1
|
Hoffmann A, Steffens U, Maček B, Franz-Wachtel M, Nieselt K, Harbig TA, Scherlach K, Hertweck C, Sahl HG, Bierbaum G. The unusual mode of action of the polyketide glycoside antibiotic cervimycin C. mSphere 2024; 9:e0076423. [PMID: 38722162 PMCID: PMC11237698 DOI: 10.1128/msphere.00764-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
Cervimycins A-D are bis-glycosylated polyketide antibiotics produced by Streptomyces tendae HKI 0179 with bactericidal activity against Gram-positive bacteria. In this study, cervimycin C (CmC) treatment caused a spaghetti-like phenotype in Bacillus subtilis 168, with elongated curved cells, which stayed joined after cell division, and exhibited a chromosome segregation defect, resulting in ghost cells without DNA. Electron microscopy of CmC-treated Staphylococcus aureus (3 × MIC) revealed swollen cells, misshapen septa, cell wall thickening, and a rough cell wall surface. Incorporation tests in B. subtilis indicated an effect on DNA biosynthesis at high cervimycin concentrations. Indeed, artificial downregulation of the DNA gyrase subunit B gene (gyrB) increased the activity of cervimycin in agar diffusion tests, and, in high concentrations (starting at 62.5 × MIC), the antibiotic inhibited S. aureus DNA gyrase supercoiling activity in vitro. To obtain a more global view on the mode of action of CmC, transcriptomics and proteomics of cervimycin treated versus untreated S. aureus cells were performed. Interestingly, 3 × MIC of cervimycin did not induce characteristic responses, which would indicate disturbance of the DNA gyrase activity in vivo. Instead, cervimycin induced the expression of the CtsR/HrcA heat shock operon and the expression of autolysins, exhibiting similarity to the ribosome-targeting antibiotic gentamicin. In summary, we identified the DNA gyrase as a target, but at low concentrations, electron microscopy and omics data revealed a more complex mode of action of cervimycin, which comprised induction of the heat shock response, indicating protein stress in the cell.IMPORTANCEAntibiotic resistance of Gram-positive bacteria is an emerging problem in modern medicine, and new antibiotics with novel modes of action are urgently needed. Secondary metabolites from Streptomyces species are an important source of antibiotics, like the cervimycin complex produced by Streptomyces tendae HKI 0179. The phenotypic response of Bacillus subtilis and Staphylococcus aureus toward cervimycin C indicated a chromosome segregation and septum formation defect. This effect was at first attributed to an interaction between cervimycin C and the DNA gyrase. However, omics data of cervimycin treated versus untreated S. aureus cells indicated a different mode of action, because the stress response did not include the SOS response but resembled the response toward antibiotics that induce mistranslation or premature chain termination and cause protein stress. In summary, these results point toward a possibly novel mechanism that generates protein stress in the cells and subsequently leads to defects in cell and chromosome segregation.
Collapse
Affiliation(s)
- Alina Hoffmann
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
| | - Ursula Steffens
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
| | - Boris Maček
- University of Tübingen, Proteome Center Tübingen, Tübingen, Germany
| | | | - Kay Nieselt
- University of Tübingen, Interfaculty Institute for Bioinformatics and Medical Informatics, Tübingen, Germany
| | - Theresa Anisja Harbig
- University of Tübingen, Interfaculty Institute for Bioinformatics and Medical Informatics, Tübingen, Germany
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
- Friedrich Schiller University Jena, Institute of Microbiology, Faculty of Biological Sciences, Jena, Germany
| | - Hans-Georg Sahl
- University of Bonn, Institute for Pharmaceutical Microbiology, Bonn, Germany
| | - Gabriele Bierbaum
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
| |
Collapse
|
2
|
GyrB inhibitors as potential antibacterial agents: a review. MONATSHEFTE FUR CHEMIE 2021. [DOI: 10.1007/s00706-021-02800-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
3
|
Gurram SR, Afzal Azam M. Design, Synthesis, Antibacterial Evaluation and Molecular Docking Studies of Some Newer Baenzothiazole Containing Aryl and Alkaryl Hydrazides. Chem Biodivers 2021; 18. [PMID: 34050601 DOI: 10.1002/cbdv.202100117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/28/2021] [Indexed: 11/06/2022]
Abstract
The alarming rise of bacterial resistance is occurring worldwide and endangering the efficacy of antibiotics. Therefore, development of new and efficient antibacterial agents remains paramount. In the present work, we designed and synthesized a series of N'-(1,3-benzothiazol-2-yl)-substituted aryl/aralkyl hydrazides C1-C27 and evaluated them in vitro for their antibacterial activity. Among all tested compounds, C10, C15, and C24 showed potent activity against Staphylococcus aureus ATCC 43300 (MRSA). Minimum bactericidal concentration studies of synthesized compounds are performed against selected bacterial strains. Time kill kinetics showed that the compounds C10 and C15 possess bactericidal activity against MRSA ATCC 43300, while compound C24 possess bactericidal activity against S. aureus NCIM 5022. In the extra-precision docking, compounds C1-C27 exhibited interactions mainly with the N-terminal and central domains of S. aureus GyrB catalytic pocket. Binding free energy (ΔGbind ) of compounds C1-C27/3U2K complexes were computed by MM-GBSA approach. Free energy components indicated Coulomb energy term as favorable for binding, while van der Waals and electrostatic solvation energy terms strongly disfavored the binding. ADMET properties of synthesized compounds C1-C27 are also computed.
Collapse
Affiliation(s)
- Swarupa Rani Gurram
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research), Ooty-643001, Nilgiris, Tamil Nadu, India
| | - Mohammed Afzal Azam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research), Ooty-643001, Nilgiris, Tamil Nadu, India
| |
Collapse
|
4
|
Delgado JL, Hsieh CM, Chan NL, Hiasa H. Topoisomerases as anticancer targets. Biochem J 2018; 475:373-398. [PMID: 29363591 PMCID: PMC6110615 DOI: 10.1042/bcj20160583] [Citation(s) in RCA: 260] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/14/2017] [Accepted: 12/21/2017] [Indexed: 12/15/2022]
Abstract
Many cancer type-specific anticancer agents have been developed and significant advances have been made toward precision medicine in cancer treatment. However, traditional or nonspecific anticancer drugs are still important for the treatment of many cancer patients whose cancers either do not respond to or have developed resistance to cancer-specific anticancer agents. DNA topoisomerases, especially type IIA topoisomerases, are proved therapeutic targets of anticancer and antibacterial drugs. Clinically successful topoisomerase-targeting anticancer drugs act through topoisomerase poisoning, which leads to replication fork arrest and double-strand break formation. Unfortunately, this unique mode of action is associated with the development of secondary cancers and cardiotoxicity. Structures of topoisomerase-drug-DNA ternary complexes have revealed the exact binding sites and mechanisms of topoisomerase poisons. Recent advances in the field have suggested a possibility of designing isoform-specific human topoisomerase II poisons, which may be developed as safer anticancer drugs. It may also be possible to design catalytic inhibitors of topoisomerases by targeting certain inactive conformations of these enzymes. Furthermore, identification of various new bacterial topoisomerase inhibitors and regulatory proteins may inspire the discovery of novel human topoisomerase inhibitors. Thus, topoisomerases remain as important therapeutic targets of anticancer agents.
Collapse
Affiliation(s)
- Justine L Delgado
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA 52242, U.S.A
| | - Chao-Ming Hsieh
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan
| | - Hiroshi Hiasa
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, U.S.A.
| |
Collapse
|
5
|
Hu L, Xu J, Xie X, Zhou Y, Tao P, Li H, Han X, Wang C, Liu J, Xu P, Neculai D, Xia Z. Oligomerization-primed coiled-coil domain interaction with Ubc13 confers processivity to TRAF6 ubiquitin ligase activity. Nat Commun 2017; 8:814. [PMID: 28993672 PMCID: PMC5634496 DOI: 10.1038/s41467-017-01290-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 09/06/2017] [Indexed: 11/30/2022] Open
Abstract
Ubiquitin ligase TRAF6, together with ubiquitin-conjugating enzyme Ubc13/Uev1, catalyzes processive assembly of unanchored K63-linked polyubiquitin chains for TAK1 activation in the IL-1R/TLR pathways. However, what domain and how it functions to enable TRAF6’s processivity are largely uncharacterized. Here, we find TRAF6 coiled-coil (CC) domain is crucial to enable its processivity. The CC domain mediates TRAF6 oligomerization to ensure efficient long polyubiquitin chain assembly. Mutating or deleting the CC domain impairs TRAF6 oligomerization and processive polyubiquitin chain assembly. Fusion of the CC domain to the E3 ubiquitin ligase CHIP/STUB1 renders the latter capable of NF-κB activation. Moreover, the CC domain, after oligomerization, interacts with Ubc13/Ub~Ubc13, which further contributes to TRAF6 processivity. Point mutations within the CC domain that weaken TRAF6 interaction with Ubc13/Ub~Ubc13 diminish TRAF6 processivity. Our results reveal that the CC oligomerization primes its interaction with Ubc13/Ub~Ubc13 to confer processivity to TRAF6 ubiquitin ligase activity. Ubiquitin ligase TRAF6 catalyzes assembly of free polyubiquitin chains for TAK1 activation in the IL-1R/TLR pathways, but the mechanism underlying its processivity is unclear. Here, the authors show that TRAF6 coiled-coil oligomerization domain primes its interaction with Ubc13/Ub~Ubc13 to confer processivity.
