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Ruan S, Tu CH, Bourne CR. Friend or Foe: Protein Inhibitors of DNA Gyrase. Biology (Basel) 2024; 13:84. [PMID: 38392303 PMCID: PMC10886550 DOI: 10.3390/biology13020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as exemplified by the highly successful fluoroquinolone class of antibiotics. It is reasonable that the activity of gyrase could be intrinsically regulated within cells, thereby helping to coordinate DNA replication with doubling times. Numerous proteins have been identified to exert inhibitory effects on DNA gyrase, although at lower doses, it can appear readily reversible and therefore may have regulatory value. Some of these, such as the small protein toxins found in plasmid-borne addiction modules, can promote cell death by inducing damage to DNA, resulting in an analogous outcome as quinolone antibiotics. Others, however, appear to transiently impact gyrase in a readily reversible and non-damaging mechanism, such as the plasmid-derived Qnr family of DNA-mimetic proteins. The current review examines the origins and known activities of protein inhibitors of gyrase and highlights opportunities to further exert control over bacterial growth by targeting this validated antibacterial target with novel molecular mechanisms. Furthermore, we are gaining new insights into fundamental regulatory strategies of gyrase that may prove important for understanding diverse growth strategies among different bacteria.
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Affiliation(s)
- Shengfeng Ruan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Chih-Han Tu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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Kever L, Hünnefeld M, Brehm J, Heermann R, Frunzke J. Identification of Gip as a novel phage-encoded gyrase inhibitor protein of Corynebacterium glutamicum. Mol Microbiol 2021; 116:1268-1280. [PMID: 34536319 DOI: 10.1111/mmi.14813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/30/2022]
Abstract
By targeting key regulatory hubs of their host, bacteriophages represent a powerful source for the identification of novel antimicrobial proteins. Here, a screening of small cytoplasmic proteins encoded by the CGP3 prophage of Corynebacterium glutamicum resulted in the identification of the gyrase-inhibiting protein Cg1978, termed Gip. Pull-down assays and surface plasmon resonance revealed a direct interaction of Gip with the gyrase subunit A (GyrA). The inhibitory activity of Gip was shown to be specific to the DNA gyrase of its bacterial host C. glutamicum. Overproduction of Gip in C. glutamicum resulted in a severe growth defect as well as an induction of the SOS response. Furthermore, reporter assays revealed an RecA-independent induction of the cryptic CGP3 prophage, most likely caused by topological alterations. Overexpression of gip was counteracted by an increased expression of gyrAB and a reduction of topA expression at the same time, reflecting the homeostatic control of DNA topology. We postulate that the prophage-encoded Gip protein plays a role in modulating gyrase activity to enable efficient phage DNA replication. A detailed elucidation of the mechanism of action will provide novel directions for the design of drugs targeting DNA gyrase.
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Affiliation(s)
- Larissa Kever
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Max Hünnefeld
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Jannis Brehm
- Institut für Molekulare Physiologie, Biozentrum II, Mikrobiologie und Weinforschung, Johannes-Gutenberg-Universität Mainz, Mainz, Germany
| | - Ralf Heermann
- Institut für Molekulare Physiologie, Biozentrum II, Mikrobiologie und Weinforschung, Johannes-Gutenberg-Universität Mainz, Mainz, Germany
| | - Julia Frunzke
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
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Dewangan RP, Singh M, Ilic S, Tam B, Akabayov B. Cell-penetrating peptide conjugates of indole-3-acetic acid-based DNA primase/ Gyrase inhibitors as potent anti-tubercular agents against planktonic and biofilm culture of Mycobacterium smegmatis. Chem Biol Drug Des 2021; 98:722-732. [PMID: 34265158 DOI: 10.1111/cbdd.13925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 06/27/2021] [Indexed: 10/20/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is a pathogenic bacterium that caused 1.5 million fatalities globally in 2018. New strains of Mtb resistant to all known classes of antibiotics pose a global healthcare problem. In this work, we have conjugated novel indole-3-acetic acid-based DNA primase/gyrase inhibitor with cell-penetrating peptide via cleavable and non-cleavable bonds. For non-cleavable linkage, inhibitor was conjugated with peptide via an amide bond to the N-terminus, whereas a cleavable linkage was obtained by conjugating the inhibitor through a disulfide bond. We performed the conjugation of the inhibitor either directly on a solid surface or by using solution-phase chemistry. M. smegmatis (non-pathogenic model of Mtb) was used to determine the minimal inhibitory concentration (MIC) of the synthetic conjugates. Conjugates were found more active as compared to free inhibitor molecules. Strikingly, the conjugate also impairs the development of biofilm, showing a therapeutic potential against infections caused by both planktonic and sessile forms of mycobacterium species.
