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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.
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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
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2
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Transcriptional Responses of Pseudomonas aeruginosa to Inhibition of Lipoprotein Transport by a Small Molecule Inhibitor. J Bacteriol 2020; 202:JB.00452-20. [PMID: 32989085 PMCID: PMC7685553 DOI: 10.1128/jb.00452-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022] Open
Abstract
A key set of lipoprotein transport components, LolCDE, were inhibited by both a small molecule as well as genetic downregulation of their expression. The data show a unique signature in the Pseudomonas aeruginosa transcriptome in response to perturbation of outer membrane biogenesis. In addition, we demonstrate a transcriptional response in key genes with marked specificity compared to several antibiotic classes with different mechanisms of action. As a result of this work, we identified genes that could be of potential use as biomarkers in a cell-based screen for novel antibiotic inhibitors of lipoprotein transport in P. aeruginosa. Lipoprotein transport from the inner to the outer membrane, carried out by the Lol machinery, is essential for the biogenesis of the Gram-negative cell envelope and, consequently, for bacterial viability. Recently, small molecule inhibitors of the Lol system in Escherichia coli have been identified and shown to inhibit the growth of this organism by interfering with the function of the LolCDE complex. Analysis of the transcriptome of E. coli treated with one such molecule (compound 2) revealed that a number of envelope stress response pathways were induced in response to LolCDE inhibition. However, Pseudomonas aeruginosa is refractory to inhibition by the same small molecule, but we could demonstrate that E. colilolCDE could be substituted for the P. aeruginosa orthologues, where it functions in the correct transport of Pseudomonas lipoproteins, and the cells are inhibited by the more potent compound 2A. In the present study, we took advantage of the functionality of E. coli LolCDE in P. aeruginosa and determined the P. aeruginosa transcriptional response to LolCDE inhibition by compound 2A. We identified key genes that responded to LolCDE inhibition and also demonstrated that the same genes appeared to be affected by genetic depletion of the native P. aeruginosa LolCDE proteins. Several of the major changes were in an upregulated cluster of genes that encode determinants of alginate biosynthesis and transport, and the levels of alginate were found to be increased either by treatment with the small molecule inhibitor or upon depletion of native LolCDE. Finally, we tested several antibiotics with differing mechanisms of action to identify potential specific reporter genes for the further development of compounds that would inhibit the native P. aeruginosa Lol system. IMPORTANCE A key set of lipoprotein transport components, LolCDE, were inhibited by both a small molecule as well as genetic downregulation of their expression. The data show a unique signature in the Pseudomonas aeruginosa transcriptome in response to perturbation of outer membrane biogenesis. In addition, we demonstrate a transcriptional response in key genes with marked specificity compared to several antibiotic classes with different mechanisms of action. As a result of this work, we identified genes that could be of potential use as biomarkers in a cell-based screen for novel antibiotic inhibitors of lipoprotein transport in P. aeruginosa.
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Picconi P, Hind CK, Nahar KS, Jamshidi S, Di Maggio L, Saeed N, Evans B, Solomons J, Wand ME, Sutton JM, Rahman KM. New Broad-Spectrum Antibiotics Containing a Pyrrolobenzodiazepine Ring with Activity against Multidrug-Resistant Gram-Negative Bacteria. J Med Chem 2020; 63:6941-6958. [PMID: 32515951 DOI: 10.1021/acs.jmedchem.0c00328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It is urgent to find new antibiotic classes with activity against multidrug-resistant (MDR) Gram-negative pathogens as the pipeline of antibiotics is essentially empty. Modified pyrrolobenzodiazepines with a C8-linked aliphatic heterocycle provide a new class of broad-spectrum antibacterial agents with activity against MDR Gram-negative bacteria, including WHO priority pathogens. The structure-activity relationship established that the third ring was particularly important for Gram-negative activity. Minimum inhibitory concentrations for the lead compounds ranged from 0.125 to 2 mg/L for MDR Gram-negative, excluding Pseudomonas aeruginosa, and between 0.03 and 1 mg/L for MDR Gram-positive species. The lead compounds were rapidly bactericidal with >5 log reduction in viable count within 4 h for Acinetobacter baumannii and Klebsiella pneumoniae. The lead compound inhibited DNA gyrase in gel-based assays, with an IC50 of 3.16 ± 1.36 mg/L. This study provides a new chemical scaffold for developing novel broad-spectrum antibiotics which can help replenish the pipeline of antibiotics.
