1
|
Kamsri B, Kamsri P, Punkvang A, Chimprasit A, Saparpakorn P, Hannongbua S, Spencer J, Oliveira ASF, Mulholland AJ, Pungpo P. Signal Propagation in the ATPase Domain of Mycobacterium tuberculosis DNA Gyrase from Dynamical-Nonequilibrium Molecular Dynamics Simulations. Biochemistry 2024; 63:1493-1504. [PMID: 38742407 PMCID: PMC11154950 DOI: 10.1021/acs.biochem.4c00161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024]
Abstract
DNA gyrases catalyze negative supercoiling of DNA, are essential for bacterial DNA replication, transcription, and recombination, and are important antibacterial targets in multiple pathogens, including Mycobacterium tuberculosis, which in 2021 caused >1.5 million deaths worldwide. DNA gyrase is a tetrameric (A2B2) protein formed from two subunit types: gyrase A (GyrA) carries the breakage-reunion active site, whereas gyrase B (GyrB) catalyzes ATP hydrolysis required for energy transduction and DNA translocation. The GyrB ATPase domains dimerize in the presence of ATP to trap the translocated DNA (T-DNA) segment as a first step in strand passage, for which hydrolysis of one of the two ATPs and release of the resulting inorganic phosphate is rate-limiting. Here, dynamical-nonequilibrium molecular dynamics (D-NEMD) simulations of the dimeric 43 kDa N-terminal fragment of M. tuberculosis GyrB show how events at the ATPase site (dissociation/hydrolysis of bound nucleotides) are propagated through communication pathways to other functionally important regions of the GyrB ATPase domain. Specifically, our simulations identify two distinct pathways that respectively connect the GyrB ATPase site to the corynebacteria-specific C-loop, thought to interact with GyrA prior to DNA capture, and to the C-terminus of the GyrB transduction domain, which in turn contacts the C-terminal GyrB topoisomerase-primase (TOPRIM) domain responsible for interactions with GyrA and the centrally bound G-segment DNA. The connection between the ATPase site and the C-loop of dimeric GyrB is consistent with the unusual properties of M. tuberculosis DNA gyrase relative to those from other bacterial species.
Collapse
Affiliation(s)
- Bundit Kamsri
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Pharit Kamsri
- Division
of Chemistry, Faculty of Science, Nakhon
Phanom University, Nakhon
Phanom 48000, Thailand
| | - Auradee Punkvang
- Division
of Chemistry, Faculty of Science, Nakhon
Phanom University, Nakhon
Phanom 48000, Thailand
| | - Aunlika Chimprasit
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Bangkok 10900, Thailand
| | | | - Supa Hannongbua
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Bangkok 10900, Thailand
| | - James Spencer
- School
of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K.
| | - A. Sofia F. Oliveira
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Pornpan Pungpo
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| |
Collapse
|
2
|
Sharma V, Das R, Mehta DK, Sharma D, Aman S, Khan MU. Quinolone scaffolds as potential drug candidates against infectious microbes: a review. Mol Divers 2024:10.1007/s11030-024-10862-4. [PMID: 38683488 DOI: 10.1007/s11030-024-10862-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/26/2024] [Indexed: 05/01/2024]
Abstract
Prevalence of microbial infections and new rising pathogens are signified as causative agent for variety of serious and lethal health crisis in past years. Despite medical advances, bacterial and fungal infections continue to be a rising problem in the health care system. As more bacteria develop resistance to antibiotics used in therapy, and as more invasive microbial species develop resistance to conventional antimicrobial drugs. Relevant published publications from the last two decades, up to 2024, were systematically retrieved from the MEDLINE/PubMed, SCOPUS, EMBASE, and WOS databases using keywords such as quinolones, anti-infective, antibacterial, antimicrobial resistance and patents on quinolone derivatives. With an approach of considerable interest towards novel heterocyclic derivatives as novel anti-infective agents, researchers have explored these as essential tools in vistas of drug design and development. Among heterocycles, quinolones have been regarded extremely essential for the development of novel derivatives, even able to tackle the associated resistance issues. The quinolone scaffold with its bicyclic structure and specific functional groups such as the carbonyl and acidic groups, is indeed considered a valuable functionalities for further lead generation and optimization in drug discovery. Besides, the substitution at N-1, C-3 and C-7 positions also subjected to be having a significant role in anti-infective potential. In this article, we intend to highlight recent quinolone derivatives based on the SAR approach and anti-infective potential such as antibacterial, antifungal, antimalarial, antitubercular, antitrypanosomal and antiviral activities. Moreover, some recent patents granted on quinolone-containing derivatives as anti-infective agents have also been highlighted in tabular form. Due consideration of this, future research in this scaffold is expected to be useful for aspiring scientists to get pharmacologically significant leads.
Collapse
Affiliation(s)
- Vishal Sharma
- Department of Pharmaceutical Chemistry, MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207, India
| | - Rina Das
- Department of Pharmaceutical Chemistry, MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207, India
| | - Dinesh Kumar Mehta
- Department of Pharmaceutical Chemistry, MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207, India.
| | - Diksha Sharma
- Swami Devidyal College of Pharmacy, Barwala, 134118, India
| | - Shahbaz Aman
- Department of Microbiology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207, India
| | - M U Khan
- Department of pharmaceutical Chemistry & Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Uniazah, Al Qassim, Saudi Arabia
| |
Collapse
|
3
|
Mishra S, Tewari H, Chaudhary R, S Misra H, Kota S. Differential cellular localization of DNA gyrase and topoisomerase IB in response to DNA damage in Deinococcus radiodurans. Extremophiles 2023; 28:7. [PMID: 38062175 DOI: 10.1007/s00792-023-01323-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023]
Abstract
Topoisomerases are crucial enzymes in genome maintenance that modulate the topological changes during DNA metabolism. Deinococcus radiodurans, a Gram-positive bacterium is characterized by its resistance to many abiotic stresses including gamma radiation. Its multipartite genome encodes both type I and type II topoisomerases. Time-lapse studies using fluorescently tagged topoisomerase IB (drTopoIB-RFP) and DNA gyrase (GyrA-RFP) were performed to check the dynamics and localization with respect to DNA repair and cell division under normal and post-irradiation growth conditions. Results suggested that TopoIB and DNA gyrase are mostly found on nucleoid, highly dynamic, and show growth phase-dependent subcellular localization. The drTopoIB-RFP was also present at peripheral and septum regions but does not co-localize with the cell division protein, drFtsZ. On the other hand, DNA gyrase co-localizes with PprA a pleiotropic protein involved in radioresistance, on the nucleoid during the post-irradiation recovery (PIR). The topoIB mutant was found to be sensitive to hydroxyurea treatment, and showed more accumulation of single-stranded DNA during the PIR, compared to the wild type suggesting its role in DNA replication stress. Together, these results suggest differential localization of drTopoIB-RFP and GyrA-RFP in D. radiodurans and their interaction with PprA protein, emphasizing the functional significance and role in radioresistance.
