1
|
Guo C, Wang KKA, Nolan EM. Investigation of Siderophore-Platinum(IV) Conjugates Reveals Differing Antibacterial Activity and DNA Damage Depending on the Platinum Cargo. ACS Infect Dis 2024; 10:1250-1266. [PMID: 38436588 DOI: 10.1021/acsinfecdis.3c00686] [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] [Indexed: 03/05/2024]
Abstract
The growing threat of bacterial infections coupled with the dwindling arsenal of effective antibiotics has heightened the urgency for innovative strategies to combat bacterial pathogens, particularly Gram-negative strains, which pose a significant challenge due to their outer membrane permeability barrier. In this study, we repurpose clinically approved anticancer agents as targeted antibacterials. We report two new siderophore-platinum(IV) conjugates, both of which consist of an oxaliplatin-based Pt(IV) prodrug (oxPt(IV)) conjugated to enterobactin (Ent), a triscatecholate siderophore employed by Enterobacteriaceae for iron acquisition. We demonstrate that l/d-Ent-oxPt(IV) (l/d-EOP) are selectively delivered into the Escherichia coli cytoplasm, achieving targeted antibacterial activity, causing filamentous morphology, and leading to enhanced Pt uptake by bacterial cells but reduced Pt uptake by human cells. d-EOP exhibits enhanced potency compared to oxaliplatin and l-EOP, primarily attributed to the intrinsic antibacterial activity of its non-native siderophore moiety. To further elucidate the antibacterial activity of Ent-Pt(IV) conjugates, we probed DNA damage caused by l/d-EOP and the previously reported cisplatin-based conjugates l/d-Ent-Pt(IV) (l/d-EP). A comparative analysis of these four conjugates reveals a correlation between antibacterial activity and the ability to induce DNA damage. This work expands the scope of Pt cargos targeted to the cytoplasm of Gram-negative bacteria via Ent conjugation, provides insight into the cellular consequences of Ent-Pt(IV) conjugates in E. coli, and furthers our understanding of the potential of Pt-based therapeutics for antibacterial applications.
Collapse
Affiliation(s)
- Chuchu Guo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kwo-Kwang A Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Elizabeth M Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
2
|
Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
Collapse
Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| |
Collapse
|
3
|
Mu C, Prosser KE, Harrypersad S, MacNeil GA, Panchmatia R, Thompson JR, Sinha S, Warren JJ, Walsby CJ. Activation by Oxidation: Ferrocene-Functionalized Ru(II)-Arene Complexes with Anticancer, Antibacterial, and Antioxidant Properties. Inorg Chem 2018; 57:15247-15261. [PMID: 30495936 DOI: 10.1021/acs.inorgchem.8b02542] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Organometallic Ru(II)-cymene complexes linked to ferrocene (Fc) via nitrogen heterocycles have been synthesized and studied as cytotoxic agents. These compounds are analogues of Ru(II)-arene piano-stool anticancer complexes such as RAPTA-C. The Ru center was coordinated by pyridine, imidazole, and piperidine with 0-, 1-, or 2-carbon bridges to Fc to give six bimetallic, dinuclear compounds, and the properties of these complexes were compared with their non-Fc-functionalized parent compounds. Crystal structures for five of the compounds, their Ru-cymene parent compounds, and an unusual trinuclear compound were determined. Cyclic voltammetry was used to determine the formal MIII/II potentials of each metal center of the Ru-cymene-Fc complexes, with distinct one-electron waves observed in each case. The Fc-functionalized complexes were found to exhibit good cytotoxicity against HT29 human colon adenocarcinoma cells, whereas the parent compounds were inactive. Similarly, antibacterial activity from the Ru-cymene-Fc compounds was observed against Bacillus subtilis, but not from the unfunctionalized complexes. In both cases, the IC50 values correlated quantitatively with the Fc+/0 reduction potentials. This is consistent with more facile oxidation to give ferrocenium, and subsequent generation of toxic reactive oxygen species, leading to greater cytotoxicity. The antioxidant properties of the complexes were quantified by a 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay. EC50 values indicate that linking of the Ru and Fc centers promotes antioxidant activity.
Collapse
Affiliation(s)
- Changhua Mu
- Department of Chemistry , Simon Fraser University , 8888 University Drive , Burnaby V5A 1S6 , British Columbia , Canada
| | - Kathleen E Prosser
- Department of Chemistry , Simon Fraser University , 8888 University Drive , Burnaby V5A 1S6 , British Columbia , Canada
| | - Shane Harrypersad
- Department of Chemistry , Simon Fraser University , 8888 University Drive , Burnaby V5A 1S6 , British Columbia , Canada
| | - Gregory A MacNeil
- Department of Chemistry , Simon Fraser University , 8888 University Drive , Burnaby V5A 1S6 , British Columbia , Canada
| | - Rikesh Panchmatia
- Department of Chemistry , Simon Fraser University , 8888 University Drive , Burnaby V5A 1S6 , British Columbia , Canada
| | - John R Thompson
- Department of Chemistry , Simon Fraser University , 8888 University Drive , Burnaby V5A 1S6 , British Columbia , Canada
| | - Soumalya Sinha
- Department of Chemistry , Simon Fraser University , 8888 University Drive , Burnaby V5A 1S6 , British Columbia , Canada
| | - Jeffrey J Warren
- Department of Chemistry , Simon Fraser University , 8888 University Drive , Burnaby V5A 1S6 , British Columbia , Canada
| | - Charles J Walsby
- Department of Chemistry , Simon Fraser University , 8888 University Drive , Burnaby V5A 1S6 , British Columbia , Canada
| |
Collapse
|
4
|
de la Cruz M, González I, Parish CA, Onishi R, Tormo JR, Martín J, Peláez F, Zink D, El Aouad N, Reyes F, Genilloud O, Vicente F. Production of Ramoplanin and Ramoplanin Analogs by Actinomycetes. Front Microbiol 2017; 8:343. [PMID: 28321210 PMCID: PMC5337499 DOI: 10.3389/fmicb.2017.00343] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/20/2017] [Indexed: 01/01/2023] Open
Abstract
Ramoplanin is a glycolipodepsipeptide antibiotic obtained from fermentation of Actinoplanes sp. ATCC 33076 that exhibits activity against clinically important multi-drug-resistant, Gram-positive pathogens including vancomycin-resistant Enterococcus (VRE), methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-intermediate resistant Clostridium difficile. It disrupts bacterial cell wall through a unique mechanism of action by sequestering the peptidoglycan intermediate Lipid II and therefore does not show cross-resistance with other antibiotics. However, while demonstrating excellent antimicrobial activity in systemic use in animal models of infection, ramoplanin presents low local tolerability when injected intravenously. As a consequence of this limitation, new derivatives are desirable to overcome this issue. During a natural product screening program developed to discover compounds that disrupt bacterial cell wall synthesis by inhibiting peptidoglycan transglycosylation through binding to the intermediate Lipid II, 49 actinomycete strains were identified by HR-LCMS as producers of ramoplanin-related compounds. The producing strains were isolated from environmental samples collected worldwide comprising both tropical and temperate areas. To assess the diversity of this microbial population, the 49 isolates were initially identified to the genus level on the basis of their micromorphology, and 16S sequencing confirmed the initial identification of the strains. These analyses resulted in the identification of members of genus Streptomyces, as well as representatives of the families Micromonosporaceae, Nocardiaceae, Thermomonosporaceae, and Pseudonocardiaceae, suggesting that the production of ramoplanins is relatively widespread among Actinomycetes. In addition, all of these isolates were tested against a panel of Gram-positive and Gram-negative bacteria, filamentous fungi, and yeast in order to further characterize their antimicrobial properties. This work describes the diversity of actinomycete strains that produced ramoplanin-related compounds, and the analysis of the antimicrobial activity exhibited by these isolates. Our results strongly suggest the presence of new ramoplanin-analogs among these actinomycete producers.
Collapse
Affiliation(s)
- Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Granada, Spain
| | - Ignacio González
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Granada, Spain
| | | | | | - José R Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Granada, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Granada, Spain
| | - Fernando Peláez
- Biotechnology Programme, Spanish National Cancer Research Centre Madrid, Spain
| | - Debbie Zink
- Merck Research Laboratories, Merck Kenilworth, NJ, USA
| | | | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Granada, Spain
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Granada, Spain
| |
Collapse
|
5
|
Osterman IA, Bogdanov AA, Dontsova OA, Sergiev PV. Techniques for Screening Translation Inhibitors. Antibiotics (Basel) 2016; 5:antibiotics5030022. [PMID: 27348012 PMCID: PMC5039519 DOI: 10.3390/antibiotics5030022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 06/08/2016] [Accepted: 06/14/2016] [Indexed: 02/03/2023] Open
Abstract
The machinery of translation is one of the most common targets of antibiotics. The development and screening of new antibiotics usually proceeds by testing antimicrobial activity followed by laborious studies of the mechanism of action. High-throughput methods for new antibiotic screening based on antimicrobial activity have become routine; however, identification of molecular targets is usually a challenge. Therefore, it is highly beneficial to combine primary screening with the identification of the mechanism of action. In this review, we describe a collection of methods for screening translation inhibitors, with a special emphasis on methods which can be performed in a high-throughput manner.
