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Zhu S, Alexander MK, Paiva TO, Rachwalski K, Miu A, Xu Y, Verma V, Reichelt M, Dufrêne YF, Brown ED, Cox G. The inactivation of tolC sensitizes Escherichia coli to perturbations in lipopolysaccharide transport. iScience 2024; 27:109592. [PMID: 38628966 PMCID: PMC11019271 DOI: 10.1016/j.isci.2024.109592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/02/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
The Escherichia coli outer membrane channel TolC complexes with several inner membrane efflux pumps to export compounds across the cell envelope. All components of these complexes are essential for robust efflux activity, yet E. coli is more sensitive to antimicrobial compounds when tolC is inactivated compared to the inactivation of genes encoding the inner membrane drug efflux pumps. While investigating these susceptibility differences, we identified a distinct class of inhibitors targeting the core-lipopolysaccharide translocase, MsbA. We show that tolC null mutants are sensitized to structurally unrelated MsbA inhibitors and msbA knockdown, highlighting a synthetic-sick interaction. Phenotypic profiling revealed that tolC inactivation induced cell envelope softening and increased outer membrane permeability. Overall, this work identified a chemical probe of MsbA, revealed that tolC is associated with cell envelope mechanics and integrity, and highlighted that these findings should be considered when using tolC null mutants to study efflux deficiency.
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Affiliation(s)
- Shawna Zhu
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada
| | | | - Telmo O. Paiva
- Institute of Life Sciences, UCLouvain, Croix du Sud, 4-5, bte L7.07.06, B-1348 Louvain-la-Neuve, Belgium
| | - Kenneth Rachwalski
- Biochemistry and Biomedical Sciences and Degroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Anh Miu
- Genentech Inc, Biochemical and Cellular Pharmacology, South San Francisco, CA, USA
| | - Yiming Xu
- Genentech Inc, Infectious Diseases, South San Francisco, CA, USA
| | - Vishal Verma
- Genentech Inc, Discovery Chemistry, South San Francisco, CA, USA
| | - Mike Reichelt
- Genentech Inc, Pathology, South San Francisco, CA, USA
| | - Yves F. Dufrêne
- Institute of Life Sciences, UCLouvain, Croix du Sud, 4-5, bte L7.07.06, B-1348 Louvain-la-Neuve, Belgium
| | - Eric D. Brown
- Biochemistry and Biomedical Sciences and Degroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Georgina Cox
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Li FKK, Worrall LJ, Gale RT, Brown ED, Strynadka NCJ. Cryo-EM analysis of S. aureus TarL, a polymerase in wall teichoic acid biogenesis central to virulence and antibiotic resistance. Sci Adv 2024; 10:eadj3864. [PMID: 38416829 PMCID: PMC10901376 DOI: 10.1126/sciadv.adj3864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/23/2024] [Indexed: 03/01/2024]
Abstract
Wall teichoic acid (WTA), a covalent adduct of Gram-positive bacterial cell wall peptidoglycan, contributes directly to virulence and antibiotic resistance in pathogenic species. Polymerization of the Staphylococcus aureus WTA ribitol-phosphate chain is catalyzed by TarL, a member of the largely uncharacterized TagF-like family of membrane-associated enzymes. We report the cryo-electron microscopy structure of TarL, showing a tetramer that forms an extensive membrane-binding platform of monotopic helices. TarL is composed of an amino-terminal immunoglobulin-like domain and a carboxyl-terminal glycosyltransferase-B domain for ribitol-phosphate polymerization. The active site of the latter is complexed to donor substrate cytidine diphosphate-ribitol, providing mechanistic insights into the catalyzed phosphotransfer reaction. Furthermore, the active site is surrounded by electropositive residues that serve to retain the lipid-linked acceptor for polymerization. Our data advance general insight into the architecture and membrane association of the still poorly characterized monotopic membrane protein class and present molecular details of ribitol-phosphate polymerization that may aid in the design of new antimicrobials.
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Affiliation(s)
- Franco K K Li
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam J Worrall
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert T Gale
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
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4
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Rachwalski K, Tu MM, Madden SJ, French S, Hansen DM, Brown ED. A mobile CRISPRi collection enables genetic interaction studies for the essential genes of Escherichia coli. Cell Rep Methods 2024; 4:100693. [PMID: 38262349 PMCID: PMC10832289 DOI: 10.1016/j.crmeth.2023.100693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/27/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024]
Abstract
Advances in gene editing, in particular CRISPR interference (CRISPRi), have enabled depletion of essential cellular machinery to study the downstream effects on bacterial physiology. Here, we describe the construction of an ordered E. coli CRISPRi collection, designed to knock down the expression of 356 essential genes with the induction of a catalytically inactive Cas9, harbored on the conjugative plasmid pFD152. This mobile CRISPRi library can be conjugated into other ordered genetic libraries to assess combined effects of essential gene knockdowns with non-essential gene deletions. As proof of concept, we probed cell envelope synthesis with two complementary crosses: (1) an Lpp deletion into every CRISPRi knockdown strain and (2) the lolA knockdown plasmid into the Keio collection. These experiments revealed a number of notable genetic interactions for the essential phenotype probed and, in particular, showed suppressing interactions for the loci in question.
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Affiliation(s)
- Kenneth Rachwalski
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Megan M Tu
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Sean J Madden
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Shawn French
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Drew M Hansen
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Eric D Brown
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.
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5
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Smith KW, Alcock BP, French S, Farha MA, Raphenya AR, Brown ED, McArthur AG. A standardized nomenclature for resistance-modifying agents in the Comprehensive Antibiotic Resistance Database. Microbiol Spectr 2023; 11:e0274423. [PMID: 37971258 PMCID: PMC10714863 DOI: 10.1128/spectrum.02744-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE While increasing rates of antimicrobial resistance undermine our current arsenal of antibiotics, resistance-modifying agents (RMAs) hold promise to extend the lifetime of these important molecules. We here provide a standardized nomenclature for RMAs within the Comprehensive Antibiotic Resistance Database in aid of RMA discovery, data curation, and genome mining.
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Affiliation(s)
- Keaton W. Smith
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Brian P. Alcock
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Shawn French
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Maya A. Farha
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Amogelang R. Raphenya
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Eric D. Brown
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Andrew G. McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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6
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Yaeger LN, French S, Brown ED, Côté JP, Burrows LL. Central metabolism is a key player in E. coli biofilm stimulation by sub-MIC antibiotics. PLoS Genet 2023; 19:e1011013. [PMID: 37917668 PMCID: PMC10645362 DOI: 10.1371/journal.pgen.1011013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/14/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
Exposure of Escherichia coli to sub-inhibitory antibiotics stimulates biofilm formation through poorly characterized mechanisms. Using a high-throughput Congo Red binding assay to report on biofilm matrix production, we screened ~4000 E. coli K12 deletion mutants for deficiencies in this biofilm stimulation response. We screened using three different antibiotics to identify core components of the biofilm stimulation response. Mutants lacking acnA, nuoE, or lpdA failed to respond to sub-MIC cefixime and novobiocin, implicating central metabolism and aerobic respiration in biofilm stimulation. These genes are members of the ArcA/B regulon-controlled by a respiration-sensitive two-component system. Mutants of arcA and arcB had a 'pre-activated' phenotype, where biofilm formation was already high relative to wild type in vehicle control conditions, and failed to increase further with the addition of sub-MIC cefixime. Using a tetrazolium dye and an in vivo NADH sensor, we showed spatial co-localization of increased metabolic activity with sub-lethal concentrations of the bactericidal antibiotics cefixime and novobiocin. Supporting a role for respiratory stress, the biofilm stimulation response to cefixime and novobiocin was inhibited when nitrate was provided as an alternative electron acceptor. Deletion of a gene encoding part of the machinery for respiring nitrate abolished its ameliorating effects, and nitrate respiration increased during growth with sub-MIC cefixime. Finally, in probing the generalizability of biofilm stimulation, we found that the stimulation response to translation inhibitors, unlike other antibiotic classes, was minimally affected by nitrate supplementation, suggesting that targeting the ribosome stimulates biofilm formation in distinct ways. By characterizing the biofilm stimulation response to sub-MIC antibiotics at a systems level, we identified multiple avenues for design of therapeutics that impair bacterial stress management.
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Affiliation(s)
- Luke N. Yaeger
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Shawn French
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Eric D. Brown
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jean Philippe Côté
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Lori L. Burrows
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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7
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Tsai CN, Massicotte MA, MacNair CR, Perry JN, Brown ED, Coombes BK. Screening under infection-relevant conditions reveals chemical sensitivity in multidrug resistant invasive non-typhoidal Salmonella (iNTS). RSC Chem Biol 2023; 4:600-612. [PMID: 37547457 PMCID: PMC10398353 DOI: 10.1039/d3cb00014a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/30/2023] [Indexed: 08/08/2023] Open
Abstract
Bloodstream infections caused by invasive, non-typhoidal Salmonella (iNTS) are a major global health concern, particularly in Africa where the pathogenic variant of Salmonella Typhimurium sequence type (ST) 313 is dominant. Unlike S. Typhimurium strains that cause gastroenteritis, iNTS strains cause bloodstream infections and are resistant to multiple first-line antibiotics, thus limiting current treatment options. Here, we developed and implemented multiple small molecule screens under physiological, infection-relevant conditions to reveal chemical sensitivities in ST313 and to identify host-directed therapeutics as entry points to drug discovery to combat the clinical burden of iNTS. Screening ST313 iNTS under host-mimicking growth conditions identified 92 compounds with antimicrobial activity despite inherent multidrug resistance. We characterized the antimicrobial activity of the nucleoside analog 3'-azido-3'-deoxythymidine as an exemplary compound from this screen, which depended on bacterial thymidine kinase activity for antimicrobial activity. In a companion macrophage-based screening platform designed to enrich for host-directed therapeutics, we identified three compounds (amodiaquine, berbamine, and indatraline) as actives that required the presence of host cells for antibacterial activity. These three compounds had antimicrobial activity only in the presence of host cells that significantly inhibited intracellular ST313 iNTS replication in macrophages. This work provides evidence that despite high invasiveness and multidrug resistance, ST313 iNTS remains susceptible to unconventional drug discovery approaches.
