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Qin Z, Huang S, Yu Y, Deng H. Dithiolopyrrolone natural products: isolation, synthesis and biosynthesis. Mar Drugs 2013; 11:3970-97. [PMID: 24141227 PMCID: PMC3826145 DOI: 10.3390/md11103970] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/25/2013] [Accepted: 09/26/2013] [Indexed: 12/24/2022] Open
Abstract
Dithiolopyrrolones are a class of antibiotics that possess the unique pyrrolinonodithiole (4H-[1,2] dithiolo [4,3-b] pyrrol-5-one) skeleton linked to two variable acyl groups. To date, there are approximately 30 naturally occurring dithiolopyrrolone compounds, including holomycin, thiolutin, and aureothricin, and more recently thiomarinols, a unique class of hybrid marine bacterial natural products containing a dithiolopyrrolone framework linked by an amide bridge with an 8-hydroxyoctanoyl chain linked to a monic acid. Generally, dithiolopyrrolone antibiotics have broad-spectrum antibacterial activity against various microorganisms, including Gram-positive and Gram-negative bacteria, and even parasites. Holomycin appeared to be active against rifamycin-resistant bacteria and also inhibit the growth of the clinical pathogen methicillin-resistant Staphylococcus aureus N315. Its mode of action is believed to inhibit RNA synthesis although the exact mechanism has yet to be established in vitro. A recent work demonstrated that the fish pathogen Yersinia ruckeri employs an RNA methyltransferase for self-resistance during the holomycin production. Moreover, some dithiolopyrrolone derivatives have demonstrated promising antitumor activities. The biosynthetic gene clusters of holomycin have recently been identified in S. clavuligerus and characterized biochemically and genetically. The biosynthetic gene cluster of thiomarinol was also identified from the marine bacterium Pseudoalteromonas sp. SANK 73390, which was uniquely encoded by two independent pathways for pseudomonic acid and pyrrothine in a novel plasmid. The aim of this review is to give an overview about the isolations, characterizations, synthesis, biosynthesis, bioactivities and mode of action of this unique family of dithiolopyrrolone natural products, focusing on the period from 1940s until now.
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Affiliation(s)
- Zhiwei Qin
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; E-Mails: (Z.Q.); (S.H.)
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
| | - Sheng Huang
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; E-Mails: (Z.Q.); (S.H.)
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; E-Mails: (Z.Q.); (S.H.)
| | - Hai Deng
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
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252
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Harnessing the potential of halogenated natural product biosynthesis by mangrove-derived actinomycetes. Mar Drugs 2013; 11:3875-90. [PMID: 24129229 PMCID: PMC3826140 DOI: 10.3390/md11103875] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 09/26/2013] [Accepted: 09/27/2013] [Indexed: 12/30/2022] Open
Abstract
Mangrove-derived actinomycetes are promising sources of bioactive natural products. In this study, using homologous screening of the biosynthetic genes and anti-microorganism/tumor assaying, 163 strains of actinomycetes isolated from mangrove sediments were investigated for their potential to produce halogenated metabolites. The FADH2-dependent halogenase genes, identified in PCR-screening, were clustered in distinct clades in the phylogenetic analysis. The coexistence of either polyketide synthase (PKS) or nonribosomal peptide synthetase (NRPS) as the backbone synthetases in the strains harboring the halogenase indicated that these strains had the potential to produce structurally diversified antibiotics. As a validation, a new enduracidin producer, Streptomyces atrovirens MGR140, was identified and confirmed by gene disruption and HPLC analysis. Moreover, a putative ansamycin biosynthesis gene cluster was detected in Streptomyces albogriseolus MGR072. Our results highlight that combined genome mining is an efficient technique to tap promising sources of halogenated natural products synthesized by mangrove-derived actinomycetes.
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Shaaban KA, Wang X, Elshahawi SI, Ponomareva LV, Sunkara M, Copley GC, Hower JC, Morris AJ, Kharel MK, Thorson JS. Herbimycins D-F, ansamycin analogues from Streptomyces sp. RM-7-15. JOURNAL OF NATURAL PRODUCTS 2013; 76:1619-26. [PMID: 23947794 PMCID: PMC3852429 DOI: 10.1021/np400308w] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Bacterial strains belonging to the class actinomycetes were isolated from the soil near a thermal vent of the Ruth Mullins coal fire (Appalachian Mountains of eastern Kentucky). High-resolution electrospray ionization mass spectrometry and ultraviolet absorption profiles of metabolites from one of the isolates (Streptomyces sp. RM-7-15) revealed the presence of a unique set of metabolites ultimately determined to be herbimycins D-F (1-3). In addition, herbimycin A (4), dihydroherbimycin A (TAN 420E) (7), and the structurally distinct antibiotic bicycylomycin were isolated from the crude extract of Streptomyces sp. RM-7-15. Herbimycins A and D-F (1-3) displayed comparable binding affinities to the Hsp90α. While the new analogues were found to be inactive in cancer cell cytotoxicity and antimicrobial assays, they may offer new insights in the context of nontoxic ansamycin-based Hsp90 inhibitors for the treatment of neurodegenerative disease.