Collapse
Affiliation(s)
- Lin Hu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Jiafeng Xu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Xiaomei Xie
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Yiwen Zhou
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Panfeng Tao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Haidong Li
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Xu Han
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Chong Wang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Jian Liu
- Department of Surgical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Pinglong Xu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Dante Neculai
- College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Zongping Xia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China.
| |
Collapse
|
6
|
Chen GY, Ng FM, Tan YW, Poulsen A, Seetoh W, Lin G, Kang C, Then SW, Ahmad NH, Wong YL, Ng HQ, Chia CSB, Lau QY, Hill J, Hung AW, Keller TH. Application of Fragment-Based Drug Discovery against DNA Gyrase B. Chempluschem 2015; 80:1250-1254. [PMID: 31973307 DOI: 10.1002/cplu.201500197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 11/11/2022]
Abstract
Bacterial resistance to antibiotics remains a serious threat to global health. The gyrase B enzyme is a well-validated target for developing antibacterial drugs. Despite being an attractive target for antibiotic development, there are currently no gyrase B inhibitory drugs on the market. A fragment screen using 1,800 compounds identified 14 fragments that bind to Escherichia coli (E. coli) gyrase B. The detailed characterization of binding is described for all 14 fragments. With the aid of X-ray crystallography, modifications on a low-affinity fragment (KD =253 μM, IC50 =634 μM) has led to the development of a new class of potent phenyl aminopyrazole inhibitors against E. coli gyrase B (IC50 =160 nM). The study presented here combines the use of a set of biophysical techniques including differential scanning fluorimetry, nuclear magnetic resonance, isothermal titration calorimetry, and X-ray crystallography to methodically identify, quantify, and optimize fragments into new chemical leads.
Collapse
Affiliation(s)
- Guo-Ying Chen
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Fui Mee Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Yih Wan Tan
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Anders Poulsen
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Weiguang Seetoh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Grace Lin
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Siew Wen Then
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Nur Huda Ahmad
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Ying Lei Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - C S Brian Chia
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Qiu Ying Lau
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| |
Collapse
|
7
|
Okamura S, Nishiyama E, Yamazaki T, Otsuka N, Taniguchi S, Ogawa W, Hatano T, Tsuchiya T, Kuroda T. Action mechanism of 6, 6'-dihydroxythiobinupharidine from Nuphar japonicum, which showed anti-MRSA and anti-VRE activities. Biochim Biophys Acta Gen Subj 2015; 1850:1245-52. [PMID: 25731981 DOI: 10.1016/j.bbagen.2015.02.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 02/11/2015] [Accepted: 02/22/2015] [Indexed: 11/17/2022]
Abstract
BACKGROUND Multidrug-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin resistant enterococci (VRE), cause serious infections at clinical sites, for which the development of new drugs is necessary. We screened candidates for new antibiotics and investigated its action mechanism. METHODS An antimicrobial compound was isolated from an extract of Nuphar japonicum. Its chemical structure was determined by NMR, MS, and optical rotation. We measured its minimum inhibitory concentration (MIC) using the microdilution method. The effects of the compound on DNA gyrase and DNA topoisomerase IV were investigated with DNA supercoiling, decatenation, and cleavage assay. RESULTS We isolated and identified 6,6'-dihydroxythiobinupharidine as the antimicrobial compound. The MIC of this compound was 1-4 μg/mL against various MRSA and VRE strains. We also demonstrated that this compound inhibited DNA topoisomerase IV (IC50 was 10-15 μM), but not DNA gyrase in S. aureus, both of which are known to be the targets of quinolone antibiotics and necessary for DNA replication. However, this compound only exhibited slight cross-resistance to norfloxacin-resistant S. aureus, which indicated that DTBN might inhibit other targets besides topoisomerase IV. These results suggest that 6,6'-dihydroxythiobinupharidine may be a potent candidate or seed for novel antibacterial agents. CONCLUSIONS DTBN from N. japonicum showed anti-MRSA and anti-VRE activities. DTBN might be involved in the inhibition of DNA topoisomerase IV. GENERAL SIGNIFICANCE DTBN might be useful as a seed compound. The information on the inhibition mechanism of DTBN will be useful for the modification of DTBN towards developing novel anti-MRSA and anti-VRE drug.
Collapse
Affiliation(s)
- Shinya Okamura
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| | - Eri Nishiyama
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| | - Tomohiro Yamazaki
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| | - Nao Otsuka
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| | - Shoko Taniguchi
- Botanical Garden, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| | - Wakano Ogawa
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| | - Tsutomu Hatano
- Natural Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| | - Tomofusa Tsuchiya
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| | - Teruo Kuroda
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| |
Collapse
|
8
|
Biçer E, Özdemir N. In vitro study of the interaction of cysteine with a thiazide diuretic (hydrochlorothiazide) at different ph by voltammetric and spectroscopic techniques. RUSS J ELECTROCHEM+ 2013. [DOI: 10.1134/s1023193513100042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
9
|
Brvar M, Perdih A, Renko M, Anderluh G, Turk D, Solmajer T. Structure-based discovery of substituted 4,5'-bithiazoles as novel DNA gyrase inhibitors. J Med Chem 2012; 55:6413-26. [PMID: 22731783 DOI: 10.1021/jm300395d] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bacterial DNA gyrase is a well-established and validated target for the development of novel antibacterials. Starting from the available structural information about the binding of the natural product inhibitor, clorobiocin, we identified a novel series of 4'-methyl-N(2)-phenyl-[4,5'-bithiazole]-2,2'-diamine inhibitors of gyrase B with a low micromolar inhibitory activity by implementing a two-step structure-based design procedure. This novel class of DNA gyrase inhibitors was extensively investigated by various techniques (differential scanning fluorimetry, surface plasmon resonance, and microscale thermophoresis). The binding mode of the potent inhibitor 18 was revealed by X-ray crystallography, confirming our initial in silico binding model. Furthermore, the high resolution of the complex structure allowed for the placement of the Gly97-Ser108 flexible loop, thus revealing its role in binding of this class of compounds. The crystal structure of the complex protein G24 and inhibitor 18 provides valuable information for further optimization of this novel class of DNA gyrase B inhibitors.
Collapse
Affiliation(s)
- Matjaž Brvar
- National Institute of Chemistry, Laboratory for Biocomputing and Bioinformatics, 1001 Ljubljana, Slovenia
| | | | | | | | | | | |
Collapse
|
10
|
Chanti Babu D, Bhujanga Rao C, Ramesh D, Raghavendra Swamy S, Venkateswarlu Y. Total synthesis of the aromatase inhibitor dihydroisocoumarin via protective opening of lactones. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
11
|
Brvar M, Perdih A, Hodnik V, Renko M, Anderluh G, Jerala R, Solmajer T. In silico discovery and biophysical evaluation of novel 5-(2-hydroxybenzylidene) rhodanine inhibitors of DNA gyrase B. Bioorg Med Chem 2012; 20:2572-80. [DOI: 10.1016/j.bmc.2012.02.052] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 02/15/2012] [Accepted: 02/21/2012] [Indexed: 11/26/2022]
|
12
|
Collin F, Karkare S, Maxwell A. Exploiting bacterial DNA gyrase as a drug target: current state and perspectives. Appl Microbiol Biotechnol 2011; 92:479-97. [PMID: 21904817 PMCID: PMC3189412 DOI: 10.1007/s00253-011-3557-z] [Citation(s) in RCA: 364] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 08/08/2011] [Accepted: 08/18/2011] [Indexed: 12/17/2022]
Abstract
DNA gyrase is a type II topoisomerase that can introduce negative supercoils into DNA at the expense of ATP hydrolysis. It is essential in all bacteria but absent from higher eukaryotes, making it an attractive target for antibacterials. The fluoroquinolones are examples of very successful gyrase-targeted drugs, but the rise in bacterial resistance to these agents means that we not only need to seek new compounds, but also new modes of inhibition of this enzyme. We review known gyrase-specific drugs and toxins and assess the prospects for developing new antibacterials targeted to this enzyme.
