Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms

Bibliography

• Shuman S, Lima CD. The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases. Curr Opin Struct Biol 2004;14(6):757-64
   PubMed Web of Science ®Google Scholar
• Shuman S. DNA ligases: progress and prospects. J Biol Chem 2009;284(26):17365-9
   PubMed Web of Science ®Google Scholar
• Tomkinson AE, Vijayakumar S, Pascal JM, Ellenberger T. DNA ligases: structure, reaction mechanism, and function. Chem Rev 2006;106(2):687-99
   PubMed Web of Science ®Google Scholar
• Nair PA, Nandakumar J, Smith P, Structural basis for nick recognition by a minimal pluripotent DNA ligase. Nat Struct Mol Biol 2007;14(8):770-8
   PubMed Web of Science ®Google Scholar
• Gajiwala KS, Pinko C. Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal. Structure 2004;12(8):1449-59
   PubMed Web of Science ®Google Scholar
• Hâkansson K, Doherty AJ, Shuman S, Wigley DB. X-Ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes. Cell 1997;89(4):545-53
   PubMed Web of Science ®Google Scholar
• Swift RV, McCammon JA. Substrate induced population shifts and stochastic gating in the PBCV-1 mRNA capping enzyme. J Am Chem Soc 2009;131(14):5126-33
   PubMed Web of Science ®Google Scholar
• Schnaufer A, Ernst NL, Palazzo SS, Separate insertion and deletion subcomplexes of the Trypanosoma brucei RNA editing complex. Mol Cell 2003;12(2):307-19
   PubMed Web of Science ®Google Scholar
• Lindahl T. Instability and decay of the primary structure of DNA. Nature 1993;362(6422):709-15
   PubMed Web of Science ®Google Scholar
• Sedgwick B, Bates PA, Paik J, Repair of alkylated DNA: recent advances. DNA Repair (Amst) 2007;6(4):429-42
   PubMed Web of Science ®Google Scholar
• Kavli B, Otterlei M, Slupphaug G, Krokan HE. Uracil in DNA-general mutagen, but normal intermediate in acquired immunity. DNA Repair (Amst) 2007;6(4):505-16
   PubMed Web of Science ®Google Scholar
• Fortini P, Pascucci B, Parlanti E, Different DNA polymerases are involved in the short- and long-patch base excision repair in mammalian cells. Biochemistry 1998;37(11):3575-80
   PubMed Web of Science ®Google Scholar
• Robertson AB, Klungland A, Rognes T, Leiros I. DNA repair in mammalian cells: Base excision repair: the long and short of it. Cell Mol Life Sci 2009;66(6):981-93
   PubMed Web of Science ®Google Scholar
• Pardo B, Gomez-Gonzalez B, Aguilera A. DNA repair in mammalian cells: DNA double-strand break repair: how to fix a broken relationship. Cell Mol Life Sci 2009;66(6):1039-56
   PubMed Web of Science ®Google Scholar
• Daley JM, Palmbos PL, Wu D, Wilson TE. Nonhomologous end joining in yeast. Annu Rev Genet 2005;39:431-51
   PubMedGoogle Scholar
• Teo IA, Arlett CF, Harcourt SA, Multiple hypersensitivity to mutagens in a cell strain (46BR) derived from a patient with immuno-deficiencies. Mutat Res 1983;107(2):371-86
   PubMed Web of Science ®Google Scholar
• Barnes DE, Tomkinson AE, Lehmann AR, Mutations in the DNA ligase I gene of an individual with immunodeficiencies and cellular hypersensitivity to DNA-damaging agents. Cell 1992;69(3):495-503
   PubMed Web of Science ®Google Scholar
• Mackenney VJ, Barnes DE, Lindahl T. Specific function of DNA ligase I in simian virus 40 DNA replication by human cell-free extracts is mediated by the amino-terminal non-catalytic domain. J Biol Chem 1997;272(17):11550-6
   PubMed Web of Science ®Google Scholar
• Amitsur M, Levitz R, Kaufmann G. Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. EMBO J 1987;6(8):2499-503
