1
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Kalkreuter E, Kautsar SA, Yang D, Bader CD, Teijaro CN, Fluegel LL, Davis CM, Simpson JR, Lauterbach L, Steele AD, Gui C, Meng S, Li G, Viehrig K, Ye F, Su P, Kiefer AF, Nichols A, Cepeda AJ, Yan W, Fan B, Jiang Y, Adhikari A, Zheng CJ, Schuster L, Cowan TM, Smanski MJ, Chevrette MG, de Carvalho LPS, Shen B. The Natural Products Discovery Center: Release of the First 8490 Sequenced Strains for Exploring Actinobacteria Biosynthetic Diversity. bioRxiv 2024:2023.12.14.571759. [PMID: 38168313 PMCID: PMC10760148 DOI: 10.1101/2023.12.14.571759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Actinobacteria, the bacterial phylum most renowned for natural product discovery, has been established as a valuable source for drug discovery and biotechnology but is underrepresented within accessible genome and strain collections. Herein, we introduce the Natural Products Discovery Center (NPDC), featuring 122,449 strains assembled over eight decades, the genomes of the first 8490 NPDC strains (7142 Actinobacteria), and the online NPDC Portal making both strains and genomes publicly available. A comparative survey of RefSeq and NPDC Actinobacteria highlights the taxonomic and biosynthetic diversity within the NPDC collection, including three new genera, hundreds of new species, and ~7000 new gene cluster families. Selected examples demonstrate how the NPDC Portal's strain metadata, genomes, and biosynthetic gene clusters can be leveraged using genome mining approaches. Our findings underscore the ongoing significance of Actinobacteria in natural product discovery, and the NPDC serves as an unparalleled resource for both Actinobacteria strains and genomes.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Satria A. Kautsar
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Dong Yang
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Chantal D. Bader
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Christiana N. Teijaro
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Department of Discovery Chemistry, Bristol-Meyers Squibb, Princeton, NJ 08543
| | - Lucas L. Fluegel
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458
| | - Christina M. Davis
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458
| | - Johnathon R. Simpson
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Prepaire Labs, Pompano Beach, FL 33060
| | - Lukas Lauterbach
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Andrew D. Steele
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Chun Gui
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Song Meng
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: State Key Laboratory of Drug Research & Natural Products Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People’s Republic of China, Beijing, China 100049
| | - Gengnan Li
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Centivax Inc., South San Francisco, CA 94080
| | - Konrad Viehrig
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal 4450-208
| | - Fei Ye
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Department of Biological Chemistry & Molecular Pharmacology, Harvard University, Boston, MA 02115
| | - Ping Su
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: State Key Laboratory for Quality Assurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China 100700
| | - Alexander F. Kiefer
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Angela Nichols
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458
| | - Alexis J. Cepeda
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458
| | - Wei Yan
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: College of Plant Protection, Nanjing Agricultural University, Nanjing, China 210095
| | - Boyi Fan
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: School of Pharmacy, Nantong University, Nantong, China 226001
| | - Yanlong Jiang
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Department of Chemistry, Rice University, Houston, TX 77005
| | - Ajeeth Adhikari
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458
- Current address: Evercrisp Biosciences, San Francisco, CA 94109
| | - Cheng-Jian Zheng
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Faculty of Pharmacy, Naval Medical University, Shanghai, China 200433
| | - Layla Schuster
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603
| | - Tyler M. Cowan
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Michael J. Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN 55108
- Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108
| | - Marc G. Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603
- Genetics Institute, University of Florida, Gainesville, FL 32603
| | - Luiz P. S. de Carvalho
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Ben Shen
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458
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2
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Fu C, Liu Y, Walt C, Rasheed S, Bader CD, Lukat P, Neuber M, Haeckl FPJ, Blankenfeldt W, Kalinina OV, Müller R. Elucidation of unusual biosynthesis and DnaN-targeting mode of action of potent anti-tuberculosis antibiotics Mycoplanecins. Nat Commun 2024; 15:791. [PMID: 38278788 PMCID: PMC10817943 DOI: 10.1038/s41467-024-44953-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/08/2024] [Indexed: 01/28/2024] Open
Abstract
DNA polymerase III sliding clamp (DnaN) was recently validated as a new anti-tuberculosis target employing griselimycins. Three (2 S,4 R)-4-methylproline moieties of methylgriselimycin play significant roles in target binding and metabolic stability. Here, we identify the mycoplanecin biosynthetic gene cluster by genome mining using bait genes from the 4-methylproline pathway. We isolate and structurally elucidate four mycoplanecins comprising scarce homo-amino acids and 4-alkylprolines. Evaluating mycoplanecin E against Mycobacterium tuberculosis surprisingly reveals an excitingly low minimum inhibition concentration at 83 ng/mL, thus outcompeting griselimycin by approximately 24-fold. We show that mycoplanecins bind DnaN with nanomolar affinity and provide a co-crystal structure of mycoplanecin A-bound DnaN. Additionally, we reconstitute the biosyntheses of the unusual L-homoleucine, L-homonorleucine, and (2 S,4 R)-4-ethylproline building blocks by characterizing in vitro the full set of eight enzymes involved. The biosynthetic study, bioactivity evaluation, and drug target validation of mycoplanecins pave the way for their further development to tackle multidrug-resistant mycobacterial infections.