Collapse
Affiliation(s)
- Frédéric Collin
- Department Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | |
Collapse
|
13
|
Nagase L, Murata-Kamiya N, Hatakeyama M. Potentiation of Helicobacter pylori CagA protein virulence through homodimerization. J Biol Chem 2011; 286:33622-31. [PMID: 21813645 DOI: 10.1074/jbc.m111.258673] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Chronic infection with Helicobacter pylori cagA-positive strains is associated with atrophic gastritis, peptic ulceration, and gastric carcinoma. The cagA gene product, CagA, is delivered into gastric epithelial cells via type IV secretion, where it undergoes tyrosine phosphorylation at the EPIYA motifs. Tyrosine-phosphorylated CagA binds and aberrantly activates the oncogenic tyrosine phosphatase SHP2, which mediates induction of elongated cell morphology (hummingbird phenotype) that reflects CagA virulence. CagA also binds and inhibits the polarity-regulating kinase partitioning-defective 1 (PAR1)/microtubule affinity-regulating kinase (MARK) via the CagA multimerization (CM) sequence independently of tyrosine phosphorylation. Because PAR1 exists as a homodimer, two CagA proteins appear to be passively dimerized through complex formation with a PAR1 dimer in cells. Interestingly, a CagA mutant that lacks the CM sequence displays a reduced SHP2 binding activity and exhibits an attenuated ability to induce the hummingbird phenotype, indicating that the CagA-PAR1 interaction also influences the morphological transformation. Here we investigated the role of CagA dimerization in induction of the hummingbird phenotype with the use of a chemical dimerizer, coumermycin. We found that CagA dimerization markedly stabilizes the CagA-SHP2 complex and thereby potentiates SHP2 deregulation, causing an increase in the number of hummingbird cells. Protrusions of hummingbird cells induced by chemical dimerization of CagA are further elongated by simultaneous inhibition of PAR1. This study revealed a role of the CM sequence in amplifying the magnitude of SHP2 deregulation by CagA, which, in conjunction with the CM sequence-mediated inhibition of PAR1, evokes morphological transformation that reflects in vivo CagA virulence.
Collapse
Affiliation(s)
- Lisa Nagase
- Division of Microbiology, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | | |
Collapse
|
14
|
Panter G, Jerala R. The ectodomain of the Toll-like receptor 4 prevents constitutive receptor activation. J Biol Chem 2011; 286:23334-44. [PMID: 21543336 DOI: 10.1074/jbc.m110.205419] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Toll-like receptor 4 (TLR4) is involved in activation of the innate immune response in a large number of different diseases. Despite numerous studies, the role of separate domains of TLR4 in the regulation of receptor activation is poorly understood. Replacement of the TLR4 ectodomain with LPS-binding proteins MD-2 or CD14 resulted in a robust ligand-independent constitutive activation comparable with the maximal stimulation of the receptor with LPS. The same effect was achieved by the replacement of the ectodomain with a monomeric fluorescent protein or a 24-kDa gyrase B fragment. This demonstrates an intrinsic dimerization propensity of the transmembrane and cytoplasmic domains of TLR4 and reveals a previously unknown function of the ectodomain in inhibiting spontaneous receptor dimerization. Constitutive activation was abolished by the replacement of the ectodomain by a bulkier protein ovalbumin. N-terminal deletion variants of TLR4 revealed that the smallest segment of the ectodomain that already prevents constitutive activity comprises only 90 residues (542 to 631) of the total 608 residues. We conclude that TLR4 represents a receptor with a low threshold of activation that can be rapidly activated by the release of inhibition exerted by its ectodomain. This is important for the sensitivity of TLR4 to activation by different agonists. The TLR4 ectodomain has multiple roles in enabling ligand regulated activation, providing proper localization while serving as an inhibitor to prevent spontaneous, ligand-independent dimerization.
Collapse
Affiliation(s)
- Gabriela Panter
- Department of Biotechnology, National Institute of Chemistry, University of Ljubljana, 1000 Ljubljana, Slovenia
| | | |
Collapse
|
15
|
Škedelj V, Tomašić T, Mašič LP, Zega A. ATP-binding site of bacterial enzymes as a target for antibacterial drug design. J Med Chem 2011; 54:915-29. [PMID: 21235241 DOI: 10.1021/jm101121s] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Veronika Škedelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | | | | | | |
Collapse
|
16
|
Exploring the conformational changes of the ATP binding site of gyrase B from Escherichia coli complexed with different established inhibitors by using molecular dynamics simulation: protein-ligand interactions in the light of the alanine scanning and free energy decomposition methods. J Mol Graph Model 2010; 29:726-39. [PMID: 21216167 DOI: 10.1016/j.jmgm.2010.12.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 12/03/2010] [Accepted: 12/07/2010] [Indexed: 11/23/2022]
Abstract
Currently, bacterial diseases cause a death toll around 2 million people a year encouraging the search for new antimicrobial agents. DNA gyrase is a well-established antibacterial target consisting of two subunits, GyrA and GyrB, in a heterodimer A(2)B(2). GyrA is involved in DNA breakage and reunion and GyrB catalyzes the hydrolysis of ATP. The GyrB subunit from Escherichia coli has been investigated, namely the ATP binding pocket both considering the protein without ligands and bound with the inhibitors clorobiocin, novobiocin and 5'-adenylyl-β-γ-imidodiphosphate. The stability of the systems was studied by molecular dynamics simulation with the further analysis of the time dependent root-mean-square coordinate deviation (RMSD) from the initial structure, and temperature factors. Moreover, exploration of the conformational space of the systems during the MD simulation was carried out by a clustering data mining technique using the average-linkage algorithm. Recognizing the key residues in the binding site of the enzyme that are involved in the binding mode with the aforementioned inhibitors was investigated by using two techniques: free energy decomposition and computational alanine scanning. The results from these simulations highlight the important residues in the ATP binding site and can be useful in the design process of potential new inhibitors.
Collapse
|
17
|
Huang H, Chen Q, Ku X, Meng L, Lin L, Wang X, Zhu C, Wang Y, Chen Z, Li M, Jiang H, Chen K, Ding J, Liu H. A series of alpha-heterocyclic carboxaldehyde thiosemicarbazones inhibit topoisomerase IIalpha catalytic activity. J Med Chem 2010; 53:3048-64. [PMID: 20353152 DOI: 10.1021/jm9014394] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A series of novel thiosemicarbazone derivatives bearing condensed heterocyclic carboxaldehyde moieties were designed and synthesized. Among them, TSC24 exhibited broad antiproliferative activity in a panel of human tumor cells and suppressed tumor growth in mice. The mechanism research revealed that TSC24 was not only an iron chelator but also a topoisomerase IIalpha catalytic inhibitor. Its inhibition on topoisomerase IIalpha was due to direct interaction with the ATPase domain of topoisomerase IIalpha which led to the block of ATP hydrolysis. Molecular docking predicted that TSC24 might bind at the ATP binding site, which was confirmed by the competitive inhibition assay. These results about the mechanisms involved in the anticancer activities of thiosemicarbazones will aid in the rational design of novel topoisomerase II-targeted drugs and will provide insights into the discovery and development of novel cancer therapeutics based on the dual activity to chelate iron and to inhibit the catalytic activity of topoisomerase IIalpha.
Collapse
Affiliation(s)
- He Huang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, P. R. China
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Budin G, Dimala MM, Lamour V, Oudet P, Mioskowski C, Meunier S, Brino L, Wagner A. A Chemical Labeling Strategy for Proteomics under Nondenaturing Conditions. Chembiochem 2009; 11:79-82. [DOI: 10.1002/cbic.200900641] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
19
|
Yu H, Rick SW. Free Energies and Entropies of Water Molecules at the Inhibitor−Protein Interface of DNA Gyrase. J Am Chem Soc 2009; 131:6608-13. [DOI: 10.1021/ja809696s] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hongtao Yu
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148
| | - Steven W. Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148
| |
Collapse
|
20
|
Keightley AM, Dobrzynska M, Podbielkowska M, Renke K, Zobel AM. Coumarin and its 4- and 7- Substituted Derivatives as Retardants of Mitoses in Allium Root Promeristem. ACTA ACUST UNITED AC 2008. [DOI: 10.1076/phbi.34.2.105.13192] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- A M Keightley
- Department of Chemistry, Trent University, Peterborough, Ontario, Canada K9J 7B8
| | - M Dobrzynska
- Department of Biology, Warsaw University, Warsaw 00-927, Krakowskie Przedmiescie 26, Poland
| | - M Podbielkowska
- Department of Biology, Warsaw University, Warsaw 00-927, Krakowskie Przedmiescie 26, Poland
| | - K Renke
- Department of Pharmacy, Medical University, Gdansk, Hallera 107, Poland
| | - A M Zobel
- Department of Chemistry, Trent University, Peterborough, Ontario, Canada K9J 7B8
| |
Collapse
|
21
|
Qin Y, Meng L, Hu C, Duan W, Zuo Z, Lin L, Zhang X, Ding J. Gambogic acid inhibits the catalytic activity of human topoisomerase IIalpha by binding to its ATPase domain. Mol Cancer Ther 2007; 6:2429-40. [PMID: 17876042 DOI: 10.1158/1535-7163.mct-07-0147] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This study is intended to characterize the cellular target of gambogic acid (GA), a natural product isolated from the gamboge resin of Garcinia hurburyi tree, which possesses potent in vitro and in vivo antitumor activities. The antiproliferative activity of GA was further confirmed here in a panel of human tumor cells and multidrug-resistant cells. We found that GA significantly inhibited the catalytic activity of topoisomerase (Topo) II and, to a comparatively less extent, of Topo I, without trapping and stabilizing covalent topoisomerase-DNA cleavage complexes. Down-regulation of Topo IIalpha but not Topo I and Topo IIbeta, reduced GA-induced apoptosis and the phosphorylation of c-Jun, and restored cell proliferation upon GA treatment. Moreover, GA antagonized etoposide-induced DNA damage and abrogated the antiproliferative activity of etoposide, whereas it did not affect camptothecin-induced DNA damage. By dissecting the actions of GA on the individual steps of Topo IIalpha catalytic cycle, we found that GA inhibited DNA cleavage and ATP hydrolysis. Moreover, GA directly bound to the ATPase domain of Topo IIalpha, and may share common binding sites with ATP. The results reported here show that GA exerts its antiproliferative effect by inhibiting the catalytic activity Topo IIalpha. They also indicate that GA inhibits Topo IIalpha-mediated DNA cleavage and modulate the activity of Topo II poisons, which provide rationale for further clinical evaluation of GA.
