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Ruan S, Tu CH, Bourne CR. Friend or Foe: Protein Inhibitors of DNA Gyrase. BIOLOGY 2024; 13:84. [PMID: 38392303 PMCID: PMC10886550 DOI: 10.3390/biology13020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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2
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Bhowmick J, Nag M, Ghosh P, Rajmani RS, Chatterjee R, Karmakar K, Chandra K, Chatterjee J, Chakravortty D, Varadarajan R. A CcdB toxin-derived peptide acts as a broad-spectrum antibacterial therapeutic in infected mice. EMBO Rep 2023; 24:e55338. [PMID: 37166011 PMCID: PMC10328072 DOI: 10.15252/embr.202255338] [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: 05/02/2022] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/12/2023] Open
Abstract
The bacterial toxin CcdB (Controller of Cell death or division B) targets DNA Gyrase, an essential bacterial topoisomerase, which is also the molecular target for fluoroquinolones. Here, we present a short cell-penetrating 24-mer peptide, CP1-WT, derived from the Gyrase-binding region of CcdB and examine its effect on growth of Escherichia coli, Salmonella Typhimurium, Staphylococcus aureus and a carbapenem- and tigecycline-resistant strain of Acinetobacter baumannii in both axenic cultures and mouse models of infection. The CP1-WT peptide shows significant improvement over ciprofloxacin in terms of its in vivo therapeutic efficacy in treating established infections of S. Typhimurium, S. aureus and A. baumannii. The molecular mechanism likely involves inhibition of Gyrase or Topoisomerase IV, depending on the strain used. The study validates the CcdB binding site on bacterial DNA Gyrase as a viable and alternative target to the fluoroquinolone binding site.
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Grants
- Department of Biotechnology, Ministry of Science and Technology, India - Indian Institute of Science (DBT-IISc) partnership program
- BT/COE/34/SP15219/2015 Department of Biotechnology, Ministry of Science and Technology, India
- DT.20/11/2015 Department of Biotechnology, Ministry of Science and Technology, India
- Department of Science and Technology, Ministry of Science and Technology, India (DST FIST)
- Ministry of Education, India (MHRD)
- University Grants Commission, Ministry of Education, India (UGC Centre for Advanced Studies)
- Department of Biotechnology, Ministry of Science and Technology, India
- Ministry of Education, India (MHRD)
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Affiliation(s)
- Jayantika Bhowmick
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Manish Nag
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Pritha Ghosh
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Raju S Rajmani
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Ritika Chatterjee
- Department of Microbiology and Cell BiologyIndian Institute of ScienceBangaloreIndia
| | - Kapudeep Karmakar
- Department of Microbiology and Cell BiologyIndian Institute of ScienceBangaloreIndia
| | - Kasturi Chandra
- Department of Microbiology and Cell BiologyIndian Institute of ScienceBangaloreIndia
| | - Jayanta Chatterjee
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell BiologyIndian Institute of ScienceBangaloreIndia
- School of BiologyIndian Institute of Science Education and Research Thiruvananthapuram (IISER TVM)ThiruvananthapuramIndia
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VapC toxin switches M. smegmatis cells into dormancy through 23S rRNA cleavage. Arch Microbiol 2023; 205:28. [DOI: 10.1007/s00203-022-03363-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/18/2022] [Accepted: 12/04/2022] [Indexed: 12/23/2022]
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Abstract
Toxin-antitoxin systems are widespread in bacterial genomes. They are usually composed of two elements: a toxin that inhibits an essential cellular process and an antitoxin that counteracts its cognate toxin. In the past decade, a number of new toxin-antitoxin systems have been described, bringing new growth inhibition mechanisms to light as well as novel modes of antitoxicity. However, recent advances in the field profoundly questioned the role of these systems in bacterial physiology, stress response and antimicrobial persistence. This shifted the paradigm of the functions of toxin-antitoxin systems to roles related to interactions between hosts and their mobile genetic elements, such as viral defence or plasmid stability. In this Review, we summarize the recent progress in understanding the biology and evolution of these small genetic elements, and discuss how genomic conflicts could shape the diversification of toxin-antitoxin systems.
