1
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Tan B, Zhang Q, Zhang L, Zhu Y, Zhang C. Naturally Occurring and Widespread Resistance to Bioactive Natural Products. ChemMedChem 2024; 19:e202300619. [PMID: 38103004 DOI: 10.1002/cmdc.202300619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 12/17/2023]
Abstract
Naturally occurring resistances diminish the effectiveness of antibiotics, and present significant challenges to human health. Human activities are usually considered as the main drivers of the dissemination of antibiotic resistance, however, the origin of the clinical antibiotic resistance can be traced to the environmental microbes, and the clinically relevant resistance determinants have already pre-existed in nature before the antibiotics come into clinic. In this concept, we present the naturally occurring and widespread resistance determinants recently discovered during the biosynthesis study of bioactive compounds. These widely prevalent resistances in environmental microbes, including antibiotic producers and non-producers, advance the understanding of the origin of resistance, and provide prediction for the clinically relevant resistance to aid in the rational design of more effective drug analogues to combat resistance.
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Affiliation(s)
- Bin Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
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2
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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] [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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3
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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] [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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4
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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: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [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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5
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Newly Discovered Mechanisms of Antibiotic Self-Resistance with Multiple Enzymes Acting at Different Locations and Stages. Antibiotics (Basel) 2022; 12:antibiotics12010035. [PMID: 36671236 PMCID: PMC9854587 DOI: 10.3390/antibiotics12010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Self-resistance determinants are essential for the biosynthesis of bioactive natural products and are closely related to drug resistance in clinical settings. The study of self-resistance mechanisms has long moved forward on the discovery of new resistance genes and the characterization of enzymatic reactions catalyzed by these proteins. However, as more examples of self-resistance have been reported, it has been revealed that the enzymatic reactions contribute to self-protection are not confined to the cellular location where the final toxic compounds are present. In this review, we summarize representative examples of self-resistance mechanisms for bioactive natural products functional at different cell locations to explore the models of resistance strategies involved. Moreover, we also highlight those resistance determinants that are widespread in nature and describe the applications of self-resistance genes in natural product mining to interrogate the landscape of self-resistance genes in drug resistance-related new drug discovery.
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6
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Testolin G, Richter J, Ritter A, Prochnow H, Köhnke J, Brönstrup M. Optical Modulation of Antibiotic Resistance by Photoswitchable Cystobactamids. Chemistry 2022; 28:e202201297. [PMID: 35771231 DOI: 10.1002/chem.202201297] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 01/07/2023]
Abstract
The rise of antibiotic resistance causes a serious health care problem, and its counterfeit demands novel, innovative concepts. The combination of photopharmacology, enabling a light-controlled reversible modulation of drug activity, with antibiotic drug design has led to first photoswitchable antibiotic compounds derived from established scaffolds. In this study, we converted cystobactamids, gyrase-inhibiting natural products with an oligoaryl scaffold and highly potent antibacterial activities, into photoswitchable agents by inserting azobenzene in the N-terminal part and/or an acylhydrazone moiety near the C-terminus, yielding twenty analogs that contain mono- as well as double-switches. Antibiotic and gyrase inhibition properties could be modulated 3.4-fold and 5-fold by light, respectively. Notably, the sensitivity of photoswitchable cystobactamids towards two known resistance factors, the peptidase AlbD and the scavenger protein AlbA, was light-dependent. While irradiation of an analog with an N-terminal azobenzene with 365 nm light led to less degradation by AlbD, the AlbA-mediated inactivation was induced. This provides a proof-of-principle that resistance towards photoswitchable antibiotics can be optically controlled.
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Affiliation(s)
- Giambattista Testolin
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Jana Richter
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Antje Ritter
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Hans Prochnow
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Jesko Köhnke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,German Center for Infection Research (DZIF) Site Hannover-Braunschweig, 38124, Braunschweig, Germany.,Center of Biomolecular Drug Research (BMWZ), Leibniz University, 30159, Hannover, Germany
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7
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Gude F, Molloy EM, Horch T, Dell M, Dunbar KL, Krabbe J, Groll M, Hertweck C. A Specialized Polythioamide‐Binding Protein Confers Antibiotic Self‐Resistance in Anaerobic Bacteria. Angew Chem Int Ed Engl 2022; 61:e202206168. [PMID: 35852818 PMCID: PMC9545259 DOI: 10.1002/anie.202206168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Indexed: 12/04/2022]
Abstract
Understanding antibiotic resistance mechanisms is central to the development of anti‐infective therapies and genomics‐based drug discovery. Yet, many knowledge gaps remain regarding the resistance strategies employed against novel types of antibiotics from less‐explored producers such as anaerobic bacteria, among them the Clostridia. Through the use of genome editing and functional assays, we found that CtaZ confers self‐resistance against the copper chelator and gyrase inhibitor closthioamide (CTA) in Ruminiclostridium cellulolyticum. Bioinformatics, biochemical analyses, and X‐ray crystallography revealed CtaZ as a founding member of a new group of GyrI‐like proteins. CtaZ is unique in binding a polythioamide scaffold in a ligand‐optimized hydrophobic pocket, thereby confining CTA. By genome mining using CtaZ as a handle, we discovered previously overlooked homologs encoded by diverse members of the phylum Firmicutes, including many pathogens. In addition to characterizing both a new role for a GyrI‐like domain in self‐resistance and unprecedented thioamide binding, this work aids in uncovering related drug‐resistance mechanisms.
