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Syed A, Filandr F, Patterson-Fortin J, Bacolla A, Ravindranathan R, Zhou J, McDonald D, Albuhluli M, Verway-Cohen A, Newman J, Tsai MS, Jones D, Schriemer D, D’Andrea A, Tainer J. Novobiocin blocks nucleic acid binding to Polθ and inhibits stimulation of its ATPase activity. Nucleic Acids Res 2023; 51:9920-9937. [PMID: 37665033 PMCID: PMC10570058 DOI: 10.1093/nar/gkad727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/10/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023] Open
Abstract
Polymerase theta (Polθ) acts in DNA replication and repair, and its inhibition is synthetic lethal in BRCA1 and BRCA2-deficient tumor cells. Novobiocin (NVB) is a first-in-class inhibitor of the Polθ ATPase activity, and it is currently being tested in clinical trials as an anti-cancer drug. Here, we investigated the molecular mechanism of NVB-mediated Polθ inhibition. Using hydrogen deuterium exchange-mass spectrometry (HX-MS), biophysical, biochemical, computational and cellular assays, we found NVB is a non-competitive inhibitor of ATP hydrolysis. NVB sugar group deletion resulted in decreased potency and reduced HX-MS interactions, supporting a specific NVB binding orientation. Collective results revealed that NVB binds to an allosteric site to block DNA binding, both in vitro and in cells. Comparisons of The Cancer Genome Atlas (TCGA) tumors and matched controls implied that POLQ upregulation in tumors stems from its role in replication stress responses to increased cell proliferation: this can now be tested in fifteen tumor types by NVB blocking ssDNA-stimulation of ATPase activity, required for Polθ function at replication forks and DNA damage sites. Structural and functional insights provided in this study suggest a path for developing NVB derivatives with improved potency for Polθ inhibition by targeting ssDNA binding with entropically constrained small molecules.
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Affiliation(s)
- Aleem Syed
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Frantisek Filandr
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jeffrey Patterson-Fortin
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ramya Ravindranathan
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Jia Zhou
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Drew T McDonald
- Biological and System Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mohammed E Albuhluli
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Amy Verway-Cohen
- Biological and System Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joseph A Newman
- Center for Medicines Discovery, University of Oxford, OX1 3QU, UK
| | - Miaw-Sheue Tsai
- Biological and System Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Darin E Jones
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Alan D D’Andrea
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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2
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Ling EM, Baslé A, Cowell IG, van den Berg B, Blower TR, Austin CA. A comprehensive structural analysis of the ATPase domain of human DNA topoisomerase II beta bound to AMPPNP, ADP, and the bisdioxopiperazine, ICRF193. Structure 2022; 30:1129-1145.e3. [PMID: 35660158 PMCID: PMC9592559 DOI: 10.1016/j.str.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/25/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022]
Abstract
Human topoisomerase II beta (TOP2B) modulates DNA topology using energy from ATP hydrolysis. To investigate the conformational changes that occur during ATP hydrolysis, we determined the X-ray crystallographic structures of the human TOP2B ATPase domain bound to AMPPNP or ADP at 1.9 Å and 2.6 Å resolution, respectively. The GHKL domains of both structures are similar, whereas the QTK loop within the transducer domain can move for product release. As TOP2B is the clinical target of bisdioxopiperazines, we also determined the structure of a TOP2B:ADP:ICRF193 complex to 2.3 Å resolution and identified key drug-binding residues. Biochemical characterization revealed the N-terminal strap reduces the rate of ATP hydrolysis. Mutagenesis demonstrated residue E103 as essential for ATP hydrolysis in TOP2B. Our data provide fundamental insights into the tertiary structure of the human TOP2B ATPase domain and a potential regulatory mechanism for ATP hydrolysis. Three structures of the TOP2B ATPase domain bound to AMPPNP, ADP, or ICRF193 The QTK loop in the ADP complex is further from the active site An SO4 ion is in place of the ATP hydrolysis product, Pi Biochemical data show the N-terminal strap reduces the ATPase hydrolysis activity
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Affiliation(s)
- Elise M Ling
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ian G Cowell
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Bert van den Berg
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK.
| | - Caroline A Austin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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Purushothaman M, Dhar SK, Natesh R. Role of unique loops in oligomerization and ATPase function of Plasmodium falciparum gyrase B. Protein Sci 2022; 31:323-332. [PMID: 34716632 PMCID: PMC8820116 DOI: 10.1002/pro.4217] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 02/03/2023]
Abstract
DNA gyrase is an ATP dependent Type IIA topoisomerase that is unique to prokaryotes. Interestingly DNA gyrase has also been found in the apicoplasts of apicomplexan parasites like Plasmodium falciparum (Pf) the causative agent of Malaria. Gyrase B (GyrB), a subunit of gyrase A2 B2 complex has an N-terminal domain (GyrBN) which is endowed with ATPase activity. We reported earlier that PfGyrB exhibits ATP-independent dimerization unlike its bacterial counterparts. Here we report the role of two unique regions (L1 and L2) identified in PfGyrBN. Deletions of L1 alone (PfGyrBNΔL1), or L1 and L2 together (PfGyrBNΔL1ΔL2) have indicated that these regions may play an important role in ATPase activity and the oligomeric state of PfGyrBN. Our experiments show that the deletion of L1 region disrupts the dimer interface of PfGyrBN and reduces its ATPase activity. Further through ITC experiments we show that the binding affinity of ATP to PfGyrBN is reduced upon the deletion of L1 region. We have observed a reduction in ATPase activity for of all three proteins PfGyrBN, PfGyrBNΔL1, and PfGyrBNΔL1ΔL2 in presence of coumermycin. Our results suggests that L1 region of PfGyrBN is likely to be functionally important and may provide a unique dimer interface that affects its enzymatic activity. Since deletion of L1 region decreases the affinity of ATP to the protein, this region can be targeted toward designing novel inhibitors of ATP hydrolysis.
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Affiliation(s)
- Monica Purushothaman
- School of BiologyIndian Institute of Science Education and Research ThiruvananthapuramThiruvananthapuramKeralaIndia
| | - Suman Kumar Dhar
- Special Centre of Molecular MedicineJawaharlal Nehru UniversityNew DelhiIndia
| | - Ramanathan Natesh
- School of BiologyIndian Institute of Science Education and Research ThiruvananthapuramThiruvananthapuramKeralaIndia
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Gong L, Lu P, Lu C, Li M, Wan H, Wang Y. Design, Synthesis and Biological Evaluation of Coumarin Derivatives as NEDD8 Activating Enzyme Inhibitors in Pancreatic Cancer Cells. Med Chem 2022; 18:679-693. [PMID: 34895126 DOI: 10.2174/1573406418666211210163817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND NEDD8 (neural precursor cell expressed developmentally downregulated protein 8) is one of the ubiquitin-like proteins which is activated by the NEDD8 activating enzyme (NAE). The overexpressed NAE can cause a variety of diseases such as numerous cancer types and inflammatory diseases. The selective inhibition of NAE could mediate the rate of ubiquitination and the subsequent degradation of proteins associated with cancer so as to achieve the purpose of treatment. OBJECTIVE In this article, we decided to study the synthesis and screening of coumarin scaffold derivatives against cancer cell lines, specifically the human pancreatic cancer cell line BxPC-3. METHODS Twenty-four targeted compounds were synthesized, and their anti-proliferative activity against three cancer cell lines, cytotoxicity against three normal cell lines through CCK-8 and MTT assay were evaluated to screen out the candidate compound. Then the target was further confirmed by both enzyme and cell-based experiments, as well as cell apoptosis research. RESULTS Several new 4-position substituted coumarin derivatives (12a~x) were synthesized and most of them exhibit antiproliferative activity in three cancer cell lines. A series of experiments were performed to identify the best candidate compound 12v. This compound displayed the highest potency against BxPC-3 with an IC50 value of 0.28 μM. It can also inhibit NAE activity in enzyme and cellbased assay, and induce CRLs-mediated accumulation of the substrate and apoptosis in BxPC-3 cells. Meanwhile, it exhibited relatively low toxicity in three normal cells. CONCLUSION Based on these results, we found that compound 12v inhibited NAE activity in enzyme and cell-based systems and induced apoptosis in BxPC-3 cells. Additionally, it also had a low toxicity. These results suggested that 12v may be promising lead compounds for the development of new anticancer drugs.