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Affiliation(s)
- Chengzhang Fu
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
| | - Yunkun Liu
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Christine Walt
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), 38124, Braunschweig, Germany
| | - Sari Rasheed
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), 38124, Braunschweig, Germany
| | - Chantal D Bader
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), 38124, Braunschweig, Germany
| | - Peer Lukat
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Markus Neuber
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), 38124, Braunschweig, Germany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), 38124, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Olga V Kalinina
- Medical Faculty, Saarland University, 66421, Homburg, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Center for Bioinformatics, Saarland Informatics Campus, 66123, Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany.
- Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany.
- German Centre for Infection Research (DZIF), 38124, Braunschweig, Germany.
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3
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Bader CD, Nichols AL, Yang D, Shen B. Interplay of emerging and established technologies drives innovation in natural product antibiotic discovery. Curr Opin Microbiol 2023; 75:102359. [PMID: 37517368 DOI: 10.1016/j.mib.2023.102359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/04/2023] [Accepted: 06/21/2023] [Indexed: 08/01/2023]
Abstract
A continued rise of antibiotic resistance and shortages of effective antibiotics necessitate the discovery and development of new antibiotics with novel modes of action (MoAs) against resistant pathogens. While natural products remain the best resource for antibiotic discovery, their exploration faces many challenges, including (i) unknown MoAs, (ii) high rediscovery rates, (iii) tedious isolation and structure elucidation, and (iv) insufficient production for further development. We have identified recent innovations in screening methods, microbiology, bioinformatics, and metabolomics technologies, as well as natural product-inspired synthesis and synthetic biology, that have contributed to new natural product antibiotics in the past two years. We highlight their interplay as the key element for successful applications, driving future opportunities to increase the pool of natural product-based antibacterial antibiotics.
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Affiliation(s)
- Chantal D Bader
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, Florida 33458, United States
| | - Angela L Nichols
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, Florida 33458, United States; Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, Florida 33458, United States
| | - Dong Yang
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, Florida 33458, United States; Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, Florida 33458, United States
| | - Ben Shen
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, Florida 33458, United States; Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, Florida 33458, United States; Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, Florida 33458, United States; Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, Florida 33458, United States.
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4
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Abstract
In this study, an unprecedented myxobacterial siderophore termed sorangibactin was discovered by heterologous expression of a coelibactin-like nonribosomal peptide synthetase (NRPS) gene cluster from the Sorangiineae strain MSr11367 in the host Myxococcus xanthus DK1622. De novo structure elucidation uncovered a linear polycyclic structure consisting of an N-terminal phenol group, an oxazole, tandem N-methyl-thiazolidines, and an unusual C-terminal γ-thiolactone moiety. Except for the unprecedented oxazoline dehydrogenation to form an oxazole, which we show to be catalyzed by a cytochrome P450-dependent enzyme, other tailoring steps were found necessary for efficient downstream processing. The unusual thioesterase (TE) domain is proposed to select homocysteine or methionine for offloading involving an intramolecular γ-thiolactone formation. Its active site comprises a rare cysteine, which was found essential for product formation by point mutation to alanine or serine, which both abolished its activity. This unusual release mechanism and the resulting rare thiolactone structure can serve as a starting point for detailed biochemical investigations.
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Affiliation(s)
- Yunsheng Gao
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E8.1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Christine Walt
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Chantal D Bader
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E8.1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
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5
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Seyfert CE, Porten C, Yuan B, Deckarm S, Panter F, Bader CD, Coetzee J, Deschner F, Tehrani KHME, Higgins PG, Seifert H, Marlovits TC, Herrmann J, Müller R. Darobactins Exhibiting Superior Antibiotic Activity by Cryo-EM Structure Guided Biosynthetic Engineering. Angew Chem Int Ed Engl 2023; 62:e202214094. [PMID: 36308277 PMCID: PMC10107326 DOI: 10.1002/anie.202214094] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Indexed: 11/06/2022]
Abstract
Over recent decades, the pipeline of antibiotics acting against Gram-negative bacteria is running dry, as most discovered candidate antibiotics suffer from insufficient potency, pharmacokinetic properties, or toxicity. The darobactins, a promising new small peptide class of drug candidates, bind to novel antibiotic target BamA, an outer membrane protein. Previously, we reported that biosynthetic engineering in a heterologous host generated novel darobactins with enhanced antibacterial activity. Here we utilize an optimized purification method and present cryo-EM structures of the Bam complex with darobactin 9 (D9), which served as a blueprint for the biotechnological generation of twenty new darobactins including halogenated analogs. The newly engineered darobactin 22 binds more tightly to BamA and outperforms the favorable activity profile of D9 against clinically relevant pathogens such as carbapenem-resistant Acinetobacter baumannii up to 32-fold, without observing toxic effects.
