Molecular Recognition of Human Telomeric DNA by Phenanthroline-Based G-Quadruplex Ligands


G-quadruplexes (G4) are non-canonical DNA structures assumed by guanine rich sequences. G4 are stabilized by the presence of cations and are characterized by a high degree of structural polymorphism with different patterns of groove, loop arrangement, strand orientations and stoichiometry. G-rich sequences are over-represented in the promoter regions of many oncogenes as well as at human telomeres, d(TTAGGG) repeats, ranging in size from 3 to 15 kb, involved in protecting chromosomal ends. A specialized enzyme, called telomerase, provides a telomere maintenance mechanism by elongating the end of the G-strand and it is activated in the majority of cancer cells. Therefore there are two general strategies of telomerase targeting in cancer treatment. One is a direct targeting of telomerase to cause its inhibition; the other one is the use of G4 stabilizers which block telomerase access to telomere, thus causing an indirect enzyme inhibition. Here, we evaluated the molecular recognition of some phenanthroline-based ligands against four different experimental models of the human telomeric sequence d[AG3(T2AG3)3] by means of docking simulations. Our theoretical analysis was able to reproduce the experimental affinity measurements, with a linear squared correlation factor r2 equal to 0.719 among all the studied models. These findings highlighted the importance to consider the polymorphism of the DNA G4. Interestingly, this correlation resulted always improved with respect to that of the single folds, with the exception of the parallel structure, thus suggesting a key role of this G4 conformation in the interaction network of the tested binders. Moreover, we identified the moieties of the phenanthroline scaffold directly involved in the complex formation. This allowed to rationalize the improved binding affinity always associated with a bis-phenanthroline system and to explain why a phenanthroline substituted with a pyridine ring is favored with respect to the pyrimidine one.

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A. Artese, L. Parrotta, S. Alcaro, F. Ortuso, G. Costa and C. Sissi, "Molecular Recognition of Human Telomeric DNA by Phenanthroline-Based G-Quadruplex Ligands," Open Journal of Medicinal Chemistry, Vol. 3 No. 2, 2013, pp. 41-49. doi: 10.4236/ojmc.2013.32006.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] E. H. Blackburn, “Switching and Signaling at the Telomere,” Cell, Vol. 106, No. 6, 2001, pp. 661-673. doi:10.1016/S0092-8674(01)00492-5
[2] E. H. Blackburn and J. G. Gall, “A Tandemly Repeated Sequence at the Termini of Extrachromosomal Ribosomal RNA Genes in Tetrahymena,” Journal of Molecular Biology, Vol. 120, No. 1, 1978, pp. 33-53. doi:10.1016/0022-2836(78)90294-2
[3] R. C. Allshire, M. Dempster and N. D. Hastie, “Human Telomeres Contain at Least 3 Types of G-Rich Repeat Distributed Non-Randomly,” Nucleic Acids Research, Vol. 17, No. 12, 1989, pp. 4611-4627. doi:10.1093/nar/17.12.4611
[4] T. de Lange, L. Shiue, R. M. Myers, D. R. Cox, S. L. Naylor, et al., “Structure and Variability of Human Chromosome Ends,” Molecular and Cellular Biology, Vol. 10, No. 2, 1990, pp. 518-527. doi:10.1128/MCB.10.2.518
[5] R. K. Moyzis, J. M. Buckingham, L. S. Cram, M. Dani, L. L. Deaven, et al., “A Highly Conserved Repetitive DNA Sequence, (TTAGGG)n, Present at the Telomeres of Human Chromosomes,” Proceedings of the National Academy of Sciences of the United States of America, Vol. 85, No. 18, 1988, pp. 6622-6626. doi:10.1073/pnas.85.18.6622