Collapse
Affiliation(s)
- Shruti Mishra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute, Mumbai, 400094, India
| | - Himani Tewari
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute, Mumbai, 400094, India
| | - Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
- National Centre for Microbial Resource, National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune, 411021, India
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute, Mumbai, 400094, India
- Centre of Multidisciplinary Unit of Research On Translational Initiatives and School of Science, GITAM (Deemed to Be University), Gandhinagar, Rushikonda, Visakhapatnam, 530045, India
| | - Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.
- Homi Bhabha National Institute, Mumbai, 400094, India.
| |
Collapse
|
4
|
Deng Z, Chapagain P, Leng F. Macromolecular crowding potently stimulates DNA supercoiling activity of Mycobacterium tuberculosis DNA gyrase. J Biol Chem 2023; 299:105439. [PMID: 37944619 PMCID: PMC10731242 DOI: 10.1016/j.jbc.2023.105439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Macromolecular crowding, manifested by high concentrations of proteins and nucleic acids in living cells, significantly influences biological processes such as enzymatic reactions. Studying these reactions in vitro, using agents such as polyetthylene glycols (PEGs) and polyvinyl alcohols (PVAs) to mimic intracellular crowding conditions, is essential due to the notable differences from enzyme behaviors observed in diluted aqueous solutions. In this article, we studied Mycobacterium tuberculosis (Mtb) DNA gyrase under macromolecular crowding conditions by incorporating PEGs and PVAs into the DNA supercoiling reactions. We discovered that high concentrations of potassium glutamate, glycine betaine, PEGs, and PVA substantially stimulated the DNA supercoiling activity of Mtb DNA gyrase. Steady-state kinetic studies showed that glycine betaine and PEG400 significantly reduced the KM of Mtb DNA gyrase and simultaneously increased the Vmax or kcat of Mtb DNA gyrase for ATP and the plasmid DNA molecule. Molecular dynamics simulation studies demonstrated that PEG molecules kept the ATP lid of DNA gyrase subunit B in a closed or semiclosed conformation, which prevented ATP molecules from leaving the ATP-binding pocket of DNA gyrase subunit B. The stimulation of the DNA supercoiling activity of Mtb DNA gyrase by these molecular crowding agents likely results from a decrease in water activity and an increase in excluded volume.
Collapse
Affiliation(s)
- Zifang Deng
- Biomolecular Science Institute, Florida International University, Miami, Florida, USA; Department of Chemistry & Biochemistry, Florida International University, Miami, Florida, USA
| | - Prem Chapagain
- Biomolecular Science Institute, Florida International University, Miami, Florida, USA; Department of Physics, Florida International University, Miami, Florida, USA
| | - Fenfei Leng
- Biomolecular Science Institute, Florida International University, Miami, Florida, USA; Department of Chemistry & Biochemistry, Florida International University, Miami, Florida, USA.
| |
Collapse
|
5
|
Kamsri B, Pakamwong B, Thongdee P, Phusi N, Kamsri P, Punkvang A, Ketrat S, Saparpakorn P, Hannongbua S, Sangswan J, Suttisintong K, Sureram S, Kittakoop P, Hongmanee P, Santanirand P, Leanpolchareanchai J, Goudar KE, Spencer J, Mulholland AJ, Pungpo P. Bioisosteric Design Identifies Inhibitors of Mycobacterium tuberculosis DNA Gyrase ATPase Activity. J Chem Inf Model 2023; 63:2707-2718. [PMID: 37074047 DOI: 10.1021/acs.jcim.2c01376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Mutations in DNA gyrase confer resistance to fluoroquinolones, second-line antibiotics for Mycobacterium tuberculosis infections. Identification of new agents that inhibit M. tuberculosis DNA gyrase ATPase activity is one strategy to overcome this. Here, bioisosteric designs using known inhibitors as templates were employed to define novel inhibitors of M. tuberculosis DNA gyrase ATPase activity. This yielded the modified compound R3-13 with improved drug-likeness compared to the template inhibitor that acted as a promising ATPase inhibitor against M. tuberculosis DNA gyrase. Utilization of compound R3-13 as a virtual screening template, supported by subsequent biological assays, identified seven further M. tuberculosis DNA gyrase ATPase inhibitors with IC50 values in the range of 0.42-3.59 μM. The most active compound 1 showed an IC50 value of 0.42 μM, 3-fold better than the comparator ATPase inhibitor novobiocin (1.27 μM). Compound 1 showed noncytotoxicity to Caco-2 cells at concentrations up to 76-fold higher than its IC50 value. Molecular dynamics simulations followed by decomposition energy calculations identified that compound 1 occupies the binding pocket utilized by the adenosine group of the ATP analogue AMPPNP in the M. tuberculosis DNA gyrase GyrB subunit. The most prominent contribution to the binding of compound 1 to M. tuberculosis GyrB subunit is made by residue Asp79, which forms two hydrogen bonds with the OH group of this compound and also participates in the binding of AMPPNP. Compound 1 represents a potential new scaffold for further exploration and optimization as a M. tuberculosis DNA gyrase ATPase inhibitor and candidate anti-tuberculosis agent.