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Affiliation(s)
- Carsten E Seyfert
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Christoph Porten
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Biao Yuan
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Notkestraße 85, Building 15, 22607, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Selina Deckarm
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Fabian Panter
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Chantal D Bader
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Janetta Coetzee
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Felix Deschner
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Kamaleddin H M E Tehrani
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Paul G Higgins
- Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, Germany
| | - Harald Seifert
- Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, Germany
| | - Thomas C Marlovits
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Notkestraße 85, Building 15, 22607, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Jennifer Herrmann
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Rolf Müller
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
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6
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Haack PA, Harmrolfs K, Bader CD, Garcia R, Gunesch AP, Haid S, Popoff A, Voltz A, Kim H, Bartenschlager R, Pietschmann T, Müller R. Thiamyxins: Structure and Biosynthesis of Myxobacterial RNA-Virus Inhibitors. Angew Chem Int Ed Engl 2022; 61:e202212946. [PMID: 36208117 PMCID: PMC10100342 DOI: 10.1002/anie.202212946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Indexed: 11/07/2022]
Abstract
During our search for novel myxobacterial natural products, we discovered the thiamyxins: thiazole- and thiazoline-rich non-ribosomal peptide-polyketide hybrids with potent antiviral activity. We isolated four congeners of this unprecedented natural product family with the non-cyclized thiamyxin D fused to a glycerol unit at the C-terminus. Alongside their structure elucidation, we present a concise biosynthesis model based on biosynthetic gene cluster analysis and isotopically labelled precursor feeding. We report incorporation of a 2-(hydroxymethyl)-4-methylpent-3-enoic acid moiety by a GCN5-related N-acetyltransferase-like decarboxylase domain featuring polyketide synthase. The thiamyxins show potent inhibition of RNA viruses in cell culture models of corona, zika and dengue virus infection. Their potency up to a half maximal inhibitory concentration of 560 nM combined with milder cytotoxic effects on human cell lines indicate the potential for further development of the thiamyxins.
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Affiliation(s)
- Patrick A Haack
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
| | - Kirsten Harmrolfs
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
| | - Chantal D Bader
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
| | - Ronald Garcia
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
| | - Antonia P Gunesch
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany.,German Center for Infection Research, Hannover-Braunschweig Partner Site, and Cluster of Excellence RESIST (EXC 2155), Hannover, Germany
| | - Sibylle Haid
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany.,German Center for Infection Research, Hannover-Braunschweig Partner Site, and Cluster of Excellence RESIST (EXC 2155), Hannover, Germany
| | - Alexander Popoff
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
| | - Alexander Voltz
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
| | - Heeyoung Kim
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, German Center for Infection Research, Heidelberg Partner Site and Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, German Center for Infection Research, Heidelberg Partner Site and Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Thomas Pietschmann
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany.,German Center for Infection Research, Hannover-Braunschweig Partner Site, and Cluster of Excellence RESIST (EXC 2155), Hannover, Germany
| | - Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
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7
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Seyfert CE, Porten C, Yuan B, Deckarmb S, Panter F, Bader CD, Coetzee J, Deschner F, Tehrani KHME, Higgins PG, Seifert H, Marlovits T, Herrmann J, Müller R. Darobactins Exhibiting Superior Antibiotic Activity by Cryo‐EM Structure Guided Biosynthetic Engineering. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202217800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Carsten E. Seyfert
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Christoph Porten
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Biao Yuan
- University Medical Center Hamburg-Eppendorf (UKE) Institute of Structural and Systems Biology Notkestraße 85, Building 15 22607 Hamburg Germany
- Centre for Structural Systems Biology (CSSB) Hamburg Germany
| | - Selina Deckarmb
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Fabian Panter
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Chantal D. Bader
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Janetta Coetzee
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Felix Deschner
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Kamaleddin H. M. E. Tehrani
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Paul G. Higgins
- Microbiology, Immunology and Hygiene Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne Germany
| | - Harald Seifert
- Microbiology, Immunology and Hygiene Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne Germany
| | - Thomas Marlovits
- University Medical Center Hamburg-Eppendorf (UKE) Institute of Structural and Systems Biology Notkestraße 85, Building 15 22607 Hamburg Germany
- Centre for Structural Systems Biology (CSSB) Hamburg Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY) Hamburg Germany
| | - Jennifer Herrmann
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Rolf Müller
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
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8
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Seyfert CE, Porten C, Yuan B, Deckarmb S, Panter F, Bader CD, Coetzee J, Deschner F, Tehrani KHME, Higgins PG, Seifert H, Marlovits T, Herrmann J, Müller R. Darobactins Exhibiting Superior Antibiotic Activity by Cryo‐EM Structure Guided Biosynthetic Engineering. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/anie.202217800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Carsten E. Seyfert
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Christoph Porten
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Biao Yuan
- University Medical Center Hamburg-Eppendorf (UKE) Institute of Structural and Systems Biology Notkestraße 85, Building 15 22607 Hamburg Germany
- Centre for Structural Systems Biology (CSSB) Hamburg Germany
| | - Selina Deckarmb
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Fabian Panter
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Chantal D. Bader
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Janetta Coetzee
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Felix Deschner
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Kamaleddin H. M. E. Tehrani
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Paul G. Higgins
- Microbiology, Immunology and Hygiene Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne Germany
| | - Harald Seifert
- Microbiology, Immunology and Hygiene Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne Germany
| | - Thomas Marlovits
- University Medical Center Hamburg-Eppendorf (UKE) Institute of Structural and Systems Biology Notkestraße 85, Building 15 22607 Hamburg Germany
- Centre for Structural Systems Biology (CSSB) Hamburg Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY) Hamburg Germany
