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The RNA Polymerase Inhibitor Corallopyronin A Has a Lower Frequency of Resistance Than Rifampicin in Staphylococcus aureus. Antibiotics (Basel) 2022; 11:antibiotics11070920. [PMID: 35884174 PMCID: PMC9311656 DOI: 10.3390/antibiotics11070920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Corallopyronin A (CorA) is active against Gram-positive bacteria and targets the switch region of RNA polymerase. Because of the high frequency of mutation (FoM) leading to rifampicin resistance, we determined the CorA FoM in S. aureus using fluctuation analysis at 4 × minimum inhibitory concentration (MIC). Resistant mutants were characterized. S. aureus strains HG001, Mu50, N315, and USA300 had an MIC of 0.25 mg/L. The median FoM for CorA resistance was 1.5 × 10−8, 4.5-fold lower than the median FoM of 6.7 × 10−8 for rifampicin, and was reflected in a 4-fold lower mutation rate for CorA than rifampicin (6 × 10−9 for CorA vs. 2.5 × 10−8 for rifampicin). In CorA-resistant/rifampicin-sensitive strains, the majority of amino acid exchanges were S1127L in RpoB or K334N in RpoC. S. aureus Mu50, a rifampicin-resistant clinical isolate, yielded two further exchanges targeting amino acids L1131 and E1048 of the RpoB subunit. The plating of >1011 cells on agar containing a combination of 4 × MIC of rifampicin and 4 × MIC of CorA did not yield any growth. In conclusion, with proper usage, e.g., in combination therapy and good antibiotic stewardship, CorA is a potential antibiotic for treating S. aureus infections.
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2
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Kirsch SH, Haeckl FPJ, Müller R. Beyond the approved: target sites and inhibitors of bacterial RNA polymerase from bacteria and fungi. Nat Prod Rep 2022; 39:1226-1263. [PMID: 35507039 DOI: 10.1039/d1np00067e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2016 to 2022RNA polymerase (RNAP) is the central enzyme in bacterial gene expression representing an attractive and validated target for antibiotics. Two well-known and clinically approved classes of natural product RNAP inhibitors are the rifamycins and the fidaxomycins. Rifampicin (Rif), a semi-synthetic derivative of rifamycin, plays a crucial role as a first line antibiotic in the treatment of tuberculosis and a broad range of bacterial infections. However, more and more pathogens such as Mycobacterium tuberculosis develop resistance, not only against Rif and other RNAP inhibitors. To overcome this problem, novel RNAP inhibitors exhibiting different target sites are urgently needed. This review includes recent developments published between 2016 and today. Particular focus is placed on novel findings concerning already known bacterial RNAP inhibitors, the characterization and development of new compounds isolated from bacteria and fungi, and providing brief insights into promising new synthetic compounds.
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Affiliation(s)
- Susanne H Kirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.,Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
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3
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Design, synthesis and biological evaluation of novel hybrids of N-aryl pyrrothine-base α-pyrone as bacterial RNA polymerase inhibitors. Bioorg Med Chem Lett 2020; 30:127146. [DOI: 10.1016/j.bmcl.2020.127146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/16/2020] [Accepted: 03/26/2020] [Indexed: 12/19/2022]
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4
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C–H Bond Activation of Silyl-Substituted Pyridines with Bis(Phenolate)Yttrium Catalysts as a Facile Tool towards Hydroxyl-Terminated Michael-Type Polymers. Catalysts 2020. [DOI: 10.3390/catal10040448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Herein, silicon-protected, ortho-methylated hydroxy-pyridines were reported as initiators in 2-aminoalkoxy-bis(phenolate)yttrium complexes for rare earth metal-mediated group-transfer polymerization (REM-GTP) of Michael-type monomers. To introduce these initiators, C−H bond activation was performed by reacting [(ONOO)tBuY(X)(thf)] (X = CH2TMS, thf = tetrahydrofuran) with tert-butyl-dimethyl-silyl-functionalized α-methylpyridine to obtain the complex [(ONOOtBuY(X)(thf)] (X = 4-(4′-(((tert-butyldimethylsilyl)oxy)methyl)phenyl)-2,6-di-methylpyridine). These initiators served as functional end-groups in polymers produced via REM-GTP. In this contribution, homopolymers of 2-vinylpyridine (2VP) and diethyl vinyl phosphonate (DEVP) were produced. Activity studies and end-group analysis via mass spectrometry, size-exclusion chromatography (SEC) and NMR spectroscopy were performed to reveal the initiator efficiency, the catalyst activity towards both monomers as well as the initiation mechanism of this initiator in contrast to commonly used alkyl initiators. In addition, 2D NMR studies were used to further confirm the end-group integrity of the polymers. For all polymers, different deprotection routes were evaluated to obtain hydroxyl-terminated poly(2-vinylpyridine) (P2VP) and poly(diethyl vinyl phosphonate) (PDEVP). Such hydroxyl groups bear the potential to act as anchoring points for small bioactive molecules, for post-polymerization functionalization or as macroinitiators for further polymerizations.