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Affiliation(s)
- Caressa N Tsai
- Department of Biochemistry & Biomedical Sciences, McMaster University Hamilton ON L8S 4L8 Canada
- Michael G. DeGroote Institute for Infectious Disease Research Hamilton ON Canada
| | - Marie-Ange Massicotte
- Department of Biochemistry & Biomedical Sciences, McMaster University Hamilton ON L8S 4L8 Canada
- Michael G. DeGroote Institute for Infectious Disease Research Hamilton ON Canada
| | - Craig R MacNair
- Department of Biochemistry & Biomedical Sciences, McMaster University Hamilton ON L8S 4L8 Canada
- Michael G. DeGroote Institute for Infectious Disease Research Hamilton ON Canada
| | - Jordyn N Perry
- Department of Biochemistry & Biomedical Sciences, McMaster University Hamilton ON L8S 4L8 Canada
| | - Eric D Brown
- Department of Biochemistry & Biomedical Sciences, McMaster University Hamilton ON L8S 4L8 Canada
- Michael G. DeGroote Institute for Infectious Disease Research Hamilton ON Canada
| | - Brian K Coombes
- Department of Biochemistry & Biomedical Sciences, McMaster University Hamilton ON L8S 4L8 Canada
- Michael G. DeGroote Institute for Infectious Disease Research Hamilton ON Canada
- Farncombe Family Digestive Health Research Institute Hamilton ON Canada
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LeWinn KZ, Trasande L, Law A, Blackwell CK, Bekelman TA, Arizaga JA, Sullivan AA, Bastain TM, Breton CV, Karagas MR, Elliott AJ, Karr CJ, Carroll KN, Dunlop AL, Croen LA, Margolis AE, Alshawabkeh AN, Cordero JF, Singh AM, Seroogy CM, Jackson DJ, Wood RA, Hartert TV, Kim YS, Duarte CS, Schweitzer JB, Lester BM, McEvoy CT, O’Connor TG, Oken E, Bornkamp N, Brown ED, Porucznik CA, Ferrara A, Camargo CA, Zhao Q, Ganiban JM, Jacobson LP. Sociodemographic Differences in COVID-19 Pandemic Experiences Among Families in the United States. JAMA Netw Open 2023; 6:e2330495. [PMID: 37610749 PMCID: PMC10448300 DOI: 10.1001/jamanetworkopen.2023.30495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/17/2023] [Indexed: 08/24/2023] Open
Abstract
Importance Few population-based studies in the US collected individual-level data from families during the COVID-19 pandemic. Objective To examine differences in COVID-19 pandemic-related experiences in a large sociodemographically diverse sample of children and caregivers. Design, Setting, and Participants The Environmental influences on Child Health Outcomes (ECHO) multi-cohort consortium is an ongoing study that brings together 64 individual cohorts with participants (24 757 children and 31 700 caregivers in this study) in all 50 US states and Puerto Rico. Participants who completed the ECHO COVID-19 survey between April 2020 and March 2022 were included in this cross-sectional analysis. Data were analyzed from July 2021 to September 2022. Main Outcomes and Measures Exposures of interest were caregiver education level, child life stage (infant, preschool, middle childhood, and adolescent), and urban or rural (population <50 000) residence. Dependent variables included COVID-19 infection status and testing; disruptions to school, child care, and health care; financial hardships; and remote work. Outcomes were examined separately in logistic regression models mutually adjusted for exposures of interest and race, ethnicity, US Census division, sex, and survey administration date. Results Analyses included 14 646 children (mean [SD] age, 7.1 [4.4] years; 7120 [49%] female) and 13 644 caregivers (mean [SD] age, 37.6 [7.2] years; 13 381 [98%] female). Caregivers were racially (3% Asian; 16% Black; 12% multiple race; 63% White) and ethnically (19% Hispanic) diverse and comparable with the US population. Less than high school education (vs master's degree or more) was associated with more challenges accessing COVID-19 tests (adjusted odds ratio [aOR], 1.88; 95% CI, 1.06-1.58), lower odds of working remotely (aOR, 0.04; 95% CI, 0.03-0.07), and more food access concerns (aOR, 4.14; 95% CI, 3.20-5.36). Compared with other age groups, young children (age 1 to 5 years) were least likely to receive support from schools during school closures, and their caregivers were most likely to have challenges arranging childcare and concerns about work impacts. Rural caregivers were less likely to rank health concerns (aOR, 0.77; 95% CI, 0.69-0.86) and social distancing (aOR, 0.82; 95% CI, 0.73-0.91) as top stressors compared with urban caregivers. Conclusions Findings in this cohort study of US families highlighted pandemic-related burdens faced by families with lower socioeconomic status and young children. Populations more vulnerable to public health crises should be prioritized in recovery efforts and future planning.
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Affiliation(s)
- Kaja Z. LeWinn
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco
| | - Leonardo Trasande
- Department of Pediatrics, New York University Grossman School of Medicine, New York
- Department of Population Health, New York University Grossman School of Medicine, New York
| | - Andrew Law
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Traci A. Bekelman
- Department of Epidemiology, Lifecourse Epidemiology of Adiposity & Diabetes Center, University of Colorado Anschutz Medical Campus, Aurora
| | - Jessica A. Arizaga
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco
| | - Alexis A. Sullivan
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco
| | - Theresa M. Bastain
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
| | - Carrie V. Breton
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
| | - Margaret R. Karagas
- Department of Epidemiology, Dartmouth Geisel School of Medicine, Lebanon, New Hampshire
| | | | | | - Kecia N. Carroll
- Jack and Lucy Clark Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Anne L. Dunlop
- Department of Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, Georgia
| | | | - Amy E. Margolis
- Columbia University Irving Medical Center, New York State Psychiatric Institute, New York
| | | | - Jose F. Cordero
- Department of Epidemiology & Biostatistics, College of Public Health, University of Georgia, Athens
| | - Anne Marie Singh
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison
| | - Christine M. Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison
| | - Daniel J. Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison
| | - Robert A. Wood
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Tina V. Hartert
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Young Shin Kim
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco
| | - Cristiane S. Duarte
- Columbia University Irving Medical Center, New York State Psychiatric Institute, New York
| | - Julie B. Schweitzer
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento
- The MIND Institute, University of California, Davis, Sacramento
| | - Barry M. Lester
- Brown Center for the Study of Children at Risk, Brown Alpert Medical School and Women & Infants Hospital, Providence, Rhode Island
| | - Cynthia T. McEvoy
- Department of Pediatrics, Oregon Health and Science University School of Medicine, Portland
| | - Thomas G. O’Connor
- Department of Psychiatry, University of Rochester Medical Center, Rochester, New York
| | - Emily Oken
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - Nicole Bornkamp
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - Eric D. Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill
| | - Christina A. Porucznik
- Department of Family & Preventive Medicine, University of Utah School of Medicine, Salt Lake City
| | | | | | - Qi Zhao
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis
| | - Jody M. Ganiban
- Department of Psychological & Brain Sciences, Columbian College of Arts & Sciences, George Washington University, Washington, DC
| | - Lisa P. Jacobson
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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9
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Carfrae LA, Rachwalski K, French S, Gordzevich R, Seidel L, Tsai CN, Tu MM, MacNair CR, Ovchinnikova OG, Clarke BR, Whitfield C, Brown ED. Inhibiting fatty acid synthesis overcomes colistin resistance. Nat Microbiol 2023:10.1038/s41564-023-01369-z. [PMID: 37127701 DOI: 10.1038/s41564-023-01369-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Treating multidrug-resistant infections has increasingly relied on last-resort antibiotics, including polymyxins, for example colistin. As polymyxins are given routinely, the prevalence of their resistance is on the rise and increases mortality rates of sepsis patients. The global dissemination of plasmid-borne colistin resistance, driven by the emergence of mcr-1, threatens to diminish the therapeutic utility of polymyxins from an already shrinking antibiotic arsenal. Restoring sensitivity to polymyxins using combination therapy with sensitizing drugs is a promising approach to reviving its clinical utility. Here we describe the ability of the biotin biosynthesis inhibitor, MAC13772, to synergize with colistin exclusively against colistin-resistant bacteria. MAC13772 indirectly disrupts fatty acid synthesis (FAS) and restores sensitivity to the last-resort antibiotic, colistin. Accordingly, we found that combinations of colistin and other FAS inhibitors, cerulenin, triclosan and Debio1452-NH3, had broad potential against both chromosomal and plasmid-mediated colistin resistance in chequerboard and lysis assays. Furthermore, combination therapy with colistin and the clinically relevant FabI inhibitor, Debio1452-NH3, showed efficacy against mcr-1 positive Klebsiella pneumoniae and colistin-resistant Escherichia coli systemic infections in mice. Using chemical genomics, lipidomics and transcriptomics, we explored the mechanism of the interaction. We propose that inhibiting FAS restores colistin sensitivity by depleting lipid synthesis, leading to changes in phospholipid composition. In all, this work reveals a surprising link between FAS and colistin resistance.
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Affiliation(s)
- Lindsey A Carfrae
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Kenneth Rachwalski
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Shawn French
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Rodion Gordzevich
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Laura Seidel
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Caressa N Tsai
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Megan M Tu
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Craig R MacNair
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Olga G Ovchinnikova
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Bradley R Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Eric D Brown
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
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10
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Tong M, Brown ED. Food for thought: Opportunities to target carbon metabolism in antibacterial drug discovery. Ann N Y Acad Sci 2023. [PMID: 37005709 DOI: 10.1111/nyas.14991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Antimicrobial resistance is at an all-time high and new drugs are required to overcome this crisis. Traditional approaches to drug discovery have failed to produce novel classes of antibiotics, with only a few currently in development. It is thought that novel classes will come from antibacterial drug discovery efforts that focus on unconventional targets. One such collection of antibacterial targets are those that comprise central carbon metabolism. Targets of this kind have been largely overlooked because conventional antibacterial testing media are ill-suited for exploring carbon source utilization. Nevertheless, as a consequence of infection, bacteria must find a carbon source in order to survive. Here, we review what is known about the carbon sources available and used by bacteria in different host infection sites. We also look at discovery efforts targeting central carbon metabolism and evaluate how these processes can influence antibiotic efficacy.
