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. 1996 Dec 15;24(24):4882–4889. doi: 10.1093/nar/24.24.4882

Designer DNA-binding drugs: the crystal structure of a meta-hydroxy analogue of Hoechst 33258 bound to d(CGCGAATTCGCG)2.

G R Clark 1, C J Squire 1, E J Gray 1, W Leupin 1, S Neidle 1
PMCID: PMC146347  PMID: 9017011

Abstract

An analogue of the DNA binding compound Hoechst 33258, which has the para hydroxyl group altered to be at the meta position, together with the replacement of one benzimidazole group by pyridylimidazole, has been cocrystallized with the dodecanucleotide sequence d(CGCGAATTCGCG)2. The X-ray structure has been determined at 2.2 A resolution and refined to an R factor of 20.1%. The ligand binds in the minor groove at the sequence 5'-AATTC with the bulky piperazine group extending over the CxG base pair. This binding is stabilised by hydrogen bonding and numerous close van der Waals contacts to the surface of the groove walls. The meta-hydroxyl group was found in two distinct orientations, neither of which participates in direct hydrogen bonds to the exocyclic amino group of a guanine base. The conformation of the drug differs from that found previously in other X-ray structures of Hoechst 33258-DNA complexes. There is significant variation between the minor groove widths in the complexes of Hoechst 33258 and the meta-hydroxyl derivative as a result of these conformational differences. Reasons are discussed for the inability of this derivative to actively recognise guanine.

