메뉴 건너뛰기




Volumn 51, Issue 10, 2007, Pages 3688-3698

Discovery of novel DNA gyrase inhibitors by high-throughput virtual screening

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; ANTIBIOTIC AGENT; CIPROFLOXACIN; COUMARIN; CYCLOTHIALIDINE; DNA TOPOISOMERASE (ATP HYDROLYSING); DNA TOPOISOMERASE IV; GYRASE INHIBITOR; NOVOBIOCIN; NSC 102938; NSC 103003; NSC 130847; NSC 174069; NSC 20091; NSC 20115; NSC 20116; NSC 56902; NSC 56904; NSC 56906; NSC 72730; NSC 72739; NSC 7706; NSC 7761; NSC 7784; NSC 7791; NSC 7861; NSC 7925; NSC 7928; NSC 7936; QUINOLINE DERIVED ANTIINFECTIVE AGENT; RO 09 1437 000; UNCLASSIFIED DRUG; UNINDEXED DRUG;

EID: 34948830988     PISSN: 00664804     EISSN: None     Source Type: Journal    
DOI: 10.1128/AAC.00392-07     Document Type: Article
Times cited : (186)

References (50)
  • 2
    • 2142814314 scopus 로고    scopus 로고
    • Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): A single residue dictates differences in novobiocin potency against topoisomerase IV and DNA gyrase
    • Bellen, S., J. D. Parsons, Y. Wei, K. Hayakawa, L. L. Swenson, P. S. Charifson, J. A. Lippke, R. Aldape, and C. H. Gross. 2004. Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potency against topoisomerase IV and DNA gyrase. Antimicrob. Agents Chemother. 48:1856-1864.
    • (2004) Antimicrob. Agents Chemother , vol.48 , pp. 1856-1864
    • Bellen, S.1    Parsons, J.D.2    Wei, Y.3    Hayakawa, K.4    Swenson, L.L.5    Charifson, P.S.6    Lippke, J.A.7    Aldape, R.8    Gross, C.H.9
  • 3
    • 1642288258 scopus 로고    scopus 로고
    • Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening
    • Boehm, H. J., M. Boehringer, D. Bur, H. Gmuender, W. Huber, W. Klaus, D. Kostrewa, H. Kuehne, T. Luebbers, N. Meunier-Keller, and F. Mueller. 2000. Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening. J. Med. Chem. 43:2664-2674.
    • (2000) J. Med. Chem , vol.43 , pp. 2664-2674
    • Boehm, H.J.1    Boehringer, M.2    Bur, D.3    Gmuender, H.4    Huber, W.5    Klaus, W.6    Kostrewa, D.7    Kuehne, H.8    Luebbers, T.9    Meunier-Keller, N.10    Mueller, F.11
  • 4
    • 34948846910 scopus 로고
    • Novobiocin
    • D. Gottleib and P. D. Shaw ed, Springer-Verlag, New York, NY
    • Brock, T. D. 1967. Novobiocin, p. 651-760. In D. Gottleib and P. D. Shaw (ed.), Antibiotics, vol. 1. Springer-Verlag, New York, NY.
    • (1967) Antibiotics , vol.1 , pp. 651-760
    • Brock, T.D.1
  • 5
    • 0034923502 scopus 로고    scopus 로고
    • DNA topoisomerases: Structure, function, and mechanism
    • Champoux, J. J. 2001. DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70:369-413.
    • (2001) Annu. Rev. Biochem , vol.70 , pp. 369-413
    • Champoux, J.J.1
  • 7
    • 0026648204 scopus 로고
    • gyrB mutations which confer coumarin resistance also affect DNA supercoiling and ATP hydrolysis by Escherichia coli DNA gyrase
    • Contreras, A., and A. Maxwell. 1992. gyrB mutations which confer coumarin resistance also affect DNA supercoiling and ATP hydrolysis by Escherichia coli DNA gyrase. Mol. Microbiol. 6:1617-1624.