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Affiliation(s)
- Madeline Tong
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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11
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Abu Jarad N, Rachwalski K, Bayat F, Khan S, Shakeri A, MacLachlan R, Villegas M, Brown ED, Hosseinidoust Z, Didar TF, Soleymani L. A Bifunctional Spray Coating Reduces Contamination on Surfaces by Repelling and Killing Pathogens. ACS Appl Mater Interfaces 2023; 15:16253-16265. [PMID: 36926806 DOI: 10.1021/acsami.2c23119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Surface-mediated transmission of pathogens is a major concern with regard to the spread of infectious diseases. Current pathogen prevention methods on surfaces rely on the use of biocides, which aggravate the emergence of antimicrobial resistance and pose harmful health effects. In response, a bifunctional and substrate-independent spray coating is presented herein. The bifunctional coating relies on wrinkled polydimethylsiloxane microparticles, decorated with biocidal gold nanoparticles to induce a "repel and kill" effect against pathogens. Pathogen repellency is provided by the structural hierarchy of the microparticles and their surface chemistry, whereas the kill mechanism is achieved using functionalized gold nanoparticles embedded on the microparticles. Bacterial tests with methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa reveal a 99.9% reduction in bacterial load on spray-coated surfaces, while antiviral tests with Phi6─a bacterial virus often used as a surrogate to SARS-CoV-2─demonstrate a 98% reduction in virus load on coated surfaces. The newly developed spray coating is versatile, easily applicable to various surfaces, and effective against various pathogens, making it suitable for reducing surface contamination in frequently touched, heavy traffic, and high-risk surfaces.
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Affiliation(s)
- Noor Abu Jarad
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton L8S 4K1, ON, Canada
| | - Kenneth Rachwalski
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton L8S 4L7, ON, Canada
| | - Fereshteh Bayat
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton L8S 4L7, ON, Canada
| | - Shadman Khan
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton L8S 4L7, ON, Canada
| | - Amid Shakeri
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton L8S 4L7, ON, Canada
| | - Roderick MacLachlan
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton L8S 4L7, ON, Canada
| | - Martin Villegas
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton L8S 4L7, ON, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton L8S 4L7, ON, Canada
| | - Zeinab Hosseinidoust
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton L8S 4L7, ON, Canada
| | - Tohid F Didar
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton L8S 4K1, ON, Canada
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton L8S 4L7, ON, Canada
- School of Biomedical Engineering, Department of Mechanical Engineering, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton L8S 4L7, Canada
| | - Leyla Soleymani
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton L8S 4K1, ON, Canada
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton L8S 4L7, ON, Canada
- School of Biomedical Engineering and Department of Engineering Physics, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton L8S 4L7, Canada
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12
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Abu Jarad N, Rachwalski K, Bayat F, Khan S, Shakeri A, MacLachlan R, Villegas M, Brown ED, Soleymani L, Didar TF. An Omniphobic Spray Coating Created from Hierarchical Structures Prevents the Contamination of High-Touch Surfaces with Pathogens. Small 2023; 19:e2205761. [PMID: 36587985 DOI: 10.1002/smll.202205761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Engineered surfaces that repel pathogens are of great interest due to their role in mitigating the spread of infectious diseases. A robust, universal, and scalable omniphobic spray coating with excellent repellency against water, oil, and pathogens is presented. The coating is substrate-independent and relies on hierarchically structured polydimethylsiloxane (PDMS) microparticles, decorated with gold nanoparticles (AuNPs). Wettability studies reveal the relationship between surface texturing of micro- and/or nano-hierarchical structures and the omniphobicity of the coating. Studies of pathogen transfer with bacteria and viruses reveal that an uncoated contaminated glove transfers pathogens to >50 subsequent surfaces, while a coated glove picks up 104 (over 99.99%) less pathogens upon first contact and transfers zero pathogens after the second touch. The developed coating also provides excellent stability under harsh conditions. The remarkable anti-pathogen properties of this surface combined with its ease of implementation, substantiate its use for the prevention of surface-mediated transmission of pathogens.
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Affiliation(s)
- Noor Abu Jarad
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Kenneth Rachwalski
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada
| | - Fereshteh Bayat
- Department of Mechanical Engineering, McMaster University, Hamilton, ON, L8S 4L7, Canada
| | - Shadman Khan
- Department of Mechanical Engineering, McMaster University, Hamilton, ON, L8S 4L7, Canada
| | - Amid Shakeri
- Department of Mechanical Engineering, McMaster University, Hamilton, ON, L8S 4L7, Canada
| | - Roderick MacLachlan
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L7, Canada
| | - Martin Villegas
- Department of Mechanical Engineering, McMaster University, Hamilton, ON, L8S 4L7, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada
| | - Leyla Soleymani
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L7, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Tohid F Didar
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
- Department of Mechanical Engineering, McMaster University, Hamilton, ON, L8S 4L7, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
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13
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Abstract
Novel approaches are required to address the looming threat of pan-resistant Gram-negative pathogens and forestall the rise of untreatable infections. Unconventional targets that are uniquely important during infection and tractable to high-throughput drug discovery methods hold high potential for innovation in antibiotic discovery programs. In this context, inhibitors of bacterial nutrient stress are particularly exciting candidates for future antibiotic development. Amino acid, nucleotide, and vitamin biosynthesis pathways are critical for bacterial growth in nutrient-limiting conditions in the laboratory and the host. Although historically dismissed as dispensable for pathogens, a wealth of transposon mutagenesis and single-mutant studies have emerged which demonstrate that several such pathways are critical for infection. Indeed, high-throughput screens of diverse synthetic compounds and natural products have uncovered inhibitors of nutrient biosynthesis. Herein, we review bacterial nutrient biosynthesis and its role during host infection. Further, we explore screening platforms developed to search for inhibitors of these targets and highlight successes among these. Finally, we feature important and sometimes surprising connections between bacterial nutrient biosynthesis, antibiotic activity, and antibiotic resistance.
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Affiliation(s)
- Lindsey A Carfrae
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Eric D Brown
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada; Present address: Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada.
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14
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Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya A, Wlodarski MA, Edalatmand A, Petkau A, Syed SA, Tsang KK, Baker SJC, Dave M, McCarthy M, Mukiri KM, Nasir JA, Golbon B, Imtiaz H, Jiang X, Kaur K, Kwong M, Liang ZC, Niu KC, Shan P, Yang JYJ, Gray K, Hoad GR, Jia B, Bhando T, Carfrae L, Farha M, French S, Gordzevich R, Rachwalski K, Tu M, Bordeleau E, Dooley D, Griffiths E, Zubyk HL, Brown ED, Maguire F, Beiko R, Hsiao WWL, Brinkman FSL, Van Domselaar G, McArthur AG. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res 2022; 51:D690-D699. [PMID: 36263822 PMCID: PMC9825576 DOI: 10.1093/nar/gkac920] [Citation(s) in RCA: 187] [Impact Index Per Article: 93.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 01/30/2023] Open
Abstract
The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes. As of version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, and 5057 AMR detection models that can be used by the accompanying Resistance Gene Identifier (RGI) software to annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded β-lactamase curation, incorporation of likelihood-based AMR mutations for Mycobacterium tuberculosis, addition of disinfectants and antiseptics plus their associated ARGs, and systematic curation of resistance-modifying agents. This expanded curation includes 180 new AMR gene families, 15 new drug classes, 1 new resistance mechanism, and two new ontological relationships: evolutionary_variant_of and is_small_molecule_inhibitor. In silico prediction of resistomes and prevalence statistics of ARGs has been expanded to 377 pathogens, 21,079 chromosomes, 2,662 genomic islands, 41,828 plasmids and 155,606 whole-genome shotgun assemblies, resulting in collation of 322,710 unique ARG allele sequences. New features include the CARD:Live collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.
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Affiliation(s)
- Brian P Alcock
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - William Huynh
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Romeo Chalil
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Keaton W Smith
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Amogelang R Raphenya
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Mateusz A Wlodarski
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Arman Edalatmand
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Aaron Petkau
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Sohaib A Syed
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kara K Tsang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Sheridan J C Baker
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Mugdha Dave
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Madeline C McCarthy
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Karyn M Mukiri
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Jalees A Nasir
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Bahar Golbon
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Hamna Imtiaz
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Xingjian Jiang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Komal Kaur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Megan Kwong
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Zi Cheng Liang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Keyu C Niu
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Prabakar Shan
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Jasmine Y J Yang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kristen L Gray
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gemma R Hoad
- Research Computing Group, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Baofeng Jia
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Timsy Bhando
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Lindsey A Carfrae
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Maya A Farha
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Shawn French
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Rodion Gordzevich
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kenneth Rachwalski
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Megan M Tu
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Emily Bordeleau
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Damion Dooley
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Emma Griffiths
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Haley L Zubyk
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada,Department of Community Health & Epidemiology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - William W L Hsiao
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada,Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada,Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew G McArthur
- To whom correspondence should be addressed. Tel: +1 905 525 9140 (Ext 21663);
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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MacNair CR, Farha MA, Serrano-Wu MH, Lee KK, Hubbard B, Côté JP, Carfrae LA, Tu MM, Gaulin JL, Hunt DK, Hung DT, Brown ED. Preclinical Development of Pentamidine Analogs Identifies a Potent and Nontoxic Antibiotic Adjuvant. ACS Infect Dis 2022; 8:768-777. [PMID: 35319198 DOI: 10.1021/acsinfecdis.1c00482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The difficulty in treating Gram-negative bacteria can largely be attributed to their highly impermeable outer membrane (OM), which serves as a barrier to many otherwise active antibiotics. This can be overcome with the use of perturbant molecules, which disrupt OM integrity and sensitize Gram-negative bacteria to many clinically available Gram-positive-active antibiotics. Although many new perturbants have been identified in recent years, most of these molecules are impeded by toxicity due to the similarities between pathogen and host cell membranes. For example, our group recently reported the cryptic OM-perturbing activity of the antiprotozoal drug pentamidine. Its development as an antibiotic adjuvant is limited, however, by toxicity concerns. Herein, we took a medicinal chemistry approach to develop novel analogs of pentamidine, aiming to improve its OM activity while reducing its off-target toxicity. We identified the compound P35, which induces OM disruption and potentiates Gram-positive-active antibiotics in Acinetobacter baumannii and Klebsiella pneumoniae. Relative to pentamidine, P35 has reduced mammalian cell cytotoxicity and hERG trafficking inhibition. Additionally, P35 outperforms pentamidine in a murine model of A. baumannii bacteremia. Together, this preclinical analysis supports P35 as a promising lead for further development as an OM perturbant.