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Affiliation(s)
| | - Meenakshi Singh
- Department of Chemistry, Ben-Gurion University of Negev, Beer-Sheva, Israel
| | - Stefan Ilic
- Department of Chemistry, Ben-Gurion University of Negev, Beer-Sheva, Israel
| | - Benjamin Tam
- Department of Chemistry, Ben-Gurion University of Negev, Beer-Sheva, Israel
| | - Barak Akabayov
- Department of Chemistry, Ben-Gurion University of Negev, Beer-Sheva, Israel
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Hüttel S, Testolin G, Herrmann J, Planke T, Gille F, Moreno M, Stadler M, Brönstrup M, Kirschning A, Müller R. Discovery and Total Synthesis of Natural Cystobactamid Derivatives with Superior Activity against Gram-Negative Pathogens. Angew Chem Int Ed Engl 2017; 56:12760-12764. [PMID: 28730677 DOI: 10.1002/anie.201705913] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Indexed: 11/07/2022]
Abstract
Antibiotic discovery and development is challenging as chemical scaffolds of synthetic origin often lack the required pharmaceutical properties, and the discovery of novel ones from natural sources is tedious. Herein, we report the discovery of new cystobactamids with a significantly improved antibacterial profile in a detailed screening of myxobacterial producer strains. Some of these new derivatives display antibacterial activities in the low-μg mL-1 range against Gram-negative pathogens, including clinical isolates of Klebsiella oxytoca, Pseudomonas aeruginosa, and fluoroquinolone-resistant Enterobacteriaceae, which were not observed for previously reported cystobactamids. Our findings provide structure-activity relationships and show how pathogen resistance can be overcome by natural scaffold diversity. The most promising derivative 861-2 was prepared by total synthesis, enabling further chemical optimization of this privileged scaffold.
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Affiliation(s)
- Stephan Hüttel
- Abteilung Mikrobielle Naturstoffe, Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz-Zentrum für Infektionsforschung, Universitätscampus E8 1, 66123, Saarbrücken, Germany.,Abteilung Mikrobielle Wirkstoffe, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Deutsches Zentrum für Infektionsforschung, DZIF, Standort Hannover-Braunschweig, Germany
| | - Giambattista Testolin
- Abteilung Chemische Biologie, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Jennifer Herrmann
- Abteilung Mikrobielle Naturstoffe, Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz-Zentrum für Infektionsforschung, Universitätscampus E8 1, 66123, Saarbrücken, Germany.,Deutsches Zentrum für Infektionsforschung, DZIF, Standort Hannover-Braunschweig, Germany
| | - Therese Planke
- Institut für Organische Chemie, Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Franziska Gille
- Institut für Organische Chemie, Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Maria Moreno
- Institut für Organische Chemie, Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Marc Stadler
- Abteilung Mikrobielle Wirkstoffe, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Deutsches Zentrum für Infektionsforschung, DZIF, Standort Hannover-Braunschweig, Germany
| | - Mark Brönstrup
- Deutsches Zentrum für Infektionsforschung, DZIF, Standort Hannover-Braunschweig, Germany.,Abteilung Chemische Biologie, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Andreas Kirschning
- Institut für Organische Chemie, Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Rolf Müller
- Abteilung Mikrobielle Naturstoffe, Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz-Zentrum für Infektionsforschung, Universitätscampus E8 1, 66123, Saarbrücken, Germany.,Deutsches Zentrum für Infektionsforschung, DZIF, Standort Hannover-Braunschweig, Germany
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Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Meinke PT, Olsen D, Lagrutta A, Bradley P, Lu J, Patel S, Rickert KW, Smith RF, Soisson S, Wei C, Fukuda H, Kishii R, Takei M, Fukuda Y. Oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad spectrum antibacterial agents. ACS Med Chem Lett 2014; 5:609-14. [PMID: 24900889 DOI: 10.1021/ml500069w] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 03/12/2014] [Indexed: 01/18/2023] Open
Abstract
Bacterial resistance is eroding the clinical utility of existing antibiotics necessitating the discovery of new agents. Bacterial type II topoisomerase is a clinically validated, highly effective, and proven drug target. This target is amenable to inhibition by diverse classes of inhibitors with alternative and distinct binding sites to quinolone antibiotics, thus enabling the development of agents that lack cross-resistance to quinolones. Described here are novel bacterial topoisomerase inhibitors (NBTIs), which are a new class of gyrase and topo IV inhibitors and consist of three distinct structural moieties. The substitution of the linker moiety led to discovery of potent broad-spectrum NBTIs with reduced off-target activity (hERG IC50 > 18 μM) and improved physical properties. AM8191 is bactericidal and selectively inhibits DNA synthesis and Staphylococcus aureus gyrase (IC50 = 1.02 μM) and topo IV (IC50 = 10.4 μM). AM8191 showed parenteral and oral efficacy (ED50) at less than 2.5 mg/kg doses in a S. aureus murine infection model. A cocrystal structure of AM8191 bound to S. aureus DNA-gyrase showed binding interactions similar to that reported for GSK299423, displaying a key contact of Asp83 with the basic amine at position-7 of the linker.
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Affiliation(s)
- Sheo B. Singh
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - David E. Kaelin
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Jin Wu
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Lynn Miesel
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Christopher M. Tan
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Peter T. Meinke
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - David Olsen
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Armando Lagrutta
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Prudence Bradley
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Jun Lu
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Sangita Patel
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Keith W. Rickert
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Robert F. Smith
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Stephen Soisson
- Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | | | - Hideyuki Fukuda
- Kyorin Pharmaceutical Co., Ltd., 2399-1, Nogi,
Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryuta Kishii
- Kyorin Pharmaceutical Co., Ltd., 2399-1, Nogi,
Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masaya Takei
- Kyorin Pharmaceutical Co., Ltd., 2399-1, Nogi,
Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasumichi Fukuda
- Kyorin Pharmaceutical Co., Ltd., 2399-1, Nogi,
Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
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