1
|
Morgan IL, McKie SJ, Kim R, Seol Y, Xu J, Harami GM, Maxwell A, Neuman KC. Highly sensitive mapping of in vitro type II topoisomerase DNA cleavage sites with SHAN-seq. Nucleic Acids Res 2024:gkae638. [PMID: 39106172 DOI: 10.1093/nar/gkae638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 08/09/2024] Open
Abstract
Type II topoisomerases (topos) are a ubiquitous and essential class of enzymes that form transient enzyme-bound double-stranded breaks on DNA called cleavage complexes. The location and frequency of these cleavage complexes on DNA is important for cellular function, genomic stability and a number of clinically important anticancer and antibacterial drugs, e.g. quinolones. We developed a simple high-accuracy end-sequencing (SHAN-seq) method to sensitively map type II topo cleavage complexes on DNA in vitro. Using SHAN-seq, we detected Escherichia coli gyrase and topoisomerase IV cleavage complexes at hundreds of sites on supercoiled pBR322 DNA, approximately one site every ten bp, with frequencies that varied by two-to-three orders of magnitude. These sites included previously identified sites and 20-50-fold more new sites. We show that the location and frequency of cleavage complexes at these sites are enzyme-specific and vary substantially in the presence of the quinolone, ciprofloxacin, but not with DNA supercoil chirality, i.e. negative versus positive supercoiling. SHAN-seq's exquisite sensitivity provides an unprecedented single-nucleotide resolution view of the distribution of gyrase and topoisomerase IV cleavage complexes on DNA. Moreover, the discovery that these enzymes can cleave DNA at orders of magnitude more sites than the relatively few previously known sites resolves the apparent paradox of how these enzymes resolve topological problems throughout the genome.
Collapse
Affiliation(s)
- Ian L Morgan
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shannon J McKie
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
| | - Rachel Kim
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yeonee Seol
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jing Xu
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Physics, University of California, Merced, CA 95343, USA
| | - Gabor M Harami
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK
| | - Keir C Neuman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
2
|
Morgan IL, McKie SJ, Kim R, Seol Y, Xu J, Harami G, Maxwell A, Neuman KC. Highly sensitive mapping of in vitro type II topoisomerase DNA cleavage sites with SHAN-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594727. [PMID: 38798569 PMCID: PMC11118536 DOI: 10.1101/2024.05.17.594727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Type II topoisomerases (topos) are a ubiquitous and essential class of enzymes that form transient enzyme-bound double-stranded breaks on DNA called cleavage complexes. The location and frequency of these cleavage complexes on DNA is important for cellular function, genomic stability, and a number of clinically important anticancer and antibacterial drugs, e.g., quinolones. We developed a simple high-accuracy end-sequencing (SHAN-seq) method to sensitively map type II topo cleavage complexes on DNA in vitro. Using SHAN-seq, we detected Escherichia coli gyrase and topoisomerase IV cleavage complexes at hundreds of sites on supercoiled pBR322 DNA, approximately one site every ten bp, with frequencies that varied by two-to-three orders of magnitude. These sites included previously identified sites and 20-50 fold more new sites. We show that the location and frequency of cleavage complexes at these sites are enzyme-specific and vary substantially in the presence of the quinolone, ciprofloxacin, but not with DNA supercoil chirality, i.e., negative vs. positive supercoiling. SHAN-seq's exquisite sensitivity provides an unprecedented single-nucleotide resolution view of the distribution of gyrase and topoisomerase IV cleavage complexes on DNA. Moreover, the discovery that these enzymes can cleave DNA at orders of magnitude more sites than the relatively few previously known sites resolves the apparent paradox of how these enzymes resolve topological problems throughout the genome.
Collapse
Affiliation(s)
- Ian L Morgan
- biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shannon J McKie
- biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
- department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
| | - Rachel Kim
- biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yeonee Seol
- biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jing Xu
- biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Physics, University of California, Merced, CA 95343
| | - Gabor Harami
- biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony Maxwell
- department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
- department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK
| | - Keir C Neuman
- biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
3
|
Kumar Gandham S, Jha A, Kudale AA. Design and Synthesis of 2-Phenylindolizine Acetamides: Molecular Docking, in Vitro Antimicrobial and Anticancer Activity Evaluation. Chem Biodivers 2024; 21:e202400075. [PMID: 38466656 DOI: 10.1002/cbdv.202400075] [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: 01/10/2024] [Revised: 03/09/2024] [Accepted: 03/10/2024] [Indexed: 03/13/2024]
Abstract
In the present work, we synthesized a small library of 2-phenylindolizine acetamide derivatives 7a-i and studied their biological activity. The synthesis was accomplished starting with easily available starting material phenacyl bromide 1 proceeding through the key intermediate 6-methyl-7-nitro-2-phenylindolizine 4. All the compounds 7a-i were characterized using spectroscopy viz., 1H-NMR, 13C NMR, FTIR, and mass spectrometry. Interestingly, 2-phenylindolizine scaffolds 7c, 7f and 7g revealed a remarkable antibacterial activity against relevant organisms S. aureus, E. coli, S. pneumoniae, P. aeruginosa. The target compounds 7e and 7h showed excellent anticancer activity against Colo-205 and MDA-MB-231 cell lines with IC50 values of 68.62, 62.91, 54.23 and 46.34 μM respectively. Additionally, all the 2-phenylindolizine acetamide derivatives 7a-i were subjected to molecular docking prediction by Autodock 4.2. Compounds 7a, 7f and 7c exhibited very good hydrogen bonding amino acid interactions Asp83 (2.23 Å), Asp83 (2.08 Å), His74 (2.05 Å), His76 (1.71 Å), Ser80 (1.05 Å) with active site of Topoisomerase-IV from S. pneumoniae (4KPE). Further, the compounds 7a-i have revealed acceptable ranges for drug-likeliness properties upon evaluation using SwissADME for ADMET and physiochemical properties.
Collapse
Affiliation(s)
- Siva Kumar Gandham
- Department of Chemistry, GITAM School of Science, GITAM (Deemed to be University), Gandhi Nagar, Rushikonda, Visakhapatnam, Andhra Pradesh-530045, India
| | - Anjali Jha
- Department of Chemistry, GITAM School of Science, GITAM (Deemed to be University), Gandhi Nagar, Rushikonda, Visakhapatnam, Andhra Pradesh-530045, India
| | - Amit A Kudale
- Research and Development, ASolution Pharmaceuticals Pvt Ltd, Ambernath, Dist. Thane, Maharashtra, 421506, India
| |
Collapse
|
4
|
Sutormin D, Galivondzhyan A, Gafurov A, Severinov K. Single-nucleotide resolution detection of Topo IV cleavage activity in the Escherichia coli genome with Topo-Seq. Front Microbiol 2023; 14:1160736. [PMID: 37089538 PMCID: PMC10117906 DOI: 10.3389/fmicb.2023.1160736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/16/2023] [Indexed: 04/08/2023] Open
Abstract
Topoisomerase IV (Topo IV) is the main decatenation enzyme in Escherichia coli; it removes catenation links that are formed during DNA replication. Topo IV binding and cleavage sites were previously identified in the E. coli genome with ChIP-Seq and NorfIP. Here, we used a more sensitive, single-nucleotide resolution Topo-Seq procedure to identify Topo IV cleavage sites (TCSs) genome-wide. We detected thousands of TCSs scattered in the bacterial genome. The determined cleavage motif of Topo IV contained previously known cleavage determinants (−4G/+8C, −2A/+6 T, −1 T/+5A) and additional, not observed previously, positions −7C/+11G and −6C/+10G. TCSs were depleted in the Ter macrodomain except for two exceptionally strong non-canonical cleavage sites located in 33 and 38 bp from the XerC-box of the dif-site. Topo IV cleavage activity was increased in Left and Right macrodomains flanking the Ter macrodomain and was especially high in the 50–60 kb region containing the oriC origin of replication. Topo IV enrichment was also increased downstream of highly active transcription units, indicating that the enzyme is involved in relaxation of transcription-induced positive supercoiling.
