1
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Peng Y, Moffat JG, DuPai C, Kofoed EM, Skippington E, Modrusan Z, Gloor SL, Clark K, Xu Y, Li S, Chen L, Liu X, Wu P, Harris SF, Wang S, Crawford TD, Li CS, Liu Z, Wai J, Tan MW. Differential effects of inosine monophosphate dehydrogenase (IMPDH/GuaB) inhibition in Acinetobacter baumannii and Escherichia coli. J Bacteriol 2024:e0010224. [PMID: 39235234 DOI: 10.1128/jb.00102-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/25/2024] [Indexed: 09/06/2024] Open
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH), known as GuaB in bacteria, catalyzes the rate-limiting step in de novo guanine biosynthesis and is conserved from humans to bacteria. We developed a series of potent inhibitors that selectively target GuaB over its human homolog. Here, we show that these GuaB inhibitors are bactericidal, generate phenotypic signatures that are distinct from other antibiotics, and elicit different time-kill kinetics and regulatory responses in two important Gram-negative pathogens: Acinetobacter baumannii and Escherichia coli. Specifically, the GuaB inhibitor G6 rapidly kills A. baumannii but only kills E. coli after 24 h. After exposure to G6, the expression of genes involved in purine biosynthesis and stress responses change in opposite directions while siderophore biosynthesis is downregulated in both species. Our results suggest that different species respond to GuaB inhibition using distinct regulatory programs and possibly explain the different bactericidal kinetics upon GuaB inhibition. The comparison highlights opportunities for developing GuaB inhibitors as novel antibiotics.IMPORTANCEA. baumannii is a priority bacterial pathogen for which development of new antibiotics is urgently needed due to the emergence of multidrug resistance. We recently developed a series of specific inhibitors against GuaB, a bacterial inosine 5'-monophosphate dehydrogenase, and achieved sub-micromolar minimum inhibitory concentrations against A. baumannii. GuaB catalyzes the rate-limiting step of de novo guanine biosynthesis and is highly conserved across bacterial pathogens. This study shows that inhibition of GuaB induced a bacterial morphological profile distinct from that of other classes of antibiotics, highlighting a novel mechanism of action. Moreover, our transcriptomic analysis showed that regulation of de novo purine biosynthesis and stress responses of A. baumannii upon GuaB inhibition differed significantly from that of E. coli.
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Affiliation(s)
- Yutian Peng
- Department of Infectious Diseases, Genentech Inc., South San Francisco, California, USA
| | - John G Moffat
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, California, USA
| | - Cory DuPai
- Department of Bioinformatics, Genentech Inc., South San Francisco, California, USA
| | - Eric M Kofoed
- Department of Infectious Diseases, Genentech Inc., South San Francisco, California, USA
| | | | - Zora Modrusan
- Department of Proteomic and Genomic Technologies, Genentech Inc., South San Francisco, California, USA
| | - Susan L Gloor
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, California, USA
| | - Kevin Clark
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, California, USA
| | - Yiming Xu
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, California, USA
| | - Shuxuan Li
- Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., South San Francisco, California, USA
| | - Liuxi Chen
- Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., South San Francisco, California, USA
| | - Xingrong Liu
- Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., South San Francisco, California, USA
| | - Ping Wu
- Department of Structural Biology, Genentech Inc., South San Francisco, California, USA
| | - Seth F Harris
- Department of Structural Biology, Genentech Inc., South San Francisco, California, USA
| | - Shumei Wang
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Terry D Crawford
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Chun Sing Li
- WuXi AppTec Co., Ltd., Waigaoqiao Free Trade Zone, Shanghai, China
| | - Zhiguo Liu
- WuXi AppTec Co., Ltd., Waigaoqiao Free Trade Zone, Shanghai, China
| | - John Wai
- WuXi AppTec Co., Ltd., Waigaoqiao Free Trade Zone, Shanghai, China
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., South San Francisco, California, USA
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2
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Bakker AT, Kotsogianni I, Avalos M, Punt JM, Liu B, Piermarini D, Gagestein B, Slingerland CJ, Zhang L, Willemse JJ, Ghimire LB, van den Berg RJHBN, Janssen APA, Ottenhoff THM, van Boeckel CAA, van Wezel GP, Ghilarov D, Martin NI, van der Stelt M. Discovery of isoquinoline sulfonamides as allosteric gyrase inhibitors with activity against fluoroquinolone-resistant bacteria. Nat Chem 2024; 16:1462-1472. [PMID: 38898213 DOI: 10.1038/s41557-024-01516-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/22/2024] [Indexed: 06/21/2024]
Abstract
Bacteria have evolved resistance to nearly all known antibacterials, emphasizing the need to identify antibiotics that operate via novel mechanisms. Here we report a class of allosteric inhibitors of DNA gyrase with antibacterial activity against fluoroquinolone-resistant clinical isolates of Escherichia coli. Screening of a small-molecule library revealed an initial isoquinoline sulfonamide hit, which was optimized via medicinal chemistry efforts to afford the more potent antibacterial LEI-800. Target identification studies, including whole-genome sequencing of in vitro selected mutants with resistance to isoquinoline sulfonamides, unanimously pointed to the DNA gyrase complex, an essential bacterial topoisomerase and an established antibacterial target. Using single-particle cryogenic electron microscopy, we determined the structure of the gyrase-LEI-800-DNA complex. The compound occupies an allosteric, hydrophobic pocket in the GyrA subunit and has a mode of action that is distinct from the clinically used fluoroquinolones or any other gyrase inhibitor reported to date. LEI-800 provides a chemotype suitable for development to counter the increasingly widespread bacterial resistance to fluoroquinolones.
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Affiliation(s)
- Alexander T Bakker
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Ioli Kotsogianni
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Mariana Avalos
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Jeroen M Punt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Bing Liu
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Diana Piermarini
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Berend Gagestein
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Cornelis J Slingerland
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Le Zhang
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Joost J Willemse
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Leela B Ghimire
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | | | - Antonius P A Janssen
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Constant A A van Boeckel
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Dmitry Ghilarov
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK.
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands.
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
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3
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Zhang Y, Cai Y, Jin X, Wu Q, Bai F, Liu J. Persistent glucose consumption under antibiotic treatment protects bacterial community. Nat Chem Biol 2024:10.1038/s41589-024-01708-z. [PMID: 39138382 DOI: 10.1038/s41589-024-01708-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 07/22/2024] [Indexed: 08/15/2024]
Abstract
Antibiotics typically induce major physiological changes in bacteria. However, their effect on nutrient consumption remains unclear. Here we found that Escherichia coli communities can sustain normal levels of glucose consumption under a broad range of antibiotics. The community-living resulted in a low membrane potential in the bacteria, allowing slow antibiotic accumulation on treatment and better adaptation. Through multi-omics analysis, we identified a prevalent adaptive response characterized by the upregulation of lipid synthesis, which substantially contributes to sustained glucose consumption. The consumption was maintained by the periphery region of the community, thereby restricting glucose penetration into the community interior. The resulting spatial heterogeneity in glucose availability protected the interior from antibiotic accumulation in a membrane potential-dependent manner, ensuring rapid recovery of the community postantibiotic treatment. Our findings unveiled a community-level antibiotic response through spatial regulation of metabolism and suggested new strategies for antibiotic therapies.
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Affiliation(s)
- Yuzhen Zhang
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
| | - Yumin Cai
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Xin Jin
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
| | - Qile Wu
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Fan Bai
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Jintao Liu
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, China.
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4
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Deep A, Liang Q, Enustun E, Pogliano J, Corbett KD. Architecture and activation mechanism of the bacterial PARIS defence system. Nature 2024:10.1038/s41586-024-07772-8. [PMID: 39112702 DOI: 10.1038/s41586-024-07772-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 07/02/2024] [Indexed: 08/17/2024]
Abstract
Bacteria and their viruses (bacteriophages or phages) are engaged in an intense evolutionary arms race1-5. While the mechanisms of many bacterial antiphage defence systems are known1, how these systems avoid toxicity outside infection yet activate quickly after infection is less well understood. Here we show that the bacterial phage anti-restriction-induced system (PARIS) operates as a toxin-antitoxin system, in which the antitoxin AriA sequesters and inactivates the toxin AriB until triggered by the T7 phage counterdefence protein Ocr. Using cryo-electron microscopy, we show that AriA is related to SMC-family ATPases but assembles into a distinctive homohexameric complex through two oligomerization interfaces. In uninfected cells, the AriA hexamer binds to up to three monomers of AriB, maintaining them in an inactive state. After Ocr binding, the AriA hexamer undergoes a structural rearrangement, releasing AriB and allowing it to dimerize and activate. AriB is a toprim/OLD-family nuclease, the activation of which arrests cell growth and inhibits phage propagation by globally inhibiting protein translation through specific cleavage of a lysine tRNA. Collectively, our findings reveal the intricate molecular mechanisms of a bacterial defence system triggered by a phage counterdefence protein, and highlight how an SMC-family ATPase has been adapted as a bacterial infection sensor.
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Affiliation(s)
- Amar Deep
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Qishan Liang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Eray Enustun
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Joe Pogliano
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
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5
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Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, da Silva EB, O'Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small molecule in situ resin capture provides a compound first approach to natural product discovery. Nat Commun 2024; 15:5230. [PMID: 38898025 PMCID: PMC11187115 DOI: 10.1038/s41467-024-49367-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Culture-based microbial natural product discovery strategies fail to realize the extraordinary biosynthetic potential detected across earth's microbiomes. Here we introduce Small Molecule In situ Resin Capture (SMIRC), a culture-independent method to obtain natural products directly from the environments in which they are produced. We use SMIRC to capture numerous compounds including two new carbon skeletons that were characterized using NMR and contain structural features that are, to the best of our knowledge, unprecedented among natural products. Applications across diverse marine habitats reveal biome-specific metabolomic signatures and levels of chemical diversity in concordance with sequence-based predictions. Expanded deployments, in situ cultivation, and metagenomics facilitate compound discovery, enhance yields, and link compounds to candidate producing organisms, although microbial community complexity creates challenges for the later. This compound-first approach to natural product discovery provides access to poorly explored chemical space and has implications for drug discovery and the detection of chemically mediated biotic interactions.
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Affiliation(s)
- Alexander Bogdanov
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Mariam N Salib
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alexander B Chase
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Earth Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Heinz Hammerlindl
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Mitchell N Muskat
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Tadeusz F Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Paul R Jensen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.
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6
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Tran TA, Sridhar S, Reece ST, Lunguya O, Jacobs J, Van Puyvelde S, Marks F, Dougan G, Thomson NR, Nguyen BT, Bao PT, Baker S. Combining machine learning with high-content imaging to infer ciprofloxacin susceptibility in isolates of Salmonella Typhimurium. Nat Commun 2024; 15:5074. [PMID: 38871710 PMCID: PMC11176356 DOI: 10.1038/s41467-024-49433-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
Antimicrobial resistance (AMR) is a growing public health crisis that requires innovative solutions. Current susceptibility testing approaches limit our ability to rapidly distinguish between antimicrobial-susceptible and -resistant organisms. Salmonella Typhimurium (S. Typhimurium) is an enteric pathogen responsible for severe gastrointestinal illness and invasive disease. Despite widespread resistance, ciprofloxacin remains a common treatment for Salmonella infections, particularly in lower-resource settings, where the drug is given empirically. Here, we exploit high-content imaging to generate deep phenotyping of S. Typhimurium isolates longitudinally exposed to increasing concentrations of ciprofloxacin. We apply machine learning algorithms to the imaging data and demonstrate that individual isolates display distinct growth and morphological characteristics that cluster by time point and susceptibility to ciprofloxacin, which occur independently of ciprofloxacin exposure. Using a further set of S. Typhimurium clinical isolates, we find that machine learning classifiers can accurately predict ciprofloxacin susceptibility without exposure to it or any prior knowledge of resistance phenotype. These results demonstrate the principle of using high-content imaging with machine learning algorithms to predict drug susceptibility of clinical bacterial isolates. This technique may be an important tool in understanding the morphological impact of antimicrobials on the bacterial cell to identify drugs with new modes of action.