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Affiliation(s)
- Khaled A. Shaaban
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Xiachang Wang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Sherif I. Elshahawi
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Larissa V. Ponomareva
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Manjula Sunkara
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, KY 40536, United States
| | - Gregory C. Copley
- Center for Applied Energy Research, University of Kentucky, Lexington, KY, 40511, United States
| | - James C. Hower
- Center for Applied Energy Research, University of Kentucky, Lexington, KY, 40511, United States
| | - Andrew J. Morris
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, KY 40536, United States
| | - Madan K. Kharel
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- To whom correspondence should be addressed: ;
| | - Jon S. Thorson
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- To whom correspondence should be addressed: ;
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256
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Multilocus sequence typing reveals evidence of homologous recombination linked to antibiotic resistance in the genus Salinispora. Appl Environ Microbiol 2013; 79:5997-6005. [PMID: 23892741 DOI: 10.1128/aem.00880-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The three closely related species that currently comprise the genus Salinispora were analyzed using a multilocus sequence typing approach targeting 48 strains derived from four geographic locations. Phylogenetic congruence and a well-supported concatenated tree provide strong support for the delineation of the three species as currently described and the basal relationship of Salinispora arenicola to the more recently diverged sister taxa S. tropica and S. pacifica. The phylogeny of the initial region of the rpoB gene sequenced was atypical, placing the related genera Micromonospora and Verrucosispora within the Salinispora clade. This phylogenetic incongruence was subsequently ascribed to a homologous-recombination event in a portion of the gene associated with resistance to compounds in the rifamycin class, which target RpoB. All S. arenicola strains produced compounds in this class and possessed resistance-conferring amino acid changes in RpoB. The phylogeny of a region of the rpoB gene that is not associated with rifamycin resistance was congruent with the other housekeeping genes. The link between antibiotic resistance and homologous recombination suggests that incongruent phylogenies provide opportunities to identify the molecular targets of secondary metabolites, an observation with potential relevance for drug discovery efforts. Low ratios of interspecies recombination to mutation, even among cooccurring strains, coupled with high levels of within-species recombination suggest that the three species have been described in accordance with natural barriers to recombination.
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257
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Abstract
Long-chain-length hydrophobic acyl residues play a vital role in a multitude of essential biological structures and processes. They build the inner hydrophobic layers of biological membranes, are converted to intracellular storage compounds, and are used to modify protein properties or function as membrane anchors, to name only a few functions. Acyl thioesters are transferred by acyltransferases or transacylases to a variety of different substrates or are polymerized to lipophilic storage compounds. Lipases represent another important enzyme class dealing with fatty acyl chains; however, they cannot be regarded as acyltransferases in the strict sense. This review provides a detailed survey of the wide spectrum of bacterial acyltransferases and compares different enzyme families in regard to their catalytic mechanisms. On the basis of their studied or assumed mechanisms, most of the acyl-transferring enzymes can be divided into two groups. The majority of enzymes discussed in this review employ a conserved acyltransferase motif with an invariant histidine residue, followed by an acidic amino acid residue, and their catalytic mechanism is characterized by a noncovalent transition state. In contrast to that, lipases rely on completely different mechanism which employs a catalytic triad and functions via the formation of covalent intermediates. This is, for example, similar to the mechanism which has been suggested for polyester synthases. Consequently, although the presented enzyme types neither share homology nor have a common three-dimensional structure, and although they deal with greatly varying molecule structures, this variety is not reflected in their mechanisms, all of which rely on a catalytically active histidine residue.
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Affiliation(s)
- Annika Röttig
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
- Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia
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258
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Yim G, Spiegelman GB, Davies JE. Separate mechanisms are involved in rifampicin upmodulated and downmodulated gene expression in Salmonella Typhimurium. Res Microbiol 2013; 164:416-24. [DOI: 10.1016/j.resmic.2013.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 02/04/2013] [Indexed: 11/29/2022]
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259
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Wang Z, Liu S, Ma J, Qu G, Wang X, Yu S, He J, Liu J, Xia T, Jiang GB. Silver nanoparticles induced RNA polymerase-silver binding and RNA transcription inhibition in erythroid progenitor cells. ACS NANO 2013; 7:4171-86. [PMID: 23570347 DOI: 10.1021/nn400594s] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Due to its antimicrobial activity, nanosilver (nAg) has become the most widely used nanomaterial. Thus far, the mechanisms responsible for nAg-induced antimicrobial properties and nAg-mediated toxicity to organisms have not been clearly recognized. Silver (Ag) ions certainly play a crucial role, and the form of nanoparticles can change the dissolution rate, bioavailability, biodistribution, and cellular uptake of Ag. However, whether nAg exerts direct "particle-specific" effects has been under debate. Here we demonstrated that nAg exhibited a robust inhibition on RNA polymerase activity and overall RNA transcription through direct Ag binding to RNA polymerase, which is separated from the cytotoxicity pathway induced by Ag ions. nAg treatment in vitro resulted in reduced hemoglobin concentration in erythroid cells; in vivo administration of nAg in mice caused profound reduction of hemoglobin content in embryonic erythrocytes, associated with anemia in the embryos. Embryonic anemia and general proliferation deficit due to the significant inhibition on RNA synthesis, at least partially, accounted for embryonic developmental retardation upon nAg administration. To date, there is no conclusive answer to the sources of nAg-mediated toxicity: Ag ions or "particle-specific" effects, or both. We here demonstrated that both Ag ions and nAg particles simultaneously existed inside cells, demonstrating the "Trojan horse" effects of nAg particles in posing biological impacts on erythroid cells. Moreover, our results suggested that "particle-specific" effects could be the predominant mediator in eliciting biological influences on erythroid cells under relatively low concentrations of nAg exposure. The combined data highlighted the inhibitory effect of nAg on RNA polymerase activity through a direct reciprocal interaction.