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Affiliation(s)
- Finn Gude
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Evelyn M. Molloy
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Therese Horch
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Maria Dell
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Kyle L. Dunbar
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Jana Krabbe
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Michael Groll
- Center for Protein AssembliesTechnical University of MunichErnst-Otto-Fischer-Straße 885747GarchingGermany
| | - Christian Hertweck
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
- Faculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
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8
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Tao S, Chen H, Li N, Liang W. The Application of the CRISPR-Cas System in Antibiotic Resistance. Infect Drug Resist 2022; 15:4155-4168. [PMID: 35942309 PMCID: PMC9356603 DOI: 10.2147/idr.s370869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022] Open
Abstract
The emergence and global epidemic of antimicrobial resistance (AMR) poses a serious threat to global public health in recent years. AMR genes are shared between bacterial pathogens mainly via horizontal gene transfer (HGT) on mobile genetic elements (MGEs), thereby accelerating the spread of antimicrobial resistance (AMR) and increasing the burden of drug resistance. There is an urgent need to develop new strategies to control bacterial infections and the spread of antimicrobial resistance. The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are an RNA-guided adaptive immune system in prokaryotes that recognizes and defends against invasive genetic elements such as phages and plasmids. Because of its specifically target and cleave DNA sequences encoding antibiotic resistance genes, CRISPR/Cas system has been developed into a new gene-editing tool for the prevention and control of bacterial drug resistance. CRISPR-Cas plays a potentially important role in controlling horizontal gene transfer and limiting the spread of antibiotic resistance. In this review, we will introduce the structure and working mechanism of CRISPR-Cas systems, followed by delivery strategies, and then focus on the relationship between antimicrobial resistance and CRISPR-Cas. Moreover, the challenges and prospects of this research field are discussed, thereby providing a reference for the prevention and control of the spread of antibiotic resistance.
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Affiliation(s)
- Shuan Tao
- School of Medical, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, People’s Republic of China
- Lianyungang Clinical College of Jiangsu University, Lianyungang, Jiangsu Province, 222023, People’s Republic of China
| | - Huimin Chen
- School of Medical, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, People’s Republic of China
| | - Na Li
- Bengbu Medical College, Bengbu, Anhui Province, 233030, People’s Republic of China
| | - Wei Liang
- Lianyungang Clinical College of Jiangsu University, Lianyungang, Jiangsu Province, 222023, People’s Republic of China
- Correspondence: Wei Liang, Lianyungang Clinical College of Jiangsu University, No. 161. Xingfu Road, Haizhou District, Lianyungang, Jiangsu Province, 222023, People’s Republic of China, Tel/Fax +86-51885213100; Tel/Fax +86 15351883016, Email
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9
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Gude F, Molloy EM, Horch T, Dell M, Dunbar KL, Krabbe J, Groll M, Hertweck C. A Specialized Polythioamide‐Binding Protein Confers Antibiotic Self‐Resistance in Anaerobic Bacteria. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Finn Gude
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Evelyn M. Molloy
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Therese Horch
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Maria Dell
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Kyle L. Dunbar
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Jana Krabbe
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Michael Groll
- TU München: Technische Universitat Munchen Center for Protein Assemblies GERMANY
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI Department of Biomolecular Chemistry Beutenbergstr. 11a 07745 Jena GERMANY
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10
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Pramanik A, Sharma PC, Patibandla S, Gao Y, Ruppa-Kasani V, Goli J, Kumar A, Chatterjee A, Sinha SS, Bates JT, Bierdeman MA, Tandon R, Ray PC. Blocking SARS-CoV-2 Delta Variant (B.1.617.2) Spike Protein Receptor-Binding Domain Binding with the ACE2 Receptor of the Host Cell and Inhibiting Virus Infections Using Human Host Defense Peptide-Conjugated Graphene Quantum Dots. ACS OMEGA 2022; 7:8150-8157. [PMID: 35252734 PMCID: PMC8886715 DOI: 10.1021/acsomega.2c00113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/01/2022] [Indexed: 05/24/2023]
Abstract