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Affiliation(s)
- Lei Gong
- School of Pharmaceutical Sciences, Nanjing Technical University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China
| | - Peng Lu
- School of Pharmaceutical Sciences, Nanjing Technical University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China
| | - Cheng Lu
- School of Pharmaceutical Sciences, Nanjing Technical University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China
| | - Mengli Li
- School of Pharmaceutical Sciences, Nanjing Technical University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China
| | - Huiyang Wan
- School of Pharmaceutical Sciences, Nanjing Technical University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China
| | - Yubin Wang
- School of Pharmaceutical Sciences, Nanjing Technical University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China
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5
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Klostermeier D. Towards Conformation-Sensitive Inhibition of Gyrase: Implications of Mechanistic Insight for the Identification and Improvement of Inhibitors. Molecules 2021; 26:1234. [PMID: 33669078 DOI: 10.3390/molecules26051234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/17/2022] Open
Abstract
Gyrase is a bacterial type IIA topoisomerase that catalyzes negative supercoiling of DNA. The enzyme is essential in bacteria and is a validated drug target in the treatment of bacterial infections. Inhibition of gyrase activity is achieved by competitive inhibitors that interfere with ATP- or DNA-binding, or by gyrase poisons that stabilize cleavage complexes of gyrase covalently bound to the DNA, leading to double-strand breaks and cell death. Many of the current inhibitors suffer from severe side effects, while others rapidly lose their antibiotic activity due to resistance mutations, generating an unmet medical need for novel, improved gyrase inhibitors. DNA supercoiling by gyrase is associated with a series of nucleotide- and DNA-induced conformational changes, yet the full potential of interfering with these conformational changes as a strategy to identify novel, improved gyrase inhibitors has not been explored so far. This review highlights recent insights into the mechanism of DNA supercoiling by gyrase and illustrates the implications for the identification and development of conformation-sensitive and allosteric inhibitors.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Jogula S, Krishna VS, Meda N, Balraju V, Sriram D. Design, synthesis and biological evaluation of novel Pseudomonas aeruginosa DNA gyrase B inhibitors. Bioorg Chem 2020; 100:103905. [PMID: 32388436 DOI: 10.1016/j.bioorg.2020.103905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/22/2022]
Abstract
In the present study, we attempted to develop a novel class of compounds active against Pseudomonas aeruginosa (Pa) by exploring the pharmaceutically well exploited enzyme targets. Since, lack of Pa gyrase B crystal structures, Thermus thermophilus gyrase B in complex with novobiocin (1KIJ) was used as template to generate model structure by performing homology modeling. Further the best model was validated and used for high-throughput virtual screening, docking and dynamics simulations using the in-house database for identification of Pa DNA gyrase B inhibitors. This study led to an identification of three lead molecules with IC50 values in range of 6.25-15.6 µM against Pa gyrase supercoiling assay. Lead-1 optimization and expansion resulted in 15 compounds. Among the synthesized compounds six compounds were shown good enzyme inhibition than Lead-1 (IC50 6.25 µM). Compound 13 emerged as the most potential compound exhibiting inhibition of Pa gyrase supercoiling with an IC50 of 2.2 µM; and in-vitro Pa activity with MIC of 8 µg/mL in presence of efflux pump inhibitor; hence could be further developed as novel inhibitor for Pa gyrase B.
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Affiliation(s)
- Sridhar Jogula
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad 500078, India
| | - Vagolu Siva Krishna
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad 500078, India
| | - Nikhila Meda
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad 500078, India
| | - Vadla Balraju
- Albany Molecular Research Hyderabad Research Centre Private Limited, MN Park, Genome valley, Hyderabad 500078, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad 500078, India.
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Radwan MA, Alshubramy MA, Abdel-Motaal M, Hemdan BA, El-Kady DS. Synthesis, molecular docking and antimicrobial activity of new fused pyrimidine and pyridine derivatives. Bioorg Chem 2020; 96:103516. [DOI: 10.1016/j.bioorg.2019.103516] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022]
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10
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Vanden Broeck A, Lotz C, Ortiz J, Lamour V. Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Nat Commun 2019; 10:4935. [PMID: 31666516 PMCID: PMC6821735 DOI: 10.1038/s41467-019-12914-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022] Open
Abstract
DNA gyrase is an essential enzyme involved in the homeostatic control of DNA supercoiling and the target of successful antibacterial compounds. Despite extensive studies, a detailed architecture of the full-length DNA gyrase from the model organism E. coli is still missing. Herein, we report the complete structure of the E. coli DNA gyrase nucleoprotein complex trapped by the antibiotic gepotidacin, using phase-plate single-particle cryo-electron microscopy. Our data unveil the structural and spatial organization of the functional domains, their connections and the position of the conserved GyrA-box motif. The deconvolution of two states of the DNA-binding/cleavage domain provides a better understanding of the allosteric movements of the enzyme complex. The local atomic resolution in the DNA-bound area reaching up to 3.0 Å enables the identification of the antibiotic density. Altogether, this study paves the way for the cryo-EM determination of gyrase complexes with antibiotics and opens perspectives for targeting conformational intermediates. Bacterial DNA gyrase is the only type II DNA topoisomerase capable of introducing negative supercoils into DNA and is of interest as a drug target. Here the authors present the cryo-EM structure of the complete E. coli DNA gyrase bound to a 180 bp double-stranded DNA and the antibiotic gepotidacin, which reveals the connections between the functional domains and their spatial organization.
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Affiliation(s)
- Arnaud Vanden Broeck
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Christophe Lotz
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Julio Ortiz
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Valérie Lamour
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France. .,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France. .,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France. .,Hôpitaux Universitaires de Strasbourg, 1 Place de l'Hôpital, 67091, Strasbourg Cedex, France.
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11
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Pedersen LC, Inoue K, Kim S, Perera L, Shaw ND. A ubiquitin-like domain is required for stabilizing the N-terminal ATPase module of human SMCHD1. Commun Biol 2019; 2:255. [PMID: 31312724 PMCID: PMC6620310 DOI: 10.1038/s42003-019-0499-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/08/2019] [Indexed: 12/16/2022] Open
Abstract
Variants in the gene SMCHD1, which encodes an epigenetic repressor, have been linked to both congenital arhinia and a late-onset form of muscular dystrophy called facioscapulohumeral muscular dystrophy type 2 (FSHD2). This suggests that SMCHD1 has a diversity of functions in both developmental time and space. The C-terminal end of SMCHD1 contains an SMC-hinge domain which mediates homodimerization and chromatin association, whereas the molecular architecture of the N-terminal region, which harbors the GHKL-ATPase domain, is not well understood. We present the crystal structure of the human SMCHD1 N-terminal ATPase module bound to ATP as a functional dimer. The dimer is stabilized by a novel N-terminal ubiquitin-like fold and by a downstream transducer domain. While disease variants map to what appear to be critical interdomain/intermolecular interfaces, only the FSHD2-specific mutant constructs we tested consistently abolish ATPase activity and/or dimerization. These data suggest that the full functional profile of SMCHD1 has yet to be determined.