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Affiliation(s)
- Zhe Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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260
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Synthesis of the naphthoquinone core of divergolides (C–D) and model studies for elaboration of the ansabridge. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.03.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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261
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Hüsecken K, Negri M, Fruth M, Boettcher S, Hartmann RW, Haupenthal J. Peptide-based investigation of the Escherichia coli RNA polymerase σ(70):core interface as target site. ACS Chem Biol 2013; 8:758-66. [PMID: 23330640 DOI: 10.1021/cb3005758] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The number of bacterial strains that are resistant against antibiotics increased dramatically during the past decades. This fact stresses the urgent need for the development of new antibacterial agents with novel modes of action targeting essential enzymes such as RNA polymerase (RNAP). Bacterial RNAP is a large multi-subunit complex consisting of a core enzyme (subunits: α(2)ββ'ω) and a dissociable sigma factor (σ(70); holo enzyme: α(2)ββ'ωσ(70)) that is responsible for promoter recognition and transcription initiation. The interface between core RNAP and σ(70) represents a promising binding site. Nevertheless, detailed studies investigating its druggability are rare. Compounds binding to this region could inhibit this protein-protein interaction and thus holo enzyme formation, resulting in inhibition of transcription initiation. Sixteen peptides covering different regions of the Escherichia coli σ(70):core interface were designed; some of them-all derived from σ(70) 2.2 region-led to a strong RNAP inhibition. Indeed, an ELISA-based experiment confirmed the most active peptide P07 to inhibit the σ(70):core interaction. Furthermore, an abortive transcription assay revealed that P07 impedes transcription initiation. In order to study the mechanism of action of P07 in more detail, molecular dynamics simulations and a rational amino acid replacement study were performed, leading to the conclusion that P07 binds to the coiled-coil region in β' and that its flexible N-terminus inhibits the enzyme by interaction with the β' lid-rudder-system (LRS). This work revisits the β' coiled-coil as a hot spot for the protein-protein interaction inhibition and expands it by introduction of the LRS as target site.
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Affiliation(s)
- Kristina Hüsecken
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Matthias Negri
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Martina Fruth
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Stefan Boettcher
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Rolf W. Hartmann
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Joerg Haupenthal
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
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262
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Rasapalli S, Jarugumilli G, Yarrapothu GR, Golen JA, Rheingold AL. Studies toward Total Synthesis of Divergolides C and D. Org Lett 2013; 15:1736-9. [DOI: 10.1021/ol400528g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sivappa Rasapalli
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, United States, and Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, United States
| | - Gopalakrishna Jarugumilli
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, United States, and Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, United States
| | - Gangadhara Rao Yarrapothu
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, United States, and Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, United States
| | - James A. Golen
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, United States, and Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, United States
| | - Arnold L. Rheingold
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, United States, and Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, United States
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263
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Kozlov M, Nudler E, Nikiforov V, Mustaev A. Reactive rifampicin derivative able to damage transcription complex. Bioconjug Chem 2013; 24:443-7. [PMID: 23425196 DOI: 10.1021/bc3005667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rifampicin (Rif) is powerful broad spectrum antibiotic that targets bacterial RNA polymerase (RNAP) by blocking the transcript exit channel. The performance of the drug can be further enhanced by tagging with active chemical groups that produce collateral damage. We explored this principle by tethering Rif to Fe(2+)-EDTA chelate. Modified drug retained high binding affinity to RNAP and caused localized cleavage of the enzyme and promoter DNA. Analysis of the degradation products revealed the cleavage of RNAP β subunit at the sites involved in the drug binding, while DNA was selectively seized in the vicinity of the transcription start site. The synthesized Rif derivative exemplifies "aggressive" types of drugs that can be especially useful for TB treatment by attacking the nongrowing dormant form of the mycobacterium, which is hardly susceptible to "passive" drugs.
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Affiliation(s)
- Maxim Kozlov
- PHRI Center and New Jersey Medical School, Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry of New Jersey, 225 Warren Street, Newark, NJ 07103, USA
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264
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Yang S, Xi Y, Zhu R, Wang L, Chen J, Yang Z. Asymmetric Total Syntheses of Ansamacrolactams (+)-Q-1047H-A-A and (+)-Q-1047H-R-A. Org Lett 2013; 15:812-5. [DOI: 10.1021/ol400038h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Shouliang Yang
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China, and Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yumeng Xi
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China, and Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Rong Zhu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China, and Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Lin Wang
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China, and Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jiahua Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China, and Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Zhen Yang
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China, and Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
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265
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rRNA (rrn) operon-engineered Bacillus subtilis as a feasible test organism for antibiotic discovery. Antimicrob Agents Chemother 2013; 57:1948-51. [PMID: 23335737 DOI: 10.1128/aac.02604-12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis contains 10 rRNA (rrn) operons. We found that rRNA operon-engineered B. subtilis strain RIK543, with only the rrnO operon, is specifically hypersensitive to RNA polymerase inhibitors such as rifamycin SV and rifampin (80-fold and 20-fold, respectively). In pilot screening experiments, we found actinomycete isolates successfully at an incidence of 1.9% (18/945) that produced antibacterials that were detectable only with RIK543 as the test organism. Strain RIK543 may be a feasible test organism for the discovery of novel RNA polymerase inhibitors.
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266
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Chen M, Roush WR. Crotylboron-based synthesis of the polypropionate units of chaxamycins A/D, salinisporamycin, and rifamycin S. J Org Chem 2013; 78:3-8. [PMID: 22703288 PMCID: PMC3465507 DOI: 10.1021/jo3008226] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Syntheses of the C(15)-C(27) fragments of chaxamycins A/D, rifamycin S, and the C(12)-C(24) fragment of salinisporamycin have been accomplished in 10 steps from commercially available starting materials. Three crotylboron reagents were utilized to construct the seven contiguous stereocenters in these fragments with excellent stereoselectivity.