Collapse
Affiliation(s)
- Ilya A Osterman
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Alexey A Bogdanov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Olga A Dontsova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Petr V Sergiev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| |
Collapse
|
6
|
Sergiev P, Osterman I, Golovina A, Laptev I, Pletnev P, Evfratov S, Marusich E, Leonov S, Ivanenkov Y, Bogdanov A, Dontsova O. Application of reporter strains for new antibiotic screening. ACTA ACUST UNITED AC 2016; 62:117-23. [DOI: 10.18097/pbmc20166202117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Screening for new antibiotics remains an important area of biology and medical science. Indispensable for this type of research is early identification of antibiotic mechanism of action. Preferentially, it should be studied quickly and cost-effectively, on the stage of primary screening. In this review we describe an application of reporter strains for rapid classification of antibiotics by its target, without prior purification of an active compound and determination of chemical structure
Collapse
Affiliation(s)
- P.V. Sergiev
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - I.A. Osterman
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - A.Ya. Golovina
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - I.G. Laptev
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - P.I. Pletnev
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - S.A. Evfratov
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - E.I. Marusich
- Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow region, Russia
| | - S.V. Leonov
- Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow region, Russia
| | - Ya.A. Ivanenkov
- Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow region, Russia
| | - A.A. Bogdanov
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - O.A. Dontsova
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
7
|
Silver LL. Natural products as a source of drug leads to overcome drug resistance. Future Microbiol 2015; 10:1711-8. [DOI: 10.2217/fmb.15.67] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Novel antibacterials may be found that can enhance the pipeline of therapeutics capable of overcoming antibiotic resistance by a return to exploration of natural products. Such novel products may be derived from both standard and previously uncultivable sources, and enriched by expression of previously unseen antibiotics predicted by genome mining of productive bacterial genera. Hypersensitive whole cell phenotypic screens can be used to detect novel secondary metabolites from both standard and newly uncovered sources.
Collapse
Affiliation(s)
- Lynn L Silver
- LL Silver Consulting, LLC, 955 South Springfield Avenue, Unit C403, Springfield, NJ 07081, USA
| |
Collapse
|
8
|
Kaushik SN, Scoffield J, Andukuri A, Alexander GC, Walker T, Kim S, Choi SC, Brott BC, Eleazer PD, Lee JY, Wu H, Childers NK, Jun HW, Park JH, Cheon K. Evaluation of ciprofloxacin and metronidazole encapsulated biomimetic nanomatrix gel on Enterococcus faecalis and Treponema denticola. Biomater Res 2015; 19:9. [PMID: 26257918 PMCID: PMC4527351 DOI: 10.1186/s40824-015-0032-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/02/2015] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND A triple antibiotic mixture (ciprofloxacin; CF, metronidazole; MN, and minocycline; MC) has been used for dental root canal medicaments in pulp regeneration therapy. However, tooth discolorations, cervical root fractures, and inadequate pulp-dentin formation have been reported due to the triple antibiotic regimen. Therefore, an antibiotic encapsulated biomimetic nanomatrix gel was developed to minimize the clinical limitations and maximize a natural healing process in root canal infections. In this study, minimal bacterial concentrations (MBC) of the selected antibiotics (CF and MN) were tested in 14 representative endodontic bacterial species. Then MBC of each CF and MN were separately encapsulated within the injectable self-assembled biomimetic nanomatrix gel to evaluate antibacterial level on Enterococcus faecalis and Treponema denticola. RESULTS Antibiotic concentrations lower than 0.2 µg/mL of CF and MN demonstrated antibacterial activity on the 14 endodontic species. Furthermore, 6 different concentrations of CF and MN separately encapsulated with the injectable self-assembled biomimetic nanomatrix gel demonstrated antibacterial activity on Enterococcus faecalis and Treponema denticola at the lowest tested concentration of 0.0625 µg/mL. CONCLUSIONS These results suggest that each CF and MN encapsulated within the injectable self-assembled biomimetic nanomatrix gel demonstrated antibacterial effects, which could be effective for the root canal disinfection while eliminating MC. In the long term, the antibiotic encapsulated injectable self-assembled biomimetic nanomatrix gel can provide a multifunctional antibiotic delivery method with potential root regeneration. Further studies are currently underway to evaluate the effects of combined CF and MN encapsulated within the injectable self-assembled biomimetic nanomatrix gel on clinical samples.
Collapse
Affiliation(s)
- Sagar N Kaushik
- />Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL USA
| | - Jessica Scoffield
- />Department of Pediatric Dentistry, University of Alabama at Birmingham, SDB 304B, 1720 2nd Ave S, Birmingham, AL 35294-0007 USA
| | - Adinarayana Andukuri
- />Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL USA
| | - Grant C Alexander
- />Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL USA
| | - Taneidra Walker
- />Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL USA
| | - Seokgon Kim
- />Department of Pediatric Dentistry, School of Dentistry, Kyung Hee University, Seoul, Korea
| | - Sung Chul Choi
- />Department of Pediatric Dentistry, School of Dentistry, Kyung Hee University, Seoul, Korea
| | - Brigitta C Brott
- />Cardiovascular Division, School of Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Paul D Eleazer
- />Department of Endodontics, University of Alabama at Birmingham, Birmingham, AL USA
| | - Jin-Yong Lee
- />Department of Maxillofacial Biomedical Engineering, Kyung Hee University, Seoul, Korea
| | - Hui Wu
- />Department of Pediatric Dentistry, University of Alabama at Birmingham, SDB 304B, 1720 2nd Ave S, Birmingham, AL 35294-0007 USA
| | - Noel K Childers
- />Department of Pediatric Dentistry, University of Alabama at Birmingham, SDB 304B, 1720 2nd Ave S, Birmingham, AL 35294-0007 USA
| | - Ho-Wook Jun
- />Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL USA
| | - Jae-Hong Park
- />Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL USA
- />Department of Pediatric Dentistry, School of Dentistry, Kyung Hee University, Seoul, Korea
| | - Kyounga Cheon
- />Department of Pediatric Dentistry, University of Alabama at Birmingham, SDB 304B, 1720 2nd Ave S, Birmingham, AL 35294-0007 USA
| |
Collapse
|
9
|
Jia K, Ionescu RE. Measurement of Bacterial Bioluminescence Intensity and Spectrum: Current Physical Techniques and Principles. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 154:19-45. [PMID: 25981856 DOI: 10.1007/10_2015_324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
: Bioluminescence is light production by living organisms, which can be observed in numerous marine creatures and some terrestrial invertebrates. More specifically, bacterial bioluminescence is the "cold light" produced and emitted by bacterial cells, including both wild-type luminescent and genetically engineered bacteria. Because of the lively interplay of synthetic biology, microbiology, toxicology, and biophysics, different configurations of whole-cell biosensors based on bacterial bioluminescence have been designed and are widely used in different fields, such as ecotoxicology, food toxicity, and environmental pollution. This chapter first discusses the background of the bioluminescence phenomenon in terms of optical spectrum. Platforms for bacterial bioluminescence detection using various techniques are then introduced, such as a photomultiplier tube, charge-coupled device (CCD) camera, micro-electro-mechanical systems (MEMS), and complementary metal-oxide-semiconductor (CMOS) based integrated circuit. Furthermore, some typical biochemical methods to optimize the analytical performances of bacterial bioluminescent biosensors/assays are reviewed, followed by a presentation of author's recent work concerning the improved sensitivity of a bioluminescent assay for pesticides. Finally, bacterial bioluminescence as implemented in eukaryotic cells, bioluminescent imaging, and cancer cell therapies is discussed.
Collapse
Affiliation(s)
- Kun Jia
- Laboratoire de Nanotechnologie et d'Instrumentation Optique, Institut Charles Delaunay, Université de Technologie de Troyes, UMR CNRS 6281, 12 rue Marie Curie CS 42060, TROYES, 10004 Cedex, France
| | - Rodica Elena Ionescu
- Laboratoire de Nanotechnologie et d'Instrumentation Optique, Institut Charles Delaunay, Université de Technologie de Troyes, UMR CNRS 6281, 12 rue Marie Curie CS 42060, TROYES, 10004 Cedex, France.
| |
Collapse
|
10
|
Swift BJF, Baneyx F. Microbial Uptake, Toxicity, and Fate of Biofabricated ZnS:Mn Nanocrystals. PLoS One 2015; 10:e0124916. [PMID: 25902065 PMCID: PMC4406734 DOI: 10.1371/journal.pone.0124916] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/12/2015] [Indexed: 01/28/2023] Open
Abstract
Despite their importance in nano-environmental health and safety, interactions between engineered nanomaterials and microbial life remain poorly characterized. Here, we used the model organism E. coli to study the penetration requirements, subcellular localization, induction of stress responses, and long-term fate of luminescent Mn-doped ZnS nanocrystals fabricated under “green” processing conditions with a minimized ZnS-binding protein. We find that such protein-coated quantum dots (QDs) are unable to penetrate the envelope of unmodified E. coli but readily translocate to the cytoplasm of cells that have been made competent by chemical treatment. The process is dose-dependent and reminiscent of bacterial transformation. Cells that have internalized up to 0.5 μg/mL of nanocrystals do not experience a significant activation of the unfolded protein or SOS responses but undergo oxidative stress when exposed to high QD doses (2.5 μg/mL). Finally, although they are stable in quiescent cells over temperatures ranging from 4 to 42°C, internalized QDs are rapidly diluted by cell division in a process that does not involve TolC-dependent efflux. Taken together, our results suggest that biomimetic QDs based on low toxicity inorganic cores capped by a protein shell are unlikely to cause significant damage to the microbial ecosystem.
