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Sosio M, Gaspari E, Iorio M, Pessina S, Medema MH, Bernasconi A, Simone M, Maffioli SI, Ebright RH, Donadio S. Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics. Cell Chem Biol 2018; 25:540-549.e4. [PMID: 29551347 DOI: 10.1016/j.chembiol.2018.02.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/28/2017] [Accepted: 02/07/2018] [Indexed: 10/17/2022]
Abstract
Pseudouridimycin (PUM) is a selective nucleoside-analog inhibitor of bacterial RNA polymerase with activity against Gram-positive and Gram-negative bacteria. PUM, produced by Streptomyces sp. ID38640, consists of a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 5'-aminopseudouridine. We report the characterization of the PUM gene cluster. Bioinformatic analysis and mutational knockouts of pum genes with analysis of accumulated intermediates, define the PUM biosynthetic pathway. The work provides the first biosynthetic pathway of a C-nucleoside antibiotic and reveals three unexpected features: production of free pseudouridine by the dedicated pseudouridine synthase, PumJ; nucleoside activation by specialized oxidoreductases and aminotransferases; and peptide-bond formation by amide ligases. A central role in the PUM biosynthetic pathway is played by the PumJ, which represents a divergent branch within the TruD family of pseudouridine synthases. PumJ-like sequences are associated with diverse gene clusters likely to govern the biosynthesis of different classes of C-nucleoside antibiotics.
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Affiliation(s)
- Margherita Sosio
- Naicons Srl, Viale Ortles 22/4, 20139 Milan, Italy; KtedoGen Srl, Viale Ortles 22/4, 20139 Milan, Italy.
| | | | | | | | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | | | | | - Sonia I Maffioli
- Naicons Srl, Viale Ortles 22/4, 20139 Milan, Italy; KtedoGen Srl, Viale Ortles 22/4, 20139 Milan, Italy
| | - Richard H Ebright
- Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Stefano Donadio
- Naicons Srl, Viale Ortles 22/4, 20139 Milan, Italy; KtedoGen Srl, Viale Ortles 22/4, 20139 Milan, Italy
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52
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Glaus F, Dedić D, Tare P, Nagaraja V, Rodrigues L, Aínsa JA, Kunze J, Schneider G, Hartkoorn RC, Cole ST, Altmann KH. Total Synthesis of Ripostatin B and Structure–Activity Relationship Studies on Ripostatin Analogs. J Org Chem 2018. [DOI: 10.1021/acs.joc.8b00193] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florian Glaus
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Darija Dedić
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Priyanka Tare
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Liliana Rodrigues
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública, Facultad de Medicina and BIFI, Universidad de Zaragoza and CIBER Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
- Fundación Agencia Aragonesa para la Investigación y el Desarrollo (ARAID), 50018 Zaragoza, Spain
| | - José Antonio Aínsa
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública, Facultad de Medicina and BIFI, Universidad de Zaragoza and CIBER Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
| | - Jens Kunze
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Ruben C. Hartkoorn
- Global Health Institute, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Stewart T. Cole
- Global Health Institute, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8092 Zürich, Switzerland
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53
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Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA. Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts. eLife 2018; 7:34823. [PMID: 29480804 PMCID: PMC5837556 DOI: 10.7554/elife.34823] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/13/2018] [Indexed: 01/22/2023] Open
Abstract
Fidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against Mycobacterium tuberculosis RNAP in vitro, but clinical use of Fdx is limited to treating Clostridium difficile intestinal infections due to poor absorption. To identify the structural determinants of Fdx binding to RNAP, we determined the 3.4 Å cryo-electron microscopy structure of a complete M. tuberculosis RNAP holoenzyme in complex with Fdx. We find that the actinobacteria general transcription factor RbpA contacts fidaxomycin, explaining its strong effect on M. tuberculosis. Additional structures define conformational states of M. tuberculosis RNAP between the free apo-holoenzyme and the promoter-engaged open complex ready for transcription. The results establish that Fdx acts like a doorstop to jam the enzyme in an open state, preventing the motions necessary to secure promoter DNA in the active site. Our results provide a structural platform to guide development of anti-tuberculosis antimicrobials based on the Fdx binding pocket. Tuberculosis (TB) is an infectious disease that affects over ten million people every year. The Mycobacterium tuberculosis bacteria that cause the disease spread through the air from one person to another and mainly infect the lungs. Although curable, TB is difficult to eradicate because it is remarkably widespread, with one third of the world’s population estimated to carry the bacteria. Treatment for TB involves a mix of antibiotics that should be taken for several months to a year. The number of multidrug-resistant TB cases, where the infection is not treatable by the common cocktail of antibiotics, is rapidly increasing. There is therefore a need to discover new drugs that can kill the M. tuberculosis bacteria. An antibiotic called fidaxomicin is used to treat intestinal infections. Although it can kill Mycobacterium tuberculosis cells in culture, it is not absorbed from the intestines to the blood and thus cannot reach the lungs to kill the bacteria. It may be possible to change the structure of the drug so that it can enter the bloodstream. Before this can be done, researchers need to understand exactly how fidaxomicin kills the bacteria so that they know which parts of the drug they can alter without making it less effective. Fidaxomicin kills bacterial cells by binding to an enzyme called RNA polymerase. The antibiotic prevents the enzyme from reading and ‘transcribing’ DNA to form molecules that are essential for life. To learn more about how fidaxomicin has this effect, Boyaci, Chen et al. used cryo-electron microscopy to look at structures of the M. tuberculosis RNA polymerase in different states, including when it was bound to fidaxomicin. The structures reveal the chemical details of the interactions between the RNA polymerase and the antibiotic. The two molecules bind to each other through a region of the RNA polymerase that is unique to M. tuberculosis and closely related bacteria. Fidaxomicin acts like a doorstop to jam the RNA polymerase in an open state that cannot bind to DNA and transcribe genes. Medicinal chemists could now build on these findings to develop new drugs that might treat TB, either by modifying fidaxomicin or designing new antibiotics that bind to the same region of the RNA polymerase. Because the fidaxomicin-binding region of the RNA polymerase is specific to M. tuberculosis new antibiotics could be tailored towards the bacteria that have a minimal effect on a patient’s normal gut bacteria.
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Affiliation(s)
- Hande Boyaci
- The Rockefeller University, New York, United States
| | - James Chen
- The Rockefeller University, New York, United States
| | | | - Margaret Palka
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, United States
| | - Seth A Darst
- The Rockefeller University, New York, United States
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54
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Molodtsov V, Sineva E, Zhang L, Huang X, Cashel M, Ades SE, Murakami KS. Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA. Mol Cell 2018; 69:828-839.e5. [PMID: 29478808 DOI: 10.1016/j.molcel.2018.01.035] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/05/2017] [Accepted: 01/25/2018] [Indexed: 02/07/2023]
Abstract
DksA and ppGpp are the central players in the stringent response and mediate a complete reprogramming of the transcriptome. A major component of the response is a reduction in ribosome synthesis, which is accomplished by the synergistic action of DksA and ppGpp bound to RNA polymerase (RNAP) inhibiting transcription of rRNAs. Here, we report the X-ray crystal structures of Escherichia coli RNAP in complex with DksA alone and with ppGpp. The structures show that DksA accesses the template strand at the active site and the downstream DNA binding site of RNAP simultaneously and reveal that binding of the allosteric effector ppGpp reshapes the RNAP-DksA complex. The structural data support a model for transcriptional inhibition in which ppGpp potentiates the destabilization of open complexes by DksA. This work establishes a structural basis for understanding the pleiotropic effects of DksA and ppGpp on transcriptional regulation in proteobacteria.
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Affiliation(s)
- Vadim Molodtsov
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Elena Sineva
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Michael Cashel
- Intramural Research Program, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah E Ades
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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55
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Jeanne-Julien L, Masson G, Astier E, Genta-Jouve G, Servajean V, Beau JM, Norsikian S, Roulland E. Study of the Construction of the Tiacumicin B Aglycone. J Org Chem 2018; 83:921-929. [PMID: 29260550 DOI: 10.1021/acs.joc.7b02909] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Our study of the synthesis of the aglycone of tiacumicin B is discussed here. We imagined two possible strategies featuring a main retrosynthetic disconnection between C13 and C14. The first strategy was based on Suzuki-Miyaura cross-coupling of 1,1-dichloro-1-alkenes, but the failure of this pathway led us to use a Pd/Cu-dual-catalyzed cross-coupling of alkynes with allenes that had never been implemented before in a total synthesis context. We used density functional theory calculations to guide our strategic choices concerning a [2.3]-Wittig rearrangement step and the final ring-size selective Yamaguchi macrolactonization. This led to two syntheses of the aglycone of tiacumicin B, with one of last generation delivering ultimately an adequately protected and glycosylation-ready aglycone.
