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Bacterial DNA replication enzymes as targets for antibacterial drug discovery

, PhD (Director) & , PhD (Associate Director)
Pages 327-339 | Published online: 21 Feb 2012

Bibliography

  • Noirot-Gros MF, Dervyn E, Wu LJ, An expanded view of bacterial DNA replication. Proc Natl Acad Sci USA 2002;99:8342-7
  • Yao NY, O'Donnell M. SnapShot: the replisome. Cell 2010;141:1088
  • Marians KJ. Understanding how the replisome works. Nat Struct Mol Biol 2008;15:125-7
  • Kornberg A, Baker TA. DNA replication. 2nd edition. University Science Books; Sausalito, CA: 2005
  • Pomerantz RT, O'Donnell M. Replisome mechanics: insights into a twin DNA polymerase machine. Trends Microbiol 2007;15:156-64
  • Syson K, Thirlway J, Hounslow AM, Solution structure of the helicase-interaction domain of the primase DnaG: a model for helicase activation. Structure 2005;13:609-16
  • Mitscher LA. Bacterial topoisomerase inhibitors: quinolone and pyridone antibacterial agents. Chem Rev 2005;105:559-92
  • Maxwell A, Lawson DM. The ATP-binding site of type II topoisomerases as a target for antibacterial drugs. Curr Top Med Chem 2003;3:283-303
  • Maxwell A. DNA gyrase as a drug target. Biochem Soc Trans 1999;27:48-53
  • Maxwell A. DNA gyrase as a drug target. Trends Microbiol 1997;5:102-9
  • Hoshino K, Sato K, Une T, Inhibitory effects of quinolones on DNA gyrase of Escherichia coli and topoisomerase II of fetal calf thymus. Antimicrob Agents Chemother 1989;33:1816-18
  • Chu DT, Hallas R, Clement JJ, Synthesis and antitumour activities of quinolone antineoplastic agents. Drugs Exp Clin Res 1992;18:275-82
  • Roca J, Berger JM, Harrison SC, DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism. Proc Natl Acad Sci USA 1996;93:4057-62
  • Roca J, Wang JC. DNA transport by a type II DNA topoisomerase: evidence in favor of a two-gate mechanism. Cell 1994;77:609-16
  • Roca J, Wang JC. The capture of a DNA double helix by an ATP-dependent protein clamp: a key step in DNA transport by type II DNA topoisomerases. Cell 1992;71:833-40
  • Bates AD, Maxwell A. The role of ATP in the reactions of type II DNA topoisomerases. Biochem Soc Trans 2010;38:438-42
  • Bates AD, Maxwell A. Energy coupling in type II topoisomerases: why do they hydrolyze ATP? Biochemistry (NY) 2007;46:7929-41
  • Maxwell A, Costenaro L, Mitelheiser S, Coupling ATP hydrolysis to DNA strand passage in type IIA DNA topoisomerases. Biochem Soc Trans 2005;33:1460-4
  • Shen LL, Mitscher LA, Sharma PN, Mechanism of inhibition of DNA gyrase by quinolone antibacterials: a cooperative drug–DNA binding model. Biochemistry (NY) 1989;28:3886-94
  • Emami S, Shafiee A, Foroumadi A. Structural features of new quinolones and relationship to antibacterial activity against gram-positive bacteria. Mini Rev Med Chem 2006;6:375-86
  • Bush K, Pucci MJ. New antimicrobial agents on the horizon. Biochem Pharmacol 2011;82:1528-39
  • 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
  • Takei M, Fukuda H, Kishii R, Target preference of 15 quinolones against Staphylococcus aureus, based on antibacterial activities and target inhibition. Antimicrob Agents Chemother 2001;45:3544-7
  • Alt S, Mitchenall LA, Maxwell A, Inhibition of DNA gyrase and DNA topoisomerase IV of Staphylococcus aureus and E by aminocoumarin antibiotics. J Antimicrob Chemother 2011;66:2061-9
  • Anderle C, Stieger M, Burrell M, Biological activities of novel gyrase inhibitors of the aminocoumarin class. Antimicrob Agents Chemother 2008;52:1982-90
  • Oblak M, Kotnik M, Solmajer T. Discovery and development of ATPase inhibitors of DNA gyrase as antibacterial agents. Curr Med Chem 2007;14:2033-47
