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Di Bonaventura G, Lupetti V, Pompilio A. Impact of Growth Conditions on High-Throughput Identification of Repurposing Drugs for Pseudomonas aeruginosa Cystic Fibrosis Lung Infections. Antibiotics (Basel) 2024; 13:642. [PMID: 39061324 PMCID: PMC11273527 DOI: 10.3390/antibiotics13070642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/26/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Pseudomonas aeruginosa lung infections in cystic fibrosis (CF) patients represent a therapeutic challenge due to antibiotic resistance. Repurposing existing drugs is a promising approach for identifying new antimicrobials. A crucial factor in successful drug repurposing is using assay conditions that mirror the site of infection. Here, the impact of growth conditions on the anti-P. aeruginosa activity of a library of 3386 compounds was evaluated. To this, after 24 h exposure, the survival rate of CF P. aeruginosa RP73 planktonic cells was assessed spectrophotometrically under "CF-like" (artificial CF sputum, pH 6.8, 5% CO2) and enriched (Tryptone Soya Broth, pH 7.2, and aerobiosis) conditions. Among non-antibiotic compounds (n = 3127), 13.4% were active regardless of growth conditions, although only 3.2% had comparable activity; 4% and 6.2% were more active under CF-like or enriched conditions, respectively. Interestingly, 22.1% and 26.6% were active exclusively under CF-like and enriched conditions, respectively. Notably, 7 and 12 hits caused 100% killing under CF-like and enriched conditions, respectively. Among antibiotics (n = 234), 42.3% were active under both conditions, although only 18.4% showed comparable activity; 9.4% and 14.5% were more active under CF-like and enriched conditions, respectively. Interestingly, 23% and 16.6% were active exclusively under CF-like and enriched conditions, respectively. Sulphonamides showed higher activity under CF-like conditions, whereas tetracyclines, fluoroquinolones, and macrolides were more effective under enriched settings. Our findings indicated that growth conditions significantly affect the anti-P. aeruginosa activity of antibiotics and non-antibiotic drugs. Consequently, repurposing studies and susceptibility tests should be performed under physicochemical conditions that the pathogen tackles at the site of infection.
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Affiliation(s)
- Giovanni Di Bonaventura
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (V.L.); (A.P.)
- Center for Advanced Studies and Technology, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | - Veronica Lupetti
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (V.L.); (A.P.)
- Center for Advanced Studies and Technology, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | - Arianna Pompilio
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (V.L.); (A.P.)
- Center for Advanced Studies and Technology, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
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Rich MH, Sharrock AV, Mulligan TS, Matthews F, Brown AS, Lee-Harwood HR, Williams EM, Copp JN, Little RF, Francis JJB, Horvat CN, Stevenson LJ, Owen JG, Saxena MT, Mumm JS, Ackerley DF. A metagenomic library cloning strategy that promotes high-level expression of captured genes to enable efficient functional screening. Cell Chem Biol 2023; 30:1680-1691.e6. [PMID: 37898120 PMCID: PMC10842177 DOI: 10.1016/j.chembiol.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/17/2023] [Accepted: 10/02/2023] [Indexed: 10/30/2023]
Abstract
Functional screening of environmental DNA (eDNA) libraries is a potentially powerful approach to discover enzymatic "unknown unknowns", but is usually heavily biased toward the tiny subset of genes preferentially transcribed and translated by the screening strain. We have overcome this by preparing an eDNA library via partial digest with restriction enzyme FatI (cuts CATG), causing a substantial proportion of ATG start codons to be precisely aligned with strong plasmid-encoded promoter and ribosome-binding sequences. Whereas we were unable to select nitroreductases from standard metagenome libraries, our FatI strategy yielded 21 nitroreductases spanning eight different enzyme families, each conferring resistance to the nitro-antibiotic niclosamide and sensitivity to the nitro-prodrug metronidazole. We showed expression could be improved by co-expressing rare tRNAs and encoded proteins purified directly using an embedded His6-tag. In a transgenic zebrafish model of metronidazole-mediated targeted cell ablation, our lead MhqN-family nitroreductase proved ∼5-fold more effective than the canonical nitroreductase NfsB.
