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French S, Guo ABY, Ellis MJ, Deisinger JP, Johnson JW, Rachwalski K, Piquette ZA, Lluka T, Zary M, Gamage S, Magolan J, Brown ED. A platform for predicting mechanism of action based on bacterial transcriptional responses identifies an unusual DNA gyrase inhibitor. Cell Rep 2024; 43:114053. [PMID: 38578824 DOI: 10.1016/j.celrep.2024.114053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 02/02/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
In the search for much-needed new antibacterial chemical matter, a myriad of compounds have been reported in academic and pharmaceutical screening endeavors. Only a small fraction of these, however, are characterized with respect to mechanism of action (MOA). Here, we describe a pipeline that categorizes transcriptional responses to antibiotics and provides hypotheses for MOA. 3D-printed imaging hardware PFIboxes) profiles responses of Escherichia coli promoter-GFP fusions to more than 100 antibiotics. Notably, metergoline, a semi-synthetic ergot alkaloid, mimics a DNA replication inhibitor. In vitro supercoiling assays confirm this prediction, and a potent analog thereof (MLEB-1934) inhibits growth at 0.25 μg/mL and is highly active against quinolone-resistant strains of methicillin-resistant Staphylococcus aureus. Spontaneous suppressor mutants map to a seldom explored allosteric binding pocket, suggesting a mechanism distinct from DNA gyrase inhibitors used in the clinic. In all, the work highlights the potential of this platform to rapidly assess MOA of new antibacterial compounds.
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Affiliation(s)
- Shawn French
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Amelia Bing Ya Guo
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Michael J Ellis
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Julia P Deisinger
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Jarrod W Johnson
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Kenneth Rachwalski
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Zoë A Piquette
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Telmah Lluka
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Miranda Zary
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Sineli Gamage
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Jakob Magolan
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Eric D Brown
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada.
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Goetz JA, Kuehfuss NM, Botschner AJ, Zhu S, Thompson LK, Cox G. Exploring functional interplay amongst Escherichia coli efflux pumps. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36318669 DOI: 10.1099/mic.0.001261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bacterial efflux pumps exhibit functional interplay that can translate to additive or multiplicative effects on resistance to antimicrobial compounds. In diderm bacteria, two different efflux pump structural types - single-component inner membrane efflux pumps and cell envelope-spanning multicomponent systems - cooperatively export antimicrobials with cytoplasmic targets from the cell. Harnessing our recently developed efflux platform, which is built upon an extensively efflux-deficient strain of Escherichia coli, here we explore interplay amongst a panel of diverse E. coli efflux pumps. Specifically, we assessed the effect of simultaneously expressing two efflux pump-encoding genes on drug resistance, including single-component inner membrane efflux pumps (MdfA, MdtK and EmrE), tripartite complexes (AcrAB, AcrAD, MdtEF and AcrEF), and the acquired TetA(C) tetracycline resistance pump. Overall, the expression of two efflux pump-encoding genes from the same structural type did not enhance resistance levels regardless of the antimicrobial compound or efflux pump under investigation. In contrast, a combination of the tripartite efflux systems with single-component pumps sharing common substrates provided multiplicative increases to antimicrobial resistance levels. In some instances, resistance was increased beyond the product of resistance provided by the two pumps individually. In summary, the developed efflux platform enables the isolation of efflux pump function, facilitating the identification of interactions between efflux pumps.
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Affiliation(s)
- James A Goetz
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Noah M Kuehfuss
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Alexander J Botschner
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Shawna Zhu
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Laura K Thompson
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Georgina Cox
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
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Klobucar K, Jardine E, Farha MA, MacKinnon MR, Fragis M, Nkonge B, Bhando T, Borrillo L, Tsai CN, Johnson JW, Coombes BK, Magolan J, Brown ED. Genetic and Chemical Screening Reveals Targets and Compounds to Potentiate Gram-Positive Antibiotics against Gram-Negative Bacteria. ACS Infect Dis 2022; 8:2187-2197. [PMID: 36098580 DOI: 10.1021/acsinfecdis.2c00357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Gram-negative bacteria are intrinsically resistant to a plethora of antibiotics that effectively inhibit the growth of Gram-positive bacteria. The intrinsic resistance of Gram-negative bacteria to classes of antibiotics, including rifamycins, aminocoumarins, macrolides, glycopeptides, and oxazolidinones, has largely been attributed to their lack of accumulation within cells due to poor permeability across the outer membrane, susceptibility to efflux pumps, or a combination of these factors. Due to the difficulty in discovering antibiotics that can bypass these barriers, finding targets and compounds that increase the activity of these ineffective antibiotics against Gram-negative bacteria has the potential to expand the antibiotic spectrum. In this study, we investigated the genetic determinants for resistance to rifampicin, novobiocin, erythromycin, vancomycin, and linezolid to determine potential targets of antibiotic-potentiating compounds. We subsequently performed a high-throughput screen of ∼50,000 diverse, synthetic compounds to uncover molecules that potentiate the activity of at least one of the five Gram-positive-targeting antibiotics. This led to the discovery of two membrane active compounds capable of potentiating linezolid and an inhibitor of lipid A biosynthesis capable of potentiating rifampicin and vancomycin. Furthermore, we characterized the ability of known inhibitors of lipid A biosynthesis to potentiate the activity of rifampicin against Gram-negative pathogens.
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Affiliation(s)
- Kristina Klobucar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Emily Jardine
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Maya A Farha
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Marc R MacKinnon
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Meghan Fragis
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Brenda Nkonge
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Timsy Bhando
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Louis Borrillo
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Caressa N Tsai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Jarrod W Johnson
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Jakob Magolan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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