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Affiliation(s)
- Pietro Picconi
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
| | - Charlotte K Hind
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, U.K
| | - Kazi S Nahar
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
| | - Shirin Jamshidi
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
| | - Lucia Di Maggio
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
| | - Naima Saeed
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
| | - Bonnie Evans
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, U.K
| | - Jessica Solomons
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, U.K
| | - Matthew E Wand
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, U.K
| | - J Mark Sutton
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, U.K
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4
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A Putative Microcin Amplifies Shiga Toxin 2a Production of Escherichia coli O157:H7. J Bacteriol 2019; 202:JB.00353-19. [PMID: 31611289 DOI: 10.1128/jb.00353-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/01/2019] [Indexed: 01/15/2023] Open
Abstract
Escherichia coli O157:H7 is a foodborne pathogen implicated in various multistate outbreaks. It encodes Shiga toxin on a prophage, and Shiga toxin production is linked to phage induction. An E. coli strain, designated 0.1229, that amplified Stx2a production when cocultured with E. coli O157:H7 strain PA2 was identified. Growth of PA2 in 0.1229 cell-free supernatants had a similar effect, even when supernatants were heated to 100°C for 10 min, but not after treatment with proteinase K. The secreted molecule was shown to use TolC for export and the TonB system for import. The genes sufficient for production of this molecule were localized to a 5.2-kb region of a 12.8-kb plasmid. This region was annotated, identifying hypothetical proteins, a predicted ABC transporter, and a cupin superfamily protein. These genes were identified and shown to be functional in two other E. coli strains, and bioinformatic analyses identified related gene clusters in similar and distinct bacterial species. These data collectively suggest that E. coli 0.1229 and other E. coli strains produce a microcin that induces the SOS response in target bacteria. Besides adding to the limited number of microcins known to be produced by E. coli, this study provides an additional mechanism by which stx 2a expression is increased in response to the gut microflora.IMPORTANCE How the gut microflora influences the progression of bacterial infections is only beginning to be understood. Antibiotics are counterindicated for E. coli O157:H7 infections, limiting treatment options. An increased understanding of how the gut microflora directs O157:H7 virulence gene expression may lead to additional treatment options. This work identified E. coli strains that enhance the production of Shiga toxin by O157:H7 through the secretion of a proposed microcin. Microcins are natural antimicrobial peptides that target specific species, can act as alternatives to antibiotics, and mediate microbial competition. This work demonstrates another mechanism by which non-O157 E. coli strains may increase Shiga toxin production and adds to our understanding of microcins, a group of antimicrobials less well understood than colicins.
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Smith KP, Dowgiallo MG, Chiaraviglio L, Parvatkar P, Kim C, Manetsch R, Kirby JE. A Whole-Cell Screen for Adjunctive and Direct Antimicrobials Active against Carbapenem-Resistant Enterobacteriaceae. SLAS DISCOVERY 2019; 24:842-853. [PMID: 31268804 DOI: 10.1177/2472555219859592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) are an emerging antimicrobial resistance threat for which few if any therapeutic options remain. Identification of new agents that either inhibit CRE or restore activity of existing antimicrobials is highly desirable. Therefore, a high-throughput screen of 182,427 commercially available compounds was used to identify small molecules which either enhanced activity of meropenem against a carbapenem-resistant Klebsiella pneumoniae ST258 screening strain and/or directly inhibited its growth. The primary screening methodology was a whole-cell screen/counterscreen combination assay that tested for reduction of microbial growth in the presence or absence of meropenem, respectively. Screening hits demonstrating eukaryotic cell toxicity based on an orthogonal screening effort or identified as pan-assay interference compounds (PAINS) by computational methods were triaged. Primary screening hits were then clustered and ranked according to favorable physicochemical properties. Among remaining hits, we found 10 compounds that enhanced activity of carbapenems against a subset of CRE. Direct antimicrobials that passed toxicity and PAINS filters were not, however, identified in this relatively large screening effort. It was previously shown that the same screening strategy was productive for identifying candidates for further development when screening known bioactive libraries inclusive of natural products. Our findings therefore further highlight liabilities of commercially available small-molecule screening libraries in the Gram-negative antimicrobial space. In particular, there was especially low yield in identifying compelling activity against a representative, highly multidrug-resistant, carbapenemase-producing K. pneumoniae strain.
