Minor groove binding compounds that jump a GC base pair and bind to adjacent AT base pair sites

Biochemistry

Volumn 48, Issue 7, 2009, Pages 1573-1583

  Rahimian, Maryam ^a   Kumar, Arvind ^a   Say, Martial ^a   Bakunov, Stanislav A ^b   Boykin, David W ^a   Tidwell, Richard R ^b   Wilson, W David ^a  

^a GEORGIA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BASE PAIRS; BENZIMIDAZOLE DERIVATIVES; BINDING AFFINITIES; BINDING CONSTANTS; COMPOUND STRUCTURES; ISOTHERMAL TITRATION CALORIMETRIES; MINOR GROOVES; MODEL SYSTEMS; SOLUTION PROPERTIES; STRONG BINDINGS; SURFACE PLASMONS; SYNTHETIC COMPOUNDS; TIGHT BINDINGS;

BINDING ENERGY; DERIVATIVES; DNA; DNA SEQUENCES; GENES; ION EXCHANGE MEMBRANES; NUCLEIC ACIDS; SURFACE PLASMON RESONANCE;

BINDING SITES;

1,5 BIS(4' AMIDINO 1,1' BIPHENYL 4 YLOXY) 3 OXAPENTANE DIHYDROCHLORIDE; 1,5 BIS(4' AMIDINO 1,1' BIPHENYL 4 YLOXY)PENTANE DIHYDROCHLORIDE; 1,5 BIS(7 AMIDINO 2 NAPHTHALENOXY) 3 OXAPENTANE; 1,5 BIS(7 AMIDINO 2 NAPHTHALENOXY) 3 OXAPENTANE DIHYDROCHLORIDE; 1,5 BIS(7 AMIDINONAPHTHALEN 2 YLOXY)PENTANE DIHYDROCHLORIDE; 2 [4 [3 (4 AMIDINOPHENOXY)PROPOXY]PHENYL] 5 (4 AMIDINOPHENYL)FURAN DIHYDROCHLORIDE; ALANINE; ANTIPARASITIC AGENT; DB 1701; DB 1703; DB 1743; DB 1744; DB 1791; DNA BASE; KINETOPLAST DNA; THREONINE; UNCLASSIFIED DRUG; NUCLEIC ACID;

ARTICLE; CHEMICAL STRUCTURE; DNA SEQUENCE; DRUG DESIGN; DRUG DNA BINDING; DRUG SYNTHESIS; ENTHALPY; GAS CHROMATOGRAPHY; ISOTHERMAL TITRATION CALORIMETRY; MOLECULAR RECOGNITION; NONHUMAN; PARASITE; PRIORITY JOURNAL; PROTEIN STRUCTURE; SURFACE PLASMON RESONANCE; BASE PAIRING; BINDING SITE; CALORIMETRY; CIRCULAR DICHROISM; MASS SPECTROMETRY; METABOLISM; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

BASE PAIRING; BINDING SITES; CALORIMETRY; CIRCULAR DICHROISM; MAGNETIC RESONANCE SPECTROSCOPY; MASS SPECTROMETRY; NUCLEIC ACIDS; SURFACE PLASMON RESONANCE;

EID: 61749104117     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi801944g     Document Type: Article

References (45)