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Santos‐Filho NA, Righetto GM, Pereira MR, Piccoli JP, Almeida LMT, Leal TC, Camargo ILBC, Cilli EM. Effect of C‐terminal and N‐terminal dimerization and alanine scanning on antibacterial activity of the analogs of the peptide
p‐BthTX‐I. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Srivastava A, Pati S, Kaushik H, Singh S, Garg LC. Toxin-antitoxin systems and their medical applications: current status and future perspective. Appl Microbiol Biotechnol 2021; 105:1803-1821. [PMID: 33582835 DOI: 10.1007/s00253-021-11134-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Almost all bacteria synthesize two types of toxins-one for its survival by regulating different cellular processes and another as a strategy to interact with host cells for pathogenesis. Usually, "bacterial toxins" are contemplated as virulence factors that harm the host organism. However, toxins produced by bacteria, as a survival strategy against the host, also hamper its cellular processes. To overcome this, the bacteria have evolved with the production of a molecule, referred to as antitoxin, to negate the deleterious effect of the toxin against itself. The toxin and antitoxins are encoded by a two-component toxin-antitoxin (TA) system. The antitoxin, a protein or RNA, sequesters the toxins of the TA system for neutralization within the bacterial cell. In this review, we have described different TA systems of bacteria and their potential medical and biotechnological applications. It is of interest to note that while bacterial toxin-antitoxin systems have been well studied, the TA system in unicellular eukaryotes, though predicted by the investigators, have never been paid the desired attention. In the present review, we have also touched upon the TA system of eukaryotes identified to date. KEY POINTS: Bacterial toxins harm the host and also affect the bacterial cellular processes. The antitoxin produced by bacteria protect it from the toxin's harmful effects. The toxin-antitoxin systems can be targeted for various medical applications.
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Affiliation(s)
- Akriti Srivastava
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh, 201314, India
| | - Soumya Pati
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh, 201314, India
| | - Himani Kaushik
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Lalit C Garg
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India.
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Sanches BCP, Rocha CA, Martin Bedoya JG, da Silva VL, da Silva PB, Fusco-Almeida AM, Chorilli M, Contiero J, Crusca E, Marchetto R. Rhamnolipid-Based Liposomes as Promising Nano-Carriers for Enhancing the Antibacterial Activity of Peptides Derived from Bacterial Toxin-Antitoxin Systems. Int J Nanomedicine 2021; 16:925-939. [PMID: 33603360 PMCID: PMC7882795 DOI: 10.2147/ijn.s283400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/25/2020] [Indexed: 12/19/2022] Open
Abstract
Background Antimicrobial resistance poses substantial risks to human health. Thus, there is an urgent need for novel antimicrobial agents, including alternative compounds, such as peptides derived from bacterial toxin-antitoxin (TA) systems. ParELC3 is a synthetic peptide derived from the ParE toxin reported to be a good inhibitor of bacterial topoisomerases and is therefore a potential antibacterial agent. However, ParELC3 is inactive against bacteria due to its inability to cross the bacterial membranes. To circumvent this limitation we prepared and used rhamnolipid-based liposomes to carry and facilitate the passage of ParELC3 through the bacterial membrane to reach its intracellular target - the topoisomerases. Methods and Results Small unilamellar liposome vesicles were prepared by sonication from three formulations that included 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and cholesterol. ParELC3 was loaded with high efficiency into the liposomes. Characterization by DLS and TEM revealed the appropriate size, zeta potential, polydispersity index, and morphology. In vitro microbiological experiments showed that ParELC3 loaded-liposomes are more efficient (29 to 11 µmol·L−1) compared to the free peptide (>100 µmol·L−1) at inhibiting the growth of standard E. coli and S. aureus strains. RL liposomes showed high hemolytic activity but when prepared with POPC and Chol this activity had a significant reduction. Independently of the formulation, the vesicles had no detectable cytotoxicity to HepG2 cells, even at the highest concentrations tested (1.3 mmol·L−1 and 50 µmol·L−1 for rhamnolipid and ParELC3, respectively). Conclusion The present findings suggest the potential use of rhamnolipid-based liposomes as nanocarrier systems to enhance the bioactivity of peptides.