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Affiliation(s)
- Lars C. Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA
| | - Kaoru Inoue
- Pediatric Neuroendocrinology Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA
| | - Susan Kim
- Pediatric Neuroendocrinology Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA
| | - Natalie D. Shaw
- Pediatric Neuroendocrinology Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA
- Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114 USA
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12
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Abstract
Coumermycin A1 is a natural aminocoumarin that inhibits bacterial DNA gyrase, a member of the GHKL proteins superfamily. We report here the first cocrystal structures of gyrase B bound to coumermycin A1, revealing that one coumermycin A1 molecule traps simultaneously two ATP-binding sites. The inhibited dimers from different species adopt distinct sequence-dependent conformations, alternative to the ATP-bound form. These structures provide a basis for the rational development of coumermycin A1 derivatives for antibiotherapy and biotechnology applications.
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Affiliation(s)
- Arnaud Vanden Broeck
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France
| | - Alastair G McEwen
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France
| | - Yassmine Chebaro
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France
| | - Noëlle Potier
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes, UMR 7140 CNRS, University of Strasbourg, Strasbourg 67000 , France
| | - Valérie Lamour
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France.,Hôpitaux Universitaires de Strasbourg , Strasbourg 67000 , France
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13
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Fruci M, Poole K. Aminoglycoside-inducible expression of the mexAB-oprM multidrug efflux operon in Pseudomonas aeruginosa: Involvement of the envelope stress-responsive AmgRS two-component system. PLoS One 2018; 13:e0205036. [PMID: 30289929 DOI: 10.1371/journal.pone.0205036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/18/2018] [Indexed: 11/19/2022] Open
Abstract
Exposure of P. aeruginosa to the aminoglycoside (AG) paromomycin (PAR) induced expression of the PA3720-armR locus and the mexAB-oprM multidrug efflux operon that AmgR controls, although PAR induction of mexAB-oprM was independent of armR. Multiple AGs promoted mexAB-oprM expression and this was lost in the absence of the amgRS locus encoding an aminoglycoside-activated envelope stress-responsive 2-component system (TCS). Purified AmgR bound to the mexAB-oprM promoter region consistent with this response regulator directly regulating expression of the efflux operon. The thiol-active reagent, diamide, which, like AGs, promotes protein aggregation and cytoplasmic membrane damage also promoted AmgRS-dependent mexAB-oprM expression, a clear indication that the MexAB-OprM efflux system is recruited in response to membrane perturbation and/or circumstances that lead to this. Despite the AG and diamide induction of mexAB-oprM, however, MexAB-OprM does not appear to contribute to resistance to these agents.
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14
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Abstract
Many cancer type-specific anticancer agents have been developed and significant advances have been made toward precision medicine in cancer treatment. However, traditional or nonspecific anticancer drugs are still important for the treatment of many cancer patients whose cancers either do not respond to or have developed resistance to cancer-specific anticancer agents. DNA topoisomerases, especially type IIA topoisomerases, are proved therapeutic targets of anticancer and antibacterial drugs. Clinically successful topoisomerase-targeting anticancer drugs act through topoisomerase poisoning, which leads to replication fork arrest and double-strand break formation. Unfortunately, this unique mode of action is associated with the development of secondary cancers and cardiotoxicity. Structures of topoisomerase-drug-DNA ternary complexes have revealed the exact binding sites and mechanisms of topoisomerase poisons. Recent advances in the field have suggested a possibility of designing isoform-specific human topoisomerase II poisons, which may be developed as safer anticancer drugs. It may also be possible to design catalytic inhibitors of topoisomerases by targeting certain inactive conformations of these enzymes. Furthermore, identification of various new bacterial topoisomerase inhibitors and regulatory proteins may inspire the discovery of novel human topoisomerase inhibitors. Thus, topoisomerases remain as important therapeutic targets of anticancer agents.
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Affiliation(s)
- Justine L Delgado
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA 52242, U.S.A
| | - Chao-Ming Hsieh
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan
| | - Hiroshi Hiasa
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, U.S.A.
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15
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Lee JH, Wendorff TJ, Berger JM. Resveratrol: A novel type of topoisomerase II inhibitor. J Biol Chem 2017; 292:21011-21022. [PMID: 29074616 DOI: 10.1074/jbc.m117.810580] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/18/2017] [Indexed: 02/04/2023] Open
Abstract
Resveratrol, a polyphenol found in various plant sources, has gained attention as a possible agent responsible for the purported health benefits of certain foods, such as red wine. Despite annual multi-million dollar market sales as a nutriceutical, there is little consensus about the physiological roles of resveratrol. One suggested molecular target of resveratrol is eukaryotic topoisomerase II (topo II), an enzyme essential for chromosome segregation and DNA supercoiling homeostasis. Interestingly, resveratrol is chemically similar to ICRF-187, a clinically approved chemotherapeutic that stabilizes an ATP-dependent dimerization interface in topo II to block enzyme activity. Based on this similarity, we hypothesized that resveratrol may antagonize topo II by a similar mechanism. Using a variety of biochemical assays, we find that resveratrol indeed acts through the ICRF-187 binding locus, but that it inhibits topo II by preventing ATPase domain dimerization rather than stabilizing it. This work presents the first comprehensive analysis of the biochemical effects of both ICRF-187 and resveratrol on the human isoforms of topo II, and reveals a new mode for the allosteric regulation of topo II through modulation of ATPase status. Natural polyphenols related to resveratrol that have been shown to impact topo II function may operate in a similar manner.
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Affiliation(s)
- Joyce H Lee
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | - Timothy J Wendorff
- the Biophysics Graduate Program, University of California, Berkeley, California 94720
| | - James M Berger
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
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16
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Aswathy V, Alper-Hayta S, Yalcin G, Mary YS, Panicker CY, Jojo P, Kaynak-Onurdag F, Armaković S, Armaković SJ, Yildiz I, Van Alsenoy C. Modification of benzoxazole derivative by bromine-spectroscopic, antibacterial and reactivity study using experimental and theoretical procedures. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.04.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Łączkowski KZ, Landowska K, Biernasiuk A, Sałat K, Furgała A, Plech T, Malm A. Synthesis, biological evaluation and molecular docking studies of novel quinuclidinone derivatives as potential antimicrobial and anticonvulsant agents. Med Chem Res 2017; 26:2088-104. [DOI: 10.1007/s00044-017-1904-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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18
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Hurley KA, Santos TMA, Fensterwald MR, Rajendran M, Moore JT, Balmond EI, Blahnik BJ, Faulkner KC, Foss MH, Heinrich VA, Lammers MG, Moore LC, Reynolds GD, Shearn-Nance GP, Stearns BA, Yao ZW, Shaw JT, Weibel DB. Targeting quinolone- and aminocoumarin-resistant bacteria with new gyramide analogs that inhibit DNA gyrase. Medchemcomm 2017; 8:942-951. [PMID: 30034678 PMCID: PMC6051542 DOI: 10.1039/c7md00012j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 02/21/2017] [Indexed: 11/21/2022]
Abstract
Bacterial DNA gyrase is an essential type II topoisomerase that enables cells to overcome topological barriers encountered during replication, transcription, recombination, and repair. This enzyme is ubiquitous in bacteria and represents an important clinical target for antibacterial therapy. In this paper we report the characterization of three exciting new gyramide analogs-from a library of 183 derivatives-that are potent inhibitors of DNA gyrase and are active against clinical strains of gram-negative bacteria (Escherichia coli, Shigella flexneri, and Salmonella enterica; 3 of 10 wild-type strains tested) and gram-positive bacteria (Bacillus spp., Enterococcus spp., Staphylococcus spp., and Streptococcus spp.; all 9 of the wild-type strains tested). E. coli strains resistant to the DNA gyrase inhibitors ciprofloxacin and novobiocin display very little cross-resistance to these new gyramides. In vitro studies demonstrate that the new analogs are potent inhibitors of the DNA supercoiling activity of DNA gyrase (IC50s of 47-170 nM) but do not alter the enzyme's ATPase activity. Although mutations that confer bacterial cells resistant to these new gyramides map to the genes encoding the subunits of the DNA gyrase (gyrA and gyrB genes), overexpression of GyrA, GyrB, or GyrA and GyrB together does not suppress the inhibitory effect of the gyramides. These observations support the hypothesis that the gyramides inhibit DNA gyrase using a mechanism that is unique from other known inhibitors.