The emergence of double mutation delta (B.1.617.2) variants has dropped vaccine effectiveness against SARS-CoV-2 infection. Although COVID-19 is responsible for more than 5.4 M deaths till now, more than 40% of infected individuals are asymptomatic carriers as the immune system of the human body can control the SARS-CoV-2 infection. Herein, we report for the first time that human host defense neutrophil α-defensin HNP1 and human cathelicidin LL-37 peptide-conjugated graphene quantum dots (GQDs) have the capability to prevent the delta variant virus entry into the host cells via blocking SARS-CoV-2 delta variant (B.1.617.2) spike protein receptor-binding domain (RBD) binding with host cells' angiotensin converting enzyme 2 (ACE2). Experimental data shows that due to the binding between the delta variant spike protein RBD and bioconjugate GQDs, in the presence of the delta variant spike protein, the fluorescence signal from GQDs quenched abruptly. Experimental quenching data shows a nonlinear Stern-Volmer quenching profile, which indicates multiple binding sites. Using the modified Hill equation, we have determined n = 2.6 and the effective binding affinity 9 nM, which is comparable with the ACE2-spike protein binding affinity (8 nM). Using the alpha, beta, and gamma variant spike-RBD, experimental data shows that the binding affinity for the delta B.1.617.2 variant is higher than those for the other variants. Further investigation using the HEK293T-human ACE2 cell line indicates that peptide-conjugated GQDs have the capability for completely inhibiting the entry of delta variant SARS-CoV-2 pseudovirions into host cells via blocking the ACE2-spike protein binding. Experimental data shows that the inhibition efficiency for LL-37 peptide- and HNP1 peptide-attached GQDs are much higher than that of only one type of peptide-attached GQDs.
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Affiliation(s)
- Avijit Pramanik
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
| | - Poonam C. Sharma
- Department
of Microbiology and Immunology, University
of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Shamily Patibandla
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
| | - Ye Gao
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
| | - Vinod Ruppa-Kasani
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
| | - Jagruti Goli
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
| | - Animesh Kumar
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
| | - Abhirup Chatterjee
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
| | - Sudarson Sekhar Sinha
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
| | - John T. Bates
- Department
of Microbiology and Immunology, University
of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Michael A. Bierdeman
- Department
of Microbiology and Immunology, University
of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Ritesh Tandon
- Department
of Microbiology and Immunology, University
of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Paresh Chandra Ray
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
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11
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Reductive inactivation of the hemiaminal pharmacophore for resistance against tetrahydroisoquinoline antibiotics. Nat Commun 2021; 12:7085. [PMID: 34873166 PMCID: PMC8648761 DOI: 10.1038/s41467-021-27404-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 11/11/2021] [Indexed: 12/24/2022] Open
Abstract
Antibiotic resistance is becoming one of the major crises, among which hydrolysis reaction is widely employed by bacteria to destroy the reactive pharmacophore. Correspondingly, antibiotic producer has canonically co-evolved this approach with the biosynthetic capability for self-resistance. Here we discover a self-defense strategy featuring with reductive inactivation of hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and homW, which are integrated with the naphthyridinomycin biosynthetic pathway. We determine the crystal structure of NapW·NADPH complex and propose a catalytic mechanism by molecular dynamics simulation analysis. Additionally, a similar detoxification strategy is identified in the biosynthesis of saframycin A, another member of tetrahydroisoquinoline (THIQ) antibiotics. Remarkably, similar SDRs are widely spread in bacteria and able to inactive other THIQ members including the clinical anticancer drug, ET-743. These findings not only fill in the missing intracellular events of temporal-spatial shielding mode for cryptic self-resistance during THIQs biosynthesis, but also exhibit a sophisticated damage-control in secondary metabolism and general immunity toward this family of antibiotics. Antibiotic-producing organisms need to co-evolve self-protection mechanisms to avoid any damage to themselves caused by the antibiotic pharmacophore (the reactive part of the compound). In this study, the authors report a self-defense strategy in naphthyridinomycin (NDM)-producing Streptomyces lusitanus, that comprises reductive inactivation of the hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and HomW.
