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Maares M, Haupt A, Schüßler C, Kulike-Koczula M, Hackler J, Keil C, Mohr I, Schomburg L, Süssmuth RD, Zischka H, Merle U, Haase H. Author Correction: A fluorometric assay to determine labile copper(II) ions in serum. Sci Rep 2024; 14:8859. [PMID: 38632369 PMCID: PMC11023943 DOI: 10.1038/s41598-024-59455-z] [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: 04/19/2024] Open
Affiliation(s)
- Maria Maares
- Department of Food Chemistry and Toxicology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
| | - Alessia Haupt
- Department of Food Chemistry and Toxicology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Christoph Schüßler
- Department of Food Chemistry and Toxicology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
| | - Marcel Kulike-Koczula
- Department of Organic and Biological Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Julian Hackler
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
- Institute for Experimental Endocrinology, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Claudia Keil
- Department of Food Chemistry and Toxicology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Isabelle Mohr
- Department of Internal Medicine IV, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Lutz Schomburg
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
- Institute for Experimental Endocrinology, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Roderich D Süssmuth
- Department of Organic and Biological Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Hans Zischka
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
- School of Medicine, Institute of Toxicology and Environmental Hygiene, Technical University Munich, Biedersteiner Strasse 29, 80802, Munich, Germany
| | - Uta Merle
- Department of Internal Medicine IV, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Hajo Haase
- Department of Food Chemistry and Toxicology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.
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Maares M, Haupt A, Schüßler C, Kulike-Koczula M, Hackler J, Keil C, Mohr I, Schomburg L, Süssmuth RD, Zischka H, Merle U, Haase H. A fluorometric assay to determine labile copper(II) ions in serum. Sci Rep 2023; 13:12807. [PMID: 37550465 PMCID: PMC10406877 DOI: 10.1038/s41598-023-39841-9] [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: 04/19/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023] Open
Abstract
Labile copper(II) ions (Cu2+) in serum are considered to be readily available for cellular uptake and to constitute the biologically active Cu2+ species in the blood. It might also be suitable to reflect copper dyshomeostasis during diseases such as Wilson's disease (WD) or neurological disorders. So far, no direct quantification method has been described to determine this small Cu2+ subset. This study introduces a fluorometric high throughput assay using the novel Cu2+ binding fluoresceine-peptide sensor FP4 (Kd of the Cu2+-FP4-complex 0.38 pM) to determine labile Cu2+ in human and rat serum. Using 96 human serum samples, labile Cu2+was measured to be 0.14 ± 0.05 pM, showing no correlation with age or other serum trace elements. No sex-specific differences in labile Cu2+ concentrations were noted, in contrast to the total copper levels in serum. Analysis of the effect of drug therapy on labile Cu2+ in the sera of 19 patients with WD showed a significant decrease in labile Cu2+ following copper chelation therapy, suggesting that labile Cu2+ may be a specific marker of disease status and that the assay could be suitable for monitoring treatment progress.
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Affiliation(s)
- Maria Maares
- Department of Food Chemistry and Toxicology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
| | - Alessia Haupt
- Department of Food Chemistry and Toxicology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Christoph Schüßler
- Department of Food Chemistry and Toxicology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
| | - Marcel Kulike-Koczula
- Department of Organic and Biological Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Julian Hackler
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
- Institute for Experimental Endocrinology, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Claudia Keil
- Department of Food Chemistry and Toxicology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Isabelle Mohr
- Department of Internal Medicine IV, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Lutz Schomburg
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
- Institute for Experimental Endocrinology, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Roderich D Süssmuth
- Department of Organic and Biological Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Hans Zischka
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
- School of Medicine, Institute of Toxicology and Environmental Hygiene, Technical University Munich, Biedersteiner Strasse 29, 80802, Munich, Germany
| | - Uta Merle
- Department of Internal Medicine IV, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Hajo Haase
- Department of Food Chemistry and Toxicology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.
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3
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Saathoff M, Kosol S, Semmler T, Tedin K, Dimos N, Kupke J, Seidel M, Ghazisaeedi F, Jonske MC, Wolf SA, Kuropka B, Czyszczoń W, Ghilarov D, Grätz S, Heddle JG, Loll B, Süssmuth RD, Fulde M. Gene amplifications cause high-level resistance against albicidin in gram-negative bacteria. PLoS Biol 2023; 21:e3002186. [PMID: 37561817 PMCID: PMC10414762 DOI: 10.1371/journal.pbio.3002186] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Received: 10/04/2022] [Accepted: 06/07/2023] [Indexed: 08/12/2023] Open
Abstract
Antibiotic resistance is a continuously increasing concern for public healthcare. Understanding resistance mechanisms and their emergence is crucial for the development of new antibiotics and their effective use. The peptide antibiotic albicidin is such a promising candidate that, as a gyrase poison, shows bactericidal activity against a wide range of gram-positive and gram-negative bacteria. Here, we report the discovery of a gene amplification-based mechanism that imparts an up to 1000-fold increase in resistance levels against albicidin. RNA sequencing and proteomics data show that this novel mechanism protects Salmonella Typhimurium and Escherichia coli by increasing the copy number of STM3175 (YgiV), a transcription regulator with a GyrI-like small molecule binding domain that traps albicidin with high affinity. X-ray crystallography and molecular docking reveal a new conserved motif in the binding groove of the GyrI-like domain that can interact with aromatic building blocks of albicidin. Phylogenetic studies suggest that this resistance mechanism is ubiquitous in gram-negative bacteria, and our experiments confirm that STM3175 homologs can confer resistance in pathogens such as Vibrio vulnificus and Pseudomonas aeruginosa.
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Affiliation(s)
- Mareike Saathoff
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Simone Kosol
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Torsten Semmler
- Robert Koch-Institute (RKI), MF2—Genome Sequencing and Genomic Epidemiology, Berlin, Germany
| | - Karsten Tedin
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Nicole Dimos
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Johannes Kupke
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Maria Seidel
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Micela Condor Jonske
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Silver A. Wolf
- Robert Koch-Institute (RKI), MF2—Genome Sequencing and Genomic Epidemiology, Berlin, Germany
| | - Benno Kuropka
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Wojciech Czyszczoń
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Dmitry Ghilarov
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Stefan Grätz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Jonathan G. Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Bernhard Loll
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | | | - Marcus Fulde
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
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Saathoff M, Tedin K, Grätz S, Schwerk P, Kunert M, Süssmuth RD, Fulde M. Albicidin independency of multidrug efflux systems in Salmonella enterica serovar Typhimurium. J Antimicrob Chemother 2023:7188369. [PMID: 37264536 DOI: 10.1093/jac/dkad173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Affiliation(s)
- Mareike Saathoff
- Institute of Microbiology and Epizootics, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Karsten Tedin
- Institute of Microbiology and Epizootics, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Stefan Grätz
- Biologische Chemie, Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Peter Schwerk
- Institute of Microbiology and Epizootics, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Maria Kunert
- Biologische Chemie, Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Roderich D Süssmuth
- Biologische Chemie, Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Marcus Fulde
- Institute of Microbiology and Epizootics, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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5
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Avella I, Damm M, Freitas I, Wüster W, Lucchini N, Zuazo Ó, Süssmuth RD, Martínez-Freiría F. One Size Fits All-Venomics of the Iberian Adder ( Vipera seoanei, Lataste 1878) Reveals Low Levels of Venom Variation across Its Distributional Range. Toxins (Basel) 2023; 15:371. [PMID: 37368672 PMCID: PMC10301717 DOI: 10.3390/toxins15060371] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/18/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
European vipers (genus Vipera) are medically important snakes displaying considerable venom variation, occurring at different levels in this group. The presence of intraspecific venom variation, however, remains understudied in several Vipera species. Vipera seoanei is a venomous snake endemic to the northern Iberian Peninsula and south-western France, presenting notable phenotypic variation and inhabiting several diverse habitats across its range. We analysed the venoms of 49 adult specimens of V. seoanei from 20 localities across the species' Iberian distribution. We used a pool of all individual venoms to generate a V. seoanei venom reference proteome, produced SDS-PAGE profiles of all venom samples, and visualised patterns of variation using NMDS. By applying linear regression, we then assessed presence and nature of venom variation between localities, and investigated the effect of 14 predictors (biological, eco-geographic, genetic) on its occurrence. The venom comprised at least 12 different toxin families, of which five (i.e., PLA2, svSP, DI, snaclec, svMP) accounted for about 75% of the whole proteome. The comparative analyses of the SDS-PAGE venom profiles showed them to be remarkably similar across the sampled localities, suggesting low geographic variability. The regression analyses suggested significant effects of biological and habitat predictors on the little variation we detected across the analysed V. seoanei venoms. Other factors were also significantly associated with the presence/absence of individual bands in the SDS-PAGE profiles. The low levels of venom variability we detected within V. seoanei might be the result of a recent population expansion, or of processes other than directional positive selection.
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Affiliation(s)
- Ignazio Avella
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; (I.F.); (N.L.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Maik Damm
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany; (M.D.)
| | - Inês Freitas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; (I.F.); (N.L.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Wolfgang Wüster
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK;
| | - Nahla Lucchini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; (I.F.); (N.L.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Óscar Zuazo
- Calle La Puebla 1, 26250 Santo Domingo de la Calzada, Spain
| | - Roderich D. Süssmuth
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany; (M.D.)
| | - Fernando Martínez-Freiría
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; (I.F.); (N.L.)
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
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6
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Kosol S, Rostock L, Barsig J, Tabarelli T, Hommernick K, Kulike M, Eulberg T, Seidel M, Behroz I, Kleebauer L, Grätz S, Mainz A, Süssmuth RD. Transcription activation by the resistance protein AlbA as a tool to evaluate derivatives of the antibiotic albicidin. Chem Sci 2023; 14:5069-5078. [PMID: 37206387 PMCID: PMC10189885 DOI: 10.1039/d3sc00955f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/15/2023] [Indexed: 05/21/2023] Open
Abstract
The rising numbers of fatal infections with resistant pathogens emphasizes the urgent need for new antibiotics. Ideally, new antibiotics should be able to evade or overcome existing resistance mechanisms. The peptide antibiotic albicidin is a highly potent antibacterial compound with a broad activity spectrum but also with several known resistance mechanisms. In order to assess the effectiveness of novel albicidin derivatives in the presence of the binding protein and transcription regulator AlbA, a resistance mechanism against albicidin identified in Klebsiella oxytoca, we designed a transcription reporter assay. In addition, by screening shorter albicidin fragments, as well as various DNA-binders and gyrase poisons, we were able to gain insights into the AlbA target spectrum. We analysed the effect of mutations in the binding domain of AlbA on albicidin sequestration and transcription activation, and found that the signal transduction mechanism is complex but can be evaded. Further demonstrating AlbA's high level of specificity, we find clues for the logical design of molecules capable of avoiding the resistance mechanism.