| | - Jennifer Herrmann
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
| | - Rolf Müller
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Department of Pharmacy at Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany)
- German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig Germany
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9
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Forcisi S, Moritz F, Thompson CJ, Kanawati B, Uhl J, Afonso C, Bader CD, Barsch A, Boughton BA, Chu RK, Ferey J, Fernandez-Lima F, Guéguen C, Heintz D, Gomez-Hernandez M, Jang KS, Kessler N, Mangal V, Müller R, Nakabayashi R, Nicol E, Nicolardi S, Palmblad M, Paša-Tolić L, Porter J, Schmitz-Afonso I, Seo JB, Sommella E, van der Burgt YEM, Villette C, Witt M, Wittrig A, Wolff JJ, Easterling ML, Laukien FH, Schmitt-Kopplin P. Large-Scale Interlaboratory DI-FT-ICR MS Comparability Study Employing Various Systems. J Am Soc Mass Spectrom 2022; 33:2203-2214. [PMID: 36371691 PMCID: PMC9732881 DOI: 10.1021/jasms.2c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ultrahigh resolution mass spectrometry (UHR-MS) coupled with direct infusion (DI) electrospray ionization offers a fast solution for accurate untargeted profiling. Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers have been shown to produce a wealth of insights into complex chemical systems because they enable unambiguous molecular formula assignment even if the vast majority of signals is of unknown identity. Interlaboratory comparisons are required to apply this type of instrumentation in quality control (for food industry or pharmaceuticals), large-scale environmental studies, or clinical diagnostics. Extended comparisons employing different FT-ICR MS instruments with qualitative direct infusion analysis are scarce since the majority of detected compounds cannot be quantified. The extent to which observations can be reproduced by different laboratories remains unknown. We set up a preliminary study which encompassed a set of 17 laboratories around the globe, diverse in instrumental characteristics and applications, to analyze the same sets of extracts from commercially available standard human blood plasma and Standard Reference Material (SRM) for blood plasma (SRM1950), which were delivered at different dilutions or spiked with different concentrations of pesticides. The aim of this study was to assess the extent to which the outputs of differently tuned FT-ICR mass spectrometers, with different technical specifications, are comparable for setting the frames of a future DI-FT-ICR MS ring trial. We concluded that a cluster of five laboratories, with diverse instrumental characteristics, showed comparable and representative performance across all experiments, setting a reference to be used in a future ring trial on blood plasma.
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Affiliation(s)
- Sara Forcisi
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Franco Moritz
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | | | - Basem Kanawati
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jenny Uhl
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Carlos Afonso
- COBRA, UMR 6014 et FR 3038, INSA de Rouen, CNRS, IRCOF, Normandie Université, Université de Rouen, 76130 Cedex Mont Saint Aignan, France
| | - Chantal D Bader
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123 Saarbrücken, Germany and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Aiko Barsch
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Berin A Boughton
- Metabolomics Australia, School of BioSciences, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Justine Ferey
- COBRA, UMR 6014 et FR 3038, INSA de Rouen, CNRS, IRCOF, Normandie Université, Université de Rouen, 76130 Cedex Mont Saint Aignan, France
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, AHC4-233, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, 11200 Eighth Street, AHC4-211, Miami, Florida 33199, United States
| | - Céline Guéguen
- Chemistry Department, Trent University, 1600 West Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - Dimitri Heintz
- Plant Imaging and Mass Spectrometry (PIMS), Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Mario Gomez-Hernandez
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, AHC4-233, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, 11200 Eighth Street, AHC4-211, Miami, Florida 33199, United States
| | - Kyoung-Soon Jang
- Bio-Chemical Analysis Team, Korea Basic Science Institute, Cheongju 28119, South Korea
| | - Nikolas Kessler
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Vaughn Mangal
- Chemistry Department, Trent University, 1600 West Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123 Saarbrücken, Germany and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Ryo Nakabayashi
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Edith Nicol
- Laboratoire de Chimie Moléculaire (LCM), CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center Leiden, 2333 ZC Leiden, The Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center Leiden, 2333 ZC Leiden, The Netherlands
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jacob Porter
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, AHC4-233, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, 11200 Eighth Street, AHC4-211, Miami, Florida 33199, United States
| | - Isabelle Schmitz-Afonso
- COBRA, UMR 6014 et FR 3038, INSA de Rouen, CNRS, IRCOF, Normandie Université, Université de Rouen, 76130 Cedex Mont Saint Aignan, France
| | - Jong Bok Seo
- Seoul Center, Korea Basic Science Institute, 145, Anam-Ro, Seongbuk-Gu 02841, Seoul, South Korea
| | - Eduardo Sommella
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano (SA), Italy
| | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center Leiden, 2333 ZC Leiden, The Netherlands
| | - Claire Villette
- Plant Imaging and Mass Spectrometry (PIMS), Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Matthias Witt
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Ashley Wittrig
- ExxonMobil Research and Engineering Company, 1545 Route 22 East, Clinton, New Jersey 08869, United States
| | - Jeremy J Wolff
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | | | - Frank H Laukien
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
- Department of Chemistry & Chemical Biology, Cambridge, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Analytical Food Chemistry, Technical University of Munich, 85354 Freising, Germany
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10
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Fathalla RK, Fröhner W, Bader CD, Fischer PD, Dahlem C, Chatterjee D, Mathea S, Kiemer AK, Arthanari H, Müller R, Abdel-Halim M, Ducho C, Engel M. Identification and Biochemical Characterization of Pyrrolidinediones as Novel Inhibitors of the Bacterial Enzyme MurA. J Med Chem 2022; 65:14740-14763. [PMID: 36269107 PMCID: PMC9989942 DOI: 10.1021/acs.jmedchem.2c01275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To develop novel antibiotics, targeting the early steps of cell wall peptidoglycan biosynthesis seems to be a promising strategy that is still underutilized. MurA, the first enzyme in this pathway, is targeted by the clinically used irreversible inhibitor fosfomycin. However, mutations in its binding site can cause bacterial resistance. We herein report a series of novel reversible pyrrolidinedione-based MurA inhibitors that equally inhibit wild type (WT) MurA and the fosfomycin-resistant MurA C115D mutant, showing an additive effect with fosfomycin for the inhibition of WT MurA. For the most potent inhibitor 46 (IC50 = 4.5 μM), the mode of inhibition was analyzed using native mass spectrometry and protein NMR spectroscopy. The compound class was nontoxic against human cells and highly stable in human S9 fraction, human plasma, and bacterial cell lysate. Taken together, this novel compound class might be further developed toward antibiotic drug candidates that inhibit cell wall synthesis.