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Affiliation(s)
- Tuan-Anh Tran
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sushmita Sridhar
- The Department of Medicine, University of Cambridge, Cambridge, UK
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen T Reece
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Sanofi, Kymab, Babraham Research Campus, Cambridge, UK
| | - Octavie Lunguya
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Jan Jacobs
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sandra Van Puyvelde
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Florian Marks
- The Department of Medicine, University of Cambridge, Cambridge, UK
- International Vaccine Institute, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | - Gordon Dougan
- The Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicholas R Thomson
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Binh T Nguyen
- Faculty of Mathematics and Computer Science, University of Science, Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Pham The Bao
- Information Science Faculty, Saigon University, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- The Department of Medicine, University of Cambridge, Cambridge, UK.
- IAVI, Chelsea and Westminster Hospital, London, UK.
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7
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Muñoz KA, Ulrich RJ, Vasan AK, Sinclair M, Wen PC, Holmes JR, Lee HY, Hung CC, Fields CJ, Tajkhorshid E, Lau GW, Hergenrother PJ. A Gram-negative-selective antibiotic that spares the gut microbiome. Nature 2024; 630:429-436. [PMID: 38811738 DOI: 10.1038/s41586-024-07502-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/01/2024] [Indexed: 05/31/2024]
Abstract
Infections caused by Gram-negative pathogens are increasingly prevalent and are typically treated with broad-spectrum antibiotics, resulting in disruption of the gut microbiome and susceptibility to secondary infections1-3. There is a critical need for antibiotics that are selective both for Gram-negative bacteria over Gram-positive bacteria, as well as for pathogenic bacteria over commensal bacteria. Here we report the design and discovery of lolamicin, a Gram-negative-specific antibiotic targeting the lipoprotein transport system. Lolamicin has activity against a panel of more than 130 multidrug-resistant clinical isolates, shows efficacy in multiple mouse models of acute pneumonia and septicaemia infection, and spares the gut microbiome in mice, preventing secondary infection with Clostridioides difficile. The selective killing of pathogenic Gram-negative bacteria by lolamicin is a consequence of low sequence homology for the target in pathogenic bacteria versus commensals; this doubly selective strategy can be a blueprint for the development of other microbiome-sparing antibiotics.
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Affiliation(s)
- Kristen A Muñoz
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rebecca J Ulrich
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Archit K Vasan
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matt Sinclair
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Po-Chao Wen
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jessica R Holmes
- High-Performance Computing in Biology, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hyang Yeon Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chien-Che Hung
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J Fields
- High-Performance Computing in Biology, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emad Tajkhorshid
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gee W Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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8
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Mermans F, De Baets H, García-Timermans C, Teughels W, Boon N. Unlocking the mechanism of action: a cost-effective flow cytometry approach for accelerating antimicrobial drug development. Microbiol Spectr 2024; 12:e0393123. [PMID: 38483479 PMCID: PMC10986550 DOI: 10.1128/spectrum.03931-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/04/2024] [Indexed: 04/06/2024] Open
Abstract
Antimicrobial resistance is one of the greatest challenges to global health. While the development of new antimicrobials can combat resistance, low profitability reduces the number of new compounds brought to market. Elucidating the mechanism of action is crucial for developing new antimicrobials. This can become expensive as there are no universally applicable pipelines. Phenotypic heterogeneity of microbial populations resulting from antimicrobial treatment can be captured through flow cytometric fingerprinting. Since antimicrobials are classified into limited groups, the mechanism of action of known compounds can be used for predictive modeling. We demonstrate a cost-effective flow cytometry approach for determining the mechanism of action of new compounds. Cultures of Actinomyces viscosus and Fusobacterium nucleatum were treated with different antimicrobials and measured by flow cytometry. A Gaussian mixture mask was applied over the data to construct phenotypic fingerprints. Fingerprints were used to assess statistical differences between mechanism of action groups and to train random forest classifiers. Classifiers were then used to predict the mechanism of action of cephalothin. Statistical differences were found among the different mechanisms of action groups. Pairwise comparison showed statistical differences for 35 out of 45 pairs for A. viscosus and for 32 out of 45 pairs for F. nucleatum after 3.5 h of treatment. The best-performing random forest classifier yielded a Matthews correlation coefficient of 0.92 and the mechanism of action of cephalothin could be successfully predicted. These findings suggest that flow cytometry can be a cheap and fast alternative for determining the mechanism of action of new antimicrobials.IMPORTANCEIn the context of the emerging threat of antimicrobial resistance, the development of novel antimicrobials is a commonly employed strategy to combat resistance. Elucidating the mechanism of action of novel compounds is crucial in this development but can become expensive, as no universally applicable pipelines currently exist. We present a novel flow cytometry-based approach capable of determining the mechanism of action swiftly and cost-effectively. The workflow aims to accelerate drug discovery and could help facilitate a more targeted approach for antimicrobial treatment of patients.
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Affiliation(s)
- Fabian Mermans
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
- Department of Oral Health Sciences, KU Leuven & Dentistry (Periodontology), University Hospitals Leuven, Leuven, Belgium
| | - Hanna De Baets
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Cristina García-Timermans
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Wim Teughels
- Department of Oral Health Sciences, KU Leuven & Dentistry (Periodontology), University Hospitals Leuven, Leuven, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
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9
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Blasco B, Jang S, Terauchi H, Kobayashi N, Suzuki S, Akao Y, Ochida A, Morishita N, Takagi T, Nagamiya H, Suzuki Y, Watanabe T, Lee H, Lee S, Shum D, Cho A, Koh D, Park S, Lee H, Kim K, Ropponen HK, Augusto da Costa RM, Dunn S, Ghosh S, Sjö P, Piddock LJV. High-throughput screening of small-molecules libraries identified antibacterials against clinically relevant multidrug-resistant A. baumannii and K. pneumoniae. EBioMedicine 2024; 102:105073. [PMID: 38520916 PMCID: PMC10963893 DOI: 10.1016/j.ebiom.2024.105073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND The current pipeline for new antibiotics fails to fully address the significant threat posed by drug-resistant Gram-negative bacteria that have been identified by the World Health Organization (WHO) as a global health priority. New antibacterials acting through novel mechanisms of action are urgently needed. We aimed to identify new chemical entities (NCEs) with activity against Klebsiella pneumoniae and Acinetobacter baumannii that could be developed into a new treatment for drug-resistant infections. METHODS We developed a high-throughput phenotypic screen and selection cascade for generation of hit compounds active against multidrug-resistant (MDR) strains of K. pneumoniae and A. baumannii. We screened compound libraries selected from the proprietary collections of three pharmaceutical companies that had exited antibacterial drug discovery but continued to accumulate new compounds to their collection. Compounds from two out of three libraries were selected using "eNTRy rules" criteria associated with increased likelihood of intracellular accumulation in Escherichia coli. FINDINGS We identified 72 compounds with confirmed activity against K. pneumoniae and/or drug-resistant A. baumannii. Two new chemical series with activity against XDR A. baumannii were identified meeting our criteria of potency (EC50 ≤50 μM) and absence of cytotoxicity (HepG2 CC50 ≥100 μM and red blood cell lysis HC50 ≥100 μM). The activity of close analogues of the two chemical series was also determined against A. baumannii clinical isolates. INTERPRETATION This work provides proof of principle for the screening strategy developed to identify NCEs with antibacterial activity against multidrug-resistant critical priority pathogens such as K. pneumoniae and A. baumannii. The screening and hit selection cascade established here provide an excellent foundation for further screening of new compound libraries to identify high quality starting points for new antibacterial lead generation projects. FUNDING BMBF and GARDP.
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Affiliation(s)
- Benjamin Blasco
- Global Antibiotic Research and Development Partnership (GARDP), 15 Chemin Camille-Vidart, 1202, Geneva, Switzerland
| | - Soojin Jang
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Hiroki Terauchi
- Eisai Co., Ltd., Tsukuba Research Laboratories, 5-1-3 Tokodai, Tsukuba, Ibaraki, 300-2635, Japan
| | - Naoki Kobayashi
- Eisai Co., Ltd., Tsukuba Research Laboratories, 5-1-3 Tokodai, Tsukuba, Ibaraki, 300-2635, Japan
| | - Shuichi Suzuki
- Eisai Co., Ltd., Tsukuba Research Laboratories, 5-1-3 Tokodai, Tsukuba, Ibaraki, 300-2635, Japan
| | - Yuichiro Akao
- Takeda Pharmaceutical Company Ltd, 261, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Atsuko Ochida
- Takeda Pharmaceutical Company Ltd, 261, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Nao Morishita
- Takeda Pharmaceutical Company Ltd, 261, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Terufumi Takagi
- Takeda Pharmaceutical Company Ltd, 261, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hiroyuki Nagamiya
- Takeda Pharmaceutical Company Ltd, 261, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Yamato Suzuki
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Toshiaki Watanabe
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Hyunjung Lee
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Sol Lee
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - David Shum
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Ahreum Cho
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Dahae Koh
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Soonju Park
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Honggun Lee
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Kideok Kim
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Henni-Karoliina Ropponen
- Global Antibiotic Research and Development Partnership (GARDP), 15 Chemin Camille-Vidart, 1202, Geneva, Switzerland
| | | | | | - Sunil Ghosh
- TCG Lifesciences Private Limited, Block BN, Plot 7, Salt Lake Electronics Complex, Sector V, Kolkata, 700091, West Bengal, India
| | - Peter Sjö
- Drugs for Neglected Diseases Initiative, 15 Chemin Camille-Vidart, 1202, Geneva, Switzerland
| | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), 15 Chemin Camille-Vidart, 1202, Geneva, Switzerland.
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10
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Scaccaglia M, Birbaumer MP, Pinelli S, Pelosi G, Frei A. Discovery of antibacterial manganese(i) tricarbonyl complexes through combinatorial chemistry. Chem Sci 2024; 15:3907-3919. [PMID: 38487233 PMCID: PMC10935722 DOI: 10.1039/d3sc05326a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/23/2024] [Indexed: 03/17/2024] Open
Abstract
The continuous rise of antimicrobial resistance is a serious threat to human health and already causing hundreds of thousands of deaths each year. While natural products and synthetic organic small molecules have provided the majority of our current antibiotic arsenal, they are falling short in providing new drugs with novel modes of action able to treat multidrug resistant bacteria. Metal complexes have recently shown promising results as antimicrobial agents, but the number of studied compounds is still vanishingly small, making it difficult to identify promising compound classes or elucidate structure-activity relationships. To accelerate the pace of discovery we have applied a combinatorial chemistry approach to the synthesis of metalloantibiotics. Utilizing robust Schiff-base chemistry and combining 7 picolinaldehydes with 10 aniline derivatives, and 6 axial ligands, either imidazole/pyridine-based or solvent, we have prepared a library of 420 novel manganese tricarbonyl complexes. All compounds were evaluated for their antibacterial properties and 10 lead compounds were identified, re-synthesised and fully characterised. All 10 compounds showed high and broad activity against Gram-positive bacteria. The best manganese complex displayed low toxicity against human cells with a therapeutic index of >100. In initial mode of action studies, we show that it targets the bacterial membrane without inducing pore formation or depolarisation. Instead, it releases its carbon monoxide ligands around the membrane and inhibits the bacterial respiratory chain. This work demonstrates that large numbers of metal complexes can be accessed through combinatorial synthesis and evaluated for their antibacterial potential, allowing for the rapid identification of promising metalloantibiotic lead compounds.
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Affiliation(s)
- Mirco Scaccaglia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma 43124 Parma Italy
- Department of Chemistry, Biochemistry & Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Michael P Birbaumer
- Department of Chemistry, Biochemistry & Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Silvana Pinelli
- Department of Medicine and Surgery, University of Parma Via Gramsci 14 43126 Parma Italy
| | - Giorgio Pelosi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma 43124 Parma Italy
| | - Angelo Frei
- Department of Chemistry, Biochemistry & Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
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11
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Monterroso B, Margolin W, Boersma AJ, Rivas G, Poolman B, Zorrilla S. Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions. Chem Rev 2024; 124:1899-1949. [PMID: 38331392 PMCID: PMC10906006 DOI: 10.1021/acs.chemrev.3c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.