   PubMed Web of Science ®Google Scholar
• Abelson J, Trotta CR, Li H. tRNA splicing. J Biol Chem 1998;273(21):12685-8
   PubMed Web of Science ®Google Scholar
• Stuart K, Allen TE, Heidmann S, Seiwert SD. RNA editing in kinetoplastid protozoa. Microbiol Mol Biol Rev 1997;61(1):105-20
   PubMed Web of Science ®Google Scholar
• Simpson L, Sbicego S, Aphasizhev R. Urididine insertion/deletion RNA editing in trypanosome mitochondria: a complex business. RNA 2003;9:265-76
   PubMed Web of Science ®Google Scholar
• Schnaufer A, Panigrahi AK, Panicucci B, An RNA ligase essential for RNA editing and survival of the bloodstream form of trypanosoma brucei. Science 2001;291(5511):2159-62
   PubMed Web of Science ®Google Scholar
• Dwivedi N, Dube D, Pandey J, NAD(+)-dependent DNA ligase: a novel target waiting for the right inhibitor. Med Res Rev 2008;28(4):545-68
   PubMed Web of Science ®Google Scholar
• Korycka-Machala M, Rychta E, Brzostek A, Evaluation of NAD(+) -dependent DNA ligase of mycobacteria as a potential target for antibiotics. Antimicrob Agents Chemother 2007;51(8):2888-97
   PubMed Web of Science ®Google Scholar
• Zhong S, Chen X, Zhu X, Identification and validation of human DNA ligase inhibitors using computer-aided drug design. J Med Chem 2008;51(15):4553-62
   PubMed Web of Science ®Google Scholar
• Amaro RE, Schnaufer A, Interthal H, Discovery of drug-like inhibitors of an essential RNA-editing ligase in trypanosoma brucei. Proc Natl Acad Sci USA 2008;105(45):17278-83
   PubMed Web of Science ®Google Scholar
• Gefter ML, Becker A, Hurwitz J. The enzymatic repair of DNA. I. Formation of circular lambda-DNA. Proc Natl Acad Sci USA 1967;58(1):240-7
   PubMed Web of Science ®Google Scholar
• Gellert M. Formation of covalent circles of lambda DNA by E. coli extracts. Proc Natl Acad Sci USA 1967;57(1):148-55
   PubMed Web of Science ®Google Scholar
• Olivera BM, Lehman IR. Linkage of polynucleotides through phosphodiester bonds by an enzyme from escherichia coli. Proc Natl Acad Sci USA 1967;57(5):1426-33
   PubMed Web of Science ®Google Scholar
• Weiss B, Richardson CC. Enzymatic breakage and joining of deoxyribonucleic acid, I. Repair of single-strand breaks in DNA by an enzyme system from escherichia coli infected with T4 bacteriophage. Proc Natl Acad Sci USA 1967;57(4):1021-8
   PubMed Web of Science ®Google Scholar
• Cozzarelli NR, Melechen NE, Jovin TM, Kornberg A. Polynucleotide cellulose as a substrate for a polynucleotide ligase induced by phage T4. Biochem Biophys Res Commun 1967;28(4):578-86
   PubMed Web of Science ®Google Scholar
• Lindahl T, Edelman GM. Polynucleotide ligase from myeloid and lymphoid tissues. Proc Natl Acad Sci USA 1968;61(2):680-7
   PubMed Web of Science ®Google Scholar
• Richardson CC. Enzymes in DNA metabolism. Annu Rev Biochem 1969;38:795-840
   PubMed Web of Science ®Google Scholar
• Jung D, Giallourakis C, Mostoslavsky R, Alt FW. Mechanism and control of V(D)J recombination at the immunoglobulin heavy chain locus. Annu Rev Immunol 2006;24:541-70
   PubMed Web of Science ®Google Scholar
• Martin IV, MacNeill SA. ATP-dependent DNA ligases. Genome Biol 2002;3(4): REVIEWS3005
   PubMed Web of Science ®Google Scholar
• Horiuchi T, Sato T, Nagata T. DNA degradation in an amber mutant of escherichia coli K12 affecting DNA ligase and viability. J Mol Biol 1975;95(2):271-87
   PubMed Web of Science ®Google Scholar
• Park UE, Olivera BM, Hughes KT, DNA ligase and the pyridine nucleotide cycle in salmonella typhimurium. J Bacteriol 1989;171(4):2173-80
   PubMed Web of Science ®Google Scholar