  • Eakin AE, Green O, Hales N, Pyrrolamide DNA gyrase inhibitors: Fragment-based NMR screening to antibacterial agents. Antimicrob Agents Chemother 2012; In press
  • Hull K, Green O, Singh A, Novel DNA gyrase inhibitors: the effect of pyrrolamide variations at site 1 and site 2 upon potency [abstract F1-2027]. 48th Intersci. Conf. Antimicrob Agents Chemother; 2008
  • Sherer B, Basarab G, Hull K, Novel DNA gyrase inhibitors: The effect of pyrrolamide linker variations upon potency [abstract F1-2026]. Abstr 48th Intersci. Conf. Antimicrob Agents Chemother; 2008
  • Tsai FT, Singh OM, Skarzynski T, The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin. Proteins 1997;28:41-52
  • Lesher GY, Froelich EJ, Gruett MD, 1,8-naphthyridine derivatives. A new class of chemotherapeutic agents. J Med Pharm Chem 1962;91:1063-5
  • Aubry A, Pan XS, Fisher LM, Mycobacterium tuberculosis DNA gyrase: interaction with quinolones and correlation with antimycobacterial drug activity. Antimicrob Agents Chemother 2004;48:1281-8
  • Kern G, Basarab GS, Andrews B, A DNA gyrase inhibitor with a novel mode of inhibition and in vivo efficacy [abstract F1-1840]. 51st Intersci. Conf. Antimicrob. Agents Chemother; 2011
  • Chen CR, Malik M, Snyder M, DNA gyrase and topoisomerase IV on the bacterial chromosome: quinolone-induced DNA cleavage. J Mol Biol 1996;258:627-37
  • Drlica K, Malik M, Kerns RJ, Quinolone-mediated bacterial death. Antimicrob Agents Chemother 2008;52:385-92
  • Dwyer DJ, Kohanski MA, Hayete B, Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Mol Syst Biol 2007;3:91
  • Kohanski MA, Dwyer DJ, Collins JJ. How antibiotics kill bacteria: from targets to networks. Nat Rev Microbiol 2010;8:423-35
  • Krasin F, Hutchinson F. Repair of DNA double-strand breaks in Escherichia coli, which requires recA function and the presence of a duplicate genome. J Mol Biol 1977;116:81-98
  • Yoshida H, Bogaki M, Nakamura M, Quinolone resistance-determining region in the DNA gyrase gyrB gene of Escherichia coli. Antimicrob Agents Chemother 1991;35:1647-50
  • Heddle J, Maxwell A. Quinolone-binding pocket of DNA gyrase: role of GyrB. Antimicrob Agents Chemother 2002;46:1805-15
  • Critchlow SE, Maxwell A. DNA cleavage is not required for the binding of quinolone drugs to the DNA gyrase-DNA complex. Biochemistry (NY) 1996;35:7387-93
  • Marians KJ, Hiasa H. Mechanism of quinolone action. A drug-induced structural perturbation of the DNA precedes strand cleavage by topoisomerase IV. J Biol Chem 1997;272:9401-9
  • Kampranis SC, Maxwell A. The DNA gyrase-quinolone complex. ATP hydrolysis and the mechanism of DNA cleavage. J Biol Chem 1998;273:22615-26
  • Howard BM, Pinney RJ, Smith JT. Function of the SOS process in repair of DNA damage induced by modern 4-quinolones. J Pharm Pharmacol 1993;45:658-62
  • Kohanski MA, Dwyer DJ, Hayete B, A common mechanism of cellular death induced by bactericidal antibiotics. Cell 2007;130:797-810
  • Wang X, Zhao X, Malik M, Contribution of reactive oxygen species to pathways of quinolone-mediated bacterial cell death. J Antimicrob Chemother 2010;65:520-4
  • Bax BD, Chan PF, Eggleston DS, Type IIA topoisomerase inhibition by a new class of antibacterial agents. Nature 2010;466:935-40
  • Wohlkonig A, Chan PF, Fosberry AP, Structural basis of quinolone inhibition of type IIA topoisomerases and target-mediated resistance. Nat Struct Mol Biol 2010;17:1152-3
  • Laponogov I, Sohi MK, Veselkov DA, Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases. Nat Struct Mol Biol 2009;16:667-9
  • Laponogov I, Pan XS, Veselkov DA, Structural basis of gate-DNA breakage and resealing by type II topoisomerases. [Electronic Resource]. PLoS ONE 2010;5:e11338
