram, Srividhya / Fiedler, Jonas / Koehnke, Jesko / Hellmich, Ute A / Hertweck, Christian

    Angewandte Chemie (International ed. in English)

    2024  Volume 63, Issue 9, Page(s) e202315850

    Abstract: Modular polyketide synthases (PKSs) are giant assembly lines that produce an impressive range of biologically active compounds. However, our understanding of the structural dynamics of these megasynthases, specifically the delivery of acyl carrier ... ...

    Abstract Modular polyketide synthases (PKSs) are giant assembly lines that produce an impressive range of biologically active compounds. However, our understanding of the structural dynamics of these megasynthases, specifically the delivery of acyl carrier protein (ACP)-bound building blocks to the catalytic site of the ketosynthase (KS) domain, remains severely limited. Using a multipronged structural approach, we report details of the inter-domain interactions after C-C bond formation in a chain-branching module of the rhizoxin PKS. Mechanism-based crosslinking of an engineered module was achieved using a synthetic substrate surrogate that serves as a Michael acceptor. The crosslinked protein allowed us to identify an asymmetric state of the dimeric protein complex upon C-C bond formation by cryo-electron microscopy (cryo-EM). The possible existence of two ACP binding sites, one of them a potential "parking position" for substrate loading, was also indicated by AlphaFold2 predictions. NMR spectroscopy showed that a transient complex is formed in solution, independent of the linker domains, and photochemical crosslinking/mass spectrometry of the standalone domains allowed us to pinpoint the interdomain interaction sites. The structural insights into a branching PKS module arrested after C-C bond formation allows a better understanding of domain dynamics and provides valuable information for the rational design of modular assembly lines.
    MeSH term(s) Polyketide Synthases/metabolism ; Cryoelectron Microscopy ; Binding Sites ; Catalytic Domain ; Acyl Carrier Protein/metabolism
    Chemical Substances Polyketide Synthases (79956-01-7) ; Acyl Carrier Protein
    Language English
    Publishing date 2024-01-17
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202315850
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Heterocomplex structure of a polyketide synthase component involved in modular backbone halogenation.

    Fraley, Amy E / Dell, Maria / Schmalhofer, Maximilian / Meoded, Roy A / Bergande, Cedric / Groll, Michael / Piel, Jörn

    Structure (London, England : 1993)

    2023  Volume 31, Issue 5, Page(s) 565–572.e4

    Abstract: Bacterial modular polyketide synthases (PKSs) generate diverse, complex and bioactive natural products that are constructed mainly based on principles of fatty acid biosynthesis. The cytotoxic oocydin-type polyketides contain a vinyl chloride moiety ... ...

    Abstract Bacterial modular polyketide synthases (PKSs) generate diverse, complex and bioactive natural products that are constructed mainly based on principles of fatty acid biosynthesis. The cytotoxic oocydin-type polyketides contain a vinyl chloride moiety introduced during polyketide chain elongation. Required for modular polyketide backbone halogenation are a non-heme iron and ɑ-ketoglutarate-dependent halogenase OocP and OocQ lacking characterized homologs. This work provides structural insights into these unusual PKS components and their interactions via a high-resolution X-ray crystallography structure of the heterocomplex. By mapping the protein-protein interactions and comparison with structures of similar halogenases, we illustrate the potential of this heterodimer complex as a replacement for the conserved homodimeric structure of homologous enzymes. The OocPQ protein pair has thus evolved as a means of stabilizing the halogenase and facilitating chemical transformations with great synthetic utility.
    MeSH term(s) Polyketide Synthases/genetics ; Polyketide Synthases/metabolism ; Halogenation ; Polyketides/metabolism ; Bacteria/metabolism
    Chemical Substances Polyketide Synthases (79956-01-7) ; Polyketides
    Language English
    Publishing date 2023-03-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1213087-4
    ISSN 1878-4186 ; 0969-2126
    ISSN (online) 1878-4186
    ISSN 0969-2126
    DOI 10.1016/j.str.2023.02.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Reconstitution of polythioamide antibiotic backbone formation reveals unusual thiotemplated assembly strategy.

    Dunbar, Kyle L / Dell, Maria / Gude, Finn / Hertweck, Christian

    Proceedings of the National Academy of Sciences of the United States of America

    2020  Volume 117, Issue 16, Page(s) 8850–8858

    Abstract: Closthioamide (CTA) is a rare example of a thioamide-containing nonribosomal peptide and is one of only a handful of secondary metabolites described from obligately anaerobic bacteria. Although the biosynthetic gene cluster responsible for CTA production ...