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Affiliation(s)
- Kenneth P Smith
- 1 Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.,2 Harvard Medical School, Boston, MA, USA
| | - Matthew G Dowgiallo
- 3 Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Lucius Chiaraviglio
- 1 Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Prakash Parvatkar
- 3 Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Chungsik Kim
- 3 Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Roman Manetsch
- 3 Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.,4 Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - James E Kirby
- 1 Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.,2 Harvard Medical School, Boston, MA, USA
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6
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Peters CE, Lamsa A, Liu RB, Quach D, Sugie J, Brumage L, Pogliano J, Lopez-Garrido J, Pogliano K. Rapid Inhibition Profiling Identifies a Keystone Target in the Nucleotide Biosynthesis Pathway. ACS Chem Biol 2018; 13:3251-3258. [PMID: 30133247 DOI: 10.1021/acschembio.8b00273] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Understanding the mechanism of action (MOA) of new antimicrobial agents is a critical step in drug discovery but is notoriously difficult for compounds that appear to inhibit multiple cellular pathways. We recently described image-based approaches [bacterial cytological profiling and rapid inducible profiling (RIP)] for identifying the cellular pathways targeted by antibiotics. Here we have applied these methods to examine the effects of proteolytically degrading enzymes involved in pyrimidine nucleotide biosynthesis, a pathway that produces intermediates for transcription, DNA replication, and cell envelope synthesis. We show that rapid removal of enzymes directly involved in deoxyribonucleotide synthesis blocks DNA replication. However, degradation of cytidylate kinase (CMK), which catalyzes reactions involved in the synthesis of both ribonucleotides and deoxyribonucleotides, blocks both DNA replication and wall teichoic acid biosynthesis, producing cytological effects identical to those created by simultaneously inhibiting both processes with the antibiotics ciprofloxacin and tunicamycin. Our results suggest that RIP can be used to identify and characterize potential keystone enzymes like CMK whose inhibition dramatically affects multiple pathways, thereby revealing important metabolic connections. Identifying and understanding the role of keystone targets might also help to determine the MOAs of drugs that appear to inhibit multiple targets.
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Affiliation(s)
- Christine E. Peters
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Anne Lamsa
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Roland B. Liu
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Diana Quach
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Joseph Sugie
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Lauren Brumage
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Javier Lopez-Garrido
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Thinking Outside the Box-Novel Antibacterials To Tackle the Resistance Crisis. Angew Chem Int Ed Engl 2018; 57:14440-14475. [PMID: 29939462 DOI: 10.1002/anie.201804971] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 12/13/2022]
Abstract
The public view on antibiotics as reliable medicines changed when reports about "resistant superbugs" appeared in the news. While reasons for this resistance development are easily spotted, solutions for re-establishing effective antibiotics are still in their infancy. This Review encompasses several aspects of the antibiotic development pipeline from very early strategies to mature drugs. An interdisciplinary overview is given of methods suitable for mining novel antibiotics and strategies discussed to unravel their modes of action. Select examples of antibiotics recently identified by using these platforms not only illustrate the efficiency of these measures, but also highlight promising clinical candidates with therapeutic potential. Furthermore, the concept of molecules that disarm pathogens by addressing gatekeepers of virulence will be covered. The Review concludes with an evaluation of antibacterials currently in clinical development. Overall, this Review aims to connect select innovative antimicrobial approaches to stimulate interdisciplinary partnerships between chemists from academia and industry.
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Affiliation(s)
- Markus Lakemeyer
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Weining Zhao
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Franziska A Mandl
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases, Sanofi-Aventis (Deutschland) GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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8
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Über bisherige Denkweisen hinaus - neue Wirkstoffe zur Überwindung der Antibiotika-Krise. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804971] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Markus Lakemeyer
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Weining Zhao
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Franziska A. Mandl
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases; Sanofi-Aventis (Deutschland) GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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9
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Abstract
DNA metabolism embodies a number of biochemical pathways, which include targets of clinically used antibiotics as well as those that are only being explored as potential targets for inhibitory compounds. We give an overview of representative cell-based and enzymatic assays suitable for high-throughput-driven search for novel DNA metabolism inhibitors of established and novel DNA metabolism targets in bacteria. The protocol for a colorimetric coupled primase-inorganic pyrophosphatase assay developed by our group is described in detail.