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5
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Affiliation(s)
- Stephan Scheeff
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
| | - Dirk Menche
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
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6
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Premnath P, Reck M, Wittstein K, Stadler M, Wagner-Döbler I. Screening for inhibitors of mutacin synthesis in Streptococcus mutans using fluorescent reporter strains. BMC Microbiol 2018; 18:24. [PMID: 29580208 PMCID: PMC5870221 DOI: 10.1186/s12866-018-1170-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/20/2018] [Indexed: 01/22/2023] Open
Abstract
Background Within the polymicrobial dental plaque biofilm, bacteria kill competitors by excreting mixtures of bacteriocins, resulting in improved fitness and survival. Inhibiting their bacteriocin synthesis might therefore be a useful strategy to eliminate specific pathogens. We used Streptococcus mutans, a highly acidogenic inhabitant of dental plaque, as a model and searched for natural products that reduced mutacin synthesis. To this end we fused the promoter of mutacin VI to the GFP+ gene and integrated the construct into the genome of S. mutans UA159 by single homologous recombination. Results The resulting reporter strain 423p - gfp + was used to screen 297 secondary metabolites from different sources, mainly myxobacteria and fungi, for their ability to reduce the fluorescence of the fully induced reporter strain by > 50% while growth was almost unaffected (> 90% of control). Seven compounds with different chemical structures and different modes of action were identified. Erinacine C was subsequently validated and shown to inhibit transcription of all three mutacins of S. mutans. The areas of the inhibition zones of the sensor strains S. sanguinis and Lactococcus lactis were reduced by 35% to 61% in comparison to controls in the presence of erinacine C, demonstrating that the amount of active mutacins in the culture supernatants of S. mutans was reduced. Erinacines are cyathane diterpenes that were extracted from cultures of the edible mushroom Hericium erinaceus. They have anti-inflammatory, antimicrobial and neuroprotective effects. For erinacine C, a new biological activity was found here. Conclusions We demonstrate the successful development of a whole-cell fluorescent reporter for the screening of natural compounds and report that erinacine C suppresses mutacin synthesis in S. mutans without affecting cell viability. Electronic supplementary material The online version of this article (10.1186/s12866-018-1170-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Priyanka Premnath
- Helmholtz-Center for Infection Research, Group Microbial Communication, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Michael Reck
- Helmholtz-Center for Infection Research, Group Microbial Communication, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Kathrin Wittstein
- Helmholtz-Center for Infection Research, Department of Microbial Drugs, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Marc Stadler
- Helmholtz-Center for Infection Research, Department of Microbial Drugs, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Irene Wagner-Döbler
- Helmholtz-Center for Infection Research, Group Microbial Communication, Inhoffenstr. 7, 38124, Braunschweig, Germany.
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7
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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8
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Helfrich EJN, Piel J. Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 2016; 33:231-316. [DOI: 10.1039/c5np00125k] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review discusses the biosynthesis of natural products that are generated bytrans-AT polyketide synthases, a family of catalytically versatile enzymes that represents one of the major group of proteins involved in the production of bioactive polyketides.