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Affiliation(s)
- Craig R. MacNair
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Maya A. Farha
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Michael H. Serrano-Wu
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Katie K. Lee
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Brian Hubbard
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Jean-Philippe Côté
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Lindsey A. Carfrae
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Megan M. Tu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Jeffrey L. Gaulin
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Diana K. Hunt
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Deborah T. Hung
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Eric D. Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
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17
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Khan S, Jarad NA, Ladouceur L, Rachwalski K, Bot V, Shakeri A, Maclachlan R, Sakib S, Weitz JI, Brown ED, Soleymani L, Didar TF. Transparent and Highly Flexible Hierarchically Structured Polydimethylsiloxane Surfaces Suppress Bacterial Attachment and Thrombosis Under Static and Dynamic Conditions. Small 2022; 18:e2108112. [PMID: 35224860 DOI: 10.1002/smll.202108112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Indexed: 06/14/2023]
Abstract
The surface fouling of biomedical devices has been an ongoing issue in healthcare. Bacterial and blood adhesion in particular, severely impede the performance of such tools, leading to poor patient outcomes. Various structural and chemical modifications have been shown to reduce fouling, but all existing strategies lack the combination of physical, chemical, and economic traits necessary for widespread use. Herein, a lubricant infused, hierarchically micro- and nanostructured polydimethylsiloxane surface is presented. The surface is easy to produce and exhibits the high flexibility and optical transparency necessary for incorporation into various biomedical tools. Tests involving two clinically relevant, priority pathogens show up to a 98.5% reduction in the biofilm formation of methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa. With blood, the surface reduces staining by 95% and suppresses thrombin generation to background levels. Furthermore, the surface shows applicability within applications such as catheters, extracorporeal circuits, and microfluidic devices, through its effectiveness in dynamic conditions. The perfusion of bacterial media shows up to 96.5% reduction in bacterial adhesion. Similarly, a 95.8% reduction in fibrin networks is observed following whole blood perfusion. This substrate stands to hold high applicability within biomedical systems as a means to prevent fouling, thus improving performance.
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Affiliation(s)
- Shadman Khan
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L7, Canada
| | - Noor Abu Jarad
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L7, Canada
| | - Liane Ladouceur
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L7, Canada
| | - Kenneth Rachwalski
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada
| | - Veronica Bot
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L7, Canada
| | - Amid Shakeri
- Department of Mechanical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L7, Canada
| | - Roderick Maclachlan
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, ON, L8S4L7, Canada
| | - Sadman Sakib
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, ON, L8S4L7, Canada
| | - Jeffrey I Weitz
- Departments of Medicine and Biochemistry and Biomedical Sciences, McMaster University and the Thrombosis & Atherosclerosis Research Institute, 237 Barton Street East, Hamilton, ON, L8L 2X2, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada
| | - Leyla Soleymani
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L7, Canada
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, ON, L8S4L7, Canada
| | - Tohid F Didar
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L7, Canada
- Department of Mechanical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L7, Canada
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18
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Johnson J, Ellis MJ, Piquette ZA, MacNair C, Carfrae L, Bhando T, Ritchie NE, Saliba P, Brown ED, Magolan J. Antibacterial Activity of Metergoline Analogues: Revisiting the Ergot Alkaloid Scaffold for Antibiotic Discovery. ACS Med Chem Lett 2022; 13:284-291. [PMID: 35178184 PMCID: PMC8842143 DOI: 10.1021/acsmedchemlett.1c00648] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/19/2022] [Indexed: 12/22/2022] Open
Abstract
Metergoline is a semisynthetic ergot alkaloid identified recently as an inhibitor of the Gram-negative intracellular pathogen Salmonella Typhimurium (S. Tm). With the previously unknown antibacterial activity of metergoline, we explored structure-activity relationships (SARs) with a series of carbamate, urea, sulfonamide, amine, and amide analogues. Cinnamide and arylacrylamide derivatives show improved potency relative to metergoline against Gram-positive bacteria, and pyridine derivative 38 is also effective against methicillin-resistant Staphylococcus aureus (MRSA) in a murine skin infection model. Arylacrylamide analogues of metergoline show modest activity against wild-type (WT) Gram-negative bacteria but are more active against strains of efflux-deficient S. Tm and hyperpermeable Escherichia coli. The potencies against WT strains of E. coli, Acinetobacter baumannii, and Burkholderia cenocepacia are also improved considerably (up to >128-fold) with the outer-membrane permeabilizer SPR741, suggesting that the ergot scaffold represents a new lead for the development of new antibiotics.
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19
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Workman SD, Day J, Farha MA, El Zahed SS, Bon C, Brown ED, Organ MG, Strynadka NCJ. Structural Insights into the Inhibition of Undecaprenyl Pyrophosphate Synthase from Gram-Positive Bacteria. J Med Chem 2021; 64:13540-13550. [PMID: 34473495 DOI: 10.1021/acs.jmedchem.1c00941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The polyprenyl lipid undecaprenyl phosphate (C55P) is the universal carrier lipid for the biosynthesis of bacterial cell wall polymers. C55P is synthesized in its pyrophosphate form by undecaprenyl pyrophosphate synthase (UppS), an essential cis-prenyltransferase that is an attractive target for antibiotic development. We previously identified a compound (MAC-0547630) that showed promise as a novel class of inhibitor and an ability to potentiate β-lactam antibiotics. Here, we provide a structural model for MAC-0547630's inhibition of UppS and a structural rationale for its enhanced effect on UppS from Bacillus subtilis versus Staphylococcus aureus. We also describe the synthesis of a MAC-0547630 derivative (JPD447), show that it too can potentiate β-lactam antibiotics, and provide a structural rationale for its improved potentiation. Finally, we present an improved structural model of clomiphene's inhibition of UppS. Taken together, our data provide a foundation for structure-guided drug design of more potent UppS inhibitors in the future.
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Affiliation(s)
- Sean D Workman
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jonathan Day
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Maya A Farha
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Sara S El Zahed
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Chris Bon
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Michael G Organ
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.,Centre for Catalysis Research and Innovation, University of Ottawa, 30 Marie-Curie Private, Ottawa, Ontario K1N 6N5, Canada.,Department of Chemistry and Biomolecular Sciences, University of Ottawa, 150 Louis-Pasteur Private, Ottawa, Ontario K1N 6N5, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
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20
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Labana P, Dornan MH, Lafrenière M, Czarny TL, Brown ED, Pezacki JP, Boddy CN. Armeniaspirols inhibit the AAA+ proteases ClpXP and ClpYQ leading to cell division arrest in Gram-positive bacteria. Cell Chem Biol 2021; 28:1703-1715.e11. [PMID: 34293284 DOI: 10.1016/j.chembiol.2021.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/22/2021] [Accepted: 06/29/2021] [Indexed: 01/16/2023]
Abstract
Multi-drug-resistant bacteria present an urgent threat to modern medicine, creating a desperate need for antibiotics with new modes of action. As natural products remain an unsurpassed source for clinically viable antibiotic compounds, we investigate the mechanism of action of armeniaspirol. The armeniaspirols are a structurally unique class of Gram-positive antibiotic discovered from Streptomyces armeniacus for which resistance cannot be readily obtained. We show that armeniaspirol inhibits the ATP-dependent proteases ClpXP and ClpYQ in vitro and in the model Gram-positive Bacillus subtilis. This inhibition dysregulates the divisome and elongasome supported by an upregulation of key proteins FtsZ, DivIVA, and MreB inducing cell division arrest. The inhibition of ClpXP and ClpYQ to dysregulate cell division represents a unique antibiotic mechanism of action and armeniaspirol is the only known natural product inhibitor of the coveted anti-virulence target ClpP. Thus, armeniaspirol possesses a promising lead scaffold for antibiotic development with unique pharmacology.
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Affiliation(s)
- Puneet Labana
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Mark H Dornan
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Matthew Lafrenière
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Tomasz L Czarny
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - John P Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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21
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Bæk KT, Jensen C, Farha MA, Nielsen TK, Paknejadi E, Mebus VH, Vestergaard M, Brown ED, Frees D. A Staphylococcus aureus clpX Mutant Used as a Unique Screening Tool to Identify Cell Wall Synthesis Inhibitors that Reverse β-Lactam Resistance in MRSA. Front Mol Biosci 2021; 8:691569. [PMID: 34150853 PMCID: PMC8212132 DOI: 10.3389/fmolb.2021.691569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/14/2021] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus aureus is a leading cause of bacterial infections world-wide. Staphylococcal infections are preferentially treated with β-lactam antibiotics, however, methicillin-resistant S. aureus (MRSA) strains have acquired resistance to this superior class of antibiotics. We have developed a growth-based, high-throughput screening approach that directly identifies cell wall synthesis inhibitors capable of reversing β-lactam resistance in MRSA. The screen is based on the finding that S. aureus mutants lacking the ClpX chaperone grow very poorly at 30°C unless specific steps in teichoic acid synthesis or penicillin binding protein (PBP) activity are inhibited. This property allowed us to exploit the S. aureus clpX mutant as a unique screening tool to rapidly identify biologically active compounds that target cell wall synthesis. We tested a library of ∼50,000 small chemical compounds and searched for compounds that inhibited growth of the wild type while stimulating growth of the clpX mutant. Fifty-eight compounds met these screening criteria, and preliminary tests of 10 compounds identified seven compounds that reverse β-lactam resistance of MRSA as expected for inhibitors of teichoic acid synthesis. The hit compounds are therefore promising candidates for further development as novel combination agents to restore β-lactam efficacy against MRSA.
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Affiliation(s)
- Kristoffer T Bæk
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Jensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maya A Farha
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Tobias K Nielsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ervin Paknejadi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Viktor H Mebus
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Vestergaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Dorte Frees
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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22
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Klobucar K, Côté JP, French S, Borrillo L, Guo ABY, Serrano-Wu MH, Lee KK, Hubbard B, Johnson JW, Gaulin JL, Magolan J, Hung DT, Brown ED. Chemical Screen for Vancomycin Antagonism Uncovers Probes of the Gram-Negative Outer Membrane. ACS Chem Biol 2021; 16:929-942. [PMID: 33974796 DOI: 10.1021/acschembio.1c00179] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The outer membrane of Gram-negative bacteria is a formidable permeability barrier which allows only a small subset of chemical matter to penetrate. This outer membrane barrier can hinder the study of cellular processes and compound mechanism of action, as many compounds including antibiotics are precluded from entry despite having intracellular targets. Consequently, outer membrane permeabilizing compounds are invaluable tools in such studies. Many existing compounds known to perturb the outer membrane also impact inner membrane integrity, such as polymyxins and their derivatives, making these probes nonspecific. We performed a screen of ∼140 000 diverse synthetic compounds, for those that antagonized the growth inhibitory activity of vancomycin at 15 °C in Escherichia coli, to enrich for chemicals capable of perturbing the outer membrane. This led to the discovery that liproxstatin-1, an inhibitor of ferroptosis in human cells, and MAC-0568743, a novel cationic amphiphile, could potentiate the activity of large-scaffold antibiotics with low permeation into Gram-negative bacteria at 37 °C. Liproxstatin-1 and MAC-0568743 were found to physically disrupt the integrity of the outer membrane through interactions with lipopolysaccharide in the outer leaflet of the outer membrane. We showed that these compounds selectively disrupt the outer membrane while minimally impacting inner membrane integrity, particularly at the concentrations needed to potentiate Gram-positive-targeting antibiotics. Further exploration of these molecules and their structural analogues is a promising avenue for the development of outer membrane specific probes.
