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Bradbury JD, Hodgkinson T, Thomas AM, Tanwar O, La Monica G, Rogga VV, Mackay LJ, Taylor EK, Gilbert K, Zhu Y, Sefton AY, Edwards AM, Gray-Hammerton CJ, Smith GR, Roberts PM, Walsh TR, Lanyon-Hogg T. Development of an inhibitor of the mutagenic SOS response that suppresses the evolution of quinolone antibiotic resistance. Chem Sci 2024; 15:9620-9629. [PMID: 38939155 PMCID: PMC11206376 DOI: 10.1039/d4sc00995a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/07/2024] [Indexed: 06/29/2024] Open
Abstract
Antimicrobial resistance (AMR) is a growing threat to health globally, with the potential to render numerous medical procedures so dangerous as to be impractical. There is therefore an urgent need for new molecules that function through novel mechanisms of action to combat AMR. The bacterial DNA-repair and SOS-response pathways promote survival of pathogens in infection settings and also activate hypermutation and resistance mechanisms, making these pathways attractive targets for new therapeutics. Small molecules, such as IMP-1700, potentiate DNA damage and inhibit the SOS response in methicillin-resistant S. aureus; however, understanding of the structure-activity relationship (SAR) of this series is lacking. We report here the first comprehensive SAR study of the IMP-1700 scaffold, identifying key pharmacophoric groups and delivering the most potent analogue reported to date, OXF-077. Furthermore, we demonstrate that as a potent inhibitor of the mutagenic SOS response, OXF-077 suppresses the rate of ciprofloxacin resistance emergence in S. aureus. This work supports SOS-response inhibitors as a novel means to combat AMR, and delivers OXF-077 as a tool molecule for future development.
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Affiliation(s)
- Jacob D Bradbury
- Department of Pharmacology, University of Oxford OX1 3QT UK
- Ineos Oxford Institute for Antimicrobial Research, Sir William Dunn School of Pathology, University of Oxford OX1 3RE UK
| | | | - Adam M Thomas
- Department of Pharmacology, University of Oxford OX1 3QT UK
| | | | - Gabriele La Monica
- Department of Pharmacology, University of Oxford OX1 3QT UK
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo 90128 Italy
| | | | - Luke J Mackay
- Department of Pharmacology, University of Oxford OX1 3QT UK
| | | | - Kiera Gilbert
- Department of Pharmacology, University of Oxford OX1 3QT UK
| | - Yihua Zhu
- Fred Hutchinson Cancer Center Seattle WA 98109-1024 USA
| | - Amber Y Sefton
- Department of Infectious Disease, Faculty of Medicine, Imperial College London W2 1NY UK
| | - Andrew M Edwards
- Department of Infectious Disease, Faculty of Medicine, Imperial College London W2 1NY UK
| | - Charlotte J Gray-Hammerton
- Ineos Oxford Institute for Antimicrobial Research, Sir William Dunn School of Pathology, University of Oxford OX1 3RE UK
| | | | - Paul M Roberts
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford OX1 3TA UK
| | - Timothy R Walsh
- Ineos Oxford Institute for Antimicrobial Research, Sir William Dunn School of Pathology, University of Oxford OX1 3RE UK
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Carvajal-Garcia J, Bracey H, Johnson AE, Hernandez Viera AJ, Egli M, Simsek EN, Jaremba EA, Kim K, Merrikh H. A small molecule that inhibits the evolution of antibiotic resistance. NAR MOLECULAR MEDICINE 2024; 1:ugae001. [PMID: 38911259 PMCID: PMC11188740 DOI: 10.1093/narmme/ugae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 06/25/2024]
Abstract
Antibiotic resistance rapidly develops against almost all available therapeutics. Therefore, searching for new antibiotics to overcome the problem of antibiotic resistance alone is insufficient. Given that antibiotic resistance can be driven by mutagenesis, an avenue for preventing it is the inhibition of mutagenic processes. We previously showed that the DNA translocase Mfd is mutagenic and accelerates antibiotic resistance development. Here, we present our discovery of a small molecule that inhibits Mfd-dependent mutagenesis, ARM-1 (anti-resistance molecule 1). We found ARM-1 using a high-throughput, small molecule, in vivo screen. Using biochemical assays, we characterized the mechanism by which ARM-1 inhibits Mfd. Critically, we found that ARM-1 reduces mutagenesis and significantly delays antibiotic resistance development across highly divergent bacterial pathogens. These results demonstrate that the mutagenic proteins accelerating evolution can be directly inhibited. Furthermore, our findings suggest that Mfd inhibition, alongside antibiotics, is a potentially effective approach for prevention of antibiotic resistance development during treatment of infections.