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Affiliation(s)
- Katherine A. Hurley
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Thiago M. A. Santos
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Molly R. Fensterwald
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | - Madhusudan Rajendran
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Jared T. Moore
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | - Edward I. Balmond
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | - Brice J. Blahnik
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Katherine C. Faulkner
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Marie H. Foss
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Victoria A. Heinrich
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Matthew G. Lammers
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Lucas C. Moore
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | - Gregory D. Reynolds
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Galen P. Shearn-Nance
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | | | - Zi W. Yao
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | - Jared T. Shaw
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | - Douglas B. Weibel
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
- Department of Chemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
- Department of Biomedical Engineering
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
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19
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Chaudhari K, Surana S, Jain P, Patel HM. Mycobacterium Tuberculosis (MTB) GyrB inhibitors: An attractive approach for developing novel drugs against TB. Eur J Med Chem 2016; 124:160-185. [PMID: 27569197 DOI: 10.1016/j.ejmech.2016.08.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/03/2016] [Accepted: 08/17/2016] [Indexed: 01/24/2023]
Abstract
New classes of drugs are needed to treat tuberculosis (TB) in order to combat the emergence of resistance (MDR and XDR) to existing agents and shorten the duration of therapy. Mycobacterial DNA gyrase B subunit has been identified to be one of the potentially under exploited drug targets in the field of antitubercular drug discovery. In the present review, we discussed the synthesis, structural optimization and docking study of effective potent DNA gyrase inhibitor against M. tuberculosis, with improved properties such as enhanced activity against MDR strains, reduced toxicity. Based on this progress, if we can successfully leverage the opportunities in this target, there is hope that we will be able to raise novel gyrase inhibitor in earnest in the long.
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Affiliation(s)
- Kavita Chaudhari
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dhule, 425405, Maharashtra, India
| | - Sanjay Surana
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dhule, 425405, Maharashtra, India
| | - Pritam Jain
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dhule, 425405, Maharashtra, India.
| | - Harun M Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dhule, 425405, Maharashtra, India.
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20
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Wu H, Zeng H, Lam R, Tempel W, Kerr ID, Min J. Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome. Acta Crystallogr F Struct Biol Commun 2015; 71:981-5. [PMID: 26249686 PMCID: PMC4528928 DOI: 10.1107/s2053230x15010183] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/26/2015] [Indexed: 02/25/2023] Open
Abstract
Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson-Crick base pairs in the genome. Pathogenic mutations in the MLH1 gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. The structure shares a high degree of similarity with previously determined prokaryotic MLH1 homologs; however, this structure affords a more accurate platform for the classification of MLH1 variants.
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Affiliation(s)
- Hong Wu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Robert Lam
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Iain D. Kerr
- Myriad Genetic Laboratories Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Physiology, University of Toronto, Toronto, ON M5G 1L7, Canada
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21
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Hearnshaw SJ, Chung TTH, Stevenson CEM, Maxwell A, Lawson DM. The role of monovalent cations in the ATPase reaction of DNA gyrase. Acta Crystallogr D Biol Crystallogr 2015; 71:996-1005. [PMID: 25849408 PMCID: PMC4388272 DOI: 10.1107/s1399004715002916] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/10/2015] [Indexed: 11/25/2022]
Abstract
Four new crystal structures of the ATPase domain of the GyrB subunit of Escherichia coli DNA gyrase have been determined. One of these, solved in the presence of K(+), is the highest resolution structure reported so far for this domain and, in conjunction with the three other structures, reveals new insights into the function of this domain. Evidence is provided for the existence of two monovalent cation-binding sites: site 1, which preferentially binds a K(+) ion that interacts directly with the α-phosphate of ATP, and site 2, which preferentially binds an Na(+) ion and the functional significance of which is not clear. The crystallographic data are corroborated by ATPase data, and the structures are compared with those of homologues to investigate the broader conservation of these sites.
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Affiliation(s)
- Stephen James Hearnshaw
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
| | - Terence Tsz-Hong Chung
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
| | | | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
| | - David Mark Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
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22
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Papillon J, Ménétret JF, Batisse C, Hélye R, Schultz P, Potier N, Lamour V. [Structural insight into negative DNA supercoiling by DNA gyrase, a bacterial type 2A DNA topoisomerase]. Med Sci (Paris) 2014; 30:1081-4. [PMID: 25537036 DOI: 10.1051/medsci/20143012009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Julie Papillon
- IGBMC, départment de biologie structurale intégrative, CNRS UMR7104, Inserm U964, université de Strasbourg, 1, rue Laurent Fries, 67400 Illkirch, France
| | - Jean-François Ménétret
- IGBMC, départment de biologie structurale intégrative, CNRS UMR7104, Inserm U964, université de Strasbourg, 1, rue Laurent Fries, 67400 Illkirch, France
| | - Claire Batisse
- IGBMC, départment de biologie structurale intégrative, CNRS UMR7104, Inserm U964, université de Strasbourg, 1, rue Laurent Fries, 67400 Illkirch, France
| | - Reynald Hélye
- Institut de chimie de Strasbourg, université de Strasbourg, CNRS UMR7177, 67000 Strasbourg, France
| | - Patrick Schultz
- IGBMC, départment de biologie structurale intégrative, CNRS UMR7104, Inserm U964, université de Strasbourg, 1, rue Laurent Fries, 67400 Illkirch, France
| | - Noëlle Potier
- Institut de chimie de Strasbourg, université de Strasbourg, CNRS UMR7177, 67000 Strasbourg, France
| | - Valérie Lamour
- IGBMC, départment de biologie structurale intégrative, CNRS UMR7104, Inserm U964, université de Strasbourg, 1, rue Laurent Fries, 67400 Illkirch, France - hôpitaux universitaires de Strasbourg, fédération de médecine translationnelle de Strasbourg, 67000 Strasbourg, France
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23
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Chetty S, Soliman MES. Possible allosteric binding site on Gyrase B, a key target for novel anti-TB drugs: homology modelling and binding site identification using molecular dynamics simulation and binding free energy calculations. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1279-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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24
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Lu J, Patel S, Sharma N, Soisson SM, Kishii R, Takei M, Fukuda Y, Lumb KJ, Singh SB. Structures of kibdelomycin bound to Staphylococcus aureus GyrB and ParE showed a novel U-shaped binding mode. ACS Chem Biol 2014; 9:2023-31. [PMID: 24992706 DOI: 10.1021/cb5001197] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial resistance to antibiotics continues to pose serious challenges as the discovery rate for new antibiotics fades. Kibdelomycin is one of the rare, novel, natural product antibiotics discovered recently that inhibits the bacterial DNA synthesis enzymes gyrase and topoisomerase IV. It is a broad-spectrum, Gram-positive antibiotic without cross-resistance to known gyrase inhibitors, including clinically effective quinolones. To understand its mechanism of action, binding mode, and lack of cross-resistance, we have co-crystallized kibdelomycin and novobiocin with the N-terminal domains of Staphylococcus aureus gyrase B (24 kDa) and topo IV (ParE, 24 and 43 kDa). Kibdelomycin shows a unique "dual-arm", U-shaped binding mode in both crystal structures. The pyrrolamide moiety in the lower part of kibdelomycin penetrates deeply into the ATP-binding site pocket, whereas the isopropyl-tetramic acid and sugar moiety of the upper part thoroughly engage in polar interactions with a surface patch of the protein. The isoproramic acid (1,3-dioxopyrrolidine) and a tetrahydropyran acetate group (Sugar A) make polar contact with a surface area consisting of helix α4 and the flexible loop connecting helices α3 and α4. The two arms are connected together by a rigid decalin linker that makes van del Waals contacts with the protein backbone. This "dual-arm", U-shaped, multicontact binding mode of kibdelomycin is unique and distinctively different from binding modes of other known gyrase inhibitors (e.g., coumarins and quinolones), which explains its lack of cross-resistance and low frequency of resistance. The crystal structures reported in this paper should enable design and discovery of analogues with better properties and antibacterial spectrum.