Collapse
Affiliation(s)
- Brian J. F. Swift
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Franҫois Baneyx
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| |
Collapse
|
11
|
A novel high-throughput cell-based assay aimed at identifying inhibitors of DNA metabolism in bacteria. Antimicrob Agents Chemother 2014; 58:7264-72. [PMID: 25246396 DOI: 10.1128/aac.03475-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacterial biosensor strains can be useful tools for the discovery and characterization of antibacterial compounds. A plasmid-based reporter vector containing a transcriptional fusion between the recA promoter and green fluorescence protein gene was introduced into an Escherichia coli ΔtolC strain to create a biosensor strain that selectively senses inhibitors of DNA metabolism via the SOS response. The strain was used to develop a high-throughput assay to identify new inhibitors of DNA metabolism. Screening of the AstraZeneca compound library with this strain identified known inhibitors of DNA metabolism, as well as novel chemotypes. The cellular target of one novel series was elucidated as DNA gyrase through genetic characterization of laboratory-generated resistant mutants followed by 50% inhibitory concentration measurements in a DNA gyrase activity assay. These studies validated the use of this antibiotic biosensor strain to identify novel selective inhibitors of DNA metabolism by high-throughput screening.
Collapse
|
12
|
Biosensors, antibiotics and food. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 145:153-85. [PMID: 25216955 DOI: 10.1007/978-3-662-43619-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Antibiotics are medicine's leading asset for fighting microbial infection, which is one of the leading causes of death worldwide. However, the misuse of antibiotics has led to the rapid spread of antibiotic resistance among bacteria and the development of multiple resistant pathogens. Therefore, antibiotics are rapidly losing their antimicrobial value. The use of antibiotics in food production animals is strictly controlled by the European Union (EU). Veterinary use is regulated to prevent the spread of resistance. EU legislation establishes maximum residue limits for veterinary medicinal products in foodstuffs of animal origin and enforces the establishment and execution of national monitoring plans. Among samples selected for monitoring, suspected noncompliant samples are screened and then subjected to confirmatory analysis to establish the identity and concentration of the contaminant. Screening methods for antibiotic residues are typically based on microbiological growth inhibition, whereas physico-chemical methods are used for confirmatory analysis. This chapter discusses biosensors, especially whole-cell based biosensors, as emerging screening methods for antibiotic residues. Whole-cell biosensors can offer highly sensitive and specific detection of residues. Applications demonstrating quantitative analysis and specific analyte identification further improve their potential as screening methods.
Collapse
|
13
|
Qian G, Ping J, Zhang Z, Xu D. Sequencing and comparative genomics analysis in Senecio scandens Buch.-Ham. Ex D. Don, based on full-length cDNA library. BIOTECHNOL BIOTEC EQ 2014; 28:805-812. [PMID: 26740776 PMCID: PMC4684062 DOI: 10.1080/13102818.2014.956461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/10/2014] [Indexed: 11/23/2022] Open
Abstract
Senecio scandens Buch.-Ham. ex D. Don, an important antibacterial source of Chinese traditional medicine, has a widespread distribution in a few ecological habitats of China. We generated a full-length complementary DNA (cDNA) library from a sample of elite individuals with superior antibacterial properties, with satisfactory parameters such as library storage (4.30 × 106 CFU), efficiency of titre (1.30 × 106 CFU/mL), transformation efficiency (96.35%), full-length ratio (64.00%) and redundancy ratio (3.28%). The BLASTN search revealed the facile formation of counterparts between the experimental sample and Arabidopsis thaliana in view of high-homology cDNA sequence (90.79%) with e-values <1e - 50. Sequence similarities to known proteins indicate that the entire sequences of the full-length cDNA clones consist of the major of functional genes identified by a large set of microarray data from the present experimental material. For other Compositae species, a large set of full-length cDNA clones reported in the present article will serve as a useful resource to facilitate further research on the transferability of expressed sequence tag-derived simple sequence repeats (EST-SSR) development, comparative genomics and novel transcript profiles.
Collapse
Affiliation(s)
- Gang Qian
- Department of Cell Biology and Genetics, Zunyi Medical College, Zunyi, Guizhou, P.R. China
| | - Junjiao Ping
- Department of Cell Biology and Genetics, Zunyi Medical College, Zunyi, Guizhou, P.R. China
| | - Zhen Zhang
- Department of Cell Biology and Genetics, Zunyi Medical College, Zunyi, Guizhou, P.R. China
| | - Delin Xu
- Department of Cell Biology and Genetics, Zunyi Medical College, Zunyi, Guizhou, P.R. China
| |
Collapse
|
14
|
Qian G, Ping J, Lu J, Zhang Z, Wang L, Xu D. Construction of Full-Length cDNA Library and Development of EST-Derived Simple Sequence Repeat (EST-SSR) Markers in Senecio scandens. Biochem Genet 2014; 52:494-508. [DOI: 10.1007/s10528-014-9662-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 06/10/2014] [Indexed: 11/28/2022]
|
15
|
Arenas FA, Leal CA, Pinto CA, Arenas-Salinas MA, Morales WA, Cornejo FA, Díaz-Vásquez WA, Vásquez CC. On the mechanism underlying tellurite reduction by Aeromonas caviae ST dihydrolipoamide dehydrogenase. Biochimie 2014; 102:174-82. [PMID: 24680738 DOI: 10.1016/j.biochi.2014.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/17/2014] [Indexed: 10/25/2022]
Abstract
The dihydrolipoamide dehydrogenase (LpdA) from the tellurite-resistant bacterium Aeromonas caviae ST reduces tellurite to elemental tellurium. To characterize this NADH-dependent activity, the A. caviae lpdA gene was subjected to site-directed mutagenesis and genes containing C45A, H322Y and E354K substitutions were individually transformed into Escherichia coli Δlpd. Cells expressing the modified genes exhibited decreased pyruvate dehydrogenase, dihydrolipoamide dehydrogenase and TR activity regarding that observed with the wild type A. caviae lpdA gene. In addition, cells expressing the altered lpdA genes showed increased oxidative stress levels and tellurite sensitivity than those carrying the wild type counterpart. The involvement of Cys residues in LpdA's TR activity was analyzed using specific inhibitors that interact with catalytic cysteines and/or disulfide bridges such as aurothiomalate, zinc or nickel. TR activity of purified LpdA was drastically affected by these compounds. Since LpdA belongs to the flavoprotein family, the involvement of the FAD/NAD(P)(+)-binding domain in TR activity was determined. FAD removal from purified LpdA results in loss of TR activity, which was restored with exogenously added FAD. Substitutions in E354, involved in FAD/NADH binding, resulted in low TR activity because of flavin loss. Finally, changing H322 (involved in NAD(+)/NADH binding) by tyrosine also resulted in altered TR activity.
Collapse
Affiliation(s)
- F A Arenas
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - C A Leal
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - C A Pinto
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - M A Arenas-Salinas
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile
| | - W A Morales
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile
| | - F A Cornejo
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - W A Díaz-Vásquez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile; Facultad de Ciencia, Universidad San Sebastián, Santiago, Chile
| | - C C Vásquez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.
| |
Collapse
|
16
|
Hrast M, Anderluh M, Knez D, Randall CP, Barreteau H, O'Neill AJ, Blanot D, Gobec S. Design, synthesis and evaluation of second generation MurF inhibitors based on a cyanothiophene scaffold. Eur J Med Chem 2014; 73:83-96. [DOI: 10.1016/j.ejmech.2013.11.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 11/15/2013] [Accepted: 11/24/2013] [Indexed: 11/29/2022]
|
17
|
Hrast M, Turk S, Sosič I, Knez D, Randall CP, Barreteau H, Contreras-Martel C, Dessen A, O'Neill AJ, Mengin-Lecreulx D, Blanot D, Gobec S. Structure-activity relationships of new cyanothiophene inhibitors of the essential peptidoglycan biosynthesis enzyme MurF. Eur J Med Chem 2013; 66:32-45. [PMID: 23786712 DOI: 10.1016/j.ejmech.2013.05.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 05/10/2013] [Accepted: 05/13/2013] [Indexed: 10/26/2022]
Abstract
Peptidoglycan is an essential component of the bacterial cell wall, and enzymes involved in its biosynthesis represent validated targets for antibacterial drug discovery. MurF catalyzes the final intracellular peptidoglycan biosynthesis step: the addition of D-Ala-D-Ala to the nucleotide precursor UDP-MurNAc-L-Ala-γ-D-Glu-meso-DAP (or L-Lys). As MurF has no human counterpart, it represents an attractive target for the development of new antibacterial drugs. Using recently published cyanothiophene inhibitors of MurF from Streptococcus pneumoniae as a starting point, we designed and synthesized a series of structurally related derivatives and investigated their inhibition of MurF enzymes from different bacterial species. Systematic structural modifications of the parent compounds resulted in a series of nanomolar inhibitors of MurF from S. pneumoniae and micromolar inhibitors of MurF from Escherichia coli and Staphylococcus aureus. Some of the inhibitors also show antibacterial activity against S. pneumoniae R6. These findings, together with two new co-crystal structures, represent an excellent starting point for further optimization toward effective novel antibacterials.