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Affiliation(s)
- Reem K. Fathalla
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Wolfgang Fröhner
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Chantal D. Bader
- 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), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Patrick D. Fischer
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
- Department of Cancer Biology, Dana-Farber Cancer Institute, 02215, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 02115, Boston, MA, USA
| | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Deep Chatterjee
- Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Sebastian Mathea
- Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Alexandra K. Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, 02215, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 02115, Boston, MA, USA
| | - Rolf Müller
- 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), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Helmholtz International Lab for Antiinfectives, Campus E8 1, 66123 Saarbrücken, Germany
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Matthias Engel
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
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11
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Haack PA, Harmrolfs K, Bader CD, Garcia R, Gunesch AP, Haid S, Popoff A, Voltz A, Kim H, Bartenschlager R, Pietschmann T, Müller R. Thiamyxins: Structure and Biosynthesis of Myxobacterial RNA‐Virus Inhibitors. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202212946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Patrick A. Haack
- Helmholtz-Institut fur Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Kirsten Harmrolfs
- Helmholtz-Institut fur Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Chantal D. Bader
- Helmholtz-Institut fur Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Ronald Garcia
- Helmholtz-Institut fur Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Antonia P. Gunesch
- TWINCORE Center of Experimental and Clinical Infection Research: TWINCORE Zentrum fur Experimentelle und Klinische Infektionsforschung GmbH Experimental Virology GERMANY
| | - Sibylle Haid
- TWINCORE Center of Experimental and Clinical Infection Research: TWINCORE Zentrum fur Experimentelle und Klinische Infektionsforschung GmbH Experimental Virology GERMANY
| | - Alexander Popoff
- Helmholtz-Institut fur Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Alexander Voltz
- Helmholtz-Institut fur Pharmazeutische Forschung Saarland Microbial Natural Products GERMANY
| | - Heeyoung Kim
- Heidelberg University Molecular Virology GERMANY
| | | | - Thomas Pietschmann
- TWINCORE Center of Experimental and Clinical Infection Research: TWINCORE Zentrum fur Experimentelle und Klinische Infektionsforschung GmbH Experimental Virology GERMANY
| | - Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland Microbial Natural Products Campus Building E8.1 66123 Saarbrücken GERMANY
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12
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Bader CD, Panter F, Garcia R, Tchesnokov EP, Haid S, Walt C, Spröer C, Kiefer AF, Götte M, Overmann J, Pietschmann T, Müller R. Sandacrabins - Structurally Unique Antiviral RNA Polymerase Inhibitors from a Rare Myxobacterium. Chemistry 2022; 28:e202104484. [PMID: 34990513 PMCID: PMC9306752 DOI: 10.1002/chem.202104484] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Indexed: 12/13/2022]
Abstract
Structure elucidation and total synthesis of five unprecedented terpenoid‐alkaloids, the sandacrabins, are reported, alongside with the first description of their producing organism Sandaracinus defensii MSr10575, which expands the Sandaracineae family by only its second member. The genome sequence of S. defensii as presented in this study was utilized to identify enzymes responsible for sandacrabin formation, whereby dimethylbenzimidazol, deriving from cobalamin biosynthesis, was identified as key intermediate. Biological activity profiling revealed that all sandacrabins except congener A exhibit potent antiviral activity against the human pathogenic coronavirus HCoV229E in the three digit nanomolar range. Investigation of the underlying mode of action discloses that the sandacrabins inhibit the SARS‐CoV‐2 RNA‐dependent RNA polymerase complex, highlighting them as structurally distinct non‐nucleoside RNA synthesis inhibitors. The observed segregation between cell toxicity at higher concentrations and viral inhibition opens the possibility for their medicinal chemistry optimization towards selective inhibitors.