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Affiliation(s)
- Ming Chen
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458
| | - William R. Roush
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458
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267
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Antibiotics for Emerging Pathogens. Infect Dis (Lond) 2013. [DOI: 10.1007/978-1-4614-5719-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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268
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Chromy BA, Elsheikh M, Christensen TL, Livingston D, Petersen K, Bearinger JP, Hoeprich PD. Repurposing screens identify rifamycins as potential broad-spectrum therapy for multidrug-resistant Acinetobacter baumannii and select agent microorganisms. Future Microbiol 2012; 7:1011-20. [DOI: 10.2217/fmb.12.75] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Aims: Estimates suggest that the drug discovery and development processes take between 10 and 15 years, with costs ranging between US$500 million and $2 billion. A growing number of bacteria have become resistant to approved antimicrobials. For example, the Gram-negative bacterium Acinetobacter baumannii has become multidrug resistant (MDR) and is now an important pathogen to the US military in terms of wound infections. Industry experts have called for a ‘disruptive’ transformation of the drug discovery process to find new chemical entities for treating drug-resistant infections. One such attempt is drug ‘repurposing’ or ‘repositioning’ – that is, identification and development of new uses for existing or abandoned pharmacotherapies. Materials & methods: Using a novel combination of screening technologies based on cell growth and cellular respiration, we screened 450 US FDA-approved drugs from the NIH National Clinical Collection against a dozen clinical MDR A. baumannii (MDRAb) isolates from US soldiers and Marines. We also screened the collection against a diverse set of select agent surrogate pathogens. Results: Seventeen drugs showed promising antimicrobial activity against all MDRAb isolates and select agent surrogates; three of these compounds – all rifamycins – were found to be effective at preventing growth and preventing cellular respiration of MDRAb and select agent surrogate bacteria when evaluated in growth prevention assays, highlighting the potential for repurposing. Conclusion: We report the discovery of a class of known compounds whose repurposing may be useful in solving the current problem with MDRAb and may lead to the discovery of broad-spectrum antimicrobials.
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Affiliation(s)
- Brett A Chromy
- University of California Davis School of Medicine, Department of Pathology & Laboratory Medicine, Tupper Hall, Room 3440, Davis, CA 95616, USA
- Lawrence Livermore National Laboratory, 7000 East Avenue, PO Box 808, Livermore, CA 94550, USA
| | - Maher Elsheikh
- Lawrence Livermore National Laboratory, 7000 East Avenue, PO Box 808, Livermore, CA 94550, USA
| | - Tova L Christensen
- Lawrence Livermore National Laboratory, 7000 East Avenue, PO Box 808, Livermore, CA 94550, USA
| | - Doug Livingston
- Evotec San Francisco, Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Kyle Petersen
- Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Jane P Bearinger
- Lawrence Livermore National Laboratory, 7000 East Avenue, PO Box 808, Livermore, CA 94550, USA
| | - Paul D Hoeprich
- Lawrence Livermore National Laboratory, 7000 East Avenue, PO Box 808, Livermore, CA 94550, USA
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269
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Characterization of a rifampin-inactivating glycosyltransferase from a screen of environmental actinomycetes. Antimicrob Agents Chemother 2012; 56:5061-9. [PMID: 22802246 DOI: 10.1128/aac.01166-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Identifying and understanding the collection of all antibiotic resistance determinants presented in the global microbiota, the antibiotic resistome, provides insight into the evolution of antibiotic resistance and critical information for the development of future antimicrobials. The rifamycins are broad-spectrum antibiotics that target bacterial transcription by inhibition of RNA polymerase. Although mutational alteration of the drug target is the predominant mechanism of resistance to this family of antibiotics in the clinic, a number of diverse inactivation mechanisms have also been reported. In this report, we investigate a subset of environmental rifampin-resistant actinomycete isolates and identify a diverse collection of rifampin inactivation mechanisms. We describe a single isolate, WAC1438, capable of inactivating rifampin by glycosylation. A draft genome sequence of WAC1438 (most closely related to Streptomyces speibonae, according to a 16S rRNA gene comparison) was assembled, and the associated rifampin glycosyltransferase open reading frame, rgt1438, was identified. The role of rgt1438 in rifampin resistance was confirmed by its disruption in the bacterial chromosome, resulting in a loss of antibiotic inactivation and a 4-fold decrease in MIC. Interestingly, examination of the RNA polymerase β-subunit sequence of WAC1438 suggests that it harbors a resistant target and thus possesses dual mechanisms of rifamycin resistance. Using an in vitro assay with purified enzyme, Rgt1438 could inactivate a variety of rifamycin antibiotics with comparable steady-state kinetics constants. Our results identify rgt1438 as a rifampin resistance determinant from WAC1438 capable of inactivating an assortment of rifamycins, adding a new element to the rifampin resistome.