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Affiliation(s)
- Simone Kosol
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Lida Rostock
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Jonas Barsig
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Theresa Tabarelli
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Kay Hommernick
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Marcel Kulike
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Tobias Eulberg
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Maria Seidel
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Iraj Behroz
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Leonardo Kleebauer
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Stefan Grätz
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Andi Mainz
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
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7
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Hellinger R, Sigurdsson A, Wu W, Romanova EV, Li L, Sweedler JV, Süssmuth RD, Gruber CW. Peptidomics. Nat Rev Methods Primers 2023; 3:25. [PMID: 37250919 PMCID: PMC7614574 DOI: 10.1038/s43586-023-00205-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 05/31/2023]
Abstract
Peptides are biopolymers, typically consisting of 2-50 amino acids. They are biologically produced by the cellular ribosomal machinery or by non-ribosomal enzymes and, sometimes, other dedicated ligases. Peptides are arranged as linear chains or cycles, and include post-translational modifications, unusual amino acids and stabilizing motifs. Their structure and molecular size render them a unique chemical space, between small molecules and larger proteins. Peptides have important physiological functions as intrinsic signalling molecules, such as neuropeptides and peptide hormones, for cellular or interspecies communication, as toxins to catch prey or as defence molecules to fend off enemies and microorganisms. Clinically, they are gaining popularity as biomarkers or innovative therapeutics; to date there are more than 60 peptide drugs approved and more than 150 in clinical development. The emerging field of peptidomics comprises the comprehensive qualitative and quantitative analysis of the suite of peptides in a biological sample (endogenously produced, or exogenously administered as drugs). Peptidomics employs techniques of genomics, modern proteomics, state-of-the-art analytical chemistry and innovative computational biology, with a specialized set of tools. The complex biological matrices and often low abundance of analytes typically examined in peptidomics experiments require optimized sample preparation and isolation, including in silico analysis. This Primer covers the combination of techniques and workflows needed for peptide discovery and characterization and provides an overview of various biological and clinical applications of peptidomics.
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Affiliation(s)
- Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Arnar Sigurdsson
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Wenxin Wu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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8
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Hempel BF, Damm M, Petras D, Kazandjian TD, Szentiks CA, Fritsch G, Nebrich G, Casewell NR, Klein O, Süssmuth RD. Spatial Venomics─Cobra Venom System Reveals Spatial Differentiation of Snake Toxins by Mass Spectrometry Imaging. J Proteome Res 2023; 22:26-35. [PMID: 36521429 DOI: 10.1021/acs.jproteome.2c00424] [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] [Indexed: 12/23/2022]
Abstract
Among venomous animals, toxic secretions have evolved as biochemical weapons associated with various highly specialized delivery systems on many occasions. Despite extensive research, there is still limited knowledge of the functional biology of most animal toxins, including their venom production and storage, as well as the morphological structures within sophisticated venom producing tissues that might underpin venom modulation. Here, we report on the spatial exploration of a snake venom gland system by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), in combination with standard proteotranscriptomic approaches, to enable in situ toxin mapping in spatial intensity maps across a venom gland sourced from the Egyptian cobra (Naja haje). MALDI-MSI toxin visualization on the elapid venom gland reveals a high spatial heterogeneity of different toxin classes at the proteoform level, which may be the result of physiological constraints on venom production and/or storage that reflects the potential for venom modulation under diverse stimuli.
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Affiliation(s)
- Benjamin-Florian Hempel
- BIH Center for Regenerative Therapies BCRT, Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany.,Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Maik Damm
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Daniel Petras
- CMFI Cluster of Excellence, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen, Universität Tübingen, 72076 Tübingen, Germany
| | - Taline D Kazandjian
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Liverpool L3 5QA, U.K
| | - Claudia A Szentiks
- Department of Wildlife Diseases and Reproduction Management, Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., 10315 Berlin, Germany
| | - Guido Fritsch
- Department of Wildlife Diseases and Reproduction Management, Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., 10315 Berlin, Germany
| | - Grit Nebrich
- BIH Center for Regenerative Therapies BCRT, Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Nicholas R Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Liverpool L3 5QA, U.K
| | - Oliver Klein
- BIH Center for Regenerative Therapies BCRT, Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
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9
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Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stępień Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Süssmuth RD, Ghilarov D. Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin. Nat Catal 2023; 6:52-67. [PMID: 36741192 PMCID: PMC9886550 DOI: 10.1038/s41929-022-00904-1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/30/2022] [Indexed: 01/24/2023]
Abstract
The peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is poorly understood. We determined a 2.6 Å resolution cryoelectron microscopy structure of a ternary complex between Escherichia coli topoisomerase DNA gyrase, a 217 bp double-stranded DNA fragment and albicidin. Albicidin employs a dual binding mechanism where one end of the molecule obstructs the crucial gyrase dimer interface, while the other intercalates between the fragments of cleaved DNA substrate. Thus, albicidin efficiently locks DNA gyrase, preventing it from religating DNA and completing its catalytic cycle. Two additional structures of this trapped state were determined using synthetic albicidin analogues that demonstrate improved solubility, and activity against a range of gyrase variants and E. coli topoisomerase IV. The extraordinary promiscuity of the DNA-intercalating region of albicidins and their excellent performance against fluoroquinolone-resistant bacteria holds great promise for the development of last-resort antibiotics.
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Affiliation(s)
| | - Kay Hommernick
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Iraj Behroz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Marcel Kulike
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Zuzanna Pakosz-Stępień
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Lukasz Mazurek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Maria Seidel
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Maria Kunert
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | | | - Bernhard Loll
- moloX GmbH, Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - John B Weston
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Andi Mainz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Dmitry Ghilarov
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,John Innes Centre, Norwich Research Park, Norwich, UK
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10
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Yao G, Kosol S, Wenz MT, Irran E, Keller BG, Trapp O, Süssmuth RD. The occurrence of ansamers in the synthesis of cyclic peptides. Nat Commun 2022; 13:6488. [PMID: 36310176 PMCID: PMC9618573 DOI: 10.1038/s41467-022-34125-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
α-Amanitin is a bicyclic octapeptide composed of a macrolactam with a tryptathionine cross-link forming a handle. Previously, the occurrence of isomers of amanitin, termed atropisomers has been postulated. Although the total synthesis of α-amanitin has been accomplished this aspect still remains unsolved. We perform the synthesis of amanitin analogs, accompanied by in-depth spectroscopic, crystallographic and molecular dynamics studies. The data unambiguously confirms the synthesis of two amatoxin-type isomers, for which we propose the term ansamers. The natural structure of the P-ansamer can be ansa-selectively synthesized using an optimized synthetic strategy. We believe that the here described terminology does also have implications for many other peptide structures, e.g. norbornapeptides, lasso peptides, tryptorubins and others, and helps to unambiguously describe conformational isomerism of cyclic peptides.
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Affiliation(s)
- Guiyang Yao
- grid.6734.60000 0001 2292 8254Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany ,grid.8547.e0000 0001 0125 2443Center for Innovative Drug Discovery, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Shanghai, PR China
| | - Simone Kosol
- grid.6734.60000 0001 2292 8254Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Marius T. Wenz
- grid.14095.390000 0000 9116 4836Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Elisabeth Irran
- grid.6734.60000 0001 2292 8254Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Bettina G. Keller
- grid.14095.390000 0000 9116 4836Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Oliver Trapp
- grid.5252.00000 0004 1936 973XDepartment of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany ,grid.429508.20000 0004 0491 677XMax-Planck-Institute for Astronomy, Königstuhl 17, 69117 Heidelberg, Germany
| | - Roderich D. Süssmuth
- grid.6734.60000 0001 2292 8254Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
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11
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Knebel C, Süssmuth RD, Hammer HS, Braeuning A, Marx-Stoelting P. New Approach Methods for Hazard Identification: A Case Study with Azole Fungicides Affecting Molecular Targets Associated with the Adverse Outcome Pathway for Cholestasis. Cells 2022; 11:cells11203293. [PMID: 36291160 PMCID: PMC9600068 DOI: 10.3390/cells11203293] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 12/03/2022] Open
Abstract
Triazole fungicides such as propiconazole (Pi) or tebuconazole (Te) show hepatotoxicity in vivo, e.g., hypertrophy and vacuolization of liver cells following interaction with nuclear receptors such as PXR (pregnane-X-receptor) and CAR (constitutive androstane receptor). Accordingly, azoles affect gene expression associated with these adverse outcomes in vivo but also in human liver cells in vitro. Additionally, genes indicative of liver cholestasis are affected in vivo and in vitro. We therefore analyzed the capability of Pi and Te to cause cholestasis in an adverse outcome pathway (AOP)-driven approach in hepatic cells of human origin in vitro, considering also previous in vivo studies. Bile salt export pump (BSEP) activity assays confirmed that both azoles are weak inhibitors of BSEP. They alternate the expression of various cholestasis-associated target genes and proteins as well as the mitochondrial membrane function. Published in vivo data, however, demonstrate that neither Pi nor Te cause cholestasis in rodent bioassays. This discrepancy can be explained by the in vivo concentrations of both azoles being well below their EC50 for BSEP inhibition. From a regulatory perspective, this illustrates that toxicogenomics and human in vitro models are valuable tools to detect the potential of a substance to cause a specific type of toxicity. To come to a sound regulatory conclusion on the in vivo relevance of such a finding, results will have to be considered in a broader context also including toxicokinetics in a weight-of-evidence approach.
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Affiliation(s)
- Constanze Knebel
- Department Food Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Street 8-10, 10589 Berlin, Germany
| | - Roderich D. Süssmuth
- Institute of Chemistry, Technical University Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Helen S. Hammer
- Signatope GmbH, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Albert Braeuning
- Department Food Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Street 8-10, 10589 Berlin, Germany
- Correspondence: (A.B.); (P.M.-S.); Tel.: +49-(0)30-18412-25100 (A.B.); Fax: +49-(0)30-18412-63758 (A.B.)
| | - Philip Marx-Stoelting
- Department Pesticides Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Street 8-10, 10589 Berlin, Germany
- Correspondence: (A.B.); (P.M.-S.); Tel.: +49-(0)30-18412-25100 (A.B.); Fax: +49-(0)30-18412-63758 (A.B.)