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Affiliation(s)
- Chantal D Bader
- 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), Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Fabian Panter
- 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), Inhoffenstraße 7, 38124, Braunschweig, Germany.,Helmholtz International Lab for anti-infectives, Campus E8 1, 66123, Saarbrücken, Germany
| | - Ronald Garcia
- 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), Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Sibylle Haid
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research a joint venture between the Medical School Hannover (MHH) and, The Helmholtz Centre for Infection Research (HZI), Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Christine Walt
- 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), Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7 and German Centre of Infection Research (DZIF) Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany.,Microbiology, Technical University of Braunschweig, 38106, Braunschweig, Germany
| | - Alexander F Kiefer
- 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), Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Jörg Overmann
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7 and German Centre of Infection Research (DZIF) Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany.,Microbiology, Technical University of Braunschweig, 38106, Braunschweig, Germany
| | - Thomas Pietschmann
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research a joint venture between the Medical School Hannover (MHH) and, The Helmholtz Centre for Infection Research (HZI), Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Rolf Müller
- 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), Inhoffenstraße 7, 38124, Braunschweig, Germany.,Helmholtz International Lab for anti-infectives, Campus E8 1, 66123, Saarbrücken, Germany
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13
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Groß S, Panter F, Pogorevc D, Seyfert CE, Deckarm S, Bader CD, Herrmann J, Müller R. Improved broad-spectrum antibiotics against Gram-negative pathogens via darobactin biosynthetic pathway engineering. Chem Sci 2021; 12:11882-11893. [PMID: 34659729 PMCID: PMC8442675 DOI: 10.1039/d1sc02725e] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/30/2021] [Indexed: 12/25/2022] Open
Abstract
The development of new antibiotics is imperative to fight increasing mortality rates connected to infections caused by multidrug-resistant (MDR) bacteria. In this context, Gram-negative pathogens listed in the WHO priority list are particularly problematic. Darobactin is a ribosomally produced and post-translationally modified bicyclic heptapeptide antibiotic selectively killing Gram-negative bacteria by targeting the outer membrane protein BamA. The native darobactin A producer Photorhabdus khanii HGB1456 shows very limited production under laboratory cultivation conditions. Herein, we present the design and heterologous expression of a synthetically engineered darobactin biosynthetic gene cluster (BGC) in Escherichia coli to reach an average darobactin A production titre of 13.4 mg L-1. Rational design of darA variants, encoding the darobactin precursor peptide with altered core sequences, resulted in the production of 13 new 'non-natural' darobactin derivatives and 4 previously hypothetical natural darobactins. One of the non-natural compounds, darobactin 9, was more potent than darobactin A, and showed significantly improved activity especially against Pseudomonas aeruginosa (0.125 μg mL-1) and Acinetobacter baumannii (1-2 μg mL-1). Importantly, it also displayed superior activity against MDR clinical isolates of E. coli (1-2 μg mL-1) and Klebsiella pneumoniae (1-4 μg mL-1). Independent deletions of genes from the darobactin BGC showed that only darA and darE, encoding a radical forming S-adenosyl-l-methionine-dependent enzyme, are required for darobactin formation. Co-expression of two additional genes associated with the BGCs in hypothetical producer strains identified a proteolytic detoxification mechanism as a potential self-resistance strategy in native producers. Taken together, we describe a versatile heterologous darobactin platform allowing the production of unprecedented active derivatives in good yields, and we provide first experimental evidence for darobactin biosynthesis processes.
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Affiliation(s)
- Sebastian Groß
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus 66123 Saarbrücken Germany .,Department of Pharmacy, Saarland University 66123 Saarbrücken Germany.,DZIF - German Centre for Infection Research, Partner site Hannover-Braunschweig Germany
| | - Fabian Panter
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus 66123 Saarbrücken Germany .,Department of Pharmacy, Saarland University 66123 Saarbrücken Germany.,DZIF - German Centre for Infection Research, Partner site Hannover-Braunschweig Germany.,Helmholtz International Lab for Anti-Infectives Campus E8 1 66123 Saarbrücken Germany
| | - Domen Pogorevc
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus 66123 Saarbrücken Germany .,Department of Pharmacy, Saarland University 66123 Saarbrücken Germany.,DZIF - German Centre for Infection Research, Partner site Hannover-Braunschweig Germany
| | - Carsten E Seyfert
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus 66123 Saarbrücken Germany .,Department of Pharmacy, Saarland University 66123 Saarbrücken Germany.,DZIF - German Centre for Infection Research, Partner site Hannover-Braunschweig Germany
| | - Selina Deckarm
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus 66123 Saarbrücken Germany .,Department of Pharmacy, Saarland University 66123 Saarbrücken Germany.,DZIF - German Centre for Infection Research, Partner site Hannover-Braunschweig Germany
| | - Chantal D Bader
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus 66123 Saarbrücken Germany .,Department of Pharmacy, Saarland University 66123 Saarbrücken Germany.,DZIF - German Centre for Infection Research, Partner site Hannover-Braunschweig Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus 66123 Saarbrücken Germany .,Department of Pharmacy, Saarland University 66123 Saarbrücken Germany.,DZIF - German Centre for Infection Research, Partner site Hannover-Braunschweig Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus 66123 Saarbrücken Germany .,Department of Pharmacy, Saarland University 66123 Saarbrücken Germany.,DZIF - German Centre for Infection Research, Partner site Hannover-Braunschweig Germany.,Helmholtz International Lab for Anti-Infectives Campus E8 1 66123 Saarbrücken Germany
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14
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Ropponen HK, Bader CD, Diamanti E, Illarionov B, Rottmann M, Fischer M, Witschel M, Müller R, Hirsch AKH. Search for the Active Ingredients from a 2-Aminothiazole DMSO Stock Solution with Antimalarial Activity. ChemMedChem 2021; 16:2089-2093. [PMID: 33844432 PMCID: PMC8360061 DOI: 10.1002/cmdc.202100067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/17/2021] [Indexed: 12/31/2022]
Abstract
Chemical decomposition of DMSO stock solutions is a common incident that can mislead biological screening campaigns. Here, we share our case study of 2‐aminothiazole 1, originating from an antimalarial class that undergoes chemical decomposition in DMSO at room temperature. As previously measured biological activities observed against Plasmodium falciparum NF54 and for the target enzyme PfIspE were not reproducible for a fresh batch, we tackled the challenge to understand where the activity originated from. Solvent‐ and temperature‐dependent studies using HRMS and NMR spectroscopy to monitor the decomposition led to the isolation and in vitro evaluation of several fractions against PfIspE. After four days of decomposition, we successfully isolated the oxygenated and dimerised compounds using SFC purification and correlated the observed activities to them. Due to the unstable nature of the two isolates, it is likely that they undergo further decomposition contributing to the overall instability of the compound.