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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
| | - Jean-Philippe Côté
- 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
| | - Shawn French
- 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
| | - Amelia Bing Ya Guo
- 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
| | - Michael H. Serrano-Wu
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Katie K. Lee
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Brian Hubbard
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - 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
| | - Jeffrey L. Gaulin
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - 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
| | - Deborah T. Hung
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - 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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23
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Abstract
Drug-resistant bacterial infections pose an imminent and growing threat to public health. The discovery and development of new antibiotics of novel chemical class and mode of action that are unsusceptible to existing resistance mechanisms is imperative for tackling this threat. Modern industrial drug discovery, however, has failed to provide new drugs of this description, as it is dependent largely on a reductionist genes-to-drugs research paradigm. We posit that the lack of success in new antibiotic drug discovery is due in part to a lack of understanding of the bacterial cell system as whole. A fundamental understanding of the architecture and function of bacterial systems has been elusive but is of critical importance to design strategies to tackle drug-resistant bacterial pathogens.Increasingly, systems-level approaches are rewriting our understanding of the cell, defining a dense network of redundant and interacting components that resist perturbations of all kinds, including by antibiotics. Understanding the network properties of bacterial cells requires integrative, systematic, and genome-scale approaches. These methods strive to understand how the phenotypic behavior of bacteria emerges from the many interactions of individual molecular components that constitute the system. With the ability to examine genomic, transcriptomic, proteomic, and metabolomic consequences of, for example, genetic or chemical perturbations, researchers are increasingly moving away from one-gene-at-a-time studies to consider the system-wide response of the cell. Such measurements are demonstrating promise as quantitative tools, powerful discovery engines, and robust hypothesis generators with great value to antibiotic drug discovery.In this Account, we describe our thinking and findings using systems-level studies aimed at understanding bacterial physiology broadly and in uncovering new antibacterial chemical matter of novel mechanism. We share our systems-level toolkit and detail recent technological developments that have enabled unprecedented acquisition of genome-wide interaction data. We focus on three types of interactions: gene-gene, chemical-gene, and chemical-chemical. We provide examples of their use in understanding cell networks and how these insights might be harnessed for new antibiotic discovery. By example, we show the application of these principles in mapping genetic networks that underpin phenotypes of interest, characterizing genes of unknown function, validating small-molecule screening platforms, uncovering novel chemical probes and antibacterial leads, and delineating the mode of action of antibacterial chemicals. We also discuss the importance of computation to these approaches and its probable dominance as a tool for systems approaches in the future. In all, we advocate for the use of systems-based approaches as discovery engines in antibacterial research, both as powerful tools and to stimulate innovation.
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Affiliation(s)
- Maya A. Farha
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Shawn French
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of 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 of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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24
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Li FKK, Gale RT, Petrotchenko EV, Borchers CH, Brown ED, Strynadka NCJ. Crystallographic analysis of TarI and TarJ, a cytidylyltransferase and reductase pair for CDP-ribitol synthesis in Staphylococcus aureus wall teichoic acid biogenesis. J Struct Biol 2021; 213:107733. [PMID: 33819634 DOI: 10.1016/j.jsb.2021.107733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 11/18/2022]
Abstract
The cell wall of many pathogenic Gram-positive bacteria contains ribitol-phosphate wall teichoic acid (WTA), a polymer that is linked to virulence and regulation of essential physiological processes including cell division. CDP-ribitol, the activated precursor for ribitol-phosphate polymerization, is synthesized by a cytidylyltransferase and reductase pair known as TarI and TarJ, respectively. In this study, we present crystal structures of Staphylococcus aureus TarI and TarJ in their apo forms and in complex with substrates and products. The TarI structures illustrate the mechanism of CDP-ribitol synthesis from CTP and ribitol-phosphate and reveal structural changes required for substrate binding and catalysis. Insights into the upstream step of ribulose-phosphate reduction to ribitol-phosphate is provided by the structures of TarJ. Furthermore, we propose a general topology of the enzymes in a heterotetrameric form built using restraints from crosslinking mass spectrometry analysis. Together, our data present molecular details of CDP-ribitol production that may aid in the design of inhibitors against WTA biosynthesis.
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Affiliation(s)
- Franco K K Li
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Robert T Gale
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3ZS, Canada
| | - Evgeniy V Petrotchenko
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada; Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada; Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3ZS, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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25
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North OI, Brown ED. Phage-antibiotic combinations: a promising approach to constrain resistance evolution in bacteria. Ann N Y Acad Sci 2020; 1496:23-34. [PMID: 33175408 DOI: 10.1111/nyas.14533] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/15/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022]
Abstract
Antibiotic resistance has reached dangerously high levels throughout the world. A growing number of bacteria pose an urgent, serious, and concerning threat to public health. Few new antibiotics are available to clinicians and only few are in development, highlighting the need for new strategies to overcome the antibiotic resistance crisis. Combining existing antibiotics with phages, viruses the infect bacteria, is an attractive and promising alternative to standalone therapies. Phage-antibiotic combinations have been shown to suppress the emergence of resistance in bacteria, and sometimes even reverse it. Here, we discuss the mechanisms by which phage-antibiotic combinations reduce resistance evolution, and the potential limitations these mechanisms have in steering microbial resistance evolution in a desirable direction. We also emphasize the importance of gaining a better understanding of mechanisms behind physiological and evolutionary phage-antibiotic interactions in complex in-patient environments.
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Affiliation(s)
- Olesia I North
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Ontario, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Ontario, Canada
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26
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Farha MA, MacNair CR, Carfrae LA, El Zahed SS, Ellis MJ, Tran HKR, McArthur AG, Brown ED. Overcoming Acquired and Native Macrolide Resistance with Bicarbonate. ACS Infect Dis 2020; 6:2709-2718. [PMID: 32898415 DOI: 10.1021/acsinfecdis.0c00340] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The growing challenge of microbial resistance emphasizes the importance of new antibiotics or reviving strategies for the use of old ones. Macrolide antibiotics are potent bacterial protein synthesis inhibitors with a formidable capacity to treat life-threatening bacterial infections; however, acquired and intrinsic resistance limits their clinical application. In the work presented here, we reveal that bicarbonate is a potent enhancer of the activity of macrolide antibiotics that overcomes both acquired and intrinsic resistance mechanisms. With a focus on azithromycin, a highly prescribed macrolide antibiotic, and using clinically relevant pathogens, we show that physiological concentrations of bicarbonate overcome drug resistance by increasing the intracellular concentration of azithromycin. We demonstrate the potential of bicarbonate as a formulation additive for topical use of azithromycin in treating a murine wound infection caused by Pseudomonas aeruginosa. Further, using a systemic murine model of methicillin-resistant Staphylococcus aureus (MRSA) infection, we demonstrate the potential role of physiological bicarbonate, naturally abundant in the host, to enhance the activity of azithromycin against macrolide-resistant MRSA. In all, our findings suggest that macrolide resistance, observed in the clinical microbiology laboratory using standard culturing techniques, is a poor predictor of efficacy in the clinic and that observed resistance should not necessarily hamper the use of macrolides. Whether as a formulation additive for topical use or as a natural component of host tissues, bicarbonate is a powerful potentiator of macrolides with the capacity to overcome drug resistance in life-threatening bacterial infections.
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Affiliation(s)
- Maya A. Farha
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Craig R. MacNair
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Lindsey A. Carfrae
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Sara S. El Zahed
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Michael J. Ellis
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Hiu-Ki R. Tran
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Andrew G. McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of 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 of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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27
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Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackermann Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, Church GM, Brown ED, Jaakkola TS, Barzilay R, Collins JJ. A Deep Learning Approach to Antibiotic Discovery. Cell 2020; 180:688-702.e13. [PMID: 32084340 DOI: 10.1016/j.cell.2020.01.021] [Citation(s) in RCA: 660] [Impact Index Per Article: 165.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/04/2019] [Accepted: 01/15/2020] [Indexed: 02/06/2023]
Abstract
Due to the rapid emergence of antibiotic-resistant bacteria, there is a growing need to discover new antibiotics. To address this challenge, we trained a deep neural network capable of predicting molecules with antibacterial activity. We performed predictions on multiple chemical libraries and discovered a molecule from the Drug Repurposing Hub-halicin-that is structurally divergent from conventional antibiotics and displays bactericidal activity against a wide phylogenetic spectrum of pathogens including Mycobacterium tuberculosis and carbapenem-resistant Enterobacteriaceae. Halicin also effectively treated Clostridioides difficile and pan-resistant Acinetobacter baumannii infections in murine models. Additionally, from a discrete set of 23 empirically tested predictions from >107 million molecules curated from the ZINC15 database, our model identified eight antibacterial compounds that are structurally distant from known antibiotics. This work highlights the utility of deep learning approaches to expand our antibiotic arsenal through the discovery of structurally distinct antibacterial molecules.
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Affiliation(s)
- Jonathan M Stokes
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kevin Yang
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kyle Swanson
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wengong Jin
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andres Cubillos-Ruiz
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Nina M Donghia
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Craig R MacNair
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Shawn French
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Lindsey A Carfrae
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Zohar Bloom-Ackermann
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Victoria M Tran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anush Chiappino-Pepe
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ahmed H Badran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ian W Andrews
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Emma J Chory
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Tommi S Jaakkola
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Regina Barzilay
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Abdul Latif Jameel Clinic for Machine Learning in Health, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - James J Collins
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Abdul Latif Jameel Clinic for Machine Learning in Health, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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28
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Weber BS, De Jong AM, Guo AB, Dharavath S, French S, Fiebig-Comyn AA, Coombes BK, Magolan J, Brown ED. Genetic and Chemical Screening in Human Blood Serum Reveals Unique Antibacterial Targets and Compounds against Klebsiella pneumoniae. Cell Rep 2020; 32:107927. [DOI: 10.1016/j.celrep.2020.107927] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/30/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022] Open
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29
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French S, Farha M, Ellis MJ, Sameer Z, Côté JP, Cotroneo N, Lister T, Rubio A, Brown ED. Potentiation of Antibiotics against Gram-Negative Bacteria by Polymyxin B Analogue SPR741 from Unique Perturbation of the Outer Membrane. ACS Infect Dis 2020; 6:1405-1412. [PMID: 31566948 DOI: 10.1021/acsinfecdis.9b00159] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Therapeutics targeting Gram-negative bacteria have the challenge of overcoming a formidable outer membrane (OM) barrier. Here, we characterize the action of SPR741, a novel polymyxin B (PMB) analogue shown to potentiate several large-scaffold antibiotics in Gram-negative pathogens. Probing the surface topology of Escherichia coli using atomic force microscopy revealed substantial OM disorder at concentrations of SPR741 that lead to antibiotic potentiation. Conversely, very little cytoplasmic membrane depolarization was observed at these same concentrations, indicating that SPR741 acts predominately on the OM. Truncating the lipopolysaccharide (LPS) core with genetic perturbations uniquely sensitized E. coli to SPR741, suggesting that LPS core residues keep SPR741 at the OM, where it can potentiate a codrug, rather than permit its entry to the cytoplasmic membrane. Further, a promoter activity assay revealed that SPR741 challenge induced the expression of RcsAB, a stress sensor for OM perturbation. Together, these results indicate that SPR741 interacts predominately with the OM, in contrast to the dual action of PMB and colistin at both the outer and cytoplasmic membranes.