• Petit MA, Ehrlich SD. The NAD-dependent ligase encoded by yerG is an essential gene of bacillus subtilis. Nucleic Acids Res 2000;28(23):4642-8
   PubMed Web of Science ®Google Scholar
• Kaczmarek FS, Zaniewski RP, Gootz TD, Cloning and functional characterization of an NAD(+)-dependent DNA ligase from staphylococcus aureus. J Bacteriol 2001;183(10):3016-24
   PubMed Web of Science ®Google Scholar
• Chen XC, Hentz NG, Hubbard F, Development of a fluorescence resonance energy transfer assay for measuring the activity of streptococcus pneumoniae DNA ligase, an enzyme essential for DNA replication, repair, and recombination. Anal Biochem 2002;309(2):232-40
   PubMed Web of Science ®Google Scholar
• Akerley BJ, Rubin EJ, Novick VL, A genome-scale analysis for identification of genes required for growth or survival of haemophilus influenzae. Proc Natl Acad Sci USA 2002;99(2):966-71
   PubMed Web of Science ®Google Scholar
• Sassetti CM, Boyd DH, Rubin EJ. Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 2003;48(1):77-84
   PubMed Web of Science ®Google Scholar
• Gong C, Martins A, Bongiorno P, Biochemical and genetic analysis of the four DNA ligases of mycobacteria. J Biol Chem 2004;279(20):20594-606
   PubMed Web of Science ®Google Scholar
• Pascal JM. DNA and RNA ligases: structural variations and shared mechanisms. Curr Opin Struct Biol 2008;18(1):96-105
   PubMed Web of Science ®Google Scholar
• Deng J, Schnaufer A, Salavati R, High resolution crystal structure of a key editosome enzyme from trypanosoma brucei: RNA editing ligase 1. J Mol Biol 2004;343(3):601-13
   PubMed Web of Science ®Google Scholar
• Subramanya HS, Doherty AJ, Ashford SR, Wigley DB. Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell 1996;85(4):607-15
   PubMed Web of Science ®Google Scholar
• Odell M, Sriskanda V, Shuman S, Nikolov DB. Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining. Mol Cell 2000;6(5):1183-93
   PubMed Web of Science ®Google Scholar
• El Omari K, Ren J, Bird LE, Molecular architecture and ligand recognition determinants for T4 RNA ligase. J Biol Chem 2006;281(3):1573-9
   PubMed Web of Science ®Google Scholar
• Lee JY, Chang C, Song HK, Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications. EMBO J 2000;19(5):1119-29
   PubMed Web of Science ®Google Scholar
• Sriskanda V, Shuman S. Mutational analysis of Chlorella virus DNA ligase: catalytic roles of domain I and motif VI. Nucleic Acids Res 1998;26(20):4618-25
   PubMed Web of Science ®Google Scholar
• Wang LK, Nair PA, Shuman S. Structure-guided mutational analysis of the OB, HhH, and BRCT domains of escherichia coli DNA ligase. J Biol Chem 2008;283(34):23343-52
   PubMed Web of Science ®Google Scholar
• Srivastava SK, Dube D, Kukshal V, NAD+-dependent DNA ligase (Rv3014c) from mycobacterium tuberculosis: novel structure–function relationship and identification of a specific inhibitor. Proteins 2007;69(1):97-111
   PubMed Web of Science ®Google Scholar
• Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger T. Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 2004;432(7016):473-8
   PubMed Web of Science ®Google Scholar
• Nandakumar J, Shuman S, Lima CD. RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward. Cell 2006;127(1):71-84
   PubMed Web of Science ®Google Scholar
• 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(2):257-71
   PubMed Web of Science ®Google Scholar
• Jeon HJ, Shin HJ, Choi JJ, Mutational analyses of the thermostable NAD+-dependent DNA ligase from thermus filiformis. FEMS Microbiol Lett 2004;237(1):111-8