Collapse
Affiliation(s)
- Dmitry Sutormin
- Skolkovo Institute of Science and Technology, Moscow, Russia
- *Correspondence: Dmitry Sutormin,
| | | | - Azamat Gafurov
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
- Konstantin Severinov,
| |
Collapse
|
5
|
A 2.8 Å Structure of Zoliflodacin in a DNA Cleavage Complex with Staphylococcus aureus DNA Gyrase. Int J Mol Sci 2023; 24:ijms24021634. [PMID: 36675148 PMCID: PMC9865888 DOI: 10.3390/ijms24021634] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/17/2023] Open
Abstract
Since 2000, some thirteen quinolones and fluoroquinolones have been developed and have come to market. The quinolones, one of the most successful classes of antibacterial drugs, stabilize DNA cleavage complexes with DNA gyrase and topoisomerase IV (topo IV), the two bacterial type IIA topoisomerases. The dual targeting of gyrase and topo IV helps decrease the likelihood of resistance developing. Here, we report on a 2.8 Å X-ray crystal structure, which shows that zoliflodacin, a spiropyrimidinetrione antibiotic, binds in the same DNA cleavage site(s) as quinolones, sterically blocking DNA religation. The structure shows that zoliflodacin interacts with highly conserved residues on GyrB (and does not use the quinolone water-metal ion bridge to GyrA), suggesting it may be more difficult for bacteria to develop target mediated resistance. We show that zoliflodacin has an MIC of 4 µg/mL against Acinetobacter baumannii (A. baumannii), an improvement of four-fold over its progenitor QPT-1. The current phase III clinical trial of zoliflodacin for gonorrhea is due to be read out in 2023. Zoliflodacin, together with the unrelated novel bacterial topoisomerase inhibitor gepotidacin, is likely to become the first entirely novel chemical entities approved against Gram-negative bacteria in the 21st century. Zoliflodacin may also become the progenitor of a new safer class of antibacterial drugs against other problematic Gram-negative bacteria.
Collapse
|
6
|
Allaka TR, Kummari B, Polkam N, Kuntala N, Chepuri K, Anireddy JS. Novel heterocyclic 1,3,4-oxadiazole derivatives of fluoroquinolones as a potent antibacterial agent: Synthesis and computational molecular modeling. Mol Divers 2021; 26:1581-1596. [PMID: 34341943 DOI: 10.1007/s11030-021-10287-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/22/2021] [Indexed: 11/27/2022]
Abstract
Design and synthesis of novel series of 1,3,4-oxadiazoles containing FQs derivatives and screened their antibacterial, antimycobacterial properties. The synthesized compounds were characterized by different spectral techniques like IR, 1H NMR, 13C NMR, mass and elemental analysis. The results of the antimicrobial activity and compounds 6d, 6b, 6e, 6f and 6a demonstrated potent antibacterial activities with zone of inhibition of 42, 36, 37, 34 and 30 mm against S. aureus, E. faecalis, S. pneumoniae, E. coli and K. pneumoniae, respectively. 1,3,4-Oxadiazole derivatives 6a, 6b, 6 g were showed excellent antimycobacterial activity against M. smegmatis H37Rv with MICs 22.35, 16.20, 20.28 µg/mL, respectively. FQs 6d and 6b exhibited highest hydrogen bonding interactions with Asp83 (3.11 A˚), Ser80 (2.15 A˚) Asp27 (σ-σ), Arg87 (Π-Π), Arg87 (Π-Π), Ser80 (σ-σ), Ala84 (σ-σ) and binding energies ΔG = - 6.41, - 6.97 kcal/mol with active site of topoisomerase-IV from S. pneumoniae [4KPE]. We performed a computational investigation of compounds 6a-j for their absorption, distribution, metabolism and excretion (ADME) properties by using the Molinspiration, Molsoft toolkits. The ligands 6f, 6d and 6b reveal the highest pharmacokinetic properties and possess maximum drug-likeness model score 1.59, 1.46 and 1.23, respectively.
Collapse
Affiliation(s)
- Tejeswara Rao Allaka
- Centre for Chemical Sciences and Technology, Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad, Kukatpally, Hyderabad, Telangana, 500085, India.
| | - Bhaskar Kummari
- Centre for Chemical Sciences and Technology, Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad, Kukatpally, Hyderabad, Telangana, 500085, India
| | - Naveen Polkam
- Centre for Chemical Sciences and Technology, Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad, Kukatpally, Hyderabad, Telangana, 500085, India
| | - Naveen Kuntala
- Centre for Chemical Sciences and Technology, Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad, Kukatpally, Hyderabad, Telangana, 500085, India
| | - Kalyani Chepuri
- Centre for Biotechnology, Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad, Kukatpally, Hyderabad, Telangana, 500085, India
| | - Jaya Shree Anireddy
- Centre for Chemical Sciences and Technology, Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad, Kukatpally, Hyderabad, Telangana, 500085, India
| |
Collapse
|
7
|
In vitro antimicrobial evaluation and in silico studies of coumarin derivatives tagged with pyrano-pyridine and pyrano-pyrimidine moieties as DNA gyrase inhibitors. Mol Divers 2021; 26:341-363. [PMID: 33895960 DOI: 10.1007/s11030-021-10224-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/08/2021] [Indexed: 01/09/2023]
Abstract
Several coumarin-containing substitute nitrogen heterocycles have recently received considerable importance due to their diverse pharmacological properties. One-pot and rapid synthesis of coumarin derivatives was achieved via reactions of acetyl-coumarin with p-chloro-benzaldehyde and malononitrile to provide compound 2-containing cyano-amine using conventional heating. Compound 2 was condensed with different carbon electrophiles triethyl orthoformate, phenyl isocyanate, carbon disulfide, benzoyl chloride, and acetyl chloride that afforded the corresponding chromene derivatives 3-17. All the newly synthesized compounds were characterized by elemental and spectroscopic evidences. All of the synthesized compounds were tested for antimicrobial activity against S. Pneumoniae, S. Epidermidis, S. Aureus, and E. coli as Gram + ve Bacteria, K. Pneumoniae, S. Paratyphi as Gram -ve Bacteria, P. Italicum, A. Fumigatus representative for Fungi. The preliminary screening results showed that most of the compounds had moderate to high activity against all tested organisms. The most potent four compounds were subjected to further investigation against E. Coli DNA gyrase and topoisomerase IV inhibitory activity, and the results showed that all of these derivatives inhibit DNA gyrase and thus cell division. Also, in silico studies were done for the most active compounds which showed good results.
Collapse
|
8
|
Metwally NH, Abdallah SO, Mohsen MMA. Design, green one-pot synthesis and molecular docking study of novel N,N-bis(cyanoacetyl)hydrazines and bis-coumarins as effective inhibitors of DNA gyrase and topoisomerase IV. Bioorg Chem 2020; 97:103672. [PMID: 32145481 DOI: 10.1016/j.bioorg.2020.103672] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/24/2020] [Accepted: 02/14/2020] [Indexed: 12/15/2022]
Abstract
A novel, quick, environmentally safe, and one-pot synthesis of a series of N,N-bis(cyanoacetyl)hydrazine derivatives, bis-imino-2H-chromenes and bis-2-oxo-2H-chromene derivatives have been designed. Some selected newly synthesized compounds were investigated in vitro for their antibacterial activity. Compound 5j is the most toxic compound against Staphylococcus aureus with activity index 171%, followed by compound 15b with activity index 136% compared to standard drug ampicillin. Moreover, compound 15a is the most toxic compound against Escherichia coli with activity index 111% compared to standard drug gentamicin. Minimum inhibitory concentration (MIC) was carried out for compounds with high antibacterial activity. Compound 5j has good MIC (7.8 μg/ml) against Staphylococcus aureus while 15a has good MIC (31.25 μg/ml) against Streptococcus mutans which is better than MIC of the standard drug ampicillin (MIC = 62.5 μg/ml). Compounds 5j, 5k, 15a, 15b and 15e which have good MIC values were introduced to enzyme assay against DNA gyrase and topoisomerase IV. The results showed that compound 15a can strongly inhibit DNA gyrase and topoisomerase IV (IC50 = 27.30 and 25.52 μM respectively), compared to methotrexate as the standard drug (IC50 = 29.01 and 23.55 μM respectively). Structure-activity relationships were also discussed based on the biological and docking simulation results.