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Selected References

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  1. Bathini Y., Rao K. E., Shea R. G., Lown J. W. Molecular recognition between ligands and nucleic acids: novel pyridine- and benzoxazole-containing agents related to Hoechst 33258 that exhibit altered DNA sequence specificity deduced from footprinting analysis and spectroscopic studies. Chem Res Toxicol. 1990 May-Jun;3(3):268–280. doi: 10.1021/tx00015a013. [DOI] [PubMed] [Google Scholar]
  2. Beerman T. A., McHugh M. M., Sigmund R., Lown J. W., Rao K. E., Bathini Y. Effects of analogs of the DNA minor groove binder Hoechst 33258 on topoisomerase II and I mediated activities. Biochim Biophys Acta. 1992 May 7;1131(1):53–61. doi: 10.1016/0167-4781(92)90098-k. [DOI] [PubMed] [Google Scholar]
  3. Boykin D. W., Kumar A., Spychala J., Zhou M., Lombardy R. J., Wilson W. D., Dykstra C. C., Jones S. K., Hall J. E., Tidwell R. R. Dicationic diarylfurans as anti-Pneumocystis carinii agents. J Med Chem. 1995 Mar 17;38(6):912–916. doi: 10.1021/jm00006a009. [DOI] [PubMed] [Google Scholar]
  4. Broggini M., Erba E., Ponti M., Ballinari D., Geroni C., Spreafico F., D'Incalci M. Selective DNA interaction of the novel distamycin derivative FCE 24517. Cancer Res. 1991 Jan 1;51(1):199–204. [PubMed] [Google Scholar]
  5. Brown D. G., Sanderson M. R., Skelly J. V., Jenkins T. C., Brown T., Garman E., Stuart D. I., Neidle S. Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding. EMBO J. 1990 Apr;9(4):1329–1334. doi: 10.1002/j.1460-2075.1990.tb08242.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Brünger A. T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 1987 Jan 23;235(4787):458–460. doi: 10.1126/science.235.4787.458. [DOI] [PubMed] [Google Scholar]
  7. Carrondo M. A., Coll M., Aymami J., Wang A. H., van der Marel G. A., van Boom J. H., Rich A. Binding of a Hoechst dye to d(CGCGATATCGCG) and its influence on the conformation of the DNA fragment. Biochemistry. 1989 Sep 19;28(19):7849–7859. doi: 10.1021/bi00445a047. [DOI] [PubMed] [Google Scholar]
  8. Chen A. Y., Yu C., Gatto B., Liu L. F. DNA minor groove-binding ligands: a different class of mammalian DNA topoisomerase I inhibitors. Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):8131–8135. doi: 10.1073/pnas.90.17.8131. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chiang S. Y., Welch J., Rauscher F. J., 3rd, Beerman T. A. Effects of minor groove binding drugs on the interaction of TATA box binding protein and TFIIA with DNA. Biochemistry. 1994 Jun 14;33(23):7033–7040. doi: 10.1021/bi00189a003. [DOI] [PubMed] [Google Scholar]
  10. Coll M., Frederick C. A., Wang A. H., Rich A. A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8385–8389. doi: 10.1073/pnas.84.23.8385. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Coll M., Frederick C. A., Wang A. H., Rich A. A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8385–8389. doi: 10.1073/pnas.84.23.8385. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Cory M., Tidwell R. R., Fairley T. A. Structure and DNA binding activity of analogues of 1,5-bis(4-amidinophenoxy)pentane (pentamidine) J Med Chem. 1992 Feb 7;35(3):431–438. doi: 10.1021/jm00081a003. [DOI] [PubMed] [Google Scholar]
  13. Dervan P. B. Design of sequence-specific DNA-binding molecules. Science. 1986 Apr 25;232(4749):464–471. doi: 10.1126/science.2421408. [DOI] [PubMed] [Google Scholar]
  14. Dorn A., Affolter M., Müller M., Gehring W. J., Leupin W. Distamycin-induced inhibition of homeodomain-DNA complexes. EMBO J. 1992 Jan;11(1):279–286. doi: 10.1002/j.1460-2075.1992.tb05050.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Ebrahimi S. E., Bibby M. C., Fox K. R., Douglas K. T. Synthesis, DNA binding, footprinting and in vitro antitumour studies of a meta-hydroxy analogue of Hoechst 33258. Anticancer Drug Des. 1995 Sep;10(6):463–479. [PubMed] [Google Scholar]
  16. Edwards K. J., Jenkins T. C., Neidle S. Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties. Biochemistry. 1992 Aug 11;31(31):7104–7109. doi: 10.1021/bi00146a011. [DOI] [PubMed] [Google Scholar]
  17. Embrey K. J., Searle M. S., Craik D. J. Interaction of Hoechst 33258 with the minor groove of the A + T-rich DNA duplex d(GGTAATTACC)2 studied in solution by NMR spectroscopy. Eur J Biochem. 1993 Feb 1;211(3):437–447. doi: 10.1111/j.1432-1033.1993.tb17569.x. [DOI] [PubMed] [Google Scholar]
