Rational design of substituted diarylureas: a scaffold for binding to G-quadruplex motifs.

The design and synthesis of a series of urea-based nonpolycyclic aromatic ligands with alkylaminoanilino side chains as telomeric and genomic G-quadruplex DNA interacting agents are described. Their interactions with quadruplexes have been examined by means of fluorescent resonance energy transfer melting, circular dichroism, and surface plasmon resonance-based assays. These validate the design concept for such urea-based ligands and also show that they have significant selectivity over duplex DNA, as well as for particular G-quadruplexes. The ligand-quadruplex complexes were investigated by computational molecular modeling, providing further information on structure-activity relationships. Preliminary biological studies using short-term cell growth inhibition assays show that some of the ligands have cancer cell selectivity, although they appear to have low potency for intracellular telomeric G-quadruplex structures, suggesting that their cellular targets may be other, possibly oncogene-related quadruplexes.

[1]  Hamid Morjani,et al.  Telomestatin-induced Telomere Uncapping Is Modulated by POT1 through G-overhang Extension in HT1080 Human Tumor Cells* , 2006, Journal of Biological Chemistry.

[2]  J. Mergny,et al.  Fluorescence Resonance Energy Transfer as a Probe for G‐Quartet Formation by a Telomeric Repeat , 2001, Chembiochem : a European journal of chemical biology.

[3]  K. Shin‐ya,et al.  Telomestatin, a novel telomerase inhibitor from Streptomyces anulatus. , 2001, Journal of the American Chemical Society.

[4]  Yong Xue,et al.  Human telomeric DNA forms parallel-stranded intramolecular G-quadruplex in K+ solution under molecular crowding condition. , 2007, Journal of the American Chemical Society.

[5]  R. Gartenhaus,et al.  Telomere uncapping by the G-quadruplex ligand RHPS4 inhibits clonogenic tumour cell growth in vitro and in vivo consistent with a cancer stem cell targeting mechanism , 2007, British Journal of Cancer.

[6]  D. Hanahan,et al.  The Hallmarks of Cancer , 2000, Cell.

[7]  A. Phan,et al.  Propeller-type parallel-stranded G-quadruplexes in the human c-myc promoter. , 2004, Journal of the American Chemical Society.

[8]  Barbara Benassi,et al.  Biological Activity of the G-Quadruplex Ligand RHPS4 (3,11-Difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl]acridinium methosulfate) Is Associated with Telomere Capping Alteration , 2004, Molecular Pharmacology.

[9]  S. Neidle,et al.  Stabilization of G-quadruplex DNA by highly selective ligands via click chemistry. , 2006, Journal of the American Chemical Society.

[10]  D. Scudiero,et al.  New colorimetric cytotoxicity assay for anticancer-drug screening. , 1990, Journal of the National Cancer Institute.

[11]  Stephen Neidle,et al.  A conserved quadruplex motif located in a transcription activation site of the human c-kit oncogene. , 2006, Biochemistry.

[12]  Charles A Laughton,et al.  Antitumor polycyclic acridines. 8.(1) Synthesis and telomerase-inhibitory activity of methylated pentacyclic acridinium salts. , 2002, Journal of medicinal chemistry.

[13]  C B Harley,et al.  Specific association of human telomerase activity with immortal cells and cancer. , 1994, Science.

[14]  C. Dugave Cis-trans isomerization in biochemistry , 2006 .

[15]  D. Osguthorpe,et al.  Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase‐trimethoprim, a drug‐receptor system , 1988, Proteins.

[16]  G. Ortaggi,et al.  Specific interactions with intra- and intermolecular G-quadruplex DNA structures by hydrosoluble coronene derivatives: a new class of telomerase inhibitors. , 2007, Bioorganic & medicinal chemistry.

[17]  James M. Morrell,et al.  Evaluation of by disubstituted acridone derivatives as telomerase inhibitors: the importance of G-quadruplex binding. , 2004, Bioorganic & medicinal chemistry letters.

[18]  W. Hahn,et al.  Inhibition of telomerase limits the growth of human cancer cells , 1999, Nature Medicine.

[19]  S. Neidle,et al.  Tri- and tetra-substituted naphthalene diimides as potent G-quadruplex ligands. , 2008, Bioorganic & medicinal chemistry letters.

[20]  B. Herbert,et al.  Telomere dysfunction in aging and cancer. , 2005, The international journal of biochemistry & cell biology.

[21]  U. Steiner,et al.  Synthesis of caged nucleosides with photoremovable protecting groups linked to intramolecular antennae , 2005 .

[22]  John M Sedivy,et al.  Telomere shortening triggers senescence of human cells through a pathway involving ATM, p53, and p21(CIP1), but not p16(INK4a). , 2004, Molecular cell.

[23]  D. Bearss,et al.  Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[24]  K. Shin‐ya,et al.  The G-quadruplex ligand telomestatin inhibits POT1 binding to telomeric sequences in vitro and induces GFP-POT1 dissociation from telomeres in human cells. , 2006, Cancer research.

[25]  Sarah W. Burge,et al.  Structure of an unprecedented G-quadruplex scaffold in the human c-kit promoter. , 2007, Journal of the American Chemical Society.