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10
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Osterman IA, Komarova ES, Shiryaev DI, Korniltsev IA, Khven IM, Lukyanov DA, Tashlitsky VN, Serebryakova MV, Efremenkova OV, Ivanenkov YA, Bogdanov AA, Sergiev PV, Dontsova OA. Sorting Out Antibiotics' Mechanisms of Action: a Double Fluorescent Protein Reporter for High-Throughput Screening of Ribosome and DNA Biosynthesis Inhibitors. Antimicrob Agents Chemother 2016; 60:7481-7489. [PMID: 27736765 PMCID: PMC5119032 DOI: 10.1128/aac.02117-16] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 11/20/2022] Open
Abstract
In order to accelerate drug discovery, a simple, reliable, and cost-effective system for high-throughput identification of a potential antibiotic mechanism of action is required. To facilitate such screening of new antibiotics, we created a double-reporter system for not only antimicrobial activity detection but also simultaneous sorting of potential antimicrobials into those that cause ribosome stalling and those that induce the SOS response due to DNA damage. In this reporter system, the red fluorescent protein gene rfp was placed under the control of the SOS-inducible sulA promoter. The gene of the far-red fluorescent protein, katushka2S, was inserted downstream of the tryptophan attenuator in which two tryptophan codons were replaced by alanine codons, with simultaneous replacement of the complementary part of the attenuator to preserve the ability to form secondary structures that influence transcription termination. This genetically modified attenuator makes possible Katushka2S expression only upon exposure to ribosome-stalling compounds. The application of red and far-red fluorescent proteins provides a high signal-to-background ratio without any need of enzymatic substrates for detection of the reporter activity. This reporter was shown to be efficient in high-throughput screening of both synthetic and natural chemicals.
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Affiliation(s)
- Ilya A Osterman
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Ekaterina S Komarova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| | - Dmitry I Shiryaev
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Ilya A Korniltsev
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Irina M Khven
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| | - Dmitry A Lukyanov
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Vadim N Tashlitsky
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Marina V Serebryakova
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Olga V Efremenkova
- G. F. Gauze Institute for Search for New Antibiotics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Yan A Ivanenkov
- Moscow Institute of Physics and Technology (State University), Moscow Region, Russia
| | - Alexey A Bogdanov
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Petr V Sergiev
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Olga A Dontsova
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
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11
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Bharadwaj S, Mitchell RJ, Qureshi A, Niazi JH. Toxicity evaluation of e-juice and its soluble aerosols generated by electronic cigarettes using recombinant bioluminescent bacteria responsive to specific cellular damages. Biosens Bioelectron 2016; 90:53-60. [PMID: 27875752 DOI: 10.1016/j.bios.2016.11.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/07/2016] [Accepted: 11/08/2016] [Indexed: 11/17/2022]
Abstract
Electronic-cigarettes (e-cigarette) are widely used as an alternative to traditional cigarettes but their safety is not well established. Herein, we demonstrate and validate an analytical method to discriminate the deleterious effects of e-cigarette refills (e-juice) and soluble e-juice aerosol (SEA) by employing stress-specific bioluminescent recombinant bacterial cells (RBCs) as whole-cell biosensors. These RBCs carry luxCDABE-operon tightly controlled by promoters that specifically induced to DNA damage (recA), superoxide radicals (sodA), heavy metals (copA) and membrane damage (oprF). The responses of the RBCs following exposure to various concentrations of e-juice/SEA was recorded in real-time that showed dose-dependent stress specific-responses against both the e-juice and vaporized e-juice aerosols produced by the e-cigarette. We also established that high doses of e-juice (4-folds diluted) lead to cell death by repressing the cellular machinery responsible for repairing DNA-damage, superoxide toxicity, ion homeostasis and membrane damage. SEA also caused the cellular damages but the cells showed enhanced bioluminescence expression without significant growth inhibition, indicating that the cells activated their global defense system to repair these damages. DNA fragmentation assay also revealed the disintegration of total cellular DNA at sub-toxic doses of e-juice. Despite their state of matter, the e-juice and its aerosols induce cytotoxicity and alter normal cellular functions, respectively that raises concerns on use of e-cigarettes as alternative to traditional cigarette. The ability of RBCs in detecting both harmful effects and toxicity mechanisms provided a fundamental understanding of biological response to e-juice and aerosols.