Collapse
Affiliation(s)
- Bundit Kamsri
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Bongkochawan Pakamwong
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Paptawan Thongdee
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Naruedon Phusi
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Pharit Kamsri
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom 48000, Thailand
| | - Auradee Punkvang
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom 48000, Thailand
| | - Sombat Ketrat
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | | | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Jidapa Sangswan
- Department of Biological Science, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Khomson Suttisintong
- National Nanotechnology Center, NSTDA, 111 Thailand Science Park, Klong Luang, Pathum Thani 12120, Thailand
| | - Sanya Sureram
- Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Prasat Kittakoop
- Chulabhorn Research Institute, Bangkok 10210, Thailand
- Chulabhorn Graduate Institute, Chemical Biology Program, Chulabhorn Royal Academy, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Higher Education, Science, Research and Innovation, Bangkok 10210, Thailand
| | - Poonpilas Hongmanee
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Pitak Santanirand
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Jiraporn Leanpolchareanchai
- Department of Pharmacy, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayuthaya Road,Rajathevi, Bangkok 10400, Thailand
| | - Kirsty E Goudar
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| |
Collapse
|
6
|
Galvin CJ, Hobson M, Meng JX, Ierokomos A, Ivanov IE, Berger JM, Bryant Z. Single-molecule dynamics of DNA gyrase in evolutionarily distant bacteria Mycobacterium tuberculosis and Escherichia coli. J Biol Chem 2023; 299:103003. [PMID: 36775125 PMCID: PMC10130225 DOI: 10.1016/j.jbc.2023.103003] [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: 05/18/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
DNA gyrase is an essential nucleoprotein motor present in all bacteria and is a major target for antibiotic treatment of Mycobacterium tuberculosis (MTB) infection. Gyrase hydrolyzes ATP to add negative supercoils to DNA using a strand passage mechanism that has been investigated using biophysical and biochemical approaches. To analyze the dynamics of substeps leading to strand passage, single-molecule rotor bead tracking (RBT) has been used previously to follow real-time supercoiling and conformational transitions in Escherichia coli (EC) gyrase. However, RBT has not yet been applied to gyrase from other pathogenically relevant bacteria, and it is not known whether substeps are conserved across evolutionarily distant species. Here, we compare gyrase supercoiling dynamics between two evolutionarily distant bacterial species, MTB and EC. We used RBT to measure supercoiling rates, processivities, and the geometries and transition kinetics of conformational states of purified gyrase proteins in complex with DNA. Our results show that E. coli and MTB gyrases are both processive, with the MTB enzyme displaying velocities ∼5.5× slower than the EC enzyme. Compared with EC gyrase, MTB gyrase also more readily populates an intermediate state with DNA chirally wrapped around the enzyme, in both the presence and absence of ATP. Our substep measurements reveal common features in conformational states of EC and MTB gyrases interacting with DNA but also suggest differences in populations and transition rates that may reflect distinct cellular needs between these two species.
Collapse
Affiliation(s)
- Cooper J Galvin
- Program in Biophysics, Stanford University, Stanford, California, USA; Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Matthew Hobson
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Athena Ierokomos
- Program in Biophysics, Stanford University, Stanford, California, USA; Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Ivan E Ivanov
- Department of Bioengineering, Stanford University, Stanford, California, USA; Department of Chemical Engineering, Stanford University, Stanford, California, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zev Bryant
- Program in Biophysics, Stanford University, Stanford, California, USA; Department of Bioengineering, Stanford University, Stanford, California, USA; Department of Structural Biology, Stanford University Medical Center, Stanford, California, USA.
| |
Collapse
|
7
|
Vidmar V, Vayssières M, Lamour V. What's on the Other Side of the Gate: A Structural Perspective on DNA Gate Opening of Type IA and IIA DNA Topoisomerases. Int J Mol Sci 2023; 24:ijms24043986. [PMID: 36835394 PMCID: PMC9960139 DOI: 10.3390/ijms24043986] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
DNA topoisomerases have an essential role in resolving topological problems that arise due to the double-helical structure of DNA. They can recognise DNA topology and catalyse diverse topological reactions by cutting and re-joining DNA ends. Type IA and IIA topoisomerases, which work by strand passage mechanisms, share catalytic domains for DNA binding and cleavage. Structural information has accumulated over the past decades, shedding light on the mechanisms of DNA cleavage and re-ligation. However, the structural rearrangements required for DNA-gate opening and strand transfer remain elusive, in particular for the type IA topoisomerases. In this review, we compare the structural similarities between the type IIA and type IA topoisomerases. The conformational changes that lead to the opening of the DNA-gate and strand passage, as well as allosteric regulation, are discussed, with a focus on the remaining questions about the mechanism of type IA topoisomerases.
Collapse
Affiliation(s)
- Vita Vidmar
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, Inserm U 1258, 67400 Illkirch, France
| | - Marlène Vayssières
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, Inserm U 1258, 67400 Illkirch, France
| | - Valérie Lamour
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, Inserm U 1258, 67400 Illkirch, France
- Hôpitaux Universitaires de Strasbourg, 67098 Strasbourg, France
- Correspondence:
| |
Collapse
|
8
|
Pakamwong B, Thongdee P, Kamsri B, Phusi N, Kamsri P, Punkvang A, Ketrat S, Saparpakorn P, Hannongbua S, Ariyachaokun K, Suttisintong K, Sureram S, Kittakoop P, Hongmanee P, Santanirand P, Spencer J, Mulholland AJ, Pungpo P. Identification of Potent DNA Gyrase Inhibitors Active against Mycobacterium tuberculosis. J Chem Inf Model 2022; 62:1680-1690. [PMID: 35347987 DOI: 10.1021/acs.jcim.1c01390] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mycobacterium tuberculosis DNA gyrase manipulates the DNA topology using controlled breakage and religation of DNA driven by ATP hydrolysis. DNA gyrase has been validated as the enzyme target of fluoroquinolones (FQs), second-line antibiotics used for the treatment of multidrug-resistant tuberculosis. Mutations around the DNA gyrase DNA-binding site result in the emergence of FQ resistance in M. tuberculosis; inhibition of DNA gyrase ATPase activity is one strategy to overcome this. Here, virtual screening, subsequently validated by biological assays, was applied to select candidate inhibitors of the M. tuberculosis DNA gyrase ATPase activity from the Specs compound library (www.specs.net). Thirty compounds were identified and selected as hits for in vitro biological assays, of which two compounds, G24 and G26, inhibited the growth of M. tuberculosis H37Rv with a minimal inhibitory concentration of 12.5 μg/mL. The two compounds inhibited DNA gyrase ATPase activity with IC50 values of 2.69 and 2.46 μM, respectively, suggesting this to be the likely basis of their antitubercular activity. Models of complexes of compounds G24 and G26 bound to the M. tuberculosis DNA gyrase ATP-binding site, generated by molecular dynamics simulations followed by pharmacophore mapping analysis, showed hydrophobic interactions of inhibitor hydrophobic headgroups and electrostatic and hydrogen bond interactions of the polar tails, which are likely to be important for their inhibition. Decreasing compound lipophilicity by increasing the polarity of these tails then presents a likely route to improving the solubility and activity. Thus, compounds G24 and G26 provide attractive starting templates for the optimization of antitubercular agents that act by targeting DNA gyrase.