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270
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Rifamycin antibiotics—new compounds and synthetic methods. Part 3: Study of the reaction of 3-formylrifamycin SV with primary amines and ketones. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.04.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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271
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Wicher B, Pyta K, Przybylski P, Tykarska E, Gdaniec M. Redetermination of rifampicin pentahydrate revealing a zwitterionic form of the antibiotic. Acta Crystallogr C 2012; 68:o209-12. [PMID: 22552312 DOI: 10.1107/s0108270112015296] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 04/07/2012] [Indexed: 06/16/2024] Open
Abstract
Rifampicin belongs to the family of naphthalenic ansamycin antibiotics. The first crystal structure of rifampicin in the form of the pentahydrate was reported in 1975 [Gadret, Goursolle, Leger & Colleter (1975). Acta Cryst. B 31, 1454-1462] with the rifampicin molecule assumed to be neutral. Redetermination of this crystal structure now shows that one of the phenol -OH groups is deprotonated, with the proton transferred to a piperazine N atom, confirming earlier spectroscopic results that indicated a zwitterionic form for the molecule, namely (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-21-acetyloxy-6,9,17,19-tetrahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-8-[(E)-N-(4-methylpiperazin-4-ium-1-yl)formimidoyl]-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienimino)naphtho[2,1-b]furan-5-olate pentahydrate, C(43)H(58)N(4)O(12)·5H(2)O. The molecular structure of this antibiotic is stabilized by a system of four intramolecular O-H···O and N-H···N hydrogen bonds. Four of the symmetry-independent water molecules are arranged via hydrogen bonds into helical chains extending along [100], whereas the fifth water molecule forms only one hydrogen bond, to the amide group O atom. The rifampicin molecules interact via O-H···O hydrogen bonds, generating chains along [001]. Rifampicin pentahydrate is isostructural with recently reported rifampicin trihydrate methanol disolvate.
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Affiliation(s)
- Barbara Wicher
- Faculty of Chemistry, Adam Mickiewicz University, 60-780 Poznań, Poland
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272
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Brady PB, Yamamoto H. Rapid and stereochemically flexible synthesis of polypropionates: super-silyl-governed aldol cascades. Angew Chem Int Ed Engl 2012; 51:1942-6. [PMID: 22252969 PMCID: PMC3480201 DOI: 10.1002/anie.201108325] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Patrick B. Brady
- Department of Chemistry, The University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637 (USA)
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273
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Pyta K, Przybylski P, Wicher B, Gdaniec M, Stefańska J. Intramolecular proton transfer impact on antibacterial properties of ansamycin antibiotic rifampicin and its new amino analogues. Org Biomol Chem 2012; 10:2385-8. [PMID: 22349158 DOI: 10.1039/c2ob00008c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intramolecular proton transfer in rifampicin (1) and its analogues 2-9 with the formation of zwitterions has been indicated by multinuclear NMR and crystallographic studies. Biological tests of 1-9 in combination with the analysis of ligand-protein interactions have revealed the relationship between the protonation site and extremely high antibacterial activity.
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Affiliation(s)
- Krystian Pyta
- Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland
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274
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Mutations in the β subunit of RNA polymerase alter intrinsic cephalosporin resistance in Enterococci. Antimicrob Agents Chemother 2012; 56:2022-7. [PMID: 22290974 DOI: 10.1128/aac.06077-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As major causes of hospital-acquired infections, antibiotic-resistant enterococci are a serious public health concern. Enterococci are intrinsically resistant to many cephalosporin antibiotics, a trait that enables proliferation in patients undergoing cephalosporin therapy. Although a few genetic determinants of cephalosporin resistance in enterococci have been described, overall, many questions remain about the underlying genetic and biochemical basis for cephalosporin resistance. Here we describe an unexpected effect of specific mutations in the β subunit of RNA polymerase (RNAP) on intrinsic cephalosporin resistance in enterococci. We found that RNAP mutants, selected initially on the basis of their ability to provide resistance to rifampin, resulted in allele-specific alterations of the intrinsic resistance of enterococci toward expanded- and broad-spectrum cephalosporins. These mutations did not affect resistance toward a diverse collection of other antibiotics that target a range of alternative cellular processes. We propose that the RNAP mutations identified here lead to alterations in transcription of as-yet-unknown genes that are critical for cellular adaption to cephalosporin stress.
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275
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Brady PB, Yamamoto H. Rapid and Stereochemically Flexible Synthesis of Polypropionates: Super-Silyl-Governed Aldol Cascades. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108325] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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276
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Yasinskaya Y, Sacks L. Models and approaches for anti-TB drug testing. Expert Rev Anti Infect Ther 2012; 9:823-31. [PMID: 21810054 DOI: 10.1586/eri.11.64] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Unique challenges remain in the development of new drugs for the treatment of TB. While existing multidrug treatment regimens are prolonged and difficult for patients to adhere to, they are highly efficacious, setting a high bar for the performance of new agents. Complicating matters more, regulatory standards have changed since the first drugs for TB were introduced, with a rigorous characterization of the effect of a new drug within a combination regimen expected. If these demands are to be satisfied, innovative models will be needed to demonstrate drug efficacy. In the past, mycobacterial cultures performed on solid media at the end of treatment have been used as critical biomarkers of drug efficacy, but their inability to predict long-term outcomes with precision has limited their utility. This article reviews a range of nonclinical and clinical models to characterize the bactericidal and/or sterilizing activity of new compounds. Novel approaches, using in vitro and animal models, sensitive biomarkers, as well as creative new clinical trial designs, are discussed. These promise a timely expansion of our TB treatment armamentarium to include potent new drugs and shorter, simpler treatment regimens.
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Affiliation(s)
- Yuliya Yasinskaya
- Office of Critical Path Programs in the Office of the Chief Scientist, US FDA, 10903 New Hampshire Avenue, Building 32, Silver Spring, MD 20993, USA.
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277
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Diarylquinolines, synthesis pathways and quantitative structure--activity relationship studies leading to the discovery of TMC207. Future Med Chem 2012; 3:1345-60. [PMID: 21879841 DOI: 10.4155/fmc.11.79] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The emergence of multidrug-resistant strains of Mycobacterium tuberculosis and resistance to current anti-TB drugs call for the discovery and development of new effective anti-TB drugs. TMC207 is the lead candidate of a novel class of antimycobacterial agents, the diarylquinolines, which specifically inhibit mycobacterial ATP synthase and displays high activity against both drug-susceptible and multidrug-resistant strains of Mycobacterium tuberculosis. This article covers both synthesis pathways as well as qualitative and quantitative analyses of the structure-activity relationships of the diarylquinoline series on Mycobacterium smegmatis activity.