Collapse
Affiliation(s)
- Yuxin Qin
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, PR China
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Gradisar H, Pristovsek P, Plaper A, Jerala R. Green tea catechins inhibit bacterial DNA gyrase by interaction with its ATP binding site. J Med Chem 2007; 50:264-71. [PMID: 17228868 DOI: 10.1021/jm060817o] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catechins are the main ingredients of green tea extracts and have been shown to possess versatile biological activities, including antimicrobial. We determined that the catechins inhibit bacterial DNA gyrase by binding to the ATP binding site of the gyrase B subunit. In the group of four tested catechins, epigallocatechin gallate (EGCG) had the highest activity, followed by epicatechin gallate (ECG) and epigallocatechin (EGC). Specific binding to the N-terminal 24 kDa fragment of gyrase B was determined by fluorescence spectroscopy and confirmed using heteronuclear two-dimensional NMR spectroscopy of the EGCG-15N-labeled gyrase B fragment complex. Protein residues affected by binding to EGCG were identified through chemical shift perturbation. Molecular docking calculations suggest that the benzopyran ring of EGCG penetrates deeply into the active site while the galloyl moiety anchors it to the cleft through interactions with its hydroxyl groups, which explains the higher activity of EGCG and ECG.
Collapse
Affiliation(s)
- Helena Gradisar
- Laboratory of Biotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | | | | | | |
Collapse
|
23
|
Huang YY, Deng JY, Gu J, Zhang ZP, Maxwell A, Bi LJ, Chen YY, Zhou YF, Yu ZN, Zhang XE. The key DNA-binding residues in the C-terminal domain of Mycobacterium tuberculosis DNA gyrase A subunit (GyrA). Nucleic Acids Res 2006; 34:5650-9. [PMID: 17038336 PMCID: PMC1636481 DOI: 10.1093/nar/gkl695] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
As only the type II topoisomerase is capable of introducing negative supercoiling, DNA gyrase is involved in crucial cellular processes. Although the other domains of DNA gyrase are better understood, the mechanism of DNA binding by the C-terminal domain of the DNA gyrase A subunit (GyrA-CTD) is less clear. Here, we investigated the DNA-binding sites in the GyrA-CTD of Mycobacterium tuberculosis gyrase through site-directed mutagenesis. The results show that Y577, R691 and R745 are among the key DNA-binding residues in M.tuberculosis GyrA-CTD, and that the third blade of the GyrA-CTD is the main DNA-binding region in M.tuberculosis DNA gyrase. The substitutions of Y577A, D669A, R691A, R745A and G729W led to the loss of supercoiling and relaxation activities, although they had a little effect on the drug-dependent DNA cleavage and decatenation activities, and had no effect on the ATPase activity. Taken together, these results showed that the GyrA-CTD is essential to DNA gyrase of M.tuberculosis, and promote the idea that the M.tuberculosis GyrA-CTD is a new potential target for drug design. It is the first time that the DNA-binding sites in GyrA-CTD have been identified.
Collapse
Affiliation(s)
- You-Yi Huang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan 430071, China
- State Key Laboratory of Agromicrobiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan 430070, China
| | - Jiao-Yu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan 430071, China
| | - Jing Gu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan 430071, China
| | - Zhi-Ping Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan 430071, China
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes CentreColney, Norwich NR4 7UH, UK
| | - Li-Jun Bi
- State Key Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of SciencesBeijing 100101, China
| | - Yuan-Yuan Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan 430071, China
| | - Ya-Feng Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan 430071, China
| | - Zi-Niu Yu
- State Key Laboratory of Agromicrobiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan 430070, China
| | - Xian-En Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan 430071, China
- To whom correspondence should be addressed. Tel: +86 010 58881508, Fax: +86 027 87199492.
| |
Collapse
|
24
|
Garrido SS, Scatigno AC, Trovatti E, Carvalho DC, Marchetto R. Probing the binding of the coumarin drugs using peptide fragments of DNA gyrase B protein. ACTA ACUST UNITED AC 2005; 65:502-11. [PMID: 15853944 DOI: 10.1111/j.1399-3011.2005.00264.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial DNA gyrase, has been identified as the target of several antibacterial agents, including the coumarin drugs. The coumarins inhibit the gyrase action by competitive binding to the ATP-binding site of DNA gyrase B (GyrB) protein. The high in vitro inhibitory potency of coumarins against DNA gyrase reactions has raised interest in studies on coumarin-gyrase interactions. In this context, a series of low-molecular weight peptides, including the coumarin resistance-determining region of subunit B of Escherichia coli gyrase, has been designed and synthesized. The first peptide model was built using the natural fragment 131-146 of GyrB and was able to bind to novobiocin (K(a) = 1.8 +/- 0.2 x 10(5)/m) and ATP (K(a) = 1.9 +/- 0.4 x 10(3)/m). To build the other sequences, changes in the Arg(136) residue were introduced so that the binding to the drug was progressively reduced with the hydrophobicity of this residue (K(a) = 1.3 +/- 0.1 x 10(5)/m and 1.0 +/- 0.2 x 10(5)/m for Ser and His, respectively). No binding was observed for the change Arg(136) to Leu. In contrast, the binding to ATP was not altered, independently of the changes promoted. On the contrary, for peptide-coumarin and peptide-ATP complexes, Mg(2+) appears to modulate the binding process. Our results demonstrate the crucial role of Arg(136) residue for the stability of coumarin-gyrase complex as well as suggest a different binding site for ATP and in both cases the interactions are mediated by magnesium ions.
Collapse
Affiliation(s)
- S S Garrido
- Department of Biochemistry and Technological Chemistry, UNESP -- Institute of Chemistry, Caixa Postal 355, 14800-900 Araraquara, São Paulo, Brazil
| | | | | | | | | |
Collapse
|
25
|
Patiño LA, Chippaux M, Courvalin P, Périchon B. Silencing of Glycopeptide Resistance in
Enterococcus faecalis
BM4405 by Novobiocin. Antimicrob Agents Chemother 2005; 49:1419-25. [PMID: 15793121 PMCID: PMC1068633 DOI: 10.1128/aac.49.4.1419-1425.2005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
Enterococcus faecalis
BM4405-1, a susceptible derivative of the VanE-type vancomycin-resistant
E. faecalis
strain BM4405, was obtained after growth in the presence of novobiocin, an inhibitor of the GyrB subunit of DNA gyrase. In contrast to findings for BM4405, UDP-MurNAc-
l
-Ala-γ-
d
-Glu-
l
-Lys-
d
-Ala-
d
-Ala (pentapeptide[
d
-Ala]) was the only peptidoglycan precursor found in BM4405-1, and no VanXY
E
d
,
d
-peptidase or VanT serine racemase activities were detected in that strain, even after induction by subinhibitory concentrations of vancomycin. Sequencing of the
vanE
operon of BM4405-1 revealed two mutations leading to substitutions in VanE (D200N) and in the C-terminal amino acid of VanR
E
(Y225F). Cloning of the
vanE
,
vanXY
E
, and
vanT
E
genes of BM4405-1 into the susceptible
E. faecalis
strain JH2-2 conferred resistance to vancomycin, indicating that the mutation in
vanE
was not responsible for susceptibility. Transcriptional analysis of the
vanE
operon in BM4405 by quantitative reverse transcription-PCR indicated that novobiocin did not affect the expression level of the
vanE
operon. Sequencing of the
gyrB
gene of BM4405-1 revealed a mutation responsible for substitution of a residue (K337Y) required for ATPase activity and thus implicated in DNA supercoiling. Cloning of the
gyrB
gene of BM4405 restored vancomycin resistance to BM4405-1. Taken together, these data suggest that alteration of DNA supercoiling following a mutation in GyrB was responsible for lack of expression of the
vanE
operon and thus for vancomycin susceptibility in BM4405-1.