  • Laponogov I, Veselkov DA, Sohi MK, Breakage-reunion domain of streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target [Electronic Resource]. PLoS ONE 2007;2:e301
  • Bradbury BJ, Pucci MJ. Recent advances in bacterial topoisomerase inhibitors. Curr Opin Pharmacol 2008;8:574-81
  • Tse-Dinh YC. Exploring DNA topoisomerases as targets of novel therapeutic agents in the treatment of infectious diseases. Infect Disord Drug Targets 2007;7:3-9
  • Grossman TH, Bartels DJ, Mullin S, Dual targeting of GyrB and ParE by a novel aminobenzimidazole class of antibacterial compounds. Antimicrob Agents Chemother 2007;51:657-66
  • Mani N, Gross CH, Parsons JD, In vitro characterization of the antibacterial spectrum of novel bacterial type II topoisomerase inhibitors of the aminobenzimidazole class. Antimicrob Agents Chemother 2006;50:1228-37
  • Zhi C, Long ZY, Manikowski A, Hybrid antibacterials. DNA polymerase-topoisomerase inhibitors. J Med Chem 2006;49:1455-65
  • Black MT, Stachyra T, Platel D, Mechanism of action of the antibiotic NXL101, a novel nonfluoroquinolone inhibitor of bacterial type II topoisomerases. Antimicrob Agents Chemother 2008;52:3339-49
  • Basarab GS, Beaudoin M-, Brassil P, Gyrase inhibiting antibacterial agents: Structure-activity relationships for four isomeric tetrahydronaphthyridine spirocyclic pyrimidinetrionesimidinetriones [abstract F1-1839]. 51st Intersci. Conf. Antimicrob Agents Chemother; 2011
  • Miller AA, Bundy GL, Mott JE, Discovery and characterization of QPT-1, the progenitor of a new class of bacterial topoisomerase inhibitors. Antimicrob Agents Chemother 2008;52:2806-12
  • Reck F, Alm R, Brassil P, Novel N-linked aminopiperidine inhibitors of bacterial topoisomerase type II: broad-spectrum antibacterial agents with reduced hERG activity. J Med Chem 2011;54:7834-47
  • Gomez L, Hack MD, Wu J, Novel pyrazole derivatives as potent inhibitors of type II topoisomerases. Part 1: synthesis and preliminary SAR analysis. Bioorg Med Chem Lett 2007;17:2723-7
  • Wiener JJ, Gomez L, Venkatesan H, Tetrahydroindazole inhibitors of bacterial type II topoisomerases. Part 2: SAR development and potency against multidrug-resistant strains. Bioorg Med Chem Lett 2007;17:2718-22
  • Miles TJ, Barfoot C, Brooks G, Novel cyclohexyl-amides as potent antibacterials targeting bacterial type IIA topoisomerases. Bioorg Med Chem Lett 2011;21:7483-8
  • Miles TJ, Axten JM, Barfoot C, Novel amino-piperidines as potent antibacterials targeting bacterial type IIA topoisomerases. Bioorg Med Chem Lett 2011;21:7489-95
  • Geng B, Comita-Prevoir J, Eyermann CJ, Exploring left-hand-side substitutions in the benzoxazinone series of 4-amino-piperidine bacterial type IIa topoisomerase inhibitors. Bioorg Med Chem Lett 2011;21:5432-5
  • Frick DN, Richardson CC. DNA primases. Annu Rev Biochem 2001;70:39-80
  • Hegde VR, Pu H, Patel M, Two new bacterial DNA primase inhibitors from the plant polygonum cuspidatum. Bioorg Med Chem Lett 2004;14:2275-7
  • Chu M, Mierzwa R, Xu L, Isolation and structure elucidation of sch 642305, a novel bacterial DNA primase inhibitor produced by penicillium verrucosum. J Nat Prod 2003;66:1527-30
  • Wilson EM, Trauner D. Concise synthesis of the bacterial DNA primase inhibitor (+) -sch 642305. Org Lett 2007;9:1327-9
  • Garcia-Fortanet J, Carda M, Marco JA. Stereoselective synthesis of the bacterial DNA primase inhibitor sch 642305 and its C-4 epimer. Tetrahedron 2007;63:12131-7
  • Agarwal A, Louise-May S, Thanassi JA, Small molecule inhibitors of E. coli primase, a novel bacterial target. Bioorg Med Chem Lett 2007;17:2807-10
  • Koepsell SA, Larson MA, Frey CA, Staphylococcus aureus primase has higher initiation specificity, interacts with single-stranded DNA stronger, but is less stimulated by its helicase than Escherichia coli primase. Mol Microbiol 2008;68:1570-82