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Affiliation(s)
- Michelle H Rich
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Abigail V Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Timothy S Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Frazer Matthews
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Alistair S Brown
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Hannah R Lee-Harwood
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Elsie M Williams
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Janine N Copp
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Rory F Little
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jenni J B Francis
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Claire N Horvat
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Luke J Stevenson
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jeremy G Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Meera T Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jeff S Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand.
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Di Bonaventura G, Lupetti V, Di Giulio A, Muzzi M, Piccirilli A, Cariani L, Pompilio A. Repurposing High-Throughput Screening Identifies Unconventional Drugs with Antibacterial and Antibiofilm Activities against Pseudomonas aeruginosa under Experimental Conditions Relevant to Cystic Fibrosis. Microbiol Spectr 2023; 11:e0035223. [PMID: 37306577 PMCID: PMC10433973 DOI: 10.1128/spectrum.00352-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 05/13/2023] [Indexed: 06/13/2023] Open
Abstract
Pseudomonas aeruginosa is the most common pathogen infecting cystic fibrosis (CF) lungs, causing acute and chronic infections. Intrinsic and acquired antibiotic resistance allow P. aeruginosa to colonize and persist despite antibiotic treatment, making new therapeutic approaches necessary. Combining high-throughput screening and drug repurposing is an effective way to develop new therapeutic uses for drugs. This study screened a drug library of 3,386 drugs, mostly FDA approved, to identify antimicrobials against P. aeruginosa under physicochemical conditions relevant to CF-infected lungs. Based on the antibacterial activity, assessed spectrophotometrically against the prototype RP73 strain and 10 other CF virulent strains, and the toxic potential evaluated toward CF IB3-1 bronchial epithelial cells, five potential hits were selected for further analysis: the anti-inflammatory and antioxidant ebselen, the anticancer drugs tirapazamine, carmofur, and 5-fluorouracil, and the antifungal tavaborole. A time-kill assay showed that ebselen has the potential to cause rapid and dose-dependent bactericidal activity. The antibiofilm activity was evaluated by viable cell count and crystal violet assays, revealing carmofur and 5-fluorouracil as the most active drugs in preventing biofilm formation regardless of the concentration. In contrast, tirapazamine and tavaborole were the only drugs actively dispersing preformed biofilms. Tavaborole was the most active drug against CF pathogens other than P. aeruginosa, especially against Burkholderia cepacia and Acinetobacter baumannii, while carmofur, ebselen, and tirapazamine were particularly active against Staphylococcus aureus and B. cepacia. Electron microscopy and propidium iodide uptake assay revealed that ebselen, carmofur, and tirapazamine significantly damage cell membranes, with leakage and cytoplasm loss, by increasing membrane permeability. IMPORTANCE Antibiotic resistance makes it urgent to design new strategies for treating pulmonary infections in CF patients. The repurposing approach accelerates drug discovery and development, as the drugs' general pharmacological, pharmacokinetic, and toxicological properties are already well known. In the present study, for the first time, a high-throughput compound library screening was performed under experimental conditions relevant to CF-infected lungs. Among 3,386 drugs screened, the clinically used drugs from outside infection treatment ebselen, tirapazamine, carmofur, 5-fluorouracil, and tavaborole showed, although to different extents, anti-P. aeruginosa activity against planktonic and biofilm cells and broad-spectrum activity against other CF pathogens at concentrations not toxic to bronchial epithelial cells. The mode-of-action studies revealed ebselen, carmofur, and tirapazamine targeted the cell membrane, increasing its permeability with subsequent cell lysis. These drugs are strong candidates for repurposing for treating CF lung P. aeruginosa infections.