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Affiliation(s)
- Louis Jeanne-Julien
- UMR 8638, CNRS/Université Paris Descartes, Faculté de Pharmacie , 4, Avenue de l'Observatoire, 75006 Paris, France
| | - Guillaume Masson
- UMR 8638, CNRS/Université Paris Descartes, Faculté de Pharmacie , 4, Avenue de l'Observatoire, 75006 Paris, France
| | - Eloi Astier
- UMR 8638, CNRS/Université Paris Descartes, Faculté de Pharmacie , 4, Avenue de l'Observatoire, 75006 Paris, France
| | - Grégory Genta-Jouve
- UMR 8638, CNRS/Université Paris Descartes, Faculté de Pharmacie , 4, Avenue de l'Observatoire, 75006 Paris, France
| | - Vincent Servajean
- ICSN-CNRS Centre de Recherche de Gif, Univ. Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Jean-Marie Beau
- ICSN-CNRS Centre de Recherche de Gif, Univ. Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France.,Laboratoire de Synthèse de Biomolécules, ICMMO, Univ. Paris-Sud and CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Stéphanie Norsikian
- ICSN-CNRS Centre de Recherche de Gif, Univ. Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Emmanuel Roulland
- UMR 8638, CNRS/Université Paris Descartes, Faculté de Pharmacie , 4, Avenue de l'Observatoire, 75006 Paris, France
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56
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Antibiotic Resistances of Clostridium difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1050:137-159. [PMID: 29383668 DOI: 10.1007/978-3-319-72799-8_9] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The rapid evolution of antibiotic resistance in Clostridium difficile and the consequent effects on prevention and treatment of C. difficile infections (CDIs) are matter of concern for public health. Antibiotic resistance plays an important role in driving C. difficile epidemiology. Emergence of new types is often associated with the emergence of new resistances and most of epidemic C. difficile clinical isolates is currently resistant to multiple antibiotics. In particular, it is to worth to note the recent identification of strains with reduced susceptibility to the first-line antibiotics for CDI treatment and/or for relapsing infections. Antibiotic resistance in C. difficile has a multifactorial nature. Acquisition of genetic elements and alterations of the antibiotic target sites, as well as other factors, such as variations in the metabolic pathways and biofilm production, contribute to the survival of this pathogen in the presence of antibiotics. Different transfer mechanisms facilitate the spread of mobile elements among C. difficile strains and between C. difficile and other species. Furthermore, recent data indicate that both genetic elements and alterations in the antibiotic targets can be maintained in C. difficile regardless of the burden imposed on fitness, and therefore resistances may persist in C. difficile population in absence of antibiotic selective pressure.
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57
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Arnott S, Skancke M, Chen S, Abell B. A case report of successful management of clostridium difficile colitis with antegrade Fidaxomicin through a mucous fistula obviating the need for subtotal colectomy. Int J Surg Case Rep 2017; 42:79-81. [PMID: 29227855 PMCID: PMC5726882 DOI: 10.1016/j.ijscr.2017.11.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/22/2017] [Accepted: 11/23/2017] [Indexed: 12/03/2022] Open
Abstract
A novel case report of colon sparing treatment of clostridium difficile colitis. Topical Fidaxomicin may be used to supplement treatment of resistant clostridium difficile colitis. Antegrade administration of Fidaxomicin through a mucous fistula is feasible supplemental therapy.
Introduction Clostridium difficile is the most common cause of healthcare-associated infections and can have devastating morbidity and mortality. Traditional treatment algorithms involve intravenous metronidazole and enteric metronidazole or vancomycin. Fidaxomicin (DificidR) targets “switch regions” within RNA polymerases and effectively kills clostridium difficile bacteria and is typically administered orally primarily or through a naso/oro-gastric conduit. Presentation of case 55-year-old with a recent elective surgical procedure was hospitalized with multifocal pneumonia and subsequently developed clostridium difficile colitis. This patient failed the standard medical therapy for clostridium difficile colitis, decompensated and required surgical exploration, partial colectomy and mucous fistula creation. Following her surgery, her clinical condition improved and her colitis resolved with the antegrade administration of fidaxomicin through her mucous fistula. Discussion Fidaxomicin is a newer to market therapeutic agent that has been shown to be effective in the treatment of clostridium difficile colitis. Previously studies have shown benefit of oral fidaxomicin therapy for fulminant clostridium difficile but our study case report describes the index case of topical fidaxomicin through a mucous fistula. Conclusion In our case of fulminant clostridium difficile colitis, Fidaxomicin administered in an antegrade fashion through a mucous fistula may have reduced the need for total colectomy in the treatment of fulminant clostridium difficile colitis.
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Affiliation(s)
- Suzanne Arnott
- George Washington University School of Medicine and Health Sciences, United States
| | - Matthew Skancke
- Department of General Surgery, George Washington University Hospital, United States.
| | - Sheena Chen
- Department of General Surgery, George Washington University Hospital, United States
| | - Bruce Abell
- Department of General Surgery, George Washington University Hospital, United States
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58
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Ruthenbeck A, Elgaher WAM, Haupenthal J, Hartmann RW, Meier C. Bacterial RNAP Inhibitors: Synthesis and Evaluation of Prodrugs of Aryl-ureidothiophene-carboxylic acids. ChemistrySelect 2017. [DOI: 10.1002/slct.201702574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alexandra Ruthenbeck
- Organic Chemistry; Department of Chemistry, Faculty of Sciences; Hamburg University; Martin-Luther-King-Platz 6 20146 Hamburg Germany
| | - Walid A. M. Elgaher
- Department of Drug Design and Optimization; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Campus E8.1 66123 Saarbrücken Germany
| | - Jörg Haupenthal
- Department of Drug Design and Optimization; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Campus E8.1 66123 Saarbrücken Germany
| | - Rolf W. Hartmann
- Department of Drug Design and Optimization; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Campus E8.1 66123 Saarbrücken Germany
| | - Chris Meier
- Organic Chemistry; Department of Chemistry, Faculty of Sciences; Hamburg University; Martin-Luther-King-Platz 6 20146 Hamburg Germany
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59
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Abstract
Covering: 2006 to 2017Actinomycetes have been, for decades, one of the most important sources for the discovery of new antibiotics with an important number of drugs and analogs successfully introduced in the market and still used today in clinical practice. The intensive antibacterial discovery effort that generated the large number of highly potent broad-spectrum antibiotics, has seen a dramatic decline in the large pharma industry in the last two decades resulting in a lack of new classes of antibiotics with novel mechanisms of action reaching the clinic. Whereas the decline in the number of new chemical scaffolds and the rediscovery problem of old known molecules has become a hurdle for industrial natural products discovery programs, new actinomycetes compounds and leads have continued to be discovered and developed to the preclinical stages. Actinomycetes are still one of the most important sources of chemical diversity and a reservoir to mine for novel structures that is requiring the integration of diverse disciplines. These can range from novel strategies to isolate species previously not cultivated, innovative whole cell screening approaches and on-site analytical detection and dereplication tools for novel compounds, to in silico biosynthetic predictions from whole gene sequences and novel engineered heterologous expression, that have inspired the isolation of new NPs and shown their potential application in the discovery of novel antibiotics. This review will address the discovery of antibiotics from actinomycetes from two different perspectives including: (1) an update of the most important antibiotics that have only reached the clinical development in the recent years despite their early discovery, and (2) an overview of the most recent classes of antibiotics described from 2006 to 2017 in the framework of the different strategies employed to untap novel compounds previously overlooked with traditional approaches.
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Affiliation(s)
- Olga Genilloud
- Fundación MEDINA, Avda Conocimiento 34, 18016 Granada, Spain.
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60
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Sucipto H, Pogorevc D, Luxenburger E, Wenzel SC, Müller R. Heterologous production of myxobacterial α-pyrone antibiotics in Myxococcus xanthus. Metab Eng 2017; 44:160-170. [PMID: 29030273 DOI: 10.1016/j.ymben.2017.10.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/01/2017] [Accepted: 10/05/2017] [Indexed: 11/17/2022]
Abstract
Myxopyronins (MXN) and corallopyronins (COR) are structurally related α-pyrone antibiotics from myxobacteria that represent a highly promising compound class for the development of broad-spectrum antibacterial therapeutic agents. Their ability to inhibit RNA polymerase through interaction with the "switch region", a novel target, distant from previously characterized RNA polymerase inhibitors (e.g. rifampicin), makes them particularly promising candidates for further research. To improve compound supply for further investigation of MXN, COR and novel derivatives of these antibacterial agents, establishment of an efficient and versatile microbial production platform for myxobacterial α-pyrone antibiotics is highly desirable. Here we describe design, construction and expression of a heterologous production and engineering platforms for MXN and COR to facilitate rational structure design and yield improvement approaches in the myxobacterial host strain Myxococcus xanthus DK1622. Optimization of the cultivation medium yielded significantly higher production titers of MXN A at around 41-fold increase and COR A at around 25-fold increase, compared to the standard CTT medium.
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Affiliation(s)
- Hilda Sucipto
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
| | - Domen Pogorevc
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Eva Luxenburger
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Silke C Wenzel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany.
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany.