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Affiliation(s)
- Shawn French
- Department of Biochemistry and Biomedical Science and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Maya Farha
- Department of Biochemistry and Biomedical Science and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Michael J. Ellis
- Department of Biochemistry and Biomedical Science and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Zaid Sameer
- Department of Biochemistry and Biomedical Science and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Jean-Philippe Côté
- Department of Biochemistry and Biomedical Science and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Nicole Cotroneo
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Troy Lister
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Aileen Rubio
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Eric D. Brown
- Department of Biochemistry and Biomedical Science and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
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30
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Tsai CN, MacNair CR, Cao MPT, Perry JN, Magolan J, Brown ED, Coombes BK. Targeting Two-Component Systems Uncovers a Small-Molecule Inhibitor of Salmonella Virulence. Cell Chem Biol 2020; 27:793-805.e7. [PMID: 32413287 DOI: 10.1016/j.chembiol.2020.04.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/27/2020] [Accepted: 04/06/2020] [Indexed: 12/27/2022]
Abstract
Salmonella serovars are leading causes of gastrointestinal disease and have become increasingly resistant to fluoroquinolone and cephalosporin antibiotics. Overcoming this healthcare crisis requires new approaches in antibiotic discovery and the identification of unique bacterial targets. In this work, we describe a chemical genomics approach to identify inhibitors of Salmonella virulence. From a cell-based, promoter reporter screen of ∼50,000 small molecules, we identified dephostatin as a non-antibiotic compound that inhibits intracellular virulence factors and polymyxin resistance genes. Dephostatin disrupts signaling through both the SsrA-SsrB and PmrB-PmrA two-component regulatory systems and restores sensitivity to the last-resort antibiotic, colistin. Cell-based experiments and mouse models of infection demonstrate that dephostatin attenuates Salmonella virulence in vitro and in vivo, suggesting that perturbing regulatory networks is a promising strategy for the development of anti-infectives.
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Affiliation(s)
- Caressa N Tsai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Craig R MacNair
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - My P T Cao
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Jordyn N Perry
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Jakob Magolan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada.
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31
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Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackermann Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, Church GM, Brown ED, Jaakkola TS, Barzilay R, Collins JJ. A Deep Learning Approach to Antibiotic Discovery. Cell 2020; 181:475-483. [DOI: 10.1016/j.cell.2020.04.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Farha MA, El-Halfawy OM, Gale RT, MacNair CR, Carfrae LA, Zhang X, Jentsch NG, Magolan J, Brown ED. Uncovering the Hidden Antibiotic Potential of Cannabis. ACS Infect Dis 2020; 6:338-346. [PMID: 32017534 DOI: 10.1021/acsinfecdis.9b00419] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The spread of antimicrobial resistance continues to be a priority health concern worldwide, necessitating the exploration of alternative therapies. Cannabis sativa has long been known to contain antibacterial cannabinoids, but their potential to address antibiotic resistance has only been superficially investigated. Here, we show that cannabinoids exhibit antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA), inhibit its ability to form biofilms, and eradicate preformed biofilms and stationary phase cells persistent to antibiotics. We show that the mechanism of action of cannabigerol is through targeting the cytoplasmic membrane of Gram-positive bacteria and demonstrate in vivo efficacy of cannabigerol in a murine systemic infection model caused by MRSA. We also show that cannabinoids are effective against Gram-negative organisms whose outer membrane is permeabilized, where cannabigerol acts on the inner membrane. Finally, we demonstrate that cannabinoids work in combination with polymyxin B against multidrug resistant Gram-negative pathogens, revealing the broad-spectrum therapeutic potential for cannabinoids.
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Affiliation(s)
- Maya A. Farha
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | - Omar M. El-Halfawy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
- Microbiology and Immunology Department, Faculty of Pharmacy, Alexandria University, 1 El-Khartoum Square, Azarita, Alexandria 21521, Egypt
| | - Robert T. Gale
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | - Craig R. MacNair
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | - Lindsey A. Carfrae
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | - Xiong Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | - Nicholas G. Jentsch
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | - Jakob Magolan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1200 Main Street West, 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 of Infectious Disease Research, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
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33
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Imani SM, Maclachlan R, Rachwalski K, Chan Y, Lee B, McInnes M, Grandfield K, Brown ED, Didar TF, Soleymani L. Flexible Hierarchical Wraps Repel Drug-Resistant Gram-Negative and Positive Bacteria. ACS Nano 2020; 14:454-465. [PMID: 31834780 DOI: 10.1021/acsnano.9b06287] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Healthcare acquired infections are a major human health problem, and are becoming increasingly troublesome with the emergence of drug resistant bacteria. Engineered surfaces that reduce the adhesion, proliferation, and spread of bacteria have promise as a mean of preventing infections and reducing the use of antibiotics. To address this need, we created a flexible plastic wrap that combines a hierarchical wrinkled structure with chemical functionalization to reduce bacterial adhesion, biofilm formation, and the transfer of bacteria through an intermediate surface. These hierarchical wraps were effective for reducing biofilm formation of World Health Organization-designated priority pathogens Gram positive methicillin-resistant Staphylococcus aureus (MRSA) and Gram negative Pseudomonas aeruginosa by 87 and 84%, respectively. In addition, these surfaces remain free of bacteria after being touched by a contaminated surface with Gram negative E. coli. We showed that these properties are the result of broad liquid repellency of the engineered surfaces and the presence of reduced anchor points for bacterial adhesion on the hierarchical structure. Such wraps are fabricated using scalable bottom-up techniques and form an effective cover on a variety of complex objects, making them superior to top-down and substrate-specific surface modification methods.
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Affiliation(s)
- Sara M Imani
- McMaster University , School of Biomedical Engineering , 1280 Main Street West , Hamilton , L8S 4L7 , Canada
| | - Roderick Maclachlan
- McMaster University , Department of Engineering Physics , 1280 Main Street West , Hamilton , L8S 4L7 , Canada
| | - Kenneth Rachwalski
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8N 3Z5 , Canada
- Michael G. DeGroote Institute of Infectious Disease Research , McMaster University , Hamilton , ON L8N 3Z5 , Canada
| | - Yuting Chan
- McMaster University , Department of Engineering Physics , 1280 Main Street West , Hamilton , L8S 4L7 , Canada
| | - Bryan Lee
- McMaster University , School of Biomedical Engineering , 1280 Main Street West , Hamilton , L8S 4L7 , Canada
| | - Mark McInnes
- OptiSolve ® , Peterborough , ON K9J 6 × 6 , Canada
| | - Kathryn Grandfield
- McMaster University , School of Biomedical Engineering , 1280 Main Street West , Hamilton , L8S 4L7 , Canada
- Department of Materials Science and Engineering , McMaster University , Hamilton , Ontario Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8N 3Z5 , Canada
- Michael G. DeGroote Institute of Infectious Disease Research , McMaster University , Hamilton , ON L8N 3Z5 , Canada
| | - Tohid F Didar
- McMaster University , School of Biomedical Engineering , 1280 Main Street West , Hamilton , L8S 4L7 , Canada
- Michael G. DeGroote Institute of Infectious Disease Research , McMaster University , Hamilton , ON L8N 3Z5 , Canada
- Department of Mechanical Engineering , McMaster University , Hamilton , Ontario Canada
| | - Leyla Soleymani
- McMaster University , School of Biomedical Engineering , 1280 Main Street West , Hamilton , L8S 4L7 , Canada
- McMaster University , Department of Engineering Physics , 1280 Main Street West , Hamilton , L8S 4L7 , Canada
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Li FKK, Rosell FI, Gale RT, Simorre JP, Brown ED, Strynadka NCJ. Crystallographic analysis of Staphylococcus aureus LcpA, the primary wall teichoic acid ligase. J Biol Chem 2020; 295:2629-2639. [PMID: 31969390 DOI: 10.1074/jbc.ra119.011469] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
Gram-positive bacteria, including major clinical pathogens such as Staphylococcus aureus, are becoming increasingly drug-resistant. Their cell walls are composed of a thick layer of peptidoglycan (PG) modified by the attachment of wall teichoic acid (WTA), an anionic glycopolymer that is linked to pathogenicity and regulation of cell division and PG synthesis. The transfer of WTA from lipid carriers to PG, catalyzed by the LytR-CpsA-Psr (LCP) enzyme family, offers a unique extracellular target for the development of new anti-infective agents. Inhibitors of LCP enzymes have the potential to manage a wide range of bacterial infections because the target enzymes are implicated in the assembly of many other bacterial cell wall polymers, including capsular polysaccharide of streptococcal species and arabinogalactan of mycobacterial species. In this study, we present the first crystal structure of S. aureus LcpA with bound substrate at 1.9 Å resolution and those of Bacillus subtilis LCP enzymes, TagT, TagU, and TagV, in the apo form at 1.6-2.8 Å resolution. The structures of these WTA transferases provide new insight into the binding of lipid-linked WTA and enable assignment of the catalytic roles of conserved active-site residues. Furthermore, we identified potential subsites for binding the saccharide core of PG using computational docking experiments, and multiangle light-scattering experiments disclosed novel oligomeric states of the LCP enzymes. The crystal structures and modeled substrate-bound complexes of the LCP enzymes reported here provide insights into key features linked to substrate binding and catalysis and may aid the structure-guided design of specific LCP inhibitors.