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Affiliation(s)
- Begoña Monterroso
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department
of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth-Houston, Houston, Texas 77030, United States
| | - Arnold J. Boersma
- Cellular
Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty
of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Germán Rivas
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - Bert Poolman
- Department
of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Zorrilla
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
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12
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Schäfer AB, Sidarta M, Abdelmesseh Nekhala I, Marinho Righetto G, Arshad A, Wenzel M. Dissecting antibiotic effects on the cell envelope using bacterial cytological profiling: a phenotypic analysis starter kit. Microbiol Spectr 2024; 12:e0327523. [PMID: 38289933 PMCID: PMC10913488 DOI: 10.1128/spectrum.03275-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Phenotypic analysis assays such as bacterial cytological profiling (BCP) have become increasingly popular for antibiotic mode of action analysis. A plethora of dyes, protein fusions, and reporter strains are available and have been used for this purpose, enabling both rapid mode of action categorization and in-depth analysis of antibiotic mechanisms. However, non-expert researchers may struggle choosing suitable assays and interpreting results. This is a particular problem for antibiotics that have multiple or complex targets, such as the bacterial cell envelope. Here, we set out to curate a minimal set of accessible and affordable phenotypic assays that allow distinction between membrane and cell wall targets, can identify dual-action inhibitors, and can be implemented in most research environments. To this end, we employed BCP, membrane potential, fluidity, and cell wall synthesis assays. To assess specificity and ease of interpretation, we tested three well-characterized and commercially available reference antibiotics: the potassium ionophore valinomycin, the lipid II-binding glycopeptide vancomycin, and the dual-action lantibiotic nisin, which binds lipid II and forms a membrane pore. Based on our experiments, we suggest a minimal set of BCP, a membrane-potentiometric probe, and fluorescent protein fusions to MinD and MreB as basic assay set and recommend complementing these assays with Laurdan-based fluidity measurements and a PliaI reporter fusion, where indicated. We believe that our results can provide guidance for researchers who wish to use phenotypic analysis for mode of action studies but do not possess the specialized equipment or expert knowledge to employ the full breadth of possible techniques.IMPORTANCEPhenotypic analysis assays using specialized fluorescence fusions and dyes have become increasingly popular in antibiotic mode of action analysis. However, it can be difficult to implement these methods due to the need for specialized equipment and/or the complexity of bacterial cell biology and physiology, making the interpretation of results difficult for non-experts. This is especially problematic for compounds that have multiple or pleiotropic effects, such as inhibitors of the bacterial cell envelope. In order to make phenotypic analysis assays accessible to labs, whose primary expertise is not bacterial cell biology, or with limited equipment and resources, a set of simple and broadly accessible assays is needed that is easy to implement, execute, and interpret. Here, we have curated a set of assays and strains that does not need highly specialized equipment, can be performed in most labs, and is straightforward to interpret without knowing the intricacies of bacterial cell biology.
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Affiliation(s)
- Ann-Britt Schäfer
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Margareth Sidarta
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Ireny Abdelmesseh Nekhala
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Gabriela Marinho Righetto
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Aysha Arshad
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Michaela Wenzel
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
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13
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Liu GY, Yu D, Fan MM, Zhang X, Jin ZY, Tang C, Liu XF. Antimicrobial resistance crisis: could artificial intelligence be the solution? Mil Med Res 2024; 11:7. [PMID: 38254241 PMCID: PMC10804841 DOI: 10.1186/s40779-024-00510-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Antimicrobial resistance is a global public health threat, and the World Health Organization (WHO) has announced a priority list of the most threatening pathogens against which novel antibiotics need to be developed. The discovery and introduction of novel antibiotics are time-consuming and expensive. According to WHO's report of antibacterial agents in clinical development, only 18 novel antibiotics have been approved since 2014. Therefore, novel antibiotics are critically needed. Artificial intelligence (AI) has been rapidly applied to drug development since its recent technical breakthrough and has dramatically improved the efficiency of the discovery of novel antibiotics. Here, we first summarized recently marketed novel antibiotics, and antibiotic candidates in clinical development. In addition, we systematically reviewed the involvement of AI in antibacterial drug development and utilization, including small molecules, antimicrobial peptides, phage therapy, essential oils, as well as resistance mechanism prediction, and antibiotic stewardship.
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Affiliation(s)
- Guang-Yu Liu
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Key Laboratory of Inflammation and Immunoregulation of Hangzhou, Hangzhou Normal University, Hangzhou, 311121, China
| | - Dan Yu
- National Key Discipline of Pediatrics Key Laboratory of Major Diseases in Children Ministry of Education, Laboratory of Dermatology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Mei-Mei Fan
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Key Laboratory of Inflammation and Immunoregulation of Hangzhou, Hangzhou Normal University, Hangzhou, 311121, China
| | - Xu Zhang
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ze-Yu Jin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christoph Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
| | - Xiao-Fen Liu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission of the People's Republic of China, National Clinical Research Centre for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
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14
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Kratz JC, Banerjee S. Gene expression tradeoffs determine bacterial survival and adaptation to antibiotic stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576495. [PMID: 38328084 PMCID: PMC10849509 DOI: 10.1101/2024.01.20.576495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
To optimize their fitness, cells face the crucial task of efficiently responding to various stresses. This necessitates striking a balance between conserving resources for survival and allocating resources for growth and division. The fundamental principles governing these tradeoffs is an outstanding challenge in the physics of living systems. In this study, we introduce a coarse-grained theoretical framework for bacterial physiology that establishes a connection between the physiological state of cells and their survival outcomes in dynamic environments, particularly in the context of antibiotic exposure. Predicting bacterial survival responses to varying antibiotic doses proves challenging due to the profound influence of the physiological state on critical parameters, such as the Minimum Inhibitory Concentration (MIC) and killing rates, even within an isogenic cell population. Our proposed theoretical model bridges the gap by linking extracellular antibiotic concentration and nutrient quality to intracellular damage accumulation and gene expression. This framework allows us to predict and explain the control of cellular growth rate, death rate, MIC and survival fraction in a wide range of time-varying environments. Surprisingly, our model reveals that cell death is rarely due to antibiotic levels being above the maximum physiological limit, but instead survival is limited by the inability to alter gene expression sufficiently quickly to transition to a less susceptible physiological state. Moreover, bacteria tend to overexpress stress response genes at the expense of reduced growth, conferring greater protection against further antibiotic exposure. This strategy is in contrast to those employed in different nutrient environments, in which bacteria allocate resources to maximize growth rate. This highlights an important tradeoff between the cellular capacity for growth and the ability to survive antibiotic exposure.
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Affiliation(s)
- Josiah C. Kratz
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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15
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Beyer L, Schäfer AB, Undabarrena A, Mattsby-Baltzer I, Tietze D, Svensson E, Stubelius A, Wenzel M, Cámara B, Tietze AA. Mimicking Nonribosomal Peptides from the Marine Actinomycete Streptomyces sp. H-KF8 Leads to Antimicrobial Peptides. ACS Infect Dis 2024; 10:79-92. [PMID: 38113038 PMCID: PMC10788856 DOI: 10.1021/acsinfecdis.3c00206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023]
Abstract
Microorganisms within the marine environment have been shown to be very effective sources of naturally produced antimicrobial peptides (AMPs). Several nonribosomal peptides were identified based on genome mining predictions of Streptomyces sp. H-KF8, a marine Actinomycetota isolated from a remote Northern Chilean Patagonian fjord. Based on these predictions, a series of eight peptides, including cyclic peptides, were designed and chemically synthesized. Six of these peptides showed antimicrobial activity. Mode of action studies suggest that two of these peptides potentially act on the cell membrane via a novel mechanism allowing the passage of small ions, resulting in the dissipation of the membrane potential. This study shows that though structurally similar peptides, determined by NMR spectroscopy, the incorporation of small sequence mutations results in a dramatic influence on their bioactivity including mode of action. The qualified hit sequence can serve as a basis for more potent AMPs in future studies.
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Affiliation(s)
- Luisa
I. Beyer
- Department
of Chemistry and Molecular Biology, Wallenberg Centre for Molecular
and Translational Medicine, University of
Gothenburg, Medicinaregatan
7B, Gothenburg 413 90, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg, University of Gothenburg, Box 100, Göteborg 405 30, Sweden
| | - Ann-Britt Schäfer
- Department
of Life Sciences, Chalmers University of
Technology, Kemigården 4, Göteborg 412 96, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg, University of Gothenburg, Box 100, Göteborg 405 30, Sweden
| | - Agustina Undabarrena
- Departamento
de Química & Centro de Biotecnología Daniel Alkalay
Lowitt, Laboratorio de Microbiología Molecular y Biotecnología
Ambiental, Universidad Técnica Federico
Santa María, Valparaíso 2340000, Chile
| | - Inger Mattsby-Baltzer
- Department
of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska
Academy at University of Gothenburg, University
of Gothenburg, Box 440, Göteborg 405 30, Sweden
| | - Daniel Tietze
- Department
of Chemistry and Molecular Biology, Wallenberg Centre for Molecular
and Translational Medicine, University of
Gothenburg, Medicinaregatan
7B, Gothenburg 413 90, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg, University of Gothenburg, Box 100, Göteborg 405 30, Sweden
| | - Elin Svensson
- Department
of Life Sciences, Chalmers University of
Technology, Kemigården 4, Göteborg 412 96, Sweden
| | - Alexandra Stubelius
- Department
of Life Sciences, Chalmers University of
Technology, Kemigården 4, Göteborg 412 96, Sweden
| | - Michaela Wenzel
- Department
of Life Sciences, Chalmers University of
Technology, Kemigården 4, Göteborg 412 96, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg, University of Gothenburg, Box 100, Göteborg 405 30, Sweden
| | - Beatriz Cámara
- Departamento
de Química & Centro de Biotecnología Daniel Alkalay
Lowitt, Laboratorio de Microbiología Molecular y Biotecnología
Ambiental, Universidad Técnica Federico
Santa María, Valparaíso 2340000, Chile
| | - Alesia A. Tietze
- Department
of Chemistry and Molecular Biology, Wallenberg Centre for Molecular
and Translational Medicine, University of
Gothenburg, Medicinaregatan
7B, Gothenburg 413 90, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg, University of Gothenburg, Box 100, Göteborg 405 30, Sweden
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16
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Deep A, Liang Q, Enustun E, Pogliano J, Corbett KD. Architecture and infection-sensing mechanism of the bacterial PARIS defense system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573835. [PMID: 38260510 PMCID: PMC10802264 DOI: 10.1101/2024.01.02.573835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Bacteria and the viruses that infect them (bacteriophages or phages) are engaged in an evolutionary arms race that has resulted in the development of hundreds of bacterial defense systems and myriad phage-encoded counterdefenses1-5. While the mechanisms of many bacterial defense systems are known1, how these systems avoid toxicity outside infection yet activate quickly upon sensing phage infection is less well understood. Here, we show that the bacterial Phage Anti-Restriction-Induced System (PARIS) operates as a toxin-antitoxin system, in which the antitoxin AriA sequesters and inactivates the toxin AriB until triggered by the T7 phage counterdefense protein Ocr. Using cryoelectron microscopy (cryoEM), we show that AriA is structurally similar to dimeric SMC-family ATPases but assembles into a distinctive homohexameric complex through two distinct oligomerization interfaces. In the absence of infection, the AriA hexamer binds up to three monomers of AriB, maintaining them in an inactive state. Ocr binding to the AriA-AriB complex triggers rearrangement of the AriA hexamer, releasing AriB and allowing it to dimerize and activate. AriB is a toprim/OLD-family nuclease whose activation arrests cell growth and inhibits phage propagation by globally inhibiting protein translation. Collectively, our findings reveal the intricate molecular mechanisms of a bacterial defense system that evolved in response to a phage counterdefense protein, and highlight how an SMC-family ATPase has been adapted as a bacterial infection sensor.