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Affiliation(s)
- Shiv Bharadwaj
- Sabanci University Nanotechnology Research and Application Center, Orta Mahalle 34956, Tuzla, Istanbul, Turkey
| | - Robert J Mitchell
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea
| | - Anjum Qureshi
- Sabanci University Nanotechnology Research and Application Center, Orta Mahalle 34956, Tuzla, Istanbul, Turkey
| | - Javed H Niazi
- Sabanci University Nanotechnology Research and Application Center, Orta Mahalle 34956, Tuzla, Istanbul, Turkey.
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12
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Bioluminescent Reporters for Rapid Mechanism of Action Assessment in Tuberculosis Drug Discovery. Antimicrob Agents Chemother 2016; 60:6748-6757. [PMID: 27572410 DOI: 10.1128/aac.01178-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/26/2016] [Indexed: 12/12/2022] Open
Abstract
The tuberculosis (TB) drug discovery pipeline is fueled by compounds identified in whole-cell screens against the causative agent, Mycobacterium tuberculosis Phenotypic screening enables the selection of molecules that inhibit essential cellular functions in live, intact bacilli grown under a chosen in vitro condition. However, deducing the mechanism of action (MOA), which is important to avoid promiscuous targets, often requires significant biological resources in a lengthy process that risks decoupling medicinal chemistry and biology efforts. Therefore, there is a need to develop methods enabling rapid MOA assessment of putative "actives" for triage decisions. Here, we describe a modified version of a bioluminescence reporter assay that allows nondestructive detection of compounds targeting either of two macromolecular processes in M. tuberculosis: cell wall biosynthesis or maintenance of DNA integrity. Coupling the luxCDABE operon from Photorhabdus luminescens to mycobacterial promoters driving expression of the iniBAC operon (PiniB-LUX) or the DNA damage-inducible genes, recA (PrecA-LUX) or radA (PradA-LUX), provided quantitative detection in real time of compounds triggering expression of any of these promoters over an extended 10- to 12-day incubation. Testing against known anti-TB agents confirmed the specificity of each reporter in registering the MOA of the applied antibiotic in M. tuberculosis, independent of bactericidal or bacteriostatic activity. Moreover, profiles obtained for experimental compounds indicated the potential to infer complex MOAs in which multiple cellular processes are disrupted. These results demonstrate the utility of the reporters for early triage of compounds based on the provisional MOA and suggest their application to investigate polypharmacology in known and experimental anti-TB agents.
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13
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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
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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
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14
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Kern G, Palmer T, Ehmann DE, Shapiro AB, Andrews B, Basarab GS, Doig P, Fan J, Gao N, Mills SD, Mueller J, Sriram S, Thresher J, Walkup GK. Inhibition of Neisseria gonorrhoeae Type II Topoisomerases by the Novel Spiropyrimidinetrione AZD0914. J Biol Chem 2015; 290:20984-20994. [PMID: 26149691 DOI: 10.1074/jbc.m115.663534] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 11/06/2022] Open
Abstract
We characterized the inhibition of Neisseria gonorrhoeae type II topoisomerases gyrase and topoisomerase IV by AZD0914 (AZD0914 will be henceforth known as ETX0914 (Entasis Therapeutics)), a novel spiropyrimidinetrione antibacterial compound that is currently in clinical trials for treatment of drug-resistant gonorrhea. AZD0914 has potent bactericidal activity against N. gonorrhoeae, including multidrug-resistant strains and key Gram-positive, fastidious Gram-negative, atypical, and anaerobic bacterial species (Huband, M. D., Bradford, P. A., Otterson, L. G., Basrab, G. S., Giacobe, R. A., Patey, S. A., Kutschke, A. C., Johnstone, M. R., Potter, M. E., Miller, P. F., and Mueller, J. P. (2014) In Vitro Antibacterial Activity of AZD0914: A New Spiropyrimidinetrione DNA Gyrase/Topoisomerase Inhibitor with Potent Activity against Gram-positive, Fastidious Gram-negative, and Atypical Bacteria. Antimicrob. Agents Chemother. 59, 467-474). AZD0914 inhibited DNA biosynthesis preferentially to other macromolecules in Escherichia coli and induced the SOS response to DNA damage in E. coli. AZD0914 stabilized the enzyme-DNA cleaved complex for N. gonorrhoeae gyrase and topoisomerase IV. The potency of AZD0914 for inhibition of supercoiling and the stabilization of cleaved complex by N. gonorrhoeae gyrase increased in a fluoroquinolone-resistant mutant enzyme. When a mutation, conferring mild resistance to AZD0914, was present in the fluoroquinolone-resistant mutant, the potency of ciprofloxacin for inhibition of supercoiling and stabilization of cleaved complex was increased greater than 20-fold. In contrast to ciprofloxacin, religation of the cleaved DNA did not occur in the presence of AZD0914 upon removal of magnesium from the DNA-gyrase-inhibitor complex. AZD0914 had relatively low potency for inhibition of human type II topoisomerases α and β.