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Affiliation(s)
- Jun Lu
- Merck Research
Laboratories, West Point, Pennsylvania 19486, United States
| | - Sangita Patel
- Merck Research
Laboratories, West Point, Pennsylvania 19486, United States
| | - Nandini Sharma
- Merck Research
Laboratories, West Point, Pennsylvania 19486, United States
| | - Stephen M. Soisson
- Merck Research
Laboratories, West Point, Pennsylvania 19486, United States
| | - Ryuta Kishii
- Kyorin
Pharmaceutical
Co., Ltd., 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masaya Takei
- Kyorin
Pharmaceutical
Co., Ltd., 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasumichi Fukuda
- Kyorin
Pharmaceutical
Co., Ltd., 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Kevin J. Lumb
- Merck Research
Laboratories, West Point, Pennsylvania 19486, United States
| | - Sheo B. Singh
- Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
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25
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Werner MM, Li Z, Zauhar RJ. Computer-aided identification of novel 3,5-substituted rhodanine derivatives with activity against Staphylococcus aureus DNA gyrase. Bioorg Med Chem 2014; 22:2176-87. [DOI: 10.1016/j.bmc.2014.02.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 02/06/2014] [Accepted: 02/14/2014] [Indexed: 11/26/2022]
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26
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Radwan AA, Abdel-Mageed WM. In silico studies of quinoxaline-2-carboxamide 1,4-di-n-oxide derivatives as antimycobacterial agents. Molecules 2014; 19:2247-60. [PMID: 24566302 DOI: 10.3390/molecules19022247] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/08/2014] [Accepted: 02/10/2014] [Indexed: 11/17/2022] Open
Abstract
Molecular modelling studies were performed on some previously reported novel quinoxaline-2-carboxamide 1,4-di-N-oxide derivatives (series 1–9). Using the LigandScout program, a pharmacophore model was developed to further optimize the antimycobacterial activity of this series of compounds. Using the Dock6 program, docking studies were performed in order to investigate the mode of binding of these compounds. The molecular modeling study allowed us to confirm the preferential binding mode of these quinoxaline-2-carboxamide 1,4-di-N-oxide derivatives inside the active site. The obtained binding mode was as same as that of the novobiocin X-ray structure.
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27
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Agrawal A, Roué M, Spitzfaden C, Petrella S, Aubry A, Hann M, Bax B, Mayer C. Mycobacterium tuberculosis DNA gyrase ATPase domain structures suggest a dissociative mechanism that explains how ATP hydrolysis is coupled to domain motion. Biochem J 2013; 456:263-73. [PMID: 24015710 DOI: 10.1042/BJ20130538] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DNA gyrase, a type II topoisomerase, regulates DNA topology by creating a double-stranded break in one DNA duplex and transporting another DNA duplex [T-DNA (transported DNA)] through this break. The ATPase domains dimerize, in the presence of ATP, to trap the T-DNA segment. Hydrolysis of only one of the two ATPs, and release of the resulting Pi, is rate-limiting in DNA strand passage. A long unresolved puzzle is how the non-hydrolysable ATP analogue AMP-PNP (adenosine 5'-[β,γ-imido]triphosphate) can catalyse one round of DNA strand passage without Pi release. In the present paper we discuss two crystal structures of the Mycobacterium tuberculosis DNA gyrase ATPase domain: one complexed with AMP-PCP (adenosine 5'-[β,γ-methylene]triphosphate) was unexpectedly monomeric, the other, an AMP-PNP complex, crystallized as a dimer. In the AMP-PNP structure, the unprotonated nitrogen (P-N=P imino) accepts hydrogen bonds from a well-ordered 'ATP lid', which is known to be required for dimerization. The equivalent CH2 group, in AMP-PCP, cannot accept hydrogen bonds, leaving the 'ATP lid' region disordered. Further analysis suggested that AMP-PNP can be converted from the imino (P-N=P) form into the imido form (P-NH-P) during the catalytic cycle. A main-chain NH is proposed to move to either protonate AMP-P-N=P to AMP-P-NH-P, or to protonate ATP to initiate ATP hydrolysis. This suggests a novel dissociative mechanism for ATP hydrolysis that could be applicable not only to GHKL phosphotransferases, but also to unrelated ATPases and GTPases such as Ras. On the basis of the domain orientation in our AMP-PCP structure we propose a mechanochemical scheme to explain how ATP hydrolysis is coupled to domain motion.
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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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Papillon J, Ménétret JF, Batisse C, Hélye R, Schultz P, Potier N, Lamour V. Structural insight into negative DNA supercoiling by DNA gyrase, a bacterial type 2A DNA topoisomerase. Nucleic Acids Res 2013; 41:7815-27. [PMID: 23804759 PMCID: PMC3763546 DOI: 10.1093/nar/gkt560] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Type 2A DNA topoisomerases (Topo2A) remodel DNA topology during replication, transcription and chromosome segregation. These multisubunit enzymes catalyze the transport of a double-stranded DNA through a transient break formed in another duplex. The bacterial DNA gyrase, a target for broad-spectrum antibiotics, is the sole Topo2A enzyme able to introduce negative supercoils. We reveal here for the first time the architecture of the full-length Thermus thermophilus DNA gyrase alone and in a cleavage complex with a 155 bp DNA duplex in the presence of the antibiotic ciprofloxacin, using cryo-electron microscopy. The structural organization of the subunits of the full-length DNA gyrase points to a central role of the ATPase domain acting like a 'crossover trap' that may help to sequester the DNA positive crossover before strand passage. Our structural data unveil how DNA is asymmetrically wrapped around the gyrase-specific C-terminal β-pinwheel domains and guided to introduce negative supercoils through cooperativity between the ATPase and β-pinwheel domains. The overall conformation of the drug-induced DNA binding-cleavage complex also suggests that ciprofloxacin traps a DNA pre-transport conformation.