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Affiliation(s)
- Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA, USA
| | - Qishan Liang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla CA, USA
| | - Eray Enustun
- Department of Molecular Biology, University of California San Diego, La Jolla CA, USA
| | - Joe Pogliano
- Department of Molecular Biology, University of California San Diego, La Jolla CA, USA
| | - Kevin D. Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA, USA
- Department of Molecular Biology, University of California San Diego, La Jolla CA, USA
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17
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Guo LD, Wu Y, Xu X, Lin Z, Tong R. Bent π-Conjugation within a Macrocycle: Asymmetric Total Syntheses of Spirohexenolides A and B. Angew Chem Int Ed Engl 2024; 63:e202316259. [PMID: 37988261 DOI: 10.1002/anie.202316259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 11/23/2023]
Abstract
Macrocycles with bent π-conjugation motif are extremely rare in nature and synthetically daunting and anticancer haouamines and spirohexenolides were representative of such rare natural products with synthetically challenging bent π-conjugation within a macrocycle. While the total synthesis of haouamines has been elegantly achieved, spirohexenolides remains an unmet synthetic challenge due to the highly strained bent 1,3,5-triene conjugation within C15 macrocycle. Inspired by the chemical synthesis of cycloparaphenylenes (CPPs) and haouamines, herein we devise a synthetic strategy to overcome the highly strained bent 1,3,5-triene conjugation within the macrocycle and achieve the first, asymmetric total synthesis of spirohexenolides A (>20 mg) and B (>50 mg). Our synthesis features strategic design of ring-closing metathesis (RCM) macrocyclization followed by double dehydration to achieve the C15 macrocycle with the deformed nonplanar 1,3,5-triene conjugation. In addition, we have developed a new enantioselective construction of highly functionalized spirotetronate fragment (northeast moiety) through RCM and Ireland-Claisen rearrangement. Our in vitro bioassay studies reveal that both spirohexenolides are cytotoxic against a panel of human cancer cells with IC50 1.2-13.3 μM and spirohexenolide A is consistently more potent (up to 3 times) than spirohexenolide B, suggesting the importance of alcohol for their bioactivity and for medicinal chemistry development.
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Affiliation(s)
- Lian-Dong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, 999077, China
| | - Yanting Wu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, 999077, China
| | - Xin Xu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, 999077, China
| | - Zhenyang Lin
- Department of Chemistry, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, 999077, China
| | - Rongbiao Tong
- Department of Chemistry, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, 999077, China
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18
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Nazli A, Qiu J, Tang Z, He Y. Recent Advances and Techniques for Identifying Novel Antibacterial Targets. Curr Med Chem 2024; 31:464-501. [PMID: 36734893 DOI: 10.2174/0929867330666230123143458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly. METHODS In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification. RESULTS Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well. CONCLUSION The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
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19
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Kamal El-sagheir A, Abdelmesseh Nekhala I, Abd El-Gaber MK, Aboraia AS, Persson J, Schäfer AB, Wenzel M, Omar FA. N4-Substituted Piperazinyl Norfloxacin Derivatives with Broad-Spectrum Activity and Multiple Mechanisms on Gyrase, Topoisomerase IV, and Bacterial Cell Wall Synthesis. ACS BIO & MED CHEM AU 2023; 3:494-506. [PMID: 38144255 PMCID: PMC10739246 DOI: 10.1021/acsbiomedchemau.3c00038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 12/26/2023]
Abstract
Fluoroquinolones are an important class of antibiotics with broad-spectrum antibacterial and antitubercular activity. Here, we describe the design and synthesis of a series of 38 N4-substituted piperazinyl norfloxacin derivatives. Their activity and mechanism of action were characterized using in silico, in vitro, and in vivo approaches. Several compounds displayed interesting activities against both Gram-negative and Gram-positive bacteria, and few displayed antimycobacterial activity, whereby some were as potent as norfloxacin and ciprofloxacin. Molecular docking experiments suggested that the new derivatives inhibit both DNA gyrase and DNA topoisomerase IV in a similar manner as norfloxacin. Selecting the most promising candidates for experimental mode of action analysis, we confirmed DNA gyrase and topoisomerase IV as targets of all tested compounds using enzymatic in vitro assays. Phenotypic analysis of both Escherichia coli and Bacillus subtilis confirmed a typical gyrase inhibition phenotype for all of the tested compounds. Assessment of possible additional targets revealed three compounds with unique effects on the B. subtilis cell wall synthesis machinery, suggesting that they may have an additional target in this pathway. Comparison with known cell wall synthesis inhibitors showed that the new compounds elicit a distinct and, so far, unique phenotype, suggesting that they act differently from known cell wall synthesis inhibitors. Interestingly, our phenotypic analysis revealed that both norfloxacin and ciprofloxacin displayed additional cellular effects as well, which may be indicative of the so far unknown additional mechanisms of fluoroquinolones.
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Affiliation(s)
| | - Ireny Abdelmesseh Nekhala
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | | | - Ahmed S. Aboraia
- Medicinal
Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Jonatan Persson
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg (CARe), 405 30 Gothenburg, Sweden
| | - Ann-Britt Schäfer
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg (CARe), 405 30 Gothenburg, Sweden
| | - Michaela Wenzel
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg (CARe), 405 30 Gothenburg, Sweden
| | - Farghaly A. Omar
- Medicinal
Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
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20
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Ausbacher D, Miller LA, Goeres DM, Stewart PS, Strøm MB, Fallarero A. α,α-disubstituted β-amino amides eliminate Staphylococcus aureus biofilms by membrane disruption and biomass removal. Biofilm 2023; 6:100151. [PMID: 37662850 PMCID: PMC10474319 DOI: 10.1016/j.bioflm.2023.100151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/12/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023] Open
Abstract
Bacterial biofilms account for up to 80% of all infections and complicate successful therapies due to their intrinsic tolerance to antibiotics. Biofilms also cause serious problems in the industrial sectors, for instance due to the deterioration of metals or microbial contamination of products. Efforts are put in finding novel strategies in both avoiding and fighting biofilms. Biofilm control is achieved by killing and/or removing biofilm or preventing transition to the biofilm lifestyle. Previous research reported on the anti-biofilm potency of α,α-disubstituted β-amino amides A1, A2 and A3, which are small antimicrobial peptidomimetics with a molecular weight below 500 Da. In the current study it was investigated if these derivatives cause a fast disintegration of biofilm bacteria and removal of Staphylococcus aureus biofilms. One hour incubation of biofilms with all three derivatives resulted in reduced metabolic activity and membrane permeabilization in S. aureus (ATCC 25923) biofilms. Bactericidal properties of these derivatives were attributed to a direct effect on membranes of biofilm bacteria. The green fluorescence protein expressing Staphylococcus aureus strain AH2547 was cultivated in a CDC biofilm reactor and utilized for disinfectant efficacy testing of A3, following the single tube method (American Society for Testing and Materials designation number E2871). A3 at a concentration of 90 μM acted as fast as 100 μM chlorhexidine and was equally effective. Confocal laser scanning microscopy studies showed that chlorhexidine treatment lead to fluorescence fading indicating membrane permeabilization but did not cause biomass removal. In contrast, A3 treatment caused a simultaneous biofilm fluorescence loss and biomass removal. These dual anti-biofilm properties make α,α-disubstituted β-amino amides promising scaffolds in finding new control strategies against recalcitrant biofilms.
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Affiliation(s)
- Dominik Ausbacher
- Natural Products and Medicinal Chemistry Research Group, Department of Pharmacy, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Lindsey A. Miller
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
| | - Darla M. Goeres
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
| | - Philip S. Stewart
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
| | - Morten B. Strøm
- Natural Products and Medicinal Chemistry Research Group, Department of Pharmacy, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Adyary Fallarero
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, FI-00014, Helsinki, Finland
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21
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Kamal El-Sagheir AM, Abdelmesseh Nekhala I, Abd El-Gaber MK, Aboraia AS, Persson J, Schäfer AB, Wenzel M, Omar FA. Rational design, synthesis, molecular modeling, biological activity, and mechanism of action of polypharmacological norfloxacin hydroxamic acid derivatives. RSC Med Chem 2023; 14:2593-2610. [PMID: 38099058 PMCID: PMC10718593 DOI: 10.1039/d3md00309d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/11/2023] [Indexed: 12/17/2023] Open
Abstract
Fluoroquinolones are broad-spectrum antibiotics that target gyrase and topoisomerase IV, involved in DNA compaction and segregation. We synthesized 28 novel norfloxacin hydroxamic acid derivatives with additional metal-chelating and hydrophobic pharmacophores, designed to enable interactions with additional drug targets. Several compounds showed equal or better activity than norfloxacin against Gram-positive, Gram-negative, and mycobacteria, with MICs as low as 0.18 μM. The most interesting derivatives were selected for in silico, in vitro, and in vivo mode of action studies. Molecular docking, enzyme inhibition, and bacterial cytological profiling confirmed inhibition of gyrase and topoisomerase IV for all except two tested derivatives (10f and 11f). Further phenotypic analysis revealed polypharmacological effects on peptidoglycan synthesis for four derivatives (16a, 17a, 17b, 20b). Interestingly, compounds 17a, 17b, and 20b, showed never seen before effects on cell wall synthetic enzymes, including MreB, MurG, and PonA, suggesting a novel mechanism of action, possibly impairing the lipid II cycle.
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Affiliation(s)
| | - Ireny Abdelmesseh Nekhala
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
| | | | - Ahmed S Aboraia
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University Assiut 71526 Egypt
| | - Jonatan Persson
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Ann-Britt Schäfer
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Michaela Wenzel
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Farghaly A Omar
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University Assiut 71526 Egypt
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22
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Shrestha S, Taib N, Gribaldo S, Shen A. Diversification of division mechanisms in endospore-forming bacteria revealed by analyses of peptidoglycan synthesis in Clostridioides difficile. Nat Commun 2023; 14:7975. [PMID: 38042849 PMCID: PMC10693644 DOI: 10.1038/s41467-023-43595-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/14/2023] [Indexed: 12/04/2023] Open
Abstract
The bacterial enzymes FtsW and FtsI, encoded in the highly conserved dcw gene cluster, are considered to be universally essential for the synthesis of septal peptidoglycan (PG) during cell division. Here, we show that the pathogen Clostridioides difficile lacks a canonical FtsW/FtsI pair, and its dcw-encoded PG synthases have undergone a specialization to fulfill sporulation-specific roles, including synthesizing septal PG during the sporulation-specific mode of cell division. Although these enzymes are directly regulated by canonical divisome components during this process, dcw-encoded PG synthases and their divisome regulators are dispensable for cell division during normal growth. Instead, C. difficile uses a bifunctional class A penicillin-binding protein as the core divisome PG synthase, revealing a previously unreported role for this class of enzymes. Our findings support that the emergence of endosporulation in the Firmicutes phylum facilitated the functional repurposing of cell division factors. Moreover, they indicate that C. difficile, and likely other clostridia, assemble a distinct divisome that therefore may represent a unique target for therapeutic interventions.
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Affiliation(s)
- Shailab Shrestha
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
- Program in Molecular Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, MA, USA
| | - Najwa Taib
- Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell Unit, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell Unit, Paris, France
| | - Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
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23
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Boyang H, Yangyanqiu W, Wenting R, Chenxin Y, Jian C, Zhanbo Q, Yanjun Y, Qiang Y, Shuwen H. Application and progress of highcontent imaging in molecular biology. Biotechnol J 2023; 18:e2300170. [PMID: 37639283 DOI: 10.1002/biot.202300170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/03/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
Humans have adopted many different methods to explore matter imaging, among which high content imaging (HCI) could conduct automated imaging analysis of cells while maintaining its structural and functional integrity. Meanwhile, as one of the most important research tools for diagnosing human diseases, HCI is widely used in the frontier of medical research, and its future application has attracted researchers' great interests. Here, the meaning of HCI was briefly explained, the history of optical imaging and the birth of HCI were described, and the experimental methods of HCI were described. Furthermore, the directions of the application of HCI were highlighted in five aspects: protein localization changes, gene identification, chemical and genetic analysis, microbiology, and drug discovery. Most importantly, some challenges and future directions of HCI were discussed, and the application and optimization of HCI were expected to be further explored.