[6] Y. Xu, “Chemistry in Human Telomere Biology: Structure, Function and Targeting of Telomere DNA/RNA,” Chemical Society Reviews, Vol. 40, No. 5, 2011, pp. 2719-2740. doi:10.1039/C0CS00134A
[7] H. Riethman, “Human Telomere Structure and Biology,” Annual Review of Genomics and Human Genetics, Vol. 9, 2008, pp. 1-19. doi:10.1146/annurev.genom.8.021506.172017
[8] C. B. Harley, A.B. Futcher and C. W. Greider, “Telomeres Shorten during Ageing of Human Fibroblasts,” Nature, Vol. 345, No. 6274, 1990, pp. 458-460. doi:10.1038/345458a0
[9] R. C. Allsopp, H. Vaziri, C. Patterson, S. Goldstein, E. V. Younglai, et al., “Telomere Length Predicts Replicative Capacity of Human Fibroblasts,” Proceedings of the National Academy of Sciences of the United States of America, Vol. 89, No. 21, 1992, pp. 10114-10118. doi:10.1073/pnas.89.21.10114
[10] J. A. Thomson, J. Itskovitz-Eldor, S. S. Shapiro, M. A. Waknitz, J. J. Swiergiel, et al., “Embryonic Stem Cell Lines Derived from Human Blastocysts,” Science, Vol. 282, No. 5391, 1998, pp. 1145-1147. doi:10.1126/science.282.5391.1145
[11] N. W. Kim, M. A. Piatyszek, K. R. Prowse, C. B. Harley, M. D. West, et al., “Specific Association of Human Telomerase Activity with Immortal Cells and Cancer,” Science, Vol. 266, No. 5193, 1994, pp. 2011-2015. doi:10.1126/science.7605428
[12] A. Ambrus, D. Chen, J. X. Dai, R. A. Jones and D. Z. Yang, “Solution Structure of the Biologically Relevant g-Quadruplex Element in the Human c-MYC Promoter. Implications for G-Quadruplex Stabilization,” Biochemistry, Vol. 44, No. 6, 2005, pp. 2048-2058. doi:10.1021/bi048242p
[13] S. T. Hsu, P. Varnai, A. Bugaut, A. P. Reszka, S. Neidle, et al., ”A G-Rich Sequence within the c-Kit Oncogene Promoter Forms a Parallel G-Quadruplex Having Asymmetric G-Tetrad Dynamics,” Journal of the American Chemical Society, Vol. 131, No. 37, 2009, pp. 13399-13409. doi:10.1021/ja904007p
[14] J. Dai, D. Chen, R. A. Jones, L. H. Hurley and D. Yang, “NMR Solution Structure of the Major G-Quadruplex Structure Formed in the Human BCL2 Promoter Region,” Nucleic Acids Research, Vol. 34, No. 18, 2006, pp. 5133-5144. doi:10.1093/nar/gkl610
[15] D. Y. Sun, K. X. Guo, J. J. Rusche and L. H. Hurley, “Facilitation of a Structural Transition in the Polypurine/ Polypyrimidine Tract within the Proximal Promoter Region of the Human VEGF Gene by the Presence of Potassium and G-Quadruplex-Interactive Agents,” Nucleic Acids Research, Vol. 33, No. 18, 2005, pp. 6070-6080. doi:10.1093/nar/gki917
[16] R. De Armond, S. Wood, D. Y. Sun, L. H. Hurley and S. W. Ebbinghaus, “Evidence for the Presence of a Guanine Quadruplex Forming Region within a Polypurine Tract of the Hypoxia Inducible Factor 1 Alpha Promoter,” Biochemistry, Vol. 44, No. 49, 2005, pp. 16341-16350. doi:10.1021/bi051618u
[17] G. Laughlan, A. I. Murchie, D. G. Norman, M. H. Moore, P. C. Moody, et al., “The High Resolution Crystal Structure of a Parallel-Stranded Guanine Tetraplex,” Science, Vol. 265, No. 5171, 1994, pp. 520-524. doi:10.1126/science.8036494
[18] K. Phillips, Z. Dauter, A. I. Murchie, D. M. Lilley and B. Luisi, “The Crystal Structure of a Parallel Stranded Guanine Tetraplex at 0.95Å Resolution,” Journal of molecular biology, Vol. 273, No. 1, 1997, pp. 171-182. doi:10.1006/jmbi.1997.1292
[19] M. Adrian, B. Heddi and A. T. Phan, “NMR Spectroscopy of G-Quadruplexes,” Methods, Vol. 57, No. 1, 2012, pp. 11-24. doi:10.1016/j.ymeth.2012.05.003
[20] Y. Wang and D. J. Patel, “Solution Structure of the Human Telomeric Repeat d[AG3(T2AG3)3] G-tetraplex,” Structure, Vol. 1, No. 4, 1993, pp. 263-282. doi:10.1016/0969-2126(93)90015-9