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Affiliation(s)
- Beatriz Cristina Pecoraro Sanches
- São Paulo State University (UNESP), Institute of Chemistry, Department of Biochemistry and Organic Chemistry, Araraquara, SP, Brazil
| | - Camila Aguiar Rocha
- São Paulo State University (UNESP), Institute of Chemistry, Department of Biochemistry and Organic Chemistry, Araraquara, SP, Brazil
| | - Jose Gregorio Martin Bedoya
- São Paulo State University (UNESP), Institute of Chemistry, Department of Biochemistry and Organic Chemistry, Araraquara, SP, Brazil
| | - Vinicius Luiz da Silva
- São Paulo State University (UNESP), Institute of Biosciences, Department of General and Applied Biology, Rio Claro, SP, Brazil
| | - Patrícia Bento da Silva
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Department of Drugs and Medicines, Araraquara, SP, Brazil
| | - Ana Marisa Fusco-Almeida
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Department of Clinical Analysis, Araraquara, SP, Brazil
| | - Marlus Chorilli
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Department of Drugs and Medicines, Araraquara, SP, Brazil
| | - Jonas Contiero
- São Paulo State University (UNESP), Institute of Biosciences, Department of General and Applied Biology, Rio Claro, SP, Brazil
| | - Edson Crusca
- São Paulo State University (UNESP), Institute of Chemistry, Department of Biochemistry and Organic Chemistry, Araraquara, SP, Brazil
| | - Reinaldo Marchetto
- São Paulo State University (UNESP), Institute of Chemistry, Department of Biochemistry and Organic Chemistry, Araraquara, SP, Brazil
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Zamakhaev MV, Goncharenko AV, Shumkov MS. Toxin-Antitoxin Systems and Bacterial Persistence (Review). APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819060140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Yi L, Lü X. New Strategy on Antimicrobial-resistance: Inhibitors of DNA Replication Enzymes. Curr Med Chem 2019; 26:1761-1787. [PMID: 29110590 DOI: 10.2174/0929867324666171106160326] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/31/2017] [Accepted: 10/30/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Antimicrobial resistance is found in all microorganisms and has become one of the biggest threats to global health. New antimicrobials with different action mechanisms are effective weapons to fight against antibiotic-resistance. OBJECTIVE This review aims to find potential drugs which can be further developed into clinic practice and provide clues for developing more effective antimicrobials. METHODS DNA replication universally exists in all living organisms and is a complicated process in which multiple enzymes are involved in. Enzymes in bacterial DNA replication of initiation and elongation phases bring abundant targets for antimicrobial development as they are conserved and indispensable. In this review, enzyme inhibitors of DNA helicase, DNA primase, topoisomerases, DNA polymerase and DNA ligase were discussed. Special attentions were paid to structures, activities and action modes of these enzyme inhibitors. RESULTS Among these enzymes, type II topoisomerase is the most validated target with abundant inhibitors. For type II topoisomerase inhibitors (excluding quinolones), NBTIs and benzimidazole urea derivatives are the most promising inhibitors because of their good antimicrobial activity and physicochemical properties. Simultaneously, DNA gyrase targeted drugs are particularly attractive in the treatment of tuberculosis as DNA gyrase is the sole type II topoisomerase in Mycobacterium tuberculosis. Relatively, exploitation of antimicrobial inhibitors of the other DNA replication enzymes are primeval, in which inhibitors of topo III are even blank so far. CONCLUSION This review demonstrates that inhibitors of DNA replication enzymes are abundant, diverse and promising, many of which can be developed into antimicrobials to deal with antibioticresistance.