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Affiliation(s)
- Hu Boyang
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Wang Yangyanqiu
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Rui Wenting
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Yan Chenxin
- Shulan International Medical School, Zhejiang Shuren University, Hangzhou, China
| | - Chu Jian
- Fifth Affiliated Clinical Medical College of Zhejiang Chinese Medical University, Huzhou Central Hospital, Huzhou, China
| | - Qu Zhanbo
- Fifth Affiliated Clinical Medical College of Zhejiang Chinese Medical University, Huzhou Central Hospital, Huzhou, China
| | - Yao Yanjun
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Yan Qiang
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Han Shuwen
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, China
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24
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Upender I, Yoshida O, Schrecengost A, Ranson H, Wu Q, Rowley DC, Kishore S, Cywes C, Miller EL, Whalen KE. A marine-derived fatty acid targets the cell membrane of Gram-positive bacteria. J Bacteriol 2023; 205:e0031023. [PMID: 37905811 PMCID: PMC10662121 DOI: 10.1128/jb.00310-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE With the lack of new antibiotics in the drug discovery pipeline, coupled with accelerated evolution of antibiotic resistance, new sources of antibiotics that target pathogens of clinical importance are paramount. Here, we use bacterial cytological profiling to identify the mechanism of action of the monounsaturated fatty acid (Z)-13-methyltetra-4-decenoic acid isolated from the marine bacterium Olleya marilimosa with antibacterial effects against Gram-positive bacteria. The fatty acid antibiotic was found to rapidly destabilize the cell membrane by pore formation and membrane aggregation in Bacillus subtilis, suggesting that this fatty acid may be a promising adjuvant used in combination to enhance antibiotic sensitivity.
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Affiliation(s)
- Isha Upender
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Olivia Yoshida
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Anna Schrecengost
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Hilary Ranson
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
- College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
| | - Qihao Wu
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
- College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
| | - David C. Rowley
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
- College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
| | - Shreya Kishore
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Claire Cywes
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Eric L. Miller
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Kristen E. Whalen
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
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25
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Soonthonsrima T, Htoo HH, Thiennimitr P, Srisuknimit V, Nonejuie P, Chaikeeratisak V. Phage-induced bacterial morphological changes reveal a phage-derived antimicrobial affecting cell wall integrity. Antimicrob Agents Chemother 2023; 67:e0076423. [PMID: 37843261 PMCID: PMC10648931 DOI: 10.1128/aac.00764-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/24/2023] [Indexed: 10/17/2023] Open
Abstract
In a looming post-antibiotic era, antibiotic alternatives have become key players in the combat against pathogens. Although recent advances in genomic research allow scientists to fully explore an organism's genome in the search for novel antibacterial molecules, laborious work is still needed in order to dissect each individual gene product for its antibacterial activity. Here, we exploited phage-induced bacterial morphological changes as anchors to explore and discover a potential phage-derived antimicrobial embedded in the phage genome. We found that, upon vibriophage KVP40 infection, Vibrio parahaemolyticus exhibited morphological changes similar to those observed when treated with mecillinam, a cell wall synthesis inhibitor, suggesting the mechanism of pre-killing that KVP40 exerts inside the bacterial cell upon sieging the host. Genome analysis revealed that, of all the annotated gene products in the KVP40 genome that are involved in cell wall degradation, lytic transglycosylase (LT) is of particular interest for subsequent functional studies. A single-cell morphological analysis revealed that heterologous expression of wild-type KVP40-LT induced similar bacterial morphological changes to those treated with the whole phage or mecillinam, prior to cell burst. On the contrary, neither the morphology nor the viability of the bacteria expressing signal-peptide truncated- or catalytic mutant E80A- KVP40-LT was affected, suggesting the necessity of these domains for the antibacterial activities. Altogether, this research paves the way for the future development of the discovery of phage-derived antimicrobials that is guided through phage-induced morphological changes.
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Affiliation(s)
- Tanapon Soonthonsrima
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Htut Htut Htoo
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Veerasak Srisuknimit
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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26
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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27
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Zagajewski A, Turner P, Feehily C, El Sayyed H, Andersson M, Barrett L, Oakley S, Stracy M, Crook D, Nellåker C, Stoesser N, Kapanidis AN. Deep learning and single-cell phenotyping for rapid antimicrobial susceptibility detection in Escherichia coli. Commun Biol 2023; 6:1164. [PMID: 37964031 PMCID: PMC10645916 DOI: 10.1038/s42003-023-05524-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023] Open
Abstract
The rise of antimicrobial resistance (AMR) is one of the greatest public health challenges, already causing up to 1.2 million deaths annually and rising. Current culture-based turnaround times for bacterial identification in clinical samples and antimicrobial susceptibility testing (AST) are typically 18-24 h. We present a novel proof-of-concept methodological advance in susceptibility testing based on the deep-learning of single-cell specific morphological phenotypes directly associated with antimicrobial susceptibility in Escherichia coli. Our models can reliably (80% single-cell accuracy) classify untreated and treated susceptible cells for a lab-reference fully susceptible E. coli strain, across four antibiotics (ciprofloxacin, gentamicin, rifampicin and co-amoxiclav). For ciprofloxacin, we demonstrate our models reveal significant (p < 0.001) differences between bacterial cell populations affected and unaffected by antibiotic treatment, and show that given treatment with a fixed concentration of 10 mg/L over 30 min these phenotypic effects correlate with clinical susceptibility defined by established clinical breakpoints. Deploying our approach on cell populations from six E. coli strains obtained from human bloodstream infections with varying degrees of ciprofloxacin resistance and treated with a range of ciprofloxacin concentrations, we show single-cell phenotyping has the potential to provide equivalent information to growth-based AST assays, but in as little as 30 min.
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Affiliation(s)
- Alexander Zagajewski
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Piers Turner
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Conor Feehily
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Hafez El Sayyed
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Monique Andersson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Lucinda Barrett
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Sarah Oakley
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Mathew Stracy
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Christoffer Nellåker
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Big Data Institute, Oxford, OX3 7LF, UK.
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK.
| | - Achillefs N Kapanidis
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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28
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Kamal El-sagheir A, Abdelmesseh Nekhala I, Abd El-Gaber MK, Aboraia AS, Persson J, Schäfer AB, Wenzel M, Omar FA. Design, Synthesis, Molecular Modeling, Biological Activity, and Mechanism of Action of Novel Amino Acid Derivatives of Norfloxacin. ACS OMEGA 2023; 8:43271-43284. [PMID: 38024743 PMCID: PMC10653056 DOI: 10.1021/acsomega.3c07221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
Two series of N4-substituted piperazinyl amino acid derivatives of norfloxacin (24 new compounds) were designed and synthesized to attain structural surrogates with additional binding sites and enhanced antibacterial activity. Synthesized derivatives showed increased antibacterial and antimycobacterial activity compared to their lead structure, norfloxacin. Molecular modeling studies supported the notion that the derivatives can establish additional bonds with the target enzymes gyrase and topoisomerase IV. In vitro enzyme inhibition assays confirmed that the tested compounds were significant inhibitors of these enzymes. Inhibition of gyrase and topoisomerase IV was then confirmed in living bacterial cells using bacterial cytological profiling of both Gram-negative Escherichia coli and Gram-positive Bacillus subtilis, revealing a typical topoisomerase inhibition phenotype characterized by severe nucleoid packing defects. Several derivatives exhibited additional effects on the Gram-positive cell wall synthesis machinery and/or the cytoplasmic membrane, which likely contributed to their increased antibacterial activity. While we could not identify specific cell wall or membrane targets, membrane depolarization was not observed. Our experiments further suggest that cell wall synthesis inhibition most likely occurs outside the membrane-bound lipid II cycle.
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Affiliation(s)
| | - Ireny Abdelmesseh Nekhala
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | | | - Ahmed S. Aboraia
- Medicinal
Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Jonatan Persson
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg 405 30, Sweden
| | - Ann-Britt Schäfer
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg 405 30, Sweden
| | - Michaela Wenzel
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg 405 30, Sweden
| | - Farghaly A. Omar
- Medicinal
Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
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29
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Grucela PK, Zhang YE. Basal level of ppGpp coordinates Escherichia coli cell heterogeneity and ampicillin resistance and persistence. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:248-260. [PMID: 37933276 PMCID: PMC10625690 DOI: 10.15698/mic2023.11.808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/20/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
The universal stringent response alarmone ppGpp (guanosine penta and tetra phosphates) plays a crucial role in various aspects of fundamental cell physiology (e.g., cell growth rate, cell size) and thus bacterial tolerance to and survival of external stresses, including antibiotics. Besides transient antibiotic tolerance (persistence), ppGpp was recently found to contribute to E. coli resistance to ampicillin. How ppGpp regulates both the persistence and resistance to antibiotics remains incompletely understood. In this study, we first clarified that the absence of ppGpp in E. coli (ppGpp0 strain) resulted in a decreased minimal inhibition concentration (MIC) value of ampicillin but, surprisingly, a higher persistence level to ampicillin during exponential growth in MOPS rich medium. High basal ppGpp levels, thus lower growth rate, did not produce high ampicillin persistence. Importantly, we found that the high ampicillin persistence of the ppGpp0 strain is not due to dormant overnight carry-over cells. Instead, the absence of ppGpp produced higher cell heterogeneity, propagating during the regrowth and the killing phases, leading to higher ampicillin persistence. Consistently, we isolated a suppressor mutation of the ppGpp0 strain that restored the standard MIC value of ampicillin and reduced its cell heterogeneity and the ampicillin persistence level concomitantly. Altogether, we discussed the fundamental role of basal level of ppGpp in regulating cell homogeneity and ampicillin persistence.
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Affiliation(s)
| | - Yong Everett Zhang
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
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30
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Podoll JD, Rosen E, Wang W, Gao Y, Zhang J, Wang X. A small-molecule membrane fluidizer re-sensitizes methicillin-resistant Staphylococcus aureus (MRSA) to β-lactam antibiotics. Antimicrob Agents Chemother 2023; 67:e0005123. [PMID: 37681969 PMCID: PMC10583677 DOI: 10.1128/aac.00051-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 06/04/2023] [Indexed: 09/09/2023] Open
Abstract
Novel antibacterial agents and strategies are urgently needed to fight against the ongoing global antibiotic resistance problem. While natural products remain the main source in antibiotic discovery, synthetic antibacterials provide an attractive alternative and may evade the ancient antibiotic resistance. Herein, we report a small molecule that re-sensitizes methicillin-resistant Staphylococcus aureus to β-lactam antibiotics with extremely low potential for resistance development. It belongs to a new class of broad-spectrum antibacterials, trypyricins, which share similar structural characteristics and mechanism of action to the cationic antimicrobial peptides. Mechanistic studies indicated that trypyricins fluidize and disrupt bacterial cytoplasmic membrane. These results suggested that trypyricins represent a promising new class of antibacterials and may be further developed as antibiotic adjuvants to fight against resistant bacteria in the clinic.
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Affiliation(s)
| | - Emma Rosen
- Recreo Pharmaceuticals Inc, Yale Circle, Boulder, Colorado, USA
| | - Wei Wang
- Department of Chemistry, University of Colorado, Boulder, Colorado, USA
| | - Yuefeng Gao
- Department of Chemistry, University of Colorado, Boulder, Colorado, USA
| | - Jing Zhang
- Recreo Pharmaceuticals Inc, Yale Circle, Boulder, Colorado, USA
| | - Xiang Wang
- Department of Chemistry, University of Colorado, Boulder, Colorado, USA
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31
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Khunti P, Chantakorn K, Tantibhadrasapa A, Htoo HH, Thiennimitr P, Nonejuie P, Chaikeeratisak V. A novel coli myophage and antibiotics synergistically inhibit the growth of the uropathogenic E. coli strain CFT073 in stoichiometric niches. Microbiol Spectr 2023; 11:e0088923. [PMID: 37732769 PMCID: PMC10580823 DOI: 10.1128/spectrum.00889-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/20/2023] [Indexed: 09/22/2023] Open
Abstract
Urinary tract infections are widespread bacterial infections affecting millions of people annually, with Escherichia coli being the most prevalent. Although phage therapy has recently gained interest as a promising alternative therapy for antibiotic-resistant bacteria, several studies have raised concerns regarding the evolution of phage resistance, making the therapy ineffective. In this study, we discover a novel coli myophage designated as Killian that targets E. coli strains, including the uropathogenic E. coli (UPEC) strain CFT073. It requires at least 20 minutes for 90% of its particles to adsorb to the host cells, undergoes subcellular activities for replication for 30 minutes, and eventually lyses the cells with a burst size of about 139 particles per cell. Additionally, Killian can withstand a wide variety of temperatures (4-50°C) and pHs (4-10). Genome analysis reveals that Killian's genome consists of 169,905 base pairs with 35.5% GC content, encoding 276 open reading frames; of these, 209 are functionally annotated with no undesirable genes detected, highlighting its potential as an antibiotic alternative against UPEC. However, after an 8-hour phage treatment at high multiplicities of infection, bacterial density continuously increases, indicating an onset of bacterial growth revival. Thus, the combination study between the phage and three different antibiotics, including amikacin, ciprofloxacin, and piperacillin, was performed and showed that certain pairs of phage and antibiotics exhibited synergistic interactions in suppressing the bacterial growth revival. These findings suggest that Killian-antibiotic combinations are effective in inhibiting the growth of UPEC. IMPORTANCE Phage therapy has recently been in the spotlight as a viable alternative therapy for bacterial infections. However, several studies have raised concerns about the emergence of phage resistance that occurs during treatment, making the therapy not much effective. Here, we present the discovery of a novel E. coli myophage that, by itself, can effectively kill the uropathogenic E. coli, but the emergence of bacterial growth revival was detected during the treatment. Phage and antibiotics are then combined to improve the efficiency of the phage in suppressing the bacterial re-growth. This research would pave the way for the future development of phage-antibiotic cocktails for the sustainable use of phages for therapeutic purposes.