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Affiliation(s)
| | - Harrison Bracey
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Anna E Johnson
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Esra N Simsek
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Emily A Jaremba
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Kwangho Kim
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Houra Merrikh
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
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3
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Ding D, Wang B, Zhang X, Zhang J, Zhang H, Liu X, Gao Z, Yu Z. The spread of antibiotic resistance to humans and potential protection strategies. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 254:114734. [PMID: 36950985 DOI: 10.1016/j.ecoenv.2023.114734] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Antibiotic resistance is currently one of the greatest threats to human health. Widespread use and residues of antibiotics in humans, animals, and the environment can exert selective pressure on antibiotic resistance bacteria (ARB) and antibiotic resistance gene (ARG), accelerating the flow of antibiotic resistance. As ARG spreads to the population, the burden of antibiotic resistance in humans increases, which may have potential health effects on people. Therefore, it is critical to mitigate the spread of antibiotic resistance to humans and reduce the load of antibiotic resistance in humans. This review briefly described the information of global antibiotic consumption information and national action plans (NAPs) to combat antibiotic resistance and provided a set of feasible control strategies for the transmission of ARB and ARG to humans in three areas including (a) Reducing the colonization capacity of exogenous ARB, (b) Enhancing human colonization resistance and mitigating the horizontal gene transfer (HGT) of ARG, (c) Reversing ARB antibiotic resistance. With the hope of achieving interdisciplinary one-health prevention and control of bacterial resistance.
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Affiliation(s)
- Dong Ding
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China; College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Bin Wang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiaoan Zhang
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junxi Zhang
- NHC Key Laboratory of Birth Defects Prevention & Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Huanhuan Zhang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xinxin Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Zhan Gao
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Zengli Yu
- College of Public Health, Zhengzhou University, Zhengzhou, China; The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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4
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Ledger EVK, Lau K, Tate EW, Edwards AM. XerC Is Required for the Repair of Antibiotic- and Immune-Mediated DNA Damage in Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0120622. [PMID: 36802166 PMCID: PMC10019262 DOI: 10.1128/aac.01206-22] [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] [Indexed: 02/23/2023] Open
Abstract
To survive in the host environment, pathogenic bacteria need to be able to repair DNA damage caused by both antibiotics and the immune system. The SOS response is a key bacterial pathway to repair DNA double-strand breaks and may therefore be a good target for novel therapeutics to sensitize bacteria to antibiotics and the immune response. However, the genes required for the SOS response in Staphylococcus aureus have not been fully established. Therefore, we carried out a screen of mutants involved in various DNA repair pathways to understand which were required for induction of the SOS response. This led to the identification of 16 genes that may play a role in SOS response induction and, of these, 3 that affected the susceptibility of S. aureus to ciprofloxacin. Further characterization revealed that, in addition to ciprofloxacin, loss of the tyrosine recombinase XerC increased the susceptibility of S. aureus to various classes of antibiotics, as well as to host immune defenses. Therefore, the inhibition of XerC may be a viable therapeutic approach to sensitize S. aureus to both antibiotics and the immune response.
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Affiliation(s)
- Elizabeth V. K. Ledger
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Katie Lau
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Edward W. Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - Andrew M. Edwards
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
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5
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Wilkinson M, Wilkinson OJ, Feyerherm C, Fletcher EE, Wigley DB, Dillingham MS. Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub. eLife 2022; 11:e83409. [PMID: 36533901 PMCID: PMC9836394 DOI: 10.7554/elife.83409] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/18/2022] [Indexed: 12/23/2022] Open
Abstract
Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, we present biochemical and structural analysis of two phage proteins, gp5.9 and Abc2, which target the DNA break resection complex RecBCD. These exemplify two contrasting mechanisms for control of DNA break repair in which the RecBCD complex is either inhibited or co-opted for the benefit of the invading phage. Gp5.9 completely inhibits RecBCD by preventing it from binding to DNA. The RecBCD-gp5.9 structure shows that gp5.9 acts by substrate mimicry, binding predominantly to the RecB arm domain and competing sterically for the DNA binding site. Gp5.9 adopts a parallel coiled-coil architecture that is unprecedented for a natural DNA mimic protein. In contrast, binding of Abc2 does not substantially affect the biochemical activities of isolated RecBCD. The RecBCD-Abc2 structure shows that Abc2 binds to the Chi-recognition domains of the RecC subunit in a position that might enable it to mediate the loading of phage recombinases onto its single-stranded DNA products.