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Affiliation(s)
- Julie Papillon
- IGBMC, Integrated Structural Biology Department, UMR7104 CNRS, U964 Inserm, Université de Strasbourg, 67400 Illkirch, France, Institut de Chimie de Strasbourg, Université de Strasbourg, UMR7177 CNRS, 67000 Strasbourg, France and Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Jean-François Ménétret
- IGBMC, Integrated Structural Biology Department, UMR7104 CNRS, U964 Inserm, Université de Strasbourg, 67400 Illkirch, France, Institut de Chimie de Strasbourg, Université de Strasbourg, UMR7177 CNRS, 67000 Strasbourg, France and Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Claire Batisse
- IGBMC, Integrated Structural Biology Department, UMR7104 CNRS, U964 Inserm, Université de Strasbourg, 67400 Illkirch, France, Institut de Chimie de Strasbourg, Université de Strasbourg, UMR7177 CNRS, 67000 Strasbourg, France and Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Reynald Hélye
- IGBMC, Integrated Structural Biology Department, UMR7104 CNRS, U964 Inserm, Université de Strasbourg, 67400 Illkirch, France, Institut de Chimie de Strasbourg, Université de Strasbourg, UMR7177 CNRS, 67000 Strasbourg, France and Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Patrick Schultz
- IGBMC, Integrated Structural Biology Department, UMR7104 CNRS, U964 Inserm, Université de Strasbourg, 67400 Illkirch, France, Institut de Chimie de Strasbourg, Université de Strasbourg, UMR7177 CNRS, 67000 Strasbourg, France and Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Noëlle Potier
- IGBMC, Integrated Structural Biology Department, UMR7104 CNRS, U964 Inserm, Université de Strasbourg, 67400 Illkirch, France, Institut de Chimie de Strasbourg, Université de Strasbourg, UMR7177 CNRS, 67000 Strasbourg, France and Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Valérie Lamour
- IGBMC, Integrated Structural Biology Department, UMR7104 CNRS, U964 Inserm, Université de Strasbourg, 67400 Illkirch, France, Institut de Chimie de Strasbourg, Université de Strasbourg, UMR7177 CNRS, 67000 Strasbourg, France and Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
- *To whom correspondence should be addressed. Tel: +33 3 88 65 32 36; Fax: +33 3 88 65 32 01;
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Saíz-Urra L, Pérez MÁC, Froeyen M. Thermodynamic computational approach to capture molecular recognition in the binding of different inhibitors to the DNA gyrase B subunit from Escherichia coli. J Mol Model 2013; 19:3187-200. [PMID: 23625033 DOI: 10.1007/s00894-013-1849-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 04/04/2013] [Indexed: 11/29/2022]
Abstract
DNA gyrase subunit B, that catalyzes the hydrolysis of ATP, is an attractive target for the development of antibacterial drugs. This work is intended to rationalize molecular recognition at DNA gyrase B enzyme - inhibitor binding interface through the evaluation of different scoring functions in finding the correct pose and scoring properly 50 Escherichia coli DNA Gyrase B inhibitors belonging to five different classes. Improving the binding free energy calculation accuracy is further attempted by using rescoring schemes after short molecular dynamic simulations of the obtained docked complexes. These data are then compared with the corresponding experimental enzyme activity data. The results are analyzed from a structural point of view emphasizing the strengths and limitations of the techniques applied in the study.
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Affiliation(s)
- Liane Saíz-Urra
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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Schmidt BH, Osheroff N, Berger JM. Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity. Nat Struct Mol Biol 2012; 19:1147-54. [PMID: 23022727 DOI: 10.1038/nsmb.2388] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 08/23/2012] [Indexed: 11/22/2022]
Abstract
Type IIA topoisomerases control DNA supercoiling and disentangle chromosomes by a complex, ATP-dependent strand passage mechanism. Although a general framework exists for type IIA topoisomerase function, the architecture of the full-length enzyme has remained undefined. Here we present the first structure of a fully-catalytic Saccharomyces cerevisiae topoisomerase II homodimer, complexed with DNA and a nonhydrolyzable ATP analog. The enzyme adopts a domain-swapped configuration wherein the ATPase domain of one protomer sits atop the nucleolytic region of its partner subunit. This organization produces an unexpected interaction between the bound DNA and a conformational transducing element in the ATPase domain, which we show is critical for both DNA-stimulated ATP hydrolysis and global topoisomerase activity. Our data indicate that the ATPase domains pivot about each other to ensure unidirectional strand passage and that this state senses bound DNA to promote ATP turnover and enzyme reset.
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32
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Abstract
The capability to accurately, rapidly, and reproducibly determine the affinity of a ligand for a target protein or enzyme is a vital component for a successful structure-based drug design effort. In order to successfully drive a structure-based drug design (SBDD) project forward, multiple distinct assays, each with particular strengths and weaknesses, need to be employed. Using bacterial DNA gyrase as an example, a range of assays are described that will fully support an SBDD program.
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Siwek A, Stączek P, Stefańska J. Synthesis and structure-activity relationship studies of 4-arylthiosemicarbazides as topoisomerase IV inhibitors with Gram-positive antibacterial activity. Search for molecular basis of antibacterial activity of thiosemicarbazides. Eur J Med Chem 2011; 46:5717-26. [PMID: 21978836 DOI: 10.1016/j.ejmech.2011.09.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 09/16/2011] [Accepted: 09/20/2011] [Indexed: 11/25/2022]
Abstract
1-(indol-2-carbonyl)-4-(4-nitrophenyl)-thiosemicarbazide was synthesized and antibacterial and type IIA topoisomerases (DNA gyrase and topoisomerase IV) activity was evaluated. It was found that it shows activity against Gram-positive bacteria with MICs of 50 μg/mL and inhibitory action against topoisomerase IV with an IC(50) of 14 μM. Although modification of its structure resulted in molecules with a lower biological profile, our observations strongly implicate that thiosemicarbazide derivatives participate in at least two different mechanisms of antibacterial activity; one is connected with the inhibition of topoisomerase IV, while the nature of the other cannot be elucidated from the limited data collected thus far. The differences in bioactivity further investigated by the molecular modeling approach and docking studies suggest that inhibitory activity of 4-arylthiosemicarbazides is connected with electronic structure rather than the geometry of the molecule.
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Affiliation(s)
- Agata Siwek
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University, Chodźki 4a, 20-093 Lublin, Poland.
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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: 355] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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35
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Akanuma S, Iwami S, Yokoi T, Nakamura N, Watanabe H, Yokobori SI, Yamagishi A. Phylogeny-Based Design of a B-Subunit of DNA Gyrase and Its ATPase Domain Using a Small Set of Homologous Amino Acid Sequences. J Mol Biol 2011; 412:212-25. [DOI: 10.1016/j.jmb.2011.07.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 10/17/2022]
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36
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Tambo-ong A, Chopra S, Glaser BT, Matsuyama K, Tran T, Madrid PB. Mannich reaction derivatives of novobiocin with modulated physiochemical properties and their antibacterial activities. Bioorg Med Chem Lett 2011; 21:5697-700. [PMID: 21871799 DOI: 10.1016/j.bmcl.2011.08.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 08/05/2011] [Accepted: 08/05/2011] [Indexed: 11/30/2022]
Abstract
Synthetic derivatives of the natural product antibiotic novobiocin were synthesized in order to improve their physiochemical properties. A Mannich reaction was used to introduce new side chains at a solvent-exposed position of the molecule, and a diverse panel of functional groups was evaluated at this position. Novobiocin and the new derivatives were tested for their binding to gyrase B and their antibacterial activities against Staphylococcus aureus, Mycobacterium tuberculosis, Francisella tularensis and Escherichia coli. While the new derivatives still bound the gyrase B protein potently (0.07-1.8 μM, IC(50)), they had significantly less antibacterial activity. Two compounds were identified with increased antibacterial activity against M. tuberculosis, with a minimum inhibitory concentration of 2.5 μg/ml.