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Affiliation(s)
- Patiphan Khunti
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | | | - Htut Htut Htoo
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
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32
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Baranova AA, Tyurin AP, Korshun VA, Alferova VA. Sensing of Antibiotic-Bacteria Interactions. Antibiotics (Basel) 2023; 12:1340. [PMID: 37627760 PMCID: PMC10451291 DOI: 10.3390/antibiotics12081340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Sensing of antibiotic-bacteria interactions is an important area of research that has gained significant attention in recent years. Antibiotic resistance is a major public health concern, and it is essential to develop new strategies for detecting and monitoring bacterial responses to antibiotics in order to maintain effective antibiotic development and antibacterial treatment. This review summarizes recent advances in sensing strategies for antibiotic-bacteria interactions, which are divided into two main parts: studies on the mechanism of action for sensitive bacteria and interrogation of the defense mechanisms for resistant ones. In conclusion, this review provides an overview of the present research landscape concerning antibiotic-bacteria interactions, emphasizing the potential for method adaptation and the integration of machine learning techniques in data analysis, which could potentially lead to a transformative impact on mechanistic studies within the field.
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Affiliation(s)
| | | | | | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (A.P.T.); (V.A.K.)
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33
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Wang C, Nguyen T, Yang X, Mellick GD, Feng Y. Phytochemical investigation of Asarum sieboldii var. seoulense and the phenotypic profiles of its constituents against a Parkinson's Disease olfactory cell line. Bioorg Med Chem Lett 2023; 92:129386. [PMID: 37355024 DOI: 10.1016/j.bmcl.2023.129386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 06/26/2023]
Abstract
Asarum sieboldii var. seoulense is a plant species under the family Aristolochiaceae and has been used for centuries as an ingredient in a well-known Traditional Chinese medicine (TCM), "Xixin", to treat symptoms of the neurodegenerative condition Parkinson's Disease (PD). Although there have been studies on the neuroprotective effect of this TCM, the phenotypic profiles of its chemical constituents against PD-implicated cellular organelles have not been reported. This research investigated the chemistry of A. sieboldii var. seoulense extract to identify the active small molecules that exhibited perturbation to the cellular compartments related to PD, potentially supporting its traditional application in treating this condition. 1H NMR-guided chemical investigation of this plant yielded twenty secondary metabolites which belong to isobutylamides, lignans and phenolics. The compounds were evaluated against an olfactory cell line derived from a PD patient using phenotypic assay. Several isolates, 2, 3, 7, 11, 13-16 and 18-20, were found to induce moderate perturbation to the staining of mitochondria, autophagosome and α-tubulin of the cells. Considering that PD pathogenesis is closely related to these cellular compartments, the results provided a rationale for the traditional application of Xixin in the treatment of PD.
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Affiliation(s)
- Chao Wang
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Thanh Nguyen
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Xinzhou Yang
- College of Pharmacy, South-Central University for Nationalities, Wuhan 430074, China
| | - George D Mellick
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia.
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34
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Shrestha S, Taib N, Gribaldo S, Shen A. Analyses of cell wall synthesis in Clostridioides difficile reveal a diversification in cell division mechanisms in endospore-forming bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.06.552200. [PMID: 37609260 PMCID: PMC10441361 DOI: 10.1101/2023.08.06.552200] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Current models of bacterial cell division assume that the core synthases of the multiprotein divisome complex, FtsW-FtsI, are the primary drivers of septal peptidoglycan (PG) synthesis. These enzymes are typically encoded in the highly conserved division and cell wall (dcw) cluster and are considered to be universally essential for cell division. Here, we combine bioinformatics analyses with functional characterization in the pathogen Clostridioides difficile to show that dcw-encoded PG synthases have undergone a surprising specialization in the sole endospore-forming phylum, Firmicutes, to fulfill sporulation-specific roles. We describe a novel role for these enzymes in synthesizing septal PG during the sporulation-specific mode of cell division in C. difficile. Although these enzymes are directly regulated by canonical divisome components during this process, dcw-encoded PG synthases and their divisome regulators are unexpectedly dispensable for cell division during normal growth. Instead, C. difficile uses its sole bifunctional class A penicillin-binding protein (aPBP) to drive cell division, revealing a previously unreported role for this class of PG synthases as the core divisome enzyme. Collectively, our findings reveal how the emergence of endosporulation in the Firmicutes phylum was a key driver for the functional repurposing of an otherwise universally conserved cellular process such as cell division. Moreover, they indicate that C. difficile, and likely other clostridia, assemble a divisome that differs markedly from previously studied bacteria, thus representing an attractive, unique target for therapeutic purposes.
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Affiliation(s)
- Shailab Shrestha
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
- Program in Molecular Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, MA, USA
| | - Najwa Taib
- Institut Pasteur, Université de Paris, Unit Evolutionary Biology of the Microbial Cell, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université de Paris, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
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35
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Dixneuf S, Chareire-Kleiberg AC, Mahé P, El Azami M, Kolytcheff C, Bellais S, Guyard C, Védrine C, Mallard F, Josso Q, Rol F. Single-cell scattering and auto-fluorescence-based fast antibiotic susceptibility testing for gram-negative and gram-positive bacteria. Front Microbiol 2023; 14:1232250. [PMID: 37601345 PMCID: PMC10436599 DOI: 10.3389/fmicb.2023.1232250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
In this study, we assess the scattering of light and auto-fluorescence from single bacterial cells to address the challenge of fast (<2 h), label-free phenotypic antimicrobial susceptibility testing (AST). Label-free flow cytometry is used for monitoring both the respiration-related auto-fluorescence in two different fluorescence channels corresponding to FAD and NADH, and the morphological and structural information contained in the light scattered by individual bacteria during incubation with or without antibiotic. Large multi-parameter data are analyzed using dimensionality reduction methods, based either on a combination of 2D binning and Principal Component Analysis, or with a one-class Support Vector Machine approach, with the objective to predict the Susceptible or Resistant phenotype of the strain. For the first time, both Escherichia coli (Gram-negative) and Staphylococcus epidermidis (Gram-positive) isolates were tested with a label-free approach, and, in the presence of two groups of bactericidal antibiotic molecules, aminoglycosides and beta-lactams. Our results support the feasibility of label-free AST in less than 2 h and suggest that single cell auto-fluorescence adds value to the Susceptible/Resistant phenotyping over single-cell scattering alone, in particular for the mecA+ Staphylococcus (i.e., resistant) strains treated with oxacillin.
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Affiliation(s)
| | | | | | | | | | | | - Cyril Guyard
- BIOASTER Technology Research Institute, Lyon, France
| | | | | | | | | |
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36
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Winkler KR, Mizrahi V, Warner DF, De Wet TJ. High-throughput functional genomics: A (myco)bacterial perspective. Mol Microbiol 2023; 120:141-158. [PMID: 37278255 PMCID: PMC10953053 DOI: 10.1111/mmi.15103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/06/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023]
Abstract
Advances in sequencing technologies have enabled unprecedented insights into bacterial genome composition and dynamics. However, the disconnect between the rapid acquisition of genomic data and the (much slower) confirmation of inferred genetic function threatens to widen unless techniques for fast, high-throughput functional validation can be applied at scale. This applies equally to Mycobacterium tuberculosis, the leading infectious cause of death globally and a pathogen whose genome, despite being among the first to be sequenced two decades ago, still contains many genes of unknown function. Here, we summarize the evolution of bacterial high-throughput functional genomics, focusing primarily on transposon (Tn)-based mutagenesis and the construction of arrayed mutant libraries in diverse bacterial systems. We also consider the contributions of CRISPR interference as a transformative technique for probing bacterial gene function at scale. Throughout, we situate our analysis within the context of functional genomics of mycobacteria, focusing specifically on the potential to yield insights into M. tuberculosis pathogenicity and vulnerabilities for new drug and regimen development. Finally, we offer suggestions for future approaches that might be usefully applied in elucidating the complex cellular biology of this major human pathogen.
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Affiliation(s)
- Kristy R. Winkler
- Molecular Mycobacteriology Research Unit and DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownRondeboschSouth Africa
| | - Valerie Mizrahi
- Molecular Mycobacteriology Research Unit and DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownRondeboschSouth Africa
- Wellcome Centre for Infectious Diseases Research in AfricaUniversity of Cape TownRondeboschSouth Africa
| | - Digby F. Warner
- Molecular Mycobacteriology Research Unit and DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownRondeboschSouth Africa
- Wellcome Centre for Infectious Diseases Research in AfricaUniversity of Cape TownRondeboschSouth Africa
| | - Timothy J. De Wet
- Molecular Mycobacteriology Research Unit and DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownRondeboschSouth Africa
- Wellcome Centre for Infectious Diseases Research in AfricaUniversity of Cape TownRondeboschSouth Africa
- Department of Integrative Biomedical SciencesUniversity of Cape TownRondeboschSouth Africa
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37
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Tsunemoto H, Sugie J, Enustun E, Pogliano K, Pogliano J. Bacterial cytological profiling reveals interactions between jumbo phage φKZ infection and cell wall active antibiotics in Pseudomonas aeruginosa. PLoS One 2023; 18:e0280070. [PMID: 37418366 PMCID: PMC10328376 DOI: 10.1371/journal.pone.0280070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/20/2022] [Indexed: 07/09/2023] Open
Abstract
The emergence of antibiotic resistance in bacteria has led to the investigation of alternative treatments, such as phage therapy. In this study, we examined the interactions between the nucleus-forming jumbo phage ФKZ and antibiotic treatment against Pseudomonas aeruginosa. Using the fluorescence microscopy technique of bacterial cytological profiling, we identified mechanism-of-action-specific interactions between antibiotics that target different biosynthetic pathways and ФKZ infection. We found that certain classes of antibiotics strongly inhibited phage replication, while others had no effect or only mildly affected progression through the lytic cycle. Antibiotics that caused an increase in host cell length, such as the cell wall active antibiotic ceftazidime, prevented proper centering of the ФKZ nucleus via the PhuZ spindle at midcell, leading us to hypothesize that the kinetic parameters of the PhuZ spindle evolved to match the average length of the host cell. To test this, we developed a computational model explaining how the dynamic properties of the PhuZ spindle contribute to phage nucleus centering and why some antibiotics affect nucleus positioning while others do not. These findings provide an understanding of the molecular mechanisms underlying the interactions between antibiotics and jumbo phage replication.
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Affiliation(s)
- Hannah Tsunemoto
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Joseph Sugie
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Eray Enustun
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
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38
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Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, Barbosa da Silva E, O’Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small Molecule in situ Resin Capture - A Compound First Approach to Natural Product Discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.02.530684. [PMID: 37398257 PMCID: PMC10312467 DOI: 10.1101/2023.03.02.530684] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Microbial natural products remain an important resource for drug discovery. Yet, commonly employed discovery techniques are plagued by the rediscovery of known compounds, the relatively few microbes that can be cultured, and laboratory growth conditions that do not elicit biosynthetic gene expression among myriad other challenges. Here we introduce a culture independent approach to natural product discovery that we call the Small Molecule In situ Resin Capture (SMIRC) technique. SMIRC exploits in situ environmental conditions to elicit compound production and represents a new approach to access poorly explored chemical space by capturing natural products directly from the environments in which they are produced. In contrast to traditional methods, this compound-first approach can capture structurally complex small molecules across all domains of life in a single deployment while relying on Nature to provide the complex and poorly understood environmental cues needed to elicit biosynthetic gene expression. We illustrate the effectiveness of SMIRC in marine habitats with the discovery of numerous new compounds and demonstrate that sufficient compound yields can be obtained for NMR-based structure assignment. Two new compound classes are reported including one novel carbon skeleton that possesses a functional group not previously observed among natural products and a second that possesses potent biological activity. We introduce expanded deployments, in situ cultivation, and metagenomics as methods to facilitate compound discovery, enhance yields, and link compounds to producing organisms. This compound first approach can provide unprecedented access to new natural product chemotypes with broad implications for drug discovery.