Collapse
Affiliation(s)
- Lorena Abadía Patiño
- Unité des Agents Antibactériens, Institut Pasteur, 25, Rue du Dr. Roux, 75724 Paris cedex 15, France
| | | | | | | |
Collapse
|
26
|
Zhao HF, Boyd J, Jolicoeur N, Shen SH. A Coumermycin/Novobiocin-Regulated Gene Expression System. Hum Gene Ther 2003; 14:1619-29. [PMID: 14633404 DOI: 10.1089/104303403322542266] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Regulated expression of transgenes in mammals is an important technique in both functional genomic studies and clinical applications. Here we describe a regulated gene expression system for mammals, based on coumarin-switched dimerization of the bacterial DNA gyrase B subunit (GyrB). The transactivator was constructed by fusing the GyrB activator to the bacterial lambda repressor-binding domain. The antibiotic coumermycin in nanomolar concentrations activated the transgene through binding of the homodimerized chimeric transactivator to the lambda operator located upstream of a minipromoter. More significantly, addition of novobiocin, an antagonist of coumermycin, promptly switched off expression of the gene by abolishing coumermycin-induced dimerization of the transactivator. Site-directed mutagenesis of the lambda repressor-binding domain resulted in significant reduction of basal expression levels and an induction reaching four orders of magnitude in stably transfected 293A cells in response to coumermycin. The capability of this inducible system for tightly regulated gene expression was demonstrated by the ready generation of stable cell lines inducibly expressing the proapoptotic bax gene in mammalian cells. Hence, this novel coumarin switch-on/switch-off system should broaden the utility of regulated gene expression, particularly when rapid on/off interchange is required.
Collapse
Affiliation(s)
- Hui-Fen Zhao
- Mammalian Cell Genetics, Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada H4P 2R2
| | | | | | | |
Collapse
|
27
|
Sifaoui F, Lamour V, Varon E, Moras D, Gutmann L. ATP-bound conformation of topoisomerase IV: a possible target for quinolones in Streptococcus pneumoniae. J Bacteriol 2003; 185:6137-46. [PMID: 14526026 PMCID: PMC225018 DOI: 10.1128/jb.185.20.6137-6146.2003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Topoisomerase IV, a C(2)E(2) tetramer, is involved in the topological changes of DNA during replication. This enzyme is the target of antibacterial compounds, such as the coumarins, which target the ATP binding site in the ParE subunit, and the quinolones, which bind, outside the active site, to the quinolone resistance-determining region (QRDR). After site-directed and random mutagenesis, we found some mutations in the ATP binding site of ParE near the dimeric interface and outside the QRDR that conferred quinolone resistance to Streptococcus pneumoniae, a bacterial pathogen. Modeling of the N-terminal, 43-kDa ParE domain of S. pneumoniae revealed that the most frequent mutations affected conserved residues, among them His43 and His103, which are involved in the hydrogen bond network supporting ATP hydrolysis, and Met31, at the dimeric interface. All mutants showed a particular phenotype of resistance to fluoroquinolones and an increase in susceptibility to novobiocin. All mutations in ParE resulted in resistance only when associated with a mutation in the QRDR of the GyrA subunit. Our models of the closed and open conformations of the active site indicate that quinolones preferentially target topoisomerase IV of S. pneumoniae in its ATP-bound closed conformation.
Collapse
Affiliation(s)
- Farid Sifaoui
- INSERM E0004, Laboratoire de Recherche Moléculaire sur les Antibiotiques, UFR Broussais-Hôtel-Dieu, Université Paris VI, 75270 Paris Cedex 06, France
| | | | | | | | | |
Collapse
|
28
|
Perron A, Chen ZG, Gingras D, Dupre DJ, Stankova J, Rola-Pleszczynski M. Agonist-independent desensitization and internalization of the human platelet-activating factor receptor by coumermycin-gyrase B-induced dimerization. J Biol Chem 2003; 278:27956-65. [PMID: 12756251 DOI: 10.1074/jbc.m212302200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Platelet-activating factor (PAF) is a phospholipid with potent and diverse physiological actions, particularly as a mediator of inflammation. We have reported previously that mutant G protein-coupled receptors (GPCRs) affect the functional properties of coexpressed wild-type human PAF receptor (hPAFR) (Le Gouill, C., Parent, J. L., Caron, C. A., Gaudreau, R., Volkov, L., Rola-Pleszczynski, M., and Stankova, J. (1999) J. Biol. Chem. 274, 12548-12554). Increasing evidence suggests that dimerization of GPCRs may play an important role in the regulation of their biological activity. Additional data have also suggested that dimerization may be important in the subsequent internalization of the delta-opioid receptor. To investigate the specific role of dimerization in the internalization process of GPCRs, we generated a fusion protein of hPAFR and bacterial DNA gyrase B (GyrB), dimerized through the addition of coumermycin. We found that dimerization potentiates PAF-induced internalization of hPAFR-GyrB in Chinese hamster ovary cells stably expressing c-Myc-hPAFR-GyrB. Coumermycin-driven dimerization was also sufficient to induce an agonist-independent sequestration process in an arrestin- and clathrin-independent manner. Moreover, the protein kinase C inhibitors staurosporine and GF109203X blocked the coumermycin-induced desensitization of hPAFR-GyrB, suggesting the implication of protein kinase C in the molecular mechanism mediating the agonist-independent desensitization of the receptor. Taken together, these findings suggest a novel mechanism of GPCR desensitization and internalization triggered by dimerization.
Collapse
Affiliation(s)
- Amelie Perron
- Immunology Division, Department of Pediatrics, Faculty of Medicine, University of Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | | | | | | | | | | |
Collapse
|
29
|
Plaper A, Golob M, Hafner I, Oblak M, Solmajer T, Jerala R. Characterization of quercetin binding site on DNA gyrase. Biochem Biophys Res Commun 2003; 306:530-6. [PMID: 12804597 DOI: 10.1016/s0006-291x(03)01006-4] [Citation(s) in RCA: 209] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gyrases are DNA topology modifying enzymes present only in prokaryotes which makes them an attractive target for antibacterial drugs. Quercetin, one of the most abundant natural flavonoids, inhibits supercoiling activity of bacterial gyrase and induces DNA cleavage. It has been generally assumed that the mechanism of flavonoid inhibition is based on interaction with DNA. We show that quercetin binds to the 24 kDa fragment of gyrase B of Escherichia coli with a K(D) value of 15 microM and inhibits ATPase activity of gyrase B. Its binding site overlaps with ATP binding pocket and could be competitively replaced by either ATP or novobiocin. The structural model of quercetin-gyrase complex was prepared, based on the close similarity with ATP and quercetin binding sites of the src family tyrosine kinase Hck. We propose that quercetin inhibits gyrases through two different mechanisms based either on interaction with DNA or with ATP binding site of gyrase.
Collapse
Affiliation(s)
- Andreja Plaper
- Research and Development, Krka, d.d., 8000 Novo mesto, Slovenia
| | | | | | | | | | | |
Collapse
|
30
|
Lamour V, Hoermann L, Jeltsch JM, Oudet P, Moras D. An open conformation of the Thermus thermophilus gyrase B ATP-binding domain. J Biol Chem 2002; 277:18947-53. [PMID: 11850422 DOI: 10.1074/jbc.m111740200] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA gyrase forms an A(2)B(2) tetramer involved in DNA replication, repair, recombination, and transcription in which the B subunit catalyzes ATP hydrolysis. The Thermus thermophilus and Escherichia coli gyrases are homologues and present the same catalytic activity. When compared with that of the E. coli 43K-5'-adenylyl-beta,gamma-imidodiphosphate complex, the crystal structure of Gyrase B 43K ATPase domain in complex with novobiocin, one of the most potent inhibitors of gyrase shows large conformational changes of the subdomains within the dimer. The stabilization of loop 98-118 closing the active site through dimeric contacts and interaction with domain 2 allows to observe novobiocin-protein interactions that could not be seen in the 24K-inhibitor complexes. Furthermore, this loop adopts a position which defines an "open" conformation of the active site in absence of ATP, in contrast with the "closed" conformation adopted upon ATP binding. All together, these results indicate how the subdomains may propagate conformational changes from the active site and provide crucial information for the design of more specific inhibitors.