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Affiliation(s)
- Lanhua Yi
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province 712100, China
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10
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Klimina KM, Poluektova EU, Danilenko VN. Bacterial toxin–antitoxin systems: Properties, functional significance, and possibility of use (Review). APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817050076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Bielenica A, Stępień K, Napiórkowska A, Augustynowicz-Kopeć E, Krukowski S, Włodarczyk M, Struga M. Synthesis and Antimicrobial Activity of 4-Chloro-3-Nitrophenylthiourea Derivatives Targeting Bacterial Type II Topoisomerases. Chem Biol Drug Des 2016; 87:905-17. [PMID: 26804238 DOI: 10.1111/cbdd.12723] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/07/2016] [Accepted: 01/07/2016] [Indexed: 12/22/2022]
Abstract
A series of novel 4-chloro-3-nitrophenylthiourea derivatives were synthesized and evaluated for their antimicrobial, antibiofilm and tuberculostatic activities. Most of compounds exhibited high antibacterial activity against both standard and hospital strains (MIC values 0.5-2 μg/mL), as compared to Ciprofloxacin. Derivatives with 3,4-dichlorophenyl (11) and 3-chloro-4-methylphenyl (13) substituents were the most promising towards Gram-positive pathogens. Both of them exhibited antibiofilm potency and effectively inhibited the formation of biofilms of methicillin-resistant and standard strains of Staphylococcus epidermidis. Two N-alkylthioureas (20, 21) showed twofold to fourfold increase in in vitro potency against isolates of Mycobacterium tuberculosis, as compared to Isoniazid. An action of 7, 10, 11, 13, 20 and 21 against activity of topoisomerases isolated from Staphylococcus aureus was studied. Synthesized compounds were found as non-genotoxic.
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Affiliation(s)
- Anna Bielenica
- Chair and Department of Biochemistry, Medical University, 02-097, Warszawa, Poland
| | - Karolina Stępień
- Department of Pharmaceutical Microbiology, Medical University, 02-007, Warszawa, Poland
| | - Agnieszka Napiórkowska
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, 01-138, Warszawa, Poland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, 01-138, Warszawa, Poland
| | - Sylwester Krukowski
- Department of Inorganic and Analytical Chemistry, Faculty of Pharmacy, Medical University, 02-097, Warszawa, Poland
| | - Marta Włodarczyk
- Department of Pharmacogenomics, Faculty of Pharmacy, Medical University, 02-097, Warszawa, Poland
| | - Marta Struga
- Department of Pharmacogenomics, Faculty of Pharmacy, Medical University, 02-097, Warszawa, Poland
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12
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Santos-Filho NA, Lorenzon EN, Ramos MAS, Santos CT, Piccoli JP, Bauab TM, Fusco-Almeida AM, Cilli EM. Synthesis and characterization of an antibacterial and non-toxic dimeric peptide derived from the C-terminal region of Bothropstoxin-I. Toxicon 2015; 103:160-8. [PMID: 26160494 DOI: 10.1016/j.toxicon.2015.07.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 06/28/2015] [Accepted: 07/01/2015] [Indexed: 12/14/2022]
Abstract
Infectious diseases are among the leading global causes of death, increasing the search for novel antibacterial agents. Among these, biologically active peptides are an excellent research tool. Using solid-phase peptide synthesis (SPPS), this work aimed to synthesize the peptide derived from the C-terminal region of Bothropstoxin-I (BthTX-I) (p-BthTX-I, sequence: KKYRYHLKPFCKK), and its disulfide-linked dimeric form, obtained via air oxidation (p-BthTX-I)2. Two other peptides were synthesized to evaluate the dimerization effect on antimicrobial activity. In both sequences, the cysteine (Cys) residue was replaced by the serine (Ser) residue, differing, however, in their C-terminus position. The antimicrobial activity of the peptides against gram-negative (Escherichia (E.) coli) and gram-positive (Staphylococcus (S.) aureus) bacteria and yeast (Candida (C.) albicans) was evaluated. Interestingly, only peptides containing the Cys residue showed antimicrobial activity, suggesting the importance of Cys residue and its dimerization for the observed activity. Apparently, p-BthTX-I and (p-BthTX-I)2 did not promote lysis or form pores and were not able to interact with membranes. Furthermore, they neither showed antifungal activity against C. albicans nor toxicity against erythrocytes, epithelial cells, or macrophages, indicating a potential specificity against prokaryotic cells.
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Affiliation(s)
| | - Esteban N Lorenzon
- Instituto de Química, UNESP - Univ. Estadual Paulista, Araraquara, SP, Brazil
| | - Matheus A S Ramos
- Faculdade de Ciências Farmacêuticas, UNESP - Univ. Estadual Paulista, Araraquara, SP, Brazil
| | - Claudia T Santos
- Faculdade de Ciências Farmacêuticas, UNESP - Univ. Estadual Paulista, Araraquara, SP, Brazil
| | - Julia P Piccoli
- Instituto de Química, UNESP - Univ. Estadual Paulista, Araraquara, SP, Brazil
| | - Tais M Bauab
- Faculdade de Ciências Farmacêuticas, UNESP - Univ. Estadual Paulista, Araraquara, SP, Brazil
| | - Ana M Fusco-Almeida
- Faculdade de Ciências Farmacêuticas, UNESP - Univ. Estadual Paulista, Araraquara, SP, Brazil
| | - Eduardo M Cilli
- Instituto de Química, UNESP - Univ. Estadual Paulista, Araraquara, SP, Brazil.