Collapse
Affiliation(s)
- Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Ooi N, Chopra I, Eady A, Cove J, Bojar R, O'Neill AJ. Antibacterial activity and mode of action of tert-butylhydroquinone (TBHQ) and its oxidation product, tert-butylbenzoquinone (TBBQ). J Antimicrob Chemother 2013; 68:1297-304. [PMID: 23463211 DOI: 10.1093/jac/dkt030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES The antioxidant tert-butylhydroquinone (TBHQ) is a food additive reported to have antibacterial activity, and may therefore have application in the healthcare setting. This study sought to characterize the antibacterial activity and mode of action of TBHQ and its oxidation product, tert-butylbenzoquinone (TBBQ). METHODS The stability of TBHQ/TBBQ was studied in buffer. Susceptibility testing was performed by broth microdilution, and killing and lytic activity were evaluated by viable counting and culture turbidity measurements. Mode of action studies included following the incorporation of radiolabelled precursors into macromolecules. The effect of TBHQ/TBBQ upon bacterial and mammalian membranes was assessed using the BacLight(TM) assay and by monitoring the haemolysis of equine erythrocytes. RESULTS TBHQ underwent oxidation in solution to form TBBQ. When oxidation was prevented, TBHQ lacked useful antibacterial activity, indicating that TBBQ is responsible for the antibacterial activity attributed to TBHQ. TBBQ demonstrated activity against Staphylococcus aureus SH1000 (MIC 8 mg/L) and against a panel of clinical S. aureus isolates (MIC90 16 mg/L). TBBQ at 4× MIC caused a >4 log10 drop in cell viability within 6 h without lysis, and eradicated staphylococcal biofilms at 8× MIC. TBBQ did not display preferential inhibition of any single macromolecular synthetic pathway, but caused loss of staphylococcal membrane integrity without haemolytic activity. CONCLUSIONS TBBQ is responsible for the antibacterial activity previously ascribed to TBHQ. TBBQ prompts loss of staphylococcal membrane integrity; it is rapidly and extensively bactericidal, but is non-lytic. In view of the potent and selective bactericidal activity of TBBQ, this compound warrants further investigation as a candidate antistaphylococcal agent.
Collapse
Affiliation(s)
- N Ooi
- Antimicrobial Research Centre and School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | | | | | | | | | | |
Collapse
|
19
|
Prosser GA, Copp JN, Mowday AM, Guise CP, Syddall SP, Williams EM, Horvat CN, Swe PM, Ashoorzadeh A, Denny WA, Smaill JB, Patterson AV, Ackerley DF. Creation and screening of a multi-family bacterial oxidoreductase library to discover novel nitroreductases that efficiently activate the bioreductive prodrugs CB1954 and PR-104A. Biochem Pharmacol 2013; 85:1091-103. [PMID: 23399641 DOI: 10.1016/j.bcp.2013.01.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 01/28/2013] [Accepted: 01/30/2013] [Indexed: 01/14/2023]
Abstract
Two potentially complementary approaches to improve the anti-cancer strategy gene-directed enzyme prodrug therapy (GDEPT) are discovery of more efficient prodrug-activating enzymes, and development of more effective prodrugs. Here we demonstrate the utility of a flexible screening system based on the Escherichia coli SOS response to evaluate novel nitroreductase enzymes and prodrugs in concert. To achieve this, a library of 47 candidate genes representing 11 different oxidoreductase families was created and screened to identify the most efficient activators of two different nitroaromatic prodrugs, CB1954 and PR-104A. The most catalytically efficient nitroreductases were found in the NfsA and NfsB enzyme families, with NfsA homologues generally more active than NfsB. Some members of the AzoR, NemA and MdaB families also exhibited low-level activity with one or both prodrugs. The results of SOS screening in our optimised E. coli reporter strain SOS-R2 were generally predictive of the ability of nitroreductase candidates to sensitise E. coli to CB1954, and of the kcat/Km for each prodrug substrate at a purified protein level. However, we also found that not all nitroreductases express stably in human (HCT-116 colon carcinoma) cells, and that activity at a purified protein level did not necessarily predict activity in stably transfected HCT-116. These results highlight a need for all enzyme-prodrug partners for GDEPT to be assessed in the specific context of the vector and cell line that they are intended to target. Nonetheless, our oxidoreductase library and optimised screens provide valuable tools to identify preferred nitroreductase-prodrug combinations to advance to preclinical evaluation.
Collapse
Affiliation(s)
- Gareth A Prosser
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, New Zealand
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Amin RM, Abdel-Kader NS, El-Ansary AL. Microplate assay for screening the antibacterial activity of Schiff bases derived from substituted benzopyran-4-one. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 95:517-525. [PMID: 22591797 DOI: 10.1016/j.saa.2012.04.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 03/22/2012] [Accepted: 04/08/2012] [Indexed: 05/31/2023]
Abstract
Schiff bases (SB(1)-SB(3)) were synthesized from the condensation of 6-formyl-7-hydroxy-5-methoxy-2-methylbenzopyran-4-one with 2-aminopyridine (SB(1)), p-phenylenediamine (SB(2)) and o-phenylenediamine (SB(3)), while Schiff bases (SB(4)-SB(6)) were synthesized by condensation of 5,7-dihydroxy-6-formyl-2-methylbenzopyran-4-one with 2-aminopyridine (SB(4)), p-phenylenediamine (SB(5)) and o-phenylenediamine (SB(6)). Schiff bases were characterized using elemental analysis, IR, UV-Vis, (1)H NMR, (13)C NMR and mass spectroscopy. These compounds were screened for antibacterial activities by micro-plate assay technique. Escherichia coli and Staphylococcus capitis were exposed to different concentrations of the Schiff bases. Results showed that the antibacterial effect of these Schiff bases on Gram-negative bacteria were higher than that on Gram-positive bacteria moreover, the Schiff bases containing substituent OCH(3) on position five have higher antibacterial activity than that containing hydroxy group on the same position.
Collapse
Affiliation(s)
- Rehab M Amin
- National Institute of Laser Enhanced Sciences, Cairo University, Giza, Egypt.
| | | | | |
Collapse
|
21
|
Škedelj V, Arsovska E, Tomašić T, Kroflič A, Hodnik V, Hrast M, Bešter-Rogač M, Anderluh G, Gobec S, Bostock J, Chopra I, O'Neill AJ, Randall C, Zega A. 6-Arylpyrido[2,3-d]pyrimidines as novel ATP-competitive inhibitors of bacterial D-alanine:D-alanine ligase. PLoS One 2012; 7:e39922. [PMID: 22876277 PMCID: PMC3410885 DOI: 10.1371/journal.pone.0039922] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 05/29/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND ATP-dependent D-alanine:D-alanine ligase (Ddl) is a part of biochemical machinery involved in peptidoglycan biosynthesis, as it catalyzes the formation of the terminal D-ala-D-ala dipeptide of the peptidoglycan precursor UDPMurNAc-pentapeptide. Inhibition of Ddl prevents bacterial growth, which makes this enzyme an attractive and viable target in the urgent search of novel effective antimicrobial drugs. To address the problem of a relentless increase in resistance to known antimicrobial agents we focused our attention to discovery of novel ATP-competitive inhibitors of Ddl. METHODOLOGY/PRINCIPAL FINDINGS Encouraged by recent successful attempts to find selective ATP-competitive inhibitors of bacterial enzymes we designed, synthesized and evaluated a library of 6-arylpyrido[2,3-d]pyrimidine-based compounds as inhibitors of Escherichia coli DdlB. Inhibitor binding to the target enzyme was subsequently confirmed by surface plasmon resonance and studied with isothermal titration calorimetry. Since kinetic analysis indicated that 6-arylpyrido[2,3-d]pyrimidines compete with the enzyme substrate ATP, inhibitor binding to the ATP-binding site was additionally studied with docking. Some of these inhibitors were found to possess antibacterial activity against membrane-compromised and efflux pump-deficient strains of E. coli. CONCLUSIONS/SIGNIFICANCE We discovered new ATP-competitive inhibitors of DdlB, which may serve as a starting point for development of more potent inhibitors of DdlB that could include both, an ATP-competitive and D-Ala competitive moiety.
Collapse
Affiliation(s)
- Veronika Škedelj
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Emilija Arsovska
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Tihomir Tomašić
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Ana Kroflič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Vesna Hodnik
- Biotechnical faculty, Infrastructural Center for Surface Plasmon Resonance, University of Ljubljana, Ljubljana, Slovenia
| | - Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Marija Bešter-Rogač
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Gregor Anderluh
- Biotechnical faculty, Infrastructural Center for Surface Plasmon Resonance, University of Ljubljana, Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Julieanne Bostock
- Antimicrobial Research Centre and Instititue of Molecular & Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Ian Chopra
- Antimicrobial Research Centre and Instititue of Molecular & Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Alex J. O'Neill
- Antimicrobial Research Centre and Instititue of Molecular & Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Christopher Randall
- Antimicrobial Research Centre and Instititue of Molecular & Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Anamarija Zega
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
| |
Collapse
|
22
|
Osterman IA, Prokhorova IV, Sysoev VO, Boykova YV, Efremenkova OV, Svetlov MS, Kolb VA, Bogdanov AA, Sergiev PV, Dontsova OA. Attenuation-based dual-fluorescent-protein reporter for screening translation inhibitors. Antimicrob Agents Chemother 2012; 56:1774-83. [PMID: 22252829 PMCID: PMC3318315 DOI: 10.1128/aac.05395-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 12/28/2011] [Indexed: 11/20/2022] Open
Abstract
A reporter construct was created on the basis of the transcription attenuator region of the Escherichia coli tryptophan operon. Dual-fluorescent-protein genes for red fluorescent protein and cerulean fluorescent protein were used as a sensor and internal control of gene expression. The sequence of the attenuator was modified to avoid tryptophan sensitivity while preserving sensitivity to ribosome stalling. Antimicrobial compounds which cause translation arrest at the stage of elongation induce the reporter both in liquid culture and on an agar plate. This reporter could be used for high-throughput screening of translation inhibitors.