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12
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Mann A, Nehra K, Rana J, Dahiya T. Antibiotic resistance in agriculture: Perspectives on upcoming strategies to overcome upsurge in resistance. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100030. [PMID: 34841321 PMCID: PMC8610298 DOI: 10.1016/j.crmicr.2021.100030] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance is a massive problem rising constantly and spreading rapidly since the past decade. The major underlying mechanism responsible for this problem is an overuse or severe misuse of antibiotics. Regardless of this emerging global threat, antibiotics are still being widely used, not only for treatment of human infections, but also to a great extent in agriculture, livestock and animal husbandry. If the current scenario persists, we might enter into a post-antibiotic era where drugs might not be able to treat even the simplest of infections. This review discusses the current status of antibiotic utilization and molecular basis of antibiotic resistance mechanisms acquired by bacteria, along with the modes of transmittance of the resultant resistant genes into human pathogens through their cycling among different ecosystems. The main focus of the article is to provide an insight into the different molecular and other strategies currently being studied worldwide for their use as an alternate to antibiotics with an overall aim to overcome or minimize the global problem of antibiotic resistance.
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13
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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: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [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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14
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Pan Z, Huang J, Zhuang W. Protein-Ligand Binding Molecular Details Revealed by Terahertz Optical Kerr Spectroscopy: A Simulation Study. JACS AU 2021; 1:1788-1797. [PMID: 34723281 PMCID: PMC8549111 DOI: 10.1021/jacsau.1c00356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Indexed: 06/13/2023]
Abstract
Picosecond fast motions and their involvement in the biochemical processes such as protein-ligand binding has engaged significant attention. Terahertz optical Kerr spectroscopy (OKE) has the superior potential to probe these fast motions directly. Application of OKE in protein-ligand binding study is, however, limited by the difficulty of quantitative atomistic interpretation, and the calculation of Kerr spectrum for entire solvated protein complex was considered not yet feasible, due to the lack of one consistent polarizable model for both configuration sampling and polarizability calculation. Here, we analyzed the biochemical relevance of OKE to the lysozyme-triacetylchitotriose binding based on the first OKE simulation using one consistent Drude polarizable model. An analytical multipole and induced dipole scheme was employed to calculate the off-diagonal Drude polarizability more efficiently and accurately. Further theoretical analysis revealed how the subtle twisting and stiffening of aromatic protein residues' spatial arrangement as well as the confinement of small water clusters between ligand and protein cavity due to the ligand binding can be examined using Kerr spectroscopy. Comparison between the signals of bound complex and that of uncorrelated protein/ligand demonstrated that binding action alone has reflection in the OKE spectrum. Our study indicated OKE as a powerful terahertz probe for protein-ligand binding chemistry and dynamics.
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Affiliation(s)
- Zhijun Pan
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, Fuzhou, Fujian 35000, China
- Shenzhen
Bay Laboratory, Guangming
District, Shenzhen 518107, China
| | - Jing Huang
- Westlake
Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural
Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Wei Zhuang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, Fuzhou, Fujian 35000, China
- Institute
of Urban Environment, Chinese Academy of
Sciences, XiaMen, Fujian 361021, China
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15
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Structure and dynamics of UBA5-UFM1 complex formation showing new insights in the UBA5 activation mechanism. J Struct Biol 2021; 213:107796. [PMID: 34508858 DOI: 10.1016/j.jsb.2021.107796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/17/2021] [Accepted: 09/05/2021] [Indexed: 11/21/2022]
Abstract
Ubiquitin fold modifier 1 (UFM1) is an ubiquitin-like protein (Ubl) involved especially in endoplasmic stress response. Activation occurs via a three-step mechanism like other Ubls. Data obtained reveal that UFM1 regulates the oligomeric state of ubiquitin activating enzyme 5 (UBA5) to initiate the activation step. Mixtures of homodimers and heterotrimers are observed in solution at the equilibrium state, demonstrating that the UBA5-UFM1 complex undergoes several concentration dependent oligomeric translational states to form a final functional complex. The oligomerization state of unbound UBA5 is also concentration dependent and shifts from the monomeric to the dimeric state. Data describing different oligomeric states are complemented with binding studies that reveal a negative cooperativity for the complex formation and thereby provide more detailed insights into the complex formation mechanism.