   PubMed Web of Science ®Google Scholar
• Ellenberger T, Tomkinson AE. Eukaryotic DNA ligases: structural and functional insights. Annu Rev Biochem 2008;77:313-38
   PubMed Web of Science ®Google Scholar
• Feng H, Parker JM, Lu J, Cao W. Effects of deletion and site-directed mutations on ligation steps of NAD+-dependent DNA ligase: a biochemical analysis of BRCA1 C-terminal domain. Biochemistry 2004;43(39):12648-59
   PubMed Web of Science ®Google Scholar
• Lim JH, Choi J, Kim W, Mutational analyses of Aquifex pyrophilus DNA ligase define essential domains for self-adenylation and DNA binding activity. Arch Biochem Biophys 2001;388(2):253-60
   PubMed Web of Science ®Google Scholar
• Miesel L, Kravec C, Xin AT, A high-throughput assay for the adenylation reaction of bacterial DNA ligase. Anal Biochem 2007;366(1):9-17
   PubMed Web of Science ®Google Scholar
• Brotz-Oesterhelt H, Knezevic I, Bartel S, Specific and potent inhibition of NAD+-dependent DNA ligase by pyridochromanones. J Biol Chem 2003;278(41):39435-42
   PubMed Web of Science ®Google Scholar
• Tanifum EA, Kots AY, Choi BK, Novel pyridopyrimidine derivatives as inhibitors of stable toxin a (STa) induced cGMP synthesis. Bioorg Med Chem Lett 2009;19(11):3067-71
   PubMed Web of Science ®Google Scholar
• Kots AY, Choi BK, Estrella-Jimenez ME, Pyridopyrimidine derivatives as inhibitors of cyclic nucleotide synthesis: Application for treatment of diarrhea. Proc Natl Acad Sci USA 2008;105(24):8440-5
   PubMed Web of Science ®Google Scholar
• Debenham JS, Madsen-Duggan CB, Wang J, Pyridopyrimidine based cannabinoid-1 receptor inverse agonists: synthesis and biological evaluation. Bioorg Med Chem Lett 2009;19(9):2591-4
   PubMed Web of Science ®Google Scholar
• Martin-Martinez M, Marty A, Jourdan M, Combination of molecular modeling, site-directed mutagenesis, and SAR studies to delineate the binding site of pyridopyrimidine antagonists on the human CCK1 receptor. J Med Chem 2005;48(15):4842-50
   PubMed Web of Science ®Google Scholar
• Nakayama K, Kawato H, Watanabe J, MexAB-OprM specific efflux pump inhibitors in pseudomonas aeruginosa. Part 3: Optimization of potency in the pyridopyrimidine series through the application of a pharmacophore model. Bioorg Med Chem Lett 2004;14(2):475-9
   PubMed Web of Science ®Google Scholar
• Meier TI, Yan D, Peery RB, Identification and characterization of an inhibitor specific to bacterial NAD+-dependent DNA ligases. FEBS J 2008;275(21):5258-71
   PubMed Web of Science ®Google Scholar
• Foley M, Tilley L. Quinoline antimalarials: mechanisms of action and resistance and prospects for new agents. Pharmacol Ther 1998;79(1):55-87
   PubMed Web of Science ®Google Scholar
• Ridley RG, Matile H, Jaquet C, Antimalarial activity of the bisquinoline trans-N1,N2-bis (7-chloroquinolin-4-yl)cyclohexane-1,2-diamine: comparison of two stereoisomers and detailed evaluation of the S,S enantiomer, Ro 47-7737. Antimicrob Agents Chemother 1997;41(3):677-86
   PubMed Web of Science ®Google Scholar
• Dascombe MJ, Drew MG, Morris H, Mapping antimalarial pharmacophores as a useful tool for the rapid discovery of drugs effective in vivo: design, construction, characterization, and pharmacology of metaquine. J Med Chem 2005;48(17):5423-36
   PubMed Web of Science ®Google Scholar
• Raynes K. Bisquinoline antimalarials: their role in malaria chemotherapy. Int J Parasitol 1999;29(3):367-79
   PubMed Web of Science ®Google Scholar