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Affiliation(s)
- Eric J. N. Helfrich
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
| | - Jörn Piel
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
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Preindl J, Jouvin K, Laurich D, Seidel G, Fürstner A. Gold- or Silver-Catalyzed Syntheses of Pyrones and Pyridine Derivatives: Mechanistic and Synthetic Aspects. Chemistry 2015; 22:237-47. [DOI: 10.1002/chem.201503403] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Indexed: 01/18/2023]
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10
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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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11
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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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12
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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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13
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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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14
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Sahner JH, Groh M, Negri M, Haupenthal J, Hartmann RW. Novel small molecule inhibitors targeting the "switch region" of bacterial RNAP: structure-based optimization of a virtual screening hit. Eur J Med Chem 2013; 65:223-31. [PMID: 23711833 DOI: 10.1016/j.ejmech.2013.04.060] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 04/26/2013] [Accepted: 04/27/2013] [Indexed: 11/30/2022]
Abstract
Rising resistance against current antibiotics necessitates the development of antibacterial agents with alternative targets. The "switch region" of RNA polymerase (RNAP), addressed by the myxopyronins, could be such a novel target site. Based on a hit candidate discovered by virtual screening, a small library of 5-phenyl-3-ureidothiophene-2-carboxylic acids was synthesized resulting in compounds with increased RNAP inhibition. Hansch analysis revealed π (lipophilicity constant) and σ (Hammet substituent constant) of the substituents at the 5-phenyl moiety to be crucial for activity. The binding mode was proven by the targeted introduction of a moiety mimicking the enecarbamate side chain of myxopyronin into the hit compound, accompanied by enhanced RNAP inhibitory potency. The new compounds displayed good antibacterial activities against Gram positive bacteria and Gram negative Escherichia coli TolC and a reduced resistance frequency compared to the established antibiotic rifampicin.
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Affiliation(s)
- J Henning Sahner
- Pharmaceutical and Medicinal Chemistry, Saarland University & Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Drug Design and Optimization, Campus C2 3, 66123 Saarbrücken, Germany
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15
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Yakushiji F, Miyamoto Y, Kunoh Y, Okamoto R, Nakaminami H, Yamazaki Y, Noguchi N, Hayashi Y. Novel hybrid-type antimicrobial agents targeting the switch region of bacterial RNA polymerase. ACS Med Chem Lett 2013; 4:220-4. [PMID: 24900654 DOI: 10.1021/ml300350p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 12/30/2012] [Indexed: 11/28/2022] Open
Abstract
The bacterial RNA polymerase (RNAP) is an ideal target for the development of antimicrobial agents against drug-resistant bacteria. Especially, the switch region within RNAP has been considered as an attractive binding site for drug discovery. Here, we designed and synthesized a series of novel hybrid-type inhibitors of bacterial RNAP. The antimicrobial activities were evaluated using a paper disk diffusion assay, and selected derivatives were tested to determine their MIC values. The hybrid-type antimicrobial agent 29 showed inhibitory activity against Escherichia coli RNAP. The molecular docking study suggested that the RNAP switch region would be the binding site of 29.
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Affiliation(s)
- Fumika Yakushiji
- Departments of †Medicinal Chemistry and ‡Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1
Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yuko Miyamoto
- Departments of †Medicinal Chemistry and ‡Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1
Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yuki Kunoh
- Departments of †Medicinal Chemistry and ‡Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1
Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Reiko Okamoto
- Departments of †Medicinal Chemistry and ‡Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1
Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Hidemasa Nakaminami
- Departments of †Medicinal Chemistry and ‡Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1
Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yuri Yamazaki
- Departments of †Medicinal Chemistry and ‡Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1
Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Norihisa Noguchi
- Departments of †Medicinal Chemistry and ‡Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1
Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yoshio Hayashi
- Departments of †Medicinal Chemistry and ‡Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1
Horinouchi, Hachioji, Tokyo 192-0392, Japan
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McPhillie MJ, Trowbridge R, Mariner KR, O’Neill AJ, Johnson AP, Chopra I, Fishwick CWG. Structure-based ligand design of novel bacterial RNA polymerase inhibitors. ACS Med Chem Lett 2011; 2:729-34. [PMID: 24900260 DOI: 10.1021/ml200087m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 07/29/2011] [Indexed: 11/28/2022] Open
Abstract
Bacterial RNA polymerase (RNAP) is essential for transcription and is an antibacterial target for small molecule inhibitors. The binding region of myxopyronin B (MyxB), a bacterial RNAP inhibitor, offers the possibility of new inhibitor design. The molecular design program SPROUT has been used in conjunction with the X-ray cocrystal structure of Thermus thermophilus RNAP with MyxB to design novel inhibitors based on a substituted pyridyl-benzamide scaffold. A series of molecules, with molecular masses <350 Da, have been prepared using a simple synthetic approach. A number of these compounds inhibited Escherichia coli RNAP.