Collapse
Affiliation(s)
- Valérie Lamour
- Institut de Génétique et de Biologie Moléculaire, CNRS/INSERM/ULP, BP163, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | | | | | | | | |
Collapse
|
31
|
Desplancq D, Kieffer B, Schmidt K, Posten C, Forster A, Oudet P, Strub JM, Van Dorsselaer A, Weiss E. Cost-effective and uniform (13)C- and (15)N-labeling of the 24-kDa N-terminal domain of the Escherichia coli gyrase B by overexpression in the photoautotrophic cyanobacterium Anabaena sp. PCC 7120. Protein Expr Purif 2001; 23:207-17. [PMID: 11570864 DOI: 10.1006/prep.2001.1496] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Structural studies of biomolecules using nuclear magnetic resonance (NMR) rely on the availability of samples enriched in (13)C and (15)N isotopes. While (13)C/(15)N-labeled proteins are generally obtained by overexpression in transformed Escherichia coli cells cultured in the presence of an expensive mixture of labeled precursors, those of the photoautotrophic cyanobacterium Anabaena sp. PCC 7120 can be uniformly labeled by growing them in medium containing Na(15)NO(3) and NaH(13)CO(3) as the sole nitrogen and carbon sources. We report here a novel vector-host system suitable for the efficient preparation of uniformly (13)C/(15)N-labeled proteins in Anabaena sp. PCC 7120. The 24-kDa N-terminal domain of the E. coli gyrase B subunit, used as a test protein, was cloned into the pRL25C shuttle vector under the control of the tac promoter. The transformed Anabaena cells were grown in the presence of the labeled mineral salts and culture conditions were optimized to obtain over 90% of (13)C and (15)N enrichment in the constitutively expressed 24-kDa polypeptide. The yield of purified 24-kDa protein after dual isotope labeling under anaerobic conditions was similar to that obtained with E. coli cells bearing a comparable expression vector and cultured in parallel in a commercially available labeling medium. Furthermore, as probed by NMR spectroscopy and mass spectrometry, the 24-kDa N-terminal domain expressed in Anabaena was identical to the E. coli sample, demonstrating that it was of sufficient quality for 3D-structure determination. Because the Anabaena system was far more advantageous taking into consideration the expense for the labels that were necessary, these results indicate that Anabaena sp. PCC 7120 is an economic alternative for the (13)C/(15)N-labeling of soluble recombinant proteins destined for structural studies.
Collapse
Affiliation(s)
- D Desplancq
- Laboratoire de Biotechnologie des Interactions Macromoléculaires, FRE-CNRS 2370, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Farrar MA, Olson SH, Perlmutter RM. Coumermycin-induced dimerization of GyrB-containing fusion proteins. Methods Enzymol 2001; 327:421-9. [PMID: 11045000 DOI: 10.1016/s0076-6879(00)27293-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- M A Farrar
- Merck Research Laboratories, Rahway, New Jersey 07065-0900, USA
| | | | | |
Collapse
|
33
|
Knight EL, Warner AJ, Maxwell A, Prigent SA. Chimeric VEGFRs are activated by a small-molecule dimerizer and mediate downstream signalling cascades in endothelial cells. Oncogene 2000; 19:5398-405. [PMID: 11103941 DOI: 10.1038/sj.onc.1203915] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Despite much interest in vascular endothelial growth factor (VEGF) and its receptors (VEGFRs -1 and -2), VEGF-induced signalling cascades remain incompletely defined. Attempts to assign individual responses to a particular receptor have used either transfected cell lines, receptor-specific growth factors or antisense oligonucleotides. Such studies have attributed the majority of VEGF-induced responses to activation of VEGFR-2. As a consequence of poor growth factor-induced VEGFR-1 autophosphorylation however, observations from these studies may instead reflect the relative activation of the two receptors. We have generated novel chimeric VEGF receptors in which the dimerization domain of the B subunit of DNA gyrase is fused to the cytoplasmic domain of VEGFRs -1 and -2. When expressed in porcine aortic endothelial cells, both chimeric VEGFR-1 and -2 autophosphorylate in response to addition of the small-molecule dimerizing agent, coumermycin. Once activated, both receptors induce downstream signalling cascades, exemplified here by the activation of MAPK, PLCgamma and PKB/Akt. Furthermore, we demonstrate that the Y1175 residue of VEGFR-2 is essential for the activation of PLCgamma mediated by this chimeric receptor. In contrast to previous reports which show a limited ability of VEGFR-1 to mediate signalling cascades, we show that once sufficiently activated, VEGFR-1 signals in a similar manner to VEGFR-2 in endothelial cells.
Collapse
Affiliation(s)
- E L Knight
- Department of Biochemistry, University of Leicester, UK
| | | | | | | |
Collapse
|
34
|
Heddle JG, Barnard FM, Wentzell LM, Maxwell A. The interaction of drugs with DNA gyrase: a model for the molecular basis of quinolone action. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:1249-64. [PMID: 11097055 DOI: 10.1080/15257770008033048] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
DNA gyrase supercoils DNA in bacteria. The fact that it is essential in all bacteria and absent from eukaryotes makes it an ideal drug target. We discuss the action of coumarin and quinolone drugs on gyrase. In the case of coumarins, the drugs are known to be competitive inhibitors of the gyrase ATPase reaction. From a combination of structural and biochemical studies, the molecular details of the gyrase-coumarin complex are well established. In the case of quinolones, the drugs are thought to act by stabilising a cleavage complex between gyrase and DNA that arrests polymerases in vivo. The exact nature of the gyrase-quinolone-DNA complex is not known; we propose a model for this complex based on structural and biochemical data.
Collapse
Affiliation(s)
- J G Heddle
- Department of Biochemistry, University of Leicester, UK
| | | | | | | |
Collapse
|
35
|
de la Campa AG, García E, Fenoll A, Muñoz R. Molecular bases of three characteristic phenotypes of pneumococcus: optochin-sensitivity, coumarin-sensitivity, and quinolone-resistance. Microb Drug Resist 2000; 3:177-93. [PMID: 9185146 DOI: 10.1089/mdr.1997.3.177] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Streptococcus pneumoniae is uniquely sensitive to amino alcohol antimalarials in the erythro configuration, such as optochin, quinine, and quinidine. The protein responsible for the optochin (quinine)-sensitive (Opts, Qins) phenotype of pneumococcus is the proteolipid c subunit of the FzeroF1 H(+)-ATPase. OptR/QinR isolates arose by point mutations in the atpC gene and produce different amino acid changes in one of the two transmembrane alpha-helices of the c subunit. In addition, comparison of the sequence of the atpCAB genes of S. pneumoniae R6 (Opts) and M222 (an OptR strain produced by interspecies recombination between pneumococcus and S. oralis), and S. oralis (OptR) revealed that, in M222, an interchange of atpC and atpA had occurred. We also demonstrate that optochin, quinine, and related compounds specifically inhibited the membrane-bound ATPase activity. Equivalent differences between Opts/Qins and OptR/QinR strains, both in growth inhibition and in membrane ATPase resistance, were found. Pneumococci also show a characteristic sensitivity to coumarin drugs, and a relatively high level of resistance to most quinolones. We have cloned and sequenced the gyrB gene, and characterized novobiocin resistant mutants. The same amino acid substitution (Ser-127 to Leu) confers novobiocin resistance on four isolates. This residue position is equivalent to Val-120 of Escherichia coli ryGB, a residue that lies inside the ATP-binding domain but is not involved in novobiocin binding in E. coli, as revealed by crystallographic data. In addition, the genes encoding the ParC and ParE subunits of topoisomerase IV, together with the region encoding amino acids 46 to 172 (residue numbers as in E. coli) of the pneumococcal ryGA subunit, were characterized in respect to fluoroquinolone resistance. The gyrA gene maps to a physical location distant from the gyrB and parEC loci on the chromosome. Ciprofloxacin-resistant (CpR) clinical isolates had mutations affecting amino acid residues of the quinolone resistance-determining region of ParC (low-level CpR), or in both resistance-determining regions of ParC and GyrA (high-level CpR). Mutations were found in residue positions equivalent to Ser-83 and Asp-87 of the E. coli GyrA subunit. Transformation experiments demonstrated that topoisomerase IV is the primary target of ciprofloxacin, DNA gyrase being a secondary one.
Collapse
Affiliation(s)
- A G de la Campa
- Centro Nacional de Biología Fundamental, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | | |
Collapse
|
36
|
Zobel AM, Schellenberger SE. Paclitaxel in combination with coumarin as a potentially effective anticancer agent. PHARMACEUTICAL BIOLOGY 2000; 38:192-196. [PMID: 21214461 DOI: 10.1076/1388-0209(200007)3831-sft192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The antimitotic and clastogenic effects induced by paclitaxel alone, and when combined with coumarin at varying concentrations and volume ratios, were investigated on meristematic cells of Allium sativum L. root tips. Paclitaxel exhibited antimitotic effects by blocking cell division in metaphase at concentrations ranging from saturated to 10 -12 ppm. Paclitaxel when used alone at high concentrations (saturated, 10 -3 ppm, 10 -6 ppm) induced cytotoxic and chromosomal aberrations after 1 and 3 h incubation and cell death after 24 h incubation. Paclitaxel demonstrated fewer cytotoxic and clastogenic effects when combined with coumarin in a 1:9 ratio at low concentrations. The combination of 10 -12 ppm of paclitaxel with 200 ppm coumarin (1:9) produced the best results as these agents worked together synergistically at the biochemical level to produce antimitotic effects with the fewest chromosomal aberrations. This mixture exhibited the potential to be used as an anticancer drug owing to its abilities to exert antimitotic activity without causing extreme clastogenic effects. Paclitaxel, when used alone or in combination with coumarin at high concentrations (greater than 10 -12 ppm), demonstrated possible carcinogenic potential when used in cancer therapy.