Collapse
Affiliation(s)
- Bongkochawan Pakamwong
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Paptawan Thongdee
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Bundit Kamsri
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Naruedon Phusi
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Pharit Kamsri
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom 48000, Thailand
| | - Auradee Punkvang
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom 48000, Thailand
| | - Sombat Ketrat
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | | | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kanchiyaphat Ariyachaokun
- Department of Biological Science, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Khomson Suttisintong
- National Nanotechnology Center, NSTDA, 111 Thailand Science Park, Klong Luang, Pathum Thani 12120, Thailand
| | - Sanya Sureram
- Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Prasat Kittakoop
- Chulabhorn Research Institute, Bangkok 10210, Thailand
- Chulabhorn Graduate Institute, Chemical Biology Program, Chulabhorn Royal Academy, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok 10300, Thailand
| | - Poonpilas Hongmanee
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Pitak Santanirand
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| |
Collapse
|
9
|
Hirsch J, Klostermeier D. What makes a type IIA topoisomerase a gyrase or a Topo IV? Nucleic Acids Res 2021; 49:6027-6042. [PMID: 33905522 PMCID: PMC8216471 DOI: 10.1093/nar/gkab270] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 12/14/2022] Open
Abstract
Type IIA topoisomerases catalyze a variety of different reactions: eukaryotic topoisomerase II relaxes DNA in an ATP-dependent reaction, whereas the bacterial representatives gyrase and topoisomerase IV (Topo IV) preferentially introduce negative supercoils into DNA (gyrase) or decatenate DNA (Topo IV). Gyrase and Topo IV perform separate, dedicated tasks during replication: gyrase removes positive supercoils in front, Topo IV removes pre-catenanes behind the replication fork. Despite their well-separated cellular functions, gyrase and Topo IV have an overlapping activity spectrum: gyrase is also able to catalyze DNA decatenation, although less efficiently than Topo IV. The balance between supercoiling and decatenation activities is different for gyrases from different organisms. Both enzymes consist of a conserved topoisomerase core and structurally divergent C-terminal domains (CTDs). Deletion of the entire CTD, mutation of a conserved motif and even by just a single point mutation within the CTD converts gyrase into a Topo IV-like enzyme, implicating the CTDs as the major determinant for function. Here, we summarize the structural and mechanistic features that make a type IIA topoisomerase a gyrase or a Topo IV, and discuss the implications for type IIA topoisomerase evolution.
Collapse
Affiliation(s)
- Jana Hirsch
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, 48149 Muenster, Germany
| | - Dagmar Klostermeier
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, 48149 Muenster, Germany
| |
Collapse
|
10
|
Vanden Broeck A, Lotz C, Drillien R, Haas L, Bedez C, Lamour V. Structural basis for allosteric regulation of Human Topoisomerase IIα. Nat Commun 2021; 12:2962. [PMID: 34016969 PMCID: PMC8137924 DOI: 10.1038/s41467-021-23136-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 04/15/2021] [Indexed: 12/01/2022] Open
Abstract
The human type IIA topoisomerases (Top2) are essential enzymes that regulate DNA topology and chromosome organization. The Topo IIα isoform is a prime target for antineoplastic compounds used in cancer therapy that form ternary cleavage complexes with the DNA. Despite extensive studies, structural information on this large dimeric assembly is limited to the catalytic domains, hindering the exploration of allosteric mechanism governing the enzyme activities and the contribution of its non-conserved C-terminal domain (CTD). Herein we present cryo-EM structures of the entire human Topo IIα nucleoprotein complex in different conformations solved at subnanometer resolutions (3.6-7.4 Å). Our data unveils the molecular determinants that fine tune the allosteric connections between the ATPase domain and the DNA binding/cleavage domain. Strikingly, the reconstruction of the DNA-binding/cleavage domain uncovers a linker leading to the CTD, which plays a critical role in modulating the enzyme's activities and opens perspective for the analysis of post-translational modifications.
Collapse
Affiliation(s)
- Arnaud Vanden Broeck
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Christophe Lotz
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Robert Drillien
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Léa Haas
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Claire Bedez
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Valérie Lamour
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.
- Department of Integrated Structural Biology, IGBMC, Illkirch, France.
- Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
| |
Collapse
|
11
|
Umumararungu T, Mukazayire MJ, Mpenda M, Mukanyangezi MF, Nkuranga JB, Mukiza J, Olawode EO. A review of recent advances in anti-tubercular drug development. Indian J Tuberc 2020; 67:539-559. [PMID: 33077057 DOI: 10.1016/j.ijtb.2020.07.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/24/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
Abstract
Tuberculosis is a global threat but in particular affects people from developing countries. It is thought that nearly a third of the population of the world live with its causative bacteria in a dormant form. Although tuberculosis is a curable disease, the chances of cure become slim as the disease becomes multidrug-resistant and the situation gets even worse as the disease becomes extensively drug-resistant. After approximately 5 decades without any new TB drug in the pipeline, there has been some good news in the recent years with the discovery of new drugs such as bedaquiline and delamanid as well as the discovery of new classes of anti-tubercular drugs. Some old drugs such as clofazimine, linezolid and many others which were not previously indicated for tuberculosis have been also repurposed for tuberculosis and they are performing well.