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12
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Scholz S, Kerestetzopoulou S, Wiebach V, Schnegotzki R, Schmid B, Reyna‐González E, Ding L, Süssmuth RD, Dittmann E, Baunach M. One-Pot Chemoenzymatic Synthesis of Microviridin Analogs Containing Functional Tags. Chembiochem 2022; 23:e202200345. [PMID: 35995730 PMCID: PMC9826346 DOI: 10.1002/cbic.202200345] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/31/2022] [Indexed: 01/11/2023]
Abstract
Microviridins are a prominent family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) featuring characteristic lactone and lactam rings. Their unusual cage-like architecture renders them highly potent serine protease inhibitors of which individual variants specifically inhibit different types of proteases of pharmacological interest. While posttranslational modifications are key for the stability and bioactivity of RiPPs, additional attractive properties can be introduced by functional tags. To date - although highly desirable - no method has been reported to incorporate functional tags in microviridin scaffolds or the overarching class of graspetides. In this study, a chemoenzymatic in vitro platform is used to introduce functional tags in various microviridin variants yielding biotinylated, dansylated or propargylated congeners. This straightforward approach paves the way for customized protease inhibitors with built-in functionalities that can help to unravel the still elusive ecological roles and targets of this remarkable class of compounds and to foster applications based on protease inhibition.
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Affiliation(s)
- Stella Scholz
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Sofia Kerestetzopoulou
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Vincent Wiebach
- Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts Plads, Building 221DK-2800 Kgs.LyngbyDenmark
| | - Romina Schnegotzki
- Institute of ChemistryTechnical University BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Bianca Schmid
- Institute of ChemistryTechnical University BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Emmanuel Reyna‐González
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Ling Ding
- Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts Plads, Building 221DK-2800 Kgs.LyngbyDenmark
| | - Roderich D. Süssmuth
- Institute of ChemistryTechnical University BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Elke Dittmann
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Martin Baunach
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany,Institute of Pharmaceutical BiologyUniversity of BonnNussallee 653115BonnGermany
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13
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Stieger CE, Park Y, de Geus MAR, Kim D, Huhn C, Slenczka JS, Ochtrop P, Müchler JM, Süssmuth RD, Broichhagen J, Baik M, Hackenberger CPR. Back Cover: DFT‐Guided Discovery of Ethynyl‐Triazolyl‐Phosphinates as Modular Electrophiles for Chemoselective Cysteine Bioconjugation and Profiling (Angew. Chem. Int. Ed. 41/2022). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/anie.202212509] [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: 11/11/2022]
Affiliation(s)
- Christian E. Stieger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
- Department of Chemistry Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Yerin Park
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Mark A. R. de Geus
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
| | - Dongju Kim
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Christiane Huhn
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
- Department of Chemistry Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - J. Sophia Slenczka
- Institut für Chemie Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Philipp Ochtrop
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
- Department of Chemistry Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Judith M. Müchler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
- Department of Chemistry Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Roderich D. Süssmuth
- Institut für Chemie Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
| | - Mu‐Hyun Baik
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
- Department of Chemistry Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
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14
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Stieger CE, Park Y, de Geus MAR, Kim D, Huhn C, Slenczka JS, Ochtrop P, Müchler JM, Süssmuth RD, Broichhagen J, Baik M, Hackenberger CPR. DFT-Guided Discovery of Ethynyl-Triazolyl-Phosphinates as Modular Electrophiles for Chemoselective Cysteine Bioconjugation and Profiling. Angew Chem Int Ed Engl 2022; 61:e202205348. [PMID: 35792701 PMCID: PMC9804898 DOI: 10.1002/anie.202205348] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 04/12/2022] [Indexed: 01/09/2023]
Abstract
We report the density functional theory (DFT) guided discovery of ethynyl-triazolyl-phosphinates (ETPs) as a new class of electrophilic warheads for cysteine selective bioconjugation. By using CuI -catalysed azide alkyne cycloaddition (CuAAC) in aqueous buffer, we were able to access a variety of functional electrophilic building blocks, including proteins, from diethynyl-phosphinate. ETP-reagents were used to obtain fluorescent peptide-conjugates for receptor labelling on live cells and a stable and a biologically active antibody-drug-conjugate. Moreover, we were able to incorporate ETP-electrophiles into an azide-containing ubiquitin under native conditions and demonstrate their potential in protein-protein conjugation. Finally, we showcase the excellent cysteine-selectivity of this new class of electrophile in mass spectrometry based, proteome-wide cysteine profiling, underscoring the applicability in homogeneous bioconjugation strategies to connect two complex biomolecules.
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Affiliation(s)
- Christian E. Stieger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Yerin Park
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea,Center for Catalytic Hydrocarbon FunctionalizationsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Mark A. R. de Geus
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Dongju Kim
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea,Center for Catalytic Hydrocarbon FunctionalizationsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Christiane Huhn
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - J. Sophia Slenczka
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 12410623BerlinGermany
| | - Philipp Ochtrop
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Judith M. Müchler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Roderich D. Süssmuth
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 12410623BerlinGermany
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Mu‐Hyun Baik
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea,Center for Catalytic Hydrocarbon FunctionalizationsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
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15
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Schnegotzki R, Koopman J, Grimme S, Süssmuth RD. Quantum Chemistry-based Molecular Dynamics Simulations as a Tool for the Assignment of ESI-MS/MS Spectra of Drug Molecules. Chemistry 2022; 28:e202200318. [PMID: 35235707 PMCID: PMC9325386 DOI: 10.1002/chem.202200318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 02/05/2022] [Indexed: 11/08/2022]
Abstract
In organic mass spectrometry, fragment ions provide important information on the analyte as a central part of its structure elucidation. With increasing molecular size and possible protonation sites, the potential energy surface (PES) of the analyte can become very complex, which results in a large number of possible fragmentation patterns. Quantum chemical (QC) calculations can help here, enabling the fast calculation of the PES and thus enhancing the mass spectrometry-based structure elucidation processes. In this work, the previously unknown fragmentation pathways of the two drug molecules Nateglinide (45 atoms) and Zopiclone (51 atoms) were investigated using a combination of generic formalisms and calculations conducted with the Quantum Chemical Mass Spectrometry (QCxMS) program. The computations of the de novo fragment spectra were conducted with the semi-empirical GFNn-xTB (n=1, 2) methods and compared against Orbitrap measured electrospray ionization (ESI) spectra in positive ion mode. It was found that the unbiased QC calculations are particularly suitable to predict non-evident fragment ion structures, sometimes contrasting the accepted generic formulation of fragment ion structures from electron migration rules, where the "true" ion fragment structures are approximated. For the first time, all fragment and intermediate structures of these large-sized molecules could be elucidated completely and routinely using this merger of methods, finding new undocumented mechanisms, that are not considered in common rules published so far. Given the importance of ESI for medicinal chemistry, pharmacokinetics, and metabolomics, this approach can significantly enhance the mass spectrometry-based structure elucidation processes and contribute to the understanding of previously unknown fragmentation pathways.
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Affiliation(s)
- Romina Schnegotzki
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Jeroen Koopman
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115, Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115, Bonn, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
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16
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Schnegotzki R, Wiebach V, Sánchez-Hidalgo M, Tietzmann M, zur Bonsen AB, Genilloud O, Süssmuth RD. Total Synthesis and Biosynthesis of Cyclodepsipeptide Cochinmicin I. Org Lett 2022; 24:2344-2348. [DOI: 10.1021/acs.orglett.2c00525] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Romina Schnegotzki
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | | | - Marina Sánchez-Hidalgo
- Department of Microbiology, Fundación MEDINA, Av. Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Marcel Tietzmann
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Andreas B. zur Bonsen
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Olga Genilloud
- Department of Microbiology, Fundación MEDINA, Av. Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Roderich D. Süssmuth
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
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17
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Barbosa JC, Gonçalves S, Makowski M, Silva ÍC, Caetano T, Schneider T, Mösker E, Süssmuth RD, Santos NC, Mendo S. Insights into the mode of action of the two-peptide lantibiotic lichenicidin. Colloids Surf B Biointerfaces 2022; 211:112308. [PMID: 34973602 DOI: 10.1016/j.colsurfb.2021.112308] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 11/04/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/30/2022]
Abstract
Lantibiotics are promising candidates to address the worldwide problem of antibiotic resistance. They belong to a class of natural compounds exhibiting strong activity against clinically relevant Gram-positive bacterial strains, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE). Lichenicidin is a class II two-peptide lantibiotic. The presence of the two mature peptides, Bliα and Bliβ, is necessary for full activity against target bacteria. This work aims at clarifying the synergistic activity of both peptides in their interaction with the target membranes. The effect of lichenicidin was tested against S. aureus cells and large unilamellar vesicles. Lichenicidin increases the net surface charge of S. aureus, as shown by zeta-potential measurements, without reaching electroneutralization. In addition, lichenicidin causes cell surface perturbations that culminate in the leakage of its internal contents, as observed by atomic force microscopy. Bliα seems to have low affinity for S. aureus, however, it contributes to increase the affinity of Bliβ, because together they present higher affinity than separately. In contrast, Bliα seems to provide an anchoring site for lichenicidin in lipid II-containing membranes. Interestingly, Bliβ alone can induce high levels of membrane leakage, but this effect appears to be faster in the presence of Bliα. Based on this information, we propose a mechanism of action of lichenicidin.
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Affiliation(s)
- Joana C Barbosa
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal.
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal.
| | - Marcin Makowski
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal.
| | - Ítala C Silva
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal.
| | - Tânia Caetano
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal.
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany.
| | - Eva Mösker
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany.
| | | | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal.
| | - Sónia Mendo
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal.
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18
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Süssmuth RD, Lensch A, Pelzer S. Does Bacillus velezensis Strain RP137 from the Persian Gulf Really Produce an Aminoglycoside? Curr Microbiol 2022; 79:75. [DOI: 10.1007/s00284-022-02765-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/11/2022] [Indexed: 11/03/2022]
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19
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Baltzer S, Bulatov T, Schmied C, Krämer A, Berger BT, Oder A, Walker-Gray R, Kuschke C, Zühlke K, Eichhorst J, Lehmann M, Knapp S, Weston J, von Kries JP, Süssmuth RD, Klussmann E. Aurora Kinase A Is Involved in Controlling the Localization of Aquaporin-2 in Renal Principal Cells. Int J Mol Sci 2022; 23:ijms23020763. [PMID: 35054947 PMCID: PMC8776063 DOI: 10.3390/ijms23020763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 12/01/2021] [Revised: 12/30/2021] [Accepted: 01/08/2022] [Indexed: 02/01/2023] Open
Abstract
The cAMP-dependent aquaporin-2 (AQP2) redistribution from intracellular vesicles into the plasma membrane of renal collecting duct principal cells induces water reabsorption and fine-tunes body water homeostasis. However, the mechanisms controlling the localization of AQP2 are not understood in detail. Using immortalized mouse medullary collecting duct (MCD4) and primary rat inner medullary collecting duct (IMCD) cells as model systems, we here discovered a key regulatory role of Aurora kinase A (AURKA) in the control of AQP2. The AURKA-selective inhibitor Aurora-A inhibitor I and novel derivatives as well as a structurally different inhibitor, Alisertib, prevented the cAMP-induced redistribution of AQP2. Aurora-A inhibitor I led to a depolymerization of actin stress fibers, which serve as tracks for the translocation of AQP2-bearing vesicles to the plasma membrane. The phosphorylation of cofilin-1 (CFL1) inactivates the actin-depolymerizing function of CFL1. Aurora-A inhibitor I decreased the CFL1 phosphorylation, accounting for the removal of the actin stress fibers and the inhibition of the redistribution of AQP2. Surprisingly, Alisertib caused an increase in actin stress fibers and did not affect CFL1 phosphorylation, indicating that AURKA exerts its control over AQP2 through different mechanisms. An involvement of AURKA and CFL1 in the control of the localization of AQP2 was hitherto unknown.