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Affiliation(s)
- Arlyn Tambo-ong
- Center for Infectious Disease and Biodefense Research, Biosciences Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
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37
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Phillips J, Goetz M, Smith S, Zink D, Polishook J, Onishi R, Salowe S, Wiltsie J, Allocco J, Sigmund J, Dorso K, Lee S, Skwish S, de la Cruz M, Martín J, Vicente F, Genilloud O, Lu J, Painter R, Young K, Overbye K, Donald R, Singh S. Discovery of Kibdelomycin, A Potent New Class of Bacterial Type II Topoisomerase Inhibitor by Chemical-Genetic Profiling in Staphylococcus aureus. ACTA ACUST UNITED AC 2011; 18:955-65. [DOI: 10.1016/j.chembiol.2011.06.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 06/25/2011] [Accepted: 06/28/2011] [Indexed: 11/27/2022]
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38
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Bates AD, Berger JM, Maxwell A. The ancestral role of ATP hydrolysis in type II topoisomerases: prevention of DNA double-strand breaks. Nucleic Acids Res 2011; 39:6327-39. [PMID: 21525132 PMCID: PMC3159449 DOI: 10.1093/nar/gkr258] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 04/04/2011] [Accepted: 04/06/2011] [Indexed: 12/27/2022] Open
Abstract
Type II DNA topoisomerases (topos) catalyse changes in DNA topology by passing one double-stranded DNA segment through another. This reaction is essential to processes such as replication and transcription, but carries with it the inherent danger of permanent double-strand break (DSB) formation. All type II topos hydrolyse ATP during their reactions; however, only DNA gyrase is able to harness the free energy of hydrolysis to drive DNA supercoiling, an energetically unfavourable process. A long-standing puzzle has been to understand why the majority of type II enzymes consume ATP to support reactions that do not require a net energy input. While certain type II topos are known to 'simplify' distributions of DNA topoisomers below thermodynamic equilibrium levels, the energy required for this process is very low, suggesting that this behaviour is not the principal reason for ATP hydrolysis. Instead, we propose that the energy of ATP hydrolysis is needed to control the separation of protein-protein interfaces and prevent the accidental formation of potentially mutagenic or cytotoxic DSBs. This interpretation has parallels with the actions of a variety of molecular machines that catalyse the conformational rearrangement of biological macromolecules.
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Affiliation(s)
- Andrew D Bates
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK.
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39
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Saíz-Urra L, Cabrera Pérez MÁ, Helguera AM, Froeyen M. Combining molecular docking and QSAR studies for modelling the antigyrase activity of cyclothialidine derivatives. Eur J Med Chem 2011; 46:2736-47. [PMID: 21530019 DOI: 10.1016/j.ejmech.2011.03.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 03/21/2011] [Accepted: 03/29/2011] [Indexed: 11/20/2022]
Abstract
DNA gyrase is a well-established antibacterial target consisting of two subunits, GyrA and GyrB, in a heterodimer A(2)B(2), where GyrB catalyzes the hydrolysis of ATP. Cyclothialidine (Ro 09-1437) has been considered as a promising inhibitor whose modifications might lead to more potent compounds against the enzyme. We report here for the first time, QSAR studies regarding to ATPase inhibitors of DNA Gyrase. 1D, 2D and 3D descriptors from DRAGON software were used on a set of 42 cyclothialidine derivatives. Based on the core of the cyclothialidine GR122222X, different conformations were created by using OMEGA. FRED was used to dock these conformers in the cavity of the GyrB subunit to select the best conformations, paying special attention to the 12-membered ring. Three QSAR models were developed considering the dimension of the descriptors. The models were robust, predictive and good in statistical significance, over 70% of the experimental variance was explained. Interpretability of the models was possible by extracting the SAR(s) encoded by these predictive models. Analyzing the compound-enzyme interactions of the complexes obtained by docking allowed us to increase the reliability of the information obtained for the QSAR models.
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Affiliation(s)
- Liane Saíz-Urra
- Centro de Bioactivos Quimicos, Universidad Central "Marta Abreu" de las Villas, Carretera a Camajuani Km 5.5, Santa Clara (54830), Villa Clara, Cuba.
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40
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Glaser BT, Malerich JP, Duellman SJ, Fong J, Hutson C, Fine RM, Keblansky B, Tang MJ, Madrid PB. A high-throughput fluorescence polarization assay for inhibitors of gyrase B. ACTA ACUST UNITED AC 2011; 16:230-8. [PMID: 21245469 DOI: 10.1177/1087057110392038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
DNA gyrase, a type II topoisomerase that introduces negative supercoils into DNA, is a validated antibacterial drug target. The holoenzyme is composed of 2 subunits, gyrase A (GyrA) and gyrase B (GyrB), which form a functional A(2)B(2) heterotetramer required for bacterial viability. A novel fluorescence polarization (FP) assay has been developed and optimized to detect inhibitors that bind to the adenosine triphosphate (ATP) binding domain of GyrB. Guided by the crystal structure of the natural product novobiocin bound to GyrB, a novel novobiocin-Texas Red probe (Novo-TRX) was designed and synthesized for use in a high-throughput FP assay. The binding kinetics of the interaction of Novo-TRX with GyrB from Francisella tularensis has been characterized, as well as the effect of common buffer additives on the interaction. The assay was developed into a 21-µL, 384-well assay format and has been validated for use in high-throughput screening against a collection of Food and Drug Administration-approved compounds. The assay performed with an average Z' factor of 0.80 and was able to identify GyrB inhibitors from a screening library.
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41
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Affiliation(s)
- Veronika Škedelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
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42
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Abstract
Protein crystallography emerged in the early 1970s and is, to this day, one of the most powerful techniques for the analysis of enzyme mechanisms and macromolecular interactions at the atomic level. It is also an extremely powerful tool for drug design. This field has evolved together with developments in computer science and molecular biology, allowing faster three-dimensional structure determination of complex biological assemblies. In recent times, structural genomics initiatives have pushed the development of methods to further speed up this process. The algorithms initially defined in the last decade for structure determination are now more and more elaborate, but the computational tools have evolved toward simpler and more user-friendly packages and web interfaces. We present here a modest overview of the popular software packages that have been developed for solving protein structures, and give a few guidelines and examples for structure determination using the two most popular methods, molecular replacement and multiple anomalous dispersion.
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Affiliation(s)
- Deepti Jain
- National Centre for Biological Sciences, Bangalore, India
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43
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Saíz-Urra L, Cabrera MA, Froeyen M. Exploring the conformational changes of the ATP binding site of gyrase B from Escherichia coli complexed with different established inhibitors by using molecular dynamics simulation: protein-ligand interactions in the light of the alanine scanning and free energy decomposition methods. J Mol Graph Model 2011; 29:726-39. [PMID: 21216167 DOI: 10.1016/j.jmgm.2010.12.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 12/03/2010] [Accepted: 12/07/2010] [Indexed: 11/23/2022]
Abstract
Currently, bacterial diseases cause a death toll around 2 million people a year encouraging the search for new antimicrobial agents. DNA gyrase is a well-established antibacterial target consisting of two subunits, GyrA and GyrB, in a heterodimer A(2)B(2). GyrA is involved in DNA breakage and reunion and GyrB catalyzes the hydrolysis of ATP. The GyrB subunit from Escherichia coli has been investigated, namely the ATP binding pocket both considering the protein without ligands and bound with the inhibitors clorobiocin, novobiocin and 5'-adenylyl-β-γ-imidodiphosphate. The stability of the systems was studied by molecular dynamics simulation with the further analysis of the time dependent root-mean-square coordinate deviation (RMSD) from the initial structure, and temperature factors. Moreover, exploration of the conformational space of the systems during the MD simulation was carried out by a clustering data mining technique using the average-linkage algorithm. Recognizing the key residues in the binding site of the enzyme that are involved in the binding mode with the aforementioned inhibitors was investigated by using two techniques: free energy decomposition and computational alanine scanning. The results from these simulations highlight the important residues in the ATP binding site and can be useful in the design process of potential new inhibitors.