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16
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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] [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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17
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Kortright KE, Doss-Gollin S, Chan BK, Turner PE. Evolution of Bacterial Cross-Resistance to Lytic Phages and Albicidin Antibiotic. Front Microbiol 2021; 12:658374. [PMID: 34220747 PMCID: PMC8245764 DOI: 10.3389/fmicb.2021.658374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/10/2021] [Indexed: 11/21/2022] Open
Abstract
Due to concerns over the global increase of antibiotic-resistant bacteria, alternative antibacterial strategies, such as phage therapy, are increasingly being considered. However, evolution of bacterial resistance to new therapeutics is almost a certainty; indeed, it is possible that resistance to alternative treatments might result in an evolved trade-up such as enhanced antibiotic resistance. Here, we hypothesize that selection for Escherichia coli bacteria to resist phage T6, phage U115, or albicidin, a DNA gyrase inhibitor, should often result in a pleiotropic trade-up in the form of cross-resistance, because all three antibacterial agents interact with the Tsx porin. Selection imposed by any one of the antibacterials resulted in cross-resistance to all three of them, in each of the 29 spontaneous bacterial mutants examined in this study. Furthermore, cross-resistance did not cause measurable fitness (growth) deficiencies for any of the bacterial mutants, when competed against wild-type E. coli in both low-resource and high-resource environments. A combination of whole-genome and targeted sequencing confirmed that mutants differed from wild-type E. coli via change(s) in the tsx gene. Our results indicate that evolution of cross-resistance occurs frequently in E. coli subjected to independent selection by phage T6, phage U115 or albicidin. This study cautions that deployment of new antibacterial therapies such as phage therapy, should be preceded by a thorough investigation of evolutionary consequences of the treatment, to avoid the potential for evolved trade-ups.
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Affiliation(s)
- Kaitlyn E Kortright
- Program in Microbiology, Yale School of Medicine, New Haven, CT, United States
| | - Simon Doss-Gollin
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Paul E Turner
- Program in Microbiology, Yale School of Medicine, New Haven, CT, United States.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
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18
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Borjihan Q, Dong A. Design of nanoengineered antibacterial polymers for biomedical applications. Biomater Sci 2021; 8:6867-6882. [PMID: 32756731 DOI: 10.1039/d0bm00788a] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pathogenic bacteria have become global threats to public health. Since the advent of antibiotics about 100 years ago, their use has been embraced with great enthusiasm because of their effective treatment of bacterial infections. However, the evolution of pathogenic bacteria with resistance to conventional antibiotics has resulted in an urgent need for the development of a new generation of antibiotics. The use of antimicrobial polymers offers the promise of enhancing the efficacy of antimicrobial agents. Of the various antibacterial polymers that effectively eradicate pathogenic bacteria, those that are nanoengineered have garnered significant research interest in their design and biomedical applications. Because of their high surface area and high reactivity, these polymers show greater antibacterial activity than conventional antibacterial agents, by inhibiting the growth or destroying the cell membrane of pathogenic bacteria. This review summarizes several strategies for designing nanoengineered antibacterial polymers, explores the factors that affect their antibacterial properties, and examines key features of their design. It then comments briefly on the future prospects for nanoengineered antibacterial polymers. This review thus provides a feasible guide to developing nanoengineered antibacterial polymers by presenting both broad and in-depth bench research, and it offers suggestions for their potential in biomedical applications.
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Affiliation(s)
- Qinggele Borjihan
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot 010021, People's Republic of China.
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19
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Prajapati JD, Kleinekathöfer U, Winterhalter M. How to Enter a Bacterium: Bacterial Porins and the Permeation of Antibiotics. Chem Rev 2021; 121:5158-5192. [PMID: 33724823 DOI: 10.1021/acs.chemrev.0c01213] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite tremendous successes in the field of antibiotic discovery seen in the previous century, infectious diseases have remained a leading cause of death. More specifically, pathogenic Gram-negative bacteria have become a global threat due to their extraordinary ability to acquire resistance against any clinically available antibiotic, thus urging for the discovery of novel antibacterial agents. One major challenge is to design new antibiotics molecules able to rapidly penetrate Gram-negative bacteria in order to achieve a lethal intracellular drug accumulation. Protein channels in the outer membrane are known to form an entry route for many antibiotics into bacterial cells. Up until today, there has been a lack of simple experimental techniques to measure the antibiotic uptake and the local concentration in subcellular compartments. Hence, rules for translocation directly into the various Gram-negative bacteria via the outer membrane or via channels have remained elusive, hindering the design of new or the improvement of existing antibiotics. In this review, we will discuss the recent progress, both experimentally as well as computationally, in understanding the structure-function relationship of outer-membrane channels of Gram-negative pathogens, mainly focusing on the transport of antibiotics.
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Affiliation(s)
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
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20
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Ding HH, Chigan JZ, Zhen JB, Liu L, Xu YS, Chen C, Yang KW. Cholesteroled polymer (Chol-b-Lys)-based nanoparticles (CL-NPs) confer antibacterial efficacy without resistance. NEW J CHEM 2021. [DOI: 10.1039/d1nj03944j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nanoparticles CL-NPs assembled by polymer Chol-b-Lys confer antibacterial efficacy without resistance.