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Abstract
DNA topoisomerases are enzymes that control the topology of DNA in all cells. There are two types, I and II, classified according to whether they make transient single- or double-stranded breaks in DNA. Their reactions generally involve the passage of a single- or double-strand segment of DNA through this transient break, stabilized by DNA-protein covalent bonds. All topoisomerases can relax DNA, but DNA gyrase, present in all bacteria, can also introduce supercoils into DNA. Because of their essentiality in all cells and the fact that their reactions proceed via DNA breaks, topoisomerases have become important drug targets; the bacterial enzymes are key targets for antibacterial agents. This article discusses the structure and mechanism of topoisomerases and their roles in the bacterial cell. Targeting of the bacterial topoisomerases by inhibitors, including antibiotics in clinical use, is also discussed.
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Wen Y, Behiels E, Devreese B. Toxin-Antitoxin systems: their role in persistence, biofilm formation, and pathogenicity. Pathog Dis 2014; 70:240-9. [DOI: 10.1111/2049-632x.12145] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/15/2014] [Accepted: 01/15/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Yurong Wen
- Unit for Biological Mass Spectrometry and Proteomics; Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Ghent University; Ghent Belgium
| | - Ester Behiels
- Unit for Biological Mass Spectrometry and Proteomics; Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Ghent University; Ghent Belgium
| | - Bart Devreese
- Unit for Biological Mass Spectrometry and Proteomics; Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Ghent University; Ghent Belgium
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15
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Mayer C, Janin YL. Non-quinolone inhibitors of bacterial type IIA topoisomerases: a feat of bioisosterism. Chem Rev 2013; 114:2313-42. [PMID: 24313284 DOI: 10.1021/cr4003984] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Claudine Mayer
- Unité de Microbiologie Structurale, Département de Biologie Structurale et Chimie, Institut Pasteur , 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
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Toxin-antitoxin genes of the Gram-positive pathogen Streptococcus pneumoniae: so few and yet so many. Microbiol Mol Biol Rev 2013. [PMID: 23204366 DOI: 10.1128/mmbr.00030-12] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Pneumococcal infections cause up to 2 million deaths annually and raise a large economic burden and thus constitute an important threat to mankind. Because of the increase in the antibiotic resistance of Streptococcus pneumoniae clinical isolates, there is an urgent need to find new antimicrobial approaches to triumph over pneumococcal infections. Toxin-antitoxin (TA) systems (TAS), which are present in most living bacteria but not in eukaryotes, have been proposed as an effective strategy to combat bacterial infections. Type II TAS comprise a stable toxin and a labile antitoxin that form an innocuous TA complex under normal conditions. Under stress conditions, TA synthesis will be triggered, resulting in the degradation of the labile antitoxin and the release of the toxin protein, which would poison the host cells. The three functional chromosomal TAS from S. pneumoniae that have been studied as well as their molecular characteristics are discussed in detail in this review. Furthermore, a meticulous bioinformatics search has been performed for 48 pneumococcal genomes that are found in public databases, and more putative TAS, homologous to well-characterized ones, have been revealed. Strikingly, several unusual putative TAS, in terms of components and genetic organizations previously not envisaged, have been discovered and are further discussed. Previously, we reported a novel finding in which a unique pneumococcal DNA signature, the BOX element, affected the regulation of the pneumococcal yefM-yoeB TAS. This BOX element has also been found in some of the other pneumococcal TAS. In this review, we also discuss possible relationships between some of the pneumococcal TAS with pathogenicity, competence, biofilm formation, persistence, and an interesting phenomenon called bistability.