1. Wilson, W. D., Nguyen, B., Tanious, F. A., Mathis, A., Hall, J. E., Stephens, C. E., and Boykin, D. W. (2005) Dications that target the DNA minor groove: compound design and preparation, DNA interactions, cellular distribution and biological activity. Curr. Med. Chem. Anti-Cancer Agents 5, 389-408.
2. Mathis, A. M., Holman, J. L., Sturk, L. M., Ismail, M. A., Boykin, D. W., Tidwell, R. R., and Hall, J. E. (2006) Accumulation and intracellular distribution of antitrypanosomal diamidine compounds DB75 and DB820 in African trypanosomes. Antimicrob. Agents Chemother. 50, 2185-2191.
3. Mathis, A. M., Bridges, A. S., Ismail, M. A., Kumar, A., Francesconi, I., Anbazhagan, M., Hu, Q., Tanious, F. A., Wenzler, T., Saulter, J., Wilson, W. D., Brun, R., Boykin, D. W., Tidwell, R. R., and Hall, J. E. (2007) Diphenyl furans and aza analogs: effects of structural modification on in vitro activity, DNA binding, and accumulation and distribution in trypanosomes. Antimicrob. Agents Chemother. 51, 2801-2810.
4. Tidwell, R. R., and Boykin, D. W. (2003) Dicationic DNA minorgroove binders as antimicrobial agents. In DNA and RNA Binders: From Small Molecules to Drugs (Demeunynck, M., Bailly, C., and Wilson, W. D., Eds.), pp 414-460, Wiley-VCH, Weinheim, Germany.
5. Wilson, W. D., Tanious, F. A., Mathis, A., Tevis, D., Hall, J. E., and Boykin, D. W. (2008) Antiparasitic compounds that target DNA. Biochimie 90, 999-1014.
6. Thuita, J. K., Karanja, S. M., Wenzler, T., Mdachi, R. E., Ngotho, J. M., Kagira, J. M., Tidwell, R., and Brun, R. (2008) Efficacy of the diamidine DB75 and its prodrug DB289, against murine models of human African trypanosomiasis, Acta Trop. 108, 6-10.
7. Bray, P. G., Barrett, M. P., Ward, S. A., and de Koning, H. P. (2003) Pentamidine uptake and resistance in pathogenic protozoa: past, present and future. Trends Parasitol. 19, 232-239.
8. Bouteille, B., Oukem, O., Bisser, S., and Dumas, M. (2003) Treatment perspectives for human African trypanosomiasis. Fundam. Clin. Pharmacol. 17, 171-181.
9. Rosypal, A. C., Werbovetz, K. A., Salem, M., Stephens, C. E., Kumar, A., Boykin, D. W., Hall, J. E., and Tidwell, R. R. (2008) Inhibition by dications of in vitro growth of Leishmania major and Leishmania tropica: causative agents of old world cutaneous leishmaniasis. J. Parasitol. 94, 743-749.
10. Peixoto, P., Liu, Y., Depauw, S., Hildebrand, M. P., Boykin, D. W., Bailly, C., Wilson, W. D., and David-Cordonnier, M. H. (2008) Direct inhibition of the DNA-binding activity of POU transcription factors Pit-1 and Brn-3 by selective binding of a phenyl-furan-benzimidazole dication. Nucleic Acids Res. 36, 3341-3353.
11. Dervan, P. B., Doss, R. M., and Marques, M. A. (2005) Programmable DNA binding oligomers for control of transcription. Curr. Med. Chem.: Anti-Cancer Agents 5, 373-387.
12. Shapiro, T. A., and Englund, P. T. (1995) The structure and replication of kinetoplast DNA. Annu. Rev. Microbiol. 49, 117-143.
13. Shlomai, J. (2004) The structure and replication of kinetoplast DNA. Curr. Mol. Med. 4, 623-647.
14. Gavathiotis, E., Sharman, G. J., and Searle, M. S. (2000) Sequencedependent variation in DNA minor groove width dictates orientational preference of Hoechst 33258 in A-tract recognition: solution NMR structure of the 2:1 complex with d(CTTTTGCAAAAG)(2). Nucleic Acids Res. 28, 728-735.
15. Rahimian, M., Miao, Y., and Wilson, W. D. (2008) Influence of DNA structure on adjacent site cooperative binding. J. Phys. Chem. B 112, 8770-8778.
16. Thomas, S., Martinez, L. L. I. T., Westenberger, S. J., and Sturm, N. R. (2007) A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing. BMC Genomics 8, 133.
17. Tidwell, R. R., Geratz, J. D., Dann, O., Volz, G., Zeh, D., and Loewe, H. (1978) Diarylamidine derivatives with one or both of the aryl moieties consisting of an indole or indole-like ring. Inhibitors of arginine-specific esteroproteases. J. Med. Chem. 21, 613-623.
18. Cantor, C. R., Warshaw, M. M., and Shapiro, H. (1970) Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers 9, 1059-1077.
19. Nguyen, B., Tanious, F. A., and Wilson, W. D. (2007) Biosensorsurface plasmon resonance: Quantitative analysis of small moleculenucleic acid interactions. Methods 42, 150-161.
20. Davis, T. M., and Wilson, W. D. (2001) Surface plasmon resonance biosensor analysis of RNA-small molecule interactions. Methods Enzymol. 340, 22-51.
21. Haq, I., Ladbury, J. E., Chowdhry, B. Z., Jenkins, T. C., and Chaires, J. B. (1997) Specific binding of hoechst 33258 to the d(CGCAAATTTGCG)2 duplex: calorimetric and spectroscopic studies. J. Mol. Biol. 271, 244-257.
22. Kiser, J. R., Monk, R. W., Smalls, R. L., and Petty, J. T. (2005) Hydration changes in the association of Hoechst 33258 with DNA. Biochemistry 44, 16988-16997.