    Abstract Closthioamide (CTA) is a rare example of a thioamide-containing nonribosomal peptide and is one of only a handful of secondary metabolites described from obligately anaerobic bacteria. Although the biosynthetic gene cluster responsible for CTA production and the thioamide synthetase that catalyzes sulfur incorporation were recently discovered, the logic for peptide backbone assembly has remained a mystery. Here, through the use of in vitro biochemical assays, we demonstrate that the amide backbone of CTA is assembled in an unusual thiotemplated pathway involving the cooperation of a transacylating member of the papain-like cysteine protease family and an iteratively acting ATP-grasp protein. Using the ATP-grasp protein as a bioinformatic handle, we identified hundreds of such thiotemplated yet nonribosomal peptide synthetase (NRPS)-independent biosynthetic gene clusters across diverse bacterial phyla. The data presented herein not only clarify the pathway for the biosynthesis of CTA, but also provide a foundation for the discovery of additional secondary metabolites produced by noncanonical biosynthetic pathways.
    MeSH term(s) Adenosine Triphosphate/metabolism ; Anti-Bacterial Agents/metabolism ; Bacteria, Anaerobic/enzymology ; Bacteria, Anaerobic/genetics ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Binding Sites ; Biosynthetic Pathways/genetics ; Computational Biology ; Cysteine Endopeptidases/genetics ; Cysteine Endopeptidases/metabolism ; Genes, Bacterial ; Multigene Family ; Peptide Biosynthesis, Nucleic Acid-Independent/genetics ; Secondary Metabolism/genetics ; Thioamides/metabolism
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Thioamides ; closthioamide ; Adenosine Triphosphate (8L70Q75FXE) ; Cysteine Endopeptidases (EC 3.4.22.-)
    Language English
    Publishing date 2020-04-07
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1918759117
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A Specialized Polythioamide-Binding Protein Confers Antibiotic Self-Resistance in Anaerobic Bacteria.

    Gude, Finn / Molloy, Evelyn M / Horch, Therese / Dell, Maria / Dunbar, Kyle L / Krabbe, Jana / Groll, Michael / Hertweck, Christian

    Angewandte Chemie (International ed. in English)

    2022  Volume 61, Issue 37, Page(s) e202206168

    Abstract: Understanding antibiotic resistance mechanisms is central to the development of anti-infective therapies and genomics-based drug discovery. Yet, many knowledge gaps remain regarding the resistance strategies employed against novel types of antibiotics ... ...

    Abstract Understanding antibiotic resistance mechanisms is central to the development of anti-infective therapies and genomics-based drug discovery. Yet, many knowledge gaps remain regarding the resistance strategies employed against novel types of antibiotics from less-explored producers such as anaerobic bacteria, among them the Clostridia. Through the use of genome editing and functional assays, we found that CtaZ confers self-resistance against the copper chelator and gyrase inhibitor closthioamide (CTA) in Ruminiclostridium cellulolyticum. Bioinformatics, biochemical analyses, and X-ray crystallography revealed CtaZ as a founding member of a new group of GyrI-like proteins. CtaZ is unique in binding a polythioamide scaffold in a ligand-optimized hydrophobic pocket, thereby confining CTA. By genome mining using CtaZ as a handle, we discovered previously overlooked homologs encoded by diverse members of the phylum Firmicutes, including many pathogens. In addition to characterizing both a new role for a GyrI-like domain in self-resistance and unprecedented thioamide binding, this work aids in uncovering related drug-resistance mechanisms.
    MeSH term(s) Anti-Bacterial Agents/chemistry ; Bacteria, Anaerobic/genetics ; Carrier Proteins/genetics ; Drug Resistance, Microbial ; Gene Editing
    Chemical Substances Anti-Bacterial Agents ; Carrier Proteins
    Language English
    Publishing date 2022-08-03
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202206168
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: An Unexpected Split-Merge Pathway in the Assembly of the Symmetric Nonribosomal Peptide Antibiotic Closthioamide.

    Dunbar, Kyle L / Dell, Maria / Molloy, Evelyn M / Büttner, Hannah / Kumpfmüller, Jana / Hertweck, Christian

    Angewandte Chemie (International ed. in English)

    2020  Volume 60, Issue 8, Page(s) 4104–4109

    Abstract: Closthioamide (CTA) is a symmetric nonribosomal peptide (NRP) comprised of two diaminopropane-linked polythioamidated monomers. CTA is biosynthesized by Ruminiclostridium cellulolyticum via an atypical NRP synthetase (NRPS)-independent biosynthetic ... ...

