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Henderson SR, Stevenson CEM, Malone B, Zholnerovych Y, Mitchenall LA, Pichowicz M, McGarry DH, Cooper IR, Charrier C, Salisbury AM, Lawson DM, Maxwell A. Structural and mechanistic analysis of ATPase inhibitors targeting mycobacterial DNA gyrase. J Antimicrob Chemother 2020; 75:2835-2842. [PMID: 32728686 PMCID: PMC7556816 DOI: 10.1093/jac/dkaa286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/28/2020] [Accepted: 05/30/2020] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES To evaluate the efficacy of two novel compounds against mycobacteria and determine the molecular basis of their action on DNA gyrase using structural and mechanistic approaches. METHODS Redx03863 and Redx04739 were tested in antibacterial assays, and also against their target, DNA gyrase, using DNA supercoiling and ATPase assays. X-ray crystallography was used to determine the structure of the gyrase B protein ATPase sub-domain from Mycobacterium smegmatis complexed with the aminocoumarin drug novobiocin, and structures of the same domain from Mycobacterium thermoresistibile complexed with novobiocin, and also with Redx03863. RESULTS Both compounds, Redx03863 and Redx04739, were active against selected Gram-positive and Gram-negative species, with Redx03863 being the more potent, and Redx04739 showing selectivity against M. smegmatis. Both compounds were potent inhibitors of the supercoiling and ATPase reactions of DNA gyrase, but did not appreciably affect the ATP-independent relaxation reaction. The structure of Redx03863 bound to the gyrase B protein ATPase sub-domain from M. thermoresistibile shows that it binds at a site adjacent to the ATP- and novobiocin-binding sites. We found that most of the mutations that we made in the Redx03863-binding pocket, based on the structure, rendered gyrase inactive. CONCLUSIONS Redx03863 and Redx04739 inhibit gyrase by preventing the binding of ATP. The fact that the Redx03863-binding pocket is distinct from that of novobiocin, coupled with the lack of activity of resistant mutants, suggests that such compounds could have potential to be further exploited as antibiotics.
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Affiliation(s)
- Sara R Henderson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Norwich Medical School, University of East Anglia, Norwich NR4 7UQ, UK
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Brandon Malone
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Yelyzaveta Zholnerovych
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Lesley A Mitchenall
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mark Pichowicz
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- Sygnature Discovery, The Discovery Building, Biocity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - David H McGarry
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- Globachem Discovery Ltd, Mereside, Alderley Park SK10 4TG, UK
| | - Ian R Cooper
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- AMR Centre Ltd, Mereside, Alderley Park SK10 4TG, UK
| | - Cedric Charrier
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- IHMA Europe Sàrl, Rte. de I’lle-au-Bois 1A, 1870 Monthey/VS, Switzerland
| | - Anne-Marie Salisbury
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- 5D Health Protection Group Ltd, William Henry Duncan Building, West Derby Street, Liverpool L7 8TX, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Gupta R, China A, Manjunatha UH, Ponnanna NM, Nagaraja V. A complex of DNA gyrase and RNA polymerase fosters transcription in Mycobacterium smegmatis. Biochem Biophys Res Commun 2006; 343:1141-5. [PMID: 16579974 DOI: 10.1016/j.bbrc.2006.02.195] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Accepted: 02/23/2006] [Indexed: 11/24/2022]
Abstract
We report here the existence of a complex between RNA polymerase (RNAP) and DNA gyrase in Mycobacterium smegmatis. The interaction between the two enzymes was detected during our attempts to purify DNA gyrase from M. smegmatis. RNAP subunits co-eluted along with DNA gyrase in two different affinity chromatography column procedures employed to purify the latter enzyme. A complex containing both the enzymes was isolated through gel filtration chromatography and sucrose density gradient centrifugation of the cell free extracts. The complex exhibited both DNA supercoiling and transcription activities. Reduction in the transcription activity of the complex in the presence of DNA gyrase inhibitor indicates a role for DNA gyrase in stimulating transcription.