Collapse
Affiliation(s)
- Théoneste Umumararungu
- Department of Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda.
| | - Marie Jeanne Mukazayire
- Department of Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Matabishi Mpenda
- Department of Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Marie Françoise Mukanyangezi
- Department of Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Jean Bosco Nkuranga
- Department of Chemistry, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Janvier Mukiza
- Department of Mathematical Science and Physical Education, School of Education, College of Education, University of Rwanda, Rwanda
| | | |
Collapse
|
12
|
Structure-Based Drug Design for Tuberculosis: Challenges Still Ahead. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10124248] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structure-based and computer-aided drug design approaches are commonly considered to have been successful in the fields of cancer and antiviral drug discovery but not as much for antibacterial drug development. The search for novel anti-tuberculosis agents is indeed an emblematic example of this trend. Although huge efforts, by consortiums and groups worldwide, dramatically increased the structural coverage of the Mycobacterium tuberculosis proteome, the vast majority of candidate drugs included in clinical trials during the last decade were issued from phenotypic screenings on whole mycobacterial cells. We developed here three selected case studies, i.e., the serine/threonine (Ser/Thr) kinases—protein kinase (Pkn) B and PknG, considered as very promising targets for a long time, and the DNA gyrase of M. tuberculosis, a well-known, pharmacologically validated target. We illustrated some of the challenges that rational, target-based drug discovery programs in tuberculosis (TB) still have to face, and, finally, discussed the perspectives opened by the recent, methodological developments in structural biology and integrative techniques.
Collapse
|
13
|
Sachdeva E, Kaur G, Tiwari P, Gupta D, Singh TP, Ethayathulla AS, Kaur P. The pivot point arginines identified in the β-pinwheel structure of C-terminal domain from Salmonella Typhi DNA Gyrase A subunit. Sci Rep 2020; 10:7817. [PMID: 32385379 PMCID: PMC7210945 DOI: 10.1038/s41598-020-64792-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/13/2020] [Indexed: 11/17/2022] Open
Abstract
The essentiality of DNA Gyrase in basic cellular processes in bacterial pathogens makes it an ideal drug target. Though the Gyrase has a conserved mechanism of action, the complete DNA wrapping and binding process is still unknown. In this study, we have identified six arginine residues R556, R612, R667, R716, R766, and R817 in the DNA GyraseA – C-terminal domain from Salmonella enterica serovar Typhi (StGyrA-CTD) to be essential for DNA wrapping and sliding by a sequence and structure analysis. Through site-directed mutagenesis and EMSA studies, we observed that the substitution of R667 (blade 3) and R716 (blade 4) in StGyrA-CTD led to loss of DNA binding. Whereas, upon mutation of residue R612 (blade2), R766 (blade5) and R817 (blade6) along with supporting residue R712 (blade 4) a decrease in binding affinity was seen. Our results indicate that R667 and R716 act as a pivot point in DNA wrapping and sliding during gyrase catalytic activity. In this study, we propose that the DNA wrapping mechanism commences with DNA binding at blade3 and blade4 followed by other blades to facilitate the DNA sliding during supercoiling activity. This study provides a better understanding of the DNA binding and wrapping mechanism of GyrA-CTD in DNA Gyrase.
Collapse
Affiliation(s)
- Ekta Sachdeva
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Gurpreet Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Pragya Tiwari
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Deepali Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Abdul S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India.
| |
Collapse
|
14
|
Hobson MJ, Bryant Z, Berger JM. Modulated control of DNA supercoiling balance by the DNA-wrapping domain of bacterial gyrase. Nucleic Acids Res 2020; 48:2035-2049. [PMID: 31950157 PMCID: PMC7038939 DOI: 10.1093/nar/gkz1230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/18/2019] [Accepted: 01/15/2020] [Indexed: 01/26/2023] Open
Abstract
Negative supercoiling by DNA gyrase is essential for maintaining chromosomal compaction, transcriptional programming, and genetic integrity in bacteria. Questions remain as to how gyrases from different species have evolved profound differences in their kinetics, efficiency, and extent of negative supercoiling. To explore this issue, we analyzed homology-directed mutations in the C-terminal, DNA-wrapping domain of the GyrA subunit of Escherichia coli gyrase (the 'CTD'). The addition or removal of select, conserved basic residues markedly impacts both nucleotide-dependent DNA wrapping and supercoiling by the enzyme. Weakening CTD-DNA interactions slows supercoiling, impairs DNA-dependent ATP hydrolysis, and limits the extent of DNA supercoiling, while simultaneously enhancing decatenation and supercoil relaxation. Conversely, strengthening DNA wrapping does not result in a more extensively supercoiled DNA product, but partially uncouples ATP turnover from strand passage, manifesting in futile cycling. Our findings indicate that the catalytic cycle of E. coli gyrase operates at high thermodynamic efficiency, and that the stability of DNA wrapping by the CTD provides one limit to DNA supercoil introduction, beyond which strand passage competes with ATP-dependent supercoil relaxation. These results highlight a means by which gyrase can evolve distinct homeostatic supercoiling setpoints in a species-specific manner.
Collapse
Affiliation(s)
- Matthew J Hobson
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
15
|
Surana P, Jainarayanan AK, Anand NM, Sharma M. Analysing non-synonymous mutations in XDR and MDR tuberculosis drugs. J Clin Tuberc Other Mycobact Dis 2019; 17:100124. [PMID: 31788566 PMCID: PMC6880092 DOI: 10.1016/j.jctube.2019.100124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis is a bacterial disease caused by Mycobacterium tuberculosis. It is known to be the second-largest cause of death and models a severe risk to public health throughout the world. Though it affects people of almost every age, individuals with weakened immune systems, (e.g., HIV infection) are more likely to get infected. The present study deals with analyzing non-synonymous mutations in anti-tuberculosis drugs, which may have a significant role in causing XDR and MDR tuberculosis drug resistance. Continued use of tuberculosis drugs, discontinuation of medicines and various other factors can promote drug resistance in the host's body. To understand the actual cause of resistance, we have identified some patterns of mutations which might be responsible for a change in the structure of the protein, ultimately causing drug resistance. Here, we aim to present some of the unique mutation patterns in the genes associated with the marketed drugs that might have a deleterious effect. In this study, we have used molecular docking approach for understanding the ligand binding affinity of the mutated drugs. The results are further validated by molecular dynamics studies.