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Affiliation(s)
- Alexander Bogdanov
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mariam N. Salib
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexander B. Chase
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Earth Sciences, Southern Methodist University, Dallas, TX 75275, USA
| | - Heinz Hammerlindl
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mitchell N. Muskat
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Lani F. Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven J. Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tadeusz F. Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Paul R. Jensen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
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39
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Mitchell RJ, Kriger SM, Fenton AD, Havrylyuk D, Pandeya A, Sun Y, Smith T, DeRouchey JE, Unrine JM, Oza V, Blackburn JS, Wei Y, Heidary DK, Glazer EC. A monoadduct generating Ru(ii) complex induces ribosome biogenesis stress and is a molecular mimic of phenanthriplatin. RSC Chem Biol 2023; 4:344-353. [PMID: 37181632 PMCID: PMC10170627 DOI: 10.1039/d2cb00247g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/01/2023] [Indexed: 03/03/2023] Open
Abstract
Ruthenium complexes are often investigated as potential replacements for platinum-based chemotherapeutics in hopes of identifying systems with improved tolerability in vivo and reduced susceptibility to cellular resistance mechanisms. Inspired by phenanthriplatin, a non-traditional platinum agent that contains only one labile ligand, monofunctional ruthenium polypyridyl agents have been developed, but until now, few demonstrated promising anticancer activity. Here we introduce a potent new scaffold, based on [Ru(tpy)(dip)Cl]Cl (tpy = 2,2':6',2''-terpyridine and dip = 4,7-diphenyl-1,10-phenanthroline) in pursuit of effective Ru(ii)-based monofunctional agents. Notably, the extension of the terpyridine at the 4' position with an aromatic ring resulted in a molecule that was cytotoxic in several cancer cell lines with sub-micromolar IC50 values, induced ribosome biogenesis stress, and exhibited minimal zebrafish embryo toxicity. This study demonstrates the successful design of a Ru(ii) agent that mimics many of the biological effects and phenotypes seen with phenanthriplatin, despite numerous differences in both the ligands and metal center structure.
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Affiliation(s)
- Richard J Mitchell
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - Sarah M Kriger
- Department of Chemistry, North Carolina State University 2620 Yarbrough DriveRaleigh NC 27695 USA
| | - Alexander D Fenton
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - Dmytro Havrylyuk
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - Ankit Pandeya
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - Yang Sun
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - Tami Smith
- Department of Plant and Soil Sciences, University of Kentucky 1100 S. Limestone St Lexington KY 40546 USA
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - Jason M Unrine
- Department of Plant and Soil Sciences, University of Kentucky 1100 S. Limestone St Lexington KY 40546 USA
| | - Viral Oza
- Department of Molecular and Cellular Biochemistry, University of Kentucky 741 S. Limestone St. Lexington KY 40536 USA
| | - Jessica S Blackburn
- Department of Molecular and Cellular Biochemistry, University of Kentucky 741 S. Limestone St. Lexington KY 40536 USA
| | - Yinan Wei
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - David K Heidary
- Department of Chemistry, North Carolina State University 2620 Yarbrough DriveRaleigh NC 27695 USA
| | - Edith C Glazer
- Department of Chemistry, North Carolina State University 2620 Yarbrough DriveRaleigh NC 27695 USA
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40
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Sharma AK, Poddar SM, Chakraborty J, Nayak BS, Kalathil S, Mitra N, Gayathri P, Srinivasan R. A mechanism of salt bridge-mediated resistance to FtsZ inhibitor PC190723 revealed by a cell-based screen. Mol Biol Cell 2023; 34:ar16. [PMID: 36652338 PMCID: PMC10011733 DOI: 10.1091/mbc.e22-12-0538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Bacterial cell division proteins, especially the tubulin homologue FtsZ, have emerged as strong targets for developing new antibiotics. Here, we have utilized the fission yeast heterologous expression system to develop a cell-based assay to screen for small molecules that directly and specifically target the bacterial cell division protein FtsZ. The strategy also allows for simultaneous assessment of the toxicity of the drugs to eukaryotic yeast cells. As a proof-of-concept of the utility of this assay, we demonstrate the effect of the inhibitors sanguinarine, berberine, and PC190723 on FtsZ. Though sanguinarine and berberine affect FtsZ polymerization, they exert a toxic effect on the cells. Further, using this assay system, we show that PC190723 affects Helicobacter pylori FtsZ function and gain new insights into the molecular determinants of resistance to PC190723. On the basis of sequence and structural analysis and site-specific mutations, we demonstrate that the presence of salt bridge interactions between the central H7 helix and β-strands S9 and S10 mediates resistance to PC190723 in FtsZ. The single-step in vivo cell-based assay using fission yeast enabled us to dissect the contribution of sequence-specific features of FtsZ and cell permeability effects associated with bacterial cell envelopes. Thus, our assay serves as a potent tool to rapidly identify novel compounds targeting polymeric bacterial cytoskeletal proteins like FtsZ to understand how they alter polymerization dynamics and address resistance determinants in targets.
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Affiliation(s)
- Ajay Kumar Sharma
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Sakshi Mahesh Poddar
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Joyeeta Chakraborty
- Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Bhagyashri Soumya Nayak
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Srilakshmi Kalathil
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Nivedita Mitra
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Pananghat Gayathri
- Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
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41
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Herschede SR, Salam R, Gneid H, Busschaert N. Bacterial cytological profiling identifies transmembrane anion transport as the mechanism of action for a urea-based antibiotic. Supramol Chem 2023. [DOI: 10.1080/10610278.2023.2178921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- Sarah R. Herschede
- Department of Chemistry, Tulane University, New Orleans, Louisiana, United States
| | - Rayhanus Salam
- Department of Chemistry, Tulane University, New Orleans, Louisiana, United States
| | - Hassan Gneid
- Department of Chemistry, Tulane University, New Orleans, Louisiana, United States
| | - Nathalie Busschaert
- Department of Chemistry, Tulane University, New Orleans, Louisiana, United States
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42
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High-Resolution Bacterial Cytological Profiling Reveals Intrapopulation Morphological Variations upon Antibiotic Exposure. Antimicrob Agents Chemother 2023; 67:e0130722. [PMID: 36625642 PMCID: PMC9933734 DOI: 10.1128/aac.01307-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Phenotypic heterogeneity is crucial to bacterial survival and could provide insights into the mechanism of action (MOA) of antibiotics, especially those with polypharmacological actions. Although phenotypic changes among individual cells could be detected by existing profiling methods, due to the data complexity, only population average data were commonly used, thereby overlooking the heterogeneity. In this study, we developed a high-resolution bacterial cytological profiling method that can capture morphological variations of bacteria upon antibiotic treatment. With an unprecedented single-cell resolution, this method classifies morphological changes of individual cells into known MOAs with an overall accuracy above 90%. We next showed that combinations of two antibiotics induce altered cell morphologies that are either unique or similar to that of an antibiotic in the combinations. With these combinatorial profiles, this method successfully revealed multiple cytological changes caused by a natural product-derived compound that, by itself, is inactive against Acinetobacter baumannii but synergistically exerts its multiple antibacterial activities in the presence of colistin. The findings have paved the way for future single-cell profiling in bacteria and have highlighted previously underappreciated intrapopulation variations caused by antibiotic perturbation.
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43
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Zhang Y, Kepiro I, Ryadnov MG, Pagliara S. Single Cell Killing Kinetics Differentiate Phenotypic Bacterial Responses to Different Antibacterial Classes. Microbiol Spectr 2023; 11:e0366722. [PMID: 36651776 PMCID: PMC9927147 DOI: 10.1128/spectrum.03667-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023] Open
Abstract
With the spread of multidrug-resistant bacteria, there has been an increasing focus on molecular classes that have not yet yielded an antibiotic. A key capability for assessing and prescribing new antibacterial treatments is to compare the effects antibacterial agents have on bacterial growth at a phenotypic, single-cell level. Here, we combined time-lapse microscopy with microfluidics to investigate the concentration-dependent killing kinetics of stationary-phase Escherichia coli cells. We used antibacterial agents from three different molecular classes, β-lactams and fluoroquinolones, with the known antibiotics ampicillin and ciprofloxacin, respectively, and a new experimental class, protein Ψ-capsids. We found that bacterial cells elongated when treated with ampicillin and ciprofloxacin used at their minimum inhibitory concentration (MIC). This was in contrast to Ψ-capsids, which arrested bacterial elongation within the first two hours of treatment. At concentrations exceeding the MIC, all the antibacterial agents tested arrested bacterial growth within the first 2 h of treatment. Further, our single-cell experiments revealed differences in the modes of action of three different agents. At the MIC, ampicillin and ciprofloxacin caused the lysis of bacterial cells, whereas at higher concentrations, the mode of action shifted toward membrane disruption. The Ψ-capsids killed cells by disrupting their membranes at all concentrations tested. Finally, at increasing concentrations, ampicillin and Ψ-capsids reduced the fraction of the population that survived treatment in a viable but nonculturable state, whereas ciprofloxacin increased this fraction. This study introduces an effective capability to differentiate the killing kinetics of antibacterial agents from different molecular classes and offers a high content analysis of antibacterial mechanisms at the single-cell level. IMPORTANCE Antibiotics act against bacterial pathogens by inhibiting their growth or killing them directly. Different modes of action determine different antibacterial responses, whereas phenotypic differences in bacteria can challenge the efficacy of antibiotics. Therefore, it is important to be able to differentiate the concentration-dependent killing kinetics of antibacterial agents at a single-cell level, in particular for molecular classes which have not yielded an antibiotic before. Here, we measured single-cell responses using microfluidics-enabled imaging, revealing that a novel class of antibacterial agents, protein Ψ-capsids, arrests bacterial elongation at the onset of treatment, whereas elongation continues for cells treated with β-lactam and fluoroquinolone antibiotics. The study advances our current understanding of antibacterial function and offers an effective strategy for the comparative design of new antibacterial therapies, as well as clinical antibiotic susceptibility testing.
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Affiliation(s)
- Yuewen Zhang
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
- National Physical Laboratory, Teddington, United Kingdom
| | - Ibolya Kepiro
- National Physical Laboratory, Teddington, United Kingdom
| | - Maxim G. Ryadnov
- National Physical Laboratory, Teddington, United Kingdom
- Department of Physics, King’s College London, London, United Kingdom
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
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44
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He Q, Yang Z, Zou Z, Qian M, Wang X, Zhang X, Yin Z, Wang J, Ye X, Liu D, Guo M. Combating Escherichia coli O157:H7 with Functionalized Chickpea-Derived Antimicrobial Peptides. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205301. [PMID: 36563134 PMCID: PMC9951321 DOI: 10.1002/advs.202205301] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The rapid dissemination of antibiotic resistance accelerates the desire for new antibacterial agents. Here, a class of antimicrobial peptides (AMPs) is designed by modifying the structural parameters of a natural chickpea-derived AMP-Leg2, termed "functionalized chickpea-derived Leg2 antimicrobial peptides" (FCLAPs). Among the FCLAPs, KTA and KTR show superior antibacterial efficacy against the foodborne pathogen Escherichia coli (E. coli) O157:H7 (with MICs in the range of 2.5-4.7 µmol L-1 ) and demonstrate satisfactory feasibility in alleviating E. coli O157:H7-induced intestinal infection. Additionally, the low cytotoxicity along with insusceptibility to antimicrobial resistance increases the potential of FCLAPs as appealing antimicrobials. Combining the multi-omics profiling andpeptide-membrane interaction assays, a unique dual-targeting mode of action is characterized. To specify the antibacterial mechanism, microscopical observations, membrane-related physicochemical properties studies, and mass spectrometry assays are further performed. Data indicate that KTA and KTR induce membrane damage by initially targeting the lipopolysaccharide (LPS), thus promoting the peptides to traverse the outer membrane. Subsequently, the peptides intercalate into the peptidoglycan (PGN) layer, blocking its synthesis, and causing a collapse of membrane structure. These findings altogether imply the great potential of KTA and KTR as promising antibacterial candidates in combating the growing threat of E. coli O157:H7.