• Ciarrocchi G, MacPhee DG, Deady LW, Tilley L. Specific inhibition of the eubacterial DNA ligase by arylamino compounds. Antimicrob Agents Chemother 1999;43(11):2766-72
   PubMed Web of Science ®Google Scholar
• Smith KT, Dawes IW. The preferential inhibition of Bacillus subtilis spore outgrowth by chloroquine. Arch Microbiol 1989;152(3):251-7
   PubMed Web of Science ®Google Scholar
• Srivastava SK, Tripathi RP, Ramachandran R. NAD+-dependent DNA Ligase (Rv3014c) from Mycobacterium tuberculosis. Crystal structure of the adenylation domain and identification of novel inhibitors. J Biol Chem 2005;280(34):30273-81
   PubMed Web of Science ®Google Scholar
• 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(22):7090-101
   PubMed Web of Science ®Google Scholar
• WHO Report on Global Surveillance of Epidemic-prone Infectious Diseases: World Health Organization; 2003
   Google Scholar
• Croft SL, Barrett MP, Urbina JA. Chemotherapy of trypanosomiases and leishmaniasis. Trends Parasitol 2005;21(11):508-12
   PubMed Web of Science ®Google Scholar
• Stuart KD, Schnaufer A, Ernst NL, Panigrahi AK. Complex management: RNA editing in trypanosomes. Trends Biochem Sci 2005;30(2):97-105
   PubMed Web of Science ®Google Scholar
• Worthey EA, Schnaufer A, Mian IS, Comparative analysis of editosome proteins in trypanosomatids. Nucleic Acids Res 2003;31(22):6392-408
   PubMed Web of Science ®Google Scholar
• Panigrahi AK, Ernst NL, Domingo GJ, Compositionally and functionally distinct editosomes in trypanosoma brucei. RNA 2006;12(6):1038-49
   PubMed Web of Science ®Google Scholar
• Carnes J, Trotter JR, Peltan A, RNA editing in trypanosoma brucei requires three different editosomes. Mol Cell Biol 2008;28(1):122-30
   PubMed Web of Science ®Google Scholar
• Blum B, Simpson L. Formation of guide RNA/messenger RNA chimeric molecules in vitro, the initial step of RNA editing, is dependent on an anchor sequence. Proc Natl Acad Sci USA 1992;89(24):11944-8
   PubMed Web of Science ®Google Scholar
• Seiwert SD, Heidmann S, Stuart K. Direct visualization of uridylate deletion in vitro suggests a mechanism for kinetoplastid RNA editing. Cell 1996;84(6):831-41
   PubMed Web of Science ®Google Scholar
• Drozdz M, Palazzo SS, Salavati R, TbMP81 is required for RNA editing in trypanosoma brucei. EMBO J 2002;21(7):1791-9
   PubMed Web of Science ®Google Scholar
• Ho CK, Wang LK, Lima CD, Shuman S. Structure and mechanism of RNA ligase. Structure 2004;12(2):327-39
   PubMed Web of Science ®Google Scholar
• Yin S, Ho CK, Shuman S. Structure-function analysis of T4 RNA ligase 2. J Biol Chem 2003;278(20):17601-8
   PubMed Web of Science ®Google Scholar
• Amaro RE, Swift RV, McCammon JA. Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in trypanosoma brucei. PLoS Neglected Trop Dis 2007; in press
   PubMed Web of Science ®Google Scholar
• Ryan AJ, Gray NM, Lowe PN, Chung CW. Effect of detergent on “promiscuous” inhibitors. J Med Chem 2003;46(16):3448-51
   PubMed Web of Science ®Google Scholar
• Chellappan S, Kiran Kumar Reddy GS, Ali A, Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem Biol Drug Des 2007;69(5):298-313
   PubMed Web of Science ®Google Scholar
• Chellappan S, Kairys V, Fernandes MX, Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease. Proteins 2007;68(2):561-7
   PubMed Web of Science ®Google Scholar
• Schnaufer A. Personal Communication. 2009
   Google Scholar
• Swift RV, Durrant J, Amaro RE, McCammon JA. Toward understanding the conformational dynamics of RNA ligation. Biochemistry 2009;48(4):709-19
   PubMed Web of Science ®Google Scholar