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Affiliation(s)
- Franco K K Li
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Federico I Rosell
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Robert T Gale
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Jean-Pierre Simorre
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
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French S, Guo ABY, Brown ED. A comprehensive guide to dynamic analysis of microbial gene expression using the 3D-printed PFIbox and a fluorescent reporter library. Nat Protoc 2020; 15:575-603. [DOI: 10.1038/s41596-019-0257-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 10/11/2019] [Indexed: 01/25/2023]
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MacNair CR, Tsai CN, Brown ED. Creative targeting of the Gram-negative outer membrane in antibiotic discovery. Ann N Y Acad Sci 2019; 1459:69-85. [PMID: 31762048 DOI: 10.1111/nyas.14280] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/13/2022]
Abstract
The rising threat of multidrug-resistant Gram-negative bacteria is exacerbated by the scarcity of new antibiotics in the development pipeline. Permeability through the outer membrane remains one of the leading hurdles in discovery efforts. However, the essentiality of a robust outer membrane makes itself an intriguing antimicrobial target. Herein, we review drug discovery efforts targeting the outer membrane and the prospective antimicrobial leads identified.
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Affiliation(s)
- Craig R MacNair
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Caressa N Tsai
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Lacasse MJ, Sebastiampillai S, Côté JP, Hodkinson N, Brown ED, Zamble DB. A whole-cell, high-throughput hydrogenase assay to identify factors that modulate [NiFe]-hydrogenase activity. J Biol Chem 2019; 294:15373-15385. [PMID: 31455635 DOI: 10.1074/jbc.ra119.008101] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
[NiFe]-hydrogenases have attracted attention as potential therapeutic targets or components of a hydrogen-based economy. [NiFe]-hydrogenase production is a complicated process that requires many associated accessory proteins that supply the requisite cofactors and substrates. Current methods for measuring hydrogenase activity have low throughput and often require specialized conditions and reagents. In this work, we developed a whole-cell high-throughput hydrogenase assay based on the colorimetric reduction of benzyl viologen to explore the biological networks of these enzymes in Escherichia coli We utilized this assay to screen the Keio collection, a set of nonlethal single-gene knockouts in E. coli BW25113. The results of this screen highlighted the assay's specificity and revealed known components of the intricate network of systems that underwrite [NiFe]-hydrogenase activity, including nickel homeostasis and formate dehydrogenase activities as well as molybdopterin and selenocysteine biosynthetic pathways. The screen also helped identify several new genetic components that modulate hydrogenase activity. We examined one E. coli strain with undetectable hydrogenase activity in more detail (ΔeutK), finding that nickel delivery to the enzyme active site was completely abrogated, and tracked this effect to an ancillary and unannotated lack of the fumarate and nitrate reduction (FNR) anaerobic regulatory protein. Collectively, these results demonstrate that the whole-cell assay developed here can be used to uncover new information about bacterial [NiFe]-hydrogenase production and to probe the cellular components of microbial nickel homeostasis.
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Affiliation(s)
- Michael J Lacasse
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | | | - Jean-Philippe Côté
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Nicholas Hodkinson
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada .,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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Poole K, Gilmour C, Farha MA, Parkins MD, Klinoski R, Brown ED. Meropenem potentiation of aminoglycoside activity against Pseudomonas aeruginosa: involvement of the MexXY-OprM multidrug efflux system. J Antimicrob Chemother 2019; 73:1247-1255. [PMID: 29420743 DOI: 10.1093/jac/dkx539] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/20/2017] [Indexed: 12/25/2022] Open
Abstract
Objectives To assess the ability of meropenem to potentiate aminoglycoside (AG) activity against laboratory and AG-resistant cystic fibrosis (CF) isolates of Pseudomonas aeruginosa and to elucidate its mechanism of action. Methods AG resistance gene deletions were engineered into P. aeruginosa laboratory and CF isolates using standard gene replacement technology. Susceptibility to AGs ± meropenem (at ½ MIC) was assessed using a serial 2-fold dilution assay. mexXY expression and MexXY-OprM efflux activity were quantified using quantitative PCR and an ethidium bromide accumulation assay, respectively. Results A screen for agents that rendered WT P. aeruginosa susceptible to a sub-MIC concentration of the AG paromomycin identified the carbapenem meropenem, which potentiated several additional AGs. Meropenem potentiation of AG activity was largely lost in a mutant lacking the MexXY-OprM multidrug efflux system, an indication that it was targeting this efflux system in enhancing P. aeruginosa susceptibility to AGs. Meropenem failed to block AG induction of mexXY expression or MexXY-OprM efflux activity, suggesting that it may be interfering with some MexXY-dependent process linked to AG susceptibility. Meropenem potentiated AG activity versus AG-resistant CF isolates, enhancing susceptibility to at least one AG in all isolates and susceptibility to all tested AGs in 50% of the isolates. Notably, meropenem potentiation of AG activity was linked to MexXY in some but not all CF isolates in which this was examined. Conclusions Meropenem potentiates AG activity against laboratory and CF strains of P. aeruginosa, both dependent on and independent of MexXY, highlighting the complexity of AG resistance in this organism.
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Affiliation(s)
- Keith Poole
- Department of Biomedical and Molecular Sciences, Botterell Hall, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Christie Gilmour
- Department of Biomedical and Molecular Sciences, Botterell Hall, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Maya A Farha
- M.G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Michael D Parkins
- Department of Microbiology Immunology and Infectious Diseases and Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Rachael Klinoski
- Department of Biomedical and Molecular Sciences, Botterell Hall, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Eric D Brown
- M.G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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39
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Stokes JM, Gutierrez A, Lopatkin AJ, Andrews IW, French S, Matic I, Brown ED, Collins JJ. A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria. Nat Methods 2019; 16:303-306. [DOI: 10.1038/s41592-019-0333-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/29/2019] [Indexed: 02/06/2023]
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Abstract
Antimicrobial resistance continues to be a public threat on a global scale. The ongoing need to develop new antimicrobial drugs that are effective against multi-drug-resistant pathogens has spurred the research community to invest in various drug discovery strategies, one of which is drug repurposing-the process of finding new uses for existing drugs. While still nascent in the antimicrobial field, the approach is gaining traction in both the public and private sector. While the approach has particular promise in fast-tracking compounds into clinical studies, it nevertheless has substantial obstacles to success. This Review covers the art of repurposing existing drugs for antimicrobial purposes. We discuss enabling screening platforms for antimicrobial discovery and present encouraging findings of novel antimicrobial therapeutic strategies. Also covered are general advantages of repurposing over de novo drug development and challenges of the strategy, including scientific, intellectual property and regulatory issues.
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Affiliation(s)
- Maya A Farha
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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41
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Ellis MJ, Tsai CN, Johnson JW, French S, Elhenawy W, Porwollik S, Andrews-Polymenis H, McClelland M, Magolan J, Coombes BK, Brown ED. A macrophage-based screen identifies antibacterial compounds selective for intracellular Salmonella Typhimurium. Nat Commun 2019; 10:197. [PMID: 30643129 PMCID: PMC6331611 DOI: 10.1038/s41467-018-08190-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/19/2018] [Indexed: 12/24/2022] Open
Abstract
Salmonella Typhimurium (S. Tm) establishes systemic infection in susceptible hosts by evading the innate immune response and replicating within host phagocytes. Here, we sought to identify inhibitors of intracellular S. Tm replication by conducting parallel chemical screens against S. Tm growing in macrophage-mimicking media and within macrophages. We identify several compounds that inhibit Salmonella growth in the intracellular environment and in acidic, ion-limited media. We report on the antimicrobial activity of the psychoactive drug metergoline, which is specific against intracellular S. Tm. Screening an S. Tm deletion library in the presence of metergoline reveals hypersensitization of outer membrane mutants to metergoline activity. Metergoline disrupts the proton motive force at the bacterial cytoplasmic membrane and extends animal survival during a systemic S. Tm infection. This work highlights the predictive nature of intracellular screens for in vivo efficacy, and identifies metergoline as a novel antimicrobial active against Salmonella.
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Affiliation(s)
- Michael J Ellis
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
| | - Caressa N Tsai
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
| | - Jarrod W Johnson
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
| | - Shawn French
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
| | - Wael Elhenawy
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697-4025, USA
| | - Helene Andrews-Polymenis
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, 8447 Riverside Pkwy, Bryan, TX, 77807, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697-4025, USA
| | - Jakob Magolan
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada.
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada.
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Abstract
The world is heading toward a dangerous post-antibiotic era where antibiotics fail to treat infections. Staphylococcus aureus is the leading cause of healthcare-associated infections worldwide, and an ever-increasing percentage of them are methicillin-resistant (MRSA). New strategies are urgently needed to combat this pathogen. Wall teichoic acids (WTA) in S. aureus are polyribitol phosphate polymers that play important roles in virulence and resistance to β-lactam antibiotics. Here, we describe a high-throughput whole-cell screening platform for inhibitors targeting WTA biosynthesis. This platform takes advantage of the unique dispensability patterns of genes encoding WTA biosynthesis. We further describe follow-up dose-response assays to identify WTA inhibitors among the primary bioactives. WTA inhibitors offer an exciting opportunity for the development of novel antibacterial leads of unique mechanism in the fight against drug-resistant staphylococcal infections.
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Affiliation(s)
- Omar M El-Halfawy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- Microbiology and Immunology Department, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
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Klobucar K, Brown ED. Use of genetic and chemical synthetic lethality as probes of complexity in bacterial cell systems. FEMS Microbiol Rev 2018; 42:4563584. [PMID: 29069427 DOI: 10.1093/femsre/fux054] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/23/2017] [Indexed: 12/22/2022] Open
Abstract
Different conditions and genomic contexts are known to have an impact on gene essentiality and interactions. Synthetic lethal interactions occur when a combination of perturbations, either genetic or chemical, result in a more profound fitness defect than expected based on the effect of each perturbation alone. Synthetic lethality in bacterial systems has long been studied; however, during the past decade, the emerging fields of genomics and chemical genomics have led to an increase in the scale and throughput of these studies. Here, we review the concepts of genomics and chemical genomics in the context of synthetic lethality and their revolutionary roles in uncovering novel biology such as the characterization of genes of unknown function and in antibacterial drug discovery. We provide an overview of the methodologies, examples and challenges of both genetic and chemical synthetic lethal screening platforms. Finally, we discuss how to apply genetic and chemical synthetic lethal approaches to rationalize the synergies of drugs, screen for new and improved antibacterial therapies and predict drug mechanism of action.