    • (1992) Mol. Microbiol , vol.6 , pp. 1617-1624
    • Contreras, A.1    Maxwell, A.2
  • 8
    • 0024383245 scopus 로고
    • Cloning and characterization of a DNA gyrase A gene from Escherichia coli that confers clinical resistance to 4-quinolones
    • Cullen, M. E., A. W. Wyke, R. Kuroda, and L. M. Fisher. 1989. Cloning and characterization of a DNA gyrase A gene from Escherichia coli that confers clinical resistance to 4-quinolones. Antimicrob. Agents Chemother. 33:886-894.
    • (1989) Antimicrob. Agents Chemother , vol.33 , pp. 886-894
    • Cullen, M.E.1    Wyke, A.W.2    Kuroda, R.3    Fisher, L.M.4
  • 9
    • 13544251502 scopus 로고    scopus 로고
    • The case for open-source software in drug discovery
    • Delano, W. L. 2005. The case for open-source software in drug discovery. Drug Discov. Today 10:213-217.
    • (2005) Drug Discov. Today , vol.10 , pp. 213-217
    • Delano, W.L.1
  • 12
    • 0038121041 scopus 로고    scopus 로고
    • Fluoroquinolones: Action and resistance
    • Drlica, K., and M. Malik. 2003. Fluoroquinolones: action and resistance. Curr. Top. Med. Chem. 3:249-282.
    • (2003) Curr. Top. Med. Chem , vol.3 , pp. 249-282
    • Drlica, K.1    Malik, M.2
  • 13
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • Ewing, T. J., S. Makino, A. G. Skillman, and I. D. Kuntz. 2001. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J. Comput.-Aided Mol. Des. 15:411-428.
    • (2001) J. Comput.-Aided Mol. Des , vol.15 , pp. 411-428
    • Ewing, T.J.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 14
    • 0034925137 scopus 로고    scopus 로고
    • Mutation in the DNA gyrase A gene of Escherichia coli that expands the quinolone resistance-determining region
    • Friedman, S. M., T. Lu, and K. Drlica. 2001. Mutation in the DNA gyrase A gene of Escherichia coli that expands the quinolone resistance-determining region. Antimicrob. Agents Chemother. 45:2378-2380.
    • (2001) Antimicrob. Agents Chemother , vol.45 , pp. 2378-2380
    • Friedman, S.M.1    Lu, T.2    Drlica, K.3
  • 15
    • 0037335662 scopus 로고    scopus 로고
    • Phylogenomics of type II DNA topoisomerases
    • Gadelle, D., J. Filee, C. Buhler, and P. Forterre. 2003. Phylogenomics of type II DNA topoisomerases. Bioessays 25:232-242.
    • (2003) Bioessays , vol.25 , pp. 232-242
    • Gadelle, D.1    Filee, J.2    Buhler, C.3    Forterre, P.4
  • 16
    • 0035154372 scopus 로고    scopus 로고
    • Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: Combined transcription and translation analysis
    • Gmuender, H., K. Kuratli, K. Di Padova, C. P. Gray, W. Keck, and S. Evers. 2001. Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis. Genome Res. 11:28-42.
    • (2001) Genome Res , vol.11 , pp. 28-42
    • Gmuender, H.1    Kuratli, K.2    Di Padova, K.3    Gray, C.P.4    Keck, W.5    Evers, S.6
  • 18
    • 0036093581 scopus 로고    scopus 로고
    • Quinolone-binding pocket of DNA gyrase: Role of GyrB
    • Heddle, J., and A. Maxwell. 2002. Quinolone-binding pocket of DNA gyrase: role of GyrB. Antimicrob. Agents Chemother. 46:1805-1815.
    • (2002) Antimicrob. Agents Chemother , vol.46 , pp. 1805-1815
    • Heddle, J.1    Maxwell, A.2
  • 20
    • 17644405067 scopus 로고    scopus 로고
    • Mechanisms of quinolone resistance in Escherichia coli and Salmonella: Recent developments
    • Hopkins, K. L., R. H. Davies, and E. J. Threlfall. 2005. Mechanisms of quinolone resistance in Escherichia coli and Salmonella: recent developments. Int. J. Antimicrob. Agents 25:358-373.