Collapse
Affiliation(s)
| | - Ashwin Kumar Jainarayanan
- Indian Institute of Science Education and Research, Mohali, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Mukta Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| |
Collapse
|
16
|
Petrella S, Capton E, Raynal B, Giffard C, Thureau A, Bonneté F, Alzari PM, Aubry A, Mayer C. Overall Structures of Mycobacterium tuberculosis DNA Gyrase Reveal the Role of a Corynebacteriales GyrB-Specific Insert in ATPase Activity. Structure 2019; 27:579-589.e5. [PMID: 30744994 DOI: 10.1016/j.str.2019.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/13/2018] [Accepted: 01/14/2019] [Indexed: 01/03/2023]
Abstract
Despite sharing common features, previous studies have shown that gyrases from different species have been modified throughout evolution to modulate their properties. Here, we report two crystal structures of Mycobacterium tuberculosis DNA gyrase, an apo and AMPPNP-bound form at 2.6-Å and 3.3-Å resolution, respectively. These structures provide high-resolution structural data on the quaternary organization and interdomain connections of a gyrase (full-length GyrB-GyrA57)2 thus providing crucial inputs on this essential drug target. Together with small-angle X-ray scattering studies, they revealed an "extremely open" N-gate state, which persists even in the DNA-free gyrase-AMPPNP complex and an unexpected connection between the ATPase and cleavage core domains mediated by two Corynebacteriales-specific motifs, respectively the C-loop and DEEE-loop. We show that the C-loop participates in the stabilization of this open conformation, explaining why this gyrase has a lower ATPase activity. Our results image a conformational state which might be targeted for drug discovery.
Collapse
Affiliation(s)
- Stéphanie Petrella
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France; Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France.
| | - Estelle Capton
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses-Paris, Cimi-Paris, INSERM U1135, National Reference Center for Mycobacteria, Laboratoire de Bactériologie-Hygiène, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, 75013 Paris, France
| | - Bertrand Raynal
- Plateforme de Biophysique Moléculaire, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Clément Giffard
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France; Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France
| | - Aurélien Thureau
- Synchrotron SOLEIL, l'Orme des Merisiers, 91410 Saint Aubin, France
| | - Françoise Bonneté
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS UMR7099 and Université Paris Didérot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Pedro M Alzari
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France; Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France
| | - Alexandra Aubry
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses-Paris, Cimi-Paris, INSERM U1135, National Reference Center for Mycobacteria, Laboratoire de Bactériologie-Hygiène, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, 75013 Paris, France.
| | - Claudine Mayer
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France; Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France
| |
Collapse
|
17
|
Chowdhury SR, Majumder HK. DNA Topoisomerases in Unicellular Pathogens: Structure, Function, and Druggability. Trends Biochem Sci 2019; 44:415-432. [PMID: 30609953 DOI: 10.1016/j.tibs.2018.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/20/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023]
Abstract
All organisms, including unicellular pathogens, compulsorily possess DNA topoisomerases for successful nucleic acid metabolism. But particular subtypes of topoisomerases exist, in all prokaryotes and in some unicellular eukaryotes, that are absent in higher eukaryotes. Moreover, topoisomerases from pathogenic members of a niche possess some unique molecular architecture and functionalities completely distinct from their nonpathogenic colleagues. This review will highlight the unique attributes associated with the structures and functions of topoisomerases from the unicellular pathogens, with special reference to bacteria and protozoan parasites. It will also summarise the progress made in the domain pertaining to the druggability of these topoisomerases, upon which a future platform for therapeutic development can be successfully constructed.
Collapse
Affiliation(s)
- Somenath Roy Chowdhury
- Laboratory of Molecular Parasitology, Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Hemanta K Majumder
- Laboratory of Molecular Parasitology, Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
| |
Collapse
|
18
|
Carta A, Bua A, Corona P, Piras S, Briguglio I, Molicotti P, Zanetti S, Laurini E, Aulic S, Fermeglia M, Pricl S. Design, synthesis and antitubercular activity of 4-alkoxy-triazoloquinolones able to inhibit the M. tuberculosis DNA gyrase. Eur J Med Chem 2018; 161:399-415. [PMID: 30384044 DOI: 10.1016/j.ejmech.2018.10.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/09/2018] [Accepted: 10/12/2018] [Indexed: 01/30/2023]
Abstract
A number of new F-triazolequinolones (FTQs) and alkoxy-triazolequinolones (ATQs) were designed, synthesized and evaluated for their activity against Mycobacterium tuberculosis H37Rv. Five out of 21 compounds exhibited interesting minimum inhibitory concentration (MIC) values (6.6-57.9 μM), ATQs generally being more potent than FTQs. Two ATQs, 21a and 30a, were endowed with the best anti-Mtb potency (MIC = 6.9 and 6.6 μM, respectively), and were not cytotoxic in a Vero cell line. Tested for activity against M. tuberculosis DNA gyrase in a DNA supercoiling activity assay, 21a and 30a showed IC50 values (27-28 μM) comparable to that of ciprofloxacin (10.6 μM). 21a was next selected for screening against several Mtb strains obtained from clinical isolates, including multi-drug-resistant (MDR) variants. Importantly, this compound was effective in all cases, with very promising MIC values (4 μM) in the case of some isoniazid/rifampicin-resistant Mtb strains. Finally, computer-based simulations revealed that the binding mode of 21a in the Mtb gyrase cleavage core complexed with DNA and the relevant network of intermolecular interactions are utterly similar to those described for ciprofloxacin, yielding a molecular rationale for the comparable anti-mycobacterial and DNA gyrase inhibition activity of this quinolone.