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Affiliation(s)
- Huan-Huan Ding
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Jia-Zhu Chigan
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Jian-Bin Zhen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Lu Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Yin-Sui Xu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
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21
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Jiang X, Zhang L, Teng M, Li X. Antibiotic binding releases autoinhibition of the TipA multidrug-resistance transcriptional regulator. J Biol Chem 2020; 295:17865-17876. [PMID: 33454020 PMCID: PMC7762955 DOI: 10.1074/jbc.ra120.016295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/21/2020] [Indexed: 11/29/2022] Open
Abstract
Investigations of bacterial resistance strategies can aid in the development of new antimicrobial drugs as a countermeasure to the increasing worldwide prevalence of bacterial antibiotic resistance. One such strategy involves the TipA class of transcription factors, which constitute minimal autoregulated multidrug resistance (MDR) systems against diverse antibiotics. However, we have insufficient information regarding how antibiotic binding induces transcriptional activation to design molecules that could interfere with this process. To learn more, we determined the crystal structure of SkgA from Caulobacter crescentus as a representative TipA protein. We identified an unexpected spatial orientation and location of the antibiotic-binding TipAS effector domain in the apo state. We observed that the α6–α7 region of the TipAS domain, which is canonically responsible for forming the lid of antibiotic-binding cleft to tightly enclose the bound antibiotic, is involved in the dimeric interface and stabilized via interaction with the DNA-binding domain in the apo state. Further structural and biochemical analyses demonstrated that the unliganded TipAS domain sterically hinders promoter DNA binding but undergoes a remarkable conformational shift upon antibiotic binding to release this autoinhibition via a switch of its α6–α7 region. Hence, the promoters for MDR genes including tipA and RNA polymerases become available for transcription, enabling efficient antibiotic resistance. These insights into the molecular mechanism of activation of TipA proteins advance our understanding of TipA proteins, as well as bacterial MDR systems, and may provide important clues to block bacterial resistance.
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Affiliation(s)
- Xuguang Jiang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, China; Department of Cell Biology and Anatomy, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.
| | - Linjuan Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, China.
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22
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Gupta MN, Alam A, Hasnain SE. Protein promiscuity in drug discovery, drug-repurposing and antibiotic resistance. Biochimie 2020; 175:50-57. [PMID: 32416199 DOI: 10.1016/j.biochi.2020.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/01/2022]
Abstract
Proteins are supposed to bind to their substrates/ligands in a specific manner via their pre-formed binding sites, according to classical biochemistry. In recent years, several types of deviations from this norm have been observed and called promiscuous behavior. Enzymatic promiscuities allow several biochemical functions to be carried out by the same enzyme. The promiscuous activity can also be the origin of "new proteins" via gene duplication. In more recent years, proteins from prokaryotes, eukaryotes and viruses have been found to have intrinsic disorder and lack a preformed binding site. Intrinsic disorder is exploited in regulatory proteins such as those that are involved in transcription and signal transduction. Such proteins function by folding locally while binding to their ligands or interacting with other proteins. These phenomena have also been classified as examples of protein promiscuity and encompass diverse kinds of ligands that can bind to a protein. Given the significant extent of structural homology in many protein families, it is not surprising that ligands also have been found to display promiscuity. Promiscuous behavior of proteins offers both challenges and opportunities to the drug discovery programs such as drug repurposing. Pathogens when exposed to antibiotics exploit protein promiscuity in several ways to develop resistance to the drug. There is increasing evidence now to support that the disorder in proteins is a major tool used by pathogens for virulence and evade drug action by exploiting protein promiscuity. This review provides a holistic view of this multi-faceted phenomenon called protein promiscuity.
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Affiliation(s)
- Munishwar N Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Anwar Alam
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Seyed E Hasnain
- JH-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India; Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Professor CR Rao Road, Hyderabad, 500046, India.