    • (2005) Int. J. Antimicrob. Agents , vol.25 , pp. 358-373
    • Hopkins, K.L.1    Davies, R.H.2    Threlfall, E.J.3
  • 21
    • 13844312649 scopus 로고    scopus 로고
    • ZINC - a free database of commercially available compounds for virtual screening
    • Irwin, J. J., and B. K. Shoichet. 2005. ZINC - a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 45:177-182.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 22
    • 0035501756 scopus 로고    scopus 로고
    • Structure-based inhibitor screening: A family of sulfonated dye inhibitors for malaria parasite triosephosphate isomerase
    • Joubert, F., A. W. Neitz, and A. I. Louw. 2001. Structure-based inhibitor screening: a family of sulfonated dye inhibitors for malaria parasite triosephosphate isomerase. Proteins 45:136-143.
    • (2001) Proteins , vol.45 , pp. 136-143
    • Joubert, F.1    Neitz, A.W.2    Louw, A.I.3
  • 23
    • 13444291112 scopus 로고    scopus 로고
    • Expression and characterization of the ATP-binding domain of a malarial Plasmodium vivax gene homologous to the B-subunit of the bacterial topoisomerase DNA gyrase
    • Khor, V., C. Yowell, J. B. Dame, and T. C. Rowe. 2005. Expression and characterization of the ATP-binding domain of a malarial Plasmodium vivax gene homologous to the B-subunit of the bacterial topoisomerase DNA gyrase. Mol. Biochem. Parasitol. 140:107-117.
    • (2005) Mol. Biochem. Parasitol , vol.140 , pp. 107-117
    • Khor, V.1    Yowell, C.2    Dame, J.B.3    Rowe, T.C.4
  • 25
    • 0037062576 scopus 로고    scopus 로고
    • DNA gyrase interaction with coumarin-based inhibitors: The role of the hydroxybenzoate isopentenyl moiety and the 5′-methyl group of the noviose
    • Lafitte, D., V. Lamour, P. O. Tsvetkov, A. A. Makarov, M. Klich, P. Deprez, D. Moras, C. Briand, and R. Gilli. 2002. DNA gyrase interaction with coumarin-based inhibitors: the role of the hydroxybenzoate isopentenyl moiety and the 5′-methyl group of the noviose. Biochemistry 41:7217-7223.
    • (2002) Biochemistry , vol.41 , pp. 7217-7223
    • Lafitte, D.1    Lamour, V.2    Tsvetkov, P.O.3    Makarov, A.A.4    Klich, M.5    Deprez, P.6    Moras, D.7    Briand, C.8    Gilli, R.9
  • 26
    • 0036023671 scopus 로고    scopus 로고
    • Crystallization of the 43 kDa ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin
    • Lamour, V., L. Hoermann, J. M. Jeltsch, P. Oudet, and D. Moras. 2002. Crystallization of the 43 kDa ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin. Acta Crystallogr. Sect. D 58:1376-1378.
    • (2002) Acta Crystallogr. Sect. D , vol.58 , pp. 1376-1378
    • Lamour, V.1    Hoermann, L.2    Jeltsch, J.M.3    Oudet, P.4    Moras, D.5
  • 27
    • 0037166285 scopus 로고    scopus 로고
    • An open conformation of the Thermus thermophilus gyrase B ATP-binding domain
    • Lamour, V., L. Hoermann, J. M. Jeltsch, P. Oudet, and D. Moras. 2002. An open conformation of the Thermus thermophilus gyrase B ATP-binding domain. J. Biol. Chem. 277:18947-18953.