Collapse
Affiliation(s)
- Ilya A. Osterman
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Irina V. Prokhorova
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Vasily O. Sysoev
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Yulia V. Boykova
- G. F. Gauze Institute for Search for New Antibiotics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Olga V. Efremenkova
- G. F. Gauze Institute for Search for New Antibiotics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Maxim S. Svetlov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Vyacheslav A. Kolb
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Alexey A. Bogdanov
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Petr V. Sergiev
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Olga A. Dontsova
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| |
Collapse
|
23
|
Nithya V, Halami PM. Novel whole-cell Reporter Assay for Stress-Based Classification of Antibacterial Compounds Produced by Locally Isolated Bacillus spp. Indian J Microbiol 2012; 52:180-4. [PMID: 23729879 DOI: 10.1007/s12088-012-0256-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 01/31/2012] [Indexed: 10/28/2022] Open
Abstract
Reporter bacteria are beneficial for the rapid and sensitive screening of cultures producing peptide antibiotics, which can be an addition or alternative to the established antibiotics. This study was carried out to validate the usability of specific reporter strains for the target mediated identification of antibiotics produced by native Bacillus spp. isolated from different food sources. During preliminary classification, cell wall stress causing Bacillus isolates were screened by using reporter strain Bacillus subtilis BSF2470. The isolates which induced cell wall stress were further characterized for their specific mode of action by using other B. subtilis reporter strains (TMB 488, TMB 299 and TMB 279). The isolate B. licheniformis N12 was found to produce bacitracin confirmed by the response to reporter strain B. subtilis TMB 279 and by putative identification of bacitracin biosynthetic loci. The other isolate B. subtilis EC1 also induced B. subtilis TMB 279, but does not possess the bacitracin gene cluster indicating that it can be a novel, bacitracin like antibiotic. The different but related subsets of peptide antibiotics that bind the pyrophosphate moiety of the lipid carrier of cell wall biosynthesis can be identified using this whole cell based reporter strains.
Collapse
Affiliation(s)
- Vadakedath Nithya
- Department of Food Microbiology, CSIR-Central Food Technological Research Institute, Mysore, 570 020 India
| | | |
Collapse
|
24
|
Activity of and development of resistance to corallopyronin A, an inhibitor of RNA polymerase. Antimicrob Agents Chemother 2011; 55:2413-6. [PMID: 21321139 DOI: 10.1128/aac.01742-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We explored the properties of corallopyronin A (CorA), a poorly characterized inhibitor of bacterial RNA polymerase (RNAP). It displayed a 50% inhibitory concentration of 0.73 μM against RNAP, compared with 11.5 nM for rifampin. The antibacterial activity of CorA was also inferior to rifampin, and resistant mutants of Staphylococcus aureus were easily selected. The mutations conferring resistance resided in the rpoB and rpoC subunits of RNAP. We conclude that CorA is not a promising antibacterial drug candidate.
Collapse
|
25
|
Arenas FA, Covarrubias PC, Sandoval JM, Pérez-Donoso JM, Imlay JA, Vásquez CC. The Escherichia coli BtuE protein functions as a resistance determinant against reactive oxygen species. PLoS One 2011; 6:e15979. [PMID: 21264338 PMCID: PMC3018469 DOI: 10.1371/journal.pone.0015979] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 12/01/2010] [Indexed: 11/19/2022] Open
Abstract
This work shows that the recently described Escherichia coli BtuE peroxidase protects the bacterium against oxidative stress that is generated by tellurite and by other reactive oxygen species elicitors (ROS). Cells lacking btuE (ΔbtuE) displayed higher sensitivity to K(2)TeO(3) and other oxidative stress-generating agents than did the isogenic, parental, wild-type strain. They also exhibited increased levels of cytoplasmic reactive oxygen species, oxidized proteins, thiobarbituric acid reactive substances, and lipoperoxides. E. coli ΔbtuE that was exposed to tellurite or H(2)O(2) did not show growth changes relative to wild type cells either in aerobic or anaerobic conditions. Nevertheless, the elimination of btuE from cells deficient in catalases/peroxidases (Hpx(-)) resulted in impaired growth and resistance to these toxicants only in aerobic conditions, suggesting that BtuE is involved in the defense against oxidative damage. Genetic complementation of E. coli ΔbtuE restored toxicant resistance to levels exhibited by the wild type strain. As expected, btuE overexpression resulted in decreased amounts of oxidative damage products as well as in lower transcriptional levels of the oxidative stress-induced genes ibpA, soxS and katG.
Collapse
Affiliation(s)
- Felipe A. Arenas
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Paulo C. Covarrubias
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Juan M. Sandoval
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - José M. Pérez-Donoso
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - James A. Imlay
- Department of Microbiology, University of Illinois, Urbana-Champaign, Illinois, United States of America
| | - Claudio C. Vásquez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| |
Collapse
|
26
|
Mondal R, Chanda PK, Bandhu A, Jana B, Lee CY, Sau S. Detection of the cell wall-affecting antibiotics at sublethal concentrations using a reporter Staphylococcus aureus harboring drp35 promoter - lacZ transcriptional fusion. BMB Rep 2010; 43:468-73. [PMID: 20663407 DOI: 10.5483/bmbrep.2010.43.7.468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously, various inhibitors of cell wall synthesis induced the drp35 gene of Staphylococcus aureus efficiently. To determine whether drp35 could be exploited in antistaphylococcal drug discovery, we cloned the promoter of drp35 (P(d)) and developed different biological assay systems using an engineered S. aureus strain that harbors a chromosomally-integrated P(d) - lacZ transcriptional fusion. An agarose-based assay showed that P(d) is induced not only by the cell wall-affecting antibiotics but also by rifampicin and ciprofloxacin. In contrast, a liquid medium-based assay revealed the induction of P(d) specifically by the cell wall-affecting antibiotics. Induction of P(d) by sublethal concentrations of cell wall-affecting antibiotics was even assessable in a microtiter plate assay format, indicating that this assay system could be potentially used for high-throughput screening of new cell wall-inhibiting compounds.
Collapse
Affiliation(s)
- Rajkrishna Mondal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | | | | | | | | | | |
Collapse
|
27
|
Upgrading bioluminescent bacterial bioreporter performance by splitting the lux operon. Anal Bioanal Chem 2010; 400:1071-82. [DOI: 10.1007/s00216-010-4266-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 09/28/2010] [Accepted: 09/28/2010] [Indexed: 11/25/2022]
|
28
|
|
29
|
Antibacterial effect of some benzopyrone derivatives. Eur J Med Chem 2010; 45:372-8. [DOI: 10.1016/j.ejmech.2009.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 07/27/2009] [Accepted: 10/01/2009] [Indexed: 11/17/2022]
|
30
|
Prosser GA, Copp JN, Syddall SP, Williams EM, Smaill JB, Wilson WR, Patterson AV, Ackerley DF. Discovery and evaluation of Escherichia coli nitroreductases that activate the anti-cancer prodrug CB1954. Biochem Pharmacol 2009; 79:678-87. [PMID: 19852945 DOI: 10.1016/j.bcp.2009.10.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 10/07/2009] [Accepted: 10/09/2009] [Indexed: 10/20/2022]
Abstract
Gene-directed enzyme prodrug therapy (GDEPT) aims to achieve highly selective tumor-cell killing through the use of tumor-tropic gene delivery vectors coupled with systemic administration of otherwise inert prodrugs. Nitroaromatic prodrugs such as CB1954 hold promise for GDEPT as they are readily reduced to potent DNA alkylating agents by bacterial nitroreductase enzymes (NTRs). Transfection with the nfsB gene from Escherichia coli can increase the sensitivity of tumor cells to CB1954 by greater than 1000-fold. However, poor catalytic efficiency limits the activation of CB1954 by NfsB at clinically relevant doses. A lack of flexible, high-throughput screening technology has hindered efforts to discover superior NTR candidates. Here we demonstrate how the SOS chromotest and complementary screening technologies can be used to evaluate novel enzymes that activate CB1954 and other bioreductive and/or genotoxic prodrugs. We identify the major E. coli NTR, NfsA, as 10-fold more efficient than NfsB in activating CB1954 as purified protein (k(cat)/K(m)) and when over-expressed in an E. coli nfsA(-)/nfsB(-) gene deleted strain. NfsA also confers sensitivity to CB1954 when expressed in HCT-116 human colon carcinoma cells, with similar efficiency to NfsB. In addition, we identify two novel E. coli NTRs, AzoR and NemA, that have not previously been characterized in the context of nitroaromatic prodrug activation.