[21] G. N. Parkinson, M. P. H. Lee and S. Neidle, “Crystal Structure of Parallel Quadruplexes from Human Telomeric DNA,” Nature, Vol. 417, No. 6891, 2002, pp. 876-880. doi:10.1038/nature755
[22] K. N. Luu, A. T. Phan, V. Kuryavyi, L. Lacroix and D. J. Patel, “Structure of the Human Telomere in K+ Solution: an Intramolecular (3+1) G-Quadruplex Scaffold,” Journal of the American Chemical Society, Vol. 128, No. 30, 2006, pp. 9963-9970. doi:10.1021/ja062791w
[23] J. Dai, C. Punchihewa, A. Ambrus, D. Chen, R. A. Jones, et al., “Structure of the Intramolecular Human Telomeric G-Quadruplex in Potassium Solution: A Novel Adenine Triple Formation,” Nucleic Acids Research, Vol. 35, No. 7, 2007, pp. 2440-2450. doi:10.1093/nar/gkm009
[24] A. T. Phan, V. Kuryavyi, K. N. Luu and D. J. Patel “Structure of Two Intramolecular G-Quadruplexes Formed by Natural Human Telomere Sequences in K+ Solution,” Nucleic Acids Research, Vol. 35, No. 19, 2007, 6517-6525. doi:10.1093/nar/gkm706
[25] J. Dai, M. Carver, C. Punchihewa, R. A. Jones and D. Yang, “Structure of the Hybrid-2 Type Intramolecular Human Telomeric G-Quadruplex in K+ Solution: Insights into Structure Polymorphism of the Human Telomeric Sequence,” Nucleic Acids Research, Vol. 35, No. 15, 2007, pp. 4927-4940. doi:10.1093/nar/gkm522
[26] D. Monchaud and M. P. Teulade-Fichou, “A Hitchhiker’s Guide to G-Quadruplex Ligands,” Organic & Biomolecular Chemistry, Vol. 6, No. 4, 2008, pp. 627-636. doi:10.1039/B714772B
[27] S. Neidle, “Human Telomeric G-Quadruplex: The Current Status of Telomeric G-Quadruplexes as Therapeutic Targets in Human Cancer,” The FEBS Journal, Vol. 277, No. 5, 2010, pp. 1118-1125. doi:10.1111/j.1742-4658.2009.07463.x
[28] M. Ruden and N. Puri, “Novel Anticancer Therapeutics Targeting Telomerase,” Cancer Treatment Reviews, Vol. 39, No. 5, 2013, pp. 444-456. doi:10.1016/j.ctrv.2012.06.007
[29] A. De Cian, L. Lacroix, C. Dourre, N. Temime-Smaali, C. Trentesaux, et al., “Targeting Telomeres and Telomerase,” Biochimie, Vol. 90, No. 1, 2008, pp. 131-155. doi:10.1016/j.biochi.2007.07.011
[30] F. Doria, M. Nadai, M. Folini, M. Di Antonio, L. Germani, et al., “Hybrid Ligand-Alkylating Agents Targeting Telomeric G-Quadruplex Structures,” Organic & Biomolecular Chemistry, Vol. 10, No. 14, 2012, pp. 2798- 2806. doi:10.1039/C2OB06816H
[31] R. Rodriguez, S. Müller, J. A. Yeoman, C. Trentesaux, J. F. Riou, et al., “A Novel Small Molecule That Alters Shelterin Integrity and Triggers a DNA-Damage Response at Telomeres,” Journal of the American Chemical Society, Vol. 130, No. 47, 2008, pp. 15758-15759. doi:10.1021/ja805615w
[32] A. De Cian, E. DeLemos, J. L. Mergny, M. P. Teulade-Fichou and D. Monchaud “Highly Efficient G-Quadruplex Recognition by Bisquinolinium Compounds,” Journal of the American Chemical Society, Vol. 129, No. 7, 2007, pp. 1856-1857. doi:10.1021/ja067352b
[33] R. Halder, J. F. Riou, M. P. Teulade-Fichou, T. Frickey and J. Hartig “Bisquinolinium Compounds Induce Quadruplex-Specific Transcriptome Changes in HeLa S3 Cell Lines,” BMC Research Notes, Vol. 5, 2012, 138. doi:10.1186/1756-0500-5-138
[34] S. Müller, S. Kumari, R. Rodriguez and S. Balasubramanian, “Small-Molecule-Mediated G-Quadruplex Isolation from Human Cells,” Nature Chemistry, Vol. 2, No. 12, 2010, pp. 1095-1098. doi:10.1038/nchem.842
[35] R. Rodriguez, K. M. Miller, J. V. Forment, C. R. Bradshaw, M. Nikan, et al., ”Small-Molecule-Induced DNA Damage Identifies Alternative DNA Structures in Human Genes,” Nature chemical biology, Vol. 8, No. 3, pp. 301-310. doi:10.1038/nchembio.780
[36] J. E. Reed, A. J. White, S. Neidle and R. Vilar, “Effect of Metal Coordination on the Interaction of Substituted Phenanthroline and Pyridine Ligands with Quadruplex DNA,” Dalton Transactions, No. 14, 2009, pp. 2558-2568. doi:10.1039/B820086F