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Affiliation(s)
- Qiao He
- College of Biosystems Engineering and Food ScienceNational‐Local Joint Engineering Laboratory of Intelligent Food Technology and EquipmentZhejiang Key Laboratory for Agro‐Food ProcessingZhejiang UniversityHangzhouZhejiang Province310058P. R. China
| | - Zhehao Yang
- College of Biosystems Engineering and Food ScienceNational‐Local Joint Engineering Laboratory of Intelligent Food Technology and EquipmentZhejiang Key Laboratory for Agro‐Food ProcessingZhejiang UniversityHangzhouZhejiang Province310058P. R. China
| | - Zhipeng Zou
- College of Biosystems Engineering and Food ScienceNational‐Local Joint Engineering Laboratory of Intelligent Food Technology and EquipmentZhejiang Key Laboratory for Agro‐Food ProcessingZhejiang UniversityHangzhouZhejiang Province310058P. R. China
| | - Mengyan Qian
- College of Biosystems Engineering and Food ScienceNational‐Local Joint Engineering Laboratory of Intelligent Food Technology and EquipmentZhejiang Key Laboratory for Agro‐Food ProcessingZhejiang UniversityHangzhouZhejiang Province310058P. R. China
| | - Xiaolei Wang
- College of Biosystems Engineering and Food ScienceNational‐Local Joint Engineering Laboratory of Intelligent Food Technology and EquipmentZhejiang Key Laboratory for Agro‐Food ProcessingZhejiang UniversityHangzhouZhejiang Province310058P. R. China
| | - Xinhui Zhang
- College of Biosystems Engineering and Food ScienceNational‐Local Joint Engineering Laboratory of Intelligent Food Technology and EquipmentZhejiang Key Laboratory for Agro‐Food ProcessingZhejiang UniversityHangzhouZhejiang Province310058P. R. China
| | - Zhongping Yin
- Jiangxi Key Laboratory of Natural Products and Functional FoodsJiangxi Agricultural UniversityNanchangJiangxi Province330045P. R. China
| | - Jinhai Wang
- Department of Colorectal SurgeryThe First Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhouZhejiang Province310058P. R. China
| | - Xingqian Ye
- College of Biosystems Engineering and Food ScienceNational‐Local Joint Engineering Laboratory of Intelligent Food Technology and EquipmentZhejiang Key Laboratory for Agro‐Food ProcessingZhejiang UniversityHangzhouZhejiang Province310058P. R. China
- Fuli Institute of Food ScienceZhejiang UniversityHangzhouZhejiang Province310058P. R. China
| | - Donghong Liu
- College of Biosystems Engineering and Food ScienceNational‐Local Joint Engineering Laboratory of Intelligent Food Technology and EquipmentZhejiang Key Laboratory for Agro‐Food ProcessingZhejiang UniversityHangzhouZhejiang Province310058P. R. China
- Fuli Institute of Food ScienceZhejiang UniversityHangzhouZhejiang Province310058P. R. China
| | - Mingming Guo
- College of Biosystems Engineering and Food ScienceNational‐Local Joint Engineering Laboratory of Intelligent Food Technology and EquipmentZhejiang Key Laboratory for Agro‐Food ProcessingZhejiang UniversityHangzhouZhejiang Province310058P. R. China
- Fuli Institute of Food ScienceZhejiang UniversityHangzhouZhejiang Province310058P. R. China
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45
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Biosynthesized Silver Nanoparticles Using Morus alba (White Mulberry) Leaf Extract as Potential Antibacterial and Anticancer Agents. Molecules 2023; 28:molecules28031213. [PMID: 36770881 PMCID: PMC9920803 DOI: 10.3390/molecules28031213] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/28/2023] Open
Abstract
In this study, we report the green synthesis of silver nanoparticles (AgNPs) from Morus alba or white mulberry leaf extract (MLE) and assess their antibacterial and anticancer potential. The GC-MS analysis of MLE confirmed the existence of phenolic compounds, serving as reducing, capping, and stabilizing agents in the biosynthesis of AgNPs. The MLE-AgNPs were spherical, with an average particle size of 20-44.5 nm and a face-centered cubic structure. EDX spectra confirmed the formation of AgNPs, and a negative zeta potential value (-14.5 mV) suggested their physicochemical stability. Excellent antibacterial activity was demonstrated by MLE-AgNPs against Acinetobacter baumannii strains with a MIC of 2 μg/mL, while good activity was observed against other Gram-negative (Escherichia coli and Salmonella typhimurium) and Gram-positive (Bacillus subtilis and Staphylococcus aureus) bacteria with a MIC of 32 μg/mL. In vitro cytotoxic effects on MCF-7 (human breast cancer cells) and MCF-10A (normal human mammary epithelial cells) were investigated by the MTT assay. The half-maximal inhibitory concentrations (IC50) against MCF-7 cells were 18 and 33 μg/mL for MLE-AgNPs and MLE, respectively, with no effect on normal MCF-10A cells. Altogether, the results support the high antibacterial and anticancer potential of biosynthesized AgNPs by white mulberry leaf extract.
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46
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Krentzel D, Shorte SL, Zimmer C. Deep learning in image-based phenotypic drug discovery. Trends Cell Biol 2023:S0962-8924(22)00262-8. [PMID: 36623998 DOI: 10.1016/j.tcb.2022.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 01/08/2023]
Abstract
Modern drug discovery approaches often use high-content imaging to systematically study the effect on cells of large libraries of chemical compounds. By automatically screening thousands or millions of images to identify specific drug-induced cellular phenotypes, for example, altered cellular morphology, these approaches can reveal 'hit' compounds offering therapeutic promise. In the past few years, artificial intelligence (AI) methods based on deep learning (DL) [a family of machine learning (ML) techniques] have disrupted virtually all image analysis tasks, from image classification to segmentation. These powerful methods also promise to impact drug discovery by accelerating the identification of effective drugs and their modes of action. In this review, we highlight applications and adaptations of ML, especially DL methods for cell-based phenotypic drug discovery (PDD).
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Affiliation(s)
- Daniel Krentzel
- Institut Pasteur, Université Paris Cité, Imaging and Modeling Unit, F-75015 Paris, France; Institut Pasteur, Joint International Unit Artificial Intelligence for Image-based Drug Discovery & Development (PIU-Ai3D), F-75015 Paris, France.
| | - Spencer L Shorte
- Institut Pasteur, Joint International Unit Artificial Intelligence for Image-based Drug Discovery & Development (PIU-Ai3D), F-75015 Paris, France; Institut Pasteur, Université Paris Cité, Photonic Bio-Imaging, Centre de Ressources et Recherches Technologiques (UTechS-PBI, C2RT), F-75015 Paris, France
| | - Christophe Zimmer
- Institut Pasteur, Université Paris Cité, Imaging and Modeling Unit, F-75015 Paris, France; Institut Pasteur, Joint International Unit Artificial Intelligence for Image-based Drug Discovery & Development (PIU-Ai3D), F-75015 Paris, France.
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47
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Abstract
As the global burden of antibiotic resistance continues to grow, creative approaches to antibiotic discovery are needed to accelerate the development of novel medicines. A rapidly progressing computational revolution-artificial intelligence-offers an optimistic path forward due to its ability to alleviate bottlenecks in the antibiotic discovery pipeline. In this review, we discuss how advancements in artificial intelligence are reinvigorating the adoption of past antibiotic discovery models-namely natural product exploration and small molecule screening. We then explore the application of contemporary machine learning approaches to emerging areas of antibiotic discovery, including antibacterial systems biology, drug combination development, antimicrobial peptide discovery, and mechanism of action prediction. Lastly, we propose a call to action for open access of high-quality screening datasets and interdisciplinary collaboration to accelerate the rate at which machine learning models can be trained and new antibiotic drugs can be developed.
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Affiliation(s)
- Telmah Lluka
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Jonathan M Stokes
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
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48
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Matos de Opitz CL, Sass P. Microscopy-Based Multiwell Assay to Characterize Disturbed Bacterial Morphogenesis Upon Antibiotic Action. Methods Mol Biol 2023; 2601:171-190. [PMID: 36445584 DOI: 10.1007/978-1-0716-2855-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The urgent need of new antimicrobial agents to combat life-threatening bacterial infections demands the identification and characterization of novel compounds that interfere with new and unprecedented target pathways or structures in multiresistant bacteria. Here, bacterial cell division has emerged as a new and promising target pathway for antibiotic intervention. Compounds, which inhibit division, commonly induce a characteristic filamentation phenotype of rod-shaped bacteria, such as Bacillus subtilis. Hence, this filamentation phenotype can be used to identify and characterize novel compounds that primarily target bacterial cell division. Since novel compounds of both synthetic and natural product origin are often available in small amounts only, thereby limiting the number of assays during mode of action studies, we here describe a semiautomated, microscopy-based approach that requires only small volumes of compounds to allow for the real-time observation of their effects on living bacteria, such as filamentation or cell lysis, in high-throughput 96-well-based formats. We provide a detailed workflow for the initial characterization of multiple compounds at once and further tools for the initial, microscopy-based characterization of their antibacterial mode of action.
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Affiliation(s)
- Cruz L Matos de Opitz
- Interfaculty Institute of Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
| | - Peter Sass
- Interfaculty Institute of Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany.
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49
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Walesch S, Birkelbach J, Jézéquel G, Haeckl FPJ, Hegemann JD, Hesterkamp T, Hirsch AKH, Hammann P, Müller R. Fighting antibiotic resistance-strategies and (pre)clinical developments to find new antibacterials. EMBO Rep 2022; 24:e56033. [PMID: 36533629 PMCID: PMC9827564 DOI: 10.15252/embr.202256033] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Antibacterial resistance is one of the greatest threats to human health. The development of new therapeutics against bacterial pathogens has slowed drastically since the approvals of the first antibiotics in the early and mid-20th century. Most of the currently investigated drug leads are modifications of approved antibacterials, many of which are derived from natural products. In this review, we highlight the challenges, advancements and current standing of the clinical and preclinical antibacterial research pipeline. Additionally, we present novel strategies for rejuvenating the discovery process and advocate for renewed and enthusiastic investment in the antibacterial discovery pipeline.
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Affiliation(s)
- Sebastian Walesch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Joy Birkelbach
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Gwenaëlle Jézéquel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Thomas Hesterkamp
- Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany,Helmholtz International Lab for Anti‐InfectivesSaarbrückenGermany
| | - Peter Hammann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany,Helmholtz International Lab for Anti‐InfectivesSaarbrückenGermany
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50
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Serbanescu D, Ojkic N, Banerjee S. Cellular resource allocation strategies for cell size and shape control in bacteria. FEBS J 2022; 289:7891-7906. [PMID: 34665933 PMCID: PMC9016100 DOI: 10.1111/febs.16234] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/21/2021] [Accepted: 10/18/2021] [Indexed: 01/14/2023]
Abstract
Bacteria are highly adaptive microorganisms that thrive in a wide range of growth conditions via changes in cell morphologies and macromolecular composition. How bacterial morphologies are regulated in diverse environmental conditions is a long-standing question. Regulation of cell size and shape implies control mechanisms that couple the growth and division of bacteria to their cellular environment and macromolecular composition. In the past decade, simple quantitative laws have emerged that connect cell growth to proteomic composition and the nutrient availability. However, the relationships between cell size, shape, and growth physiology remain challenging to disentangle and unifying models are lacking. In this review, we focus on regulatory models of cell size control that reveal the connections between bacterial cell morphology and growth physiology. In particular, we discuss how changes in nutrient conditions and translational perturbations regulate the cell size, growth rate, and proteome composition. Integrating quantitative models with experimental data, we identify the physiological principles of bacterial size regulation, and discuss the optimization strategies of cellular resource allocation for size control.
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Affiliation(s)
- Diana Serbanescu
- Department of Physics and Astronomy, University College London, UK
| | - Nikola Ojkic
- Department of Physics and Astronomy, University College London, UK
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