  • Borowiec JA. DNA helicases. In: ML DePamphilis. editor. DNA Replication in Eukaryotic Cells. Cold Spring Harbor Laboratory Press; NY: 1996. p. 545-74
  • Schaeffer P, Headlam M, Dixon N. Protein-protein interactions in the bacterial replisome. Aust Biochem 2004;35:9-12
  • Wing RA, Bailey S, Steitz TA. Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit. J Mol Biol 2008;382:859-69
  • Bailey S, Eliason WK, Steitz TA. Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase. Science 2007;318:459-63
  • Aiello D, Barnes MH, Biswas EE, Discovery, characterization and comparison of inhibitors of Bacillus anthracis and Staphylococcus aureus replicative DNA helicases. Bioorg Med Chem 2009;17:4466-76
  • Moir DT, Li B, Pai R, Optimization of coumarin-based inhibitors of Staphylococcus aureus and Bacillus anthracis replicative DNA helicases [abstract. F1-1838]. 51st Intersci. Conf. Antimicrob Agents Chemother; 2011
  • Inoue R, Kaito C, Tanabe M, Genetic identification of two distinct DNA polymerases, DnaE and PolC, that are essential for chromosomal DNA replication in Staphylococcus aureus. Molecular Genet Genomics 2001;266:564-71
  • Tarantino PM Jr, Zhi C, Wright GE, Inhibitors of DNA polymerase III as novel antimicrobial agents against gram-positive eubacteria. Antimicrob Agents Chemother 1999;43:1982-7
  • Daly JS, Giehl TJ, Brown NC, In vitro antimicrobial activities of novel anilinouracils which selectively inhibit DNA polymerase III of gram-positive bacteria. Antimicrob Agents & Chemother 2000;44:2217-21
  • Huang YP, Ito J. The hyperthermophilic bacterium thermotoga maritima has two different classes of family C DNA polymerases: evolutionary implications. Nucleic Acids Res 1998;26:5300-9
  • Payne DJ, Gwynn MN, Holmes DJ, Drugs for bad bugs: confronting the challenges of antibacterial discovery. Nat Rev Drug Discov 2007;6:29-40
  • Gwynn MN, Portnoy A, Rittenhouse SF, Challenges of antibacterial discovery revisited. Ann N Y Acad Sci 2010;1213:5-19
  • Svenstrup N, Ehlert K, Ladel C, New DNA polymerase IIIC inhibitors: 3-subtituted anilinouracils with potent antibacterial activity in vitro and in vivo. ChemMedChem 2008;3:1604-15
  • Srivastava SK, Dube D, Tewari N, Mycobacterium tuberculosis NAD+- dependent DNA ligase is selectively inhibited by glycosylamines compared with human DNA ligase I. Nucleic Acids Res 2005;33:7090-101
  • Nandakumar J, Nair PA, Shuman S. Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate. Mol Cell 2007;26:257-71
  • Odell M, Sriskanda V, Shuman S, Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining. Mol Cell 2000;6:1183-93
  • Wilkinson A, Day J, Bowater R. Bacterial DNA ligases. Mol Microbiol 2001;40:1241-8
  • Shuman S. DNA ligases: progress and prospects. J Biol Chem 2009;284:17365-9
  • Pascal JM. DNA and RNA ligases: structural variations and shared mechanisms. Curr Opin Struct Biol 2008;18:96-105
  • Barrow EW, Westbrook L, Bansal N, Antimycobacterial activity of 2-methyl-adenosine. J Antimicrob Chemother 2003;52:801-8
  • Lahiri SD, Gu R, Gao N, Structure guided understanding of NAD+ recognition in bacterial DNA ligases. Chem Biol 2012; In press
  • Zhu H, Shuman S. Structure-guided mutational analysis of the nucleotidyltransferase domain of Escherichia coli NAD+-dependent DNA ligase (LigA). J Biol Chem 2005;280:12137-44
  • Han S, Chang JS, Griffor M. Structure of the adenylation domain of NAD(+)-dependent DNA ligase from Staphylococcus aureus. Acta Crystallograph Sect F Struct Biol Cryst Commun 2009;65:1078-82
  • Brotz-Oesterhelt H, Knezevic I, Bartel S, Specific and potent inhibition of NAD+-dependent DNA ligase by pyridochromanones. J Biol Chem 2003;278:39435-42