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Affiliation(s)
- Martin J. McPhillie
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Rachel Trowbridge
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Katherine R. Mariner
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Alex J. O’Neill
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - A. Peter Johnson
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Ian Chopra
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Colin W. G. Fishwick
- School of Chemistry and ‡Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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17
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Srivastava A, Talaue M, Liu S, Degen D, Ebright RY, Sineva E, Chakraborty A, Druzhinin SY, Chatterjee S, Mukhopadhyay J, Ebright YW, Zozula A, Shen J, Sengupta S, Niedfeldt RR, Xin C, Kaneko T, Irschik H, Jansen R, Donadio S, Connell N, Ebright RH. New target for inhibition of bacterial RNA polymerase: 'switch region'. Curr Opin Microbiol 2011; 14:532-43. [PMID: 21862392 PMCID: PMC3196380 DOI: 10.1016/j.mib.2011.07.030] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Revised: 07/28/2011] [Accepted: 07/28/2011] [Indexed: 01/08/2023]
Abstract
A new drug target - the 'switch region' - has been identified within bacterial RNA polymerase (RNAP), the enzyme that mediates bacterial RNA synthesis. The new target serves as the binding site for compounds that inhibit bacterial RNA synthesis and kill bacteria. Since the new target is present in most bacterial species, compounds that bind to the new target are active against a broad spectrum of bacterial species. Since the new target is different from targets of other antibacterial agents, compounds that bind to the new target are not cross-resistant with other antibacterial agents. Four antibiotics that function through the new target have been identified: myxopyronin, corallopyronin, ripostatin, and lipiarmycin. This review summarizes the switch region, switch-region inhibitors, and implications for antibacterial drug discovery.
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Affiliation(s)
- Aashish Srivastava
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Meliza Talaue
- Center for Biodefense, University of Medicine and Dentistry of New Jersey, Newark NJ 07101, USA
| | - Shuang Liu
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - David Degen
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Richard Y. Ebright
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Elena Sineva
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Anirban Chakraborty
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Sergey Y. Druzhinin
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Sujoy Chatterjee
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Jayanta Mukhopadhyay
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Yon W. Ebright
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Alex Zozula
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Juan Shen
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Sonali Sengupta
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Rui Rong Niedfeldt
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
| | - Cai Xin
- College of Chemical Engineering, Sichuan University, Sichuan, Chengdu 610065, PRC
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, New York NY 10004, USA
| | - Herbert Irschik
- Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Rolf Jansen
- Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Stefano Donadio
- NAICONS--New Anti-Infectives Consortium, 20138 Milano, Italy
| | - Nancy Connell
- Center for Biodefense, University of Medicine and Dentistry of New Jersey, Newark NJ 07101, USA
| | - Richard H. Ebright
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854, USA
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18
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Moy TI, Daniel A, Hardy C, Jackson A, Rehrauer O, Hwang YS, Zou D, Nguyen K, Silverman JA, Li Q, Murphy C. Evaluating the activity of the RNA polymerase inhibitor myxopyronin B against Staphylococcus aureus. FEMS Microbiol Lett 2011; 319:176-9. [PMID: 21477256 DOI: 10.1111/j.1574-6968.2011.02282.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Myxopyronin B (MyxB) binds to the switch region of RNA polymerase (RNAP) and inhibits transcriptional initiation. To evaluate the potential development of MyxB as a novel class of antibiotic, we characterized the antimicrobial activity of MyxB against Staphylococcus aureus. Spontaneous MyxB resistance in S. aureus occurred at a frequency of 8 × 10(-8) , similar to that of rifampin. The MyxB-resistant mutants were found to be altered in single amino acid residues in the RNAP subunits that form the MyxB-binding site. In the presence of human serum albumin, the MyxB minimum inhibitory concentration against S. aureus increased drastically (≥128-fold) and 99.5% of MyxB was protein bound. Because of the high serum protein binding and resistance rate, we conclude that MyxB is not a viable starting point for antibiotic development.
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Affiliation(s)
- Terence I Moy
- Cubist Pharmaceuticals Inc., Lexington, MA 02421, USA.