23. Kapinos, L. E., Bin, Song, and Sigel, H. (1999) Acid-Base and Metal-Ion-Coordinating Properties of Benzimidazole and Derivatives (=1,3-Dideazapurines) in Aqueous Solution: Interrelation between Complex Stability and Ligand Basicity. Chem.-Eur. J. 5 (9), 1794-1802.
24. Wilson, W. D., Tanious, F. A., Fernandez-Saiz, M., and Rigl, C. T. (1997) Evaluation of drug-nucleic acid interactions by thermal melting curves. Methods Mol. Biol. (Totowa, NJ) 90, 219-240.
25. Lyng, R., Rodger, A., and Norden, B. (1992) The CD of ligand-DNA systems. 2. Poly(dA-dT) B-DNA. Biopolymers 32, 1201-1214.
26. Rodger, A., and Nordén, B. (1997) Circular Dichroism and Linear Dichroism, Oxford University Press, New York.
27. Nguyen, B., Tardy, C., Bailly, C., Colson, P., Houssier, C., Kumar, A., Boykin, D. W., and Wilson, W. D. (2002) Influence of compound structure on affinity, sequence selectivity, and mode of binding to DNA for unfused aromatic dications related to furamidine. Biopolymers 63, 281-297.
28. Liu, Y., Kumar, A., Boykin, D. W., and Wilson, W. D. (2007) Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove. Biophys. Chem. 131, 1-14.
29. Myszka, D. G. (2000) Kinetic, equilibrium, and thermodynamic analysis of macromolecular interactions with BIACORE. Methods Enzymol. 323, 325-340.
30. Day, Y. S., Baird, C. L., Rich, R. L., and Myszka, D. G. (2002) Direct comparison of binding equilibrium, thermodynamic, and rate constants determined by surface- and solution-based biophysical methods. Protein Sci. 11, 1017-1025.
31. Mazur, S., Tanious, F. A., Ding, D., Kumar, A., Boykin, D. W., Simpson, I. J., Neidle, S., and Wilson, W. D. (2000) A thermodynamic and structural analysis of DNA minor-groove complex formation. J. Mol. Biol. 300, 321-337.
32. Liu, Y., Kumar, A., Boykin, D. W., and Wilson, W. D. (2007) Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove. Biophys. Chem. 131, 1-14.
33. Ladbury, J. E., and Chowdhry, B. Z. (1996) Sensing the heat: the application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions. Chem. Biol. 3, 791-801.
34. Ladbury, J. E. (2004) Application of isothermal titration calorimetry in the biological sciences: things are heating up. Biotechniques 37, 885-887.
35. Haq, I. (2002) Thermodynamics of drug-DNA interactions. Arch. Biochem. Biophys. 403, 1-15.
36. Freyer, M. W., Buscaglia, R., Hollingsworth, A., Ramos, J., Blynn, M., Pratt, R., Wilson, W. D., and Lewis, E. A. (2007) Break in the heat capacity change at 303 K for complex binding of netropsin to AATT containing hairpin DNA constructs. Biophys. J. 92, 2516-2522.
37. Freyer, M. W., Buscaglia, R., Nguyen, B., Wilson, W. D., and Lewis, E. A. (2006) Binding of netropsin and 4,6-diamidino-2-phenylindole to an A2T2 DNA hairpin: a comparison of biophysical techniques. Anal. Biochem. 355, 259-266.
38. Freyer, M. W., Buscaglia, R., Cashman, D., Hyslop, S., Wilson, W. D., Chaires, J. B., and Lewis, E. A. (2006) Binding of netropsin to several DNA constructs: Evidence for at least two different 1:1 complexes formed from an -AATT-containing ds-DNA construct and a single minor groove binding ligand, Biophys. Chem. 126, 186-196.
39. Degtyareva, N. N., Fresia, M. J., and Petty, J. T. (2007) DNA Conformational Effects on the Interaction of Netropsin with A-tract Sequences. Biochemistry 46, 15136-15143.
40. Dervan, P. B. (1986) Design of sequence-specific DNA-binding molecules. Science 232, 464-471.
41. Lee, M., Pon, R. T., Krowicki, K., and Lown, J. W. (1988) Structural and dynamic aspects of the sequence specific binding of netropsin and its bis-imidazole analogue on the decadeoxyri-bonucleotide d-[CGCAATTGCG]2. J. Biomol. Struct. Dyn. 5, 939-949.
42. Lee, M., Rhodes, A. L., Wyatt, M. D., D'Incalci, M., Forrow, S., and Hartley, J. A. (1993) In vitro cytotoxicity of GC sequence directed alkylating agents related to distamycin. J. Med. Chem. 36, 863-870.
43. Sharma, S. K., Morrissey, A. T., Miller, G. G., Gmeiner, W. H., and Lown, J. W. (2001) Design, synthesis, and intracellular localization of a fluorescently labeled DNA binding polyamide related to the antibiotic distamycin. Bioorg. Med. Chem. Lett. 11, 769-772.
44. Laughton, C. A., Tanious, F., Nunn, C. M., Boykin, D. W., Wilson, W. D., and Neidle, S. (1996) A crystallographic and spectroscopic study of the complex between d(CGCGAATTCGCG)2 and 2,5-bis(4-guanylphenyl)furan, an analogue of berenil. Structural origins of enhanced DNA-binding affinity. Biochemistry 35, 5655-5661.
45. Wang, L., Kumar, A., Boykin, D. W, Bailly, C., and Wilson, W. D. (2002) Comparative thermodynamics for monomer and dimer sequence-dependent binding of a heterocyclic dication in the DNA minor groove. J. Mol. Biol. 317, 361-374.