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61
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Maffioli SI, Zhang Y, Degen D, Carzaniga T, Del Gatto G, Serina S, Monciardini P, Mazzetti C, Guglierame P, Candiani G, Chiriac AI, Facchetti G, Kaltofen P, Sahl HG, Dehò G, Donadio S, Ebright RH. Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase. Cell 2017. [PMID: 28622509 DOI: 10.1016/j.cell.2017.05.042] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Drug-resistant bacterial pathogens pose an urgent public-health crisis. Here, we report the discovery, from microbial-extract screening, of a nucleoside-analog inhibitor that inhibits bacterial RNA polymerase (RNAP) and exhibits antibacterial activity against drug-resistant bacterial pathogens: pseudouridimycin (PUM). PUM is a natural product comprising a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 6'-amino-pseudouridine. PUM potently and selectively inhibits bacterial RNAP in vitro, inhibits bacterial growth in culture, and clears infection in a mouse model of Streptococcus pyogenes peritonitis. PUM inhibits RNAP through a binding site on RNAP (the NTP addition site) and mechanism (competition with UTP for occupancy of the NTP addition site) that differ from those of the RNAP inhibitor and current antibacterial drug rifampin (Rif). PUM exhibits additive antibacterial activity when co-administered with Rif, exhibits no cross-resistance with Rif, and exhibits a spontaneous resistance rate an order-of-magnitude lower than that of Rif. PUM is a highly promising lead for antibacterial therapy.
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Affiliation(s)
- Sonia I Maffioli
- NAICONS Srl, 20139 Milan, Italy; Vicuron Pharmaceuticals, 21040 Gerenzano, Italy
| | - Yu Zhang
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - David Degen
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Thomas Carzaniga
- Department of Bioscience, University of Milan, 20122 Milan, Italy
| | | | - Stefania Serina
- NAICONS Srl, 20139 Milan, Italy; Vicuron Pharmaceuticals, 21040 Gerenzano, Italy
| | - Paolo Monciardini
- NAICONS Srl, 20139 Milan, Italy; Vicuron Pharmaceuticals, 21040 Gerenzano, Italy
| | | | | | | | - Alina Iulia Chiriac
- Institute of Medical Microbiology, Immunology, and Parasitology, University of Bonn, D-53012 Bonn, Germany
| | | | | | - Hans-Georg Sahl
- Institute of Medical Microbiology, Immunology, and Parasitology, University of Bonn, D-53012 Bonn, Germany
| | - Gianni Dehò
- Department of Bioscience, University of Milan, 20122 Milan, Italy
| | - Stefano Donadio
- NAICONS Srl, 20139 Milan, Italy; Vicuron Pharmaceuticals, 21040 Gerenzano, Italy.
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.
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62
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Jeanne-Julien L, Masson G, Astier E, Genta-Jouve G, Servajean V, Beau JM, Norsikian S, Roulland E. Synthesis of a Tiacumicin B Protected Aglycone. Org Lett 2017; 19:4006-4009. [PMID: 28723103 DOI: 10.1021/acs.orglett.7b01744] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tiacumicin B is an antibiotic endowed with the remarkable ability to interact with a new biological target, giving it an inestimable potential in the context of the ever-growing and worrisome appearance of resistances of bacteria and mycobacteria to antibiotics. The synthesis of an aglycone of tiacumicin B ready for glycosylation is reported. The key steps of this approach are a [2,3]-Wittig rearrangement, a Pd/Cu-catalyzed allene-alkyne cross-coupling, a E-selective cross-metathesis, and a final ring-size selective macrolactonization.
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Affiliation(s)
- Louis Jeanne-Julien
- C-TAC, UMR 8638, CNRS/Université Parie Descartes , 4, avenue de l'Observatoire, 75006 Paris, France
| | - Guillaume Masson
- C-TAC, UMR 8638, CNRS/Université Parie Descartes , 4, avenue de l'Observatoire, 75006 Paris, France
| | - Eloi Astier
- C-TAC, UMR 8638, CNRS/Université Parie Descartes , 4, avenue de l'Observatoire, 75006 Paris, France
| | - Grégory Genta-Jouve
- C-TAC, UMR 8638, CNRS/Université Parie Descartes , 4, avenue de l'Observatoire, 75006 Paris, France
| | - Vincent Servajean
- ICSN-CNRS Centre de Recherche de Gif, Univ Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Jean-Marie Beau
- ICSN-CNRS Centre de Recherche de Gif, Univ Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France.,Laboratoire de Synthèse de Biomolécules, ICMMO, Univ.Paris-Sud and CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Stéphanie Norsikian
- ICSN-CNRS Centre de Recherche de Gif, Univ Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Emmanuel Roulland
- C-TAC, UMR 8638, CNRS/Université Parie Descartes , 4, avenue de l'Observatoire, 75006 Paris, France
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63
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Feklistov A, Bae B, Hauver J, Lass-Napiorkowska A, Kalesse M, Glaus F, Altmann KH, Heyduk T, Landick R, Darst SA. RNA polymerase motions during promoter melting. Science 2017; 356:863-866. [PMID: 28546214 PMCID: PMC5696265 DOI: 10.1126/science.aam7858] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/27/2017] [Indexed: 12/17/2022]
Abstract
All cellular RNA polymerases (RNAPs), from those of bacteria to those of man, possess a clamp that can open and close, and it has been assumed that the open RNAP separates promoter DNA strands and then closes to establish a tight grip on the DNA template. Here, we resolve successive motions of the initiating bacterial RNAP by studying real-time signatures of fluorescent reporters placed on RNAP and DNA in the presence of ligands locking the clamp in distinct conformations. We report evidence for an unexpected and obligatory step early in the initiation involving a transient clamp closure as a prerequisite for DNA melting. We also present a 2.6-angstrom crystal structure of a late-initiation intermediate harboring a rotationally unconstrained downstream DNA duplex within the open RNAP active site cleft. Our findings explain how RNAP thermal motions control the promoter search and drive DNA melting in the absence of external energy sources.
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Affiliation(s)
- Andrey Feklistov
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Brian Bae
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jesse Hauver
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Agnieszka Lass-Napiorkowska
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, USA
| | - Markus Kalesse
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Brunswick, Germany
| | - Florian Glaus
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 1-5/10 8093 Zürich, Switzerland
| | - Karl-Heinz Altmann
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 1-5/10 8093 Zürich, Switzerland
| | - Tomasz Heyduk
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Seth A Darst
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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64
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Elmasri WA, Zhu R, Peng W, Al-Hariri M, Kobeissy F, Tran P, Hamood AN, Hegazy MF, Paré PW, Mechref Y. Multitargeted Flavonoid Inhibition of the Pathogenic Bacterium Staphylococcus aureus: A Proteomic Characterization. J Proteome Res 2017; 16:2579-2586. [PMID: 28541047 DOI: 10.1021/acs.jproteome.7b00137] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Growth inhibition of the pathogen Staphylococcus aureus with currently available antibiotics is problematic in part due to bacterial biofilm protection. Although recently characterized natural products, including 3',4',5-trihydroxy-6,7-dimethoxy-flavone [1], 3',4',5,6,7-pentahydroxy-flavone [2], and 5-hydroxy-4',7-dimethoxy-flavone [3], exhibit both antibiotic and biofilm inhibitory activities, the mode of action of such hydroxylated flavonoids with respect to S. aureus inhibition is yet to be characterized. Enzymatic digestion and high-resolution MS analysis of differentially expressed proteins from S. aureus with and without exposure to antibiotic flavonoids (1-3) allowed for the characterization of global protein alterations induced by metabolite treatment. A total of 56, 92, and 110 proteins were differentially expressed with bacterial exposure to 1, 2, or 3, respectively. The connectivity of the identified proteins was characterized using a search tool for the retrieval of interacting genes/proteins (STRING) with multitargeted S. aureus inhibition of energy metabolism and biosynthesis by the assayed flavonoids. Identifying the mode of action of natural products as antibacterial agents is expected to provide insight into the potential use of flavonoids alone or in combination with known therapeutic agents to effectively control S. aureus infection.
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Affiliation(s)
- Wael A Elmasri
- Department of Chemistry & Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States
| | - Rui Zhu
- Department of Chemistry & Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States
| | - Wenjing Peng
- Department of Chemistry & Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States
| | - Moustafa Al-Hariri
- Department of Biochemistry & Molecular Genetics, Faculty of Medicine, American University of Beirut , Beirut 1107 2020, Lebanon
| | - Firas Kobeissy
- Department of Biochemistry & Molecular Genetics, Faculty of Medicine, American University of Beirut , Beirut 1107 2020, Lebanon
| | | | | | - Mohamed F Hegazy
- Department of Phytochemistry, National Research Centre , Giza 12311, Egypt
| | - Paul W Paré
- Department of Chemistry & Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States
| | - Yehia Mechref
- Department of Chemistry & Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States
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65
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Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH. Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition. Mol Cell 2017; 66:169-179.e8. [PMID: 28392175 DOI: 10.1016/j.molcel.2017.03.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 02/15/2017] [Accepted: 02/28/2017] [Indexed: 01/22/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, which kills 1.8 million annually. Mtb RNA polymerase (RNAP) is the target of the first-line antituberculosis drug rifampin (Rif). We report crystal structures of Mtb RNAP, alone and in complex with Rif, at 3.8-4.4 Å resolution. The results identify an Mtb-specific structural module of Mtb RNAP and establish that Rif functions by a steric-occlusion mechanism that prevents extension of RNA. We also report non-Rif-related compounds-Nα-aroyl-N-aryl-phenylalaninamides (AAPs)-that potently and selectively inhibit Mtb RNAP and Mtb growth, and we report crystal structures of Mtb RNAP in complex with AAPs. AAPs bind to a different site on Mtb RNAP than Rif, exhibit no cross-resistance with Rif, function additively when co-administered with Rif, and suppress resistance emergence when co-administered with Rif.