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Affiliation(s)
- Sandrine Baltzer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (S.B.); (R.W.-G.); (C.K.); (K.Z.)
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany; (T.B.); (R.D.S.)
| | - Timur Bulatov
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany; (T.B.); (R.D.S.)
| | - Christopher Schmied
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (C.S.); (A.O.); (J.E.); (M.L.); (J.P.v.K.)
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany; (A.K.); (B.-T.B.); (S.K.)
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
- DKTK (German Translational Research Network), Partner Site Frankfurt/Mainz, 60590 Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany; (A.K.); (B.-T.B.); (S.K.)
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Andreas Oder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (C.S.); (A.O.); (J.E.); (M.L.); (J.P.v.K.)
| | - Ryan Walker-Gray
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (S.B.); (R.W.-G.); (C.K.); (K.Z.)
| | - Christin Kuschke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (S.B.); (R.W.-G.); (C.K.); (K.Z.)
| | - Kerstin Zühlke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (S.B.); (R.W.-G.); (C.K.); (K.Z.)
| | - Jenny Eichhorst
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (C.S.); (A.O.); (J.E.); (M.L.); (J.P.v.K.)
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (C.S.); (A.O.); (J.E.); (M.L.); (J.P.v.K.)
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany; (A.K.); (B.-T.B.); (S.K.)
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
- DKTK (German Translational Research Network), Partner Site Frankfurt/Mainz, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
| | - John Weston
- JQuest Consulting, Carl-Orff-Weg 25, 65779 Kelkheim, Germany;
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (C.S.); (A.O.); (J.E.); (M.L.); (J.P.v.K.)
| | - Roderich D. Süssmuth
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany; (T.B.); (R.D.S.)
| | - Enno Klussmann
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (S.B.); (R.W.-G.); (C.K.); (K.Z.)
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
- Correspondence: ; Tel.: +49-30-9406-2596
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20
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Hugouvieux-Cotte-Pattat N, Royer M, Gueguen E, Le Guen P, Süssmuth RD, Reverchon S, Cociancich S. Specificity and genetic polymorphism in the Vfm quorum sensing system of plant pathogenic bacteria of the genus Dickeya. Environ Microbiol 2022; 24:1467-1483. [PMID: 35014170 PMCID: PMC9306890 DOI: 10.1111/1462-2920.15889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/12/2021] [Accepted: 12/26/2021] [Indexed: 12/11/2022]
Abstract
The Vfm quorum sensing (QS) system is preponderant for the virulence of different species of the bacterial genus Dickeya. The vfm gene cluster encodes 26 genes involved in the production, sensing or transduction of the QS signal. To date, the Vfm QS signal has escaped detection by analytical chemistry methods. However, we report here a strain‐specific polymorphism in the biosynthesis genes vfmO and vfmP, which is predicted to be related to the production of different analogues of the QS signal. Consequently, the Vfm communication could be impossible between strains possessing different variants of the genes vfmO/P. We constructed three Vfm QS biosensor strains possessing different vfmO/P variants and compared these biosensors for their responses to samples prepared from 34 Dickeya strains possessing different vfmO/P variants. A pattern of specificity was demonstrated, providing evidence that the polymorphism in the genes vfmO/P determines the biosynthesis of different analogues of the QS signal. Unexpectedly, this vfmO/P‐dependent pattern of specificity is linked to a polymorphism in the ABC transporter gene vfmG, suggesting an adaptation of the putative permease VfmG to specifically bind different analogues of the QS signal. Accordingly, we discuss the possible involvement of VfmG as co‐sensor of the Vfm two‐component regulatory system.
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Affiliation(s)
| | - Monique Royer
- CIRAD, UMR PHIM, Montpellier, F-34398, France.,PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Erwan Gueguen
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240 MAP, Villeurbanne, F-69622, France
| | - Paul Le Guen
- CIRAD, UMR PHIM, Montpellier, F-34398, France.,PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Berlin, D-10623, Germany
| | - Sylvie Reverchon
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240 MAP, Villeurbanne, F-69622, France
| | - Stéphane Cociancich
- CIRAD, UMR PHIM, Montpellier, F-34398, France.,PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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21
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Bulatov T, Gensel S, Mainz A, Dang T, Koller TO, Voigt K, Ebeling J, Wilson DN, Genersch E, Süssmuth RD. Total Synthesis and Biological Evaluation of Paenilamicins from the Honey Bee Pathogen Paenibacillus larvae. J Am Chem Soc 2021; 144:288-296. [PMID: 34968060 DOI: 10.1021/jacs.1c09616] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Paenilamicins are a group of complex polycationic peptide secondary metabolites with antibacterial and antifungal activities produced by the devastating honey bee brood pathogen Paenibacillus larvae causing the lethal brood disease American Foulbrood (AFB). Here, we report the convergent total synthesis and structural revision of paenilamicin B2. Specific stereoisomers of paenilamicin B2 were synthesized for unambiguous confirmation of the natural product structure and for evaluation of biological activities. These studies revealed the N-terminal fragment of paenilamicin as an important pharmacophore. Infection assays using bee larvae and the insect pathogen Bacillus thuringiensis demonstrated that paenilamicins outcompete bacterial competitors in the ecological niche of P. larvae. Finally, we show first data that classifies paenilamicins as potential ribosome inhibitors. Hence, our synthesis route is a further step for understanding the pathogenicity of P. larvae and for thorough structure-activity-relationship as well as mode-of-action studies in the near future.
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Affiliation(s)
- Timur Bulatov
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Sebastian Gensel
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Andi Mainz
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Tam Dang
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Timm O Koller
- Institut für Biochemie und Molekularbiologie, Universität Hamburg, 20146 Hamburg, Germany
| | - Kerstin Voigt
- Jena Microbial Resource Collection (JMRC), Hans-Knöll-Institut, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Julia Ebeling
- Institute for Bee Research, Friedrich-Engels-Strasse 32, 16540 Hohen Neuendorf, Germany
| | - Daniel N Wilson
- Institut für Biochemie und Molekularbiologie, Universität Hamburg, 20146 Hamburg, Germany
| | - Elke Genersch
- Institute for Bee Research, Friedrich-Engels-Strasse 32, 16540 Hohen Neuendorf, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
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22
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Hegemann JD, Süssmuth RD. Identification of the Catalytic Residues in the Cyclase Domain of the Class IV Lanthipeptide Synthetase SgbL. Chembiochem 2021; 22:3169-3172. [PMID: 34490957 PMCID: PMC9292228 DOI: 10.1002/cbic.202100391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/03/2021] [Revised: 09/06/2021] [Indexed: 11/08/2022]
Abstract
Lanthipeptides belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs) and are subdivided into different classes based on their processing enzymes. The three-domain class IV lanthipeptide synthetases (LanL enzymes) consist of N-terminal lyase, central kinase, and C-terminal cyclase domains. While the catalytic residues of the kinase domains (mediating ATP-dependent Ser/Thr phosphorylations) and the lyase domains (carrying out subsequent phosphoserine/phosphothreonine (pSer/pThr) eliminations to yield dehydroalanine/dehydrobutyrine (Dha/Dhb) residues) have been characterized previously, such studies are missing for LanL cyclase domains. To close this gap of knowledge, this study reports on the identification and validation of the catalytic residues in the cyclase domain of the class IV lanthipeptide synthetase SgbL, which facilitate the nucleophilic attacks by Cys thiols on Dha/Dhb residues for the formation of β-thioether crosslinks.
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Affiliation(s)
- Julian D Hegemann
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Roderich D Süssmuth
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 124, 10623, Berlin, Germany
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23
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Zborovsky L, Kleebauer L, Seidel M, Kostenko A, von Eckardstein L, Gombert FO, Weston J, Süssmuth RD. Improvement of the antimicrobial potency, pharmacokinetic and pharmacodynamic properties of albicidin by incorporation of nitrogen atoms. Chem Sci 2021; 12:14606-14617. [PMID: 34881013 PMCID: PMC8580050 DOI: 10.1039/d1sc04019g] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/17/2021] [Indexed: 01/22/2023] Open
Abstract
The worrisome development and spread of multidrug-resistant bacteria demands new antibacterial agents with strong bioactivities particularly against Gram-negative bacteria. Albicidins were recently structurally characterized as highly active antibacterial natural products from the bacterium Xanthomonas albilineans. Albicidin, which effectively targets the bacterial DNA-gyrase, is a lipophilic hexapeptide mostly consisting of para amino benzoic acid units and only one α-amino acid. In this study, we report on the design and synthesis of new albicidins, containing N-atoms on each of the 5 different phenyl rings. We systematically introduced N-atoms into the aromatic backbone to monitor intramolecular H-bonds and for one derivative correlated them with a significant enhancement of the antibacterial activity and activity spectrum, particularly also towards Gram-positive bacteria. In parallel we conducted DFT calculations to find the most stable conformation of each derivative. A drastic angle-change was observed for the lead compound and shows a preferred planarity through H-bonding with the introduced N-atom at the D-fragment of albicidin. Finally, we went to the next level and conducted the first in vivo experiments with an albicidin analogue. Our lead compound was evaluated in two different mouse experiments: In the first we show a promising PK profile and the absence of toxicity and in the second very good efficiency and reduction of the bacterial titre in an E. coli infection model with FQ-resistant clinically relevant strains. These results qualify albicidins as active antibacterial substances with the potential to be developed as a drug for treatment of infections caused by Gram-negative and Gram-positive bacteria.