Collapse
Affiliation(s)
- G A Prosser
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, New Zealand
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Amin RM, Mohamed MB, Ramadan MA, Verwanger T, Krammer B. Rapid and sensitive microplate assay for screening the effect of silver and gold nanoparticles on bacteria. Nanomedicine (Lond) 2009; 4:637-43. [DOI: 10.2217/nnm.09.50] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background & aim: Nanomaterials are the leading requirement of the rapidly developing field of nanomedicine and bionanotechnology, and in this respect, nanotoxicology research is gaining great importance. In the field of infections, nanoparticles are being utilized as therapeutic tools against microbes, thus understanding the properties of nanoparticles and their effect on microbes is essential prior to clinical application. The aim of this study was to evaluate a microplate-based assay for monitoring the toxicity of silver and gold nanoparticles on bacteria. Method: Escherichia coli, a Gram-negative bacteria, and Staphylococcus capitis, a Gram-positive bacteria, were exposed to different concentrations of gold and silver nanoparticles. Results: Analysis of bacterial growth showed that the toxicity of silver nanospheres is higher than that of gold nanospheres. The toxicity of silver nanoparticles is dependent on their concentration, whereas in the case of gold nanoparticles, there is no significant toxic effect. Therefore, the described microplate assay could be used as a rapid and sensitive method for detection of bacterial growth inhibition.
Collapse
Affiliation(s)
- Rehab M Amin
- Department of Laser Applications in Photochemistry, National Institute of Laser Enhanced Sciences, Cairo University, Egypt
| | - Mona B Mohamed
- Department of Laser Applications in Photochemistry, National Institute of Laser Enhanced Sciences, Cairo University, Egypt
| | - Marwa A Ramadan
- Department of Laser Applications in Photochemistry, National Institute of Laser Enhanced Sciences, Cairo University, Egypt
| | - Thomas Verwanger
- Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Hellbrunnerstr. 34, Austria
| | - Barbara Krammer
- Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Hellbrunnerstr. 34, Austria
| |
Collapse
|
32
|
Expression of Aeromonas caviae ST pyruvate dehydrogenase complex components mediate tellurite resistance in Escherichia coli. Biochem Biophys Res Commun 2009; 380:148-52. [DOI: 10.1016/j.bbrc.2009.01.078] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 01/13/2009] [Indexed: 11/23/2022]
|
33
|
Abstract
In Escherichia coli, the molecular chaperone HSP70 (DnaK) is necessary for 30S and 50S ribosomal subunit assembly at temperatures above 37 degrees C. Inhibitors of DnaK should therefore hinder ribosome biogenesis, in addition to all of the other DnaK-dependent cellular functions. An easily testable phenotype of DnaK is described here based on alpha-complementation of beta-galactosidase. This protein fragment complementation requires a functional DnaK in vivo, offering a suitable method for screening for DnaK inhibitors. Subsequently, it will be of great importance to check whether inhibitors of bacterial DnaK selected in this way have an effect (inhibitory or stimulatory) on the activities of eukaryotic HSP70 and HSC70 chaperones, because of the universal conservation in all biota of these chaperones in both their structural and functional properties. This question is important due to their implication in many pathways in immunology, cancer biology, and neurodegenerative disorders.
Collapse
|
34
|
Biological activities of novel gyrase inhibitors of the aminocoumarin class. Antimicrob Agents Chemother 2008; 52:1982-90. [PMID: 18347114 DOI: 10.1128/aac.01235-07] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thirty-one aminocoumarin antibiotics derived from mutasynthesis experiments were investigated for their biological activities. Their inhibitory activities toward Escherichia coli DNA gyrase were determined in two different in vitro assays: an ATPase assay and a DNA supercoiling assay. The assays gave a similar rank order of the activities of the compounds tested, although the absolute 50% inhibitory concentrations (IC(50)s) obtained in each assay were different. To confirm that the compounds also acted as gyrase inhibitors in vivo, reporter gene assays were carried out with E. coli by using gyrA and sulA promoter fusions with the luxCDABE operon. A strong induction of both promoters was observed for those compounds that showed gyrase inhibitory activity in the biochemical assays. Compounds carrying analogs of the prenylated benzoyl moiety (ring A) of clorobiocin that were structurally very different showed high levels of activity both in the biochemical assay and in the reporter gene assay, indicating that the structure of this moiety can be varied considerably without a loss of affinity for bacterial gyrase. The experimentally determined IC(50)s were compared to the binding energies calculated in silico, which indicated that a shift of the pyrrole carboxylic acid moiety from the O-3'' to the O-2'' position of the deoxysugar moiety has a significant impact on the binding mode of the compounds. The aminocoumarin compounds were also investigated for their MICs against different bacterial pathogens. Several compounds showed high levels of activity against staphylococci, including a methicillin-resistant Staphylococcus aureus strain. However, they showed only poor activities against gram-negative strains.
Collapse
|
35
|
Chanda PK, Ganguly T, Das M, Lee CY, Luong TT, Sau S. Detection of antistaphylococcal and toxic compounds by biological assay systems developed with a reporter Staphylococcus aureus strain harboring a heat inducible promoter - lacZ transcriptional fusion. BMB Rep 2008; 40:936-43. [PMID: 18047789 DOI: 10.5483/bmbrep.2007.40.6.936] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously it was reported that promoter of groES-groEL operon of Staphylococcus aureus is induced by various cell-wall active antibiotics. In order to exploit the above promoter for identifying novel antistaphylococcal drugs, we have cloned the promoter containing region (P(g)) of groES-groEL operon of S. aureus Newman and found that the above promoter is induced by sublethal concentrations of many antibiotics including cell-wall active antibiotics. A reporter S. aureus RN4220 strain (designated SAU006) was constructed by inserting the P(g)-lacZ transcriptional fusion into its chromosome. Agarose-based assay developed with SAU006 shows that P(g) in single-copy is also induced distinctly by different classes of antibiotics. Data indicate that ciprofloxacin, rifampicin, ampicillin, and cephalothin are strong inducers, whereas, tetracycline, streptomycin and vancomycin induce the above promoter weakly. Sublethal concentrations of ciprofloxacin and ampicilin even have induced P(g) efficiently in microtiter plate grown SAU006. Additional studies show for the first time that above promoter is also induced weakly by arsenate salt and hydrogen peroxide. Taken together, we suggest that our simple and sensitive assay systems with SAU006 could be utilized for screening and detecting not only novel antistaphylococcal compounds but also different toxic chemicals.
Collapse
Affiliation(s)
- Palas Kumar Chanda
- Department of Biochemistry, Bose Institute, P1/12-CIT Scheme VII M, Calcutta 700 054, India
| | | | | | | | | | | |
Collapse
|
36
|
Pérez JM, Arenas FA, Pradenas GA, Sandoval JM, Vásquez CC. Escherichia coli YqhD exhibits aldehyde reductase activity and protects from the harmful effect of lipid peroxidation-derived aldehydes. J Biol Chem 2008; 283:7346-53. [PMID: 18211903 DOI: 10.1074/jbc.m708846200] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Evidence that Escherichia coli YqhD is involved in bacterial response to compounds that generate membrane lipid peroxidation is presented. Overexpression of yqhD results in increased resistance to the reactive oxygen species-generating compounds hydrogen peroxide, paraquat, chromate, and potassium tellurite. Increased tolerance was also observed for the lipid peroxidation-derived aldehydes butanaldehyde, propanaldehyde, acrolein, and malondialdehyde and the membrane-peroxidizing compound tert-butylhydroperoxide. Expression of yqhD was also associated with changes in the concentration of intracellular peroxides and cytoplasmic protein carbonyl content and with a reduction in intracellular acrolein levels. When compared with the wild type strain, an yqhD mutant exhibited a sensitive phenotype to all these compounds and also augmented levels of thiobarbituric acid-reactive substances, which may indicate an increased level of lipid peroxidation. Purified YqhD catalyzes the in vitro reduction of acetaldehyde, malondialdehyde, propanaldehyde, butanaldehyde, and acrolein in a NADPH-dependent reaction. Finally, yqhD transcription was induced in cells that had been exposed to conditions favoring lipid peroxidation. Taken together these results indicate that this enzyme may have a physiological function by protecting the cell against the toxic effect of aldehydes derived from lipid oxidation. We speculate that in Escherichia coli YqhD is part of a glutathione-independent, NADPH-dependent response mechanism to lipid peroxidation.
Collapse
Affiliation(s)
- José Manuel Pérez
- Laboratorio de Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170019, Chile
| | | | | | | | | |
Collapse
|
37
|
De Pascale G, Grigoriadou C, Losi D, Ciciliato I, Sosio M, Donadio S. Validation for high-throughput screening of a VanRS-based reporter gene assay for bacterial cell wall inhibitors. J Appl Microbiol 2008; 103:133-40. [PMID: 17584459 DOI: 10.1111/j.1365-2672.2006.03231.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIMS The present study was undertaken to validate, for antibiotic discovery, a reporter gene assay based on a Bacillus subtilis strain expressing the Enterococcusfaecium vanRS genes and a vanH-lacZ fusion, which produced beta-galactosidase activity in the presence of cell wall inhibitors (CWI) and lysozyme. METHODS AND RESULTS The reporter assay was miniaturized, automated and validated with antibiotics and tested against portions of chemical and microbial extract libraries. The assay is simple, fast and reproducible and can detect all CWI, sometimes at concentrations lower than those necessary to inhibit bacterial growth. However, some membrane-interfering compounds also generate comparable signals. While most CWI elicit a signal that is transcription-dependent and abolished in an osmoprotective medium, transcription is not required for beta-galactosidase activity brought about by the membrane-interfering compounds. CONCLUSIONS At least two distinct mechanisms appear to lead to enzymatic activity in the reporter strain. Effective counterscreens can be designed to discard the undesired classes of compounds. SIGNIFICANCE AND IMPACT OF THE STUDY Extensive validation is required before introducing a reporter assay in high-throughput screening. However, the ease of operation and manipulation makes the reporter assays powerful tools for antibiotic discovery.