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Affiliation(s)
- Richa Gupta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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Manjunatha UH, Maxwell A, Nagaraja V. A monoclonal antibody that inhibits mycobacterial DNA gyrase by a novel mechanism. Nucleic Acids Res 2005; 33:3085-94. [PMID: 15930158 PMCID: PMC1142348 DOI: 10.1093/nar/gki622] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
DNA gyrase is a DNA topoisomerase indispensable for cellular functions in bacteria. We describe a novel, hitherto unknown, mechanism of specific inhibition of Mycobacterium smegmatis and Mycobacterium tuberculosis DNA gyrase by a monoclonal antibody (mAb). Binding of the mAb did not affect either GyrA–GyrB or gyrase–DNA interactions. More importantly, the ternary complex of gyrase–DNA–mAb retained the ATPase activity of the enzyme and was competent to catalyse DNA cleavage–religation reactions, implying a new mode of action different from other classes of gyrase inhibitors. DNA gyrase purified from fluoroquinolone-resistant strains of M.tuberculosis and M.smegmatis were inhibited by the mAb. The absence of cross-resistance of the drug-resistant enzymes from two different sources to the antibody-mediated inhibition corroborates the new mechanism of inhibition. We suggest that binding of the mAb in the proximity of the primary dimer interface region of GyrA in the heterotetrameric enzyme appears to block the release of the transported segment after strand passage, leading to enzyme inhibition. The specific inhibition of mycobacterial DNA gyrase with the mAb opens up new avenues for designing novel lead molecules for drug discovery and for probing gyrase mechanism.
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Affiliation(s)
- Ujjini H Manjunatha
- Department of Microbiology and Cell Biology, Indian Institute of Science Bangalore, 560 012, India
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Tyagi AK, Dhar N. Recent advances in tuberculosis research in India. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2003; 84:211-73. [PMID: 12934938 DOI: 10.1007/3-540-36488-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Tuberculosis (TB) continues to be the leading killer of mankind among all infectious diseases, especially in the developing countries. Since the discovery of tubercle bacillus more than 100 years ago, TB has been the subject of research in an attempt to develop tools and strategies to combat this disease. Research in Indian laboratories has contributed significantly towards developing the DOTS strategy employed worldwide in tuberculosis control programmes and elucidating the biological properties of its etiologic agent, M. tuberculosis. In recent times, the development of tools for manipulation of mycobacteria has given a boost to researchers working in this field. New strategies are being employed towards understanding the mechanisms of protection and pathogenesis of this disease. Molecular methods are being applied to develop new tools and reagents for prevention, diagnosis and treatment of tuberculosis. With the sequencing of the genome of M. tuberculosis, molecules are being identified for the development of new drugs and vaccines. In this chapter, the advances made in these areas by Indian researchers mainly during the last five years are reviewed.
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Affiliation(s)
- Anil K Tyagi
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, India.
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Jain P, Nagaraja V. An orphan gyrB in the Mycobacterium smegmatis genome uncovered by comparative genomics. J Genet 2002; 81:105-10. [PMID: 12717039 DOI: 10.1007/bf02715907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA gyrase is an essential topoisomerase found in all bacteria. It is encoded by gyrB and gyrA genes. These genes are organized differently in different bacteria. Direct comparison of Mycobacterium tuberculosis and Mycobacterium smegmatis genomes reveals presence of an additional gyrB in M. smegmatis flanked by novel genes. Analysis of the amino acid sequence of GyrB from different organisms suggests that the orphan GyrB in M. smegmatis may have an important cellular role.
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Affiliation(s)
- P Jain
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India.
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Abstract
We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Manjunatha UH, Dalal M, Chatterji M, Radha DR, Visweswariah SS, Nagaraja V. Functional characterisation of mycobacterial DNA gyrase: an efficient decatenase. Nucleic Acids Res 2002; 30:2144-53. [PMID: 12000834 PMCID: PMC115291 DOI: 10.1093/nar/30.10.2144] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A rapid single step immunoaffinity purification procedure is described for Mycobacterium smegmatis DNA gyrase. The mycobacterial enzyme is a 340 kDa heterotetrameric protein comprising two subunits each of GyrA and GyrB, exhibiting subtle differences and similarities to the well-characterised Escherichia coli gyrase. In contrast to E.coli gyrase, the M.smegmatis enzyme exhibits strong decatenase activity at physiological Mg2+ concentrations. Further, the enzymes exhibited marked differences in ATPase activity, DNA binding characteristics and susceptibility to fluoroquinolones. The holoenzyme showed very low intrinsic ATPase activity and was stimulated 20-fold in the presence of DNA. The DNA-stimulated ATPase kinetics revealed apparent K0.5 and kcat of 0.68 mM and 0.39 s(-1), respectively. The dissociation constant for DNA was found to be 9.2 nM, which is 20 times weaker than that of E.coli DNA gyrase. The differences between the enzymes were further substantiated as they exhibited varied sensitivity to moxifloxacin and ciprofloxacin. In spite of these differences, mycobacterial DNA gyrase is a functionally and mechanistically conserved enzyme and the variations in activity seem to reflect functional optimisation for its physiological role during mycobacterial genome replication.
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Affiliation(s)
- U H Manjunatha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
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