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23
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Microbial disease management in agriculture: Current status and future prospects. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2019.101468] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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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] [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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25
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Testolin G, Cirnski K, Rox K, Prochnow H, Fetz V, Grandclaudon C, Mollner T, Baiyoumy A, Ritter A, Leitner C, Krull J, van den Heuvel J, Vassort A, Sordello S, Hamed MM, Elgaher WAM, Herrmann J, Hartmann RW, Müller R, Brönstrup M. Synthetic studies of cystobactamids as antibiotics and bacterial imaging carriers lead to compounds with high in vivo efficacy. Chem Sci 2019; 11:1316-1334. [PMID: 34123255 PMCID: PMC8148378 DOI: 10.1039/c9sc04769g] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
There is an alarming scarcity of novel chemical matter with bioactivity against multidrug-resistant Gram-negative bacterial pathogens. Cystobactamids, recently discovered natural products from myxobacteria, are an exception to this trend. Their unusual chemical structure, composed of oligomeric para-aminobenzoic acid moieties, is associated with a high antibiotic activity through the inhibition of gyrase. In this study, structural determinants of cystobactamid's antibacterial potency were defined at five positions, which were varied using three different synthetic routes to the cystobactamid scaffold. The potency against Acinetobacter baumannii could be increased ten-fold to an MIC (minimum inhibitory concentration) of 0.06 μg mL-1, and the previously identified spectrum gap of Klebsiella pneumoniae could be closed compared to the natural products (MIC of 0.5 μg mL-1). Proteolytic degradation of cystobactamids by the resistance factor AlbD was prevented by an amide-triazole replacement. Conjugation of cystobactamid's N-terminal tetrapeptide to a Bodipy moiety induced the selective localization of the fluorophore for bacterial imaging purposes. Finally, a first in vivo proof of concept was obtained in an E. coli infection mouse model, where derivative 22 led to the reduction of bacterial loads (cfu, colony-forming units) in muscle, lung and kidneys by five orders of magnitude compared to vehicle-treated mice. These findings qualify cystobactamids as highly promising lead structures against infections caused by Gram-positive and Gram-negative bacterial pathogens.
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Affiliation(s)
- Giambattista Testolin
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Katarina Cirnski
- German Center for Infection Research (DZIF) Site Hannover-Braunschweig Germany.,Helmholtz Institute for Pharmaceutical Research Saarland Universitätscampus E8.1 66123 Saarbrücken Germany
| | - Katharina Rox
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany .,German Center for Infection Research (DZIF) Site Hannover-Braunschweig Germany
| | - Hans Prochnow
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Verena Fetz
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Charlotte Grandclaudon
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany .,German Center for Infection Research (DZIF) Site Hannover-Braunschweig Germany
| | - Tim Mollner
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Alain Baiyoumy
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Antje Ritter
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Christian Leitner
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany .,German Center for Infection Research (DZIF) Site Hannover-Braunschweig Germany
| | - Jana Krull
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Joop van den Heuvel
- Group Recombinant Protein Expression, Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Aurelie Vassort
- Evotec ID 1541 Avenue Marcel Merieux 69289 Marcy l'Etoile France
| | | | - Mostafa M Hamed
- Helmholtz Institute for Pharmaceutical Research Saarland Universitätscampus E8.1 66123 Saarbrücken Germany
| | - Walid A M Elgaher
- Helmholtz Institute for Pharmaceutical Research Saarland Universitätscampus E8.1 66123 Saarbrücken Germany
| | - Jennifer Herrmann
- German Center for Infection Research (DZIF) Site Hannover-Braunschweig Germany.,Helmholtz Institute for Pharmaceutical Research Saarland Universitätscampus E8.1 66123 Saarbrücken Germany
| | - Rolf W Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland Universitätscampus E8.1 66123 Saarbrücken Germany
| | - Rolf Müller
- German Center for Infection Research (DZIF) Site Hannover-Braunschweig Germany.,Helmholtz Institute for Pharmaceutical Research Saarland Universitätscampus E8.1 66123 Saarbrücken Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany .,German Center for Infection Research (DZIF) Site Hannover-Braunschweig Germany.,Center of Biomolecular Drug Research (BMWZ), Leibniz Universität 30167 Hannover Germany
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26
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Hashimi SM. Albicidin, a potent DNA gyrase inhibitor with clinical potential. J Antibiot (Tokyo) 2019; 72:785-792. [PMID: 31451755 DOI: 10.1038/s41429-019-0228-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/23/2019] [Accepted: 08/14/2019] [Indexed: 11/09/2022]
Abstract
The emergence of multiple antibiotic-resistant bacteria is a serious global problem which requires the development of new effective antimicrobial therapeutics. Albicidin produced by the sugarcane pathogen Xanthomonas albilineans is a potent DNA gyrase inhibitor with inhibitory effects significantly better than most DNA gyrase inhibitors. Albicidin acts primarily by inhibiting the religation of the cleaved DNA intermediate during the gyrase catalytic sequence similar to quinolones. The clinical realization of albicidin has been hampered by limited production and its unsolved structure. In this review, the relationship between albicidin and sugarcane leaf-scald disease is described. Furthermore, the biosynthesis and resistance mechanisms of albicidin are discussed. Finally, recent efforts to solve the structure and produce albicidin in a heterologous host and chemically are summarized.