[26]  C. Harley,et al.  Telomerase and cancer therapeutics , 2008, Nature Reviews Cancer.

[27]  Roger A. Jones,et al.  Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution , 2006, Nucleic acids research.

[28]  G. W. Anderson,et al.  N,N'-Carbonyldiimidazole, a New Peptide Forming Reagent1 , 1960 .

[29]  T. Lange,et al.  POT1 as a terminal transducer of TRF1 telomere length control , 2003, Nature.

[30]  S. Neidle,et al.  Click chemistry assembly of G-quadruplex ligands incorporating a diarylurea scaffold and triazole linkers. , 2008, Chemical communications.

[31]  A. Smogorzewska,et al.  Regulation of telomerase by telomeric proteins. , 2004, Annual review of biochemistry.

[32]  Binh Nguyen,et al.  Biosensor-surface plasmon resonance: quantitative analysis of small molecule-nucleic acid interactions. , 2007, Methods.

[33]  C. Harley,et al.  Lipid modification of GRN163, an N3′ → P5′ thio-phosphoramidate oligonucleotide, enhances the potency of telomerase inhibition , 2005, Oncogene.

[34]  G. Parkinson,et al.  Topology conservation and loop flexibility in quadruplex-drug recognition: crystal structures of inter- and intramolecular telomeric DNA quadruplex-drug complexes. , 2008, Journal of molecular biology.

[35]  J. Shay,et al.  Telomere-end processing the terminal nucleotides of human chromosomes. , 2005, Molecular cell.

[36]  K. Dimitriadis,et al.  Optimization of the sulforhodamine B colorimetric assay. , 1997, Journal of immunological methods.

[37]  S. Neidle,et al.  Structure-based design of benzylamino-acridine compounds as G-quadruplex DNA telomere targeting agents. , 2007, Bioorganic & medicinal chemistry letters.

[38]  Y. Hashimoto,et al.  Specific nonpeptide inhibitors of puromycin-sensitive aminopeptidase with a 2,4(1H,3H)-quinazolinedione skeleton. , 2003, Chemical & pharmaceutical bulletin.

[39]  Stephen Neidle,et al.  Putative DNA quadruplex formation within the human c-kit oncogene. , 2005, Journal of the American Chemical Society.

[40]  J. Shay,et al.  A survey of telomerase activity in human cancer. , 1997, European journal of cancer.

[41]  B. Gilchrest,et al.  Signaling pathway requirements for induction of senescence by telomere homolog oligonucleotides. , 2004, Experimental cell research.

[42]  Stephen Neidle,et al.  Structural basis of DNA quadruplex recognition by an acridine drug. , 2008, Journal of the American Chemical Society.

[43]  G. Morin The human telomere terminal transferase enzyme is a ribonucleoprotein that synthesizes TTAGGG repeats , 1989, Cell.

[44]  Stephen Neidle,et al.  Crystal structure of parallel quadruplexes from human telomeric DNA , 2002, Nature.

[45]  S. Balasubramanian,et al.  Tetrapeptides induce selective recognition for G-quadruplexes when conjugated to a DNA-binding platform. , 2004, Organic & biomolecular chemistry.

[46]  S. Neidle,et al.  Human telomerase inhibition by substituted acridine derivatives. , 1999, Bioorganic & medicinal chemistry letters.

[47]  D. Davies,et al.  Helix formation by guanylic acid. , 1962, Proceedings of the National Academy of Sciences of the United States of America.

[48]  M. Searle,et al.  Drug recognition and stabilisation of the parallel-stranded DNA quadruplex d(TTAGGGT)4 containing the human telomeric repeat. , 2003, Journal of Molecular Biology.

[49]  C Roskelley,et al.  A biomarker that identifies senescent human cells in culture and in aging skin in vivo. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[50]  J. Murnane Telomeres and chromosome instability. , 2006, DNA repair.

[51]  M. Teulade‐Fichou,et al.  A hitchhiker's guide to G-quadruplex ligands. , 2008, Organic & biomolecular chemistry.

[52]  Stephen Neidle,et al.  The G-quadruplex-interactive molecule BRACO-19 inhibits tumor growth, consistent with telomere targeting and interference with telomerase function. , 2005, Cancer research.

[53]  Kazuo Shin-Ya,et al.  Telomestatin, a potent telomerase inhibitor that interacts quite specifically with the human telomeric intramolecular g-quadruplex. , 2002, Journal of the American Chemical Society.

[54]  A. Phan,et al.  Two-repeat human telomeric d(TAGGGTTAGGGT) sequence forms interconverting parallel and antiparallel G-quadruplexes in solution: distinct topologies, thermodynamic properties, and folding/unfolding kinetics. , 2003, Journal of the American Chemical Society.

[55]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.

[56]  E. Blackburn Switching and Signaling at the Telomere , 2001, Cell.

[57]  S Neidle,et al.  DNA minor-groove recognition by small molecules. , 2001, Natural product reports.

[58]  Stephen Neidle,et al.  Trisubstituted acridines as G-quadruplex telomere targeting agents. Effects of extensions of the 3,6- and 9-side chains on quadruplex binding, telomerase activity, and cell proliferation. , 2006, Journal of medicinal chemistry.