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Affiliation(s)
- Henni-Karoliina Ropponen
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz-Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Chantal D Bader
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz-Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Eleonora Diamanti
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz-Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.,Helmholtz International Lab for Anti-Infectives, Campus E8.1, 66123, Saarbrücken, Germany
| | - Boris Illarionov
- Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Matthias Rottmann
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland.,Universität Basel, Petersplatz 1, 4003, Basel, Switzerland
| | - Markus Fischer
- Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | | | - Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz-Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.,Helmholtz International Lab for Anti-Infectives, Campus E8.1, 66123, Saarbrücken, Germany
| | - Anna K H Hirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz-Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.,Helmholtz International Lab for Anti-Infectives, Campus E8.1, 66123, Saarbrücken, Germany
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15
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Panter F, Bader CD, Müller R. The Sandarazols are Cryptic and Structurally Unique Plasmid-Encoded Toxins from a Rare Myxobacterium*. Angew Chem Int Ed Engl 2021; 60:8081-8088. [PMID: 33534143 PMCID: PMC8048970 DOI: 10.1002/anie.202014671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/12/2021] [Indexed: 11/20/2022]
Abstract
Herein, we describe a new plasmid found in Sandaracinus sp. MSr10575 named pSa001 spanning 209.7 kbp that harbors a cryptic secondary metabolite biosynthesis gene cluster (BGC). Activation of this BGC by homologous-recombination-mediated exchange of the native promoter sequence against a vanillate inducible system led to the production and subsequent isolation and structure elucidation of novel secondary metabolites, the sandarazols A-G. The sandarazols contain intriguing structural features and very reactive functional groups such as an α-chlorinated ketone, an epoxyketone, and a (2R)-2-amino-3-(N,N-dimethylamino)-propionic acid building block. In-depth investigation of the underlying biosynthetic machinery led to a concise biosynthetic model for the new compound family, including several uncommon biosynthetic steps. The chlorinated congener sandarazol C shows an IC50 value of 0.5 μm against HCT 116 cells and a MIC of 14 μm against Mycobacterium smegmatis, which points at the sandarazols' potential function as defensive secondary metabolites or toxins.
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Affiliation(s)
- Fabian Panter
- Department of Microbial Natural ProductsHelmholtz-Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University, Campus E8 166123SaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner SiteHannover-BraunschweigGermany
- Helmholtz International Lab for Anti-Infectives, Campus E8 166123SaarbrückenGermany
| | - Chantal D. Bader
- Department of Microbial Natural ProductsHelmholtz-Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University, Campus E8 166123SaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner SiteHannover-BraunschweigGermany
| | - Rolf Müller
- Department of Microbial Natural ProductsHelmholtz-Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University, Campus E8 166123SaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner SiteHannover-BraunschweigGermany
- Helmholtz International Lab for Anti-Infectives, Campus E8 166123SaarbrückenGermany
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16
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Panter F, Bader CD, Müller R. Die Sandarazole sind kryptische und strukturell einzigartige, Plasmid‐codierte Toxine aus einem seltenen Myxobakterium**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fabian Panter
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Zentrum für Infektionsforschung (HZI) und Fachbereich Pharmazie Universität des Saarlandes, Campus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hannover-Braunschweig Deutschland
- Helmholtz International Lab for Anti-Infectives, Campus E8 1 66123 Saarbrücken Deutschland
| | - Chantal D. Bader
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Zentrum für Infektionsforschung (HZI) und Fachbereich Pharmazie Universität des Saarlandes, Campus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hannover-Braunschweig Deutschland
| | - Rolf Müller
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Zentrum für Infektionsforschung (HZI) und Fachbereich Pharmazie Universität des Saarlandes, Campus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hannover-Braunschweig Deutschland
- Helmholtz International Lab for Anti-Infectives, Campus E8 1 66123 Saarbrücken Deutschland
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17
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Panter F, Bader CD, Müller R. Synergizing the potential of bacterial genomics and metabolomics to find novel antibiotics. Chem Sci 2021; 12:5994-6010. [PMID: 33995996 PMCID: PMC8098685 DOI: 10.1039/d0sc06919a] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic development based on natural products has faced a long lasting decline since the 1970s, while both the speed and the extent of antimicrobial resistance (AMR) development have been severely underestimated. The discovery of antimicrobial natural products of bacterial and fungal origin featuring new chemistry and previously unknown mode of actions is increasingly challenged by rediscovery issues. Natural products that are abundantly produced by the corresponding wild type organisms often featuring strong UV signals have been extensively characterized, especially the ones produced by extensively screened microbial genera such as streptomycetes. Purely synthetic chemistry approaches aiming to replace the declining supply from natural products as starting materials to develop novel antibiotics largely failed to provide significant numbers of antibiotic drug leads. To cope with this fundamental issue, microbial natural products science is being transformed from a 'grind-and-find' study to an integrated approach based on bacterial genomics and metabolomics. Novel technologies in instrumental analytics are increasingly employed to lower detection limits and expand the space of detectable substance classes, while broadening the scope of accessible and potentially bioactive natural products. Furthermore, the almost exponential increase in publicly available bacterial genome data has shown that the biosynthetic potential of the investigated strains by far exceeds the amount of detected metabolites. This can be judged by the discrepancy between the number of biosynthetic gene clusters (BGC) encoded in the genome of each microbial strain and the number of secondary metabolites actually detected, even when considering the increased sensitivity provided by novel analytical instrumentation. In silico annotation tools for biosynthetic gene cluster classification and analysis allow fast prioritization in BGC-to-compound workflows, which is highly important to be able to process the enormous underlying data volumes. BGC prioritization is currently accompanied by novel molecular biology-based approaches to access the so-called orphan BGCs not yet correlated with a secondary metabolite. Integration of metabolomics, in silico genomics and molecular biology approaches into the mainstream of natural product research will critically influence future success and impact the natural product field in pharmaceutical, nutritional and agrochemical applications and especially in anti-infective research.