Collapse
|
9
|
Sutormin D, Rubanova N, Logacheva M, Ghilarov D, Severinov K. Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome. Nucleic Acids Res 2019; 47:1373-1388. [PMID: 30517674 PMCID: PMC6379681 DOI: 10.1093/nar/gky1222] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/19/2018] [Accepted: 11/23/2018] [Indexed: 12/31/2022] Open
Abstract
An important antibiotic target, DNA gyrase is an essential bacterial enzyme that introduces negative supercoils into DNA and relaxes positive supercoils accumulating in front of moving DNA and RNA polymerases. By altering the superhelical density, gyrase may regulate expression of bacterial genes. The information about how gyrase is distributed along genomic DNA and whether its distribution is affected by drugs is scarce. During catalysis, gyrase cleaves both DNA strands forming a covalently bound intermediate. By exploiting the ability of several topoisomerase poisons to stabilize this intermediate we developed a ChIP-Seq-based approach to locate, with single nucleotide resolution, DNA gyrase cleavage sites (GCSs) throughout the Escherichia coli genome. We identified an extended gyrase binding motif with phased 10-bp G/C content variation, indicating that bending ability of DNA contributes to gyrase binding. We also found that GCSs are enriched in extended regions located downstream of highly transcribed operons. Transcription inhibition leads to redistribution of gyrase suggesting that the enrichment is functionally significant. Our method can be applied for precise mapping of prokaryotic and eukaryotic type II topoisomerases cleavage sites in a variety of organisms and paves the way for future studies of various topoisomerase inhibitors.
Collapse
Affiliation(s)
- Dmitry Sutormin
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Natalia Rubanova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Maria Logacheva
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Dmitry Ghilarov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Malopolska Centre of Biotechnology, Jagiellonian University, 30387 Cracow, Poland
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| |
Collapse
|
10
|
Chowdhury SR, Majumder HK. DNA Topoisomerases in Unicellular Pathogens: Structure, Function, and Druggability. Trends Biochem Sci 2019; 44:415-432. [PMID: 30609953 DOI: 10.1016/j.tibs.2018.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/20/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023]
Abstract
All organisms, including unicellular pathogens, compulsorily possess DNA topoisomerases for successful nucleic acid metabolism. But particular subtypes of topoisomerases exist, in all prokaryotes and in some unicellular eukaryotes, that are absent in higher eukaryotes. Moreover, topoisomerases from pathogenic members of a niche possess some unique molecular architecture and functionalities completely distinct from their nonpathogenic colleagues. This review will highlight the unique attributes associated with the structures and functions of topoisomerases from the unicellular pathogens, with special reference to bacteria and protozoan parasites. It will also summarise the progress made in the domain pertaining to the druggability of these topoisomerases, upon which a future platform for therapeutic development can be successfully constructed.
Collapse
Affiliation(s)
- Somenath Roy Chowdhury
- Laboratory of Molecular Parasitology, Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Hemanta K Majumder
- Laboratory of Molecular Parasitology, Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
| |
Collapse
|
11
|
Ubiquitous Nature of Fluoroquinolones: The Oscillation between Antibacterial and Anticancer Activities. Antibiotics (Basel) 2017; 6:antibiotics6040026. [PMID: 29112154 PMCID: PMC5745469 DOI: 10.3390/antibiotics6040026] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 10/26/2017] [Accepted: 11/03/2017] [Indexed: 12/15/2022] Open
Abstract
Fluoroquinolones are synthetic antibacterial agents that stabilize the ternary complex of prokaryotic topoisomerase II enzymes (gyrase and Topo IV), leading to extensive DNA fragmentation and bacteria death. Despite the similar structural folds within the critical regions of prokaryotic and eukaryotic topoisomerases, clinically relevant fluoroquinolones display a remarkable selectivity for prokaryotic topoisomerase II, with excellent safety records in humans. Typical agents that target human topoisomerases (such as etoposide, doxorubicin and mitoxantrone) are associated with significant toxicities and secondary malignancies, whereas clinically relevant fluoroquinolones are not known to exhibit such propensities. Although many fluoroquinolones have been shown to display topoisomerase-independent antiproliferative effects against various human cancer cells, those that are significantly active against eukaryotic topoisomerase show the same DNA damaging properties as other topoisomerase poisons. Empirical models also show that fluoroquinolones mediate some unique immunomodulatory activities of suppressing pro-inflammatory cytokines and super-inducing interleukin-2. This article reviews the extended roles of fluoroquinolones and their prospects as lead for the unmet needs of "small and safe" multimodal-targeting drug scaffolds.
Collapse
|
12
|
de la Campa AG, Ferrándiz MJ, Martín-Galiano AJ, García MT, Tirado-Vélez JM. The Transcriptome of Streptococcus pneumoniae Induced by Local and Global Changes in Supercoiling. Front Microbiol 2017; 8:1447. [PMID: 28824578 PMCID: PMC5534458 DOI: 10.3389/fmicb.2017.01447] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/17/2017] [Indexed: 01/28/2023] Open
Abstract
The bacterial chromosome is compacted in a manner optimal for DNA transactions to occur. The degree of compaction results from the level of DNA-supercoiling and the presence of nucleoid-binding proteins. DNA-supercoiling is homeostatically maintained by the opposing activities of relaxing DNA topoisomerases and negative supercoil-inducing DNA gyrase. DNA-supercoiling acts as a general cis regulator of transcription, which can be superimposed upon other types of more specific trans regulatory mechanism. Transcriptomic studies on the human pathogen Streptococcus pneumoniae, which has a relatively small genome (∼2 Mb) and few nucleoid-binding proteins, have been performed under conditions of local and global changes in supercoiling. The response to local changes induced by fluoroquinolone antibiotics, which target DNA gyrase subunit A and/or topoisomerase IV, involves an increase in oxygen radicals which reduces cell viability, while the induction of global supercoiling changes by novobiocin (a DNA gyrase subunit B inhibitor), or by seconeolitsine (a topoisomerase I inhibitor), has revealed the existence of topological domains that specifically respond to such changes. The control of DNA-supercoiling in S. pneumoniae occurs mainly via the regulation of topoisomerase gene transcription: relaxation triggers the up-regulation of gyrase and the down-regulation of topoisomerases I and IV, while hypernegative supercoiling down-regulates the expression of topoisomerase I. Relaxation affects 13% of the genome, with the majority of the genes affected located in 15 domains. Hypernegative supercoiling affects 10% of the genome, with one quarter of the genes affected located in 12 domains. However, all the above domains overlap, suggesting that the chromosome is organized into topological domains with fixed locations. Based on its response to relaxation, the pneumococcal chromosome can be said to be organized into five types of domain: up-regulated, down-regulated, position-conserved non-regulated, position-variable non-regulated, and AT-rich. The AT content is higher in the up-regulated than in the down-regulated domains. Genes within the different domains share structural and functional characteristics. It would seem that a topology-driven selection pressure has defined the chromosomal location of the metabolism, virulence and competence genes, which suggests the existence of topological rules that aim to improve bacterial fitness.
Collapse
Affiliation(s)
- Adela G de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos IIIMadrid, Spain.,Presidencia, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - María J Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos IIIMadrid, Spain
| | - Antonio J Martín-Galiano
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos IIIMadrid, Spain
| | - María T García
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad ComplutenseMadrid, Spain
| | - Jose M Tirado-Vélez
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos IIIMadrid, Spain
| |
Collapse
|
13
|
A spontaneous mutation in kdsD, a biosynthesis gene for 3 Deoxy-D-manno-Octulosonic Acid, occurred in a ciprofloxacin resistant strain of Francisella tularensis and caused a high level of attenuation in murine models of tularemia. PLoS One 2017; 12:e0174106. [PMID: 28328947 PMCID: PMC5362203 DOI: 10.1371/journal.pone.0174106] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/03/2017] [Indexed: 12/26/2022] Open
Abstract
Francisella tularensis, a gram-negative facultative intracellular bacterial pathogen, is the causative agent of tularemia and able to infect many mammalian species, including humans. Because of its ability to cause a lethal infection, low infectious dose, and aerosolizable nature, F. tularensis subspecies tularensis is considered a potential biowarfare agent. Due to its in vitro efficacy, ciprofloxacin is one of the antibiotics recommended for post-exposure prophylaxis of tularemia. In order to identify therapeutics that will be efficacious against infections caused by drug resistant select-agents and to better understand the threat, we sought to characterize an existing ciprofloxacin resistant (CipR) mutant in the Schu S4 strain of F. tularensis by determining its phenotypic characteristics and sequencing the chromosome to identify additional genetic alterations that may have occurred during the selection process. In addition to the previously described genetic alterations, the sequence of the CipR mutant strain revealed several additional mutations. Of particular interest was a frameshift mutation within kdsD which encodes for an enzyme necessary for the production of 3-Deoxy-D-manno-Octulosonic Acid (KDO), an integral component of the lipopolysaccharide (LPS). A kdsD mutant was constructed in the Schu S4 strain. Although it was not resistant to ciprofloxacin, the kdsD mutant shared many phenotypic characteristics with the CipR mutant, including growth defects under different conditions, sensitivity to hydrophobic agents, altered LPS profiles, and attenuation in multiple models of murine tularemia. This study demonstrates that the KdsD enzyme is essential for Francisella virulence and may be an attractive therapeutic target for developing novel medical countermeasures.