Collapse
|
37
|
Kume A, Ito K, Ueda Y, Hasegawa M, Urabe M, Mano H, Ozawa K. A G-CSF receptor-gyrase B fusion gene: A new type of molecular switch for expansion of genetically modified hematopoietic cells. Biochem Biophys Res Commun 1999; 260:9-12. [PMID: 10381335 DOI: 10.1006/bbrc.1999.0859] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have developed a novel system for expansion of transduced hematopoietic cells. This system involves "selective amplifier genes" encoding fusion proteins between the granulocyte colony-stimulating factor receptor (Gcr) and the estrogen receptor (Er). The GcrEr chimeric gene conferred estrogen-dependent growth ability on murine hematopoietic cells. Here, we constructed a modified "selective amplifier gene" to circumvent possible concerns with the Er/estrogen switching system. The bacterial gyrase B (Gyr) gene was fused to the Gcr gene, and the GcrGyr fusion construct was introduced into interleukin-3 (IL-3)-dependent Ba/F3 cells. The dimeric antibiotic coumermycin induced IL-3-independent growth in Ba/F3 cells expressing GcrGyr. This stimulatory effect was antagonized by an excess amount of novobiocin, a monomeric form of coumermycin. These results suggest the feasibility of using Gyr as a molecular switch to regulate a growth signal in hematopoietic cells.
Collapse
Affiliation(s)
- A Kume
- Division of Genetic Therapeutics, Center for Molecular Medicine, Tochigi, 3311-1 Yakushiji, 329-0498, Japan
| | | | | | | | | | | | | |
Collapse
|
38
|
Paitan Y, Boulton N, Ron EZ, Rosenberg E, Orr E. Molecular analysis of the DNA gyrB gene from Myxococcus xanthus. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 6):1641-1647. [PMID: 9639935 DOI: 10.1099/00221287-144-6-1641] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DNA gyrase, an essential type II topoisomerase, mediates negative supercoiling of the bacterial chromosome, thereby affecting the processes of DNA replication, transcription, recombination and repair. The gyrB gene from the Gram-negative soil bacterium Myxococcus xanthus was sequenced. The sequence predicts a protein of 815 amino acid residues displaying significant homology to all known GyrB proteins. A 6-His-GyrB fusion protein was overexpressed in Escherichia coli and purified to near homogeneity using affinity chromatography on Ni-nitrilotriacetic acid-agarose and novobiocin-Sepharose columns. The fusion protein bound novobiocin and cross-reacted with anti-E. coli GyrB antibodies, indicating structural and functional similarities to the E. coli DNA GyrB. The gene was mapped to the region of the origin of replication (oriC) of M. xanthus.
Collapse
Affiliation(s)
- Yossi Paitan
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Neil Boulton
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Eliora Z Ron
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Eugene Rosenberg
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Elisha Orr
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| |
Collapse
|
39
|
Li TK, Liu LF. Modulation of gyrase-mediated DNA cleavage and cell killing by ATP. Antimicrob Agents Chemother 1998; 42:1022-7. [PMID: 9593120 PMCID: PMC105738 DOI: 10.1128/aac.42.5.1022] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
An uncoupler of oxidative phosphorylation, 2,4-dinitrophenol, and an aconitase inhibitor, fluoroacetic acid, both of which are known to lower the cellular ATP pool, protected Escherichia coli cells from the bactericidal actions of gyrase poisons including quinolone antibiotics, nalidixic acid and ciprofloxacin, and the epipodophyllotoxins VP-16 and VM-26. Using purified E. coli DNA gyrase, we examined the effect of ATP on gyrase-mediated DNA cleavage in the presence of these gyrase poisons. ATP was shown to stimulate gyrase-mediated DNA cleavage from 10- to more than 100-fold in the presence of these gyrase poisons. ADP antagonized the stimulatory effect of ATP. Consequently, gyrase-mediated DNA cleavage induced by gyrase poisons is modulated by the ATP concentration/ADP concentration ([ATP]/[ADP]) ratio. Coumermycin A1, an inhibitor of the ATPase subunit of DNA gyrase, like ADP, also effectively antagonized the stimulatory effect of ATP on gyrase-mediated DNA cleavage induced by gyrase poisons. Furthermore, coumermycin A1, like DNP and fluoroacetic acid, also protected cells from the bactericidal action of gyrase poisons. In the aggregate, our results are consistent with the notion that the [ATP]/[ADP] ratio, through its modulatory effect on the gyrase-mediated DNA cleavage, is an important determinant of cellular susceptibility to gyrase poisons.
Collapse
Affiliation(s)
- T K Li
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway 08854, USA
| | | |
Collapse
|
40
|
Fournier B, Hooper DC. Mutations in topoisomerase IV and DNA gyrase of Staphylococcus aureus: novel pleiotropic effects on quinolone and coumarin activity. Antimicrob Agents Chemother 1998; 42:121-8. [PMID: 9449271 PMCID: PMC105466 DOI: 10.1128/aac.42.1.121] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Previous studies have shown that topoisomerase IV and DNA gyrase interact with quinolones and coumarins in different ways. The MICs of coumarins (novobiocin and coumermycin) for MT5, a Staphylococcus aureus nov mutant, are higher than those for wild-type strains. Sequencing the gyrB gene encoding one subunit of the DNA gyrase revealed the presence of a double mutation likely to be responsible for this resistance: at codon 102 (Ile to Ser) and at codon 144 (Arg to Ile). For single-step flqA mutant MT5224c9, previously selected on ciprofloxacin, the fluoroquinolone MIC was higher and the coumarin MIC was lower than those for its parent, MT5. Sequencing the grlB and grlA genes of topoisomerase IV of MT5224c9 showed a single Asn-470-to-Asp mutation in GrlB. Genetic outcrosses by transformation with chromosomal DNA and introduction of plasmids carrying either the wild-type or the mutated grlB gene indicated that this mutation causes both increased MICs of fluoroquinolones and decreased MICs of coumarins and that the mutant grlB allele is codominant for both phenotypes with multicopy alleles. Integration of these plasmids into the chromosome confirmed the codominance of fluoroquinolone resistance, but grlB+ appeared dominant over grlB (Asp-470) for coumarin resistance. Finally, the gyrA (Leu-84) mutation previously described as silent for fluoroquinolone resistance increased the MIC of nalidixic acid, a nonfluorinated quinolone. Combining the grlA (Phe-80) and grlB (Asp-470) mutations with this gyrA mutation also had differing effects. The findings indicate that alterations in topoisomerases may have pleiotropic effects on different classes of inhibitors as well as on inhibitors within the same class. A full understanding of drug action and resistance at the molecular level must take into account both inhibitor structure-activity relationships and the effects of different classes of topoisomerase mutants.
Collapse
Affiliation(s)
- B Fournier
- Infectious Disease Division, Massachusetts General Hospital, Harvard Medical School, Boston 02114-2696, USA
| | | |
Collapse
|
41
|
Prodromou C, Roe SM, O'Brien R, Ladbury JE, Piper PW, Pearl LH. Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone. Cell 1997; 90:65-75. [PMID: 9230303 DOI: 10.1016/s0092-8674(00)80314-1] [Citation(s) in RCA: 959] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Hsp90 molecular chaperones in eukaryotic cells play essential roles in the folding and activation of a range of client proteins involved in cell cycle regulation, steroid hormone responsiveness, and signal transduction. The biochemical mechanism of Hsp90 is poorly understood, and the involvement of ATP in particular is controversial. Crystal structures of complexes between the N-terminal domain of the yeast Hsp90 chaperone and ADP/ATP unambiguously identify a specific adenine nucleotide binding site homologous to the ATP-binding site of DNA gyrase B. This site is the same as that identified for the antitumor agent geldanamycin, suggesting that geldanamycin acts by blocking the binding of nucleotides to Hsp90 and not the binding of incompletely folded client polypeptides as previously suggested. These results finally resolve the question of the direct involvement of ATP in Hsp90 function.
Collapse
Affiliation(s)
- C Prodromou
- Department of Biochemistry and Molecular Biology, University College London, United Kingdom
| | | | | | | | | | | |
Collapse
|
42
|
Abstract
DNA gyrase is a remarkable enzyme, catalysing the seemingly complex reaction of DNA supercoiling. As gyrase is essential in prokaryotes, it is a good target for antibacterial agents. These agents have diverse chemical structures and interact with gyrase in a variety of ways.