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Affiliation(s)
- Wei Lin
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Soma Mandal
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - David Degen
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Liu
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yon W Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shengjian Li
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Feng
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Zhang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Sukhendu Mandal
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yi Jiang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shuang Liu
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Matthew Gigliotti
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Meliza Talaue
- Center for Biodefense and Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Nancy Connell
- Center for Biodefense and Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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66
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Zarins-Tutt JS, Abraham ER, Bailey CS, Goss RJM. Bluegenics: Bioactive Natural Products of Medicinal Relevance and Approaches to Their Diversification. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 55:159-186. [PMID: 28238038 DOI: 10.1007/978-3-319-51284-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Nature provides a valuable resource of medicinally relevant compounds, with many antimicrobial and antitumor agents entering clinical trials being derived from natural products. The generation of analogues of these bioactive natural products is important in order to gain a greater understanding of structure activity relationships; probing the mechanism of action, as well as to optimise the natural product's bioactivity and bioavailability. This chapter critically examines different approaches to generating natural products and their analogues, exploring the way in which synthetic and biosynthetic approaches may be blended together to enable expeditious access to new designer natural products.
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Affiliation(s)
| | - Emily R Abraham
- School of Chemistry, University of St Andrews, St Andrews, Scotland, UK
| | | | - Rebecca J M Goss
- School of Chemistry, University of St Andrews, St Andrews, Scotland, UK.
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67
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Aljarallah KM. Conventional and alternative treatment approaches for Clostridium difficile infection. Int J Health Sci (Qassim) 2017; 11:1-10. [PMID: 28293151 PMCID: PMC5327666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Clostridium difficile-associated disease continues to be one of the leading health concerns worldwide. C. difficile is considered as a causative agent of nosocomial diarrhea that causes serious infection, which may result in death. The incidences of C. difficile infection (CDI) in developed countries have become increasingly high which may be attributed to the emergence of newer epidemic strains, extensive use of antibiotics, and limited alternative therapies. The available treatment options against CDI are expensive and promote resistance. Therefore, there is urgent need for new approaches to meet these challenges. This review discusses the current understanding of CDI, the existing clinical treatment strategies and future potential options as antidifficile agents based on the available published works.
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Affiliation(s)
- Khalid M. Aljarallah
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, KSA,Address for correspondence: Dr. Khalid M. Aljarallah, Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, KSA. E-mail:
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68
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Herrmann J, Fayad AA, Müller R. Natural products from myxobacteria: novel metabolites and bioactivities. Nat Prod Rep 2016; 34:135-160. [PMID: 27907217 DOI: 10.1039/c6np00106h] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: 2011-July 2016Myxobacteria are a rich source for structurally diverse secondary metabolites with intriguing biological activities. Here we report on new natural products that were isolated from myxobacteria in the period of 2011 to July 2016. Some examples of recent advances on modes-of-action are also summarised along with a more detailed overview on five compound classes currently assessed in preclinical studies.
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Affiliation(s)
- J Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland, Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
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69
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New antibiotics from Nature’s chemical inventory. Bioorg Med Chem 2016; 24:6227-6252. [DOI: 10.1016/j.bmc.2016.09.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/07/2016] [Indexed: 01/07/2023]
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70
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Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP. Nat Commun 2016; 7:13595. [PMID: 27882920 PMCID: PMC5123050 DOI: 10.1038/ncomms13595] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 10/18/2016] [Indexed: 12/15/2022] Open
Abstract
Little is known about how archaeal viruses perturb the transcription machinery of their hosts. Here we provide the first example of an archaeo-viral transcription factor that directly targets the host RNA polymerase (RNAP) and efficiently represses its activity. ORF145 from the temperate Acidianus two-tailed virus (ATV) forms a high-affinity complex with RNAP by binding inside the DNA-binding channel where it locks the flexible RNAP clamp in one position. This counteracts the formation of transcription pre-initiation complexes in vitro and represses abortive and productive transcription initiation, as well as elongation. Both host and viral promoters are subjected to ORF145 repression. Thus, ORF145 has the properties of a global transcription repressor and its overexpression is toxic for Sulfolobus. On the basis of its properties, we have re-named ORF145 RNAP Inhibitory Protein (RIP).
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71
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Lee J, Borukhov S. Bacterial RNA Polymerase-DNA Interaction-The Driving Force of Gene Expression and the Target for Drug Action. Front Mol Biosci 2016; 3:73. [PMID: 27882317 PMCID: PMC5101437 DOI: 10.3389/fmolb.2016.00073] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/24/2016] [Indexed: 11/17/2022] Open
Abstract
DNA-dependent multisubunit RNA polymerase (RNAP) is the key enzyme of gene expression and a target of regulation in all kingdoms of life. It is a complex multifunctional molecular machine which, unlike other DNA-binding proteins, engages in extensive and dynamic interactions (both specific and nonspecific) with DNA, and maintains them over a distance. These interactions are controlled by DNA sequences, DNA topology, and a host of regulatory factors. Here, we summarize key recent structural and biochemical studies that elucidate the fine details of RNAP-DNA interactions during initiation. The findings of these studies help unravel the molecular mechanisms of promoter recognition and open complex formation, initiation of transcript synthesis and promoter escape. We also discuss most current advances in the studies of drugs that specifically target RNAP-DNA interactions during transcription initiation and elongation.
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Affiliation(s)
- Jookyung Lee
- Department of Cell Biology, Rowan University School of Osteopathic Medicine Stratford, NJ, USA
| | - Sergei Borukhov
- Department of Cell Biology, Rowan University School of Osteopathic Medicine Stratford, NJ, USA
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72
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Elgaher WAM, Sharma KK, Haupenthal J, Saladini F, Pires M, Real E, Mély Y, Hartmann RW. Discovery and Structure-Based Optimization of 2-Ureidothiophene-3-carboxylic Acids as Dual Bacterial RNA Polymerase and Viral Reverse Transcriptase Inhibitors. J Med Chem 2016; 59:7212-22. [PMID: 27339173 DOI: 10.1021/acs.jmedchem.6b00730] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We are concerned with the development of novel anti-infectives with dual antibacterial and antiretroviral activities for MRSA/HIV-1 co-infection. To achieve this goal, we exploited for the first time the mechanistic function similarity between the bacterial RNA polymerase (RNAP) "switch region" and the viral non-nucleoside reverse transcriptase inhibitor (NNRTI) binding site. Starting from our previously discovered RNAP inhibitors, we managed to develop potent RT inhibitors effective against several resistant HIV-1 strains with maintained or enhanced RNAP inhibitory properties following a structure-based design approach. A quantitative structure-activity relationship (QSAR) analysis revealed distinct molecular features necessary for RT inhibition. Furthermore, mode of action (MoA) studies revealed that these compounds inhibit RT noncompetitively, through a new mechanism via closing of the RT clamp. In addition, the novel RNAP/RT inhibitors are characterized by a potent antibacterial activity against S. aureus and in cellulo antiretroviral activity against NNRTI-resistant strains. In HeLa and HEK 293 cells, the compounds showed only marginal cytotoxicity.
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Affiliation(s)
- Walid A M Elgaher
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); and Pharmaceutical and Medicinal Chemistry, Saarland University , Campus E8.1, 66123 Saarbrücken, Germany
| | - Kamal K Sharma
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Jörg Haupenthal
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); and Pharmaceutical and Medicinal Chemistry, Saarland University , Campus E8.1, 66123 Saarbrücken, Germany
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena , Viale Mario Bracci 16, 53100 Siena, Italy
| | - Manuel Pires
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Eleonore Real
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Rolf W Hartmann
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); and Pharmaceutical and Medicinal Chemistry, Saarland University , Campus E8.1, 66123 Saarbrücken, Germany
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73
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Korp J, Vela Gurovic MS, Nett M. Antibiotics from predatory bacteria. Beilstein J Org Chem 2016; 12:594-607. [PMID: 27340451 PMCID: PMC4902038 DOI: 10.3762/bjoc.12.58] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/11/2016] [Indexed: 11/23/2022] Open
Abstract
Bacteria, which prey on other microorganisms, are commonly found in the environment. While some of these organisms act as solitary hunters, others band together in large consortia before they attack their prey. Anecdotal reports suggest that bacteria practicing such a wolfpack strategy utilize antibiotics as predatory weapons. Consistent with this hypothesis, genome sequencing revealed that these micropredators possess impressive capacities for natural product biosynthesis. Here, we will present the results from recent chemical investigations of this bacterial group, compare the biosynthetic potential with that of non-predatory bacteria and discuss the link between predation and secondary metabolism.