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Affiliation(s)
- Martin Wilkinson
- Section of Structural Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College LondonLondonUnited Kingdom
| | - Oliver J Wilkinson
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Connie Feyerherm
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Emma E Fletcher
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Dale B Wigley
- Section of Structural Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College LondonLondonUnited Kingdom
| | - Mark S Dillingham
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
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IPA-3: An Inhibitor of Diadenylate Cyclase of Streptococcus suis with Potent Antimicrobial Activity. Antibiotics (Basel) 2022; 11:antibiotics11030418. [PMID: 35326881 PMCID: PMC8944544 DOI: 10.3390/antibiotics11030418] [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: 02/17/2022] [Revised: 03/13/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022] Open
Abstract
Antimicrobial resistance (AMR) poses a huge threat to public health. The development of novel antibiotics is an effective strategy to tackle AMR. Cyclic diadenylate monophosphate (c-di-AMP) has recently been identified as an essential signal molecule for some important bacterial pathogens involved in various bacterial physiological processes, leading to its synthase diadenylate cyclase becoming an attractive antimicrobial drug target. In this study, based on the enzymatic activity of diadenylate cyclase of Streptococcus suis (ssDacA), we established a high-throughput method of screening for ssDacA inhibitors. Primary screening with a compound library containing 1133 compounds identified IPA-3 (2,2′-dihydroxy-1,1′-dinapthyldisulfide) as an ssDacA inhibitor. High-performance liquid chromatography (HPLC) analysis further indicated that IPA-3 could inhibit the production of c-di-AMP by ssDacA in vitro in a dose-dependent manner. Notably, it was demonstrated that IPA-3 could significantly inhibit the growth of several Gram-positive bacteria which harbor an essential diadenylate cyclase but not E. coli, which is devoid of the enzyme, or Streptococcus mutans, in which the diadenylate cyclase is not essential. Additionally, the binding site in ssDacA for IPA-3 was predicted by molecular docking, and contains residues that are relatively conserved in diadenylate cyclase of Gram-positive bacteria. Collectively, our results illustrate the feasibility of ssDacA as an antimicrobial target and consider IPA-3 as a promising starting point for the development of a novel antibacterial.
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Mercolino J, Lo Sciuto A, Spinnato MC, Rampioni G, Imperi F. RecA and Specialized Error-Prone DNA Polymerases are not Required for Mutagenesis and Antibiotic Resistance Induced by Fluoroquinolones in Pseudomonas aeruginosa. Antibiotics (Basel) 2022; 11:antibiotics11030325. [PMID: 35326787 PMCID: PMC8944484 DOI: 10.3390/antibiotics11030325] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 02/05/2023] Open
Abstract
To cope with stressful conditions, including antibiotic exposure, bacteria activate the SOS response, a pathway that induces error-prone DNA repair and mutagenesis mechanisms. In most bacteria, the SOS response relies on the transcriptional repressor LexA and the co-protease RecA, the latter being also involved in homologous recombination. The role of the SOS response in stress- and antibiotic-induced mutagenesis has been characterized in detail in the model organism Escherichia coli. However, its effect on antibiotic resistance in the human pathogen Pseudomonas aeruginosa is less clear. Here, we analyzed a recA deletion mutant and confirmed, by conjugation and gene expression assays, that RecA is required for homologous recombination and SOS response induction in P. aeruginosa. MIC assays demonstrated that RecA affects P. aeruginosa resistance only towards fluoroquinolones and genotoxic agents. The comparison of antibiotic-resistant mutant frequency between treated and untreated cultures revealed that, among the antibiotics tested, only fluoroquinolones induced mutagenesis in P. aeruginosa. Notably, both RecA and error-prone DNA polymerases were found to be dispensable for this process. These data demonstrate that the SOS response is not required for antibiotic-induced mutagenesis in P. aeruginosa, suggesting that RecA inhibition is not a suitable strategy to target antibiotic-induced emergence of resistance in this pathogen.