Collapse
Affiliation(s)
- Antonio Carta
- Department of Chemistry and Pharmacy, University of Sassari, Via Muroni 23, 07100, Sassari, Italy.
| | - Alessandra Bua
- Department of Biomedical Sciences, University of Sassari, V.le San Pietro 43/C, 07100, Sassari, Italy
| | - Paola Corona
- Department of Chemistry and Pharmacy, University of Sassari, Via Muroni 23, 07100, Sassari, Italy
| | - Sandra Piras
- Department of Chemistry and Pharmacy, University of Sassari, Via Muroni 23, 07100, Sassari, Italy
| | - Irene Briguglio
- Department of Chemistry and Pharmacy, University of Sassari, Via Muroni 23, 07100, Sassari, Italy
| | - Paola Molicotti
- Department of Biomedical Sciences, University of Sassari, V.le San Pietro 43/C, 07100, Sassari, Italy
| | - Stefania Zanetti
- Department of Biomedical Sciences, University of Sassari, V.le San Pietro 43/C, 07100, Sassari, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy.
| |
Collapse
|
19
|
Patkari M, Kumbhar C, Nag A, Mehra S. Distinct transcriptomic response of S. coelicolor to ciprofloxacin in a nutrient-rich environment. Appl Microbiol Biotechnol 2018; 102:10623-10643. [PMID: 30327831 DOI: 10.1007/s00253-018-9398-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 02/07/2023]
Abstract
With the rising threat of anti-microbial resistance (AMR), there is an urgent need to enhance efficacy of existing antibiotics. Understanding the myriad mechanisms through which bacteria evade these drugs would be of immense value to designing novel strategies against them. Streptomyces coelicolor A3(2) M145 belongs to the actinomyctes species that are responsible for more than two-thirds of antibiotics. This group of bacteria therefore encodes for various mechanisms that can resist both endogenous and non-endogenous antibiotics. In an earlier study, we had studied the transcriptomic response of these bacteria to ciprofloxacin, when cultured in a minimal media. In this work, we investigate why the minimum inhibitory concentration of the drug increases by fourfold when the bacteria are grown in a nutrient-rich media. Through transcriptomic, biochemical, and microscopic studies, we show that S. coelicolor responds to ciprofloxacin in a concentration-dependent manner. While, sub-inhibitory concentration of the drug primarily causes oxidative stress, the inhibitory concentration of ciprofloxacin evokes a more severe genome-wide response in the cell, which ranges from the familiar upregulation of the SOS response and DNA repair pathways to the widespread alterations in the central metabolism pathway to accommodate the increased needs of nucleotides and other precursors. Further, the upregulation of peptidoglycan synthesis genes, along with microscopy images, suggest alterations in the cell morphology to increase fitness of the bacteria during the antibiotic stress. The data also points to the enhanced efflux activity in cells cultured in rich media that contributes significantly towards reducing intracellular drug concentration and thus promotes survival.
Collapse
Affiliation(s)
- Minal Patkari
- Department of Chemical Engineering, IIT Bombay, Powai, 400076, India
- Department of Civil and Environmental Engineering, University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | - Ankita Nag
- Department of Chemical Engineering, IIT Bombay, Powai, 400076, India
| | - Sarika Mehra
- Department of Chemical Engineering, IIT Bombay, Powai, 400076, India.
| |
Collapse
|
20
|
Ashley RE, Blower TR, Berger JM, Osheroff N. Recognition of DNA Supercoil Geometry by Mycobacterium tuberculosis Gyrase. Biochemistry 2017; 56:5440-5448. [PMID: 28921956 PMCID: PMC5637011 DOI: 10.1021/acs.biochem.7b00681] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Mycobacterium
tuberculosis encodes only a single
type II topoisomerase, gyrase. As a result, this enzyme likely carries
out the cellular functions normally performed by canonical gyrase
and topoisomerase IV, both in front of and behind the replication
fork. In addition, it is the sole target for quinolone antibacterials
in this species. Because quinolone-induced DNA strand breaks generated
on positively supercoiled DNA ahead of replication forks and transcription
complexes are most likely to result in permanent genomic damage, the
actions of M. tuberculosis gyrase on positively supercoiled
DNA were investigated. Results indicate that the enzyme acts rapidly
on overwound DNA and removes positive supercoils much faster than
it introduces negative supercoils into relaxed DNA. Canonical gyrase
and topoisomerase IV distinguish supercoil handedness differently
during the DNA cleavage reaction: while gyrase maintains lower levels
of cleavage complexes on overwound DNA, topoisomerase IV maintains
similar levels of cleavage complexes on both over- and underwound
substrates. M. tuberculosis gyrase maintained lower
levels of cleavage complexes on positively supercoiled DNA in the
absence and presence of quinolone-based drugs. By retaining this important
feature of canonical gyrase, the dual function M. tuberculosis type II enzyme remains a safe enzyme to act in front of replication
forks and transcription complexes. Finally, the N-terminal gate region
of the enzyme appears to be necessary to distinguish supercoil handedness
during DNA cleavage, suggesting that the capture of the transport
segment may influence how gyrase maintains cleavage complexes on substrates
with different topological states.
Collapse
Affiliation(s)
| | - Tim R Blower
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , Baltimore, Maryland 21205-2185, United States
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , Baltimore, Maryland 21205-2185, United States
| | - Neil Osheroff
- VA Tennessee Valley Healthcare System , Nashville, Tennessee 37212, United States
| |
Collapse
|
21
|
Ashley RE, Lindsey RH, McPherson SA, Turnbough CL, Kerns RJ, Osheroff N. Interactions between Quinolones and Bacillus anthracis Gyrase and the Basis of Drug Resistance. Biochemistry 2017; 56:4191-4200. [PMID: 28708938 PMCID: PMC5560241 DOI: 10.1021/acs.biochem.7b00203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Gyrase appears to
be the primary cellular target for quinolone
antibacterials in multiple pathogenic bacteria, including Bacillus anthracis, the causative agent of anthrax. Given
the significance of this type II topoisomerase as a drug target, it
is critical to understand how quinolones interact with gyrase and
how specific mutations lead to resistance. However, these important
issues have yet to be addressed for a canonical gyrase. Therefore,
we utilized a mechanistic approach to characterize interactions of
quinolones with wild-type B. anthracis gyrase and
enzymes containing the most common quinolone resistance mutations.