Collapse
|
14
|
Murugavel S, Stephen CJP, Subashini R, Reddy HR, AnanthaKrishnan D. Synthesis, crystal structure investigation, spectroscopic characterizations and DFT computations on a novel 1-(2-chloro-4-phenylquinolin-3-yl)ethanone. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.05.095] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
15
|
Laponogov I, Pan XS, Veselkov DA, Cirz RT, Wagman A, Moser HE, Fisher LM, Sanderson MR. Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones. Open Biol 2016; 6:rsob.160157. [PMID: 27655731 PMCID: PMC5043579 DOI: 10.1098/rsob.160157] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/26/2016] [Indexed: 12/16/2022] Open
Abstract
As part of a programme of synthesizing and investigating the biological properties of new fluoroquinolone antibacterials and their targeting of topoisomerase IV from Streptococcus pneumoniae, we have solved the X-ray structure of the complexes of two new 7,8-bridged fluoroquinolones (with restricted C7 group rotation favouring tight binding) in complex with the topoisomerase IV from S. pneumoniae and an 18-base-pair DNA binding site—the E-site—found by our DNA mapping studies to bind drug strongly in the presence of topoisomerase IV (Leo et al. 2005 J. Biol. Chem.280, 14 252–14 263, doi:10.1074/jbc.M500156200). Although the degree of antibiotic resistance towards fluoroquinolones is much lower than that of β-lactams and a range of ribosome-bound antibiotics, there is a pressing need to increase the diversity of members of this successful clinically used class of drugs. The quinolone moiety of the new 7,8-bridged agents ACHN-245 and ACHN-454 binds similarly to that of clinafloxocin, levofloxacin, moxifloxacin and trovofloxacin but the cyclic scaffold offers the possibility of chemical modification to produce interactions with other topoisomerase residues at the active site.
Collapse
Affiliation(s)
- Ivan Laponogov
- Randall Division of Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, UK Molecular and Clinical Sciences Research Institute, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Xiao-Su Pan
- Molecular and Clinical Sciences Research Institute, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Dennis A Veselkov
- Randall Division of Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, UK
| | - Ryan T Cirz
- Achaogen, 7000 Shoreline Ct. No. 371, San Francisco, CA 94080, USA
| | - Allan Wagman
- Achaogen, 7000 Shoreline Ct. No. 371, San Francisco, CA 94080, USA
| | - Heinz E Moser
- Achaogen, 7000 Shoreline Ct. No. 371, San Francisco, CA 94080, USA
| | - L Mark Fisher
- Molecular and Clinical Sciences Research Institute, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Mark R Sanderson
- Randall Division of Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, UK
| |
Collapse
|
16
|
Cui SF, Addla D, Zhou CH. Novel 3-Aminothiazolquinolones: Design, Synthesis, Bioactive Evaluation, SARs, and Preliminary Antibacterial Mechanism. J Med Chem 2016; 59:4488-510. [DOI: 10.1021/acs.jmedchem.5b01678] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Sheng-Feng Cui
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
- Department of Public Security Technology, Railway Police College, Zhengzhou 450053, China
| | - Dinesh Addla
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| |
Collapse
|
17
|
Veselkov DA, Laponogov I, Pan XS, Selvarajah J, Skamrova GB, Branstrom A, Narasimhan J, Prasad JVNV, Fisher LM, Sanderson MR. Structure of a quinolone-stabilized cleavage complex of topoisomerase IV from Klebsiella pneumoniae and comparison with a related Streptococcus pneumoniae complex. Acta Crystallogr D Struct Biol 2016; 72:488-96. [PMID: 27050128 PMCID: PMC4822561 DOI: 10.1107/s2059798316001212] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/19/2016] [Indexed: 11/24/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative bacterium that is responsible for a range of common infections, including pulmonary pneumonia, bloodstream infections and meningitis. Certain strains of Klebsiella have become highly resistant to antibiotics. Despite the vast amount of research carried out on this class of bacteria, the molecular structure of its topoisomerase IV, a type II topoisomerase essential for catalysing chromosomal segregation, had remained unknown. In this paper, the structure of its DNA-cleavage complex is reported at 3.35 Å resolution. The complex is comprised of ParC breakage-reunion and ParE TOPRIM domains of K. pneumoniae topoisomerase IV with DNA stabilized by levofloxacin, a broad-spectrum fluoroquinolone antimicrobial agent. This complex is compared with a similar complex from Streptococcus pneumoniae, which has recently been solved.
Collapse
Affiliation(s)
- Dennis A. Veselkov
- Randall Division of Cell and Molecular Biophysics, King’s College London, 3rd Floor, New Hunt’s House, Guy’s Campus, London SE1 1UL, England
| | - Ivan Laponogov
- Randall Division of Cell and Molecular Biophysics, King’s College London, 3rd Floor, New Hunt’s House, Guy’s Campus, London SE1 1UL, England
- Cardiovascular and Cell Sciences Research Institute, St George’s, University of London, Cranmer Terrace, London SW17 0RE, England
| | - Xiao-Su Pan
- Cardiovascular and Cell Sciences Research Institute, St George’s, University of London, Cranmer Terrace, London SW17 0RE, England
| | - Jogitha Selvarajah
- Cardiovascular and Cell Sciences Research Institute, St George’s, University of London, Cranmer Terrace, London SW17 0RE, England
| | - Galyna B. Skamrova
- Randall Division of Cell and Molecular Biophysics, King’s College London, 3rd Floor, New Hunt’s House, Guy’s Campus, London SE1 1UL, England
| | - Arthur Branstrom
- PTC Therapeutics Inc., 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Jana Narasimhan
- PTC Therapeutics Inc., 100 Corporate Court, South Plainfield, NJ 07080, USA
| | | | - L. Mark Fisher
- Cardiovascular and Cell Sciences Research Institute, St George’s, University of London, Cranmer Terrace, London SW17 0RE, England
| | - Mark R. Sanderson
- Randall Division of Cell and Molecular Biophysics, King’s College London, 3rd Floor, New Hunt’s House, Guy’s Campus, London SE1 1UL, England
| |
Collapse
|
18
|
Zhang L, Addla D, Ponmani J, Wang A, Xie D, Wang YN, Zhang SL, Geng RX, Cai GX, Li S, Zhou CH. Discovery of membrane active benzimidazole quinolones-based topoisomerase inhibitors as potential DNA-binding antimicrobial agents. Eur J Med Chem 2016; 111:160-82. [PMID: 26871658 DOI: 10.1016/j.ejmech.2016.01.052] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/25/2016] [Accepted: 01/28/2016] [Indexed: 01/10/2023]
Abstract
A series of novel benzimidazole quinolones as potential antimicrobial agents were designed and synthesized. Most of the prepared compounds exhibited good or even stronger antimicrobial activities in comparison with reference drugs. The most potent compound 15m was membrane active and did not trigger the development of resistance in bacteria. It not only inhibited the formation of biofilms but also disrupted the established Staphylococcus aureus and Escherichia coli biofilms. It was able to inhibit the relaxation activity of E. coli topoisomerase IV at 10 μM concentration. Moreover, this compound also showed low toxicity against mammalian cells. Molecular modeling and experimental investigation of compound 15m with DNA suggested that this compound could effectively bind with DNA to form a steady 15m-DNA complex which might further block DNA replication to exert the powerful bioactivities.