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Purification of GidA protein, a novel topoisomerase II inhibitor produced by Streptomyces flavoviridis. World J Microbiol Biotechnol 2013; 30:555-65. [PMID: 23996636 DOI: 10.1007/s11274-013-1475-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 08/23/2013] [Indexed: 10/26/2022]
Abstract
The presence of topoisomerase II inhibition activities in the intracellular extract of Streptomyces flavoviridis was investigated. One active compound inhibiting relaxation activity of topoisomerase II was determined to be a protein. This active principle was purified to homogeneity by gel filtration followed by ion exchange chromatography. The apparent molecular mass was 42 kDa as determined by SDS-PAGE. MALDI TOF peptide mass fingerprinting analysis confirmed this topoisomerase II inhibitor, as glucose-inhibited division protein A (GidA) by MOWSE score of 72. The effects of purified GidA protein on DNA relaxation and decatenation by topoisomerase II were investigated. It inhibited topoisomerase II activity and acted as a topoisomerase poison that significantly stabilized the covalent DNA-topoisomerase II reaction intermediate "cleavable complex", as observed with etoposide. Collectively, these findings indicate that GidA is a potent inhibitor of topoisomerase II enzyme, which can be exploited for rational drug design in human carcinomas.
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Mapping the Spectrum of Conformational States of the DNA- and C-Gates in Bacillus subtilis Gyrase. J Mol Biol 2013; 425:2632-40. [DOI: 10.1016/j.jmb.2013.04.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/04/2013] [Accepted: 04/07/2013] [Indexed: 11/19/2022]
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Barbosa LCB, Garrido SS, Garcia A, Delfino DB, Santos LDN, Marchetto R. Design and synthesis of peptides from bacterial ParE toxin as inhibitors of topoisomerases. Eur J Med Chem 2012; 54:591-6. [PMID: 22749642 DOI: 10.1016/j.ejmech.2012.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 06/04/2012] [Accepted: 06/05/2012] [Indexed: 12/16/2022]
Abstract
Toxin-antitoxin (TA) proteic systems encode a toxin and an antitoxin that regulate the growth and death of bacterial cells under various stress conditions. The ParE protein is a toxin that inhibits DNA gyrase activity and thereby blocks DNA replication. Based on the Escherichia coli ParE structure, a series of linear peptides were designed and synthesized by solid-phase methodology. The ability of the peptides to inhibit the activity of bacterial topoisomerases was investigated. Four peptides (ParELC3, ParELC8, ParELC10 and ParELC12), showed complete inhibition of DNA gyrase supercoiling activity with an IC(100) between 20 and 40 μmol L(-1). In contrast to wild-type ParE, the peptide analogues were able to inhibit the DNA relaxation of topoisomerase IV, another type IIA bacterial topoisomerase, with lower IC(100) values. Interestingly only ParELC12 displayed inhibition of the relaxation activity of human topoisomerase II. Our findings reveal new inhibitors of bacterial topoisomerases and are a good starting point for the development of a new class of antibacterial agents that targets the DNA topoisomerases.
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Affiliation(s)
- Luiz Carlos Bertucci Barbosa
- UNESP - Institute of Chemistry, Department of Biochemistry and Technological Chemistry, Caixa Postal 355, 14800-900 Araraquara, São Paulo, Brazil
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Collin F, Karkare S, Maxwell A. Exploiting bacterial DNA gyrase as a drug target: current state and perspectives. Appl Microbiol Biotechnol 2011; 92:479-97. [PMID: 21904817 PMCID: PMC3189412 DOI: 10.1007/s00253-011-3557-z] [Citation(s) in RCA: 364] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 08/08/2011] [Accepted: 08/18/2011] [Indexed: 12/17/2022]
Abstract
DNA gyrase is a type II topoisomerase that can introduce negative supercoils into DNA at the expense of ATP hydrolysis. It is essential in all bacteria but absent from higher eukaryotes, making it an attractive target for antibacterials. The fluoroquinolones are examples of very successful gyrase-targeted drugs, but the rise in bacterial resistance to these agents means that we not only need to seek new compounds, but also new modes of inhibition of this enzyme. We review known gyrase-specific drugs and toxins and assess the prospects for developing new antibacterials targeted to this enzyme.