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Affiliation(s)
- Juliane Korp
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - María S Vela Gurovic
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS) -CONICET- Carrindanga Km 11, Bahía Blanca 8000, Argentina
| | - Markus Nett
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Beutenbergstr. 11, 07745 Jena, Germany
- Department of Biochemical and Chemical Engineering, Technical Biology, Technical University Dortmund, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
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74
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TFE and Spt4/5 open and close the RNA polymerase clamp during the transcription cycle. Proc Natl Acad Sci U S A 2016; 113:E1816-25. [PMID: 26979960 DOI: 10.1073/pnas.1515817113] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription is an intrinsically dynamic process and requires the coordinated interplay of RNA polymerases (RNAPs) with nucleic acids and transcription factors. Classical structural biology techniques have revealed detailed snapshots of a subset of conformational states of the RNAP as they exist in crystals. A detailed view of the conformational space sampled by the RNAP and the molecular mechanisms of the basal transcription factors E (TFE) and Spt4/5 through conformational constraints has remained elusive. We monitored the conformational changes of the flexible clamp of the RNAP by combining a fluorescently labeled recombinant 12-subunit RNAP system with single-molecule FRET measurements. We measured and compared the distances across the DNA binding channel of the archaeal RNAP. Our results show that the transition of the closed to the open initiation complex, which occurs concomitant with DNA melting, is coordinated with an opening of the RNAP clamp that is stimulated by TFE. We show that the clamp in elongation complexes is modulated by the nontemplate strand and by the processivity factor Spt4/5, both of which stimulate transcription processivity. Taken together, our results reveal an intricate network of interactions within transcription complexes between RNAP, transcription factors, and nucleic acids that allosterically modulate the RNAP during the transcription cycle.
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75
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Spigaglia P. Recent advances in the understanding of antibiotic resistance in Clostridium difficile infection. Ther Adv Infect Dis 2016; 3:23-42. [PMID: 26862400 DOI: 10.1177/2049936115622891] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Clostridium difficile epidemiology has changed in recent years, with the emergence of highly virulent types associated with severe infections, high rates of recurrences and mortality. Antibiotic resistance plays an important role in driving these epidemiological changes and the emergence of new types. While clindamycin resistance was driving historical endemic types, new types are associated with resistance to fluoroquinolones. Furthermore, resistance to multiple antibiotics is a common feature of the newly emergent strains and, in general, of many epidemic isolates. A reduced susceptibility to antibiotics used for C. difficile infection (CDI) treatment, in particular to metronidazole, has recently been described in several studies. Furthermore, an increased number of strains show resistance to rifamycins, used for the treatment of relapsing CDI. Several mechanisms of resistance have been identified in C. difficile, including acquisition of genetic elements and alterations of the antibiotic target sites. The C. difficile genome contains a plethora of mobile genetic elements, many of them involved in antibiotic resistance. Transfer of genetic elements among C. difficile strains or between C. difficile and other bacterial species can occur through different mechanisms that facilitate their spread. Investigations of the fitness cost in C. difficile indicate that both genetic elements and mutations in the molecular targets of antibiotics can be maintained regardless of the burden imposed on fitness, suggesting that resistances may persist in the C. difficile population also in absence of antibiotic selective pressure. The rapid evolution of antibiotic resistance and its composite nature complicate strategies in the treatment and prevention of CDI. The rapid identification of new phenotypic and genotypic traits, the implementation of effective antimicrobial stewardship and infection control programs, and the development of alternative therapies are needed to prevent and contain the spread of resistance and to ensure an efficacious therapy for CDI.
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76
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Assembly and clustering of natural antibiotics guides target identification. Nat Chem Biol 2016; 12:233-9. [PMID: 26829473 DOI: 10.1038/nchembio.2018] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/09/2015] [Indexed: 12/25/2022]
Abstract
Antibiotics are essential for numerous medical procedures, including the treatment of bacterial infections, but their widespread use has led to the accumulation of resistance, prompting calls for the discovery of antibacterial agents with new targets. A majority of clinically approved antibacterial scaffolds are derived from microbial natural products, but these valuable molecules are not well annotated or organized, limiting the efficacy of modern informatic analyses. Here, we provide a comprehensive resource defining the targets, chemical origins and families of the natural antibacterial collective through a retrobiosynthetic algorithm. From this we also detail the directed mining of biosynthetic scaffolds and resistance determinants to reveal structures with a high likelihood of having previously unknown modes of action. Implementing this pipeline led to investigations of the telomycin family of natural products from Streptomyces canus, revealing that these bactericidal molecules possess a new antibacterial mode of action dependent on the bacterial phospholipid cardiolipin.
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77
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Leeds JA. Antibacterials Developed to Target a Single Organism: Mechanisms and Frequencies of Reduced Susceptibility to the Novel Anti-Clostridium difficile Compounds Fidaxomicin and LFF571. Cold Spring Harb Perspect Med 2016; 6:a025445. [PMID: 26834162 PMCID: PMC4743069 DOI: 10.1101/cshperspect.a025445] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Clostridium difficile is the most common cause of antibacterial-associated diarrhea. Clear clinical presentation and rapid diagnostics enable targeted therapy for C. difficile infection (CDI) to start quickly. CDI treatment includes metronidazole and vancomycin (VAN). Despite decades of use for CDI, no clinically meaningful resistance to either agent has emerged. Fidaxomicin (FDX), an RNA polymerase inhibitor, is also approved to treat CDI. Mutants with reduced susceptibility to FDX have been selected in vitro by single and multistep methods. Strains with elevated FDX minimum inhibitory concentrations (MICs) were also identified from FDX-treated patients in clinical trials. LFF571 is an exploratory agent that inhibits EF-Tu. In a proof-of-concept study, LFF571 was safe and effective for treating CDI. Spontaneous mutants with reduced susceptibility to LFF571 were selected in vitro in a single step, but not via serial passage. Although there are several agents in development for treatment of CDI, this review summarizes the frequencies and mechanisms of C. difficile mutants displaying reduced susceptibility to FDX or LFF71.
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Affiliation(s)
- Jennifer A Leeds
- Infectious Disease Area, Novartis Institutes for BioMedical Research, Emeryville, California 94608
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78
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Bacterial Transcription as a Target for Antibacterial Drug Development. Microbiol Mol Biol Rev 2016; 80:139-60. [PMID: 26764017 DOI: 10.1128/mmbr.00055-15] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design.
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79
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Morichaud Z, Chaloin L, Brodolin K. Regions 1.2 and 3.2 of the RNA Polymerase σ Subunit Promote DNA Melting and Attenuate Action of the Antibiotic Lipiarmycin. J Mol Biol 2016; 428:463-76. [DOI: 10.1016/j.jmb.2015.12.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 01/24/2023]
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80
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References. Antibiotics (Basel) 2015. [DOI: 10.1128/9781555819316.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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81
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Single-stranded DNA aptamers for functional probing of bacterial RNA polymerase. Methods Mol Biol 2015; 1276:165-83. [PMID: 25665563 DOI: 10.1007/978-1-4939-2392-2_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Bacterial RNA polymerase (RNAP) is the main regulatory hub of gene transcription. During transcription, RNAP interacts with the DNA template, RNA product, nucleotide substrates, metal cofactors, and regulatory molecules that bind to distinct RNAP sites to modulate its activity. RNAP is also inhibited by several known antibiotics and is a promising target for development of novel antibacterial compounds. Despite great progress in structural analysis of RNAP in recent years, many details of RNAP interactions with nucleic acids, regulatory molecules and antibiotics remain insufficiently understood. Aptamers that target various epitopes on the RNAP molecule represent a useful tool for functional analysis of transcription. Here, we describe protocols for selection of highly specific aptamers to different components of RNAP and their applications for analysis of RNAP-ligand interactions and RNAP inhibition.
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82
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Painter RE, Adam GC, Arocho M, DiNunzio E, Donald RGK, Dorso K, Genilloud O, Gill C, Goetz M, Hairston NN, Murgolo N, Nare B, Olsen DB, Powles M, Racine F, Su J, Vicente F, Wisniewski D, Xiao L, Hammond M, Young K. Elucidation of DnaE as the Antibacterial Target of the Natural Product, Nargenicin. ACTA ACUST UNITED AC 2015; 22:1362-73. [PMID: 26456734 DOI: 10.1016/j.chembiol.2015.08.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/10/2015] [Accepted: 08/25/2015] [Indexed: 01/14/2023]
Abstract
Resistance to existing classes of antibiotics drives the need for discovery of novel compounds with unique mechanisms of action. Nargenicin A1, a natural product with limited antibacterial spectrum, was rediscovered in a whole-cell antisense assay. Macromolecular labeling in both Staphylococcus aureus and an Escherichia coli tolC efflux mutant revealed selective inhibition of DNA replication not due to gyrase or topoisomerase IV inhibition. S. aureus nargenicin-resistant mutants were selected at a frequency of ∼1 × 10(-9), and whole-genome resequencing found a single base-pair change in the dnaE gene, a homolog of the E. coli holoenzyme α subunit. A DnaE single-enzyme assay was exquisitely sensitive to inhibition by nargenicin, and other in vitro characterization studies corroborated DnaE as the target. Medicinal chemistry efforts may expand the spectrum of this novel mechanism antibiotic.