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Affiliation(s)
- Saeed Mujahid Hashimi
- Department of Basic Science, Biology Unit, Deanship of Preparatory Year and Supporting Studies, and Department of Stem Cell Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 34212, Saudi Arabia.
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27
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Wencewicz TA. Crossroads of Antibiotic Resistance and Biosynthesis. J Mol Biol 2019; 431:3370-3399. [PMID: 31288031 DOI: 10.1016/j.jmb.2019.06.033] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/20/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022]
Abstract
The biosynthesis of antibiotics and self-protection mechanisms employed by antibiotic producers are an integral part of the growing antibiotic resistance threat. The origins of clinically relevant antibiotic resistance genes found in human pathogens have been traced to ancient microbial producers of antibiotics in natural environments. Widespread and frequent antibiotic use amplifies environmental pools of antibiotic resistance genes and increases the likelihood for the selection of a resistance event in human pathogens. This perspective will provide an overview of the origins of antibiotic resistance to highlight the crossroads of antibiotic biosynthesis and producer self-protection that result in clinically relevant resistance mechanisms. Some case studies of synergistic antibiotic combinations, adjuvants, and hybrid antibiotics will also be presented to show how native antibiotic producers manage the emergence of antibiotic resistance.
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Affiliation(s)
- Timothy A Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, USA.
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28
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Sikandar A, Cirnski K, Testolin G, Volz C, Brönstrup M, Kalinina OV, Müller R, Koehnke J. Adaptation of a Bacterial Multidrug Resistance System Revealed by the Structure and Function of AlbA. J Am Chem Soc 2018; 140:16641-16649. [PMID: 30422653 DOI: 10.1021/jacs.8b08895] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To combat the rise of antimicrobial resistance, the discovery of new antibiotics is paramount. Albicidin and cystobactamid are related natural product antibiotics with potent activity against Gram-positive and, crucially, Gram-negative pathogens. AlbA has been reported to neutralize albicidin by binding it with nanomolar affinity. To understand this potential resistance mechanism, we determined structures of AlbA and its complex with albicidin. The structures revealed AlbA to be comprised of two domains, each unexpectedly resembling the multiantibiotic neutralizing protein TipA. Binding of the long albicidin molecule was shared pseudosymmetrically between the two domains. The structure also revealed an unexpected chemical modification of albicidin, which we demonstrate to be promoted by AlbA, and to reduce albicidin potency; we propose a mechanism for this reaction. Overall, our findings suggest that AlbA arose through internal duplication in an ancient TipA-like gene, leading to a new binding scaffold adapted to the sequestration of long-chain antibiotics.
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Affiliation(s)
- Asfandyar Sikandar
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland , Helmholtz Centre for Infection Research, Saarland University , Campus Geb. E8.1 , Saarbrücken 66123 , Germany
| | - Katarina Cirnski
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products , Helmholtz Centre for Infection Research, and Department of Pharmaceutical Biotechnology, Saarland University , Campus E8.1 , Saarbrücken 66123 , Germany.,German Centre for Infection Research (DZIF) , Site Hannover Braunschweig , Braunschweig 38124 , Germany
| | - Giambattista Testolin
- German Centre for Infection Research (DZIF) , Site Hannover Braunschweig , Braunschweig 38124 , Germany.,Department of Chemical Biology , Helmholtz Centre for Infection Research, and Institute of Systems Biotechnology, Saarland University , Saarbrücken 66123 , Germany
| | - Carsten Volz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products , Helmholtz Centre for Infection Research, and Department of Pharmaceutical Biotechnology, Saarland University , Campus E8.1 , Saarbrücken 66123 , Germany.,German Centre for Infection Research (DZIF) , Site Hannover Braunschweig , Braunschweig 38124 , Germany
| | - Mark Brönstrup
- German Centre for Infection Research (DZIF) , Site Hannover Braunschweig , Braunschweig 38124 , Germany.,Department of Chemical Biology , Helmholtz Centre for Infection Research, and Institute of Systems Biotechnology, Saarland University , Saarbrücken 66123 , Germany
| | - Olga V Kalinina
- Department for Computational Biology and Applied Algorithmics , Max Planck Institute for Informatics , Saarbrücken D-66123 , Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products , Helmholtz Centre for Infection Research, and Department of Pharmaceutical Biotechnology, Saarland University , Campus E8.1 , Saarbrücken 66123 , Germany.,German Centre for Infection Research (DZIF) , Site Hannover Braunschweig , Braunschweig 38124 , Germany
| | - Jesko Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland , Helmholtz Centre for Infection Research, Saarland University , Campus Geb. E8.1 , Saarbrücken 66123 , Germany
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