  • Pinko C, Chu S, Su Y, Crystal structures of DNA ligase from pathogenic bacteria reveal extensive structural conservation and provide critical insight into protein-ligand interaction. 43rd Interscience Conference on Antimicrobial Agents and Chemotherapy; 2003
  • Gajiwala KS, Pinko C. Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal. Structure 2004;12:1449-59
  • Meier TI, Yan D, Peery RB, Identification and characterization of an inhibitor specific to bacterial NAD+-dependent DNA ligases. FEBS J 2008;275:5258-71
  • Mills SD, Eakin AE, Buurman ET, Novel bacterial NAD+-dependent DNA ligase inhibitors with broad-spectrum activity and antibacterial efficacy in vivo. Antimicrob Agents Chemother 2011;55:1088-96
  • Stokes SS, Huynh H, Gowravaram M, Discovery of bacterial NAD+-dependent DNA ligase inhibitors: optimization of antibacterial activity. Bioorg Med Chem Lett 2011;21:4556-60
  • Berman HM, Westbrook J, Feng Z, The protein data bank. Nucleic Acids Res 2000;28:235-42
  • Ramachandran GN, Sasisekharan V. Conformation of polypeptides and proteins. Adv Protein Chem 1968;23:283-438
  • Morris GM, Goodsell DS, Halliday RS, Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function J Comput Chem. 1998;19:1639-62
  • Sriskanda V, Shuman S. A second NAD(+)-dependent DNA ligase (LigB) in Escherichia coli. Nucleic Acids Res 2001;29:4930-4
  • Charifson PS, Grillot AL, Grossman TH, Novel dual-targeting benzimidazole urea inhibitors of DNA gyrase and topoisomerase IV possessing potent antibacterial activity: intelligent design and evolution through the judicious use of structure-guided design and structure-activity relationships. J Med Chem 2008;51:5243-63
  • Wang G, Klein MG, Tokonzaba E, The structure of a DnaB-family replicative helicase and its interactions with primase. Nat Struct Mol Biol 2008;15:94-100
  • Albert JS, Blomberg N, Breeze AL, An integrated approach to fragment-based lead generation: philosophy, strategy and case studies from AstraZeneca's drug discovery programmes. Curr Top Med Chem 2007;7:1600-29
  • Murray CW, Blundell TL. Structural biology in fragment-based drug design. Curr Opin Struct Biol 2010;20:497-507
  • Green O, Ni H, Singh A, Novel DNA gyrase inhibitors: Structure-guided discovery and optimization of pyrrolamides [Abstract F-2025]. 48th Intersci. Con. Antimibrobial Agents Chemother; 2008
  • Wiles JA, Hashimoto A, Thanassi JA, Isothiazolopyridones: synthesis, structure, and biological activity of a new class of antibacterial agents. J Med Chem 2006;49:39-42
  • Wiles JA, Wang Q, Lucien E, Isothiazoloquinolones containing functionalized aromatic hydrocarbons at the 7-position: synthesis and in vitro activity of a series of potent antibacterial agents with diminished cytotoxicity in human cells. Bioorg Med Chem Lett 2006;16:1272-6
  • Hutchings KM, Tran TP, Ellsworth EL, Synthesis and antibacterial activity of the C-7 side chain of 3-aminoquinazolinediones. Bioorg Med Chem Lett 2008;18:5087-90
  • Tran TP, Ellsworth EL, Sanchez JP, Structure-activity relationships of 3-aminoquinazolinediones, a new class of bacterial type-2 topoisomerase (DNA gyrase and topo IV) inhibitors. Bioorg Med Chem Lett 2007;17:1312-20
  • Lubbers T, Angehrn P, Gmunder H, Design, synthesis, and structure-activity relationship studies of new phenolic DNA gyrase inhibitors. Bioorg Med Chem Lett 2007;17:4708-14
  • Angehrn P, Goetschi E, Gmuender H, A new DNA gyrase inhibitor subclass of the cyclothialidine family based on a bicyclic dilactam-lactone scaffold. synthesis and antibacterial properties. J Med Chem 2011;54:2207-24
  • Angehrn P, Buchmann S, Funk C, New antibacterial agents derived from the DNA gyrase inhibitor cyclothialidine. J Med Chem 2004;47:1487-513

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