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Affiliation(s)
- Lieby Zborovsky
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Leonardo Kleebauer
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Maria Seidel
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Arseni Kostenko
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Leonard von Eckardstein
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Frank Otto Gombert
- Gombert Pharma Research Solutions (GPRS) Dornacherstrasse 120 CH 4053 Basel Switzerland
| | - John Weston
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Roderich D Süssmuth
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
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24
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Calvete JJ, Pla D, Els J, Carranza S, Damm M, Hempel BF, John EBO, Petras D, Heiss P, Nalbantsoy A, Göçmen B, Süssmuth RD, Calderón-Celis F, Nosti AJ, Encinar JR. Combined Molecular and Elemental Mass Spectrometry Approaches for Absolute Quantification of Proteomes: Application to the Venomics Characterization of the Two Species of Desert Black Cobras, Walterinnesia aegyptia and Walterinnesia morgani. J Proteome Res 2021; 20:5064-5078. [PMID: 34606723 PMCID: PMC8576837 DOI: 10.1021/acs.jproteome.1c00608] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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] [Indexed: 01/07/2023]
Abstract
![]()
We report a novel hybrid, molecular
and elemental mass spectrometry
(MS) setup for the absolute quantification of snake venom proteomes
shown here for two desert black cobra species within the genus Walterinnesia, Walterinnesia aegyptia and Walterinnesia morgani. The experimental
design includes the decomplexation of the venom samples by reverse-phase
chromatography independently coupled to four mass spectrometry systems:
the combined bottom-up and top-down molecular MS for protein identification
and a parallel reverse-phase microbore high-performance liquid chromatograph
(RP-μHPLC) on-line to inductively coupled plasma (ICP-MS/MS)
elemental mass spectrometry and electrospray ionization quadrupole
time-of-flight mass spectrometry (ESI-QToF MS). This allows to continuously
record the absolute sulfur concentration throughout the chromatogram
and assign it to the parent venom proteins separated in the RP-μHPLC-ESI-QToF
parallel run via mass profiling. The results provide a locus-resolved
and quantitative insight into the three desert black cobra venom proteome
samples. They also validate the units of measure of our snake venomics
strategy for the relative quantification of snake venom proteomes
as % of total venom peptide bonds as a proxy for the % by weight of
the venom toxins/toxin families. In a more general context, our work
may pave the way for broader applications of hybrid elemental/molecular
MS setups in diverse areas of proteomics.
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Affiliation(s)
- Juan J Calvete
- Laboratorio de Venómica Evolutiva y Traslational, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Jaume Roig 11, 46010 Valencia, Spain
| | - Davinia Pla
- Laboratorio de Venómica Evolutiva y Traslational, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Jaume Roig 11, 46010 Valencia, Spain
| | - Johannes Els
- Environment and Protected Areas Authority, 82828 Sharjah, United Arab Emirates
| | - Salvador Carranza
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Maik Damm
- Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
| | - Benjamin-Florian Hempel
- Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany.,BIH Center for Regenerative Therapies BCRT, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Elisa B O John
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul, CEP 91501-970 Porto Alegre, RS, Brazil
| | - Daniel Petras
- CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Túbingen, 72076 Tübingen, Germany
| | - Paul Heiss
- Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
| | - Ayse Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Bornova, Izmir, Turkey
| | - Bayram Göçmen
- Zoology Section, Department of Biology, Faculty of Science, Ege University, 35100 Bornova, Izmir, Turkey
| | - Roderich D Süssmuth
- Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
| | | | - Alicia Jiménez Nosti
- Department of Physical and Analytical Chemistry, University of Oviedo, 33006 Oviedo, Spain
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, 33006 Oviedo, Spain
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25
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Kleebauer L, Zborovsky L, Hommernick K, Seidel M, Weston JB, Süssmuth RD. Overcoming AlbD Protease Resistance and Improving Potency: Synthesis and Bioactivity of Antibacterial Albicidin Analogues with Amide Bond Isosteres. Org Lett 2021; 23:7023-7027. [PMID: 34398605 DOI: 10.1021/acs.orglett.1c02312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Albicidin is a potent antibacterial oligoaromatic peptide that is susceptible to the protease AlbD, a resistance factor. This potentially restricts the use of albicidin as a drug. To overcome this obstacle, we synthesized and evaluated six analogues with isosteric replacement of the key amide link. Protease stability was established while maintaining the antibacterial activity, including three analogues with up to eight times higher activity compared with the natural albicidin.
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Affiliation(s)
- Leonardo Kleebauer
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Lieby Zborovsky
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Kay Hommernick
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Maria Seidel
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - John B Weston
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
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26
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Yao G, Knittel CH, Kosol S, Wenz MT, Keller BG, Gruß H, Braun AC, Lutz C, Hechler T, Pahl A, Süssmuth RD. Iodine-Mediated Tryptathionine Formation Facilitates the Synthesis of Amanitins. J Am Chem Soc 2021; 143:14322-14331. [PMID: 34459587 DOI: 10.1021/jacs.1c06565] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Synthetic methods on the macrocyclization of peptides are of high interest since they facilitate the synthesis of various types of potentially bioactive compounds, e.g. addressing targets like protein-protein-interactions. Herein, we report on an efficient method to construct tryptathionine-cross-links in peptides between the amino acids Trp and Cys. This reaction not only is the basis for the total synthesis of the death cap toxin α-amanitin but also provides rapid access to various new amanitin analogues. This study for the first time presents a systematic compilation of structure-activity relations (SAR) of amatoxins with regard to RNA polymerase II inhibition and cytotoxicity with one amanitin derivative of superior RNAP II inhibition. The present approach paves the way for the synthesis of structurally diverse amatoxins as future payloads for antibody-toxin conjugates in cancer therapy.
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Affiliation(s)
- Guiyang Yao
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Caroline H Knittel
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Simone Kosol
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Marius T Wenz
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Hendrik Gruß
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Alexandra C Braun
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Christian Lutz
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Torsten Hechler
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Andreas Pahl
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
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27
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Rügen N, Jenkins TP, Wielsch N, Vogel H, Hempel BF, Süssmuth RD, Ainsworth S, Cabezas-Cruz A, Vilcinskas A, Tonk M. Hexapod Assassins' Potion: Venom Composition and Bioactivity from the Eurasian Assassin Bug Rhynocoris iracundus. Biomedicines 2021; 9:biomedicines9070819. [PMID: 34356883 PMCID: PMC8301361 DOI: 10.3390/biomedicines9070819] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
Assassin bug venoms are potent and exert diverse biological functions, making them potential biomedical goldmines. Besides feeding functions on arthropods, assassin bugs also use their venom for defense purposes causing localized and systemic reactions in vertebrates. However, assassin bug venoms remain poorly characterized. We collected the venom from the assassin bug Rhynocoris iracundus and investigated its composition and bioactivity in vitro and in vivo. It caused lysis of murine neuroblastoma, hepatoma cells, and healthy murine myoblasts. We demonstrated, for the first time, that assassin bug venom induces neurolysis and suggest that it counteracts paralysis locally via the destruction of neural networks, contributing to tissue digestion. Furthermore, the venom caused paralysis and melanization of Galleria mellonella larvae and pupae, whilst also possessing specific antibacterial activity against Escherichia coli, but not Listeria grayi and Pseudomonas aeruginosa. A combinatorial proteo-transcriptomic approach was performed to identify potential toxins responsible for the observed effects. We identified neurotoxic Ptu1, an inhibitory cystin knot (ICK) toxin homologous to ω-conotoxins from cone snails, cytolytic redulysins homologous to trialysins from hematophagous kissing bugs, and pore-forming hemolysins. Additionally, chitinases and kininogens were found and may be responsible for insecticidal and cytolytic activities. We demonstrate the multifunctionality and complexity of assassin bug venom, which renders its molecular components interesting for potential biomedical applications.
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Affiliation(s)
- Nicolai Rügen
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany; (N.R.); (A.V.)
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Natalie Wielsch
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745 Jena, Germany;
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany;
| | - Benjamin-Florian Hempel
- Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany; (B.-F.H.); (R.D.S.)
- BIH Center for Regenerative Therapies BCRT, Charité—Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Roderich D. Süssmuth
- Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany; (B.-F.H.); (R.D.S.)
| | - Stuart Ainsworth
- Centre for Snakebite Research and Interventions, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK;
| | - Alejandro Cabezas-Cruz
- UMR BIPAR, Laboratoire de Santé Animale, Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, F-94700 Maisons-Alfort, France;
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany; (N.R.); (A.V.)
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Miray Tonk
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany
- Correspondence:
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Oeyen M, Meyen E, Noppen S, Claes S, Doijen J, Vermeire K, Süssmuth RD, Schols D. Labyrinthopeptin A1 inhibits dengue and Zika virus infection by interfering with the viral phospholipid membrane. Virology 2021; 562:74-86. [PMID: 34274562 DOI: 10.1016/j.virol.2021.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 11/18/2022]
Abstract
To date, there are no broad-spectrum antivirals available to treat infections with flaviviruses such as dengue (DENV) and Zika virus (ZIKV). In this study, we determine the broad antiviral activity of the lantibiotic Labyrinthopeptin A1. We show that Laby A1 inhibits all DENV serotypes and various ZIKV strains with IC50 around 1 μM. The structurally related Laby A2 also displayed a consistent, but about tenfold lower, antiviral activity. Furthermore, Laby A1 inhibits many viruses from divergent families such as HIV, YFV, RSV and Punta Torovirus. Of interest, Laby A1 does not show activity against non-enveloped viruses. Its antiviral activity is independent of the cell line or the used evaluation method, and can also be observed in MDDC, a physiologically relevant primary cell type. Furthermore, Laby A1 demonstrates low cellular toxicity and has a more favorable SI compared to duramycin, a well-described lantibiotic with broad-spectrum antiviral activity. Time-of-drug addition experiments demonstrate that Laby A1 inhibits infection and entry processes of ZIKV and DENV. We reveal that Laby A1 performs its broad antiviral activity by interacting with a viral factor rather than a cellular factor, and that it has virucidal properties. Finally, using SPR interaction studies we demonstrate that Laby A1 interacts with several phospholipids (i.e. PE and PS) present in the viral envelope. Together with other recent Labyrinthopeptin antiviral publications, this work validates the activity of Laby A1 as broad antiviral entry inhibitor with a unique mechanism of action and demonstrates its potential value as antiviral agent against emerging flaviviruses.
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Affiliation(s)
- Merel Oeyen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000 Leuven, Belgium
| | - Eef Meyen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000 Leuven, Belgium
| | - Sam Noppen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000 Leuven, Belgium
| | - Sandra Claes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000 Leuven, Belgium
| | - Jordi Doijen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000 Leuven, Belgium
| | - Kurt Vermeire
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000 Leuven, Belgium
| | - Roderich D Süssmuth
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124/TC 2, D-10623 Berlin, Germany
| | - Dominique Schols
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000 Leuven, Belgium.