    • (2002) J. Biol. Chem , vol.277 , pp. 18947-18953
    • Lamour, V.1    Hoermann, L.2    Jeltsch, J.M.3    Oudet, P.4    Moras, D.5
  • 28
    • 0029826375 scopus 로고    scopus 로고
    • Delayed cytotoxicity and cleavage of mitochondrial DNA in ciprofloxacin-treated mammalian cells
    • Lawrence, J. W., D. C. Claire, V. Weissig, and T. C. Rowe. 1996. Delayed cytotoxicity and cleavage of mitochondrial DNA in ciprofloxacin-treated mammalian cells. Mol. Pharmacol. 50:1178-1188.
    • (1996) Mol. Pharmacol , vol.50 , pp. 1178-1188
    • Lawrence, J.W.1    Claire, D.C.2    Weissig, V.3    Rowe, T.C.4
  • 29
    • 0032189275 scopus 로고    scopus 로고
    • DNA gyrase and topoisomerase IV: Biochemical activities, physiological roles during chromosome replication, and drug sensitivities
    • Levine, C., H. Hiasa, and K. J. Marians. 1998. DNA gyrase and topoisomerase IV: biochemical activities, physiological roles during chromosome replication, and drug sensitivities. Biochim. Biophys. Acta 1400:29-43.
    • (1998) Biochim. Biophys. Acta , vol.1400 , pp. 29-43
    • Levine, C.1    Hiasa, H.2    Marians, K.J.3
  • 30
    • 0029978822 scopus 로고    scopus 로고
    • The nature of inhibition of DNA gyrase by the coumarins and the cyclothialidines revealed by X-ray crystallography
    • Lewis, R. J., O. M. Singh, C. V. Smith, T. Skarzynski, A. Maxwell, A. J. Wonacott, and D. B. Wigley. 1996. The nature of inhibition of DNA gyrase by the coumarins and the cyclothialidines revealed by X-ray crystallography. EMBO J. 15:1412-1420.
    • (1996) EMBO J , vol.15 , pp. 1412-1420
    • Lewis, R.J.1    Singh, O.M.2    Smith, C.V.3    Skarzynski, T.4    Maxwell, A.5    Wonacott, A.J.6    Wigley, D.B.7
  • 31
    • 0035227959 scopus 로고    scopus 로고
    • Use of a real-time, coupled assay to measure the ATPase activity of DNA topoisomerase II
    • Lindsley, J. E. 2001. Use of a real-time, coupled assay to measure the ATPase activity of DNA topoisomerase II. Methods Mol. Biol 95:57-64.
    • (2001) Methods Mol. Biol , vol.95 , pp. 57-64
    • Lindsley, J.E.1
  • 32
    • 0342313482 scopus 로고    scopus 로고
    • Design, synthesis, and structure-activity relationship studies of ATP analogues as DNA gyrase inhibitors
    • Lubbers, T., P. Angehrn, H. Gmunder, S. Herzig, and J. Kulhanek. 2000. Design, synthesis, and structure-activity relationship studies of ATP analogues as DNA gyrase inhibitors. Bioorg. Med. Chem. Lett. 10:821-826.
    • (2000) Bioorg. Med. Chem. Lett , vol.10 , pp. 821-826
    • Lubbers, T.1    Angehrn, P.2    Gmunder, H.3    Herzig, S.4    Kulhanek, J.5
  • 34
    • 4444363101 scopus 로고    scopus 로고
    • Overexpression and purification of bacterial DNA gyrase
    • Maxwell, A., and A. J. Howells. 1999. Overexpression and purification of bacterial DNA gyrase. Methods Mol. Biol 94:135-144.
    • (1999) Methods Mol. Biol , vol.94 , pp. 135-144
    • Maxwell, A.1    Howells, A.J.2
  • 35
    • 0012684806 scopus 로고    scopus 로고
    • The ATP-binding site of type II topoisomerases as a target for antibacterial drugs
    • Maxwell, A., and D. M. Lawson. 2003. The ATP-binding site of type II topoisomerases as a target for antibacterial drugs. Curr. Top. Med. Chem. 3:283-303.
    • (2003) Curr. Top. Med. Chem , vol.3 , pp. 283-303
    • Maxwell, A.1    Lawson, D.M.2
  • 36
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald, I. K., and J. M. Thornton. 1994. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238:777-793.