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Affiliation(s)
- Jessica Mercolino
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
| | - Alessandra Lo Sciuto
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
| | - Maria Concetta Spinnato
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
| | - Giordano Rampioni
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
- IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
| | - Francesco Imperi
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
- IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
- Correspondence:
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8
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Welcome to Volume 14 of Future Medicinal Chemistry. Future Med Chem 2021; 14:1-3. [PMID: 34927463 DOI: 10.4155/fmc-2021-0300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Abstract
Staphylococcus aureus is a common cause of both superficial and invasive infections of humans and animals. Despite a potent host response and apparently appropriate antibiotic therapy, staphylococcal infections frequently become chronic or recurrent, demonstrating a remarkable ability of S. aureus to withstand the hostile host environment. There is growing evidence that staphylococcal DNA repair makes important contributions to the survival of the pathogen in host tissues, as well as promoting the emergence of mutants that resist host defenses and antibiotics. While much of what we know about DNA repair in S. aureus is inferred from studies with model organisms, the roles of specific repair mechanisms in infection are becoming clear and differences with Bacillus subtilis and Escherichia coli have been identified. Furthermore, there is growing interest in staphylococcal DNA repair as a target for novel therapeutics that sensitize the pathogen to host defenses and antibiotics. In this review, we discuss what is known about staphylococcal DNA repair and its role in infection, examine how repair in S. aureus is similar to, or differs from, repair in well-characterized model organisms, and assess the potential of staphylococcal DNA repair as a novel therapeutic target.
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RexAB promotes the survival of Staphylococcus aureus exposed to multiple classes of antibiotics. Antimicrob Agents Chemother 2021; 65:e0059421. [PMID: 34310219 PMCID: PMC8448105 DOI: 10.1128/aac.00594-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antibiotics inhibit essential bacterial processes, resulting in arrest of growth and, in some cases, cell death. Many antibiotics are also reported to trigger endogenous production of reactive oxygen species (ROS), which damage DNA, leading to induction of the mutagenic SOS response associated with the emergence of drug resistance. However, the type of DNA damage that arises and how this triggers the SOS response are largely unclear. We found that several different classes of antibiotic triggered dose-dependent induction of the SOS response in Staphylococcus aureus, indicative of DNA damage, including some bacteriostatic drugs. The SOS response was heterogenous and varied in magnitude between strains and antibiotics. However, in many cases, full induction of the SOS response was dependent upon the RexAB helicase/nuclease complex, which processes DNA double-strand breaks to produce single-stranded DNA and facilitate RecA nucleoprotein filament formation. The importance of RexAB in repair of DNA was confirmed by measuring bacterial survival during antibiotic exposure, with most drugs having significantly greater bactericidal activity against rexB mutants than against wild-type strains. For some, but not all, antibiotics there was no difference in bactericidal activity between wild type and rexB mutant under anaerobic conditions, indicative of a role for reactive oxygen species in mediating DNA damage. Taken together, this work confirms previous observations that several classes of antibiotics cause DNA damage in S. aureus and extends them by showing that processing of DNA double-strand breaks by RexAB is a major trigger of the mutagenic SOS response and promotes bacterial survival.
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Ning Q, Wang D, You J. Joint effects of antibiotics and quorum sensing inhibitors on resistance development in bacteria. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:995-1005. [PMID: 34060581 DOI: 10.1039/d1em00047k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Quorum sensing inhibitors (QSIs) are promising alternatives to antibiotics. While QSIs have great application potential in a variety of fields, their joint effects with antibiotics on bacteria, especially on antibiotic resistance mutations, remain largely unexplored. Herein, we report the joint effects of four commonly used antibiotics and two QSIs on bacterial growth and resistance mutations in E. coli. It was found that QSIs presented antagonistic or additive effects with antibiotics on bacterial growth, and more importantly, QSIs exhibited an attenuating effect on antibiotic-induced resistance mutations. Further analysis demonstrated that antibiotics might enhance resistance mutations by promoting the expressions of rpoS, lexA and recA, while QSIs attenuated the mutations by promoting the expressions of mutS and uvrD. The present research provides a comprehensive understanding of the joint effects of antibiotics and QSIs on bacteria, which may benefit the risk assessment of their combined exposure.
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Affiliation(s)
- Qing Ning
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China.
| | - Dali Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China.
| | - Jing You
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China.
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