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Affiliation(s)
- Ronald E Painter
- In vitro Pharmacology, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Gregory C Adam
- Screening and Protein Sciences, Merck Research Laboratories, North Wales, PA 19454, USA
| | - Marta Arocho
- Medicinal Chemistry, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Edward DiNunzio
- In vitro Pharmacology, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Robert G K Donald
- Infectious Disease Biology, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Karen Dorso
- Infectious Disease Biology, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Olga Genilloud
- Centro de Investigación Básica (CIBE), Merck Sharp & Dhome de España, S.A., 28027 Madrid, Spain
| | - Charles Gill
- Infectious Disease Biology, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Michael Goetz
- Medicinal Chemistry, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Nichelle N Hairston
- Infectious Disease Biology, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Nicholas Murgolo
- Discovery Pharmacogenomics, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Bakela Nare
- Infectious Disease Biology, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - David B Olsen
- Infectious Disease Biology, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Maryann Powles
- Infectious Disease Biology, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Fred Racine
- Infectious Disease Biology, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Jing Su
- Medicinal Chemistry, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Francisca Vicente
- Centro de Investigación Básica (CIBE), Merck Sharp & Dhome de España, S.A., 28027 Madrid, Spain
| | - Douglas Wisniewski
- Infectious Disease Biology, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Li Xiao
- Medicinal Chemistry, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Milton Hammond
- Infectious Disease Biology, Merck Research Laboratories, Kenilworth, NJ 07033, USA
| | - Katherine Young
- Infectious Disease Biology, Merck Research Laboratories, Kenilworth, NJ 07033, USA.
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83
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Zhang N, Schäfer J, Sharma A, Rayner L, Zhang X, Tuma R, Stockley P, Buck M. Mutations in RNA Polymerase Bridge Helix and Switch Regions Affect Active-Site Networks and Transcript-Assisted Hydrolysis. J Mol Biol 2015; 427:3516-3526. [PMID: 26365052 PMCID: PMC4641871 DOI: 10.1016/j.jmb.2015.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 11/21/2022]
Abstract
In bacterial RNA polymerase (RNAP), the bridge helix and switch regions form an intricate network with the catalytic active centre and the main channel. These interactions are important for catalysis, hydrolysis and clamp domain movement. By targeting conserved residues in Escherichia coli RNAP, we are able to show that functions of these regions are differentially required during σ70-dependent and the contrasting σ54-dependent transcription activations and thus potentially underlie the key mechanistic differences between the two transcription paradigms. We further demonstrate that the transcription factor DksA directly regulates σ54-dependent activation both positively and negatively. This finding is consistent with the observed impacts of DksA on σ70-dependent promoters. DksA does not seem to significantly affect RNAP binding to a pre-melted promoter DNA but affects extensively activity at the stage of initial RNA synthesis on σ54-regulated promoters. Strikingly, removal of the σ54 Region I is sufficient to invert the action of DksA (from stimulation to inhibition or vice versa) at two test promoters. The RNAP mutants we generated also show a strong propensity to backtrack. These mutants increase the rate of transcript-hydrolysis cleavage to a level comparable to that seen in the Thermus aquaticus RNAP even in the absence of a non-complementary nucleotide. These novel phenotypes imply an important function of the bridge helix and switch regions as an anti-backtracking ratchet and an RNA hydrolysis regulator. The bridge helix and switch regions form an intricate network in RNAP. The σ70 and σ54 transcription systems differentially use this interaction network. Transcription factor DksA and σ54 Region I also contribute to this network. Disruption of this network enhances backtracking and intrinsic RNA hydrolysis.
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Affiliation(s)
- Nan Zhang
- Division of Cell and Molecular Biology, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom.
| | - Jorrit Schäfer
- Division of Cell and Molecular Biology, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Amit Sharma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lucy Rayner
- Division of Cell and Molecular Biology, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Xiaodong Zhang
- Division of Macromolecular Structure and Function, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Peter Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Martin Buck
- Division of Cell and Molecular Biology, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom.
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84
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Feng Y, Degen D, Wang X, Gigliotti M, Liu S, Zhang Y, Das D, Michalchuk T, Ebright YW, Talaue M, Connell N, Ebright RH. Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles. Structure 2015; 23:1470-1481. [PMID: 26190576 DOI: 10.1016/j.str.2015.06.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 11/30/2022]
Abstract
CBR hydroxamidines are small-molecule inhibitors of bacterial RNA polymerase (RNAP) discovered through high-throughput screening of synthetic-compound libraries. CBR pyrazoles are structurally related RNAP inhibitors discovered through scaffold hopping from CBR hydroxamidines. CBR hydroxamidines and pyrazoles selectively inhibit Gram-negative bacterial RNAP and exhibit selective antibacterial activity against Gram-negative bacteria. Here, we report crystal structures of the prototype CBR hydroxamidine, CBR703, and a CBR pyrazole in complex with E. coli RNAP holoenzyme. In addition, we define the full resistance determinant for CBR703, show that the binding site and resistance determinant for CBR703 do not overlap the binding sites and resistance determinants of other characterized RNAP inhibitors, show that CBR703 exhibits no or minimal cross-resistance with other characterized RNAP inhibitors, and show that co-administration of CBR703 with other RNAP inhibitors results in additive antibacterial activities. The results set the stage for structure-based optimization of CBR inhibitors as antibacterial drugs.
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Affiliation(s)
- Yu Feng
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - David Degen
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Xinyue Wang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Matthew Gigliotti
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shuang Liu
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Zhang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Deepankar Das
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Trevor Michalchuk
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yon W Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Meliza Talaue
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Nancy Connell
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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85
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Molodtsov V, Fleming PR, Eyermann CJ, Ferguson AD, Foulk MA, McKinney DC, Masse CE, Buurman ET, Murakami KS. X-ray crystal structures of Escherichia coli RNA polymerase with switch region binding inhibitors enable rational design of squaramides with an improved fraction unbound to human plasma protein. J Med Chem 2015; 58:3156-71. [PMID: 25798859 DOI: 10.1021/acs.jmedchem.5b00050] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Squaramides constitute a novel class of RNA polymerase inhibitors of which genetic evidence and computational modeling previously have suggested an inhibitory mechanism mediated by binding to the RNA polymerase switch region. An iterative chemistry program increased the fraction unbound to human plasma protein from below minimum detection levels, i.e., <1% to 4-6%, while retaining biochemical potency. Since in vitro antimicrobial activity against an efflux-negative strain of Haemophilus influenzae was 4- to 8-fold higher, the combined improvement was at least 20- to 60-fold. Cocrystal structures of Escherichia coli RNA polymerase with two key squaramides showed displacement of the switch 2, predicted to interfere with the conformational change of the clamp domain and/or with binding of template DNA, a mechanism akin to that of natural product myxopyronin. Furthermore, the structures confirmed the chemical features required for biochemical potency. The terminal isoxazole and benzyl rings bind into distinct relatively narrow, hydrophobic pockets, and both are required for biochemical potency. In contrast, the linker composed of squarate and piperidine accesses different conformations in their respective cocrystal structures with RNA polymerase, reflecting its main role of proper orientation of the aforementioned terminal rings. These observations further explain the tolerance of hydrophilic substitutions in the linker region that was exploited to improve the fraction unbound to human plasma protein while retaining biochemical potency.
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Affiliation(s)
- Vadim Molodtsov
- †Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | | | | | | | | | | | - Craig E Masse
- ⊥Nimbus Therapeutics, Inc., Cambridge, Massachusetts 02141, United States
| | | | - Katsuhiko S Murakami
- †Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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86
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Sahner JH, Sucipto H, Wenzel SC, Groh M, Hartmann RW, Müller R. Advanced Mutasynthesis Studies on the Natural α-Pyrone Antibiotic Myxopyronin fromMyxococcus fulvus. Chembiochem 2015; 16:946-53. [DOI: 10.1002/cbic.201402666] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Indexed: 01/27/2023]
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87
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Hassan HM, Degen D, Jang KH, Ebright RH, Fenical W. Salinamide F, new depsipeptide antibiotic and inhibitor of bacterial RNA polymerase from a marine-derived Streptomyces sp. J Antibiot (Tokyo) 2015; 68:206-9. [PMID: 25227504 PMCID: PMC4363298 DOI: 10.1038/ja.2014.122] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/10/2014] [Accepted: 08/13/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Hossam M Hassan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - David Degen
- Department of Chemistry and Chemical Biology, Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - Kyoung Hwa Jang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Richard H Ebright
- Department of Chemistry and Chemical Biology, Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
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88
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Fruth M, Plaza A, Hinsberger S, Sahner JH, Haupenthal J, Bischoff M, Jansen R, Müller R, Hartmann RW. Binding mode characterization of novel RNA polymerase inhibitors using a combined biochemical and NMR approach. ACS Chem Biol 2014; 9:2656-63. [PMID: 25207839 DOI: 10.1021/cb5005433] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial RNA polymerase (RNAP) represents a validated target for the development of broad-spectrum antibiotics. However, the medical value of RNAP inhibitors in clinical use is limited by the prevalence of resistant strains. To overcome this problem, we focused on the exploration of alternative target sites within the RNAP. Previously, we described the discovery of a novel RNAP inhibitor class containing an ureidothiophene-2-carboxylic acid core structure. Herein, we demonstrate that these compounds are potent against a set of methicillin-resistant Staphylococcus aureus (MRSA) strains (MIC 2-16 μg mL(-1)) and rifampicin-resistant Escherichia coli TolC strains (MIC 12.5-50 μg mL(-1)). Additionally, an abortive transcription assay revealed that these compounds inhibit the bacterial transcription process during the initiation phase. Furthermore, the binding mode of the ureidothiophene-2-carboxylic acids was characterized by mutagenesis studies and ligand-based NMR spectroscopy. Competition saturation transfer difference (STD) NMR experiments with the described RNAP inhibitor myxopyronin A (Myx) suggest that the ureidothiophene-2-carboxylic acids compete with Myx for the same binding site in the RNAP switch region. INPHARMA (interligand NOE for pharmacophore mapping) experiments and molecular docking simulations provided a binding model in which the ureidothiophene-2-carboxylic acids occupy the region of the Myx western chain binding site and slightly occlude that of the eastern chain. These results demonstrate that the ureidothiophene-2-carboxylic acids are a highly attractive new class of RNAP inhibitors that can avoid the problem of resistance.