    Abstract Closthioamide (CTA) is a symmetric nonribosomal peptide (NRP) comprised of two diaminopropane-linked polythioamidated monomers. CTA is biosynthesized by Ruminiclostridium cellulolyticum via an atypical NRP synthetase (NRPS)-independent biosynthetic pathway. Although the logic for monomer assembly was recently elucidated, the strategy for the biosynthesis and incorporation of the diamine linker remained a mystery. By means of genome editing, synthesis, and in vitro biochemical assays, we demonstrate that the final steps in CTA maturation proceed through a surprising split-merge pathway involving the dual use of a thiotemplated intermediate. This pathway includes the first examples of an aldo-keto reductase catalyzing the reductive release of a thiotemplated product, and of a transthioamidating transglutaminase. In addition to clarifying the remaining steps in CTA assembly, our data shed light on largely unexplored pathways for NRPS-independent peptide biosynthesis.
    MeSH term(s) Aldo-Keto Reductases/genetics ; Aldo-Keto Reductases/metabolism ; Anti-Bacterial Agents/analysis ; Anti-Bacterial Agents/biosynthesis ; Anti-Bacterial Agents/chemistry ; Biocatalysis ; Chromatography, High Pressure Liquid ; Clostridiales/genetics ; Clostridiales/metabolism ; Gene Editing ; Multigene Family ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Thioamides/analysis ; Thioamides/chemistry ; Thioamides/metabolism ; Transaminases/genetics ; Transaminases/metabolism ; Transglutaminases/genetics ; Transglutaminases/metabolism
    Chemical Substances Anti-Bacterial Agents ; Thioamides ; closthioamide ; Aldo-Keto Reductases (EC 1.1.1.-) ; Transglutaminases (EC 2.3.2.13) ; Transaminases (EC 2.6.1.-)
    Language English
    Publishing date 2020-12-23
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202011741
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Analysis of Rhizonin Biosynthesis Reveals Origin of Pharmacophoric Furylalanine Moieties in Diverse Cyclopeptides.

    Ehinger, Friedrich J / Niehs, Sarah P / Dose, Benjamin / Dell, Maria / Krabbe, Jana / Pidot, Sacha J / Stinear, Timothy P / Scherlach, Kirstin / Ross, Claudia / Lackner, Gerald / Hertweck, Christian

    Angewandte Chemie (International ed. in English)

    2023  Volume 62, Issue 42, Page(s) e202308540

    Abstract: Rhizonin A and B are hepatotoxic cyclopeptides produced by bacterial endosymbionts (Mycetohabitans endofungorum) of the fungus Rhizopus microsporus. Their toxicity critically depends on the presence of 3-furylalanine (Fua) residues, which also occur in ... ...

    Abstract Rhizonin A and B are hepatotoxic cyclopeptides produced by bacterial endosymbionts (Mycetohabitans endofungorum) of the fungus Rhizopus microsporus. Their toxicity critically depends on the presence of 3-furylalanine (Fua) residues, which also occur in pharmaceutically relevant cyclopeptides of the endolide and bingchamide families. The biosynthesis and incorporation of Fua by non-ribosomal peptide synthetases (NRPS), however, has remained elusive. By genome sequencing and gene inactivation we elucidated the gene cluster responsible for rhizonin biosynthesis. A suite of isotope labeling experiments identified tyrosine and l-DOPA as Fua precursors and provided the first mechanistic insight. Bioinformatics, mutational analysis and heterologous reconstitution identified dioxygenase RhzB as necessary and sufficient for Fua formation. RhzB is a novel type of heme-dependent aromatic oxygenases (HDAO) that enabled the discovery of the bingchamide biosynthesis gene cluster through genome mining.
    MeSH term(s) Humans ; Peptides, Cyclic/chemistry ; Computational Biology ; Multigene Family ; Fungi/metabolism ; Peptide Synthases/genetics ; Peptide Synthases/metabolism
    Chemical Substances Peptides, Cyclic ; Peptide Synthases (EC 6.3.2.-)
    Language English
    Publishing date 2023-09-13
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202308540
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Reconstitution of Iterative Thioamidation in Closthioamide Biosynthesis Reveals Tailoring Strategy for Nonribosomal Peptide Backbones.