Collapse
Affiliation(s)
- Ling Zhang
- Key Laboratory of Applied Chemistry of Chongqing Municipality, Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Dinesh Addla
- Key Laboratory of Applied Chemistry of Chongqing Municipality, Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Jeyakkumar Ponmani
- Key Laboratory of Applied Chemistry of Chongqing Municipality, Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ao Wang
- Key Laboratory of Applied Chemistry of Chongqing Municipality, Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Dan Xie
- Key Laboratory of Applied Chemistry of Chongqing Municipality, Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ya-Nan Wang
- Key Laboratory of Applied Chemistry of Chongqing Municipality, Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Shao-Lin Zhang
- Key Laboratory of Applied Chemistry of Chongqing Municipality, Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Rong-Xia Geng
- Key Laboratory of Applied Chemistry of Chongqing Municipality, Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Gui-Xin Cai
- Key Laboratory of Applied Chemistry of Chongqing Municipality, Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Shuo Li
- School of Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Cheng-He Zhou
- Key Laboratory of Applied Chemistry of Chongqing Municipality, Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China.
| |
Collapse
|
19
|
|
20
|
Reactive Oxygen Species Contribute to the Bactericidal Effects of the Fluoroquinolone Moxifloxacin in Streptococcus pneumoniae. Antimicrob Agents Chemother 2015; 60:409-17. [PMID: 26525786 DOI: 10.1128/aac.02299-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/24/2015] [Indexed: 11/20/2022] Open
Abstract
We studied the transcriptomic response of Streptococcus pneumoniae to the fluoroquinolone moxifloxacin at a concentration that inhibits DNA gyrase. Treatment of the wild-type strain R6, at a concentration of 10× the MIC, triggered a response involving 132 genes after 30 min of treatment. Genes from several metabolic pathways involved in the production of pyruvate were upregulated. These included 3 glycolytic enzymes, which ultimately convert fructose 6-phosphate to pyruvate, and 2 enzymes that funnel phosphate sugars into the glycolytic pathway. In addition, acetyl coenzyme A (acetyl-CoA) carboxylase was downregulated, likely leading to an increase in acetyl-CoA. When coupled with an upregulation in formate acetyltransferase, an increase in acetyl-CoA would raise the production of pyruvate. Since pyruvate is converted by pyruvate oxidase (SpxB) into hydrogen peroxide (H2O2), an increase in pyruvate would augment intracellular H2O2. Here, we confirm a 21-fold increase in the production of H2O2 and a 55-fold increase in the amount of hydroxyl radical in cultures treated during 4 h with moxifloxacin. This increase in hydroxyl radical through the Fenton reaction would damage DNA, lipids, and proteins. These reactive oxygen species contributed to the lethality of the drug, a conclusion supported by the observed protective effects of an SpxB deletion. These results support the model whereby fluoroquinolones cause redox alterations. The transcriptional response of S. pneumoniae to moxifloxacin is compared with the response to levofloxacin, an inhibitor of topoisomerase IV. Levofloxacin triggers the transcriptional activation of iron transport genes and also enhances the Fenton reaction.
Collapse
|
21
|
Baylay AJ, Ivens A, Piddock LJV. A novel gene amplification causes upregulation of the PatAB ABC transporter and fluoroquinolone resistance in Streptococcus pneumoniae. Antimicrob Agents Chemother 2015; 59:3098-108. [PMID: 25779578 PMCID: PMC4432121 DOI: 10.1128/aac.04858-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/01/2015] [Indexed: 01/14/2023] Open
Abstract
Overexpression of the ABC transporter genes patA and patB confers efflux-mediated fluoroquinolone resistance in Streptococcus pneumoniae and is also linked to pneumococcal stress responses. Although upregulation of patAB has been observed in many laboratory mutants and clinical isolates, the regulatory mechanisms controlling expression of these genes are unknown. In this study, we aimed to identify the cause of high-level constitutive overexpression of patAB in M184, a multidrug-resistant mutant of S. pneumoniae R6. Using a whole-genome transformation and sequencing approach, we identified a novel duplication of a 9.2-kb region of the M184 genome which included the patAB genes. This duplication did not affect growth and was semistable with a low segregation rate. The expression levels of patAB in M184 were much higher than those that could be fully explained by doubling of the gene dosage alone, and inactivation of the first copy of patA had no effect on multidrug resistance. Using a green fluorescent protein reporter system, increased patAB expression was ascribed to transcriptional read-through from a tRNA gene upstream of the second copy of patAB. This is the first report of a large genomic duplication causing antibiotic resistance in S. pneumoniae and also of a genomic duplication causing antibiotic resistance by a promoter switching mechanism.
Collapse
Affiliation(s)
- Alison J Baylay
- Antimicrobials Research Group, School of Immunity and Infection, Institute of Microbiology and Infection, and College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Alasdair Ivens
- Centre for Immunity, Infection and Evolution, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura J V Piddock
- Antimicrobials Research Group, School of Immunity and Infection, Institute of Microbiology and Infection, and College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| |
Collapse
|
22
|
Cui SF, Peng LP, Zhang HZ, Rasheed S, Vijaya Kumar K, Zhou CH. Novel hybrids of metronidazole and quinolones: synthesis, bioactive evaluation, cytotoxicity, preliminary antimicrobial mechanism and effect of metal ions on their transportation by human serum albumin. Eur J Med Chem 2014; 86:318-34. [PMID: 25173851 DOI: 10.1016/j.ejmech.2014.08.063] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 08/22/2014] [Accepted: 08/23/2014] [Indexed: 02/05/2023]
Abstract
A novel series of hybrids of metronidazole and quinolones as antimicrobial agents were designed and synthesized. Most prepared compounds exhibited good or even stronger antimicrobial activities in comparison with reference drugs. Furthermore, these highly active metronidazole-quinolone hybrids showed appropriate ranges of pKa, log P and aqueous solubility to pharmacokinetic behaviors and no obvious toxicity to A549 and human hepatocyte LO2 cells. Their competitive interactions with metal ions to HSA revealed that the participation of Mg(2+) ion in compound 7d-HSA association could result in a concentration increase of free compound 7d. Molecular modeling and experimental investigation of compound 7d with DNA suggested that possible antibacterial mechanism might be in relation with multiple binding sites between bioactive molecules and topo IV-DNA complex.
Collapse
Affiliation(s)
- Sheng-Feng Cui
- Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Li-Ping Peng
- Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Hui-Zhen Zhang
- Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Syed Rasheed
- Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Kannekanti Vijaya Kumar
- Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China.
| |
Collapse
|
23
|
Mayer C, Janin YL. Non-quinolone inhibitors of bacterial type IIA topoisomerases: a feat of bioisosterism. Chem Rev 2013; 114:2313-42. [PMID: 24313284 DOI: 10.1021/cr4003984] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Claudine Mayer
- Unité de Microbiologie Structurale, Département de Biologie Structurale et Chimie, Institut Pasteur , 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | | |
Collapse
|
24
|
Laponogov I, Veselkov DA, Crevel IMT, Pan XS, Fisher LM, Sanderson MR. Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport. Nucleic Acids Res 2013; 41:9911-23. [PMID: 23965305 PMCID: PMC3834822 DOI: 10.1093/nar/gkt749] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Type II topoisomerases regulate DNA supercoiling and chromosome segregation. They act as ATP-operated clamps that capture a DNA duplex and pass it through a transient DNA break in a second DNA segment via the sequential opening and closure of ATPase-, G-DNA- and C-gates. Here, we present the first ‘open clamp’ structures of a 3-gate topoisomerase II-DNA complex, the seminal complex engaged in DNA recognition and capture. A high-resolution structure was solved for a (full-length ParE-ParC55)2 dimer of Streptococcus pneumoniae topoisomerase IV bound to two DNA molecules: a closed DNA gate in a B-A-B form double-helical conformation and a second B-form duplex associated with closed C-gate helices at a novel site neighbouring the catalytically important β-pinwheel DNA-binding domain. The protein N gate is present in an ‘arms-wide-open’ state with the undimerized N-terminal ParE ATPase domains connected to TOPRIM domains via a flexible joint and folded back allowing ready access both for gate and transported DNA segments and cleavage-stabilizing antibacterial drugs. The structure shows the molecular conformations of all three gates at 3.7 Å, the highest resolution achieved for the full complex to date, and illuminates the mechanism of DNA capture and transport by a type II topoisomerase.