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278
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Walsh CT, Haynes SW, Ames BD. Aminobenzoates as building blocks for natural productassembly lines. Nat Prod Rep 2012; 29:37-59. [DOI: 10.1039/c1np00072a] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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279
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280
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Antibiotics for Emerging Pathogens. Infect Dis (Lond) 2012. [DOI: 10.1007/978-1-0716-2463-0_523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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281
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Pyta K, Przybylski P, Klich K, Stefańska J. A new model of binding of rifampicin and its amino analogues as zwitterions to bacterial RNA polymerase. Org Biomol Chem 2012; 10:8283-97. [DOI: 10.1039/c2ob26317c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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282
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Yuan H, Zhao W, Zhong Y, Wang J, Qin Z, Ding X, Zhao GP. Two genes, rif15 and rif16, of the rifamycin biosynthetic gene cluster in Amycolatopsis mediterranei likely encode a transketolase and a P450 monooxygenase, respectively, both essential for the conversion of rifamycin SV into B. Acta Biochim Biophys Sin (Shanghai) 2011; 43:948-56. [PMID: 21986914 DOI: 10.1093/abbs/gmr091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Amycolatopsis mediterranei produces an important antibiotic rifamycin, the biosynthesis of which involves many unusual modifications. Previous work suggested a putative P450 enzyme encoded by rif16 within the rifamycin biosynthetic gene cluster (rif) was required for the conversion of the intermediate rifamycin SV into the end product rifamycin B. In this study, we genetically proved that a putative transketolase encoded by rif15 is another essential enzyme for this conversion. Expression of merely rif15 and rif16 in a rif cluster null mutant of A. mediterranei U32 was able to convert rifamycin SV into B. However, this Rif15- and Rif16-mediated conversion was only detected in intact cells of A. meidterranei, but not in Streptomyce coelicolor or Mycobacterium smegmatis, suggesting that yet-characterized gene(s) in A. mediterranei other than those encoded by the rif cluster should be involved in this process.
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Affiliation(s)
- Hua Yuan
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China
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283
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Freel KC, Edlund A, Jensen PR. Microdiversity and evidence for high dispersal rates in the marine actinomycete 'Salinispora pacifica'. Environ Microbiol 2011; 14:480-93. [PMID: 22117917 DOI: 10.1111/j.1462-2920.2011.02641.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In July of 2006 and January of 2008, a total of 671 marine sediment samples were collected at depths from 5 to 2012 m throughout the Fijian islands and selectively processed for the cultivation of marine actinomycetes belonging to the genus Salinispora. The primary objectives were to assess the diversity, distribution and phylogeny of 'S. pacifica', the least well studied of the three species in the genus. Employing a sequential screening method based on antibiotic sensitivity, RFLP patterns, and 16S rRNA and ITS sequence analyses, 42 of 750 isolates with Salinispora-like features were identified as 'S. pacifica'. These strains represent the first report of 'S. pacifica' from Fiji and include 15 representatives of 4 new 'S. pacifica' 16S rRNA sequence types. Among the 'S. pacifica' strains isolated, little evidence for geographical isolation emerged based on 16S, ITS or secondary metabolite biosynthetic gene fingerprinting. The inclusion of isolates from additional collection sites and other Salinispora spp. revealed a high degree of dispersal among 'S. pacifica' populations and phylogenetic support for the delineation of this lineage as a third species.
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Affiliation(s)
- Kelle C Freel
- Scripps Institution of Oceanography, Center for Marine Biotechnology and Biomedicine, University of California-San Diego, La Jolla, CA 92093, USA
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284
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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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285
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Synthesis and structure–activity relationships of novel substituted 8-amino, 8-thio, and 1,8-pyrazole congeners of antitubercular rifamycin S and rifampin. Bioorg Med Chem Lett 2011; 21:6094-9. [DOI: 10.1016/j.bmcl.2011.08.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 08/09/2011] [Accepted: 08/11/2011] [Indexed: 11/18/2022]
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286
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Rifamycin inhibition of WT and Rif-resistant Mycobacterium tuberculosis and Escherichia coli RNA polymerases in vitro. Tuberculosis (Edinb) 2011; 91:361-9. [DOI: 10.1016/j.tube.2011.05.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 04/28/2011] [Accepted: 05/09/2011] [Indexed: 11/24/2022]
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287
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Pronin SV, Martinez A, Kuznedelov K, Severinov K, Shuman HA, Kozmin SA. Chemical synthesis enables biochemical and antibacterial evaluation of streptolydigin antibiotics. J Am Chem Soc 2011; 133:12172-84. [PMID: 21714556 PMCID: PMC3174773 DOI: 10.1021/ja2041964] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Inhibition of bacterial transcription represents an effective and clinically validated anti-infective chemotherapeutic strategy. We describe the evolution of our approach to the streptolydigin class of antibiotics that target bacterial RNA polymerases (RNAPs). This effort resulted in the synthesis and biological evaluation of streptolydigin, streptolydiginone, streptolic acid, and a series of new streptolydigin-based agents. Subsequent biochemical evaluation of RNAP inhibition demonstrated that the presence of both streptolic acid and tetramic acid subunits was required for activity of this class of antibiotics. In addition, we identified 10,11-dihydrostreptolydigin as a new RNAP-targeting agent, which was assembled with high synthetic efficiency of 15 steps in the longest linear sequence. Dihydrostreptolydigin inhibited three representative bacterial RNAPs and displayed in vitro antibacterial activity against S. salivarius . The overall increase in synthetic efficiency combined with substantial antibacterial activity of this fully synthetic antibiotic demonstrates the power of organic synthesis in enabling design and comprehensive in vitro pharmacological evaluation of new chemical agents that target bacterial transcription.