    Dunbar, Kyle L / Dell, Maria / Molloy, Evelyn M / Kloss, Florian / Hertweck, Christian

    Angewandte Chemie (International ed. in English)

    2019  Volume 58, Issue 37, Page(s) 13014–13018

    Abstract: Thioamide-containing nonribosomal peptides (NRPs) are exceedingly rare. Recently the biosynthetic gene cluster for the thioamidated NRP antibiotic closthioamide (CTA) was reported, however, the enzyme responsible for and the timing of thioamide formation ...

    Abstract Thioamide-containing nonribosomal peptides (NRPs) are exceedingly rare. Recently the biosynthetic gene cluster for the thioamidated NRP antibiotic closthioamide (CTA) was reported, however, the enzyme responsible for and the timing of thioamide formation remained enigmatic. Here, genome editing, biochemical assays, and mutational studies are used to demonstrate that an Fe-S cluster containing member of the adenine nucleotide α-hydrolase protein superfamily (CtaC) is responsible for sulfur incorporation during CTA biosynthesis. However, unlike all previously characterized members, CtaC functions in a thiotemplated manner. In addition to prompting a revision of the CTA biosynthetic pathway, the reconstitution of CtaC provides the first example of a NRP thioamide synthetase. Finally, CtaC is used as a bioinformatic handle to demonstrate that thioamidated NRP biosynthetic gene clusters are more widespread than previously appreciated.
    MeSH term(s) Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biosynthetic Pathways ; Clostridiales/chemistry ; Clostridiales/genetics ; Clostridiales/metabolism ; Genes, Bacterial ; Multigene Family ; Peptide Synthases/genetics ; Peptide Synthases/metabolism ; Peptides/chemistry ; Peptides/genetics ; Peptides/metabolism ; Thioamides/chemistry ; Thioamides/metabolism
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Peptides ; Thioamides ; closthioamide ; Peptide Synthases (EC 6.3.2.-)
    Language English
    Publishing date 2019-08-07
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.201905992
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Genome Editing Reveals Novel Thiotemplated Assembly of Polythioamide Antibiotics in Anaerobic Bacteria.

    Dunbar, Kyle L / Büttner, Hannah / Molloy, Evelyn M / Dell, Maria / Kumpfmüller, Jana / Hertweck, Christian

    Angewandte Chemie (International ed. in English)

    2018  Volume 57, Issue 43, Page(s) 14080–14084

    Abstract: Closthioamide (CTA) is a unique symmetric nonribosomal peptide with six thioamide moieties that is produced by the Gram-positive obligate anaerobe Ruminiclostridium cellulolyticum. CTA displays potent inhibitory activity against important clinical ... ...

    Abstract Closthioamide (CTA) is a unique symmetric nonribosomal peptide with six thioamide moieties that is produced by the Gram-positive obligate anaerobe Ruminiclostridium cellulolyticum. CTA displays potent inhibitory activity against important clinical pathogens, making it a promising drug candidate. Yet, the biosynthesis of this DNA gyrase-targeting antibiotic has remained enigmatic. Using a combination of genome mining, genome editing (targeted group II intron, CRISPR/Cas9), and heterologous expression, we show that CTA biosynthesis involves specialized enzymes for starter unit biosynthesis, amide bond formation, thionation, and dimerization. Surprisingly, CTA biosynthesis involves a novel thiotemplated peptide assembly line that markedly differs from known nonribosomal peptide synthetases. These findings provide the first insights into the biosynthesis of thioamide-containing nonribosomal peptides and offer a starting point for the discovery of related natural products.
    MeSH term(s) Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Bacteria, Anaerobic/chemistry ; Bacteria, Anaerobic/genetics ; CRISPR-Cas Systems ; Carbon-13 Magnetic Resonance Spectroscopy ; Chromatography, High Pressure Liquid ; Clostridiales/chemistry ; Clostridiales/genetics ; DNA Gyrase/drug effects ; Gene Editing ; Genes, Bacterial ; Introns ; Mass Spectrometry ; Multigene Family ; Peptide Synthases/chemistry ; Proton Magnetic Resonance Spectroscopy ; Thioamides/chemistry ; Thioamides/pharmacology
    Chemical Substances Anti-Bacterial Agents ; Thioamides ; DNA Gyrase (EC 5.99.1.3) ; Peptide Synthases (EC 6.3.2.-) ; non-ribosomal peptide synthase (EC 6.3.2.-)
    Language English
    Publishing date 2018-10-03
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.201807970
    Database MEDical Literature Analysis and Retrieval System OnLINE

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