Collapse
|
38
|
Shapiro E, Baneyx F. Stress-activated bioluminescent Escherichia coli sensors for antimicrobial agents detection. J Biotechnol 2007; 132:487-93. [PMID: 17897748 DOI: 10.1016/j.jbiotec.2007.08.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 07/29/2007] [Accepted: 08/09/2007] [Indexed: 11/23/2022]
Abstract
A DNA cartridge encoding Photinus pyralis luciferase (luc), lacZ homology extensions and an excisable marker was constructed to facilitate the conversion of Escherichia coli lacZ fusions to luc fusions by lambda Red-mediated recombination. This tool was used to transform a cspA::lacZ strain into a luminescent biosensor for C-group translational inhibitors. Comparison of cspA::lacZ and cspA::luc cells showed native firefly luciferase to be a more rapid and sensitive reporter than beta-galactosidase for chloramphenicol detection. To evaluate the usefulness of a red-shifted variant of P. pyralis luciferase (LucR1) for biosensor development, a single copy translational fusion between the SOS-inducible sulA promoter and the lucR1 gene was inserted at the malP site of the E. coli chromosome. The sulA::lucR1 fusion allowed high signal detection of the quinolone ofloxacin to levels as low as 15% of the minimum inhibitory concentration and could be combined with a cspA::lacZ fusion to yield a biosensor suitable for the independent and dual detection of chloramphenicol and ofloxacin.
Collapse
Affiliation(s)
- Elyse Shapiro
- Department of Chemical Engineering, University of Washington, Box 351750, Seattle, WA 98195, USA
| | | |
Collapse
|
39
|
Cysteine metabolism-related genes and bacterial resistance to potassium tellurite. J Bacteriol 2007; 189:8953-60. [PMID: 17951385 DOI: 10.1128/jb.01252-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tellurite exerts a deleterious effect on a number of small molecules containing sulfur moieties that have a recognized role in cellular oxidative stress. Because cysteine is involved in the biosynthesis of glutathione and other sulfur-containing compounds, we investigated the expression of Geobacillus stearothermophilus V cysteine-related genes cobA, cysK, and iscS and Escherichia coli cysteine regulon genes under conditions that included the addition of K2TeO3 to the culture medium. Results showed that cell tolerance to tellurite correlates with the expression level of the cysteine metabolic genes and that these genes are up-regulated when tellurite is present in the growth medium.
Collapse
|
40
|
Urban A, Eckermann S, Fast B, Metzger S, Gehling M, Ziegelbauer K, Rübsamen-Waigmann H, Freiberg C. Novel whole-cell antibiotic biosensors for compound discovery. Appl Environ Microbiol 2007; 73:6436-43. [PMID: 17720843 PMCID: PMC2075059 DOI: 10.1128/aem.00586-07] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cells containing reporters which are specifically induced via selected promoters are used in pharmaceutical drug discovery and in environmental biology. They are used in screening for novel drug candidates and in the detection of bioactive compounds in environmental samples. In this study, we generated and validated a set of five Bacillus subtilis promoters fused to the firefly luciferase reporter gene suitable for cell-based screening, enabling the as yet most-comprehensive high-throughput diagnosis of antibiotic interference in the major biosynthetic pathways of bacteria: the biosynthesis of DNA by the yorB promoter, of RNA by the yvgS promoter, of proteins by the yheI promoter, of the cell wall by the ypuA promoter, and of fatty acids by the fabHB promoter. The reporter cells mainly represent novel antibiotic biosensors compatible with high-throughput screening. We validated the strains by developing screens with a set of 14,000 pure natural products, representing a source of highly diverse chemical entities, many of them with antibiotic activity (6% with anti-Bacillus subtilis activity of </=25 mug/ml]). Our screening approach is exemplified by the discovery of classical and novel DNA synthesis and translation inhibitors. For instance, we show that the mechanistically underexplored antibiotic ferrimycin A1 selectively inhibits protein biosynthesis.
Collapse
Affiliation(s)
- Andreas Urban
- Pharma Research & Development, Discovery Europe, Bayer HealthCare AG, D-42096 Wuppertal, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Pérez JM, Calderón IL, Arenas FA, Fuentes DE, Pradenas GA, Fuentes EL, Sandoval JM, Castro ME, Elías AO, Vásquez CC. Bacterial toxicity of potassium tellurite: unveiling an ancient enigma. PLoS One 2007; 2:e211. [PMID: 17299591 PMCID: PMC1784070 DOI: 10.1371/journal.pone.0000211] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Accepted: 01/22/2007] [Indexed: 11/19/2022] Open
Abstract
Biochemical, genetic, enzymatic and molecular approaches were used to demonstrate, for the first time, that tellurite (TeO32−) toxicity in E. coli involves superoxide formation. This radical is derived, at least in part, from enzymatic TeO32− reduction. This conclusion is supported by the following observations made in K2TeO3-treated E. coli BW25113: i) induction of the ibpA gene encoding for the small heat shock protein IbpA, which has been associated with resistance to superoxide, ii) increase of cytoplasmic reactive oxygen species (ROS) as determined with ROS-specific probe 2′7′-dichlorodihydrofluorescein diacetate (H2DCFDA), iii) increase of carbonyl content in cellular proteins, iv) increase in the generation of thiobarbituric acid-reactive substances (TBARs), v) inactivation of oxidative stress-sensitive [Fe-S] enzymes such as aconitase, vi) increase of superoxide dismutase (SOD) activity, vii) increase of sodA, sodB and soxS mRNA transcription, and viii) generation of superoxide radical during in vitro enzymatic reduction of potassium tellurite.
Collapse
Affiliation(s)
- José M. Pérez
- Laboratorio de Microbiología Molecular, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Iván L. Calderón
- Laboratorio de Microbiología Molecular, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Felipe A. Arenas
- Laboratorio de Microbiología Molecular, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Derie E. Fuentes
- Laboratorio de Microbiología Molecular, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Gonzalo A. Pradenas
- Laboratorio de Microbiología Molecular, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Eugenia L. Fuentes
- Laboratorio de Microbiología Molecular, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Juan M. Sandoval
- Laboratorio de Microbiología Molecular, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Miguel E. Castro
- Laboratorio de Microbiología Molecular, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Alex O. Elías
- Laboratorio de Microbiología Molecular, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Claudio C. Vásquez
- Laboratorio de Microbiología Molecular, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
42
|
Fischer HP, Freiberg C. Applications of transcriptional profiling in antibiotics discovery and development. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2007; 64:21, 23-47. [PMID: 17195470 DOI: 10.1007/978-3-7643-7567-6_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
This chapter will review specific applications of microarray technology and related data analysis strategies in antibacterial research and development. We present examples of microarray applications spanning the entire antibiotics research and development pipeline, from target discovery, assay development, pharmacological evaluation, to compound safety studies. This review emphasizes the utility of microarrays for a systematic evaluation of novel chemistry as antibiotic agents. Transcriptional profiling has revolutionized the process of target elucidation and has the potential to offer substantial guidance in the identification of new targets. Microarrays will continue to be a workhorse of anti-infectives discovery programs ranging from efficacy assessments of antibiotics ('forward pharmacology') to drug safety evaluations ('toxicogenomics').
Collapse
|
43
|
Freiberg C, Brunner N, Macko L, Fischer HP. Discovering Antibiotic Efficacy Biomarkers. Mol Cell Proteomics 2006; 5:2326-35. [PMID: 16940496 DOI: 10.1074/mcp.m600127-mcp200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As current antibiotic therapy is increasingly challenged by emerging drug-resistant bacteria, new technologies are required to identify and develop novel classes of antibiotics. A major bottleneck in today's discovery efforts, however, is a lack of an efficient and standardized method for assaying the efficacy of a drug candidate. We propose a new high content screening approach for identifying efficacious molecules suitable for development of antibiotics. Key to our approach is a new microarray-based efficacy biomarker discovery strategy. We first produced a large dataset of transcriptional responses of Bacillus subtilis to numerous structurally diverse antibacterial drugs. Second we evaluated different protocols to optimize drug concentration and exposure time selection for profiling compounds of unknown mechanism. Finally we identified a surprisingly low number of gene transcripts (approximately 130) that were sufficient for identifying the mechanism of novel substances with reasonable accuracy (approximately 90%). We show that the statistics-based approach reveals a physiologically meaningful set of biomarkers that can be related to major bacterial defense mechanisms against antibiotics. We provide statistical evidence that a parallel measurement of the expression of the biomarkers guarantees optimal performance when using expression systems for screening libraries of novel substances. The general approach is also applicable to drug discovery for medical indications other than infectious diseases.