Collapse
Affiliation(s)
- Ivan Laponogov
- Randall Division of Cell and Molecular Biophysics, 3rd floor New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK and Division of Biomedical Sciences, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
| | | | | | | | | | | |
Collapse
|
25
|
Arnoldi E, Pan XS, Fisher LM. Functional determinants of gate-DNA selection and cleavage by bacterial type II topoisomerases. Nucleic Acids Res 2013; 41:9411-23. [PMID: 23939623 PMCID: PMC3814380 DOI: 10.1093/nar/gkt696] [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] [Indexed: 11/17/2022] Open
Abstract
Antibacterial fluoroquinolones trap a cleavage complex of gyrase and topoisomerase (topo) IV inducing site-specific DNA breakage within a bent DNA gate engaged in DNA transport. Despite its importance for drug action and in revealing potential sites of topoisomerase catalysis, the mechanism of DNA selectivity is poorly understood. To explore its functional basis, we generated mutant versions of the strongly cleaved E-site and used a novel competitive assay to examine their gemifloxacin-mediated DNA breakage by Streptococcus pneumoniae topo IV and gyrase. Parallel studies of Ca2+-induced cleavage distinguished ‘intrinsic recognition’ of DNA cleavage sites by topo IV from drug-induced preferences. Analysis revealed strong enzyme-determined requirements for −4G, −2A and −1T bases preceding the breakage site (between −1 and +1) and enzyme-unique or degenerate determinants at −3, plus drug-specific preferences at +2/+3 and for +1 purines associated with drug intercalation. Similar cleavage rules were seen additionally at the novel V-site identified here in ColE1-derived plasmids. In concert with DNA binding data, our results provide functional evidence for DNA, enzyme and drug contributions to DNA cleavage at the gate, suggest a mechanism for DNA discrimination involving enzyme-induced DNA bending/helix distortion and cleavage complex stabilization and advance understanding of fluoroquinolones as important cleavage-enhancing therapeutics.
Collapse
Affiliation(s)
- Elisa Arnoldi
- Division of Biomedical Sciences, St.George's, University of London, London SW17 0RE, UK
| | | | | |
Collapse
|
26
|
Zhang H, Guo J, Li D, Ng MTT, Lee JY, Lv B, Ng CW, Lee S, Shao F, Li T. Confirmation of quinolone-induced formation of gyrase–DNA conjugates using AFM. Bioorg Med Chem Lett 2013; 23:4622-6. [DOI: 10.1016/j.bmcl.2013.06.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 05/29/2013] [Accepted: 06/10/2013] [Indexed: 11/28/2022]
|
27
|
New insights into DNA-binding by type IIA topoisomerases. Curr Opin Struct Biol 2013; 23:125-33. [DOI: 10.1016/j.sbi.2012.11.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 11/28/2012] [Accepted: 11/29/2012] [Indexed: 11/18/2022]
|
28
|
Heeb S, Fletcher MP, Chhabra SR, Diggle SP, Williams P, Cámara M. Quinolones: from antibiotics to autoinducers. FEMS Microbiol Rev 2011; 35:247-74. [PMID: 20738404 PMCID: PMC3053476 DOI: 10.1111/j.1574-6976.2010.00247.x] [Citation(s) in RCA: 386] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Since quinine was first isolated, animals, plants and microorganisms producing a wide variety of quinolone compounds have been discovered, several of which possess medicinally interesting properties ranging from antiallergenic and anticancer to antimicrobial activities. Over the years, these have served in the development of many synthetic drugs, including the successful fluoroquinolone antibiotics. Pseudomonas aeruginosa and related bacteria produce a number of 2-alkyl-4(1H)-quinolones, some of which exhibit antimicrobial activity. However, quinolones such as the Pseudomonas quinolone signal and 2-heptyl-4-hydroxyquinoline act as quorum-sensing signal molecules, controlling the expression of many virulence genes as a function of cell population density. Here, we review selectively this extensive family of bicyclic compounds, from natural and synthetic antimicrobials to signalling molecules, with a special emphasis on the biology of P. aeruginosa. In particular, we review their nomenclature and biochemistry, their multiple properties as membrane-interacting compounds, inhibitors of the cytochrome bc1 complex and iron chelators, as well as the regulation of their biosynthesis and their integration into the intricate quorum-sensing regulatory networks governing virulence and secondary metabolite gene expression.
Collapse
Affiliation(s)
- Stephan Heeb
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham, UK
| | | | | | | | | | | |
Collapse
|
29
|
Laponogov I, Pan XS, Veselkov DA, McAuley KE, Fisher LM, Sanderson MR. Structural basis of gate-DNA breakage and resealing by type II topoisomerases. PLoS One 2010; 5:e11338. [PMID: 20596531 PMCID: PMC2893164 DOI: 10.1371/journal.pone.0011338] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 06/07/2010] [Indexed: 11/23/2022] Open
Abstract
Type II DNA topoisomerases are ubiquitous enzymes with essential functions in DNA replication, recombination and transcription. They change DNA topology by forming a transient covalent cleavage complex with a gate-DNA duplex that allows transport of a second duplex though the gate. Despite its biological importance and targeting by anticancer and antibacterial drugs, cleavage complex formation and reversal is not understood for any type II enzyme. To address the mechanism, we have used X-ray crystallography to study sequential states in the formation and reversal of a DNA cleavage complex by topoisomerase IV from Streptococcus pneumoniae, the bacterial type II enzyme involved in chromosome segregation. A high resolution structure of the complex captured by a novel antibacterial dione reveals two drug molecules intercalated at a cleaved B-form DNA gate and anchored by drug-specific protein contacts. Dione release generated drug-free cleaved and resealed DNA complexes in which the DNA gate instead adopts an unusual A/B-form helical conformation with a Mg2+ ion repositioned to coordinate each scissile phosphodiester group and promote reversible cleavage by active-site tyrosines. These structures, the first for putative reaction intermediates of a type II topoisomerase, suggest how a type II enzyme reseals DNA during its normal reaction cycle and illuminate aspects of drug arrest important for the development of new topoisomerase-targeting therapeutics.
Collapse
Affiliation(s)
- Ivan Laponogov
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
- Division of Basic Medical Sciences, St George's University of London, London, United Kingdom
| | - Xiao-Su Pan
- Division of Basic Medical Sciences, St George's University of London, London, United Kingdom
| | - Dennis A. Veselkov
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | | | - L. Mark Fisher
- Division of Basic Medical Sciences, St George's University of London, London, United Kingdom
- * E-mail: (LMF); (MRS)
| | - Mark R. Sanderson
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
- * E-mail: (LMF); (MRS)
| |
Collapse
|
30
|
Loveless BM, Yermakova A, Christensen DR, Kondig JP, Heine HS, Wasieloski LP, Kulesh DA. Identification of ciprofloxacin resistance by SimpleProbe™, High Resolution Melt and Pyrosequencing™ nucleic acid analysis in biothreat agents: Bacillus anthracis, Yersinia pestis and Francisella tularensis. Mol Cell Probes 2010; 24:154-60. [DOI: 10.1016/j.mcp.2010.01.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 01/11/2010] [Accepted: 01/12/2010] [Indexed: 10/19/2022]
|
31
|
Probing the differential interactions of quinazolinedione PD 0305970 and quinolones with gyrase and topoisomerase IV. Antimicrob Agents Chemother 2009; 53:3822-31. [PMID: 19564360 DOI: 10.1128/aac.00113-09] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Quinazoline-2,4-diones, such as PD 0305970, are new DNA gyrase and topoisomerase IV (topo IV) inhibitors with potent activity against gram-positive pathogens, including quinolone-resistant isolates. The mechanistic basis of dione activity vis-à-vis quinolones is not understood. We present evidence for Streptococcus pneumoniae gyrase and topo IV that PD 0305970 and quinolones interact differently with the enzyme breakage-reunion and Toprim domains, DNA, and Mg2+-four components that are juxtaposed in the topoisomerase cleavage complex to effect DNA scission. First, PD 0305970 targets primarily gyrase in Streptococcus pneumoniae. However, unlike quinolones, which select predominantly for gyrA (or topo IV parC) mutations in the breakage-reunion domain, unusually the dione selected for novel mutants with alterations that map to a region of the Toprim domain of GyrB (R456H and E474A or E474D) or ParE (D435H and E475A). This "dione resistance-determining region" overlaps the GyrB quinolone resistance-determining region and the region that binds essential Mg2+ ions, each function involving conserved EGDSA and PLRGK motifs. Second, dione-resistant gyrase and topo IV were inhibited by ciprofloxacin, whereas quinolone-resistant enzymes (GyrA S81F and ParC S79F) remained susceptible to PD 0305970. Third, dione-promoted DNA cleavage by gyrase occurred at a distinct repertoire of sites, implying that structural differences with quinolones are sensed at the DNA level. Fourth, unlike the situation with quinolones, the Mg2+ chelator EDTA did not reverse dione-induced gyrase cleavage nor did the dione promote Mg2+-dependent DNA unwinding. It appears that PD 0305970 interacts uniquely to stabilize the cleavage complex of gyrase/topo IV perhaps via an altered orientation directed by the bidentate 3-amino-2,4-dione moiety.