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Affiliation(s)
- Frédéric Collin
- Department Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Diago-Navarro E, Hernandez-Arriaga AM, López-Villarejo J, Muñoz-Gómez AJ, Kamphuis MB, Boelens R, Lemonnier M, Díaz-Orejas R. parD toxin-antitoxin system of plasmid R1 - basic contributions, biotechnological applications and relationships with closely-related toxin-antitoxin systems. FEBS J 2010; 277:3097-117. [DOI: 10.1111/j.1742-4658.2010.07722.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sissi C, Palumbo M. In front of and behind the replication fork: bacterial type IIA topoisomerases. Cell Mol Life Sci 2010; 67:2001-24. [PMID: 20165898 PMCID: PMC11115839 DOI: 10.1007/s00018-010-0299-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 01/26/2010] [Accepted: 02/01/2010] [Indexed: 01/03/2023]
Abstract
Topoisomerases are vital enzymes specialized in controlling DNA topology, in particular supercoiling and decatenation, to properly handle nucleic acid packing and cell dynamics. The type IIA enzymes act by cleaving both strands of a double helix and having another strand from the same or another molecule cross the DNA gate before a re-sealing event completes the catalytic cycle. Here, we will consider the two types of IIA prokaryotic topoisomerases, DNA Gyrase and Topoisomerase IV, as crucial regulators of bacterial cell cycle progression. Their synergistic action allows control of chromosome packing and grants occurrence of functional transcription and replication processes. In addition to displaying a fascinating molecular mechanism of action, which transduces chemical energy into mechanical energy by means of large conformational changes, these enzymes represent attractive pharmacological targets for antibacterial chemotherapy.
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Affiliation(s)
- Claudia Sissi
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131, Padua, Italy.
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Barbosa LCB, Garrido SS, Garcia A, Delfino DB, Marchetto R. Function inferences from a molecular structural model of bacterial ParE toxin. Bioinformation 2010; 4:438-40. [PMID: 20975905 PMCID: PMC2951705 DOI: 10.6026/97320630004438] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 04/09/2010] [Indexed: 11/26/2022] Open
Abstract
Toxin-antitoxin (TA) systems contribute to plasmid stability by a mechanism that relies on the differential stabilities of the toxin and antitoxin proteins and leads to the killing of daughter bacteria that did not receive a plasmid copy at the cell division. ParE is the toxic component of a TA system that constitutes along with RelE an important class of bacterial toxin called RelE/ParE superfamily. For ParE toxin, no crystallographic structure is available so far and rare in vitro studies demonstrated that the target of toxin activity is E. coli DNA gyrase. Here, a 3D Model for E. coli ParE toxin by molecular homology modeling was built using MODELLER, a program for comparative modeling. The Model was energy minimized by CHARMM and validated using PROCHECK and VERIFY3D programs. Resulting Ramachandran plot analysis it was found that the portion residues failing into the most favored and allowed regions was 96.8%. Structural similarity search employing DALI server showed as the best matches RelE and YoeB families. The Model also showed similarities with other microbial ribonucleases but in a small score. A possible homologous deep cleft active site was identified in the Model using CASTp program. Additional studies to investigate the nuclease activity in members of ParE family as well as to confirm the inhibitory replication activity are needed. The predicted Model allows initial inferences about the unexplored 3D structure of the ParE toxin and may be further used in rational design of molecules for structure-function studies.
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Affiliation(s)
- Luiz Carlos Bertucci Barbosa
- Institute of Chemistry, UNESP ‐ Univ Estadual Paulista, Department of Biochemistry and Technological Chemistry, Araraquara, São Paulo, Brazil
| | - Saulo Santesso Garrido
- Institute of Chemistry, UNESP ‐ Univ Estadual Paulista, Department of Biochemistry and Technological Chemistry, Araraquara, São Paulo, Brazil
| | - Anderson Garcia
- Institute of Chemistry, UNESP ‐ Univ Estadual Paulista, Department of Biochemistry and Technological Chemistry, Araraquara, São Paulo, Brazil
| | - Davi Barbosa Delfino
- Institute of Chemistry, UNESP ‐ Univ Estadual Paulista, Department of Biochemistry and Technological Chemistry, Araraquara, São Paulo, Brazil
| | - Reinaldo Marchetto
- Institute of Chemistry, UNESP ‐ Univ Estadual Paulista, Department of Biochemistry and Technological Chemistry, Araraquara, São Paulo, Brazil
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