    • (1994) J. Mol. Biol , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 38
    • 0036233675 scopus 로고    scopus 로고
    • Developmental therapeutics program at the NCI: Molecular target and drug discovery process
    • Monga, M., and E. A. Sausville. 2002. Developmental therapeutics program at the NCI: molecular target and drug discovery process. Leukemia 16:520-526.
    • (2002) Leukemia , vol.16 , pp. 520-526
    • Monga, M.1    Sausville, E.A.2
  • 40
  • 41
    • 3042806401 scopus 로고    scopus 로고
    • A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
    • Perola, E., W. P. Walters, and P. S. Charifson. 2004. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 56:235-249.
    • (2004) Proteins , vol.56 , pp. 235-249
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 44
    • 0019321370 scopus 로고
    • The intrinsic ATPase of DNA gyrase
    • Sugino, A., and N. R. Cozzarelli. 1980. The intrinsic ATPase of DNA gyrase. J. Biol. Chem. 255:6299-6306.
    • (1980) J. Biol. Chem , vol.255 , pp. 6299-6306
    • Sugino, A.1    Cozzarelli, N.R.2
  • 45
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
    • Wallace, A. C., R. A. Laskowski, and J. M. Thornton. 1995. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8:127-134.
    • (1995) Protein Eng , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 46
    • 0036085460 scopus 로고    scopus 로고
    • Cellular roles of DNA topoisomerases: A molecular perspective
    • Wang, J. C. 2002. Cellular roles of DNA topoisomerases: a molecular perspective. Nat. Rev. Mol. Cell Biol. 3:430-440.
    • (2002) Nat. Rev. Mol. Cell Biol , vol.3 , pp. 430-440
    • Wang, J.C.1
  • 47
    • 0042990131 scopus 로고    scopus 로고
    • Effects of DNA supercoiling on gene expression
    • E. C. C. Lin and A. S. Lynch ed, coli. Landes Company, Austin, TX
    • Wang, J. C., and A. S. Lynch. 1996. Effects of DNA supercoiling on gene expression, p. 127-147. In E. C. C. Lin and A. S. Lynch (ed.), Regulation of gene expression in Escherichia coli. Landes Company, Austin, TX.
    • (1996) Regulation of gene expression in Escherichia , pp. 127-147
    • Wang, J.C.1    Lynch, A.S.2
  • 48
    • 0026428621 scopus 로고
    • Crystal structure of an N-terminal fragment of the DNA gyrase B protein
    • Wigley, D. B., G. J. Davies, E. J. Dodson, A. Maxwell, and G. Dodson. 1991. Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 351:624-629.
    • (1991) Nature , vol.351 , pp. 624-629
    • Wigley, D.B.1    Davies, G.J.2    Dodson, E.J.3    Maxwell, A.4    Dodson, G.5
  • 49
    • 16644376474 scopus 로고    scopus 로고
    • Evaluation and application of multiple scoring functions for a virtual screening experiment
    • Xing, L., E. Hodgkin, Q. Liu, and D. Sedlock. 2004. Evaluation and application of multiple scoring functions for a virtual screening experiment. J. Comput.-Aided Mol. Des. 18:333-344.
    • (2004) J. Comput.-Aided Mol. Des , vol.18 , pp. 333-344
    • Xing, L.1    Hodgkin, E.2    Liu, Q.3    Sedlock, D.4
  • 50
    • 0025282176 scopus 로고
    • Quinolone resistance-determining region in the DNA gyrase gyrA gene of Escherichia coli
    • Yoshida, H., M. Bogaki, M. Nakamura, and S. Nakamura. 1990. Quinolone resistance-determining region in the DNA gyrase gyrA gene of Escherichia coli. Antimicrob. Agents Chemother. 34:1271-1272.
    • (1990) Antimicrob. Agents Chemother , vol.34 , pp. 1271-1272
    • Yoshida, H.1    Bogaki, M.2    Nakamura, M.3    Nakamura, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.