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19
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Weissman KJ, Müller R. Myxobacterial secondary metabolites: bioactivities and modes-of-action. Nat Prod Rep 2010; 27:1276-95. [DOI: 10.1039/c001260m] [Citation(s) in RCA: 225] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Ho MX, Hudson BP, Das K, Arnold E, Ebright RH. Structures of RNA polymerase-antibiotic complexes. Curr Opin Struct Biol 2009; 19:715-23. [PMID: 19926275 DOI: 10.1016/j.sbi.2009.10.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 10/19/2009] [Accepted: 10/20/2009] [Indexed: 01/22/2023]
Abstract
Inhibition of bacterial RNA polymerase (RNAP) is an established strategy for antituberculosis therapy and broad-spectrum antibacterial therapy. Crystal structures of RNAP-inhibitor complexes are available for four classes of antibiotics: rifamycins, sorangicin, streptolydigin, and myxopyronin. The structures define three different targets, and three different mechanisms, for inhibition of bacterial RNAP: (1) rifamycins and sorangicin bind near the RNAP active center and block extension of RNA products; (2) streptolydigin interacts with a target that overlaps the RNAP active center and inhibits conformational cycling of the RNAP active center; and (3) myxopyronin interacts with a target remote from the RNAP active center and functions by interfering with opening of the RNAP active-center cleft to permit entry and unwinding of DNA and/or by interfering with interactions between RNAP and the DNA template strand. The structures enable construction of homology models of pathogen RNAP-antibiotic complexes, enable in silico screening for new antibacterial agents, and enable rational design of improved antibacterial agents.
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Affiliation(s)
- Mary X Ho
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854, USA
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21
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Haebich D, von Nussbaum F. Lost in transcription--inhibition of RNA polymerase. Angew Chem Int Ed Engl 2009; 48:3397-400. [PMID: 19294713 DOI: 10.1002/anie.200900338] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Form and function: The natural product myxopyronin A provides the key to understanding the inhibition of bacterial RNA polymerase and should spark new ideas for the design of new antibiotics against tuberculosis and other infectious diseases.
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Affiliation(s)
- Dieter Haebich
- Bayer Schering Pharma AG, Medicinal Chemistry Europe, 42096 Wuppertal, Germany.
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22
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23
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Mukhopadhyay J, Das K, Ismail S, Koppstein D, Jang M, Hudson B, Sarafianos S, Tuske S, Patel J, Jansen R, Irschik H, Arnold E, Ebright RH. The RNA polymerase "switch region" is a target for inhibitors. Cell 2008; 135:295-307. [PMID: 18957204 PMCID: PMC2580802 DOI: 10.1016/j.cell.2008.09.033] [Citation(s) in RCA: 187] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 07/28/2008] [Accepted: 09/11/2008] [Indexed: 01/22/2023]
Abstract
The alpha-pyrone antibiotic myxopyronin (Myx) inhibits bacterial RNA polymerase (RNAP). Here, through a combination of genetic, biochemical, and structural approaches, we show that Myx interacts with the RNAP "switch region"--the hinge that mediates opening and closing of the RNAP active center cleft--to prevent interaction of RNAP with promoter DNA. We define the contacts between Myx and RNAP and the effects of Myx on RNAP conformation and propose that Myx functions by interfering with opening of the RNAP active-center cleft during transcription initiation. We further show that the structurally related alpha-pyrone antibiotic corallopyronin (Cor) and the structurally unrelated macrocyclic-lactone antibiotic ripostatin (Rip) function analogously to Myx. The RNAP switch region is distant from targets of previously characterized RNAP inhibitors, and, correspondingly, Myx, Cor, and Rip do not exhibit crossresistance with previously characterized RNAP inhibitors. The RNAP switch region is an attractive target for identification of new broad-spectrum antibacterial therapeutic agents.