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Affiliation(s)
- Giovanni Di Bonaventura
- Department of Medical, Oral, and Biotechnological Sciences, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
- Center for Advanced Studies and Technology, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
| | - Veronica Lupetti
- Department of Medical, Oral, and Biotechnological Sciences, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
- Center for Advanced Studies and Technology, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
| | | | | | - Alessandra Piccirilli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L’Aquila, Italy
| | - Lisa Cariani
- Microbiology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Arianna Pompilio
- Department of Medical, Oral, and Biotechnological Sciences, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
- Center for Advanced Studies and Technology, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
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Ayon NJ. High-Throughput Screening of Natural Product and Synthetic Molecule Libraries for Antibacterial Drug Discovery. Metabolites 2023; 13:625. [PMID: 37233666 PMCID: PMC10220967 DOI: 10.3390/metabo13050625] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Due to the continued emergence of resistance and a lack of new and promising antibiotics, bacterial infection has become a major public threat. High-throughput screening (HTS) allows rapid screening of a large collection of molecules for bioactivity testing and holds promise in antibacterial drug discovery. More than 50% of the antibiotics that are currently available on the market are derived from natural products. However, with the easily discoverable antibiotics being found, finding new antibiotics from natural sources has seen limited success. Finding new natural sources for antibacterial activity testing has also proven to be challenging. In addition to exploring new sources of natural products and synthetic biology, omics technology helped to study the biosynthetic machinery of existing natural sources enabling the construction of unnatural synthesizers of bioactive molecules and the identification of molecular targets of antibacterial agents. On the other hand, newer and smarter strategies have been continuously pursued to screen synthetic molecule libraries for new antibiotics and new druggable targets. Biomimetic conditions are explored to mimic the real infection model to better study the ligand-target interaction to enable the designing of more effective antibacterial drugs. This narrative review describes various traditional and contemporaneous approaches of high-throughput screening of natural products and synthetic molecule libraries for antibacterial drug discovery. It further discusses critical factors for HTS assay design, makes a general recommendation, and discusses possible alternatives to traditional HTS of natural products and synthetic molecule libraries for antibacterial drug discovery.
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Affiliation(s)
- Navid J Ayon
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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Rich MH, Sharrock AV, Mulligan TS, Matthews F, Brown AS, Lee-Harwood HR, Williams EM, Copp JN, Little RF, Francis JJB, Horvat CN, Stevenson LJ, Owen JG, Saxena MT, Mumm JS, Ackerley DF. A metagenomic library cloning strategy that promotes high-level expression of captured genes to enable efficient functional screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534183. [PMID: 36993673 PMCID: PMC10055417 DOI: 10.1101/2023.03.24.534183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Functional screening of environmental DNA (eDNA) libraries is a potentially powerful approach to discover enzymatic "unknown unknowns", but is usually heavily biased toward the tiny subset of genes preferentially transcribed and translated by the screening strain. We have overcome this by preparing an eDNA library via partial digest with restriction enzyme FatI (cuts CATG), causing a substantial proportion of ATG start codons to be precisely aligned with strong plasmid-encoded promoter and ribosome-binding sequences. Whereas we were unable to select nitroreductases from standard metagenome libraries, our FatI strategy yielded 21 nitroreductases spanning eight different enzyme families, each conferring resistance to the nitro-antibiotic niclosamide and sensitivity to the nitro-prodrug metronidazole. We showed expression could be improved by co-expressing rare tRNAs and encoded proteins purified directly using an embedded His6-tag. In a transgenic zebrafish model of metronidazole-mediated targeted cell ablation, our lead MhqN-family nitroreductase proved ~5-fold more effective than the canonical nitroreductase NfsB.
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Affiliation(s)
- Michelle H Rich
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Abigail V Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Timothy S Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Frazer Matthews
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Alistair S Brown
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Hannah R Lee-Harwood
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Elsie M Williams
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Current address: Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Janine N Copp
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Current addresses: Michael Smith Laboratories, University of British Columbia, Vancouver BC V6T 1Z4, Canada; Abcellera Biologics Inc, Vancouver BC V5Y 0A1, Canada
| | - Rory F Little
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Current address: Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Jenni JB Francis
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Claire N Horvat
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Current address: Teva Pharmaceuticals, Sydney, New South Wales 2113, Australia
| | - Luke J Stevenson
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jeremy G Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Meera T Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jeff S Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
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Sionov RV, Steinberg D. Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria. Microorganisms 2022; 10:1239. [PMID: 35744757 PMCID: PMC9228545 DOI: 10.3390/microorganisms10061239] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.
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Affiliation(s)
- Ronit Vogt Sionov
- The Biofilm Research Laboratory, The Institute of Biomedical and Oral Research, The Faculty of Dental Medicine, Hadassah Medical School, The Hebrew University, Jerusalem 9112102, Israel;
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