  18. Fede A., Billeter M., Leupin W., Wüthrich K. Determination of the NMR solution structure of the Hoechst 33258-d(GTGGAATTCCAC)2 complex and comparison with the X-ray crystal structure. Structure. 1993 Nov 15;1(3):177–186. doi: 10.1016/0969-2126(93)90019-d. [DOI] [PubMed] [Google Scholar]
  19. Fede A., Labhardt A., Bannwarth W., Leupin W. Dynamics and binding mode of Hoechst 33258 to d(GTGGAATTCCAC)2 in the 1:1 solution complex as determined by two-dimensional 1H NMR. Biochemistry. 1991 Dec 3;30(48):11377–11388. doi: 10.1021/bi00112a004. [DOI] [PubMed] [Google Scholar]
  20. Geierstanger B. H., Jacobsen J. P., Mrksich M., Dervan P. B., Wemmer D. E. Structural and dynamic characterization of the heterodimeric and homodimeric complexes of distamycin and 1-methylimidazole-2-carboxamide-netropsin bound to the minor groove of DNA. Biochemistry. 1994 Mar 15;33(10):3055–3062. doi: 10.1021/bi00176a039. [DOI] [PubMed] [Google Scholar]
  21. Gravatt G. L., Baguley B. C., Wilson W. R., Denny W. A. DNA-directed alkylating agents. 6. Synthesis and antitumor activity of DNA minor groove-targeted aniline mustard analogues of pibenzimol (Hoechst 33258) J Med Chem. 1994 Dec 9;37(25):4338–4345. doi: 10.1021/jm00051a010. [DOI] [PubMed] [Google Scholar]
  22. Henderson D., Hurley L. H. Molecular struggle for transcriptional control. Nat Med. 1995 Jun;1(6):525–527. doi: 10.1038/nm0695-525. [DOI] [PubMed] [Google Scholar]
  23. Jenkins T. C., Lane A. N., Neidle S., Brown D. G. NMR and molecular modeling studies of the interaction of berenil and pentamidine with d(CGCAAATTTGCG)2. Eur J Biochem. 1993 May 1;213(3):1175–1184. doi: 10.1111/j.1432-1033.1993.tb17868.x. [DOI] [PubMed] [Google Scholar]
  24. Kopka M. L., Yoon C., Goodsell D., Pjura P., Dickerson R. E. Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G. J Mol Biol. 1985 Jun 25;183(4):553–563. doi: 10.1016/0022-2836(85)90171-8. [DOI] [PubMed] [Google Scholar]
  25. Kumar S., Yadagiri B., Zimmermann J., Pon R. T., Lown J. W. Sequence specific molecular recognition and binding by a GC recognizing Hoechst 33258 analogue to the decadeoxyribonucleotide d-[CATGGCCATG]2: structural and dynamic aspects deduced from high field 1H-NMR studies. J Biomol Struct Dyn. 1990 Oct;8(2):331–357. doi: 10.1080/07391102.1990.10507809. [DOI] [PubMed] [Google Scholar]
  26. Lavery R., Sklenar H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J Biomol Struct Dyn. 1988 Aug;6(1):63–91. doi: 10.1080/07391102.1988.10506483. [DOI] [PubMed] [Google Scholar]
  27. Mrksich M., Wade W. S., Dwyer T. J., Geierstanger B. H., Wemmer D. E., Dervan P. B. Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin. Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7586–7590. doi: 10.1073/pnas.89.16.7586. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Neidle S. Minor-groove width and accessibility in B-DNA drug and protein complexes. FEBS Lett. 1992 Feb 17;298(1):97–99. doi: 10.1016/0014-5793(92)80030-k. [DOI] [PubMed] [Google Scholar]
  29. Nunn C. M., Jenkins T. C., Neidle S. Crystal structure of d(CGCGAATTCGCG) complexed with propamidine, a short-chain homologue of the drug pentamidine. Biochemistry. 1993 Dec 21;32(50):13838–13843. doi: 10.1021/bi00213a012. [DOI] [PubMed] [Google Scholar]
  30. Nunn C. M., Neidle S. Sequence-dependent drug binding to the minor groove of DNA: crystal structure of the DNA dodecamer d(CGCAAATTTGCG)2 complexed with propamidine. J Med Chem. 1995 Jun 23;38(13):2317–2325. doi: 10.1021/jm00013a008. [DOI] [PubMed] [Google Scholar]
  31. Parkinson J. A., Ebrahimi S. E., McKie J. H., Douglas K. T. Molecular design of DNA-directed ligands with specific interactions: solution NMR studies of the interaction of a m-hydroxy analogue of Hoechst 33258 with d(CGCGAATTCGCG)2. Biochemistry. 1994 Jul 19;33(28):8442–8452. doi: 10.1021/bi00194a008. [DOI] [PubMed] [Google Scholar]
  32. Pjura P. E., Grzeskowiak K., Dickerson R. E. Binding of Hoechst 33258 to the minor groove of B-DNA. J Mol Biol. 1987 Sep 20;197(2):257–271. doi: 10.1016/0022-2836(87)90123-9. [DOI] [PubMed] [Google Scholar]