[37] J. E. Reed, A. A. Arnal, S. Neidle and R. Vilar, “Stabilization of G-Quadruplex DNA and Inhibition of Telomerase Activity by Square-Planar Nickel(II) Complexes,” Journal of the American Chemical Society, Vol. 128, No. 18, 2006, pp. 5992-5993. doi:10.1021/ja058509n
[38] D. Monchaud, P. Yang, L. Lacroix, M. P. Teulade-Fichou and J. L. Mergny, “A Metal-Mediated Conformational Switch Controls G-Quadruplex Binding Affinity,” Angewandte Chemie, Vol. 120, No. 26, 2008, pp. 4858-4861. doi:10.1002/ange.200800468
[39] C. Musetti, L. Lucatello, S. Bianco, A. P. Krapcho, S. A. Cadamuro, et al., “Metal Ion-Mediated Assembly of Effective Phenanthroline-Based G-Quadruplex Ligands,” Dalton Transactions, No. 19, 2009, pp. 3657-3660. doi:10.1039/B904630P
[40] C. Musetti, A. P. Krapcho, M. Palumbo and C. Sissi, “Effect of G-Quadruplex Polymorphism on the Recognition of Telomeric DNA by a Metal Complex,” Plos One, Vol. 8, No. 3, 2013. doi:10.1371/journal.pone.0058529
[41] S. Bianco, C. Musetti, A. Waldeck, S. Sparapani, J. D. Seitz, et al., “Bisphenanthroline Derivatives as Suitable Scaffolds for Effective G-Quadruplex Recognition,” Dalton Transactions, Vol. 39, No. 25, 2010, pp. 5833-5841. doi:10.1039/C0DT00038H
[42] Maestro Graphics User Interface, version 9.8, Schrödinger, LLC.
[43] J. L. Banks, H. S. Beard, Y. Cao, A. E. Cho, W. Damm, et al., “Integrated Modeling Program, Applied Chemical Theory (IMPACT),” Journal of Computational Chemistry, Vol. 26, No. 16, 2005, pp. 1752-1780. doi:10.1002/jcc.20292
[44] W. C. Still, A. Tempczyk, R. C. Hawley and T. Hendrickson, “Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics,” Journal of the America Chemical Society, Vol. 112, No. 16, 1990, pp. 6127-6129. doi:10.1021/ja00172a038
[45] F. Mohamadi, N. G. J. Richards, W. C. Guida, R. Liskamp, M. Lipton, et al., “Macromodel—An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics,” Journal of Computational Chemistry, Vol. 11, No. 4, 1990, pp. 440-467. doi:10.1002/jcc.540110405
[46] The Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB).
[47] R. A. Friesner, J. L. Banks, R. B. Murphy, T. A. Halgren, J. J. Klicic, et al., “Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy,” Journal of Medicinal Chemistry, Vol. 47, No. 7, 2004, pp. 1739-1749. doi:10.1021/jm0306430
[48] S. Alcaro, C. Musetti, S. Distinto, M. Casatti, G. Zagotto, et al., “Identification and Characterization of New DNA G-Quadruplex Binders Selected by a Combination of Ligand and Structure-Based Virtual Screening Approaches,” Journal of Medicinal Chemistry, Vol. 56, No. 3, 2013, pp. 843-855. doi:10.1021/jm3013486
[49] S. Alcaro, G. Costa, S. Distinto, F. Moraca, F. Ortuso, et al., “The Polymorphisms of DNA G-Quadruplex Investigated by Docking Experiments with Telomestatin Enantiomers,” Current Pharmaceutical Design, Vol. 18, No. 14, 2012, pp. 1873-1879. doi:10.2174/138161212799958495
[50] S. Alcaro, A. Artese, J. N. Iley, S. Missailidis, F. Ortuso, et al., “Rational Design, Synthesis, Biophysical and Antiproliferative Evaluation of Fluorenone Derivatives with DNA G-Quadruplex Binding Properties,” ChemMed-Chem, Vol. 5, No. 4, 2010, pp. 575-583. doi:10.1002/cmdc.200900541
[51] A. Ambrus, D. Chen, J. X. Dai, T. Bialis, R. A. Jones, et al., “Human Telomeric Sequence Forms a Hybrid-Type Intramolecular G-Quadruplex Structure with Mixed Parallel/Antiparallel Strands in Potassium Solution, ” Nucleic Acids Research, Vol. 34, No. 9, 2006, pp. 2723-2735. doi:10.1093/nar/gkl348

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