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Affiliation(s)
- Jayanta Mukhopadhyay
- Howard Hughes Medical Institute, Rutgers University, Piscataway NJ 08854
- Waksman Institute, Rutgers University, Piscataway NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854
| | - Sajida Ismail
- Howard Hughes Medical Institute, Rutgers University, Piscataway NJ 08854
- Waksman Institute, Rutgers University, Piscataway NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854
| | - David Koppstein
- Howard Hughes Medical Institute, Rutgers University, Piscataway NJ 08854
- Waksman Institute, Rutgers University, Piscataway NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854
| | - Minyoung Jang
- Howard Hughes Medical Institute, Rutgers University, Piscataway NJ 08854
- Waksman Institute, Rutgers University, Piscataway NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854
| | - Brian Hudson
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854
| | - Stefan Sarafianos
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854
| | - Steven Tuske
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854
| | - Jay Patel
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854
| | - Rolf Jansen
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Herbert Irschik
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854
| | - Richard H. Ebright
- Howard Hughes Medical Institute, Rutgers University, Piscataway NJ 08854
- Waksman Institute, Rutgers University, Piscataway NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway NJ 08854
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Lira R, Xiang AX, Doundoulakis T, Biller WT, Agrios KA, Simonsen KB, Webber SE, Sisson W, Aust RM, Shah AM, Showalter RE, Banh VN, Steffy KR, Appleman JR. Syntheses of novel myxopyronin B analogs as potential inhibitors of bacterial RNA polymerase. Bioorg Med Chem Lett 2007; 17:6797-800. [PMID: 17980587 DOI: 10.1016/j.bmcl.2007.10.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 10/09/2007] [Accepted: 10/10/2007] [Indexed: 10/22/2022]
Abstract
Based upon observations from our initial findings, additional myxopyronin B analogs have been prepared and tested for in vitro inhibitory activity against DNA-dependent RNA polymerase and antibacterial activity against Escherichia coli and Staphylococcus aureus.
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Affiliation(s)
- Ricardo Lira
- Anadys Pharmaceuticals, Inc., 3115 Merryfield Row, San Diego, CA 92121, USA
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26
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Kanai A, Takeda Y, Kuramochi K, Nakazaki A, Kobayashi S. Synthetic Study on Telomerase Inhibitor, D8646-2-6: Synthesis of the Key Intermediate Using Sn(OTf)2 or Sc(OTf)3 Mediated Aldol-Type Reaction and Stille Coupling. Chem Pharm Bull (Tokyo) 2007; 55:495-9. [PMID: 17329902 DOI: 10.1248/cpb.55.495] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The synthesis of the key intermediate (4) in the proposed route to D8646-2-6 is described. The aldol reaction of the carbohydrate-containing pyrone 7 with the aldehyde 6 was accomplished by using LiHMDS and Sc(OTf)3 or Sn(OTf)2. The stepwise dehydration reaction of the aldol adduct 14, followed by Stille coupling with vinyl stannane 5 which contained phosphonate gave the desired 4.
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Affiliation(s)
- Akira Kanai
- Faculty of Pharmaceutical Sciences, Tokyo University of Science (RIKADAI), Chiba, Japan
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O'Neill AJ, Huovinen T, Fishwick CWG, Chopra I. Molecular genetic and structural modeling studies of Staphylococcus aureus RNA polymerase and the fitness of rifampin resistance genotypes in relation to clinical prevalence. Antimicrob Agents Chemother 2006; 50:298-309. [PMID: 16377701 PMCID: PMC1346782 DOI: 10.1128/aac.50.1.298-309.2006] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The adaptive and further evolutionary responses of Staphylococcus aureus to selection pressure with the antibiotic rifampin have not been explored in detail. We now present a detailed analysis of these systems. The use of rifampin for the chemotherapy of infections caused by S. aureus has resulted in the selection of mutants with alterations within the beta subunit of the target enzyme, RNA polymerase. Using a new collection of strains, we have identified numerous novel mutations in the beta subunits of both clinical and in vitro-derived resistant strains and established that additional, undefined mechanisms contribute to expression of rifampin resistance in clinical isolates of S. aureus. The fitness costs associated with rifampin resistance genotypes were found to have a significant influence on their clinical prevalence, with the most common clinical genotype (H481N, S529L) exhibiting no fitness cost in vitro. Intragenic mutations which compensate for the fitness costs associated with rifampin resistance in clinical strains of S. aureus were identified for the first time. Structural explanations for rifampin resistance and the loss of fitness were obtained by molecular modeling of mutated RNA polymerase enzymes.
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Affiliation(s)
- A J O'Neill
- Antimicrobial Research Centre and Division of Microbiology, University of Leeds, Leeds LS2 9JT, United Kingdom
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