  33. Prakash A. S., Valu K. K., Wakelin L. P., Woodgate P. D., Denny W. A. Synthesis and anti-tumour activity of the spatially-separated mustard bis-N,N'-[3-(N-(2-chloroethyl)-N-ethyl)amino-5-[N,N-dimethylamino)methy l)-aminophenyl]-1,4-benzenedicarboxamide, which alkylates DNA exclusively at adenines in the minor groove. Anticancer Drug Des. 1991 Jul;6(3):195–206. [PubMed] [Google Scholar]
  34. Quintana J. R., Lipanov A. A., Dickerson R. E. Low-temperature crystallographic analyses of the binding of Hoechst 33258 to the double-helical DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G. Biochemistry. 1991 Oct 22;30(42):10294–10306. doi: 10.1021/bi00106a030. [DOI] [PubMed] [Google Scholar]
  35. Rao K. E., Shea R. G., Yadagiri B., Lown J. W. Molecular recognition between oligopeptides and nucleic acids: DNA sequence specificity and binding properties of thiazole-lexitropsins incorporating the concepts of base site acceptance and avoidance. Anticancer Drug Des. 1990 Feb;5(1):3–20. [PubMed] [Google Scholar]
  36. Searle M. S., Embrey K. J. Sequence-specific interaction of Hoechst 33258 with the minor groove of an adenine-tract DNA duplex studied in solution by 1H NMR spectroscopy. Nucleic Acids Res. 1990 Jul 11;18(13):3753–3762. doi: 10.1093/nar/18.13.3753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Spink N., Brown D. G., Skelly J. V., Neidle S. Sequence-dependent effects in drug-DNA interaction: the crystal structure of Hoechst 33258 bound to the d(CGCAAATTTGCG)2 duplex. Nucleic Acids Res. 1994 May 11;22(9):1607–1612. doi: 10.1093/nar/22.9.1607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Sriram M., van der Marel G. A., Roelen H. L., van Boom J. H., Wang A. H. Conformation of B-DNA containing O6-ethyl-G-C base pairs stabilized by minor groove binding drugs: molecular structure of d(CGC[e6G]AATTCGCG complexed with Hoechst 33258 or Hoechst 33342. EMBO J. 1992 Jan;11(1):225–232. doi: 10.1002/j.1460-2075.1992.tb05045.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Tabernero L., Verdaguer N., Coll M., Fita I., van der Marel G. A., van Boom J. H., Rich A., Aymamí J. Molecular structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor groove binding drug netropsin. Biochemistry. 1993 Aug 24;32(33):8403–8410. doi: 10.1021/bi00084a004. [DOI] [PubMed] [Google Scholar]
  40. Teng M. K., Usman N., Frederick C. A., Wang A. H. The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG). Nucleic Acids Res. 1988 Mar 25;16(6):2671–2690. doi: 10.1093/nar/16.6.2671. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Tidwell R. R., Jones S. K., Geratz J. D., Ohemeng K. A., Cory M., Hall J. E. Analogues of 1,5-bis(4-amidinophenoxy)pentane (pentamidine) in the treatment of experimental Pneumocystis carinii pneumonia. J Med Chem. 1990 Apr;33(4):1252–1257. doi: 10.1021/jm00166a026. [DOI] [PubMed] [Google Scholar]
  42. Vega M. C., García Sáez I., Aymamí J., Eritja R., Van der Marel G. A., Van Boom J. H., Rich A., Coll M. Three-dimensional crystal structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor-groove-binding drug Hoechst 33258. Eur J Biochem. 1994 Jun 15;222(3):721–726. doi: 10.1111/j.1432-1033.1994.tb18917.x. [DOI] [PubMed] [Google Scholar]
  43. Welch J. J., Rauscher F. J., 3rd, Beerman T. A. Targeting DNA-binding drugs to sequence-specific transcription factor.DNA complexes. Differential effects of intercalating and minor groove binding drugs. J Biol Chem. 1994 Dec 9;269(49):31051–31058. [PubMed] [Google Scholar]
  44. Westhof E. Re-refinement of the B-dodecamer d(CGCGAATTCGCG) with a comparative analysis of the solvent in it and in the Z-hexamer d(5BrCG5BrCG5BrCG). J Biomol Struct Dyn. 1987 Dec;5(3):581–600. doi: 10.1080/07391102.1987.10506414. [DOI] [PubMed] [Google Scholar]
  45. Wood A. A., Nunn C. M., Czarny A., Boykin D. W., Neidle S. Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2. Nucleic Acids Res. 1995 Sep 25;23(18):3678–3684. doi: 10.1093/nar/23.18.3678. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Zimmer C., Wähnert U. Nonintercalating DNA-binding ligands: specificity of the interaction and their use as tools in biophysical, biochemical and biological investigations of the genetic material. Prog Biophys Mol Biol. 1986;47(1):31–112. doi: 10.1016/0079-6107(86)90005-2. [DOI] [PubMed] [Google Scholar]

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