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Häbe TT, Späth C, Schrade S, Jörg W, Süssmuth RD, Bischoff D, Luippold AH. An ultrafast and flexible liquid chromatography/tandem mass spectrometry system paves the way for machine learning driven in vivo sample processing in early drug discovery. Rapid Commun Mass Spectrom 2021; 35:e9096. [PMID: 33837598 DOI: 10.1002/rcm.9096] [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] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE The low speed and low flexibility of most liquid chromatography/tandem mass spectrometry (LC/MS/MS) approaches in early drug discovery delay sample analysis from routine in vivo studies within the same day. A high-throughput platform for the rapid quantification of drug compounds in various in vivo assays was developed and established in routine bioanalysis. METHODS Automated selection of an efficient and adequate LC method was realized by autonomous sample qualification for ultrafast batch gradients (9 s/sample) or for fast linear gradients (45 s/sample) if samples required chromatography. The hardware and software components of our Rapid and Integrated Analysis System (RIAS) were streamlined for increased analytical throughput via state-of-the-art automation while maintaining high analytical quality. RESULTS Online decision-making was based on a quick assay suitability test (AST), based on a small and dedicated sample set evaluated by two different strategies. 84% of the acquired data points were within ±30% accuracy and 93% of the deviations between the lower limit of quantitation (LLOQ) values were ≤2-fold compared with standard LC/MS/MS systems. Speed, flexibility and overall automation significantly improved. CONCLUSIONS The developed platform provided an analysis time of only 10 min (batch-mode) and 47 min (gradient-mode) per standard pharmacokinetic (PK) study (62 injections). Automation, data evaluation and results handling were optimized to pave the way for machine learning based on decision-making regarding the evaluation strategy of the AST.
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Affiliation(s)
- Tim T Häbe
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Strasse 65, Biberach an der Riss, 88397, Germany
| | - Christian Späth
- Boehringer Ingelheim Pharma GmbH & Co. KG, ISEE Infrastructure, Safety, Environment and Engineering, Birkendorfer Strasse 65, Biberach an der Riss, 88397, Germany
| | - Steffen Schrade
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Strasse 65, Biberach an der Riss, 88397, Germany
| | - Wolfgang Jörg
- Boehringer Ingelheim Pharma GmbH & Co. KG, ISEE Infrastructure, Safety, Environment and Engineering, Birkendorfer Strasse 65, Biberach an der Riss, 88397, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, Berlin, 10623, Germany
| | - Daniel Bischoff
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Strasse 65, Biberach an der Riss, 88397, Germany
| | - Andreas H Luippold
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Strasse 65, Biberach an der Riss, 88397, Germany
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Behroz I, Kleebauer L, Hommernick K, Seidel M, Grätz S, Mainz A, Weston JB, Süssmuth RD. Acetylenic Replacement of Albicidin's Methacrylamide Residue Circumvents Detrimental E/Z Photoisomerization and Preserves Antibacterial Activity. Chemistry 2021; 27:9077-9086. [PMID: 33769627 PMCID: PMC8362182 DOI: 10.1002/chem.202100523] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 01/07/2023]
Abstract
The natural product albicidin is a highly potent inhibitor of bacterial DNA gyrase. Its outstanding activity, particularly against Gram-negative pathogens, qualifies it as a promising lead structure in the search for new antibacterial drugs. However, as we show here, the N-terminal cinnamoyl moiety of albicidin is susceptible to photochemical E/Z isomerization. Moreover, the newly formed Z isomer exhibits significantly reduced antibacterial activity, which hampers the development and biological evaluation of albicidin and potent derivatives thereof. Hence, we synthesized 13 different variants of albicidin in which the vulnerable para-coumaric acid moiety was replaced; this yielded photostable analogues. Biological activity assays revealed that diaryl alkyne analogues exhibited virtually undiminished antibacterial efficacy. This promising scaffold will therefore serve as a blueprint for the design of a potent albicidin-based drug.
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Affiliation(s)
- Iraj Behroz
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Leonardo Kleebauer
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Kay Hommernick
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Maria Seidel
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Stefan Grätz
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Andi Mainz
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - John B. Weston
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Roderich D. Süssmuth
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
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31
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Damm M, Hempel BF, Süssmuth RD. Old World Vipers-A Review about Snake Venom Proteomics of Viperinae and Their Variations. Toxins (Basel) 2021; 13:toxins13060427. [PMID: 34204565 PMCID: PMC8235416 DOI: 10.3390/toxins13060427] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 05/26/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 12/12/2022] Open
Abstract
Fine-tuned by millions of years of evolution, snake venoms have frightened but also fascinated humanity and nowadays they constitute potential resources for drug development, therapeutics and antivenoms. The continuous progress of mass spectrometry techniques and latest advances in proteomics workflows enabled toxinologists to decipher venoms by modern omics technologies, so-called ‘venomics’. A tremendous upsurge reporting on snake venom proteomes could be observed. Within this review we focus on the highly venomous and widely distributed subfamily of Viperinae (Serpentes: Viperidae). A detailed public literature database search was performed (2003–2020) and we extensively reviewed all compositional venom studies of the so-called Old-World Vipers. In total, 54 studies resulted in 89 venom proteomes. The Viperinae venoms are dominated by four major, four secondary, six minor and several rare toxin families and peptides, respectively. The multitude of different venomics approaches complicates the comparison of venom composition datasets and therefore we differentiated between non-quantitative and three groups of quantitative workflows. The resulting direct comparisons within these groups show remarkable differences on the intra- and interspecies level across genera with a focus on regional differences. In summary, the present compilation is the first comprehensive up-to-date database on Viperinae venom proteomes and differentiating between analytical methods and workflows.
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Affiliation(s)
- Maik Damm
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany;
| | - Benjamin-Florian Hempel
- BIH Center for Regenerative Therapies, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, (BCRT), 10117 Berlin, Germany;
| | - Roderich D. Süssmuth
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany;
- Correspondence: ; Tel.: +49-(0)30-314-24205
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32
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Schorn MA, Verhoeven S, Ridder L, Huber F, Acharya DD, Aksenov AA, Aleti G, Moghaddam JA, Aron AT, Aziz S, Bauermeister A, Bauman KD, Baunach M, Beemelmanns C, Beman JM, Berlanga-Clavero MV, Blacutt AA, Bode HB, Boullie A, Brejnrod A, Bugni TS, Calteau A, Cao L, Carrión VJ, Castelo-Branco R, Chanana S, Chase AB, Chevrette MG, Costa-Lotufo LV, Crawford JM, Currie CR, Cuypers B, Dang T, de Rond T, Demko AM, Dittmann E, Du C, Drozd C, Dujardin JC, Dutton RJ, Edlund A, Fewer DP, Garg N, Gauglitz JM, Gentry EC, Gerwick L, Glukhov E, Gross H, Gugger M, Guillén Matus DG, Helfrich EJN, Hempel BF, Hur JS, Iorio M, Jensen PR, Kang KB, Kaysser L, Kelleher NL, Kim CS, Kim KH, Koester I, König GM, Leao T, Lee SR, Lee YY, Li X, Little JC, Maloney KN, Männle D, Martin H C, McAvoy AC, Metcalf WW, Mohimani H, Molina-Santiago C, Moore BS, Mullowney MW, Muskat M, Nothias LF, O'Neill EC, Parkinson EI, Petras D, Piel J, Pierce EC, Pires K, Reher R, Romero D, Roper MC, Rust M, Saad H, Saenz C, Sanchez LM, Sørensen SJ, Sosio M, Süssmuth RD, Sweeney D, Tahlan K, Thomson RJ, Tobias NJ, Trindade-Silva AE, van Wezel GP, Wang M, Weldon KC, Zhang F, Ziemert N, Duncan KR, Crüsemann M, Rogers S, Dorrestein PC, Medema MH, van der Hooft JJJ. A community resource for paired genomic and metabolomic data mining. Nat Chem Biol 2021; 17:363-368. [PMID: 33589842 PMCID: PMC7987574 DOI: 10.1038/s41589-020-00724-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.
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Affiliation(s)
- Michelle A Schorn
- Laboratory of Microbiology, Department of Agricultural and Food Sciences, Wageningen University, Wageningen, the Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | | | - Lars Ridder
- Netherlands eScience Center, Amsterdam, the Netherlands
| | - Florian Huber
- Netherlands eScience Center, Amsterdam, the Netherlands
| | - Deepa D Acharya
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Gajender Aleti
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jamshid Amiri Moghaddam
- Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI), Jena, Germany
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Saefuddin Aziz
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- Microbiology Department, Biology Faculty, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Anelize Bauermeister
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Katherine D Bauman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Martin Baunach
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI), Jena, Germany
| | - J Michael Beman
- Department of Life and Environmental Sciences, University of California Merced, Merced, CA, USA
- Sierra Nevada Research Institute, University of California Merced, Merced, CA, USA
| | - María Victoria Berlanga-Clavero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Alex A Blacutt
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
| | - Anne Boullie
- Institut Pasteur, Collection of Cyanobacteria, Paris, France
| | - Asker Brejnrod
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tim S Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexandra Calteau
- Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Liu Cao
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Víctor J Carrión
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands
| | - Raquel Castelo-Branco
- Interdisciplinary Centre of Marine and Environmental Research), University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Shaurya Chanana
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexander B Chase
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Marc G Chevrette
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Bart Cuypers
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tam Dang
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Elke Dittmann
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany
| | - Chao Du
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Christopher Drozd
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Anna Edlund
- J. Craig Venter Institute, Genomic Medicine Group, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - David P Fewer
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Harald Gross
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Muriel Gugger
- Institut Pasteur, Collection of Cyanobacteria, Paris, France
| | - Dulce G Guillén Matus
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Eric J N Helfrich
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Benjamin-Florian Hempel
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
- Charité, University Medicine Berlin, Berlin-Brandenburg Center for Regenerative Therapy (BCRT), Campus Virchow Klinikum, Berlin, Germany
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Sunchon, Republic of Korea
| | | | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kyo Bin Kang
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Leonard Kaysser
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Chung Sub Kim
- Department of Chemistry, Yale University, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Irina Koester
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Tiago Leao
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seoung Rak Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Yi-Yuan Lee
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xuanji Li
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jessica C Little
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Daniel Männle
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Christian Martin H
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Panama, Republic of Panama
| | - Andrew C McAvoy
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Willam W Metcalf
- Carl R. Woese Institute for Genomic Biology and Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Mitchell Muskat
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ellis C O'Neill
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - Elizabeth I Parkinson
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Emily C Pierce
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Karine Pires
- Instituto Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Raphael Reher
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - M Caroline Roper
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Michael Rust
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Hamada Saad
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- Phytochemistry and Plant Systematics Department, Division of Pharmaceutical Industries, National Research Centre, Cairo, Egypt
| | - Carmen Saenz
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | | | | | | | - Douglas Sweeney
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, Canada
| | - Regan J Thomson
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Nicholas J Tobias
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Amaro E Trindade-Silva
- Departamento de Fisiologia e Farmacologia, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Gilles P van Wezel
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Fan Zhang
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI, USA
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, UK
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Simon Rogers
- School of Computing Science, University of Glasgow, Glasgow, UK
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology and Pediatrics, University of California San Diego, La Jolla, CA, USA.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
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Mazurek Ł, Ghilarov D, Michalczyk E, Pakosz Z, Metelev M, Czyszczoń W, Wawro K, Behroz I, Dubiley S, Süssmuth RD, Heddle JG. Pentapeptide repeat protein QnrB1 requires ATP hydrolysis to rejuvenate poisoned gyrase complexes. Nucleic Acids Res 2021; 49:1581-1596. [PMID: 33434265 PMCID: PMC7897471 DOI: 10.1093/nar/gkaa1266] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/16/2020] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
DNA gyrase, a type II topoisomerase found predominantly in bacteria, is the target for a variety of 'poisons', namely natural product toxins (e.g. albicidin, microcin B17) and clinically important synthetic molecules (e.g. fluoroquinolones). Resistance to both groups can be mediated by pentapeptide repeat proteins (PRPs). Despite long-term studies, the mechanism of action of these protective PRPs is not known. We show that a PRP, QnrB1 provides specific protection against fluoroquinolones, which strictly requires ATP hydrolysis by gyrase. QnrB1 binds to the GyrB protein and stimulates ATPase activity of the isolated N-terminal ATPase domain of GyrB (GyrB43). We probed the QnrB1 binding site using site-specific incorporation of a photoreactive amino acid and mapped the crosslinks to the GyrB43 protein. We propose a model in which QnrB1 binding allosterically promotes dissociation of the fluoroquinolone molecule from the cleavage complex.