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Affiliation(s)
| | | | | | | | | | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, University of Saarland Hospital, 66421 Homburg/Saar, Germany
| | - Rolf Jansen
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | | | - Rolf W. Hartmann
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C23, 66123 Saarbrücken, Germany
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89
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Qu HQ, Jiang ZD. Clostridium difficile infection in diabetes. Diabetes Res Clin Pract 2014; 105:285-94. [PMID: 25015315 DOI: 10.1016/j.diabres.2014.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 01/26/2014] [Accepted: 06/13/2014] [Indexed: 01/08/2023]
Abstract
Diabetes-related hospitalization and hospital utilization is a serious challenge to the health care system, a situation which may be further aggravated by nosocomial Clostridium difficile (C. difficile) infection (CDI). Studies have demonstrated that diabetes increases the risk of recurrent CDI with OR (95% CI) 2.99 (1.88, 4.76). C. difficile is a gram-positive, spore-forming anaerobic bacterium which is widely distributed in the environment. Up to 7% of healthy adults and up to 45% of infants may have asymptomatic intestinal carriage of C. difficile. A large number of strains of C. difficile have been identified. A number of PCR or sequence-based molecular typing methods are available for typing C. difficile isolates. C. difficile virulence evolved independently in the highly epidemic lineages, associated with the expression of toxin genes and other virulence factors. This article briefly reviews recent progresses in the bateriology of C. difficile and highlights the limited knowledge of potential mechanisms for the increased risk of CDI in diabetes which warrants further research.
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Affiliation(s)
- Hui-Qi Qu
- Human Genetics Center, The University of Texas School of Public Health, Houston, TX, USA.
| | - Zhi-Dong Jiang
- Center for Infectious Diseases, Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas School of Public Health, Houston, TX, USA
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90
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Fair RJ, Tor Y. Antibiotics and bacterial resistance in the 21st century. PERSPECTIVES IN MEDICINAL CHEMISTRY 2014; 6:25-64. [PMID: 25232278 PMCID: PMC4159373 DOI: 10.4137/pmc.s14459] [Citation(s) in RCA: 841] [Impact Index Per Article: 84.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/24/2014] [Accepted: 06/24/2014] [Indexed: 12/11/2022]
Abstract
Dangerous, antibiotic resistant bacteria have been observed with increasing frequency over the past several decades. In this review the factors that have been linked to this phenomenon are addressed. Profiles of bacterial species that are deemed to be particularly concerning at the present time are illustrated. Factors including economic impact, intrinsic and acquired drug resistance, morbidity and mortality rates, and means of infection are taken into account. Synchronously with the waxing of bacterial resistance there has been waning antibiotic development. The approaches that scientists are employing in the pursuit of new antibacterial agents are briefly described. The standings of established antibiotic classes as well as potentially emerging classes are assessed with an emphasis on molecules that have been clinically approved or are in advanced stages of development. Historical perspectives, mechanisms of action and resistance, spectrum of activity, and preeminent members of each class are discussed.
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Affiliation(s)
- Richard J Fair
- Department for Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Berlin, Germany
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
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91
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Tang W, Liu S, Degen D, Ebright RH, Prusov EV. Synthesis and evaluation of novel analogues of ripostatins. Chemistry 2014; 20:12310-9. [PMID: 25112727 DOI: 10.1002/chem.201403176] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Indexed: 11/08/2022]
Abstract
Ripostatins are polyene macrolactones isolated from the myxobacterium Sorangium cellulosum. They exhibit antibiotic activity by inhibiting bacterial RNA polymerase (RNAP) through a binding site and mechanism that are different from those of current antibacterial drugs. Thus, the ripostatins serve as starting points for the development of new anti-infective agents with a novel mode of action. In this work, several derivatives of ripostatins were produced. 15-Desoxyripostatin A was synthesized by using a one-pot carboalumination/cross-coupling. 5,6-Dihydroripostatin A was constructed by utilizing an intramolecular Suzuki cross-coupling macrolactonization approach. 14,14'-Difluororipostatin A and both epimeric 14,14'-difluororipostatins B were synthesized by using a Reformatsky type aldol addition of a haloketone, Stille cross-coupling, and ring-closing metathesis. The RNAP-inhibitory and antibacterial activities are presented. Structure-activity relationships indicate that the monocyclic keto-ol form of ripostatin A is the active form of ripostatin A, that the ripostatin C5-C6 unsaturation is important for activity, and that C14 geminal difluorination of ripostatin B results in no loss of activity.
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Affiliation(s)
- Wufeng Tang
- Helmholtz-Zentrum für Infektionsforschung (HZI), Inhoffenstrasse 7, 38124 Braunschweig (Germany), Fax: (+49) 0531-6181-9499
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92
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C-terminal domain swapping of SSB changes the size of the ssDNA binding site. BIOMED RESEARCH INTERNATIONAL 2014; 2014:573936. [PMID: 25162017 PMCID: PMC4137731 DOI: 10.1155/2014/573936] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/09/2014] [Indexed: 01/29/2023]
Abstract
Single-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism, including DNA replication, repair, and recombination, and is therefore essential for cell survival. Bacterial SSB consists of an N-terminal ssDNA-binding/oligomerization domain and a flexible C-terminal protein-protein interaction domain. We characterized the ssDNA-binding properties of Klebsiella pneumoniae SSB (KpSSB), Salmonella enterica Serovar Typhimurium LT2 SSB (StSSB), Pseudomonas aeruginosa PAO1 SSB (PaSSB), and two chimeric KpSSB proteins, namely, KpSSBnStSSBc and KpSSBnPaSSBc. The C-terminal domain of StSSB or PaSSB was exchanged with that of KpSSB through protein chimeragenesis. By using the electrophoretic mobility shift assay, we characterized the stoichiometry of KpSSB, StSSB, PaSSB, KpSSBnStSSBc, and KpSSBnPaSSBc, complexed with a series of ssDNA homopolymers. The binding site sizes were determined to be 26 ± 2, 21 ± 2, 29 ± 2, 21 ± 2, and 29 ± 2 nucleotides (nt), respectively. Comparison of the binding site sizes of KpSSB, KpSSBnStSSBc, and KpSSBnPaSSBc showed that the C-terminal domain swapping of SSB changes the size of the binding site. Our observations suggest that not only the conserved N-terminal domain but also the C-terminal domain of SSB is an important determinant for ssDNA binding.
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93
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Identification of novel bacterial RNA polymerase “Switch Region” inhibitors using pharmacophore model based on multi-template and similarity research. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0960-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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94
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Abstract
Covering: up to the end of 2013. Myxobacteria produce a vast range of structurally diverse natural products with prominent biological activities. Here, we provide a detailed description and judge the potential of all antibiotically active myxobacterial compounds as lead structures, pointing out their particularities and, if known, their mode of action. Thus, the review provides an overview of the potential of specific compounds, suitable for future investigations and possible clinical applications.
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Affiliation(s)
- Till F Schäberle
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
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95
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Mandal SM, Roy A, Ghosh AK, Hazra TK, Basak A, Franco OL. Challenges and future prospects of antibiotic therapy: from peptides to phages utilization. Front Pharmacol 2014; 5:105. [PMID: 24860506 PMCID: PMC4027024 DOI: 10.3389/fphar.2014.00105] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/22/2014] [Indexed: 12/30/2022] Open
Abstract
Bacterial infections are raising serious concern across the globe. The effectiveness of conventional antibiotics is decreasing due to global emergence of multi-drug-resistant (MDR) bacterial pathogens. This process seems to be primarily caused by an indiscriminate and inappropriate use of antibiotics in non-infected patients and in the food industry. New classes of antibiotics with different actions against MDR pathogens need to be developed urgently. In this context, this review focuses on several ways and future directions to search for the next generation of safe and effective antibiotics compounds including antimicrobial peptides, phage therapy, phytochemicals, metalloantibiotics, lipopolysaccharide, and efflux pump inhibitors to control the infections caused by MDR pathogens.