Collapse
Affiliation(s)
- Christoph Freiberg
- Pharma Global Drug Discovery, European Research Center, Bayer HealthCare AG, D-42096 Wuppertal, Germany
| | | | | | | |
Collapse
|
44
|
Nicoloff H, Perreten V, McMurry LM, Levy SB. Role for tandem duplication and lon protease in AcrAB-TolC- dependent multiple antibiotic resistance (Mar) in an Escherichia coli mutant without mutations in marRAB or acrRAB. J Bacteriol 2006; 188:4413-23. [PMID: 16740948 PMCID: PMC1482967 DOI: 10.1128/jb.01502-05] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A spontaneous mutant (M113) of Escherichia coli AG100 with an unstable multiple antibiotic resistance (Mar) phenotype was isolated in the presence of tetracycline. Two mutations were found: an insertion in the promoter of lon (lon3::IS186) that occurred first and a subsequent large tandem duplication, dupIS186, bearing the genes acrAB and extending from the lon3::IS186 to another IS186 present 149 kb away from lon. The decreased amount of Lon protease increased the amount of MarA by stabilization of the basal quantities of MarA produced, which in turn increased the amount of multidrug effux pump AcrAB-TolC. However, in a mutant carrying only a lon mutation, the overproduced pump mediated little, if any, increased multidrug resistance, indicating that the Lon protease was required for the function of the pump. This requirement was only partial since resistance was mediated when amounts of AcrAB in a lon mutant were further increased by a second mutation. In M113, amplification of acrAB on the duplication led to increased amounts of AcrAB and multidrug resistance. Spontaneous gene duplication represents a new mechanism for mediating multidrug resistance in E. coli through AcrAB-TolC.
Collapse
Affiliation(s)
- Hervé Nicoloff
- Center for Adaptation Genetics and Drug Resistance, Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA
| | | | | | | |
Collapse
|
45
|
Abstract
The ribosome is one of the main antibiotic targets in the cell. Recent years brought important insights into the mode of interaction of antibiotics with the ribosome and mechanisms of antibiotic action. Ribosome crystallography provided a detailed view of the interactions between antibiotics and rRNA. Advances in biochemical techniques let us better understand how the binding of small organic molecules can interfere with functions of an enzyme four orders of magnitude larger than the inhibitor. These and other achievements paved the way for the development of new ribosome-targeting antibiotics, some of which have already entered medical practice. The recent progress, problems and new directions of research of ribosome-targeting antibiotics are discussed in this review.
Collapse
Affiliation(s)
- Tanel Tenson
- Institute of Technology, University of Tartu, Estonia.
| | | |
Collapse
|
46
|
O'Neill AJ, Chopra I. Preclinical evaluation of novel antibacterial agents by microbiological and molecular techniques. Expert Opin Investig Drugs 2005; 13:1045-63. [PMID: 15268641 DOI: 10.1517/13543784.13.8.1045] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The defining property of an antibacterial agent is its ability to selectively interfere with bacterial growth and/or survival. Consequently, a considerable and crucial part of the preclinical evaluation of any novel antibacterial drug involves judging and characterising its effects on bacteria in vitro. These critical stages in drug development are sometimes made to appear somewhat trivial, sandwiched as they are between the highly demanding antibacterial discovery process and the formidable task of demonstrating safety and efficacy in vivo. However, careful biological evaluation in vitro is key to quantifying and understanding the basis of the antibacterial activity, providing preliminary indications and evaluations of therapeutic potential, assessing the likelihood for the development of bacterial resistance, guiding chemical refinement and assisting subsequent stages of the appraisal of any new antibacterial drug. This review covers concepts in, and strategies for, the in vitro microbiological and molecular evaluation of antibacterial drug candidates.
Collapse
Affiliation(s)
- Alex J O'Neill
- Antimicrobial Research Centre, School of Biochemistry and Microbiology, University of Leeds, Leeds, LS2 9JT, UK.
| | | |
Collapse
|
47
|
Abstract
Antibacterial drug discovery has experienced a paradigm shift from phenotypic screening for antibacterial activity to rational inhibition of preselected targets. Functional genomics techniques are implemented at various stages of the early drug discovery process and play a central role in target validation and mode of action determination. The spectrum of methods ranges from genetic manipulations (e.g. knockout studies, mutation analyses and the construction of conditional mutants) to transcriptome and proteome expression profiling. Functional genomics supports antibacterial drug discovery by improving knowledge on gene function, bacterial physiology and virulence and the effects of antibiotics on bacterial metabolism.
Collapse
|
48
|
Norman A, Hestbjerg Hansen L, Sørensen SJ. Construction of a ColD cda promoter-based SOS-green fluorescent protein whole-cell biosensor with higher sensitivity toward genotoxic compounds than constructs based on recA, umuDC, or sulA promoters. Appl Environ Microbiol 2005; 71:2338-46. [PMID: 15870320 PMCID: PMC1087587 DOI: 10.1128/aem.71.5.2338-2346.2005] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Four different green fluorescent protein (GFP)-based whole-cell biosensors were created based on the DNA damage inducible SOS response of Escherichia coli in order to evaluate the sensitivity of individual SOS promoters toward genotoxic substances. Treatment with the known carcinogen N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) revealed that the promoter for the ColD plasmid-borne cda gene had responses 12, 5, and 3 times greater than the recA, sulA, and umuDC promoters, respectively, and also considerably higher sensitivity. Furthermore, we showed that when the SOS-GFP construct was introduced into an E. coli host deficient in the tolC gene, the minimal detection limits toward mitomycin C, MNNG, nalidixic acid, and formaldehyde were lowered to 9.1 nM, 0.16 microM, 1.1 microM, and 141 microM, respectively, which were two to six times lower than those in the wild-type strain. This study thus presents a new SOS-GFP whole-cell biosensor which is not only able to detect minute levels of genotoxins but, due to its use of the green fluorescent protein, also a reporter system which should be applicable in high-throughput screening assays as well as a wide variety of in situ detection studies.
Collapse
Affiliation(s)
- Anders Norman
- Department of Microbiology, University of Copenhagen, Sølvgade 83H, 1307 Copenhagen K, Denmark.
| | | | | |
Collapse
|
49
|
Abstract
The delicate and dynamic balance of the physiological steady state and its maintenance is well characterized by studies of bacterial stress response. Through the use of genetic analysis, numerous stress regulons, their physiological regulators and their biochemical processes have been delineated. In particular, transcriptionally activated stress regulons are subjects of study and application. These regulons include those that respond to macromolecular damage and toxicity as well as to nutrient starvation. The convenience of reporter gene fusions has allowed the creation of biosensor strains, resulting from the fusion of stress-responsive promoters with a variety of reporter genes. Such cellular biosensors are being used for monitoring dynamic systems and can report the presence of environmental stressors in real time. They provide a greater range of sensitivity, e.g. to sub-lethal concentrations of toxicants, than the simple assessment of cell viability. The underlying physiological context of the reporter strains results in the detection of bioavailable concentrations of both toxicants and nutrients. Culture conditions and host strain genotypes can be customized so as to maximize the sensitivity of the strain for a particular application. Collections of specific strains that are grouped in panels are used to diagnose targets or mode of action for unknown toxicants. Further application in massive by parallel DNA and gene fusion arrays greatly extends the information available for diagnosis of modes of action and may lead to development of novel high-throughput screens. Future studies will include more panels, arrays, as well as single reporter cell detection for a better understanding of the population heterogeneity during stress response. New knowledge of physiology gained from further studies of novel systems, or using innovative methods of analysis, will undoubtedly yield still more useful and informative environmental biosensors.
Collapse
Affiliation(s)
- Amy Cheng Vollmer
- Department of Biology, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA.
| | | |
Collapse
|
50
|
Hutter B, Fischer C, Jacobi A, Schaab C, Loferer H. Panel of Bacillus subtilis reporter strains indicative of various modes of action. Antimicrob Agents Chemother 2004; 48:2588-94. [PMID: 15215113 PMCID: PMC434206 DOI: 10.1128/aac.48.7.2588-2594.2004] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a recent project, we collected the transcriptional profiles of Bacillus subtilis 168 after treatment with a large set of diverse antibacterial agents. One result of the data analysis was the identification of marker genes that are indicative of certain compounds or compound classes. We cloned these promoter regions in front of a luciferase reporter gene and reintroduced the constructs individually into the B. subtilis chromosome. Strains were analyzed for their responsiveness after treatment with a set of 37 antibacterials. Twelve functional reporter strains were generated that were selectively and significantly upregulated by the compounds. The selectivity of the reporter strains ranged from generic pathways like protein biosynthesis, cell wall biosynthesis, and fatty acid biosynthesis to compound classes (quinolones and glycopeptides) and individual compounds (rifampin, cycloserine, and clindamycin). Five of the strains are amenable for high-throughput applications, e.g., pathway-specific screening. In summary, we successfully generated B. subtilis reporter strains that are indicative of the mechanisms of action of various classes of antibacterials. The set of reporter strains presented herein can be used for mode-of-action analyses and for whole-cell screening of compound libraries in a mode-of-action-specific manner.
Collapse
Affiliation(s)
- Bernd Hutter
- GPC Biotech AG, Fraunhoferstrasse 20, 82152 Martinsried/Munich, Germany.
| | | | | | | | | |
Collapse
|