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Affiliation(s)
- Łukasz Mazurek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Dmitry Ghilarov
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Zuzanna Pakosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | | | - Wojciech Czyszczoń
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Karolina Wawro
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Iraj Behroz
- Institute of Biological Chemistry, Technische Universität Berlin, Berlin, Germany
| | | | - Roderich D Süssmuth
- Institute of Biological Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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34
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Yushchuk O, Ostash I, Mösker E, Vlasiuk I, Deneka M, Rückert C, Busche T, Fedorenko V, Kalinowski J, Süssmuth RD, Ostash B. Eliciting the silent lucensomycin biosynthetic pathway in Streptomyces cyanogenus S136 via manipulation of the global regulatory gene adpA. Sci Rep 2021; 11:3507. [PMID: 33568768 PMCID: PMC7875965 DOI: 10.1038/s41598-021-82934-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 11/10/2020] [Accepted: 01/25/2021] [Indexed: 12/14/2022] Open
Abstract
Actinobacteria are among the most prolific sources of medically and agriculturally important compounds, derived from their biosynthetic gene clusters (BGCs) for specialized (secondary) pathways of metabolism. Genomics witnesses that the majority of actinobacterial BGCs are silent, most likely due to their low or zero transcription. Much effort is put into the search for approaches towards activation of silent BGCs, as this is believed to revitalize the discovery of novel natural products. We hypothesized that the global transcriptional factor AdpA, due to its highly degenerate operator sequence, could be used to upregulate the expression of silent BGCs. Using Streptomyces cyanogenus S136 as a test case, we showed that plasmids expressing either full-length adpA or its DNA-binding domain led to significant changes in the metabolome. These were evident as changes in the accumulation of colored compounds, bioactivity, as well as the emergence of a new pattern of secondary metabolites as revealed by HPLC-ESI-mass spectrometry. We further focused on the most abundant secondary metabolite and identified it as the polyene antibiotic lucensomycin. Finally, we uncovered the entire gene cluster for lucensomycin biosynthesis (lcm), that remained elusive for five decades until now, and outlined an evidence-based scenario for its adpA-mediated activation.
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Affiliation(s)
- Oleksandr Yushchuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm. 102, Lviv, 79005, Ukraine
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm. 102, Lviv, 79005, Ukraine
| | - Eva Mösker
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Iryna Vlasiuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm. 102, Lviv, 79005, Ukraine
| | - Maksym Deneka
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm. 102, Lviv, 79005, Ukraine
| | - Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Tobias Busche
- Technology Platform Genomics, CeBiTec, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm. 102, Lviv, 79005, Ukraine
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany.
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm. 102, Lviv, 79005, Ukraine.
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35
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 358] [Impact Index Per Article: 119.3] [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: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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Abstract
Lanthipeptides belong to the superfamily of ribosomally-synthesized and posttranslationally-modified peptides (RiPPs). Despite the fact that they represent one of the longest known RiPP subfamilies, their youngest members, classes III and IV, have only been described more recently. Since then, a plethora of studies furthered the understanding of their biosynthesis. While there are commonalities between classes III and IV due to the similar domain architectures of their processing enzymes, there are also striking differences that allow their discrimination. In this concise review article, we summarize what is known about the underlying biosynthetic principles of these lanthipeptides and discuss open questions for future research.
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Affiliation(s)
- Julian D Hegemann
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124 10623 Berlin Germany
| | - Roderich D Süssmuth
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124 10623 Berlin Germany
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37
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Wiebach V, Mainz A, Schnegotzki R, Siegert MAJ, Hügelland M, Pliszka N, Süssmuth RD. An Amphipathic Alpha-Helix Guides Maturation of the Ribosomally-Synthesized Lipolanthines. Angew Chem Int Ed Engl 2020; 59:16777-16785. [PMID: 32533616 PMCID: PMC7540663 DOI: 10.1002/anie.202003804] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 03/13/2020] [Revised: 05/15/2020] [Indexed: 12/19/2022]
Abstract
The recently discovered strongly anti‐Gram‐positive lipolanthines represent a new group of lipidated, ribosomally synthesized and post‐translationally modified peptides (RiPPs). They are bicyclic octapeptides with a central quaternary carbon atom (avionin), which is installed through the cooperative action of the class‐III lanthipeptide synthetase MicKC and the cysteine decarboxylase MicD. Genome mining efforts indicate a widespread distribution and unprecedented biosynthetic diversity of lipolanthine gene clusters, combining elements of RiPPs, polyketide and non‐ribosomal peptide biosynthesis. Utilizing NMR spectroscopy, we show that a (θxx)θxxθxxθ (θ=L, I, V, M or T) motif, which is conserved in the leader peptides of all class‐III and ‐IV lanthipeptides, forms an amphipathic α‐helix in MicA that destines the peptide substrate for enzymatic processing. Our results provide general rules of substrate recruitment and enzymatic regulation during lipolanthine maturation. These insights will facilitate future efforts to rationally design new lanthipeptide scaffolds with antibacterial potency.
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Affiliation(s)
- Vincent Wiebach
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Andi Mainz
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Romina Schnegotzki
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Mary-Ann J Siegert
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Manuela Hügelland
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Nicole Pliszka
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Roderich D Süssmuth
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
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38
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Wiebach V, Mainz A, Schnegotzki R, Siegert MJ, Hügelland M, Pliszka N, Süssmuth RD. Eine amphipathische alpha‐Helix lenkt die Modifizierung ribosomal‐synthetisierter Lipolanthine. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003804] [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: 11/05/2022]
Affiliation(s)
- Vincent Wiebach
- Institut für Chemie/ Biologische ChemieTechnische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Andi Mainz
- Institut für Chemie/ Biologische ChemieTechnische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Romina Schnegotzki
- Institut für Chemie/ Biologische ChemieTechnische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Mary‐Ann J. Siegert
- Institut für Chemie/ Biologische ChemieTechnische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Manuela Hügelland
- Institut für Chemie/ Biologische ChemieTechnische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Nicole Pliszka
- Institut für Chemie/ Biologische ChemieTechnische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Roderich D. Süssmuth
- Institut für Chemie/ Biologische ChemieTechnische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
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39
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Trünkle C, Lechner C, Korr D, Bouché L, Barak N, Fernández-Montalván A, Süssmuth RD, Reichel A. Concentration Dependence of the Unbound Partition Coefficient Kpuu and Its Application to Correct for Exposure-Related Discrepancies between Biochemical and Cellular Potency of KAT6A Inhibitors. Drug Metab Dispos 2020; 48:553-562. [DOI: 10.1124/dmd.120.090563] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/07/2020] [Indexed: 12/13/2022] Open
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40
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Siegert MJ, Knittel CH, Süssmuth RD. Back Cover: A Convergent Total Synthesis of the Death Cap Toxin α‐Amanitin (Angew. Chem. Int. Ed. 14/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/anie.202001279] [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: 11/10/2022]
Affiliation(s)
- Mary‐Ann J. Siegert
- Institute of Chemistry Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Caroline H. Knittel
- Institute of Chemistry Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Roderich D. Süssmuth
- Institute of Chemistry Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
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41
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Siegert MJ, Knittel CH, Süssmuth RD. Rücktitelbild: Eine konvergente Totalsynthese des Pilztoxins α‐Amanitin (Angew. Chem. 14/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001279] [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: 11/11/2022]
Affiliation(s)
- Mary‐Ann J. Siegert
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Caroline H. Knittel
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Roderich D. Süssmuth
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
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42
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Hempel BF, Damm M, Mrinalini, Göçmen B, Karış M, Nalbantsoy A, Kini RM, Süssmuth RD. Extended Snake Venomics by Top-Down In-Source Decay: Investigating the Newly Discovered Anatolian Meadow Viper Subspecies, Vipera anatolica senliki. J Proteome Res 2020; 19:1731-1749. [PMID: 32073270 DOI: 10.1021/acs.jproteome.9b00869] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein, we report on the venom proteome of Vipera anatolica senliki, a recently discovered and hitherto unexplored subspecies of the critically endangered Anatolian meadow viper endemic to the Antalya Province of Turkey. Integrative venomics, including venom gland transcriptomics as well as complementary bottom-up and top-down proteomics analyses, were applied to fully characterize the venom of V. a. senliki. Furthermore, the classical top-down venomics approach was extended to elucidate the venom proteome by an alternative in-source decay (ISD) proteomics workflow using the reducing matrix 1,5-diaminonaphthalene. Top-down ISD proteomics allows for disulfide bond counting and effective de novo sequencing-based identification of high-molecular-weight venom constituents, both of which are difficult to achieve by commonly established top-down approaches. Venom gland transcriptome analysis identified 96 toxin transcript annotations from 18 toxin families. Relative quantitative snake venomics revealed snake venom metalloproteinases (42.9%) as the most abundant protein family, followed by several less dominant toxin families. Online mass profiling and top-down venomics provide a detailed insight into the venom proteome of V. a. senliki and facilitate a comparative analysis of venom variability for the closely related subspecies, Vipera anatolica anatolica.