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Affiliation(s)
- Santi M Mandal
- Central Research Facility, Department of Chemistry and Department of Biotechnology, Indian Institute of Technology Kharagpur Kharagpur, India
| | - Anupam Roy
- Central Research Facility, Department of Chemistry and Department of Biotechnology, Indian Institute of Technology Kharagpur Kharagpur, India
| | - Ananta K Ghosh
- Central Research Facility, Department of Chemistry and Department of Biotechnology, Indian Institute of Technology Kharagpur Kharagpur, India
| | - Tapas K Hazra
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Texas Medical Branch at Galveston Galveston, TX, USA
| | - Amit Basak
- Central Research Facility, Department of Chemistry and Department of Biotechnology, Indian Institute of Technology Kharagpur Kharagpur, India
| | - Octavio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília Brasilia, Brazil
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96
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Degen D, Feng Y, Zhang Y, Ebright KY, Ebright YW, Gigliotti M, Vahedian-Movahed H, Mandal S, Talaue M, Connell N, Arnold E, Fenical W, Ebright RH. Transcription inhibition by the depsipeptide antibiotic salinamide A. eLife 2014; 3:e02451. [PMID: 24843001 PMCID: PMC4029172 DOI: 10.7554/elife.02451] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 04/18/2014] [Indexed: 12/12/2022] Open
Abstract
We report that bacterial RNA polymerase (RNAP) is the functional cellular target of the depsipeptide antibiotic salinamide A (Sal), and we report that Sal inhibits RNAP through a novel binding site and mechanism. We show that Sal inhibits RNA synthesis in cells and that mutations that confer Sal-resistance map to RNAP genes. We show that Sal interacts with the RNAP active-center 'bridge-helix cap' comprising the 'bridge-helix N-terminal hinge', 'F-loop', and 'link region'. We show that Sal inhibits nucleotide addition in transcription initiation and elongation. We present a crystal structure that defines interactions between Sal and RNAP and effects of Sal on RNAP conformation. We propose that Sal functions by binding to the RNAP bridge-helix cap and preventing conformational changes of the bridge-helix N-terminal hinge necessary for nucleotide addition. The results provide a target for antibacterial drug discovery and a reagent to probe conformation and function of the bridge-helix N-terminal hinge.DOI: http://dx.doi.org/10.7554/eLife.02451.001.
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Affiliation(s)
- David Degen
- Waksman Institute, Rutgers University, Piscataway, United States
| | - Yu Feng
- Waksman Institute, Rutgers University, Piscataway, United States
| | - Yu Zhang
- Waksman Institute, Rutgers University, Piscataway, United States
| | | | - Yon W Ebright
- Waksman Institute, Rutgers University, Piscataway, United States
| | | | | | - Sukhendu Mandal
- Waksman Institute, Rutgers University, Piscataway, United States
| | - Meliza Talaue
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, United States
| | - Nancy Connell
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, United States
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, United States
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97
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Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH. GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides. eLife 2014; 3:e02450. [PMID: 24755292 PMCID: PMC3994528 DOI: 10.7554/elife.02450] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic GE23077 (GE) binds directly to the bacterial RNA polymerase (RNAP) active-center ‘i’ and ‘i+1’ nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. The target-based resistance spectrum for GE is unusually small, reflecting the fact that the GE binding site on RNAP includes residues of the RNAP active center that cannot be substituted without loss of RNAP activity. The GE binding site on RNAP is different from the rifamycin binding site. Accordingly, GE and rifamycins do not exhibit cross-resistance, and GE and a rifamycin can bind simultaneously to RNAP. The GE binding site on RNAP is immediately adjacent to the rifamycin binding site. Accordingly, covalent linkage of GE to a rifamycin provides a bipartite inhibitor having very high potency and very low susceptibility to target-based resistance. DOI:http://dx.doi.org/10.7554/eLife.02450.001 As increasing numbers of bacteria become resistant to antibiotics, new drugs are needed to fight bacterial infections. To develop new antibacterial drugs, researchers need to understand how existing antibiotics work. There are many ways to kill bacteria, but one of the most effective is to target an enzyme called bacterial RNA polymerase. If bacterial RNA polymerase is prevented from working, bacteria cannot synthesize RNA and cannot survive. GE23077 (GE for short) is an antibiotic produced by bacteria found in soil. Although GE stops bacterial RNA polymerase from working, and thereby kills bacteria, it does not affect mammalian RNA polymerases, and so does not kill mammalian cells. Understanding how GE works could help with the development of new antibacterial drugs. Zhang et al. present results gathered from a range of techniques to show how GE inhibits bacterial RNA polymerase. These show that GE works by binding to a site on RNA polymerase that is different from the binding sites of previously characterized antibacterial drugs. The mechanism used to inhibit the RNA polymerase is also different. The newly identified binding site has several features that make it an unusually attractive target for development of antibacterial compounds. Bacteria can become resistant to an antibiotic if genetic mutations lead to changes in the site the antibiotic binds to. However, the site that GE binds to on RNA polymerase is essential for RNA polymerase to function and so cannot readily be changed without crippling the enzyme. Therefore, this type of antibiotic resistance is less likely to develop. In addition, the newly identified binding site for GE on RNA polymerase is located next to the binding site for a current antibacterial drug, rifampin. Zhang et al. therefore linked GE and rifampin to form a two-part (‘bipartite’) compound designed to bind simultaneously to the GE and the rifampin binding sites. This compound was able to inhibit drug-resistant RNA polymerases tens to thousands of times more potently than GE or rifampin alone. DOI:http://dx.doi.org/10.7554/eLife.02450.002
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Affiliation(s)
- Yu Zhang
- Waksman Institute, Rutgers University, Piscataway, United States
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98
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Malinen AM, NandyMazumdar M, Turtola M, Malmi H, Grocholski T, Artsimovitch I, Belogurov GA. CBR antimicrobials alter coupling between the bridge helix and the β subunit in RNA polymerase. Nat Commun 2014; 5:3408. [PMID: 24598909 PMCID: PMC3959191 DOI: 10.1038/ncomms4408] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 02/06/2014] [Indexed: 01/17/2023] Open
Abstract
Bacterial RNA polymerase (RNAP) is a validated target for antibacterial drugs. CBR703 series antimicrobials allosterically inhibit transcription by binding to a conserved α helix (β' bridge helix, BH) that interconnects the two largest RNAP subunits. Here we show that disruption of the BH-β subunit contacts by amino-acid substitutions invariably results in accelerated catalysis, slowed-down forward translocation and insensitivity to regulatory pauses. CBR703 partially reverses these effects in CBR-resistant RNAPs while inhibiting catalysis and promoting pausing in CBR-sensitive RNAPs. The differential response of variant RNAPs to CBR703 suggests that the inhibitor binds in a cavity walled by the BH, the β' F-loop and the β fork loop. Collectively, our data are consistent with a model in which the β subunit fine tunes RNAP elongation activities by altering the BH conformation, whereas CBRs deregulate transcription by increasing coupling between the BH and the β subunit.
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Affiliation(s)
- Anssi M. Malinen
- Department of Biochemistry, University of Turku, Turku 20014, Finland
| | - Monali NandyMazumdar
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Matti Turtola
- Department of Biochemistry, University of Turku, Turku 20014, Finland
| | - Henri Malmi
- Department of Biochemistry, University of Turku, Turku 20014, Finland
| | - Thadee Grocholski
- Department of Biochemistry, University of Turku, Turku 20014, Finland
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
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99
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Mullane K. Fidaxomicin in Clostridium difficile infection: latest evidence and clinical guidance. Ther Adv Chronic Dis 2014; 5:69-84. [PMID: 24587892 PMCID: PMC3926343 DOI: 10.1177/2040622313511285] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The incidence of Clostridium difficile infection (CDI) has risen 400% in the last decade. It currently ranks as the third most common nosocomial infection. CDI has now crossed over as a community-acquired infection. The major failing of current therapeutic options for the management of CDI is recurrence of disease after the completion of treatment. Fidaxomicin has been proven to be superior to vancomycin in successful sustained clinical response to therapy. Improved outcomes may be due to reduced collateral damage to the gut microflora by fidaxomicin, bactericidal activity, inhibition of Clostridial toxin formation and inhibition of new sporulation. This superiority is maintained in groups previously reported as being at high risk for CDI recurrence including those: with relapsed infection after a single treatment course; on concomitant antibiotic therapy; aged >65 years; with cancer; and with chronic renal insufficiency. Because the acquisition cost of fidaxomicin far exceeds that of metronidazole or vancomycin, in order to rationally utilize this agent, it should be targeted to those populations who are at high risk for relapse and in whom the drug has demonstrated superiority. In this manuscript is reviewed the changing epidemiology of CDI, current treatment options for this infection, proposed benefits of fidaxomicin over currently available antimicrobial options, available analysis of cost effectiveness of the drug, and is given recommendations for judicious use of the drug based upon the available published literature.
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Affiliation(s)
- Kathleen Mullane
- Department of Medicine/Division of Infectious Diseases, University of Chicago, 5841 South Maryland Avenue, MC 5065, Chicago, IL 60637, USA
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100
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Elgaher WAM, Fruth M, Groh M, Haupenthal J, Hartmann RW. Expanding the scaffold for bacterial RNA polymerase inhibitors: design, synthesis and structure–activity relationships of ureido-heterocyclic-carboxylic acids. RSC Adv 2014. [DOI: 10.1039/c3ra45820b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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