Results indicate that clinically relevant quinolones interact with
the enzyme through a water–metal ion bridge in which a noncatalytic
divalent metal ion is chelated by the C3/C4 keto acid of the drug.
In contrast to other bacterial type II topoisomerases that have been
examined, the bridge is anchored to gyrase primarily through a single
residue (Ser85). Substitution of groups at the quinolone C7 and C8
positions generated drugs that were less dependent on the water–metal
ion bridge and overcame resistance. Thus, by analyzing the interactions
of drugs with type II topoisomerases from individual bacteria, it
may be possible to identify specific quinolone derivatives that can
overcome target-mediated resistance in important pathogenic species.
Collapse
Affiliation(s)
| | | | - Sylvia A McPherson
- Department of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Charles L Turnbough
- Department of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Robert J Kerns
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa College of Pharmacy , Iowa City, Iowa 52242, United States
| | - Neil Osheroff
- VA Tennessee Valley Healthcare System , Nashville, Tennessee 37212, United States
| |
Collapse
|
22
|
Minovski N, Novič M. Integrated in Silico Methods for the Design and Optimization of Novel Drug Candidates. Oncology 2017. [DOI: 10.4018/978-1-5225-0549-5.ch016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although almost fully automated, the discovery of novel, effective, and safe drugs is still a long-term and highly expensive process. Consequently, the need for fleet, rational, and cost-efficient development of novel drugs is crucial, and nowadays the advanced in silico drug design methodologies seem to effectively meet these issues. The aim of this chapter is to provide a comprehensive overview of some of the current trends and advances in the in silico design of novel drug candidates with a special emphasis on 6-fluoroquinolone (6-FQ) antibacterials as potential novel Mycobacterium tuberculosis DNA gyrase inhibitors. In particular, the chapter covers some of the recent aspects of a wide range of in silico drug discovery approaches including multidimensional machine-learning methods, ligand-based and structure-based methodologies, as well as their proficient combination and integration into an intelligent virtual screening protocol for design and optimization of novel 6-FQ analogs.
Collapse
|
23
|
Investigating the Roles of the C-Terminal Domain of Plasmodium falciparum GyrA. PLoS One 2015; 10:e0142313. [PMID: 26566222 PMCID: PMC4643928 DOI: 10.1371/journal.pone.0142313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 10/20/2015] [Indexed: 01/11/2023] Open
Abstract
Malaria remains as one of the most deadly diseases in developing countries. The Plasmodium causative agents of human malaria such as Plasmodium falciparum possess an organelle, the apicoplast, which is the result of secondary endosymbiosis and retains its own circular DNA. A type II topoisomerase, DNA gyrase, is present in the apicoplast. In prokaryotes this enzyme is a proven, effective target for antibacterial agents, and its discovery in P. falciparum opens up the prospect of exploiting it as a drug target. Basic characterisation of P. falciparum gyrase is important because there are significant sequence differences between it and the prokaryotic enzyme. However, it has proved difficult to obtain soluble protein. Here we have predicted a new domain boundary in P. falciparum GyrA that corresponds to the C-terminal domain of prokaryotic GyrA and successfully purified it in a soluble form. Biochemical analyses revealed many similarities between the C-terminal domains of GyrA from E. coli and P. falciparum, suggesting that despite its considerably larger size, the malarial protein carries out a similar DNA wrapping function. Removal of a unique Asn-rich region in the P. falciparum protein did not result in a significant change, suggesting it is dispensable for DNA wrapping.
Collapse
|
24
|
Lin TY, Nagano S, Gardiner Heddle J. Functional Analyses of the Toxoplasma gondii DNA Gyrase Holoenzyme: A Janus Topoisomerase with Supercoiling and Decatenation Abilities. Sci Rep 2015; 5:14491. [PMID: 26412236 PMCID: PMC4585971 DOI: 10.1038/srep14491] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/19/2015] [Indexed: 12/29/2022] Open
Abstract
A number of important protozoan parasites including those responsible for toxoplasmosis and malaria belong to the phylum Apicomplexa and are characterised by their possession of a relict plastid, the apicoplast. Being required for survival, apicoplasts are potentially useful drug targets and their attractiveness is increased by the fact that they contain “bacterial” gyrase, a well-established antibacterial drug target. We have cloned and purified the gyrase proteins from the apicoplast of Toxoplasma gondii (the cause of toxoplasmosis), reconstituted the functional enzyme and succeeded in characterising it. We discovered that the enzyme is inhibited by known gyrase inhibitors and that, as well as the expected supercoiling activity, it is also able to decatenate DNA with high efficiency. This unusual dual functionality may be related to the apparent lack of topoisomerase IV in the apicoplast.
Collapse
Affiliation(s)
- Ting-Yu Lin
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Soshichiro Nagano
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | | |
Collapse
|
25
|
Eagle Effect in Nonreplicating Persister Mycobacteria. Antimicrob Agents Chemother 2015; 59:7786-9. [PMID: 26349831 PMCID: PMC4649170 DOI: 10.1128/aac.01476-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/03/2015] [Indexed: 11/25/2022] Open
Abstract
We determined the microbicidal activities of antibacterials against nonreplicating Mycobacterium smegmatis grown in a starvation-based Loebel model for persistence. Whereas most drugs lost their activity, fluoroquinolones retained lethal potency. Dose-response characterizations showed a paradoxical more-drug-kills-less Eagle effect. Pretreatment of cultures with chloramphenicol blocked the lethal action of the gyrase inhibitors. These results suggest that fluoroquinolones at low concentrations trigger a protein synthesis-dependent cell death pathway and shut off this suicide pathway at elevated concentrations.
Collapse
|
26
|
Synthesis, anti-microbial and anti-cancer evaluation study of 3-(3-benzofuranyl)-coumarin derivatives. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1449-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|