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Affiliation(s)
- Benjamin-Florian Hempel
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Maik Damm
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Mrinalini
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Bayram Göçmen
- Department of Biology, Faculty of Science, Ege University, 35100 Bornova, 35100 Izmir, Turkey
| | - Mert Karış
- Department of Biology, Faculty of Science, Ege University, 35100 Bornova, 35100 Izmir, Turkey
| | - Ayse Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Izmir, Bornova, Turkey
| | - R Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 16, Medical Drive, Singapore 117600
| | - Roderich D Süssmuth
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
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43
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Drzazgowska J, Schmid B, Süssmuth RD, Altintas Z. Self-Assembled Monolayer Epitope Bridges for Molecular Imprinting and Cancer Biomarker Sensing. Anal Chem 2020; 92:4798-4806. [DOI: 10.1021/acs.analchem.9b03813] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Julia Drzazgowska
- Institute of Chemistry, Technical University of Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Bianca Schmid
- Institute of Chemistry, Technical University of Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Roderich D. Süssmuth
- Institute of Chemistry, Technical University of Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Zeynep Altintas
- Institute of Chemistry, Technical University of Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
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Abstract
The toxic bicyclic octapeptide α-amanitin is mostly found in different species of the mushroom genus Amanita, with the death cap (Amanita phalloides) as one of the most prominent members. Due to its high selective inhibition of RNA polymerase II, which is directly linked to its high toxicity, particularly to hepatocytes, α-amanitin received an increased attention as a toxin-component of antibody-drug conjugates (ADC) in cancer research. Furthermore, the isolation of α-amanitin from mushrooms as the sole source severely restricts compound supply as well as further investigations, as structure-activity relationship (SAR) studies. Based on a straightforward access to the non-proteinogenic amino acid dihydroxyisoleucine, we herein present a robust total synthesis of α-amanitin providing options for production at larger scale as well as future structural diversifications.
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Affiliation(s)
- Mary‐Ann J. Siegert
- Institute of ChemistryTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Caroline H. Knittel
- Institute of ChemistryTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Roderich D. Süssmuth
- Institute of ChemistryTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
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45
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Affiliation(s)
- Mary‐Ann J. Siegert
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Caroline H. Knittel
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Roderich D. Süssmuth
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Deutschland
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46
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Schaefer M, Morinaga G, Saito A, Matsui A, Schänzle G, Bischoff D, Klinder K, Süssmuth RD. P117 - Impact of culture conditions on functional expression of major drug metabolizing enzymes and transporters in long-term UPCYTE® hepatocyte culture. Drug Metab Pharmacokinet 2020. [DOI: 10.1016/j.dmpk.2020.04.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Behroz I, Durkin P, Grätz S, Seidel M, Rostock L, Spinczyk M, Weston JB, Süssmuth RD. Extensive Structure-Activity Relationship Study of Albicidin's C-Terminal Dipeptidic p-Aminobenzoic Acid Moiety. Chemistry 2019; 25:16538-16543. [PMID: 31642561 PMCID: PMC6972991 DOI: 10.1002/chem.201904752] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Indexed: 01/24/2023]
Abstract
Albicidin is a recently described natural product that strongly inhibits bacterial DNA gyrase. The pronounced activity, particularly against Gram-negative bacteria, turns it into a promising lead structure for an antibacterial drug. Hence, structure-activity relationship studies are key for the in-depth understanding of structural features/moieties affecting gyrase inhibition, antibacterial activity and overcoming resistance. The 27 newly synthesized albicidins give profound insights into possibilities for variations of the C-terminus. Furthermore, in the present study, a novel derivative has been identified as overcoming resistance posed by the Klebsiella-protease AlbD. Structural modifications include, for example, azahistidine replacing the previous instable cyanoalanine as the central amino acid, as well as a triazole amide bond isostere between building blocks D and E.
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Affiliation(s)
- Iraj Behroz
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Patrick Durkin
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Stefan Grätz
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Maria Seidel
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Lida Rostock
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Marcello Spinczyk
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - John B. Weston
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Roderich D. Süssmuth
- Institut für Organische ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
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Casewell NR, Petras D, Card DC, Suranse V, Mychajliw AM, Richards D, Koludarov I, Albulescu LO, Slagboom J, Hempel BF, Ngum NM, Kennerley RJ, Brocca JL, Whiteley G, Harrison RA, Bolton FMS, Debono J, Vonk FJ, Alföldi J, Johnson J, Karlsson EK, Lindblad-Toh K, Mellor IR, Süssmuth RD, Fry BG, Kuruppu S, Hodgson WC, Kool J, Castoe TA, Barnes I, Sunagar K, Undheim EAB, Turvey ST. Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals. Proc Natl Acad Sci U S A 2019; 116:25745-25755. [PMID: 31772017 PMCID: PMC6926037 DOI: 10.1073/pnas.1906117116] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents the ancestral state in this group or is the result of multiple independent origins. We investigated the origin and evolution of venom in eulipotyphlans by characterizing the venom system of the endangered Hispaniolan solenodon (Solenodon paradoxus). We constructed a genome to underpin proteomic identifications of solenodon venom toxins, before undertaking evolutionary analyses of those constituents, and functional assessments of the secreted venom. Our findings show that solenodon venom consists of multiple paralogous kallikrein 1 (KLK1) serine proteases, which cause hypotensive effects in vivo, and seem likely to have evolved to facilitate vertebrate prey capture. Comparative analyses provide convincing evidence that the oral venom systems of solenodons and shrews have evolved convergently, with the 4 independent origins of venom in eulipotyphlans outnumbering all other venom origins in mammals. We find that KLK1s have been independently coopted into the venom of shrews and solenodons following their divergence during the late Cretaceous, suggesting that evolutionary constraints may be acting on these genes. Consequently, our findings represent a striking example of convergent molecular evolution and demonstrate that distinct structural backgrounds can yield equivalent functions.
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Affiliation(s)
- Nicholas R Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom;
| | - Daniel Petras
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, TX 76010
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Vivek Suranse
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, 560012 Bangalore, India
| | - Alexis M Mychajliw
- Department of Biology, Stanford University, Stanford, CA 94305
- Department of Rancho La Brea, Natural History Museum of Los Angeles County, Los Angeles, CA 90036
- Institute of Low Temperature Science, Hokkaido University, 060-0819 Sapporo, Japan
| | - David Richards
- School of Life Sciences, University of Nottingham, University Park, NG7 2RD Nottingham, United Kingdom
- Biomedical Research Centre, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, United Kingdom
| | - Ivan Koludarov
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Laura-Oana Albulescu
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom
| | - Julien Slagboom
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 LA Amsterdam, The Netherlands
| | | | - Neville M Ngum
- School of Life Sciences, University of Nottingham, University Park, NG7 2RD Nottingham, United Kingdom
| | - Rosalind J Kennerley
- Durrell Wildlife Conservation Trust, Les Augrès Manor, Trinity, Jersey JE3 5BP, British Channel Islands, United Kingdom
| | - Jorge L Brocca
- SOH Conservación, Apto. 401 Residencial Las Galerías, Santo Domingo, 10130, Dominican Republic
| | - Gareth Whiteley
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom
| | - Robert A Harrison
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom
| | - Fiona M S Bolton
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom
| | - Jordan Debono
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia, QLD 4067, Australia
| | - Freek J Vonk
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
| | - Jessica Alföldi
- Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Jeremy Johnson
- Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Elinor K Karlsson
- Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Kerstin Lindblad-Toh
- Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Ian R Mellor
- School of Life Sciences, University of Nottingham, University Park, NG7 2RD Nottingham, United Kingdom
| | | | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia, QLD 4067, Australia
| | - Sanjaya Kuruppu
- Monash Venom Group, Department of Pharmacology, Biomedicine Discovery Institute, Monash University, VIC 3800, Australia
- Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, VIC 3800, Australia
| | - Wayne C Hodgson
- Monash Venom Group, Department of Pharmacology, Biomedicine Discovery Institute, Monash University, VIC 3800, Australia
| | - Jeroen Kool
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 LA Amsterdam, The Netherlands
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX 76010
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, SW7 5BD London, United Kingdom
| | - Kartik Sunagar
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, 560012 Bangalore, India
| | - Eivind A B Undheim
- Centre for Advanced Imaging, The University of Queensland, Brisbane QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo 0316, Norway
| | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY London, United Kingdom
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Steiniger C, Hoffmann S, Süssmuth RD. Probing Exchange Units for Combining Iterative and Linear Fungal Nonribosomal Peptide Synthetases. Cell Chem Biol 2019; 26:1526-1534.e2. [DOI: 10.1016/j.chembiol.2019.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/08/2019] [Accepted: 08/09/2019] [Indexed: 11/30/2022]
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Mudalungu CM, von Törne WJ, Voigt K, Rückert C, Schmitz S, Sekurova ON, Zotchev SB, Süssmuth RD. Noursamycins, Chlorinated Cyclohexapeptides Identified from Molecular Networking of Streptomyces noursei NTR-SR4. J Nat Prod 2019; 82:1478-1486. [PMID: 31181917 DOI: 10.1021/acs.jnatprod.8b00967] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The noursamycins A-F are chlorinated cyclic hexapeptides, which were identified and isolated from the strain Streptomyces noursei NTR-SR4 overexpressing a LuxR-like transcriptional activator. The molecules were structurally characterized by mass spectrometric analyses and 1D and 2D NMR spectroscopic techniques. The enzymatic machinery involved in the biosynthesis of these peptides is represented by a modular nonribosomal peptide synthetase (NRPS), and the corresponding gene cluster was identified in the S. noursei genome. The latter suggested the biosynthetic pathway for the noursamycins. Spectral networking analysis uncovered noursamycin derivatives that were later found to result from a relaxed substrate specificity of the A3 and A4 adenylation domains of the NRPS. The stereochemistry of the amino acid constituents of the noursamycins was resolved by chemical derivatization, subsequent enantiomer analytics by GC-EIMS, and in silico data analyses. Noursamycins A and B exhibited antibacterial activity against Gram-positive and Gram-negative bacteria, while no apparent cytotoxicity was observed.
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Affiliation(s)
- Cynthia M Mudalungu
- Technische Universität Berlin, Institut für Chemie , Straße des 17. Juni 124 , 10623 Berlin , Germany
| | - Wipert J von Törne
- Technische Universität Berlin, Institut für Chemie , Straße des 17. Juni 124 , 10623 Berlin , Germany
| | - Kerstin Voigt
- Jena Microbial Resource Collection , Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstraße 11a , 07745 Jena , Germany
| | - Christian Rückert
- Centrum für Biotechnologie (CeBiTec) , Universität Bielefeld , Universitätsstraße 25 , 33615 Bielefeld , Germany
| | - Stefan Schmitz
- Department of Biotechnology , Norwegian University of Science and Technology , Trondheim NO-7491 , Norway
| | - Olga N Sekurova
- Department of Pharmacognosy , University of Vienna , Althanstraße 14 , 1090 Wien , Austria
| | - Sergey B Zotchev
- Department of Pharmacognosy , University of Vienna , Althanstraße 14 , 1090 Wien , Austria
| | - Roderich D Süssmuth
- Technische Universität Berlin, Institut für Chemie , Straße des 17. Juni 124 , 10623 Berlin , Germany
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