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Affiliation(s)
- Gunther Kern
- Departments of Biosciences, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451.
| | - Tiffany Palmer
- Departments of Biosciences, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | - David E Ehmann
- Departments of Biosciences, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | - Adam B Shapiro
- Departments of Biosciences, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | - Beth Andrews
- Departments of Biosciences, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | - Gregory S Basarab
- Departments of Chemistry, Infection Innovative Medicines Unit, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | - Peter Doig
- Department of Structure and Biophysics, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | - Jun Fan
- Departments of Biosciences, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | - Ning Gao
- Department of Structure and Biophysics, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | - Scott D Mills
- Departments of Biosciences, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | - John Mueller
- Departments of Biosciences, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | - Shubha Sriram
- Departments of Biosciences, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | - Jason Thresher
- Department of Structure and Biophysics, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | - Grant K Walkup
- Departments of Biosciences, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
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15
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Abstract
The dramatic rise in microbial drug resistance in recent years has led to ongoing searches for novel drugs to add to the armory against infectious disease. Nevertheless, a paucity of new antibacterial drugs in discovery and development pipelines using traditional approaches has prompted a variety of unconventional and disruptive strategies for antibacterial drug discovery. Herein, we review recent nontraditional approaches that have been piloted for early drug discovery efforts. These unique methodologies open new avenues for finding the next generation of antimicrobials.
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Affiliation(s)
- Maya A Farha
- M.G. DeGroote Institute for Infectious Disease Research, and Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario, Canada
| | - Eric D Brown
- M.G. DeGroote Institute for Infectious Disease Research, and Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario, Canada
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16
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Novel antibacterial targets and compounds revealed by a high-throughput cell wall reporter assay. J Bacteriol 2015; 197:1726-34. [PMID: 25733621 DOI: 10.1128/jb.02552-14] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 02/24/2015] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED A high-throughput phenotypic screen based on a Citrobacter freundii AmpC reporter expressed in Escherichia coli was executed to discover novel inhibitors of bacterial cell wall synthesis, an attractive, well-validated target for antibiotic intervention. Here we describe the discovery and characterization of sulfonyl piperazine and pyrazole compounds, each with novel mechanisms of action. E. coli mutants resistant to these compounds display no cross-resistance to antibiotics of other classes. Resistance to the sulfonyl piperazine maps to LpxH, which catalyzes the fourth step in the synthesis of lipid A, the outer membrane anchor of lipopolysaccharide (LPS). To our knowledge, this compound is the first reported inhibitor of LpxH. Resistance to the pyrazole compound mapped to mutations in either LolC or LolE, components of the essential LolCDE transporter complex, which is required for trafficking of lipoproteins to the outer membrane. Biochemical experiments with E. coli spheroplasts showed that the pyrazole compound is capable of inhibiting the release of lipoproteins from the inner membrane. Both of these compounds have significant promise as chemical probes to further interrogate the potential of these novel cell wall components for antimicrobial therapy. IMPORTANCE The prevalence of antibacterial resistance, particularly among Gram-negative organisms, signals a need for novel antibacterial agents. A phenotypic screen using AmpC as a sensor for compounds that inhibit processes involved in Gram-negative envelope biogenesis led to the identification of two novel inhibitors with unique mechanisms of action targeting Escherichia coli outer membrane biogenesis. One compound inhibits the transport system for lipoprotein transport to the outer membrane, while the other compound inhibits synthesis of lipopolysaccharide. These results indicate that it is still possible to uncover new compounds with intrinsic antibacterial activity that inhibit novel targets related to the cell envelope, suggesting that the Gram-negative cell envelope still has untapped potential for therapeutic intervention.
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