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Affiliation(s)
- Sergey V. Pronin
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607, United States
| | - Anthony Martinez
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607, United States
| | - Konstantin Kuznedelov
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Konstantin Severinov
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, United States
- Institutes of Gene Biology and Molecualr Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Howard A. Shuman
- Department of Microbiology, University of Chicago, Chicago, Illinois 60607, United States
| | - Sergey A. Kozmin
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607, United States
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288
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Pyta K, Przybylski P. MALDI-TOF tandem mass spectrometric analysis of novel aza-analogues of semi-synthetic ansamycin antibiotic--rifampicin. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:751-756. [PMID: 21766394 DOI: 10.1002/jms.1954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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289
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Abstract
There is a clear and urgent need for novel antibacterial agents that can address the concerns of growing resistance. This article details recent patent activity within the antibiotic field based on the emerging strategy of a multivalent approach to drug discovery. A range of heterodimer antibiotics are discussed, which consist of two antibacterial chemical classes covalently linked to afford compounds with the potential to engage multiple mechanisms of action. The possible benefits of such compounds include activity against drug-resistant bacteria, enhanced efficacy and duration, an expanded spectrum of activity and reduced potential for generating bacterial resistance. This exciting approach towards novel heterodimer antibiotics holds significant promise, but must overcome a range of challenges before yielding a successful medicine. Progress to date is encouraging and has resulted in three compounds entering clinical trials.
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290
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Eun YJ, Utada A, Copeland MF, Takeuchi S, Weibel DB. Encapsulating bacteria in agarose microparticles using microfluidics for high-throughput cell analysis and isolation. ACS Chem Biol 2011; 6:260-6. [PMID: 21142208 PMCID: PMC3060957 DOI: 10.1021/cb100336p] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The high-throughput analysis and isolation of bacterial cells encapsulated in agarose microparticles using fluorescence-activated cell sorting (FACS) is described. Flow-focusing microfluidic systems were used to create monodisperse microparticles that were ∼30 μm in diameter. The dimensions of these particles made them compatible with flow cytometry and FACS, and the sensitivity of these techniques reduced the incubation time for cell replication before analyses were carried out. The small volume of the microparticles (∼1-50 pL) minimized the quantity of reagents needed for bacterial studies. This platform made it possible to screen and isolate bacteria and apply a combination of techniques to rapidly determine the target of biologically active small molecules. As a pilot study, Escherichia coli cells were encapsulated in agarose microparticles, incubated in the presence of varying concentrations of rifampicin, and analyzed using FACS. The minimum inhibitory concentration of rifampicin was determined, and spontaneous mutants that had developed resistance to the antibiotic were isolated via FACS and characterized by DNA sequencing. The β-subunit of RNA polymerase, RpoB, was confirmed as the target of rifampicin, and Q513L was the mutation most frequently observed. Using this approach, the time and quantity of antibiotics required for the isolation of mutants was reduced by 8- and 150-fold, respectively, compared to conventional microbiological techniques using nutrient agar plates. We envision that this technique will have an important impact on research in chemical biology, natural products chemistry, and the discovery and characterization of biologically active secondary metabolites.
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Affiliation(s)
- Ye-Jin Eun
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrew Utada
- Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Matthew F. Copeland
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Shoji Takeuchi
- Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Douglas B. Weibel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
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291
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Wilson MC, Nam SJ, Gulder TAM, Kauffman CA, Jensen PR, Fenical W, Moore BS. Structure and biosynthesis of the marine streptomycete ansamycin ansalactam A and its distinctive branched chain polyketide extender unit. J Am Chem Soc 2011; 133:1971-7. [PMID: 21247149 PMCID: PMC3091981 DOI: 10.1021/ja109226s] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reported is the structure and biosynthesis of ansalactam A, an ansamycin class polyketide produced by an unusual modification of the polyketide pathway. This new metabolite, produced by a marine sediment-derived bacterium of the genus Streptomyces , possesses a novel spiro γ-lactam moiety and a distinctive isobutyryl polyketide fragment observed for the first time in this class of natural products. The structure of ansalactam A was defined by spectroscopic methods including X-ray crystallographic analysis. Biosynthetic studies with stable isotopes further led to the discovery of a new, branched chain polyketide synthase extender unit derived from (E)-4-methyl-2-pentenoic acid for polyketide assembly observed for the first time in this class of natural products.