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44
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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 DOI: 10.1007/s00018-010-0299-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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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45
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Xie P. Dynamics of strand passage catalyzed by topoisomerase II. Eur Biophys J 2010; 39:1251-9. [PMID: 20127325 DOI: 10.1007/s00249-010-0578-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 12/17/2009] [Accepted: 01/13/2010] [Indexed: 11/25/2022]
Abstract
DNA topoisomerase II is a homodimeric molecular machine that uses ATP hydrolysis to untangle DNA by passing one double-stranded DNA duplex (T-segment) through another double-stranded duplex (G-segment). However, despite extensive studies, the dynamics of ATP-dependent T-transport is still not very clear. Here, based on the proposal that transport of the T-segment through the transiently cleaved G-segment and the opened C-gate of the enzyme is via a free diffusion mechanism, the dynamics of T-transport are studied theoretically. Our results show that, to complete passage of the strand with nearly 100% efficiency, the C-gate is required to open by a width that is only slightly larger than the width of DNA duplex and for a time shorter than 100 micros in the presence of several k (B) T binding affinities of the T-segment for the B' domains. The results are implied by our understanding of the opening and closing dynamics of the C-gate. Moreover, the dependence of chemomechanical coupling efficiency on degrees of DNA supercoiling by gyrases can also be explained by using our results. On the basis of these theoretical results and previous experimental data, a modified two-gate model for chemomechanical coupling of the topoisomerase II enzyme is proposed.
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Affiliation(s)
- Ping Xie
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190, Beijing, China.
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46
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Edwards MJ, Flatman RH, Mitchenall LA, Stevenson CEM, Le TBK, Clarke TA, McKay AR, Fiedler HP, Buttner MJ, Lawson DM, Maxwell A. A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase. Science 2010; 326:1415-8. [PMID: 19965760 DOI: 10.1126/science.1179123] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets.
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Affiliation(s)
- Marcus J Edwards
- Department of Biological Chemistry, John Innes Centre, Colney, Norwich NR4 7UH, UK
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47
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Jung HY, Lee KJ, Kim KH, Hyoung JH, Han MR, Kim HK, Kang LW, Ahn YJ, Heo YS. Crystallization and preliminary X-ray crystallographic analysis of DNA gyrase GyrB subunit from Xanthomonas oryzae pv. oryzae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:48-50. [PMID: 20057069 DOI: 10.1107/s1744309109047721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 11/11/2009] [Indexed: 11/11/2022]
Abstract
DNA gyrase is a type II topoisomerase that is essential for chromosome segregation and cell division owing to its ability to modify the topological forms of bacterial DNA. In this study, the N-terminal fragment of the GyrB subunit of DNA gyrase from Xanthomonas oryzae pv. oryzae was overexpressed in Escherichia coli, purified and crystallized. Diffraction data were collected to 2.10 A resolution using a synchrotron-radiation source. The crystal belonged to space group I4(1), with unit-cell parameters a = b = 110.27, c = 70.75 A. The asymmetric unit contained one molecule, with a V(M) of 2.57 A(3) Da(-1) and a solvent content of 50.2%.
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Affiliation(s)
- Ha Yun Jung
- Department of Chemistry, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
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Gómez García I, Stevenson CEM, Usón I, Freel Meyers CL, Walsh CT, Lawson DM. The crystal structure of the novobiocin biosynthetic enzyme NovP: the first representative structure for the TylF O-methyltransferase superfamily. J Mol Biol 2009; 395:390-407. [PMID: 19857499 DOI: 10.1016/j.jmb.2009.10.045] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 10/14/2009] [Accepted: 10/19/2009] [Indexed: 12/19/2022]
Abstract
NovP is an S-adenosyl-l-methionine-dependent O-methyltransferase that catalyzes the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. Specifically, it methylates at 4-OH of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic: previous crystallographic studies have shown that this group interacts directly with the target enzyme DNA gyrase, which is a validated drug target. We have determined the high-resolution crystal structure of NovP from Streptomyces spheroides as a binary complex with its desmethylated cosubstrate S-adenosyl-l-homocysteine. The structure displays a typical class I methyltransferase fold, in addition to motifs that are consistent with a divalent-metal-dependent mechanism. This is the first representative structure of a methyltransferase from the TylF superfamily, which includes a number of enzymes implicated in the biosynthesis of antibiotics and other therapeutics. The NovP structure reveals a number of distinctive structural features that, based on sequence conservation, are likely to be characteristic of the superfamily. These include a helical 'lid' region that gates access to the cosubstrate binding pocket and an active center that contains a 3-Asp putative metal binding site. A further conserved Asp likely acts as the general base that initiates the reaction by deprotonating the 4-OH group of the noviose unit. Using in silico docking, we have generated models of the enzyme-substrate complex that are consistent with the proposed mechanism. Furthermore, these models suggest that NovP is unlikely to tolerate significant modifications at the noviose moiety, but could show increasing substrate promiscuity as a function of the distance of the modification from the methylation site. These observations could inform future attempts to utilize NovP for methylating a range of glycosylated compounds.
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Bendsen S, Oestergaard VH, Skouboe C, Brinch M, Knudsen BR, Andersen AH. The QTK loop is essential for the communication between the N-terminal atpase domain and the central cleavage--ligation region in human topoisomerase IIalpha. Biochemistry 2009; 48:6508-15. [PMID: 19485418 DOI: 10.1021/bi9005978] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have characterized a human topoisomerase IIalpha enzyme with a deletion of the conserved QTK loop, which extends from the transducer domain to the ATP-binding pocket in the GHKL domain. The loop has been suggested to play a role for interdomain communication in type II topoisomerases. The mutant enzyme performs only very low levels of strand passage, although it is able to cleave and ligate DNA as well as close the N-terminal clamp. Cleavage is nearly unaffected by ATP and ATP analogues relative to the wild-type enzyme. Although the enzyme is able to close the clamp, the clamp has altered characteristics, allowing trapping of DNA also in the absence of an ATP analogue. The enzyme furthermore retains intrinsic levels of ATPase activity, but the activity is not stimulated by DNA. Our observations demonstrate that the QTK loop is an important player for the interdomain communication in human topoisomerase IIalpha. First, the loop seems to play a role in keeping the N-terminal clamp in an open conformation when no nucleotide is present. Once the nucleotide binds, it facilitates clamp closure, although it is not essential for this event. The QTK loop, in contrast, is essential for the DNA-stimulated ATPase activity of human topoisomerase IIalpha.
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Affiliation(s)
- Simon Bendsen
- Department of Molecular Biology, C. F. Moellers Alle, Building 1130, University of Aarhus, 8000 Arhus C, Denmark
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Affiliation(s)
- Hongtao Yu
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148
| | - Steven W. Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148
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