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Affiliation(s)
- Kristina Klobucar
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St West, Hamilton, ON L8N 3Z5, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St West, Hamilton, ON L8N 3Z5, Canada
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Fang L, Zhang G, El-Halfawy O, Simon M, Brown ED, Pfeifer BA. Broadened glycosylation patterning of heterologously produced erythromycin. Biotechnol Bioeng 2018; 115:2771-2777. [PMID: 29873068 DOI: 10.1002/bit.26735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/30/2018] [Accepted: 05/29/2018] [Indexed: 11/08/2022]
Abstract
The biosynthetic flexibility associated with the antibiotic natural product erythromycin is both remarkable and utilitarian. Product formation is marked by a modular nature where directing compound variation increasingly spans both the secondary metabolite core scaffold and adorning functionalization patterns. The resulting molecular diversity allows for chemical expansion of the native compound structural space. Accordingly, associated antibiotic bioactivity is expected to expand infectious disease treatment applications. In the enclosed work, new glycosylation patterns spanning the deoxysugars d-forosamine, d-allose, l-noviose, and d-vicenisamine were engineered within the erythromycin biosynthetic system established through an Escherichia coli heterologous production platform. The resulting analogs highlight the expanded flexibility of the erythromycin biosynthetic process. In addition, the new compounds demonstrated bioactivity against multiple Gram-positive tester strains, including erythromycin-resistant Bacillus subtilis, and limited activity against a Gram-negative bacterial target.
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Affiliation(s)
- Lei Fang
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York
| | - Guojian Zhang
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York.,Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Omar El-Halfawy
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Max Simon
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York.,Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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French S, Coutts BE, Brown ED. Open-Source High-Throughput Phenomics of Bacterial Promoter-Reporter Strains. Cell Syst 2018; 7:339-346.e3. [PMID: 30172841 DOI: 10.1016/j.cels.2018.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 05/25/2018] [Accepted: 07/10/2018] [Indexed: 11/17/2022]
Abstract
Open-source electronics are becoming more prevalent in biological sciences, enabling novel and unique means of data acquisition. Here, we present 3D-printed, open-source tools to acquire fluorescence phenotypes with high temporal resolution. Printed fluorescence imaging boxes (PFIboxes) cost approximately 200 US dollars to assemble, can be placed in incubators or hypoxic chambers, and accurately read high-density colony arrays of microorganisms. We demonstrate the utility of PFIboxes using a time course gene expression approach, examining global Escherichia coli promoter activity using a fluorescent reporter library across a diverse panel of 15 antibiotics, each at several concentrations. Many secondary and indirect effects were observed when E. coli was challenged with various drugs, including increased gene expression in carbon metabolism processes. Further, kinetic data acquisition enabled non-destructive time course gene expression, clustering of which revealed patterns of co-expression. In all, PFIboxes provide an open solution to gene expression, for about 2 US dollars per treatment condition, including technical replicates.
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Affiliation(s)
- Shawn French
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Brittney E Coutts
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
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El Zahed SS, Brown ED. Chemical-Chemical Combinations Map Uncharted Interactions in Escherichia coli under Nutrient Stress. iScience 2018; 2:168-181. [PMID: 30428373 PMCID: PMC6136904 DOI: 10.1016/j.isci.2018.03.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/28/2018] [Accepted: 03/07/2018] [Indexed: 11/16/2022] Open
Abstract
Of the ∼4,400 genes that constitute Escherichia coli's genome, ∼300 genes are indispensable for its growth in nutrient-rich conditions. These encode housekeeping functions, including cell wall, DNA, RNA, and protein syntheses. Under conditions in which nutrients are limited to a carbon source, nitrogen source, essential phosphates, and salts, more than 100 additional genes become essential. These largely code for the synthesis of amino acids, vitamins, and nucleobases. Although much is known about this collection of ∼400 genes, their interactions under nutrient stress are uncharted. Using a chemical biology approach, we focused on 45 chemical probes targeting encoded proteins in this collection and mapped their interactions under nutrient-limited conditions. Encompassing 990 unique pairwise chemical combinations, we revealed a highly connected network of 186 interactions, of which 81 were synergistic and 105 were antagonistic. The network revealed signature interactions for each probe and highlighted new connectivity between housekeeping functions and those essential in nutrient stress. Chemical probes map a complex interaction network in E. coli under nutrient stress A total of 990 unique chemical combinations reveal a dense network of 186 interactions New connections between housekeeping functions and those in nutrient stress
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Affiliation(s)
- Sara S El Zahed
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada.
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47
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Abstract
The antibacterial properties of sodium bicarbonate have been known for years, yet the molecular understanding of its mechanism of action is still lacking. Utilizing chemical-chemical combinations, we first explored the effect of bicarbonate on the activity of conventional antibiotics to infer on the mechanism. Remarkably, the activity of 8 classes of antibiotics differed in the presence of this ubiquitous buffer. These interactions and a study of mechanism of action revealed that, at physiological concentrations, bicarbonate is a selective dissipater of the pH gradient of the proton motive force across the cytoplasmic membrane of both Gram-negative and Gram-positive bacteria. Further, while components that make up innate immunity have been extensively studied, a link to bicarbonate, the dominant buffer in the extracellular fluid, has never been made. Here, we also explored the effects of bicarbonate on components of innate immunity. Although the immune response and the buffering system have distinct functions in the body, we posit there is interplay between these, as the antimicrobial properties of several components of innate immunity were enhanced by a physiological concentration of bicarbonate. Our findings implicate bicarbonate as an overlooked potentiator of host immunity in the defense against pathogens. Overall, the unique mechanism of action of bicarbonate has far-reaching and predictable effects on the activity of innate immune components and antibiotics. We conclude that bicarbonate has remarkable power as an antibiotic adjuvant and suggest that there is great potential to exploit this activity in the discovery and development of new antibacterial drugs by leveraging testing paradigms that better reflect the physiological concentration of bicarbonate.
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Affiliation(s)
- Maya A. Farha
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | - Shawn French
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | - Jonathan M. Stokes
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | - Eric D. Brown
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
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48
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McAuley S, Huynh A, Czarny TL, Brown ED, Nodwell JR. Membrane activity profiling of small molecule B. subtilis growth inhibitors utilizing novel duel-dye fluorescence assay. Medchemcomm 2018; 9:554-561. [PMID: 30108946 PMCID: PMC6071753 DOI: 10.1039/c8md00009c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/14/2018] [Indexed: 01/22/2023]
Abstract
Small molecule disruption of the bacterial membrane is both a challenge and interest for drug development. While some avoid membrane activity due to toxicity issues, others are interested in leveraging the effects for new treatments. Existing assays are available for measuring disruption of membrane potential or membrane permeability, two key characteristics of the bacterial membrane, however they are limited in their ability to distinguish between these properties. Here, we demonstrate a high throughput assay for detection and characterization of membrane active compounds. The assay distinguishes the effect of small molecules on either the membrane potential or membrane permeability using the fluorescent dyes TO-PRO-3 iodide and DiOC2(3) without the need for secondary assays. We then applied this assay to a library of 3520 synthetic molecules previously shown to inhibit growth of B. subtilis in order to determine the frequency of membrane activity within such a biologically active library. From the library, we found 249 compounds that demonstrated significant membrane activity, suggesting that synthetic libraries of this kind do not contain a plurality of membrane active molecules.
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Affiliation(s)
- S McAuley
- Biochemistry , University of Toronto , Toronto , ON , Canada .
| | - A Huynh
- Biochemistry , University of Toronto , Toronto , ON , Canada .
| | - T L Czarny
- Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON , Canada
| | - E D Brown
- Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON , Canada
| | - J R Nodwell
- Biochemistry , University of Toronto , Toronto , ON , Canada .
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49
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MacNair CR, Stokes JM, Carfrae LA, Fiebig-Comyn AA, Coombes BK, Mulvey MR, Brown ED. Overcoming mcr-1 mediated colistin resistance with colistin in combination with other antibiotics. Nat Commun 2018; 9:458. [PMID: 29386620 PMCID: PMC5792607 DOI: 10.1038/s41467-018-02875-z] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/04/2018] [Indexed: 12/13/2022] Open
Abstract
Plasmid-borne colistin resistance mediated by mcr-1 may contribute to the dissemination of pan-resistant Gram-negative bacteria. Here, we show that mcr-1 confers resistance to colistin-induced lysis and bacterial cell death, but provides minimal protection from the ability of colistin to disrupt the Gram-negative outer membrane. Indeed, for colistin-resistant strains of Enterobacteriaceae expressing plasmid-borne mcr-1, clinically relevant concentrations of colistin potentiate the action of antibiotics that, by themselves, are not active against Gram-negative bacteria. The result is that several antibiotics, in combination with colistin, display growth-inhibition at levels below their corresponding clinical breakpoints. Furthermore, colistin and clarithromycin combination therapy displays efficacy against mcr-1-positive Klebsiella pneumoniae in murine thigh and bacteremia infection models at clinically relevant doses. Altogether, these data suggest that the use of colistin in combination with antibiotics that are typically active against Gram-positive bacteria poses a viable therapeutic alternative for highly drug-resistant Gram-negative pathogens expressing mcr-1.
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Affiliation(s)
- Craig R MacNair
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3ZS, Canada
| | - Jonathan M Stokes
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3ZS, Canada
| | - Lindsey A Carfrae
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3ZS, Canada
| | - Aline A Fiebig-Comyn
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3ZS, Canada
| | - Brian K Coombes
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3ZS, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Eric D Brown
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3ZS, Canada.
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50
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Abstract
Bacterial transposons were long thought of as selfish mobile genetic elements that propagate at the expense of 'host' bacterium fitness. However, limited transposition can benefit the host organism by promoting DNA rearrangements and facilitating horizontal gene transfer. Here we discuss and provide context for our recently published work which reported the surprising finding that an otherwise dormant transposon, IS200, encodes a regulatory RNA in Salmonella Typhimurium. This previous work identified a trans-acting sRNA that is encoded in the 5'UTR of IS200 transposase mRNA (tnpA). This sRNA represses expression of genes encoded within Salmonella Pathogenicity Island 1 (SPI-1), and accordingly limits invasion into non-phagocytic cells in vitro. We present new data here that shows IS200 elements are important for colonization of the mouse gastrointestinal tract. We discuss our previous and current findings in the context of transposon biology and suggest that otherwise 'silent' transposons may in fact play an important role in controlling host gene expression.
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Affiliation(s)
- Michael J Ellis
- a Department of Biochemistry , University of Western Ontario , London , ON Canada
| | - Lindsey A Carfrae
- b Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research , McMaster University , Hamilton , ON Canada
| | - Craig R Macnair
- b Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research , McMaster University , Hamilton , ON Canada
| | - Ryan S Trussler
- a Department of Biochemistry , University of Western Ontario , London , ON Canada
| | - Eric D Brown
- b Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research , McMaster University , Hamilton , ON Canada
| | - David B Haniford
- a Department of Biochemistry , University of Western Ontario , London , ON Canada
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