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Affiliation(s)
- Fabian Panter
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
| | - Chantal D Bader
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
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18
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Bader CD, Haack PA, Panter F, Krug D, Müller R. Expanding the Scope of Detectable Microbial Natural Products by Complementary Analytical Methods and Cultivation Systems. J Nat Prod 2021; 84:268-277. [PMID: 33449690 DOI: 10.1021/acs.jnatprod.0c00942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recent advances in genome sequencing have unveiled a large discrepancy between the genome-encoded capacity of microorganisms to produce secondary metabolites and the number detected. In this work, a two-platform mass spectrometry analysis for the comprehensive secondary metabolomics characterization of nine myxobacterial strains, focusing on extending the range of detectable secondary metabolites by diversifying analytical methods and cultivation conditions, is presented. Direct infusion measurements of crude extracts on a Fourier transform ion cyclotron resonance mass spectrometer are compared to a time-of-flight device coupled to liquid chromatography measurements. Both methods are successful in detecting known metabolites, whereas statistical analysis of unknowns highlights their complementarity: Strikingly, 82-99% of molecular features detected with one setup were not detectable with the other. Metabolite profile differences from our set of strains grown in liquid culture versus their swarming colonies on agar plates were evaluated. The detection of up to 96% more molecular features when both liquid and plate cultures were analyzed translates into increased chances to identify new secondary metabolites. Discrimination between primary and secondary metabolism in combination with GNPS molecular networking revealed strain Mx3 as particularly promising for the isolation of novel secondary metabolites among the nine strains investigated in this study.
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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), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Patrick A Haack
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Fabian Panter
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Daniel Krug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
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19
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Bader CD, Neuber M, Panter F, Krug D, Müller R. Supercritical Fluid Extraction Enhances Discovery of Secondary Metabolites from Myxobacteria. Anal Chem 2020; 92:15403-15411. [DOI: 10.1021/acs.analchem.0c02995] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Chantal D. Bader
- Department Microbial Natural Products, Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig) and Department of Pharmacy, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus E8.1, 66123 Saarbrücken, Germany
| | - Markus Neuber
- Department Microbial Natural Products, Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig) and Department of Pharmacy, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus E8.1, 66123 Saarbrücken, Germany
| | - Fabian Panter
- Department Microbial Natural Products, Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig) and Department of Pharmacy, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus E8.1, 66123 Saarbrücken, Germany
| | - Daniel Krug
- Department Microbial Natural Products, Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig) and Department of Pharmacy, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig) and Department of Pharmacy, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus E8.1, 66123 Saarbrücken, Germany
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20
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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: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Kiefer A, Bader CD, Held J, Esser A, Rybniker J, Empting M, Müller R, Kazmaier U. Synthesis of New Cyclomarin Derivatives and Their Biological Evaluation towards
Mycobacterium Tuberculosis
and
Plasmodium Falciparum. Chemistry 2019; 25:8894-8902. [DOI: 10.1002/chem.201901640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Alexander Kiefer
- Organic ChemistrySaarland University Campus C4.2 66123 Saarbrücken Germany
| | - Chantal D. Bader
- Department Microbial Natural Products (MINS)Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)–Helmholtz Centre for Infection Research (HZI) Campus E8.1 66123 Saarbrücken Germany
| | - Jana Held
- Department of Tropical MedicineUniversity of Tübingen Wilhelmstraße 27 72074 Tübingen Germany
| | - Anna Esser
- Center for Molecular Medicine CologneUniversity of Cologne Robert Koch Str. 21 50931 Cologne Germany
| | - Jan Rybniker
- Department I of Internal MedicineUniversity of Cologne 50937 Cologne (Germany) and German Center for Infection Research (DZIF), Partner Site Bonn-Cologne Germany
| | - Martin Empting
- Department of Drug Design and Optimization (DDOP)Helmholtz-Institute for Pharmaceutical Research Saarland, (HIPS)–Helmholtz Centre for Infection Research (HZI) Campus E8.1 66123 Saarbrücken Germany
| | - Rolf Müller
- Department Microbial Natural Products (MINS)Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)–Helmholtz Centre for Infection Research (HZI) Campus E8.1 66123 Saarbrücken Germany
- Department of PharmacySaarland University Campus E8.1 66123 Saarbrücken Germany
| | - Uli Kazmaier
- Organic ChemistrySaarland University Campus C4.2 66123 Saarbrücken Germany
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Hug JJ, Bader CD, Remškar M, Cirnski K, Müller R. Concepts and Methods to Access Novel Antibiotics from Actinomycetes. Antibiotics (Basel) 2018; 7:E44. [PMID: 29789481 PMCID: PMC6022970 DOI: 10.3390/antibiotics7020044] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/25/2022] Open
Abstract
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.
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Affiliation(s)
- Joachim J Hug
- 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, 38124 Braunschweig, Germany.
| | - 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, 38124 Braunschweig, Germany.
| | - Maja Remškar
- 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, 38124 Braunschweig, Germany.
| | - Katarina Cirnski
- 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, 38124 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, 38124 Braunschweig, Germany.
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