Collapse
|
32
|
Laponogov I, Sohi MK, Veselkov DA, Pan XS, Sawhney R, Thompson AW, McAuley KE, Fisher LM, Sanderson MR. Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases. Nat Struct Mol Biol 2009; 16:667-9. [PMID: 19448616 DOI: 10.1038/nsmb.1604] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 04/08/2009] [Indexed: 11/09/2022]
Abstract
Type II topoisomerases alter DNA topology by forming a covalent DNA-cleavage complex that allows DNA transport through a double-stranded DNA break. We present the structures of cleavage complexes formed by the Streptococcus pneumoniae ParC breakage-reunion and ParE TOPRIM domains of topoisomerase IV stabilized by moxifloxacin and clinafloxacin, two antipneumococcal fluoroquinolones. These structures reveal two drug molecules intercalated at the highly bent DNA gate and help explain antibacterial quinolone action and resistance.
Collapse
Affiliation(s)
- Ivan Laponogov
- Randall Division of Cell and Molecular Biophysics, King's College London, University of London, London, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
|
34
|
Sohi MK, Veselkov DA, Laponogov I, Pan XS, Fisher LM, Sanderson MR. The difficult case of crystallization and structure solution for the ParC55 breakage-reunion domain of topoisomerase IV from Streptococcus pneumoniae. PLoS One 2008; 3:e3201. [PMID: 18787651 PMCID: PMC2527675 DOI: 10.1371/journal.pone.0003201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Accepted: 07/08/2008] [Indexed: 11/19/2022] Open
Abstract
Background Streptococcus pneumoniae is the major cause of community-acquired pneumonia and is also associated with bronchitis, meningitis, otitis and sinusitis. The emergence and increasing prevalence of resistance to penicillin and other antibiotics has led to interest in other anti-pneumonococcal drugs such as quinolones that target the enzymes DNA gyrase and topoisomerase IV. During crystallization and in the avenues to finding a method to determine phases for the structure of the ParC55 breakage-reunion domain of topoisomerase IV from Streptococcus pneumoniae, obstacles were faced at each stage of the process. These problems included: majority of the crystals being twinned, either non-diffracting or exhibiting a high mosaic spread. The crystals, which were grown under conditions that favoured diffraction, were difficult to flash-freeze without loosing diffraction. The initial structure solution by molecular replacement failed and the approach proved to be unviable due to the complexity of the problem. In the end the successful structure solution required an in-depth data analysis and a very detailed molecular replacement search. Methodology/Principal Findings Crystal anti-twinning agents have been tested and two different methods of flash freezing have been compared. The fragility of the crystals did not allow the usual method of transferring the crystals into the heavy atom solution. Consequently, it was necessary to co-crystallize in the presence of the heavy atom compound. The multiple isomorphous replacement approach was unsuccessful because the 7 cysteine mutants which were engineered could not be successfully derivatized. Ultimately, molecular replacement was used to solve the structure by sorting through a large number of solutions in space group P1 using CNS. Conclusions/Significance The main objective of this paper is to describe the obstacles which were faced and overcome in order to acquire data sets on such difficult crystals and determine phases for successful structure solution.
Collapse
Affiliation(s)
- Maninder K. Sohi
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kingdom
| | - Dennis A. Veselkov
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kingdom
| | - Ivan Laponogov
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kingdom
| | - Xiao-Su Pan
- Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London, United Kingdom
| | - L. Mark Fisher
- Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London, United Kingdom
- * E-mail: (LMF); (MRS)
| | - Mark R. Sanderson
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kingdom
- * E-mail: (LMF); (MRS)
| |
Collapse
|
35
|
Pan XS, Dias M, Palumbo M, Fisher LM. Clerocidin selectively modifies the gyrase-DNA gate to induce irreversible and reversible DNA damage. Nucleic Acids Res 2008; 36:5516-29. [PMID: 18723572 PMCID: PMC2553588 DOI: 10.1093/nar/gkn539] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Clerocidin (CL), a microbial diterpenoid, reacts with DNA via its epoxide group and stimulates DNA cleavage by type II DNA topoisomerases. The molecular basis of CL action is poorly understood. We establish by genetic means that CL targets DNA gyrase in the gram-positive bacterium Streptococcus pneumoniae, and promotes gyrase-dependent single- and double-stranded DNA cleavage in vitro. CL-stimulated DNA breakage exhibited a strong preference for guanine preceding the scission site (-1 position). Mutagenesis of -1 guanines to A, C or T abrogated CL cleavage at a strong pBR322 site. Surprisingly, for double-strand breaks, scission on one strand consistently involved a modified (piperidine-labile) guanine and was not reversed by heat, salt or EDTA, whereas complementary strand scission occurred at a piperidine-stable -1 nt and was reversed by EDTA. CL did not induce cleavage by a mutant gyrase (GyrA G79A) identified here in CL-resistant pneumococci. Indeed, mutations at G79 and at the neighbouring S81 residue in the GyrA breakage-reunion domain discriminated poisoning by CL from that of antibacterial quinolones. The results suggest a novel mechanism of enzyme inhibition in which the -1 nt at the gyrase-DNA gate exhibit different CL reactivities to produce both irreversible and reversible DNA damage.
Collapse
Affiliation(s)
- Xiao Su Pan
- Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
| | | | | | | |
Collapse
|
36
|
Affiliation(s)
- Karl Drlica
- Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, 225 Warren St., Newark, NJ 07103, USA.
| | | | | | | |
Collapse
|
37
|
Richter SN, Giaretta G, Comuzzi V, Leo E, Mitchenall LA, Fisher LM, Maxwell A, Palumbo M. Hot-spot consensus of fluoroquinolone-mediated DNA cleavage by Gram-negative and Gram-positive type II DNA topoisomerases. Nucleic Acids Res 2007; 35:6075-85. [PMID: 17766248 PMCID: PMC2094056 DOI: 10.1093/nar/gkm653] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bacterial DNA gyrase and topoisomerase IV are selective targets of fluoroquinolones. Topoisomerase IV versus gyrase and Gram-positive versus Gram-negative behavior was studied based on the different recognition of DNA sequences by topoisomerase-quinolone complexes. A careful statistical analysis of preferred bases was performed on a large number (>400) of cleavage sites. We found discrete preferred sequences that were similar when using different enzymes (i.e. gyrase and topoisomerase IV) from the same bacterial source, but in part diverse when employing enzymes from different origins (i.e. Escherichia coli and Streptococcus pneumoniae). Subsequent analysis on the wild-type and mutated consensus sequences showed that: (i) Gn/Cn-rich sequences at and around the cleavage site are hot spots for quinolone-mediated strand breaks, especially for E. coli topoisomerases: we elucidated positions required for quinolone and enzyme recognition; (ii) for S. pneumoniae enzymes only, A and T at positions -2 and +6 are discriminating cleavage determinants; (iii) symmetry of the target sequence is a key trait to promote cleavage and (iv) the consensus sequence adopts a heteronomous A/B conformation, which may trigger DNA processing by the enzyme-drug complex.