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Affiliation(s)
- Micheal C Wilson
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, United States
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292
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Ding L, Maier A, Fiebig HH, Görls H, Lin WH, Peschel G, Hertweck C. Divergolides A-D from a Mangrove Endophyte Reveal an Unparalleled Plasticity in ansa-Macrolide Biosynthesis. Angew Chem Int Ed Engl 2011; 50:1630-4. [DOI: 10.1002/anie.201006165] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Indexed: 11/12/2022]
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293
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Ding L, Maier A, Fiebig HH, Görls H, Lin WH, Peschel G, Hertweck C. Divergolides A-D from a Mangrove Endophyte Reveal an Unparalleled Plasticity in ansa-Macrolide Biosynthesis. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006165] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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294
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Wilson MC, Gulder TAM, Mahmud T, Moore BS. Shared biosynthesis of the saliniketals and rifamycins in Salinispora arenicola is controlled by the sare1259-encoded cytochrome P450. J Am Chem Soc 2011; 132:12757-65. [PMID: 20726561 DOI: 10.1021/ja105891a] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Saliniketals A and B are unusual polyketides from the marine actinomycete Salinispora arenicola that inhibit ornithine decarboxylase induction. The structural similarities between the saliniketals and the ansa chain of the potent rifamycin antibiotics, which co-occur in the fermentation broth, suggest a common origin between the two compound classes. Using PCR-directed mutagenesis, chemical complementation studies, and stable isotope feeding experiments, we showed that the saliniketals are byproducts of the rifamycin biosynthetic pathway diverging at the stage of 34a-deoxyrifamycin W. Our results suggest that a single enzyme, the cytochrome P450 monooxygenase encoded by sare1259, catalyzes multiple oxidative rearrangement reactions on 34a-deoxyrifamyin W to yield both the saliniketal and rifamycin structural classes.
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Affiliation(s)
- Micheal C Wilson
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA
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295
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Belen’kii L, Gramenitskaya V, Evdokimenkova Y. The Literature of Heterocyclic Chemistry, Part X, 2005–2007. ADVANCES IN HETEROCYCLIC CHEMISTRY 2011. [DOI: 10.1016/b978-0-12-385464-3.00001-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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296
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Marriner GA, Nayyar A, Uh E, Wong SY, Mukherjee T, Via LE, Carroll M, Edwards RL, Gruber TD, Choi I, Lee J, Arora K, England KD, Boshoff HIM, Barry CE. The Medicinal Chemistry of Tuberculosis Chemotherapy. TOPICS IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1007/7355_2011_13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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297
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Lindqvist L, Robert F, Merrick W, Kakeya H, Fraser C, Osada H, Pelletier J. Inhibition of translation by cytotrienin A--a member of the ansamycin family. RNA (NEW YORK, N.Y.) 2010; 16:2404-2413. [PMID: 20943818 PMCID: PMC2995401 DOI: 10.1261/rna.2307710] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 09/17/2010] [Indexed: 05/30/2023]
Abstract
The ansamycins are a diverse and often physiologically active group of compounds that include geldanamycin and rifamycin, inhibitors of heat shock protein 90 and prokaryotic DNA-dependent RNA synthesis, respectively. Cytotrienin A is an ansamycin-type small molecule with potent antiproliferative and proapoptotic properties. Here, we report that this compound inhibits eukaryotic protein synthesis by targeting translation elongation and interfering with eukaryotic elongation factor 1A function. We also find that cytotrienin A prevents HUVEC tube formation and diminishes microvessel formation in the chorioallantoic membrane assay. These results provide a molecular understanding into cytotrienin A's previously reported properties as an anticancer apoptosis-inducing drug.
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Affiliation(s)
- Lisa Lindqvist
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
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298
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De Pascale G, Wright GD. Antibiotic resistance by enzyme inactivation: from mechanisms to solutions. Chembiochem 2010; 11:1325-34. [PMID: 20564281 DOI: 10.1002/cbic.201000067] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Gianfranco De Pascale
- DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street W, Hamilton, ON L8N 3Z5 Canada
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299
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Strong in vitro activities of two new rifabutin analogs against multidrug-resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 2010; 54:5363-5. [PMID: 20855731 DOI: 10.1128/aac.00149-10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two new rifabutin analogs, RFA-1 and RFA-2, show high in vitro antimycobacterial activities against Mycobacterium tuberculosis. MIC values of RFA-1 and RFA-2 were ≤0.02 μg/ml against rifamycin-susceptible strains and 0.5 μg/ml against a wide selection of multidrug-resistant strains, compared to ≥50 μg/ml for rifampin and 10 μg/ml for rifabutin. Molecular dynamic studies indicate that the compounds may exert tighter binding to mutants of RNA polymerase that have adapted to the rifamycins.
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300
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The delta subunit of RNA polymerase, RpoE, is a global modulator of Streptococcus mutans environmental adaptation. J Bacteriol 2010; 192:5081-92. [PMID: 20675470 DOI: 10.1128/jb.00653-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The delta subunit of RNA polymerase, RpoE, is widespread in low-G+C Gram-positive bacteria and is thought to play a role in enhancing transcriptional specificity by blocking RNA polymerase binding at weak promoter sites and stimulating RNA synthesis by accelerating core enzyme recycling. Despite the well-studied biochemical properties of RpoE, a role for this protein in vivo has not been defined in depth. In this study, we show that inactivation of rpoE in the human dental caries pathogen Streptococcus mutans causes impaired growth and loss of important virulence traits, including biofilm formation, resistance to antibiotics, and tolerance to environmental stresses. Complementation of the mutant with rpoE expressed in trans restored its phenotype to wild type. The luciferase fusion reporter showed that rpoE was highly transcribed throughout growth and that acid and hydrogen peroxide stresses repressed rpoE expression. Transcriptome profiling of wild-type and ΔrpoE cells in the exponential and early stationary phase of growth, under acid and hydrogen peroxide stress and under both stresses combined, revealed that genes involved in histidine synthesis, malolactic fermentation, biofilm formation, and antibiotic resistance were downregulated in the ΔrpoE mutant under all conditions. Moreover, the loss of RpoE resulted in dramatic changes in transport and metabolism of carbohydrates and amino acids. Interestingly, differential expression, mostly upregulation, of 330 noncoding regions was found. In conclusion, this study demonstrates that RpoE is an important global modulator of gene expression in S. mutans which is required for optimal growth and environmental adaptation.
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