[59]  T. Cech,et al.  Structure of human POT1 bound to telomeric single-stranded DNA provides a model for chromosome end-protection , 2004, Nature Structural &Molecular Biology.

[60]  S. Cogoi,et al.  G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription , 2006, Nucleic acids research.

[61]  S. Neidle,et al.  Inhibition of human telomerase by a G-quadruplex-interactive compound. , 1997, Journal of medicinal chemistry.

[62]  R. Batey,et al.  Parallel synthesis of tri- and tetrasubstituted ureas from carbamoyl imidazolium salts. , 2002, Combinatorial chemistry & high throughput screening.

[63]  K. Glaser,et al.  Discovery of N-(4-(3-amino-1H-indazol-4-yl)phenyl)-N'-(2-fluoro-5-methylphenyl)urea (ABT-869), a 3-aminoindazole-based orally active multitargeted receptor tyrosine kinase inhibitor. , 2007, Journal of medicinal chemistry.

[64]  R. Moyzis,et al.  Conservation of the human telomere sequence (TTAGGG)n among vertebrates. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[65]  Stephen Neidle,et al.  A G-quadruplex telomere targeting agent produces p16-associated senescence and chromosomal fusions in human prostate cancer cells. , 2004, Molecular cancer therapeutics.

[66]  T. Lange,et al.  Shelterin: the protein complex that shapes and safeguards human telomeres , 2005 .

[67]  A. Phan,et al.  Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution† , 2007, Nucleic acids research.

[68]  B. Guyen,et al.  Synthesis, biophysical and biological evaluation of 3,6-bis-amidoacridines with extended 9-anilino substituents as potent G-quadruplex-binding telomerase inhibitors. , 2004, Bioorganic & medicinal chemistry letters.

[69]  K. Shin‐ya,et al.  G-Quadruplex stabilization by telomestatin induces TRF2 protein dissociation from telomeres and anaphase bridge formation accompanied by loss of the 3′ telomeric overhang in cancer cells , 2006, Oncogene.

[70]  Shankar Balasubramanian,et al.  An RNA G-quadruplex in the 5' UTR of the NRAS proto-oncogene modulates translation. , 2007, Nature chemical biology.

[71]  E. Blackburn,et al.  Telomere states and cell fates , 2000, Nature.

[72]  J. Mergny,et al.  Telomerase inhibitors based on quadruplex ligands selected by a fluorescence assay , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[73]  S. Neidle,et al.  Structure-specific recognition of quadruplex DNA by organic cations: influence of shape, substituents and charge. , 2007, Biophysical chemistry.

[74]  Sarah W. Burge,et al.  Quadruplex DNA: sequence, topology and structure , 2006, Nucleic acids research.

[75]  L. Hurley,et al.  Deconvoluting the structural and drug-recognition complexity of the G-quadruplex-forming region upstream of the bcl-2 P1 promoter. , 2006, Journal of the American Chemical Society.

[76]  L. Kèlland,et al.  Targeting the Limitless Replicative Potential of Cancer: The Telomerase/Telomere Pathway , 2007, Clinical Cancer Research.

[77]  G. Parkinson,et al.  Structural basis for binding of porphyrin to human telomeres. , 2007, Biochemistry.

[78]  Stephen Neidle,et al.  Structure-based design of selective and potent G quadruplex-mediated telomerase inhibitors , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[79]  Shankar Balasubramanian,et al.  G-quadruplexes in promoters throughout the human genome , 2006, Nucleic acids research.

[80]  D. Loayza,et al.  DNA Binding Features of Human POT1 , 2004, Journal of Biological Chemistry.

[81]  R. Wheelhouse,et al.  Cationic Porphyrins as Telomerase Inhibitors: the Interaction of Tetra-(N-methyl-4-pyridyl)porphine with Quadruplex DNA , 1998 .

[82]  J. Langmore,et al.  Long G Tails at Both Ends of Human Chromosomes Suggest a C Strand Degradation Mechanism for Telomere Shortening , 1997, Cell.

[83]  N. Peet,et al.  Phosgenation of methyl anthranilate , 1974 .

[84]  A. Phan,et al.  Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter , 2005, Nature chemical biology.

[85]  L. S. Cram,et al.  A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[86]  J. Elguero,et al.  A New Entry to Bis‐Tröger’s Bases , 2004 .

[87]  S Neidle,et al.  Molecular modeling studies on G-quadruplex complexes of telomerase inhibitors: structure-activity relationships. , 1999, Journal of medicinal chemistry.

[88]  James M. Morrell,et al.  Trisubstituted acridine derivatives as potent and selective telomerase inhibitors. , 2003, Journal of medicinal chemistry.

[89]  S. Neidle,et al.  A G-quadruplex-interactive potent small-molecule inhibitor of telomerase exhibiting in vitro and in vivo antitumor activity. , 2002, Molecular pharmacology.

[90]  T. Duka,et al.  First evidence of a functional interaction between DNA quadruplexes and poly(ADP-ribose) polymerase-1. , 2008, ACS chemical biology.