Collapse
Affiliation(s)
- Sara N. Richter
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Giulia Giaretta
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Valentina Comuzzi
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Elisabetta Leo
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Lesley A. Mitchenall
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - L. Mark Fisher
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Anthony Maxwell
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Manlio Palumbo
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
- *To whom correspondence should be addressed. +39049 827 5699+39049 827 5366
| |
Collapse
|
38
|
Laponogov I, Veselkov DA, Sohi MK, Pan XS, Achari A, Yang C, Ferrara JD, Fisher LM, Sanderson MR. Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target. PLoS One 2007; 2:e301. [PMID: 17375187 PMCID: PMC1810434 DOI: 10.1371/journal.pone.0000301] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Accepted: 02/21/2007] [Indexed: 11/18/2022] Open
Abstract
The 2.7 A crystal structure of the 55-kDa N-terminal breakage-reunion domain of topoisomerase (topo) IV subunit A (ParC) from Streptococcus pneumoniae, the first for the quinolone targets from a gram-positive bacterium, has been solved and reveals a 'closed' dimer similar in fold to Escherichia coli DNA gyrase subunit A (GyrA), but distinct from the 'open' gate structure of Escherichia coli ParC. Unlike GyrA whose DNA binding groove is largely positively charged, the DNA binding site of ParC exhibits a distinct pattern of alternating positively and negatively charged regions coincident with the predicted positions of the grooves and phosphate backbone of DNA. Based on the ParC structure, a new induced-fit model for sequence-specific recognition of the gate (G) segment by ParC has been proposed. These features may account for the unique DNA recognition and quinolone targeting properties of pneumococcal type II topoisomerases compared to their gram-negative counterparts.
Collapse
Affiliation(s)
- Ivan Laponogov
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kindgom
| | - Dennis A. Veselkov
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kindgom
| | - Maninder K. Sohi
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kindgom
| | - Xiao-Su Pan
- Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London, United Kindgom
| | - Aniruddha Achari
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kindgom
| | - Cheng Yang
- Rigaku Americas Corporation, The Woodlands, Texas, United States of America
| | - Joseph D. Ferrara
- Rigaku Americas Corporation, The Woodlands, Texas, United States of America
| | - L. Mark Fisher
- Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London, United Kindgom
| | - Mark R. Sanderson
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kindgom
| |
Collapse
|
39
|
Aubry A, Fisher LM, Jarlier V, Cambau E. First functional characterization of a singly expressed bacterial type II topoisomerase: the enzyme from Mycobacterium tuberculosis. Biochem Biophys Res Commun 2006; 348:158-65. [PMID: 16876125 DOI: 10.1016/j.bbrc.2006.07.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Accepted: 07/07/2006] [Indexed: 10/24/2022]
Abstract
Genome deciphering revealed that Mycobacterium tuberculosis encodes a single type II topoisomerase contrary to common bacteria harboring two type II topoisomerases (DNA gyrase and topoisomerase IV). Functions of the M. tuberculosis type II topoisomerase were explored after cloning and expressing the subunits encoding genes in Escherichia coli. M. tuberculosis type II topoisomerase supercoiled relaxed pBR322 with a specific activity close to that of DNA gyrases of common bacteria whereas it exhibited DNA relaxation and formation of cleavable complexes with activities significantly higher than other DNA gyrases. Intermolecular passage activity evaluated by the decatenation of kinetoplast DNA was 25-fold lower than that of the topoisomerase IV from Streptococcus pneumoniae, but was markedly higher than that of the E. coli gyrase. Overall, the type II topoisomerase of M. tuberculosis exhibits classical polyvalent activities of DNA gyrase for supercoiling but enhanced relaxation, cleavage, and decatenation activities.
Collapse
Affiliation(s)
- Alexandra Aubry
- Laboratoire de Bactériologie, Faculté de Médecine Pitié-Salpêtrière, EA1541, Université Paris 6, France
| | | | | | | |
Collapse
|
40
|
Richter SN, Leo E, Giaretta G, Gatto B, Fisher LM, Palumbo M. Clerocidin interacts with the cleavage complex of Streptococcus pneumoniae topoisomerase IV to induce selective irreversible DNA damage. Nucleic Acids Res 2006; 34:1982-91. [PMID: 16614448 PMCID: PMC1435983 DOI: 10.1093/nar/gkl127] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clerocidin (CL), a diterpenoid natural product, alkylates DNA through its epoxide moiety and exhibits both anticancer and antibacterial activities. We have examined CL action in the presence of topoisomerase IV from Streptococcus pneumoniae. CL promoted irreversible enzyme-mediated DNA cleavage leading to single- and double-stranded DNA breaks at specific sites. Reaction required the diterpenoid function: no cleavage was seen using a naphthalene-substituted analogue. Moreover, drug-induced DNA breakage was not observed using a mutant topoisomerase IV (ParC Y118F) unable to form a cleavage complex with DNA. Sequence analysis of 102 single-stranded DNA breaks and 79 double-stranded breaks revealed an overwhelming preference for G at the -1 position, i.e. immediately 5' of the enzyme DNA scission site. This specificity contrasts with that of topoisomerase IV cleavage with antibacterial quinolones. Indeed, CL stimulated DNA breakage by a quinolone-resistant topoisomerase IV (ParC S79F). Overall, the results indicate that topoisomerase IV facilitates selective irreversible CL attack at guanine and that its cleavage complex differs markedly from that of mammalian topoisomerase II which promotes both irreversible and reversible CL attack at guanine and cytosine, respectively. The unique ability to form exclusively irreversible DNA breaks suggests topoisomerase IV may be a key intracellular target of CL in bacteria.
Collapse
Affiliation(s)
- Sara N. Richter
- Department of Pharmaceutical Sciences, University of Padova35131 Padova, Italy
| | - Elisabetta Leo
- Department of Pharmaceutical Sciences, University of Padova35131 Padova, Italy
- Department of Basic Medical Sciences, St. George's, University of LondonLondon SW17 0RE, UK
| | - Giulia Giaretta
- Department of Pharmaceutical Sciences, University of Padova35131 Padova, Italy
| | - Barbara Gatto
- Department of Pharmaceutical Sciences, University of Padova35131 Padova, Italy
| | - L. Mark Fisher
- Department of Basic Medical Sciences, St. George's, University of LondonLondon SW17 0RE, UK
| | - Manlio Palumbo
- Department of Pharmaceutical Sciences, University of Padova35131 Padova, Italy
- To whom correspondence should be addressed. Tel: +39 049 8275699; Fax: +39 049 8275366;
| |
Collapse
|
41
|
Oram M, Travers AA, Howells AJ, Maxwell A, Pato ML. Dissection of the bacteriophage Mu strong gyrase site (SGS): significance of the SGS right arm in Mu biology and DNA gyrase mechanism. J Bacteriol 2006; 188:619-32. [PMID: 16385052 PMCID: PMC1347280 DOI: 10.1128/jb.188.2.619-632.2006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacteriophage Mu strong gyrase site (SGS), required for efficient phage DNA replication, differs from other gyrase sites in the efficiency of gyrase binding coupled with a highly processive supercoiling activity. Genetic studies have implicated the right arm of the SGS as a key structural feature for promoting rapid Mu replication. Here, we show that deletion of the distal portion of the right arm abolishes efficient binding, cleavage, and supercoiling by DNA gyrase in vitro. DNase I footprinting analysis of the intact SGS revealed an adenylyl imidodiphosphate-dependent change in protection in the right arm, indicating that this arm likely forms the T segment that is passed through the cleaved G segment during the supercoiling reaction. Furthermore, in an SGS derivative with an altered right-arm sequence, the left arm showed these changes, suggesting that the selection of a T segment by gyrase is determined primarily by the sequences of the arms. Analysis of the sequences of the SGS and other gyrase sites suggests that the choice of T segment correlates with which arm possesses the more extensive set of phased anisotropic bending signals, with the Mu right arm possessing an unusually extended set of such signals. The implications of these observations for the structure of the gyrase-DNA complex and for the biological function of the Mu SGS are discussed.
Collapse
Affiliation(s)
- Mark Oram
- University of Colorado Health Sciences Center at Fitzsimons, Microbiology Department, 12800 E. 19th Ave., Aurora, CO 80045, USA
| | | | | | | | | |
Collapse
|