Collapse
Affiliation(s)
- A Maxwell
- Dept of Biochemistry, University of Leicester, UK.
| |
Collapse
|
43
|
Tingey AP, Maxwell A. Probing the role of the ATP-operated clamp in the strand-passage reaction of DNA gyrase. Nucleic Acids Res 1996; 24:4868-73. [PMID: 9016655 PMCID: PMC146357 DOI: 10.1093/nar/24.24.4868] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The high-resolution structure of the 43 kDa N-terminal fragment of the DNA gyrase B protein shows a large cavity within the protein dimer. The approximate size of this cavity is 20 A, suggesting it could accommodate a DNA helix. Computer-modelling studies of this cavity suggest that it contains a constriction, reducing the width to approximately 13 A, principally caused by the side chain of Arg286. We have used site-directed mutagenesis to alter this residue to Gln. Gyrase bearing this mutation shows virtually no supercoiling activity and near-normal relaxation and DNA cleavage activities. The mutated protein has ATPase activity which cannot be stimulated by DNA. These data support the proposed role of the 43 kDa domain as an ATP-operated clamp which binds DNA during the supercoiling cycle. The lack of DNA-dependent ATPase of the mutant may indicate that binding of DNA within the clamp is a prerequisite for stimulation of the ATPase activity.
Collapse
Affiliation(s)
- A P Tingey
- Department of Biochemistry, University of Leicester, UK
| | | |
Collapse
|
44
|
Farrar MA, Alberol-Ila J, Perlmutter RM. Activation of the Raf-1 kinase cascade by coumermycin-induced dimerization. Nature 1996; 383:178-81. [PMID: 8774884 DOI: 10.1038/383178a0] [Citation(s) in RCA: 253] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The Raf-1 serine/threonine kinase is a key component of the MAP kinase cascade, regulating both proliferation and commitment to cell fate. Raf activation is stimulated following its translocation to the plasma membrane, a process that ordinarily requires interaction with the membrane-localized GTPase, Ras-GTP. To investigate the mechanisms underlying Raf activation, we have developed a coumermycin-induced chemical dimerization method. We find that dimerization is by itself sufficient, in the absence of any membrane components, both to activate a modified Raf protein and to stimulate the MAP kinase cascade appropriately. As Ras-GTP-induced membrane localization increases the effective intracellular Raf concentration, our results indicate that homotypic oligomerization may ordinarily act to promote Raf activation in vivo.
Collapse
Affiliation(s)
- M A Farrar
- Howard Hughes Medical Institute, University of Washington, Seattle, 98195, USA
| | | | | |
Collapse
|
45
|
Abstract
DNA gyrase, an enzyme unique to prokaryotes, has been implicated in almost all processes that involve DNA. Although efficient inhibitors of this protein have been known for more than 20 years, none of them have enjoyed prolonged pharmaceutical success. It is only recently that the mechanisms of inhibition for some of these classes of drugs have been established unequivocally by X-ray crystallography. It is hoped that this detailed structural information will assist the design of novel, effective inhibitors of DNA gyrase.
Collapse
Affiliation(s)
- R J Lewis
- Laboratory of Molecular Biophysics, University of Oxford, UK
| | | | | |
Collapse
|
46
|
Stieger M, Angehrn P, Wohlgensinger B, Gmünder H. GyrB mutations in Staphylococcus aureus strains resistant to cyclothialidine, coumermycin, and novobiocin. Antimicrob Agents Chemother 1996; 40:1060-2. [PMID: 8849232 PMCID: PMC163264 DOI: 10.1128/aac.40.4.1060] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The sequence of the gyrase B subunit gene from Staphylococcus aureus strains resistant to the gyrase B subunit inhibitors cyclothialidine, coumermycin, and novobiocin has been determined. The residues altered in the resistant gyrase B subunits map to the ATP-binding region, suggesting that the drugs inhibit ATP binding and hydrolysis. The pattern of cross-resistances indicates that the detailed binding mode of the compounds differs.
Collapse
Affiliation(s)
- M Stieger
- F. Hoffmann-La Roche, Basel, Switzerland
| | | | | | | |
Collapse
|
47
|
Oram M, Dosanjh B, Gormley NA, Smith CV, Fisher LM, Maxwell A, Duncan K. Mode of action of GR122222X, a novel inhibitor of bacterial DNA gyrase. Antimicrob Agents Chemother 1996; 40:473-6. [PMID: 8834902 PMCID: PMC163138 DOI: 10.1128/aac.40.2.473] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
GR122222X is a potent inhibitor of the supercoiling reaction of bacterial DNA gyrase. We show that this compound binds stoichiometrically to inactivate the ATPase activity of a 43-kDa N-terminal fragment of the B subunit and competitively inhibits the binding of a radiolabelled coumarin drug to N-terminal fragments of GyrB. These and other data suggest that GR122222X has a mode of action similar, but not identical, to that of coumarin antibiotics.
Collapse
Affiliation(s)
- M Oram
- Department of Cellular and Molecular Sciences, University of London, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
48
|
Sekiguchi J, Stivers JT, Mildvan AS, Shuman S. Mechanism of inhibition of vaccinia DNA topoisomerase by novobiocin and coumermycin. J Biol Chem 1996; 271:2313-22. [PMID: 8567695 DOI: 10.1074/jbc.271.4.2313] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Vaccinia DNA topoisomerase, a eukaryotic type I enzyme, has unique pharmacological properties, including sensitivity to the coumarin drugs novobiocin and coumermycin, which are classical inhibitors of DNA gyrase, a type II enzyme. Whereas coumarins inhibit gyrase by binding the GyrB subunit and thereby blocking the ATP-binding site, they inhibit vaccinia topoisomerase by binding to the protein and blocking the interaction of enzyme with DNA. Noncovalent DNA binding and single-turnover DNA cleavage by topoisomerase are inhibited with K1 values of 10-25 microM for coumermycin and 350 microM for novobiocin. Spectroscopic and fluorescence measurements of drug binding t enzyme indicate a single binding site on vaccinia topoisomerase for coumermycin (KD = 27 +/- 5 microM) and two classes of binding sites for novobiocin, one tight site (KD1 = 20 +/- 5 microM) and several weak sites (KD2 = 513 +/- 125 microM; n = 4.9 +/- 0.7). Addition of a stoichiometric amount of DNA to a performed coumermycin-topoisomerase complex quantitatively displaces the drug, indicating that coumermycin binding and DNA binding to topoisomerase are mutually exclusive. A simple interpretation is that the site of drug binding coincides or overlaps with the DNA-binding site on the topoisomerase. Both novobiocin and coumermycin alter the susceptibility of vaccinia topoisomerase to proteolysis with either chymotrypsin or trypsin; similar effects occur when topoisomerase binds to duplex DNA.
Collapse
Affiliation(s)
- J Sekiguchi
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA
| | | | | | | |
Collapse
|
49
|
Ali JA, Orphanides G, Maxwell A. Nucleotide binding to the 43-kilodalton N-terminal fragment of the DNA gyrase B protein. Biochemistry 1995; 34:9801-8. [PMID: 7626649 DOI: 10.1021/bi00030a018] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The binding of ADPNP (5'-adenylyl beta,gamma-imidodiphosphate) to the 43-kDa N-terminal fragment of the DNA gyrase B protein is found to stabilize a dimer of the protein. Analysis of the kinetics of binding of ADPNP to the fragment suggests that protein dimers can contain 1 or 2 molecules of bound nucleotide. ATP, ADP, or coumarin drugs inhibit the binding of ADPNP. The rate of dissociation of ADPNP from the 43-kDa protein is found to be very slow and unaffected by the presence of other nucleotides. These data can be accommodated by a scheme in which the 43-kDa monomer forms a short-lived complex with ADPNP that can be converted into long-lived dimer complexes containing either 1 or 2 molecules of bound ADPNP; dimer formation with 2 bound ADPNPs is strongly favored. Coumarin drugs inhibit the binding of ADPNP to the 43-kDa fragment, with novobiocin binding to the protein with a stoichiometry of 1:1 and coumermycin binding with a stoichiometry of 0.5:1.
Collapse
Affiliation(s)
- J A Ali
- Department of Biochemistry, University of Leicester, U.K
| | | | | |
Collapse
|
50
|
Muñoz R, Bustamante M, de la Campa AG. Ser-127-to-Leu substitution in the DNA gyrase B subunit of Streptococcus pneumoniae is implicated in novobiocin resistance. J Bacteriol 1995; 177:4166-70. [PMID: 7608096 PMCID: PMC177155 DOI: 10.1128/jb.177.14.4166-4170.1995] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We report the cloning of the gyrB gene from Streptococcus pneumoniae 533 that carries the nov-1 allele. The gyrB gene codes for a protein homologous to the gyrase B subunit of archaebacteria and eubacteria. The same amino acid substitution (Ser-127 to Leu) confers novobiocin resistance on four isolates of S. pneumoniae. This amino acid position is equivalent to Val-120 of Escherichia coli GyrB, a residue that lies inside the ATP-binding domain as revealed by the crystal structure of the protein.
Collapse
Affiliation(s)
- R Muñoz
- Unidad de Genética Bacteriana, Instituto de Salud Carlos III, Majadahonda, Spain
| | | | | |
Collapse
|